This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.
Testing the association between copy number variation 80 arm-level events and 12 molecular subtypes across 515 patients, 192 significant findings detected with P value < 0.05 and Q value < 0.25.
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1p gain cnv correlated to 'CN_CNMF'.
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1q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
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2p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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2q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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3p gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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3q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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4p gain cnv correlated to 'CN_CNMF'.
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5p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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5q gain cnv correlated to 'METHLYATION_CNMF'.
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6p gain cnv correlated to 'METHLYATION_CNMF'.
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7p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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7q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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8p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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8q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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9p gain cnv correlated to 'MRNASEQ_CNMF'.
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10p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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10q gain cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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11p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
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11q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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12p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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12q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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14q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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15q gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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17p gain cnv correlated to 'CN_CNMF'.
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17q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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18p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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18q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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20p gain cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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20q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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21q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
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1p loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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3p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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4p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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4q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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5q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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6q loss cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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8p loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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9p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
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9q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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10p loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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10q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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11p loss cnv correlated to 'CN_CNMF'.
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12p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
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12q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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13q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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15q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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16p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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16q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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17p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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18p loss cnv correlated to 'CN_CNMF'.
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18q loss cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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19p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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19q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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20p loss cnv correlated to 'CN_CNMF'.
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21q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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22q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 192 significant findings detected.
Clinical Features |
MRNA CNMF |
MRNA CHIERARCHICAL |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
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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 | Fisher's exact test | Fisher's exact test | |
12p gain | 137 (27%) | 378 |
0.22 (1.00) |
0.0478 (1.00) |
1e-05 (0.00946) |
2e-05 (0.0169) |
