(primary solid tumor cohort)
This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.
Testing the association between copy number variation of 43 peak regions and 8 molecular subtypes across 220 patients, 64 significant findings detected with Q value < 0.25.
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Amp Peak 1(1q32.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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Amp Peak 3(7p11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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Amp Peak 4(7q32.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
-
Amp Peak 5(8q24.21) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 6(10p15.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.
-
Amp Peak 9(12p13.32) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 12(19p13.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 13(19q13.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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Amp Peak 15(Xq11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 1(1p36.31) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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Del Peak 2(1p32.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 4(2q37.3) cnvs correlated to 'METHLYATION_CNMF'.
-
Del Peak 7(4q33) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 8(4q35.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 9(5q35.2) cnvs correlated to 'METHLYATION_CNMF'.
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Del Peak 13(9p21.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 14(10q26.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 15(11p15.5) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 17(12q24.11) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 25(19q13.42) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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Del Peak 26(22q13.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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Del Peak 28(Xq21.1) cnvs correlated to 'MIRSEQ_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 | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
Del Peak 1(1p36 31) | 83 (38%) | 137 |
0.000549 (0.146) |
0.00201 (0.508) |
3.69e-31 (1.19e-28) |
3.02e-37 (9.77e-35) |
4.44e-17 (1.4e-14) |
7.5e-20 (2.39e-17) |
4.56e-11 (1.4e-08) |
0.00939 (1.00) |
Del Peak 2(1p32 3) | 77 (35%) | 143 |
0.0286 (1.00) |
0.0635 (1.00) |
2.88e-37 (9.35e-35) |
1.25e-40 (4.07e-38) |
2.7e-18 (8.55e-16) |
2.09e-23 (6.71e-21) |
3.51e-13 (1.09e-10) |
0.0009 (0.237) |
Del Peak 14(10q26 2) | 70 (32%) | 150 |
0.179 (1.00) |
0.257 (1.00) |
1.05e-17 (3.33e-15) |
1.53e-16 (4.78e-14) |
1.09e-13 (3.39e-11) |
2.8e-08 (8.42e-06) |
3.44e-06 (0.001) |
0.000724 (0.191) |
Del Peak 25(19q13 42) | 116 (53%) | 104 |
0.0353 (1.00) |
0.0105 (1.00) |
4.4e-29 (1.42e-26) |
1.12e-22 (3.57e-20) |
4.81e-11 (1.48e-08) |
3.35e-12 (1.03e-09) |
6.67e-10 (2.04e-07) |
