This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.
Testing the association between copy number variation 54 focal events and 10 molecular subtypes across 299 patients, 39 significant findings detected with P value < 0.05 and Q value < 0.25.
-
amp_1q21.3 cnv correlated to 'CN_CNMF'.
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amp_1q44 cnv correlated to 'CN_CNMF'.
-
amp_5p15.33 cnv correlated to 'CN_CNMF'.
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amp_6p24.3 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
-
amp_7p22.1 cnv correlated to 'CN_CNMF'.
-
amp_7q34 cnv correlated to 'CN_CNMF'.
-
amp_8q11.21 cnv correlated to 'CN_CNMF'.
-
amp_8q24.21 cnv correlated to 'CN_CNMF'.
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amp_13q12.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
-
amp_15q26.2 cnv correlated to 'CN_CNMF'.
-
amp_17q25.3 cnv correlated to 'CN_CNMF'.
-
amp_20q13.33 cnv correlated to 'CN_CNMF'.
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amp_22q13.2 cnv correlated to 'CN_CNMF'.
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del_1p36.31 cnv correlated to 'METHLYATION_CNMF'.
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del_1p22.1 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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del_6q22.31 cnv correlated to 'CN_CNMF'.
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del_6q26 cnv correlated to 'CN_CNMF'.
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del_9p21.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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del_10p15.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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del_10q23.31 cnv correlated to 'CN_CNMF'.
-
del_10q26.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
del_11p11.2 cnv correlated to 'CN_CNMF'.
-
del_11q23.3 cnv correlated to 'CN_CNMF'.
-
del_13q12.11 cnv correlated to 'CN_CNMF'.
-
del_13q34 cnv correlated to 'CN_CNMF'.
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del_14q23.3 cnv correlated to 'CN_CNMF'.
-
del_14q32.2 cnv correlated to 'CN_CNMF'.
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del_15q13.3 cnv correlated to 'CN_CNMF'.
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del_15q14 cnv correlated to 'CN_CNMF'.
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del_15q15.2 cnv correlated to 'CN_CNMF'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 54 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 39 significant findings detected.
Clinical Features |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE 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 | Fisher's exact test | Fisher's exact test | |
del 1p22 1 | 76 (25%) | 223 |
0.00108 (0.53) |
1e-05 (0.0054) |
0.592 (1.00) |
0.213 (1.00) |
2e-05 (0.0104) |
0.00036 (0.181) |
0.193 (1.00) |
0.451 (1.00) |
0.487 (1.00) |
0.573 (1.00) |
del 10p15 3 | 163 (55%) | 136 |
1e-05 (0.0054) |
0.00271 (1.00) |
0.833 (1.00) |
0.156 (1.00) |
7e-05 (0.036) |
0.00011 (0.056) |
0.293 (1.00) |
0.0978 (1.00) |
0.377 (1.00) |
0.792 (1.00) |
del 10q26 3 | 193 (65%) | 106 |
1e-05 (0.0054) |
0.0957 (1.00) |
0.837 (1.00) |
0.309 (1.00) |
3e-05 (0.0155) |
0.00031 (0.157) |
0.116 (1.00) |
0.109 (1.00) |
0.234 (1.00) |
0.881 (1.00) |
amp 6p24 3 | 169 (57%) | 130 |
1e-05 (0.0054) |