0.00802 (1.00) |
0.357 (1.00) |
1e-05 (0.00946) |
1e-05 (0.00946) |
1e-05 (0.00946) |
1e-05 (0.00946) |
0.371 (1.00) |
2e-05 (0.0169) |
12q gain | 130 (25%) | 385 |
0.22 (1.00) |
0.137 (1.00) |
1e-05 (0.00946) |
1e-05 (0.00946) |
0.0232 (1.00) |
0.199 (1.00) |
1e-05 (0.00946) |
1e-05 (0.00946) |
1e-05 (0.00946) |
1e-05 (0.00946) |
0.226 (1.00) |
1e-05 (0.00946) |
17q gain | 191 (37%) | 324 |
0.306 (1.00) |
0.876 (1.00) |
1e-05 (0.00946) |
4e-05 (0.0326) |
0.297 (1.00) |
0.272 (1.00) |
4e-05 (0.0326) |
1e-05 (0.00946) |
0.00012 (0.0935) |
4e-05 (0.0326) |
0.395 (1.00) |
0.00029 (0.22) |
20q gain | 199 (39%) | 316 |
0.00426 (1.00) |
0.00892 (1.00) |
1e-05 (0.00946) |
1e-05 (0.00946) |
0.109 (1.00) |
0.249 (1.00) |
2e-05 (0.0169) |
1e-05 (0.00946) |
2e-05 (0.0169) |
0.00012 (0.0935) |
0.161 (1.00) |
1e-05 (0.00946) |
4p loss | 120 (23%) | 395 |
0.184 (1.00) |
0.382 (1.00) |
3e-05 (0.0248) |
1e-05 (0.00946) |
0.523 (1.00) |
0.693 (1.00) |
0.0001 (0.0786) |
2e-05 (0.0169) |
2e-05 (0.0169) |
1e-05 (0.00946) |
0.191 (1.00) |
0.0001 (0.0786) |
4q loss | 136 (26%) | 379 |
0.00045 (0.335) |
0.00678 (1.00) |
1e-05 (0.00946) |
1e-05 (0.00946) |
0.273 (1.00) |
0.337 (1.00) |
1e-05 (0.00946) |
1e-05 (0.00946) |
1e-05 (0.00946) |
1e-05 (0.00946) |
0.0579 (1.00) |
2e-05 (0.0169) |
5q loss | 141 (27%) | 374 |
0.064 (1.00) |
0.035 (1.00) |
1e-05 (0.00946) |
1e-05 (0.00946) |
0.0654 (1.00) |
0.0544 (1.00) |
2e-05 (0.0169) |
0.0001 (0.0786) |
1e-05 (0.00946) |
1e-05 (0.00946) |
0.467 (1.00) |
2e-05 (0.0169) |
22q loss | 220 (43%) | 295 |
0.126 (1.00) |
0.168 (1.00) |
1e-05 (0.00946) |
1e-05 (0.00946) |
0.89 (1.00) |
0.62 (1.00) |
1e-05 (0.00946) |
1e-05 (0.00946) |
7e-05 (0.0557) |
3e-05 (0.0248) |
0.112 (1.00) |
0.00016 (0.123) |
2p gain | 155 (30%) | 360 |
0.301 (1.00) |
0.242 (1.00) |
1e-05 (0.00946) |
1e-05 (0.00946) |
0.819 (1.00) |
0.973 (1.00) |
3e-05 (0.0248) |
4e-05 (0.0326) |
1e-05 (0.00946) |
0.00049 (0.363) |
0.0267 (1.00) |
0.00016 (0.123) |
7p gain | 264 (51%) | 251 |
0.853 (1.00) |
0.538 (1.00) |
1e-05 (0.00946) |
0.0015 (1.00) |
0.00077 (0.561) |
0.00777 (1.00) |
1e-05 (0.00946) |
1e-05 (0.00946) |
1e-05 (0.00946) |
0.00035 (0.264) |
0.00016 (0.123) |
1e-05 (0.00946) |
8q gain | 246 (48%) | 269 |
0.0236 (1.00) |
0.0474 (1.00) |
1e-05 (0.00946) |
1e-05 (0.00946) |
0.649 (1.00) |
0.793 (1.00) |
1e-05 (0.00946) |
1e-05 (0.00946) |
1e-05 (0.00946) |
0.00362 (1.00) |
0.0149 (1.00) |
6e-05 (0.0481) |
15q loss | 242 (47%) | 273 |
0.101 (1.00) |
0.282 (1.00) |
1e-05 (0.00946) |
0.00013 (0.101) |
0.0532 (1.00) |
0.00547 (1.00) |
1e-05 (0.00946) |
1e-05 (0.00946) |
3e-05 (0.0248) |
0.00461 (1.00) |
0.308 (1.00) |
1e-05 (0.00946) |
19p loss | 244 (47%) | 271 |
0.817 (1.00) |
1 (1.00) |
1e-05 (0.00946) |
1e-05 (0.00946) |
0.877 (1.00) |
0.389 (1.00) |
1e-05 (0.00946) |
1e-05 (0.00946) |
1e-05 (0.00946) |
1e-05 (0.00946) |
0.0312 (1.00) |
0.00157 (1.00) |
19q loss | 159 (31%) | 356 |
0.344 (1.00) |
0.461 (1.00) |
1e-05 (0.00946) |
0.00012 (0.0935) |
0.267 (1.00) |
0.6 (1.00) |
0.00015 (0.116) |
5e-05 (0.0403) |
5e-05 (0.0403) |
2e-05 (0.0169) |
0.284 (1.00) |
0.00911 (1.00) |
10p gain | 112 (22%) | 403 |
0.236 (1.00) |
0.298 (1.00) |
1e-05 (0.00946) |
1e-05 (0.00946) |
0.0314 (1.00) |
0.169 (1.00) |
5e-05 (0.0403) |
1e-05 (0.00946) |
0.00043 (0.321) |
0.00018 (0.137) |