0.112 (1.00) |
Amp Peak 1(1q32 1) | 23 (10%) | 197 |
7.81e-07 (0.000231) |
8.15e-05 (0.0225) |
1.9e-05 (0.00537) |
0.378 (1.00) |
0.639 (1.00) |
0.416 (1.00) |
||
Amp Peak 3(7p11 2) | 55 (25%) | 165 |
0.864 (1.00) |
0.86 (1.00) |
1.1e-18 (3.49e-16) |
1.17e-12 (3.64e-10) |
1.17e-09 (3.55e-07) |
0.0172 (1.00) |
0.00108 (0.282) |
0.0182 (1.00) |
Amp Peak 4(7q32 3) | 77 (35%) | 143 |
0.764 (1.00) |
0.575 (1.00) |
8.39e-17 (2.63e-14) |
5.43e-07 (0.000161) |
2.53e-05 (0.0071) |
0.0286 (1.00) |
0.0551 (1.00) |
0.207 (1.00) |
Amp Peak 6(10p15 1) | 35 (16%) | 185 |
0.467 (1.00) |
0.468 (1.00) |
2.61e-09 (7.9e-07) |
9.16e-08 (2.75e-05) |
0.00335 (0.82) |
0.00473 (1.00) |
0.000613 (0.162) |
0.869 (1.00) |
Amp Peak 13(19q13 2) | 15 (7%) | 205 |
0.369 (1.00) |
0.327 (1.00) |
1.02e-06 (3e-04) |
0.000382 (0.103) |
0.000267 (0.0728) |
0.0101 (1.00) |
0.0341 (1.00) |
0.0081 (1.00) |
Amp Peak 15(Xq11 2) | 31 (14%) | 189 |
0.282 (1.00) |
0.803 (1.00) |
3.63e-06 (0.00105) |
1.97e-06 (0.000578) |
0.0118 (1.00) |
0.000397 (0.107) |
0.124 (1.00) |
0.373 (1.00) |
Del Peak 15(11p15 5) | 48 (22%) | 172 |
0.642 (1.00) |
0.184 (1.00) |
1.98e-07 (5.91e-05) |
1.03e-09 (3.15e-07) |
0.0248 (1.00) |
0.000283 (0.0768) |
0.206 (1.00) |
0.428 (1.00) |
Del Peak 26(22q13 31) | 31 (14%) | 189 |
0.25 (1.00) |
0.144 (1.00) |
2.21e-06 (0.000646) |
1.75e-05 (0.00496) |
4.5e-05 (0.0126) |
0.00189 (0.484) |
0.00961 (1.00) |
0.119 (1.00) |
Amp Peak 5(8q24 21) | 44 (20%) | 176 |
0.37 (1.00) |
1 (1.00) |
6.87e-06 (0.00198) |
1.72e-06 (0.000504) |
0.00114 (0.297) |
0.00189 (0.484) |
0.0201 (1.00) |
0.11 (1.00) |
Amp Peak 9(12p13 32) | 34 (15%) | 186 |
0.864 (1.00) |
0.86 (1.00) |
1e-05 (0.00285) |
6.33e-05 (0.0176) |
0.0134 (1.00) |
0.000959 (0.251) |
0.00802 (1.00) |
0.00986 (1.00) |
Amp Peak 12(19p13 3) | 51 (23%) | 169 |
0.186 (1.00) |
0.272 (1.00) |
1.69e-09 (5.13e-07) |
5.84e-06 (0.00169) |
0.00459 (1.00) |
0.00296 (0.732) |
0.113 (1.00) |
0.546 (1.00) |
Del Peak 7(4q33) | 61 (28%) | 159 |
1 (1.00) |
0.784 (1.00) |
0.000502 (0.134) |
0.000365 (0.0989) |
0.0319 (1.00) |
0.0186 (1.00) |
0.00194 (0.492) |
0.362 (1.00) |
Del Peak 8(4q35 2) | 62 (28%) | 158 |
1 (1.00) |
0.784 (1.00) |
8.18e-05 (0.0225) |
6.46e-05 (0.0179) |
0.019 (1.00) |
0.0166 (1.00) |
0.00505 (1.00) |
0.262 (1.00) |
Del Peak 13(9p21 3) | 78 (35%) | 142 |
0.333 (1.00) |
0.272 (1.00) |
2.4e-07 (7.15e-05) |
8.35e-06 (0.0024) |
0.00679 (1.00) |
0.0465 (1.00) |
0.256 (1.00) |
0.15 (1.00) |
Del Peak 17(12q24 11) | 30 (14%) | 190 |
1 (1.00) |
0.388 (1.00) |
4.97e-05 (0.0139) |
1.48e-05 (0.00421) |
0.312 (1.00) |
0.00896 (1.00) |
0.0154 (1.00) |
0.766 (1.00) |
Del Peak 4(2q37 3) | 32 (15%) | 188 |
0.18 (1.00) |
0.547 (1.00) |
0.00134 (0.347) |
9.19e-06 (0.00263) |
0.0218 (1.00) |
0.0217 (1.00) |
0.063 (1.00) |
0.204 (1.00) |
Del Peak 9(5q35 2) | 28 (13%) | 192 |
0.446 (1.00) |
0.61 (1.00) |
0.00261 (0.646) |
0.000447 (0.12) |
0.0301 (1.00) |
0.0054 (1.00) |
0.0269 (1.00) |
0.0798 (1.00) |