0.00098 (0.483) |
0.325 (1.00) |
0.0168 (1.00) |
0.0971 (1.00) |
0.016 (1.00) |
0.00537 (1.00) |
0.00039 (0.196) |
0.00549 (1.00) |
0.00117 (0.572) |
amp 13q12 3 | 85 (28%) | 214 |
1e-05 (0.0054) |
7e-05 (0.036) |
0.388 (1.00) |
0.749 (1.00) |
0.00463 (1.00) |
0.0286 (1.00) |
0.832 (1.00) |
0.662 (1.00) |
0.475 (1.00) |
0.932 (1.00) |
del 9p21 3 | 229 (77%) | 70 |
1e-05 (0.0054) |
0.00114 (0.559) |
0.757 (1.00) |
0.701 (1.00) |
1e-05 (0.0054) |
0.0135 (1.00) |
0.0242 (1.00) |
0.328 (1.00) |
0.471 (1.00) |
0.252 (1.00) |
amp 1q21 3 | 158 (53%) | 141 |
1e-05 (0.0054) |
0.0248 (1.00) |
0.337 (1.00) |
0.523 (1.00) |
0.00969 (1.00) |
0.0902 (1.00) |
0.0827 (1.00) |
0.081 (1.00) |
0.0959 (1.00) |
0.175 (1.00) |
amp 1q44 | 162 (54%) | 137 |
1e-05 (0.0054) |
0.00437 (1.00) |
0.162 (1.00) |
0.143 (1.00) |
0.0318 (1.00) |
0.0151 (1.00) |
0.00782 (1.00) |
0.00838 (1.00) |
0.0731 (1.00) |
0.0103 (1.00) |
amp 5p15 33 | 91 (30%) | 208 |
0.00012 (0.0608) |
0.216 (1.00) |
0.694 (1.00) |
0.739 (1.00) |
0.0949 (1.00) |
0.261 (1.00) |
0.00348 (1.00) |
0.084 (1.00) |
0.00312 (1.00) |
0.283 (1.00) |
amp 7p22 1 | 164 (55%) | 135 |
4e-05 (0.0206) |
0.825 (1.00) |
0.625 (1.00) |
0.215 (1.00) |
0.0258 (1.00) |
0.219 (1.00) |
0.567 (1.00) |
0.506 (1.00) |
0.682 (1.00) |
0.173 (1.00) |
amp 7q34 | 177 (59%) | 122 |
1e-05 (0.0054) |
0.0826 (1.00) |
0.318 (1.00) |
0.953 (1.00) |
0.0624 (1.00) |
0.0198 (1.00) |
0.671 (1.00) |
0.488 (1.00) |
0.357 (1.00) |
0.902 (1.00) |
amp 8q11 21 | 137 (46%) | 162 |
2e-05 (0.0104) |
0.0205 (1.00) |
0.57 (1.00) |
0.246 (1.00) |
0.0159 (1.00) |
0.37 (1.00) |
0.668 (1.00) |
0.772 (1.00) |
0.0499 (1.00) |
0.387 (1.00) |
amp 8q24 21 | 158 (53%) | 141 |
1e-05 (0.0054) |
0.0162 (1.00) |
0.752 (1.00) |
0.936 (1.00) |
0.00983 (1.00) |
0.688 (1.00) |
0.55 (1.00) |
0.495 (1.00) |
0.303 (1.00) |
0.357 (1.00) |
amp 15q26 2 | 99 (33%) | 200 |
0.00034 (0.172) |
0.386 (1.00) |
0.938 (1.00) |
0.807 (1.00) |
0.297 (1.00) |
0.0465 (1.00) |
0.777 (1.00) |
0.0561 (1.00) |
1 (1.00) |
0.37 (1.00) |
amp 17q25 3 | 100 (33%) | 199 |
0.0001 (0.0511) |
0.0125 (1.00) |
0.0307 (1.00) |
0.0745 (1.00) |
0.108 (1.00) |
0.828 (1.00) |
0.844 (1.00) |
0.0514 (1.00) |
0.0305 (1.00) |
0.0182 (1.00) |
amp 20q13 33 | 153 (51%) | 146 |
1e-05 (0.0054) |
0.0125 (1.00) |
0.827 (1.00) |
0.988 (1.00) |
0.00188 (0.91) |
0.0109 (1.00) |
0.261 (1.00) |
0.32 (1.00) |
0.147 (1.00) |
0.24 (1.00) |
amp 22q13 2 | 127 (42%) | 172 |
0.00011 (0.056) |
0.13 (1.00) |
0.973 (1.00) |
0.717 (1.00) |
0.426 (1.00) |
0.118 (1.00) |
0.476 (1.00) |
0.202 (1.00) |
0.317 (1.00) |
0.437 (1.00) |
del 1p36 31 | 70 (23%) | 229 |
0.125 (1.00) |
1e-05 (0.0054) |
0.577 (1.00) |
0.21 (1.00) |
0.0745 (1.00) |
0.00426 (1.00) |
0.0973 (1.00) |
0.118 (1.00) |
0.728 (1.00) |
0.341 (1.00) |
del 6q22 31 | 179 (60%) | 120 |
1e-05 (0.0054) |
0.0214 (1.00) |
0.958 (1.00) |
0.445 (1.00) |
0.00502 (1.00) |
0.193 (1.00) |
0.564 (1.00) |
0.556 (1.00) |
0.748 (1.00) |
0.341 (1.00) |
del 6q26 | 184 (62%) | 115 |
1e-05 (0.0054) |
0.0192 (1.00) |
0.839 (1.00) |
0.537 (1.00) |
0.00142 (0.692) |
0.0544 (1.00) |
0.19 (1.00) |
0.424 (1.00) |
0.861 (1.00) |
0.432 (1.00) |
del 10q23 31 | 188 (63%) | 111 |
1e-05 (0.0054) |
0.0137 (1.00) |
0.88 (1.00) |
0.207 (1.00) |
0.00065 (0.323) |
0.00056 (0.28) |
0.134 (1.00) |
0.0222 (1.00) |
0.908 (1.00) |
0.563 (1.00) |
del 11p11 2 | 96 (32%) | 203 |
0.0001 (0.0511) |