0.306 (1.00) |
0.00094 (0.683) |
21q loss | 165 (32%) | 350 |
0.185 (1.00) |
0.145 (1.00) |
1e-05 (0.00946) |
0.00048 (0.356) |
0.0146 (1.00) |
0.048 (1.00) |
1e-05 (0.00946) |
1e-05 (0.00946) |
2e-05 (0.0169) |
9e-05 (0.0709) |
0.591 (1.00) |
0.00044 (0.328) |
3q gain | 92 (18%) | 423 |
0.0561 (1.00) |
0.0708 (1.00) |
5e-05 (0.0403) |
0.00013 (0.101) |
0.483 (1.00) |
0.0994 (1.00) |
1e-05 (0.00946) |
1e-05 (0.00946) |
0.0138 (1.00) |
0.0328 (1.00) |
0.143 (1.00) |
0.00107 (0.766) |
7q gain | 217 (42%) | 298 |
0.481 (1.00) |
0.31 (1.00) |
1e-05 (0.00946) |
0.00975 (1.00) |
0.0644 (1.00) |
0.0538 (1.00) |
1e-05 (0.00946) |
1e-05 (0.00946) |
0.00308 (1.00) |
0.00125 (0.891) |
0.149 (1.00) |
2e-05 (0.0169) |
11q gain | 118 (23%) | 397 |
0.0106 (1.00) |
0.0172 (1.00) |
1e-05 (0.00946) |
0.0134 (1.00) |
0.00854 (1.00) |
0.773 (1.00) |
0.00273 (1.00) |
0.00032 (0.242) |
0.00013 (0.101) |
3e-05 (0.0248) |
0.465 (1.00) |
0.00311 (1.00) |
14q gain | 126 (24%) | 389 |
0.804 (1.00) |
0.846 (1.00) |
1e-05 (0.00946) |
0.00315 (1.00) |
0.433 (1.00) |
0.126 (1.00) |
0.00016 (0.123) |
5e-05 (0.0403) |
7e-05 (0.0557) |
0.00171 (1.00) |
0.148 (1.00) |
0.153 (1.00) |
16q loss | 140 (27%) | 375 |
0.552 (1.00) |
0.626 (1.00) |
1e-05 (0.00946) |
3e-05 (0.0248) |
0.192 (1.00) |
0.038 (1.00) |
1e-05 (0.00946) |
3e-05 (0.0248) |
0.0104 (1.00) |
0.00282 (1.00) |
0.873 (1.00) |
0.00069 (0.505) |
18q loss | 216 (42%) | 299 |
0.517 (1.00) |
0.425 (1.00) |
1e-05 (0.00946) |
0.23 (1.00) |
0.00409 (1.00) |
3e-05 (0.0248) |
0.00011 (0.086) |
0.00013 (0.101) |
0.0427 (1.00) |
0.635 (1.00) |
0.594 (1.00) |
0.167 (1.00) |
5p gain | 274 (53%) | 241 |
0.798 (1.00) |
0.361 (1.00) |
1e-05 (0.00946) |
0.0952 (1.00) |
0.0509 (1.00) |
0.00339 (1.00) |
0.0414 (1.00) |
1e-05 (0.00946) |
0.0338 (1.00) |
0.126 (1.00) |
0.654 (1.00) |
0.00016 (0.123) |
18p gain | 93 (18%) | 422 |
0.877 (1.00) |
0.637 (1.00) |
4e-05 (0.0326) |
1e-05 (0.00946) |
0.183 (1.00) |
0.894 (1.00) |
0.0223 (1.00) |
0.00327 (1.00) |
0.0249 (1.00) |
0.0178 (1.00) |
0.15 (1.00) |
0.00025 (0.189) |
18q gain | 71 (14%) | 444 |
0.595 (1.00) |
0.147 (1.00) |
1e-05 (0.00946) |
1e-05 (0.00946) |
0.0714 (1.00) |
0.234 (1.00) |
2e-05 (0.0169) |
0.0006 (0.442) |
0.0127 (1.00) |
0.00258 (1.00) |
0.0439 (1.00) |
0.0031 (1.00) |
20p gain | 173 (34%) | 342 |
0.0701 (1.00) |
0.139 (1.00) |
0.00351 (1.00) |
0.00012 (0.0935) |
0.168 (1.00) |
0.515 (1.00) |
0.00037 (0.278) |
1e-05 (0.00946) |
6e-05 (0.0481) |
0.00051 (0.376) |
0.0632 (1.00) |
0.00039 (0.292) |
1p loss | 82 (16%) | 433 |
0.0811 (1.00) |
0.126 (1.00) |
1e-05 (0.00946) |
0.00128 (0.911) |
0.133 (1.00) |
0.135 (1.00) |
0.00015 (0.116) |
1e-05 (0.00946) |
0.226 (1.00) |
0.0315 (1.00) |
0.14 (1.00) |
0.263 (1.00) |
3p loss | 213 (41%) | 302 |
0.342 (1.00) |
0.113 (1.00) |
4e-05 (0.0326) |
6e-05 (0.0481) |
0.517 (1.00) |
0.321 (1.00) |
0.0406 (1.00) |
1e-05 (0.00946) |
0.0122 (1.00) |
0.00985 (1.00) |
0.256 (1.00) |
0.018 (1.00) |
8p loss | 202 (39%) | 313 |
0.131 (1.00) |
0.0797 (1.00) |
1e-05 (0.00946) |
0.00989 (1.00) |
0.266 (1.00) |
0.00649 (1.00) |
6e-05 (0.0481) |
1e-05 (0.00946) |
0.0056 (1.00) |
0.0151 (1.00) |
0.00763 (1.00) |
0.00305 (1.00) |
9q loss | 248 (48%) | 267 |
0.5 (1.00) |
0.902 (1.00) |
0.00011 (0.086) |
0.00022 (0.167) |
0.549 (1.00) |
0.0866 (1.00) |