Del Peak 28(Xq21 1) | 30 (14%) | 190 |
0.73 (1.00) |
0.504 (1.00) |
0.468 (1.00) |
0.0585 (1.00) |
0.00838 (1.00) |
0.0258 (1.00) |
0.000193 (0.0529) |
0.363 (1.00) |
Amp Peak 2(4q12) | 10 (5%) | 210 |
0.503 (1.00) |
0.523 (1.00) |
0.393 (1.00) |
0.543 (1.00) |
0.812 (1.00) |
0.393 (1.00) |
||
Amp Peak 7(10q11 21) | 5 (2%) | 215 |
0.2 (1.00) |
0.443 (1.00) |
0.213 (1.00) |
0.176 (1.00) |
0.00949 (1.00) |
0.556 (1.00) |
||
Amp Peak 8(11q23 3) | 38 (17%) | 182 |
0.0708 (1.00) |
0.0162 (1.00) |
0.922 (1.00) |
0.0277 (1.00) |
0.217 (1.00) |
0.23 (1.00) |
0.479 (1.00) |
0.591 (1.00) |
Amp Peak 10(12p11 22) | 21 (10%) | 199 |
1 (1.00) |
0.388 (1.00) |
0.0212 (1.00) |
0.0474 (1.00) |
0.142 (1.00) |
0.00329 (0.81) |
0.00209 (0.527) |
0.0355 (1.00) |
Amp Peak 11(12q14 1) | 14 (6%) | 206 |
0.122 (1.00) |
0.398 (1.00) |
0.029 (1.00) |
0.328 (1.00) |
0.94 (1.00) |
0.909 (1.00) |
||
Amp Peak 14(Xp22 33) | 15 (7%) | 205 |
0.00248 (0.617) |
0.0073 (1.00) |
0.323 (1.00) |
0.0905 (1.00) |
0.121 (1.00) |
1 (1.00) |
||
Del Peak 3(1q43) | 13 (6%) | 207 |
0.666 (1.00) |
0.33 (1.00) |
0.202 (1.00) |
0.0861 (1.00) |
0.343 (1.00) |
0.296 (1.00) |
||
Del Peak 5(3p21 1) | 20 (9%) | 200 |
1 (1.00) |
0.413 (1.00) |
0.359 (1.00) |
0.0288 (1.00) |
0.94 (1.00) |
0.0143 (1.00) |
0.0566 (1.00) |
0.00812 (1.00) |
Del Peak 6(3q29) | 21 (10%) | 199 |
0.175 (1.00) |
1 (1.00) |
0.00982 (1.00) |
0.00218 (0.547) |
0.114 (1.00) |
0.074 (1.00) |
0.54 (1.00) |
0.136 (1.00) |
Del Peak 10(6p24 1) | 21 (10%) | 199 |
0.131 (1.00) |
0.371 (1.00) |
0.436 (1.00) |
0.233 (1.00) |
0.252 (1.00) |
0.45 (1.00) |
||
Del Peak 11(6q24 3) | 33 (15%) | 187 |
0.0479 (1.00) |
0.0407 (1.00) |
0.0158 (1.00) |
0.0015 (0.386) |
0.269 (1.00) |
0.0519 (1.00) |
0.0189 (1.00) |
0.449 (1.00) |
Del Peak 12(8p23 2) | 11 (5%) | 209 |
1 (1.00) |
0.388 (1.00) |
0.00696 (1.00) |
0.0127 (1.00) |
0.136 (1.00) |
0.36 (1.00) |
0.634 (1.00) |
0.23 (1.00) |
Del Peak 16(11q25) | 15 (7%) | 205 |
0.00183 (0.471) |
0.0165 (1.00) |
0.126 (1.00) |
0.0905 (1.00) |
0.633 (1.00) |
0.118 (1.00) |
||
Del Peak 18(13q14 2) | 65 (30%) | 155 |
0.18 (1.00) |
0.0733 (1.00) |
0.054 (1.00) |
0.00902 (1.00) |
0.482 (1.00) |
0.202 (1.00) |
0.214 (1.00) |
0.548 (1.00) |
Del Peak 19(13q34) | 50 (23%) | 170 |
0.508 (1.00) |
0.526 (1.00) |
0.244 (1.00) |
0.0929 (1.00) |
0.242 (1.00) |
0.156 (1.00) |
0.106 (1.00) |
0.316 (1.00) |
Del Peak 20(14q24 3) | 51 (23%) | 169 |
0.303 (1.00) |
0.341 (1.00) |
0.00236 (0.589) |
0.0151 (1.00) |
0.0253 (1.00) |
0.118 (1.00) |
0.00879 (1.00) |
0.0141 (1.00) |
Del Peak 21(15q21 3) | 27 (12%) | 193 |
0.839 (1.00) |
0.828 (1.00) |
0.0596 (1.00) |
0.0592 (1.00) |
0.00699 (1.00) |
0.247 (1.00) |
0.34 (1.00) |
0.841 (1.00) |
Del Peak 22(17q25 3) | 15 (7%) | 205 |
0.0206 (1.00) |
0.164 (1.00) |
0.658 (1.00) |
0.367 (1.00) |
0.354 (1.00) |
0.755 (1.00) |
||
Del Peak 23(18p11 32) | 32 (15%) | 188 |
0.321 (1.00) |
0.388 (1.00) |
0.552 (1.00) |
0.137 (1.00) |
0.481 (1.00) |
0.648 (1.00) |
0.68 (1.00) |
0.38 (1.00) |