0.00818 (1.00) |
0.65 (1.00) |
0.856 (1.00) |
0.136 (1.00) |
0.00146 (0.71) |
0.582 (1.00) |
0.228 (1.00) |
0.592 (1.00) |
0.697 (1.00) |
del 11q23 3 | 161 (54%) | 138 |
1e-05 (0.0054) |
0.21 (1.00) |
0.902 (1.00) |
0.262 (1.00) |
0.0338 (1.00) |
0.227 (1.00) |
0.296 (1.00) |
0.0173 (1.00) |
0.186 (1.00) |
0.0243 (1.00) |
del 13q12 11 | 68 (23%) | 231 |
8e-05 (0.041) |
0.0696 (1.00) |
0.245 (1.00) |
0.901 (1.00) |
0.984 (1.00) |
0.962 (1.00) |
0.645 (1.00) |
0.442 (1.00) |
0.527 (1.00) |
0.445 (1.00) |
del 13q34 | 68 (23%) | 231 |
0.00036 (0.181) |
0.00443 (1.00) |
0.0676 (1.00) |
0.747 (1.00) |
0.895 (1.00) |
0.261 (1.00) |
0.942 (1.00) |
0.849 (1.00) |
1 (1.00) |
0.39 (1.00) |
del 14q23 3 | 102 (34%) | 197 |
1e-05 (0.0054) |
0.809 (1.00) |
0.553 (1.00) |
0.246 (1.00) |
0.00272 (1.00) |
0.273 (1.00) |
0.0262 (1.00) |
0.663 (1.00) |
0.00346 (1.00) |
0.19 (1.00) |
del 14q32 2 | 100 (33%) | 199 |
1e-05 (0.0054) |
0.769 (1.00) |
0.505 (1.00) |
0.184 (1.00) |
0.00059 (0.294) |
0.386 (1.00) |
0.0201 (1.00) |
0.581 (1.00) |
0.0153 (1.00) |
0.109 (1.00) |
del 15q13 3 | 73 (24%) | 226 |
2e-05 (0.0104) |
0.0159 (1.00) |
0.0896 (1.00) |
0.305 (1.00) |
0.276 (1.00) |
0.0474 (1.00) |
0.944 (1.00) |
0.797 (1.00) |
0.6 (1.00) |
0.707 (1.00) |
del 15q14 | 73 (24%) | 226 |
1e-05 (0.0054) |
0.0116 (1.00) |
0.808 (1.00) |
0.683 (1.00) |
0.132 (1.00) |
0.0247 (1.00) |
0.892 (1.00) |
0.305 (1.00) |
0.641 (1.00) |
0.393 (1.00) |
del 15q15 2 | 78 (26%) | 221 |
1e-05 (0.0054) |
0.00964 (1.00) |
0.476 (1.00) |
0.431 (1.00) |
0.252 (1.00) |
0.0458 (1.00) |
0.891 (1.00) |
0.449 (1.00) |
0.864 (1.00) |
0.349 (1.00) |
amp 1p12 | 96 (32%) | 203 |
0.0135 (1.00) |
0.764 (1.00) |
0.706 (1.00) |
0.883 (1.00) |
0.158 (1.00) |
0.611 (1.00) |
0.0845 (1.00) |
0.782 (1.00) |
0.524 (1.00) |
0.399 (1.00) |
amp 3p13 | 78 (26%) | 221 |
0.153 (1.00) |
0.166 (1.00) |
0.0689 (1.00) |
0.113 (1.00) |
0.785 (1.00) |
0.146 (1.00) |
0.572 (1.00) |
0.0111 (1.00) |
0.823 (1.00) |
0.67 (1.00) |
amp 4q12 | 53 (18%) | 246 |
0.00058 (0.289) |
0.201 (1.00) |
0.0828 (1.00) |
0.532 (1.00) |
0.31 (1.00) |
0.121 (1.00) |
0.0407 (1.00) |
0.00127 (0.62) |
0.0081 (1.00) |
0.0393 (1.00) |
amp 5q35 3 | 48 (16%) | 251 |
0.00675 (1.00) |
0.00218 (1.00) |
0.0933 (1.00) |
0.0732 (1.00) |
0.0365 (1.00) |
0.226 (1.00) |
0.224 (1.00) |
0.098 (1.00) |
0.00457 (1.00) |
0.124 (1.00) |
amp 6q12 | 64 (21%) | 235 |
0.00509 (1.00) |
0.793 (1.00) |
0.529 (1.00) |
0.081 (1.00) |
0.113 (1.00) |
0.144 (1.00) |
0.0877 (1.00) |
0.0972 (1.00) |
0.515 (1.00) |
0.396 (1.00) |
amp 11q13 3 | 58 (19%) | 241 |
0.0265 (1.00) |
0.312 (1.00) |
0.905 (1.00) |
0.84 (1.00) |
0.406 (1.00) |
0.31 (1.00) |
0.366 (1.00) |
0.0927 (1.00) |
0.981 (1.00) |
0.349 (1.00) |
amp 11q13 4 | 54 (18%) | 245 |
0.00103 (0.507) |
0.0959 (1.00) |
0.917 (1.00) |
0.873 (1.00) |
0.148 (1.00) |
0.757 (1.00) |
0.119 (1.00) |
0.0349 (1.00) |
0.872 (1.00) |
0.237 (1.00) |
amp 12q14 1 | 51 (17%) | 248 |
0.0111 (1.00) |
0.33 (1.00) |
0.87 (1.00) |
0.286 (1.00) |
0.0558 (1.00) |
0.114 (1.00) |
0.787 (1.00) |
0.42 (1.00) |
0.138 (1.00) |
0.853 (1.00) |
amp 12q15 | 50 (17%) | 249 |
0.0116 (1.00) |
0.682 (1.00) |
0.642 (1.00) |
0.558 (1.00) |
0.272 (1.00) |
0.444 (1.00) |
0.688 (1.00) |
0.566 (1.00) |
0.463 (1.00) |
0.753 (1.00) |
amp 19p13 2 | 56 (19%) | 243 |
0.107 (1.00) |
0.366 (1.00) |
0.44 (1.00) |
0.956 (1.00) |
0.0124 (1.00) |