0.135 (1.00) |
0.00037 (0.278) |
0.00237 (1.00) |
2e-05 (0.0169) |
0.174 (1.00) |
0.00457 (1.00) |
10p loss | 110 (21%) | 405 |
0.815 (1.00) |
0.788 (1.00) |
1e-05 (0.00946) |
0.033 (1.00) |
0.0624 (1.00) |
0.0169 (1.00) |
6e-05 (0.0481) |
1e-05 (0.00946) |
0.00314 (1.00) |
0.277 (1.00) |
0.0243 (1.00) |
0.0324 (1.00) |
13q loss | 252 (49%) | 263 |
0.106 (1.00) |
0.625 (1.00) |
1e-05 (0.00946) |
0.054 (1.00) |
0.00333 (1.00) |
0.0163 (1.00) |
1e-05 (0.00946) |
1e-05 (0.00946) |
0.00998 (1.00) |
0.0225 (1.00) |
0.234 (1.00) |
0.00335 (1.00) |
16p loss | 111 (22%) | 404 |
0.452 (1.00) |
0.483 (1.00) |
1e-05 (0.00946) |
7e-05 (0.0557) |
0.744 (1.00) |
0.00301 (1.00) |
8e-05 (0.0634) |
0.00103 (0.742) |
0.00358 (1.00) |
0.00433 (1.00) |
0.504 (1.00) |
0.00225 (1.00) |
2q gain | 140 (27%) | 375 |
0.126 (1.00) |
0.289 (1.00) |
1e-05 (0.00946) |
2e-05 (0.0169) |
0.915 (1.00) |
0.707 (1.00) |
0.0786 (1.00) |
0.0145 (1.00) |
0.0019 (1.00) |
0.089 (1.00) |
0.0153 (1.00) |
0.00877 (1.00) |
3p gain | 41 (8%) | 474 |
0.00186 (1.00) |
0.0372 (1.00) |
0.926 (1.00) |
0.743 (1.00) |
3e-05 (0.0248) |
0.00015 (0.116) |
0.111 (1.00) |
0.117 (1.00) |
0.557 (1.00) |
0.0149 (1.00) |
||
8p gain | 126 (24%) | 389 |
0.15 (1.00) |
0.254 (1.00) |
1e-05 (0.00946) |
0.0952 (1.00) |
0.59 (1.00) |
0.253 (1.00) |
0.00072 (0.526) |
9e-05 (0.0709) |
0.425 (1.00) |
0.839 (1.00) |
0.395 (1.00) |
0.478 (1.00) |
10q gain | 78 (15%) | 437 |
0.00229 (1.00) |
2e-05 (0.0169) |
0.36 (1.00) |
0.195 (1.00) |
0.00049 (0.363) |
3e-05 (0.0248) |
0.147 (1.00) |
0.0415 (1.00) |
0.984 (1.00) |
0.064 (1.00) |
||
11p gain | 96 (19%) | 419 |
0.0006 (0.442) |
0.00098 (0.71) |
2e-05 (0.0169) |
0.327 (1.00) |
0.00098 (0.71) |
0.678 (1.00) |
0.104 (1.00) |
0.00045 (0.335) |
0.00095 (0.69) |
1e-05 (0.00946) |
0.395 (1.00) |
0.0279 (1.00) |
15q gain | 39 (8%) | 476 |
0.193 (1.00) |
0.147 (1.00) |
0.798 (1.00) |
0.137 (1.00) |
0.272 (1.00) |
0.349 (1.00) |
1e-05 (0.00946) |
1e-05 (0.00946) |
0.737 (1.00) |
0.661 (1.00) |
0.145 (1.00) |
0.902 (1.00) |
6q loss | 217 (42%) | 298 |
0.247 (1.00) |
0.542 (1.00) |
0.00832 (1.00) |
0.00011 (0.086) |
0.2 (1.00) |
0.235 (1.00) |
0.131 (1.00) |
0.00022 (0.167) |
0.675 (1.00) |
0.00136 (0.963) |
0.744 (1.00) |
0.173 (1.00) |
10q loss | 132 (26%) | 383 |
0.816 (1.00) |
0.789 (1.00) |
4e-05 (0.0326) |
0.0307 (1.00) |
0.0295 (1.00) |
0.0302 (1.00) |
0.00136 (0.963) |
1e-05 (0.00946) |
0.00344 (1.00) |
0.00613 (1.00) |
0.0138 (1.00) |
0.00119 (0.85) |
12q loss | 99 (19%) | 416 |
0.555 (1.00) |
0.425 (1.00) |
4e-05 (0.0326) |
0.0844 (1.00) |
0.201 (1.00) |
0.0822 (1.00) |
0.00129 (0.917) |
8e-05 (0.0634) |
0.0956 (1.00) |
0.227 (1.00) |
0.906 (1.00) |
0.213 (1.00) |
17p loss | 215 (42%) | 300 |
0.551 (1.00) |
0.362 (1.00) |
1e-05 (0.00946) |
0.0001 (0.0786) |
0.0265 (1.00) |
0.00902 (1.00) |
0.00103 (0.742) |
0.00132 (0.936) |
0.297 (1.00) |
0.128 (1.00) |
0.77 (1.00) |
0.0166 (1.00) |
1p gain | 141 (27%) | 374 |
0.631 (1.00) |
1 (1.00) |
1e-05 (0.00946) |
0.612 (1.00) |
0.0133 (1.00) |
0.0279 (1.00) |
0.204 (1.00) |
0.0484 (1.00) |
0.0442 (1.00) |
0.2 (1.00) |
0.183 (1.00) |
0.0968 (1.00) |
1q gain | 311 (60%) | 204 |
0.121 (1.00) |
1 (1.00) |
0.0134 (1.00) |
0.00805 (1.00) |
0.00102 (0.735) |
0.0067 (1.00) |
0.128 (1.00) |
0.00031 (0.234) |
0.618 (1.00) |
0.0594 (1.00) |
0.0227 (1.00) |