Del Peak 24(18q23) | 35 (16%) | 185 |
0.321 (1.00) |
0.388 (1.00) |
0.918 (1.00) |
0.108 (1.00) |
0.489 (1.00) |
0.875 (1.00) |
0.756 (1.00) |
0.54 (1.00) |
Del Peak 27(Xp22 31) | 51 (23%) | 169 |
0.73 (1.00) |
0.61 (1.00) |
0.517 (1.00) |
0.201 (1.00) |
0.548 (1.00) |
0.0926 (1.00) |
0.0789 (1.00) |
0.0865 (1.00) |
P value = 7.81e-07 (Fisher's exact test), Q value = 0.00023
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 94 | 50 | 76 |
AMP PEAK 1(1Q32.1) MUTATED | 5 | 16 | 2 |
AMP PEAK 1(1Q32.1) WILD-TYPE | 89 | 34 | 74 |
P value = 8.15e-05 (Fisher's exact test), Q value = 0.023
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 100 | 34 | 58 | 23 |
AMP PEAK 1(1Q32.1) MUTATED | 8 | 12 | 2 | 1 |
AMP PEAK 1(1Q32.1) WILD-TYPE | 92 | 22 | 56 | 22 |
P value = 1.9e-05 (Chi-square test), Q value = 0.0054
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 60 | 42 | 35 | 70 | 11 |
AMP PEAK 1(1Q32.1) MUTATED | 1 | 13 | 1 | 8 | 0 |
AMP PEAK 1(1Q32.1) WILD-TYPE | 59 | 29 | 34 | 62 | 11 |
P value = 1.1e-18 (Fisher's exact test), Q value = 3.5e-16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 94 | 50 | 76 |
AMP PEAK 3(7P11.2) MUTATED | 9 | 38 | 8 |
AMP PEAK 3(7P11.2) WILD-TYPE | 85 | 12 | 68 |
P value = 1.17e-12 (Fisher's exact test), Q value = 3.6e-10
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 100 | 34 | 58 | 23 |
AMP PEAK 3(7P11.2) MUTATED | 17 | 27 | 6 | 3 |
AMP PEAK 3(7P11.2) WILD-TYPE | 83 | 7 | 52 | 20 |
P value = 1.17e-09 (Chi-square test), Q value = 3.6e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 60 | 42 | 35 | 70 | 11 |
AMP PEAK 3(7P11.2) MUTATED | 14 | 27 | 4 | 9 | 0 |
AMP PEAK 3(7P11.2) WILD-TYPE | 46 | 15 | 31 | 61 | 11 |
P value = 8.39e-17 (Fisher's exact test), Q value = 2.6e-14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 94 | 50 | 76 |
AMP PEAK 4(7Q32.3) MUTATED | 20 | 43 | 14 |
AMP PEAK 4(7Q32.3) WILD-TYPE | 74 | 7 | 62 |
P value = 5.43e-07 (Fisher's exact test), Q value = 0.00016
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 100 | 34 | 58 | 23 |
AMP PEAK 4(7Q32.3) MUTATED | 35 | 25 | 12 | 3 |
AMP PEAK 4(7Q32.3) WILD-TYPE | 65 | 9 | 46 | 20 |
P value = 2.53e-05 (Chi-square test), Q value = 0.0071
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 60 | 42 | 35 | 70 | 11 |
AMP PEAK 4(7Q32.3) MUTATED | 26 | 26 | 7 | 16 | 1 |
AMP PEAK 4(7Q32.3) WILD-TYPE | 34 | 16 | 28 | 54 | 10 |
P value = 6.87e-06 (Fisher's exact test), Q value = 0.002
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 94 | 50 | 76 |
AMP PEAK 5(8Q24.21) MUTATED | 32 | 8 | 4 |
AMP PEAK 5(8Q24.21) WILD-TYPE | 62 | 42 | 72 |
P value = 1.72e-06 (Fisher's exact test), Q value = 5e-04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 100 | 34 | 58 | 23 |
AMP PEAK 5(8Q24.21) MUTATED | 36 | 4 | 3 | 1 |
AMP PEAK 5(8Q24.21) WILD-TYPE | 64 | 30 | 55 | 22 |
P value = 2.61e-09 (Fisher's exact test), Q value = 7.9e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 94 | 50 | 76 |
AMP PEAK 6(10P15.1) MUTATED | 31 | 3 | 1 |