0.101 (1.00) |
0.982 (1.00) |
0.371 (1.00) |
0.841 (1.00) |
0.21 (1.00) |
del 2q37 3 | 74 (25%) | 225 |
0.715 (1.00) |
0.0557 (1.00) |
0.0912 (1.00) |
0.00418 (1.00) |
0.00251 (1.00) |
0.062 (1.00) |
0.00643 (1.00) |
0.099 (1.00) |
0.217 (1.00) |
0.0567 (1.00) |
del 3p24 3 | 60 (20%) | 239 |
0.478 (1.00) |
0.375 (1.00) |
0.374 (1.00) |
0.523 (1.00) |
0.192 (1.00) |
0.391 (1.00) |
0.268 (1.00) |
0.437 (1.00) |
0.0991 (1.00) |
0.117 (1.00) |
del 3q23 | 48 (16%) | 251 |
0.144 (1.00) |
0.0532 (1.00) |
0.351 (1.00) |
0.431 (1.00) |
0.207 (1.00) |
0.543 (1.00) |
0.363 (1.00) |
0.458 (1.00) |
0.606 (1.00) |
0.447 (1.00) |
del 4q34 3 | 85 (28%) | 214 |
0.0196 (1.00) |
0.0127 (1.00) |
0.513 (1.00) |
0.552 (1.00) |
0.0561 (1.00) |
0.0129 (1.00) |
0.541 (1.00) |
0.00302 (1.00) |
0.215 (1.00) |
0.00725 (1.00) |
del 5p15 31 | 61 (20%) | 238 |
0.784 (1.00) |
0.345 (1.00) |
0.548 (1.00) |
0.538 (1.00) |
0.651 (1.00) |
0.67 (1.00) |
0.994 (1.00) |
0.583 (1.00) |
0.78 (1.00) |
0.42 (1.00) |
del 5q11 2 | 80 (27%) | 219 |
0.0015 (0.727) |
0.178 (1.00) |
0.573 (1.00) |
0.178 (1.00) |
0.468 (1.00) |
0.106 (1.00) |
0.851 (1.00) |
0.333 (1.00) |
0.613 (1.00) |
0.535 (1.00) |
del 5q31 3 | 111 (37%) | 188 |
0.00052 (0.261) |
0.00092 (0.454) |
0.62 (1.00) |
0.3 (1.00) |
0.39 (1.00) |
0.0942 (1.00) |
0.932 (1.00) |
0.352 (1.00) |
0.515 (1.00) |
0.398 (1.00) |
del 8p23 3 | 69 (23%) | 230 |
0.0799 (1.00) |
0.16 (1.00) |
0.202 (1.00) |
0.162 (1.00) |
0.0796 (1.00) |
0.793 (1.00) |
0.454 (1.00) |
0.321 (1.00) |
0.21 (1.00) |
0.782 (1.00) |
del 9p23 | 206 (69%) | 93 |
0.00083 (0.411) |
0.0199 (1.00) |
0.455 (1.00) |
0.613 (1.00) |
0.00422 (1.00) |
0.141 (1.00) |
0.0237 (1.00) |
0.0805 (1.00) |
0.568 (1.00) |
0.0589 (1.00) |
del 12q23 3 | 73 (24%) | 226 |
0.00068 (0.337) |
0.0206 (1.00) |
0.965 (1.00) |
0.822 (1.00) |
0.513 (1.00) |
0.283 (1.00) |
0.288 (1.00) |
0.224 (1.00) |
0.909 (1.00) |
0.764 (1.00) |
del 16p13 3 | 56 (19%) | 243 |
0.366 (1.00) |
0.022 (1.00) |
0.0124 (1.00) |
0.337 (1.00) |
0.0489 (1.00) |
0.874 (1.00) |
0.466 (1.00) |
0.59 (1.00) |
0.136 (1.00) |
0.238 (1.00) |
del 16q12 1 | 97 (32%) | 202 |
0.0912 (1.00) |
0.541 (1.00) |
0.0212 (1.00) |
0.685 (1.00) |
0.154 (1.00) |
0.262 (1.00) |
0.0861 (1.00) |
0.193 (1.00) |
0.22 (1.00) |
0.15 (1.00) |
del 16q24 3 | 107 (36%) | 192 |
0.0321 (1.00) |
0.652 (1.00) |
0.146 (1.00) |
0.907 (1.00) |
0.013 (1.00) |
0.051 (1.00) |
0.176 (1.00) |
0.0522 (1.00) |
0.0353 (1.00) |
0.042 (1.00) |
del 19p13 3 | 83 (28%) | 216 |
0.00677 (1.00) |
0.407 (1.00) |
0.00239 (1.00) |
0.0624 (1.00) |
0.00342 (1.00) |
0.221 (1.00) |
0.896 (1.00) |
0.443 (1.00) |
0.665 (1.00) |
0.125 (1.00) |
P value = 1e-05 (Fisher's exact test), Q value = 0.0054
Table S1. Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 85 | 57 | 51 | 106 |
AMP PEAK 2(1Q21.3) MUTATED | 76 | 13 | 37 | 32 |
AMP PEAK 2(1Q21.3) WILD-TYPE | 9 | 44 | 14 | 74 |
Figure S1. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'
![](D2V1.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0054
Table S2. Gene #3: 'amp_1q44' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 85 | 57 | 51 | 106 |
AMP PEAK 3(1Q44) MUTATED | 77 | 14 | 37 | 34 |
AMP PEAK 3(1Q44) WILD-TYPE | 8 | 43 | 14 | 72 |
Figure S2. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #1: 'CN_CNMF'
![](D3V1.png)
P value = 0.00012 (Fisher's exact test), Q value = 0.061