0.118 (1.00) |
4p gain | 83 (16%) | 432 |
0.876 (1.00) |
1 (1.00) |
2e-05 (0.0169) |
0.153 (1.00) |
0.434 (1.00) |
0.111 (1.00) |
0.043 (1.00) |
0.283 (1.00) |
0.136 (1.00) |
0.237 (1.00) |
0.915 (1.00) |
0.18 (1.00) |
5q gain | 129 (25%) | 386 |
0.196 (1.00) |
0.288 (1.00) |
0.00954 (1.00) |
8e-05 (0.0634) |
0.372 (1.00) |
0.313 (1.00) |
0.00625 (1.00) |
0.0267 (1.00) |
0.158 (1.00) |
0.00994 (1.00) |
0.429 (1.00) |
0.0721 (1.00) |
6p gain | 142 (28%) | 373 |
0.353 (1.00) |
0.0879 (1.00) |
0.00034 (0.256) |
1e-05 (0.00946) |
0.031 (1.00) |
0.856 (1.00) |
0.0761 (1.00) |
0.00895 (1.00) |
0.0615 (1.00) |
0.00732 (1.00) |
0.642 (1.00) |
0.00985 (1.00) |
9p gain | 45 (9%) | 470 |
0.00129 (0.917) |
0.137 (1.00) |
0.939 (1.00) |
0.277 (1.00) |
0.00024 (0.182) |
0.00473 (1.00) |
0.15 (1.00) |
0.639 (1.00) |
0.0952 (1.00) |
0.138 (1.00) |
||
17p gain | 85 (17%) | 430 |
0.454 (1.00) |
0.687 (1.00) |
3e-05 (0.0248) |
0.0618 (1.00) |
0.96 (1.00) |
0.691 (1.00) |
0.0124 (1.00) |
0.0384 (1.00) |
0.0041 (1.00) |
0.063 (1.00) |
0.661 (1.00) |
0.387 (1.00) |
21q gain | 97 (19%) | 418 |
0.539 (1.00) |
0.264 (1.00) |
0.00515 (1.00) |
0.673 (1.00) |
0.431 (1.00) |
0.0221 (1.00) |
0.0298 (1.00) |
7e-05 (0.0557) |
0.682 (1.00) |
0.743 (1.00) |
0.456 (1.00) |
0.406 (1.00) |
9p loss | 264 (51%) | 251 |
0.0516 (1.00) |
0.601 (1.00) |
0.00049 (0.363) |
0.0211 (1.00) |
0.813 (1.00) |
0.0567 (1.00) |
0.00097 (0.703) |
6e-05 (0.0481) |
0.0172 (1.00) |
0.00061 (0.448) |
0.194 (1.00) |
0.0684 (1.00) |
11p loss | 112 (22%) | 403 |
0.0527 (1.00) |
0.126 (1.00) |
1e-05 (0.00946) |
0.00815 (1.00) |
0.707 (1.00) |
0.755 (1.00) |
0.00276 (1.00) |
0.00705 (1.00) |
0.0251 (1.00) |
0.0418 (1.00) |
0.202 (1.00) |
0.0421 (1.00) |
12p loss | 113 (22%) | 402 |
0.63 (1.00) |
0.881 (1.00) |
0.00101 (0.729) |
0.244 (1.00) |
0.0321 (1.00) |
0.15 (1.00) |
0.00608 (1.00) |
0.0002 (0.152) |
0.106 (1.00) |
0.347 (1.00) |
0.989 (1.00) |
0.153 (1.00) |
18p loss | 181 (35%) | 334 |
0.436 (1.00) |
0.454 (1.00) |
1e-05 (0.00946) |
0.608 (1.00) |
0.0229 (1.00) |
0.021 (1.00) |
0.0193 (1.00) |
0.00234 (1.00) |
0.0401 (1.00) |
0.375 (1.00) |
0.973 (1.00) |
0.596 (1.00) |
20p loss | 117 (23%) | 398 |
0.221 (1.00) |
0.241 (1.00) |
8e-05 (0.0634) |
0.00039 (0.292) |
0.00057 (0.42) |
0.00263 (1.00) |
0.00665 (1.00) |
0.0011 (0.786) |
0.951 (1.00) |
0.959 (1.00) |
0.252 (1.00) |
0.0178 (1.00) |
4q gain | 47 (9%) | 468 |
0.33 (1.00) |
0.582 (1.00) |
0.00142 (1.00) |
0.84 (1.00) |
0.68 (1.00) |
0.163 (1.00) |
0.00754 (1.00) |
0.0035 (1.00) |
0.071 (1.00) |
0.274 (1.00) |
0.506 (1.00) |
0.198 (1.00) |
6q gain | 60 (12%) | 455 |
1 (1.00) |
1 (1.00) |
0.0435 (1.00) |
0.00335 (1.00) |
0.431 (1.00) |
0.846 (1.00) |
0.163 (1.00) |
0.0142 (1.00) |
0.00922 (1.00) |
0.00842 (1.00) |
0.981 (1.00) |
0.256 (1.00) |
9q gain | 34 (7%) | 481 |
0.0306 (1.00) |
0.452 (1.00) |
0.773 (1.00) |
0.705 (1.00) |
0.0772 (1.00) |
0.116 (1.00) |
0.194 (1.00) |
0.805 (1.00) |
0.27 (1.00) |
0.135 (1.00) |
||
13q gain | 43 (8%) | 472 |
0.413 (1.00) |
0.543 (1.00) |
0.978 (1.00) |
0.00691 (1.00) |
0.0426 (1.00) |
0.0341 (1.00) |
0.0593 (1.00) |
0.128 (1.00) |
0.83 (1.00) |
0.363 (1.00) |
0.431 (1.00) |
0.537 (1.00) |
16p gain | 136 (26%) | 379 |
0.531 (1.00) |
0.336 (1.00) |
0.00924 (1.00) |
0.0129 (1.00) |
0.0863 (1.00) |
0.0214 (1.00) |