AMP PEAK 6(10P15.1) WILD-TYPE | 63 | 47 | 75 |
P value = 9.16e-08 (Fisher's exact test), Q value = 2.7e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 100 | 34 | 58 | 23 |
AMP PEAK 6(10P15.1) MUTATED | 31 | 2 | 0 | 2 |
AMP PEAK 6(10P15.1) WILD-TYPE | 69 | 32 | 58 | 21 |
P value = 0.000613 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 50 | 50 | 32 | 87 |
AMP PEAK 6(10P15.1) MUTATED | 8 | 16 | 0 | 11 |
AMP PEAK 6(10P15.1) WILD-TYPE | 42 | 34 | 32 | 76 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 94 | 50 | 76 |
AMP PEAK 9(12P13.32) MUTATED | 27 | 4 | 3 |
AMP PEAK 9(12P13.32) WILD-TYPE | 67 | 46 | 73 |
P value = 6.33e-05 (Fisher's exact test), Q value = 0.018
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 100 | 34 | 58 | 23 |
AMP PEAK 9(12P13.32) MUTATED | 28 | 3 | 2 | 1 |
AMP PEAK 9(12P13.32) WILD-TYPE | 72 | 31 | 56 | 22 |
P value = 1.69e-09 (Fisher's exact test), Q value = 5.1e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 94 | 50 | 76 |
AMP PEAK 12(19P13.3) MUTATED | 4 | 15 | 32 |
AMP PEAK 12(19P13.3) WILD-TYPE | 90 | 35 | 44 |
P value = 5.84e-06 (Fisher's exact test), Q value = 0.0017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 100 | 34 | 58 | 23 |
AMP PEAK 12(19P13.3) MUTATED | 10 | 10 | 25 | 2 |
AMP PEAK 12(19P13.3) WILD-TYPE | 90 | 24 | 33 | 21 |
P value = 1.02e-06 (Fisher's exact test), Q value = 3e-04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 94 | 50 | 76 |
AMP PEAK 13(19Q13.2) MUTATED | 1 | 12 | 2 |
AMP PEAK 13(19Q13.2) WILD-TYPE | 93 | 38 | 74 |
P value = 0.000382 (Fisher's exact test), Q value = 0.1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 100 | 34 | 58 | 23 |
AMP PEAK 13(19Q13.2) MUTATED | 5 | 8 | 0 | 1 |
AMP PEAK 13(19Q13.2) WILD-TYPE | 95 | 26 | 58 | 22 |
P value = 0.000267 (Chi-square test), Q value = 0.073
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 60 | 42 | 35 | 70 | 11 |
AMP PEAK 13(19Q13.2) MUTATED | 3 | 9 | 0 | 1 | 1 |
AMP PEAK 13(19Q13.2) WILD-TYPE | 57 | 33 | 35 | 69 | 10 |
P value = 3.63e-06 (Fisher's exact test), Q value = 0.0011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 94 | 50 | 76 |
AMP PEAK 15(XQ11.2) MUTATED | 26 | 2 | 3 |
AMP PEAK 15(XQ11.2) WILD-TYPE | 68 | 48 | 73 |
P value = 1.97e-06 (Fisher's exact test), Q value = 0.00058
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 100 | 34 | 58 | 23 |
AMP PEAK 15(XQ11.2) MUTATED | 27 | 3 | 0 | 1 |
AMP PEAK 15(XQ11.2) WILD-TYPE | 73 | 31 | 58 | 22 |
P value = 0.000397 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 32 | 117 | 69 |
AMP PEAK 15(XQ11.2) MUTATED | 0 | 26 | 5 |
AMP PEAK 15(XQ11.2) WILD-TYPE | 32 | 91 | 64 |
P value = 0.000549 (Fisher's exact test), Q value = 0.15
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 9 | 10 | 8 |
DEL PEAK 1(1P36.31) MUTATED | 0 | 8 | 2 |
DEL PEAK 1(1P36.31) WILD-TYPE | 9 | 2 | 6 |
P value = 3.69e-31 (Fisher's exact test), Q value = 1.2e-28
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 94 | 50 | 76 |