Table S3. Gene #6: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 85 | 57 | 51 | 106 |
AMP PEAK 6(5P15.33) MUTATED | 32 | 25 | 18 | 16 |
AMP PEAK 6(5P15.33) WILD-TYPE | 53 | 32 | 33 | 90 |
Figure S3. Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'
![](D6V1.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0054
Table S4. Gene #8: 'amp_6p24.3' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 85 | 57 | 51 | 106 |
AMP PEAK 8(6P24.3) MUTATED | 67 | 45 | 15 | 42 |
AMP PEAK 8(6P24.3) WILD-TYPE | 18 | 12 | 36 | 64 |
Figure S4. Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #1: 'CN_CNMF'
![](D8V1.png)
P value = 0.00039 (Fisher's exact test), Q value = 0.2
Table S5. Gene #8: 'amp_6p24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 76 | 80 | 36 | 95 |
AMP PEAK 8(6P24.3) MUTATED | 51 | 30 | 19 | 62 |
AMP PEAK 8(6P24.3) WILD-TYPE | 25 | 50 | 17 | 33 |
Figure S5. Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
![](D8V8.png)
P value = 4e-05 (Fisher's exact test), Q value = 0.021
Table S6. Gene #10: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 85 | 57 | 51 | 106 |
AMP PEAK 10(7P22.1) MUTATED | 47 | 34 | 41 | 42 |
AMP PEAK 10(7P22.1) WILD-TYPE | 38 | 23 | 10 | 64 |
Figure S6. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'
![](D10V1.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0054
Table S7. Gene #11: 'amp_7q34' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 85 | 57 | 51 | 106 |
AMP PEAK 11(7Q34) MUTATED | 45 | 35 | 47 | 50 |
AMP PEAK 11(7Q34) WILD-TYPE | 40 | 22 | 4 | 56 |
Figure S7. Get High-res Image Gene #11: 'amp_7q34' versus Molecular Subtype #1: 'CN_CNMF'
![](D11V1.png)
P value = 2e-05 (Fisher's exact test), Q value = 0.01
Table S8. Gene #12: 'amp_8q11.21' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 85 | 57 | 51 | 106 |
AMP PEAK 12(8Q11.21) MUTATED | 44 | 37 | 29 | 27 |
AMP PEAK 12(8Q11.21) WILD-TYPE | 41 | 20 | 22 | 79 |
Figure S8. Get High-res Image Gene #12: 'amp_8q11.21' versus Molecular Subtype #1: 'CN_CNMF'
![](D12V1.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0054
Table S9. Gene #13: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 85 | 57 | 51 | 106 |
AMP PEAK 13(8Q24.21) MUTATED | 53 | 41 | 30 | 34 |
AMP PEAK 13(8Q24.21) WILD-TYPE | 32 | 16 | 21 | 72 |
Figure S9. Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'
![](D13V1.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0054
Table S10. Gene #18: 'amp_13q12.3' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 85 | 57 | 51 | 106 |
AMP PEAK 18(13Q12.3) MUTATED | 32 | 32 | 10 | 11 |
AMP PEAK 18(13Q12.3) WILD-TYPE | 53 | 25 | 41 | 95 |
Figure S10. Get High-res Image Gene #18: 'amp_13q12.3' versus Molecular Subtype #1: 'CN_CNMF'
![](D18V1.png)
P value = 7e-05 (Fisher's exact test), Q value = 0.036
Table S11. Gene #18: 'amp_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 112 | 111 | 76 |
AMP PEAK 18(13Q12.3) MUTATED | 29 | 20 | 36 |
AMP PEAK 18(13Q12.3) WILD-TYPE | 83 | 91 | 40 |
Figure S11. Get High-res Image Gene #18: 'amp_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D18V2.png)
P value = 0.00034 (Fisher's exact test), Q value = 0.17
Table S12. Gene #19: 'amp_15q26.2' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 85 | 57 | 51 | 106 |
AMP PEAK 19(15Q26.2) MUTATED | 27 | 16 | 30 | 26 |
AMP PEAK 19(15Q26.2) WILD-TYPE | 58 | 41 | 21 | 80 |