0.111 (1.00) |
0.00484 (1.00) |
0.00259 (1.00) |
0.721 (1.00) |
0.0265 (1.00) |
0.101 (1.00) |
16q gain | 102 (20%) | 413 |
0.439 (1.00) |
0.154 (1.00) |
0.00736 (1.00) |
0.0829 (1.00) |
0.0101 (1.00) |
0.0268 (1.00) |
0.45 (1.00) |
0.0219 (1.00) |
0.00147 (1.00) |
0.11 (1.00) |
0.16 (1.00) |
0.13 (1.00) |
19p gain | 33 (6%) | 482 |
0.192 (1.00) |
0.0418 (1.00) |
0.416 (1.00) |
0.735 (1.00) |
0.702 (1.00) |
0.774 (1.00) |
0.993 (1.00) |
0.746 (1.00) |
0.437 (1.00) |
0.858 (1.00) |
0.905 (1.00) |
0.475 (1.00) |
19q gain | 76 (15%) | 439 |
0.0497 (1.00) |
0.04 (1.00) |
0.00333 (1.00) |
0.0168 (1.00) |
0.872 (1.00) |
0.927 (1.00) |
0.216 (1.00) |
0.0143 (1.00) |
0.173 (1.00) |
0.478 (1.00) |
0.423 (1.00) |
0.00228 (1.00) |
22q gain | 62 (12%) | 453 |
0.11 (1.00) |
0.119 (1.00) |
0.00421 (1.00) |
0.925 (1.00) |
0.108 (1.00) |
0.282 (1.00) |
0.177 (1.00) |
0.0964 (1.00) |
0.449 (1.00) |
0.564 (1.00) |
0.278 (1.00) |
0.538 (1.00) |
xq gain | 77 (15%) | 438 |
0.658 (1.00) |
0.247 (1.00) |
0.00035 (0.264) |
0.1 (1.00) |
0.869 (1.00) |
0.151 (1.00) |
0.0516 (1.00) |
0.0201 (1.00) |
0.0448 (1.00) |
0.158 (1.00) |
0.268 (1.00) |
0.0692 (1.00) |
1q loss | 27 (5%) | 488 |
0.133 (1.00) |
0.0194 (1.00) |
0.106 (1.00) |
0.026 (1.00) |
0.0725 (1.00) |
0.173 (1.00) |
0.832 (1.00) |
0.498 (1.00) |
0.926 (1.00) |
0.146 (1.00) |
||
2p loss | 23 (4%) | 492 |
0.751 (1.00) |
0.58 (1.00) |
0.0645 (1.00) |
0.173 (1.00) |
0.549 (1.00) |
0.989 (1.00) |
0.974 (1.00) |
0.909 (1.00) |
0.0448 (1.00) |
0.491 (1.00) |
0.253 (1.00) |
0.125 (1.00) |
2q loss | 24 (5%) | 491 |
0.00066 (0.484) |
0.0478 (1.00) |
0.463 (1.00) |
0.442 (1.00) |
0.292 (1.00) |
0.39 (1.00) |
0.14 (1.00) |
0.665 (1.00) |
0.632 (1.00) |
0.223 (1.00) |
||
3q loss | 146 (28%) | 369 |
0.553 (1.00) |
0.144 (1.00) |
0.00705 (1.00) |
0.0139 (1.00) |
0.806 (1.00) |
0.491 (1.00) |
0.0741 (1.00) |
0.00103 (0.742) |
0.233 (1.00) |
0.412 (1.00) |
0.389 (1.00) |
0.866 (1.00) |
5p loss | 44 (9%) | 471 |
0.597 (1.00) |
0.308 (1.00) |
0.198 (1.00) |
0.00922 (1.00) |
0.0874 (1.00) |
0.24 (1.00) |
0.00706 (1.00) |
0.00179 (1.00) |
0.114 (1.00) |
0.00178 (1.00) |
0.624 (1.00) |
0.00164 (1.00) |
6p loss | 105 (20%) | 410 |
0.0129 (1.00) |
0.00442 (1.00) |
0.0163 (1.00) |
0.219 (1.00) |
0.522 (1.00) |
0.264 (1.00) |
0.154 (1.00) |
0.254 (1.00) |
0.336 (1.00) |
0.0236 (1.00) |
0.734 (1.00) |
0.181 (1.00) |
7p loss | 35 (7%) | 480 |
1 (1.00) |
1 (1.00) |
0.00212 (1.00) |
0.0112 (1.00) |
0.291 (1.00) |
0.993 (1.00) |
0.00534 (1.00) |
0.00175 (1.00) |
0.0906 (1.00) |
0.141 (1.00) |
0.065 (1.00) |
0.0791 (1.00) |
7q loss | 42 (8%) | 473 |
0.805 (1.00) |
0.256 (1.00) |
0.0586 (1.00) |
0.0201 (1.00) |
0.889 (1.00) |
0.961 (1.00) |
0.111 (1.00) |
0.0375 (1.00) |
0.388 (1.00) |
0.143 (1.00) |
0.728 (1.00) |
0.825 (1.00) |
8q loss | 56 (11%) | 459 |
0.031 (1.00) |
0.664 (1.00) |
0.492 (1.00) |
0.249 (1.00) |
0.23 (1.00) |
0.0778 (1.00) |
0.535 (1.00) |
0.599 (1.00) |
0.149 (1.00) |
0.254 (1.00) |
||
11q loss | 90 (17%) | 425 |
0.841 (1.00) |
0.482 (1.00) |
0.0007 (0.512) |
0.0143 (1.00) |
0.305 (1.00) |
0.231 (1.00) |
0.00104 (0.746) |
0.00639 (1.00) |
0.0423 (1.00) |
0.0302 (1.00) |
0.0364 (1.00) |
0.213 (1.00) |
14q loss | 115 (22%) | 400 |
0.929 (1.00) |
0.411 (1.00) |
0.0202 (1.00) |
0.442 (1.00) |
0.331 (1.00) |
0.107 (1.00) |
0.0308 (1.00) |