DEL PEAK 1(1P36.31) MUTATED | 7 | 9 | 67 |
DEL PEAK 1(1P36.31) WILD-TYPE | 87 | 41 | 9 |
P value = 3.02e-37 (Fisher's exact test), Q value = 9.8e-35
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 100 | 34 | 58 | 23 |
DEL PEAK 1(1P36.31) MUTATED | 6 | 8 | 58 | 7 |
DEL PEAK 1(1P36.31) WILD-TYPE | 94 | 26 | 0 | 16 |
P value = 4.44e-17 (Chi-square test), Q value = 1.4e-14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 60 | 42 | 35 | 70 | 11 |
DEL PEAK 1(1P36.31) MUTATED | 4 | 10 | 34 | 32 | 3 |
DEL PEAK 1(1P36.31) WILD-TYPE | 56 | 32 | 1 | 38 | 8 |
P value = 7.5e-20 (Fisher's exact test), Q value = 2.4e-17
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 32 | 117 | 69 |
DEL PEAK 1(1P36.31) MUTATED | 32 | 19 | 32 |
DEL PEAK 1(1P36.31) WILD-TYPE | 0 | 98 | 37 |
P value = 4.56e-11 (Fisher's exact test), Q value = 1.4e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 50 | 50 | 32 | 87 |
DEL PEAK 1(1P36.31) MUTATED | 9 | 7 | 26 | 41 |
DEL PEAK 1(1P36.31) WILD-TYPE | 41 | 43 | 6 | 46 |
P value = 2.88e-37 (Fisher's exact test), Q value = 9.4e-35
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 94 | 50 | 76 |
DEL PEAK 2(1P32.3) MUTATED | 5 | 4 | 68 |
DEL PEAK 2(1P32.3) WILD-TYPE | 89 | 46 | 8 |
P value = 1.25e-40 (Fisher's exact test), Q value = 4.1e-38
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 100 | 34 | 58 | 23 |
DEL PEAK 2(1P32.3) MUTATED | 4 | 5 | 58 | 7 |
DEL PEAK 2(1P32.3) WILD-TYPE | 96 | 29 | 0 | 16 |
P value = 2.7e-18 (Chi-square test), Q value = 8.6e-16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 60 | 42 | 35 | 70 | 11 |
DEL PEAK 2(1P32.3) MUTATED | 4 | 5 | 33 | 32 | 3 |
DEL PEAK 2(1P32.3) WILD-TYPE | 56 | 37 | 2 | 38 | 8 |
P value = 2.09e-23 (Fisher's exact test), Q value = 6.7e-21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 32 | 117 | 69 |
DEL PEAK 2(1P32.3) MUTATED | 32 | 13 | 32 |
DEL PEAK 2(1P32.3) WILD-TYPE | 0 | 104 | 37 |
P value = 3.51e-13 (Fisher's exact test), Q value = 1.1e-10
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 50 | 50 | 32 | 87 |
DEL PEAK 2(1P32.3) MUTATED | 7 | 4 | 25 | 41 |
DEL PEAK 2(1P32.3) WILD-TYPE | 43 | 46 | 7 | 46 |
P value = 9e-04 (Fisher's exact test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 88 | 13 | 118 |
DEL PEAK 2(1P32.3) MUTATED | 44 | 3 | 30 |
DEL PEAK 2(1P32.3) WILD-TYPE | 44 | 10 | 88 |
P value = 9.19e-06 (Fisher's exact test), Q value = 0.0026
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 100 | 34 | 58 | 23 |
DEL PEAK 4(2Q37.3) MUTATED | 28 | 1 | 2 | 1 |
DEL PEAK 4(2Q37.3) WILD-TYPE | 72 | 33 | 56 | 22 |
P value = 0.000502 (Fisher's exact test), Q value = 0.13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 94 | 50 | 76 |
DEL PEAK 7(4Q33) MUTATED | 25 | 5 | 31 |
DEL PEAK 7(4Q33) WILD-TYPE | 69 | 45 | 45 |
P value = 0.000365 (Fisher's exact test), Q value = 0.099
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 100 | 34 | 58 | 23 |
DEL PEAK 7(4Q33) MUTATED | 31 | 3 | 25 | 2 |
DEL PEAK 7(4Q33) WILD-TYPE | 69 | 31 | 33 | 21 |