Figure S12. Get High-res Image Gene #19: 'amp_15q26.2' versus Molecular Subtype #1: 'CN_CNMF'
![](D19V1.png)
P value = 1e-04 (Fisher's exact test), Q value = 0.051
Table S13. Gene #20: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 85 | 57 | 51 | 106 |
AMP PEAK 20(17Q25.3) MUTATED | 39 | 23 | 19 | 19 |
AMP PEAK 20(17Q25.3) WILD-TYPE | 46 | 34 | 32 | 87 |
Figure S13. Get High-res Image Gene #20: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'
![](D20V1.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0054
Table S14. Gene #22: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 85 | 57 | 51 | 106 |
AMP PEAK 22(20Q13.33) MUTATED | 47 | 36 | 36 | 34 |
AMP PEAK 22(20Q13.33) WILD-TYPE | 38 | 21 | 15 | 72 |
Figure S14. Get High-res Image Gene #22: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'
![](D22V1.png)
P value = 0.00011 (Fisher's exact test), Q value = 0.056
Table S15. Gene #23: 'amp_22q13.2' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 85 | 57 | 51 | 106 |
AMP PEAK 23(22Q13.2) MUTATED | 44 | 20 | 32 | 31 |
AMP PEAK 23(22Q13.2) WILD-TYPE | 41 | 37 | 19 | 75 |
Figure S15. Get High-res Image Gene #23: 'amp_22q13.2' versus Molecular Subtype #1: 'CN_CNMF'
![](D23V1.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0054
Table S16. Gene #24: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 112 | 111 | 76 |
DEL PEAK 1(1P36.31) MUTATED | 20 | 16 | 34 |
DEL PEAK 1(1P36.31) WILD-TYPE | 92 | 95 | 42 |
Figure S16. Get High-res Image Gene #24: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D24V2.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0054
Table S17. Gene #25: 'del_1p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 112 | 111 | 76 |
DEL PEAK 2(1P22.1) MUTATED | 19 | 22 | 35 |
DEL PEAK 2(1P22.1) WILD-TYPE | 93 | 89 | 41 |
Figure S17. Get High-res Image Gene #25: 'del_1p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D25V2.png)
P value = 2e-05 (Fisher's exact test), Q value = 0.01
Table S18. Gene #25: 'del_1p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 99 | 87 | 112 |
DEL PEAK 2(1P22.1) MUTATED | 40 | 9 | 27 |
DEL PEAK 2(1P22.1) WILD-TYPE | 59 | 78 | 85 |
Figure S18. Get High-res Image Gene #25: 'del_1p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
![](D25V5.png)
P value = 0.00036 (Fisher's exact test), Q value = 0.18
Table S19. Gene #25: 'del_1p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 70 | 178 | 50 |
DEL PEAK 2(1P22.1) MUTATED | 18 | 34 | 24 |
DEL PEAK 2(1P22.1) WILD-TYPE | 52 | 144 | 26 |
Figure S19. Get High-res Image Gene #25: 'del_1p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
![](D25V6.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0054
Table S20. Gene #33: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 85 | 57 | 51 | 106 |
DEL PEAK 10(6Q22.31) MUTATED | 55 | 46 | 40 | 38 |
DEL PEAK 10(6Q22.31) WILD-TYPE | 30 | 11 | 11 | 68 |
Figure S20. Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'
![](D33V1.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0054
Table S21. Gene #34: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 85 | 57 | 51 | 106 |
DEL PEAK 11(6Q26) MUTATED | 60 | 46 | 40 | 38 |
DEL PEAK 11(6Q26) WILD-TYPE | 25 | 11 | 11 | 68 |
Figure S21. Get High-res Image Gene #34: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'
![](D34V1.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0054
Table S22. Gene #37: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 85 | 57 | 51 | 106 |
DEL PEAK 14(9P21.3) MUTATED | 65 | 55 | 44 | 65 |
DEL PEAK 14(9P21.3) WILD-TYPE | 20 | 2 | 7 | 41 |
Figure S22. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'
![](D37V1.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0054
Table S23. Gene #37: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 99 | 87 | 112 |
DEL PEAK 14(9P21.3) MUTATED | 90 | 54 | 84 |
DEL PEAK 14(9P21.3) WILD-TYPE | 9 | 33 | 28 |
Figure S23. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
![](D37V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0054
Table S24. Gene #38: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 85 | 57 | 51 | 106 |
DEL PEAK 15(10P15.3) MUTATED | 50 | 37 | 41 | 35 |
DEL PEAK 15(10P15.3) WILD-TYPE | 35 | 20 | 10 | 71 |
Figure S24. Get High-res Image Gene #38: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'
![](D38V1.png)
P value = 7e-05 (Fisher's exact test), Q value = 0.036
Table S25. Gene #38: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 99 | 87 | 112 |
DEL PEAK 15(10P15.3) MUTATED | 72 | 38 | 53 |
DEL PEAK 15(10P15.3) WILD-TYPE | 27 | 49 | 59 |
Figure S25. Get High-res Image Gene #38: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
![](D38V5.png)
P value = 0.00011 (Fisher's exact test), Q value = 0.056
Table S26. Gene #38: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 70 | 178 | 50 |
DEL PEAK 15(10P15.3) MUTATED | 40 | 83 | 40 |
DEL PEAK 15(10P15.3) WILD-TYPE | 30 | 95 | 10 |
Figure S26. Get High-res Image Gene #38: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
![](D38V6.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0054
Table S27. Gene #39: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 85 | 57 | 51 | 106 |
DEL PEAK 16(10Q23.31) MUTATED | 51 | 42 | 48 | 47 |
DEL PEAK 16(10Q23.31) WILD-TYPE | 34 | 15 | 3 | 59 |
Figure S27. Get High-res Image Gene #39: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'
![](D39V1.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0054
Table S28. Gene #40: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 85 | 57 | 51 | 106 |
DEL PEAK 17(10Q26.3) MUTATED | 49 | 45 | 48 | 51 |
DEL PEAK 17(10Q26.3) WILD-TYPE | 36 | 12 | 3 | 55 |
Figure S28. Get High-res Image Gene #40: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'
![](D40V1.png)
P value = 3e-05 (Fisher's exact test), Q value = 0.015
Table S29. Gene #40: 'del_10q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 99 | 87 | 112 |
DEL PEAK 17(10Q26.3) MUTATED | 82 | 47 | 64 |
DEL PEAK 17(10Q26.3) WILD-TYPE | 17 | 40 | 48 |
Figure S29. Get High-res Image Gene #40: 'del_10q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
![](D40V5.png)
P value = 0.00031 (Fisher's exact test), Q value = 0.16
Table S30. Gene #40: 'del_10q26.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 70 | 178 | 50 |
DEL PEAK 17(10Q26.3) MUTATED | 43 | 106 | 44 |
DEL PEAK 17(10Q26.3) WILD-TYPE | 27 | 72 | 6 |
Figure S30. Get High-res Image Gene #40: 'del_10q26.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
![](D40V6.png)
P value = 1e-04 (Fisher's exact test), Q value = 0.051
Table S31. Gene #41: 'del_11p11.2' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 85 | 57 | 51 | 106 |
DEL PEAK 18(11P11.2) MUTATED | 42 | 13 | 19 | 22 |
DEL PEAK 18(11P11.2) WILD-TYPE | 43 | 44 | 32 | 84 |