P value = 8.18e-05 (Fisher's exact test), Q value = 0.023
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 94 | 50 | 76 |
DEL PEAK 8(4Q35.2) MUTATED | 26 | 4 | 32 |
DEL PEAK 8(4Q35.2) WILD-TYPE | 68 | 46 | 44 |
P value = 6.46e-05 (Fisher's exact test), Q value = 0.018
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 100 | 34 | 58 | 23 |
DEL PEAK 8(4Q35.2) MUTATED | 33 | 2 | 25 | 2 |
DEL PEAK 8(4Q35.2) WILD-TYPE | 67 | 32 | 33 | 21 |
P value = 0.000447 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 100 | 34 | 58 | 23 |
DEL PEAK 9(5Q35.2) MUTATED | 20 | 5 | 0 | 3 |
DEL PEAK 9(5Q35.2) WILD-TYPE | 80 | 29 | 58 | 20 |
P value = 2.4e-07 (Fisher's exact test), Q value = 7.1e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 94 | 50 | 76 |
DEL PEAK 13(9P21.3) MUTATED | 28 | 34 | 16 |
DEL PEAK 13(9P21.3) WILD-TYPE | 66 | 16 | 60 |
P value = 8.35e-06 (Fisher's exact test), Q value = 0.0024
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 100 | 34 | 58 | 23 |
DEL PEAK 13(9P21.3) MUTATED | 38 | 23 | 12 | 3 |
DEL PEAK 13(9P21.3) WILD-TYPE | 62 | 11 | 46 | 20 |
P value = 1.05e-17 (Fisher's exact test), Q value = 3.3e-15
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 94 | 50 | 76 |
DEL PEAK 14(10Q26.2) MUTATED | 27 | 39 | 4 |
DEL PEAK 14(10Q26.2) WILD-TYPE | 67 | 11 | 72 |
P value = 1.53e-16 (Fisher's exact test), Q value = 4.8e-14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 100 | 34 | 58 | 23 |
DEL PEAK 14(10Q26.2) MUTATED | 33 | 30 | 3 | 3 |
DEL PEAK 14(10Q26.2) WILD-TYPE | 67 | 4 | 55 | 20 |
P value = 1.09e-13 (Chi-square test), Q value = 3.4e-11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 60 | 42 | 35 | 70 | 11 |
DEL PEAK 14(10Q26.2) MUTATED | 18 | 34 | 2 | 13 | 1 |
DEL PEAK 14(10Q26.2) WILD-TYPE | 42 | 8 | 33 | 57 | 10 |
P value = 2.8e-08 (Fisher's exact test), Q value = 8.4e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 32 | 117 | 69 |
DEL PEAK 14(10Q26.2) MUTATED | 1 | 55 | 12 |
DEL PEAK 14(10Q26.2) WILD-TYPE | 31 | 62 | 57 |
P value = 3.44e-06 (Fisher's exact test), Q value = 0.001
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 50 | 50 | 32 | 87 |
DEL PEAK 14(10Q26.2) MUTATED | 20 | 29 | 5 | 16 |
DEL PEAK 14(10Q26.2) WILD-TYPE | 30 | 21 | 27 | 71 |
P value = 0.000724 (Fisher's exact test), Q value = 0.19
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 88 | 13 | 118 |
DEL PEAK 14(10Q26.2) MUTATED | 16 | 4 | 50 |
DEL PEAK 14(10Q26.2) WILD-TYPE | 72 | 9 | 68 |
P value = 1.98e-07 (Fisher's exact test), Q value = 5.9e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 94 | 50 | 76 |
DEL PEAK 15(11P15.5) MUTATED | 35 | 10 | 3 |
DEL PEAK 15(11P15.5) WILD-TYPE | 59 | 40 | 73 |
P value = 1.03e-09 (Fisher's exact test), Q value = 3.1e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 100 | 34 | 58 | 23 |
DEL PEAK 15(11P15.5) MUTATED | 40 | 5 | 0 | 3 |
DEL PEAK 15(11P15.5) WILD-TYPE | 60 | 29 | 58 | 20 |
P value = 0.000283 (Fisher's exact test), Q value = 0.077