Figure S31. Get High-res Image Gene #41: 'del_11p11.2' versus Molecular Subtype #1: 'CN_CNMF'
![](D41V1.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0054
Table S32. Gene #42: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 85 | 57 | 51 | 106 |
DEL PEAK 19(11Q23.3) MUTATED | 66 | 24 | 32 | 39 |
DEL PEAK 19(11Q23.3) WILD-TYPE | 19 | 33 | 19 | 67 |
Figure S32. Get High-res Image Gene #42: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'
![](D42V1.png)
P value = 8e-05 (Fisher's exact test), Q value = 0.041
Table S33. Gene #44: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 85 | 57 | 51 | 106 |
DEL PEAK 21(13Q12.11) MUTATED | 20 | 6 | 24 | 18 |
DEL PEAK 21(13Q12.11) WILD-TYPE | 65 | 51 | 27 | 88 |
Figure S33. Get High-res Image Gene #44: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'
![](D44V1.png)
P value = 0.00036 (Fisher's exact test), Q value = 0.18
Table S34. Gene #45: 'del_13q34' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 85 | 57 | 51 | 106 |
DEL PEAK 22(13Q34) MUTATED | 20 | 5 | 22 | 21 |
DEL PEAK 22(13Q34) WILD-TYPE | 65 | 52 | 29 | 85 |
Figure S34. Get High-res Image Gene #45: 'del_13q34' versus Molecular Subtype #1: 'CN_CNMF'
![](D45V1.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0054
Table S35. Gene #46: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 85 | 57 | 51 | 106 |
DEL PEAK 23(14Q23.3) MUTATED | 21 | 32 | 29 | 20 |
DEL PEAK 23(14Q23.3) WILD-TYPE | 64 | 25 | 22 | 86 |
Figure S35. Get High-res Image Gene #46: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'
![](D46V1.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0054
Table S36. Gene #47: 'del_14q32.2' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 85 | 57 | 51 | 106 |
DEL PEAK 24(14Q32.2) MUTATED | 23 | 32 | 27 | 18 |
DEL PEAK 24(14Q32.2) WILD-TYPE | 62 | 25 | 24 | 88 |
Figure S36. Get High-res Image Gene #47: 'del_14q32.2' versus Molecular Subtype #1: 'CN_CNMF'
![](D47V1.png)
P value = 2e-05 (Fisher's exact test), Q value = 0.01
Table S37. Gene #48: 'del_15q13.3' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 85 | 57 | 51 | 106 |
DEL PEAK 25(15Q13.3) MUTATED | 33 | 20 | 4 | 16 |
DEL PEAK 25(15Q13.3) WILD-TYPE | 52 | 37 | 47 | 90 |
Figure S37. Get High-res Image Gene #48: 'del_15q13.3' versus Molecular Subtype #1: 'CN_CNMF'
![](D48V1.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0054
Table S38. Gene #49: 'del_15q14' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 85 | 57 | 51 | 106 |
DEL PEAK 26(15Q14) MUTATED | 35 | 20 | 1 | 17 |
DEL PEAK 26(15Q14) WILD-TYPE | 50 | 37 | 50 | 89 |
Figure S38. Get High-res Image Gene #49: 'del_15q14' versus Molecular Subtype #1: 'CN_CNMF'
![](D49V1.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0054
Table S39. Gene #50: 'del_15q15.2' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 85 | 57 | 51 | 106 |
DEL PEAK 27(15Q15.2) MUTATED | 37 | 23 | 1 | 17 |
DEL PEAK 27(15Q15.2) WILD-TYPE | 48 | 34 | 50 | 89 |
Figure S39. Get High-res Image Gene #50: 'del_15q15.2' versus Molecular Subtype #1: 'CN_CNMF'
![](D50V1.png)
-
Copy number data file = transformed.cor.cli.txt
-
Molecular subtype file = SKCM-TM.transferedmergedcluster.txt
-
Number of patients = 299
-
Number of significantly focal cnvs = 54
-
Number of molecular subtypes = 10
-
Exclude genes 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.
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.