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 32 | 117 | 69 |
DEL PEAK 15(11P15.5) MUTATED | 0 | 34 | 13 |
DEL PEAK 15(11P15.5) WILD-TYPE | 32 | 83 | 56 |
P value = 4.97e-05 (Fisher's exact test), Q value = 0.014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 94 | 50 | 76 |
DEL PEAK 17(12Q24.11) MUTATED | 24 | 3 | 3 |
DEL PEAK 17(12Q24.11) WILD-TYPE | 70 | 47 | 73 |
P value = 1.48e-05 (Fisher's exact test), Q value = 0.0042
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 100 | 34 | 58 | 23 |
DEL PEAK 17(12Q24.11) MUTATED | 26 | 1 | 1 | 2 |
DEL PEAK 17(12Q24.11) WILD-TYPE | 74 | 33 | 57 | 21 |
P value = 4.4e-29 (Fisher's exact test), Q value = 1.4e-26
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 94 | 50 | 76 |
DEL PEAK 25(19Q13.42) MUTATED | 26 | 14 | 76 |
DEL PEAK 25(19Q13.42) WILD-TYPE | 68 | 36 | 0 |
P value = 1.12e-22 (Fisher's exact test), Q value = 3.6e-20
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 100 | 34 | 58 | 23 |
DEL PEAK 25(19Q13.42) MUTATED | 44 | 4 | 58 | 7 |
DEL PEAK 25(19Q13.42) WILD-TYPE | 56 | 30 | 0 | 16 |
P value = 4.81e-11 (Chi-square test), Q value = 1.5e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 60 | 42 | 35 | 70 | 11 |
DEL PEAK 25(19Q13.42) MUTATED | 24 | 9 | 35 | 43 | 5 |
DEL PEAK 25(19Q13.42) WILD-TYPE | 36 | 33 | 0 | 27 | 6 |
P value = 3.35e-12 (Fisher's exact test), Q value = 1e-09
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 32 | 117 | 69 |
DEL PEAK 25(19Q13.42) MUTATED | 32 | 42 | 42 |
DEL PEAK 25(19Q13.42) WILD-TYPE | 0 | 75 | 27 |
P value = 6.67e-10 (Fisher's exact test), Q value = 2e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 50 | 50 | 32 | 87 |
DEL PEAK 25(19Q13.42) MUTATED | 22 | 12 | 30 | 52 |
DEL PEAK 25(19Q13.42) WILD-TYPE | 28 | 38 | 2 | 35 |
P value = 2.21e-06 (Fisher's exact test), Q value = 0.00065
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 94 | 50 | 76 |
DEL PEAK 26(22Q13.31) MUTATED | 14 | 16 | 1 |
DEL PEAK 26(22Q13.31) WILD-TYPE | 80 | 34 | 75 |
P value = 1.75e-05 (Fisher's exact test), Q value = 0.005
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 100 | 34 | 58 | 23 |
DEL PEAK 26(22Q13.31) MUTATED | 19 | 10 | 0 | 1 |
DEL PEAK 26(22Q13.31) WILD-TYPE | 81 | 24 | 58 | 22 |
P value = 4.5e-05 (Chi-square test), Q value = 0.013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 60 | 42 | 35 | 70 | 11 |
DEL PEAK 26(22Q13.31) MUTATED | 8 | 15 | 0 | 7 | 0 |
DEL PEAK 26(22Q13.31) WILD-TYPE | 52 | 27 | 35 | 63 | 11 |
P value = 0.000193 (Fisher's exact test), Q value = 0.053
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 50 | 50 | 32 | 87 |
DEL PEAK 28(XQ21.1) MUTATED | 3 | 9 | 12 | 6 |
DEL PEAK 28(XQ21.1) WILD-TYPE | 47 | 41 | 20 | 81 |
-
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 = LGG-TP.transferedmergedcluster.txt
-
Number of patients = 220
-
Number of copy number variation regions = 43
-
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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.