0.00463 (1.00) |
0.0238 (1.00) |
0.17 (1.00) |
0.191 (1.00) |
0.0477 (1.00) |
17q loss | 58 (11%) | 457 |
0.293 (1.00) |
0.474 (1.00) |
0.00086 (0.626) |
0.0842 (1.00) |
0.00885 (1.00) |
0.0734 (1.00) |
0.138 (1.00) |
0.506 (1.00) |
0.836 (1.00) |
0.161 (1.00) |
0.98 (1.00) |
0.807 (1.00) |
20q loss | 69 (13%) | 446 |
0.256 (1.00) |
0.498 (1.00) |
0.456 (1.00) |
0.62 (1.00) |
0.105 (1.00) |
0.216 (1.00) |
0.529 (1.00) |
0.478 (1.00) |
0.497 (1.00) |
0.63 (1.00) |
0.0928 (1.00) |
0.897 (1.00) |
xq loss | 68 (13%) | 447 |
0.172 (1.00) |
0.254 (1.00) |
0.00046 (0.342) |
0.00477 (1.00) |
0.399 (1.00) |
0.813 (1.00) |
0.324 (1.00) |
0.58 (1.00) |
0.209 (1.00) |
0.13 (1.00) |
0.84 (1.00) |
0.455 (1.00) |
P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S1. Gene #1: '1p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
1P GAIN MUTATED | 81 | 44 | 16 |
1P GAIN WILD-TYPE | 110 | 185 | 79 |
Figure S1. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.23
Table S2. Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
1Q GAIN MUTATED | 54 | 38 | 15 | 46 | 36 | 36 | 30 | 6 | 31 |
1Q GAIN WILD-TYPE | 29 | 19 | 29 | 38 | 10 | 15 | 19 | 12 | 23 |
Figure S2. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S3. Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
2P GAIN MUTATED | 76 | 38 | 41 |
2P GAIN WILD-TYPE | 115 | 191 | 54 |
Figure S3. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S4. Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 125 | 108 | 116 |
2P GAIN MUTATED | 10 | 58 | 32 | 27 |
2P GAIN WILD-TYPE | 86 | 67 | 76 | 89 |
Figure S4. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025
Table S5. Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
2P GAIN MUTATED | 40 | 18 | 26 | 49 | 16 |
2P GAIN WILD-TYPE | 98 | 94 | 50 | 57 | 38 |
Figure S5. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.033
Table S6. Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
2P GAIN MUTATED | 23 | 11 | 11 | 32 | 8 | 26 | 22 | 0 | 16 |
2P GAIN WILD-TYPE | 60 | 46 | 33 | 52 | 38 | 25 | 27 | 18 | 38 |
Figure S6. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S7. Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 189 | 228 | 93 |
2P GAIN MUTATED | 40 | 95 | 19 |
2P GAIN WILD-TYPE | 149 | 133 | 74 |
Figure S7. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.12
Table S8. Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 248 | 83 |
2P GAIN MUTATED | 16 | 92 | 19 |
2P GAIN WILD-TYPE | 87 | 156 | 64 |
Figure S8. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S9. Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
2Q GAIN MUTATED | 63 | 38 | 39 |
2Q GAIN WILD-TYPE | 128 | 191 | 56 |
Figure S9. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017
Table S10. Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 125 | 108 | 116 |
2Q GAIN MUTATED | 13 | 50 | 32 | 23 |
2Q GAIN WILD-TYPE | 83 | 75 | 76 | 93 |
Figure S10. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025
Table S11. Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
3P GAIN MUTATED | 20 | 0 | 3 | 12 | 5 |
3P GAIN WILD-TYPE | 118 | 112 | 73 | 94 | 49 |
Figure S11. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.12
Table S12. Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
3P GAIN MUTATED | 11 | 0 | 4 | 17 | 1 | 2 | 2 | 0 | 3 |
3P GAIN WILD-TYPE | 72 | 57 | 40 | 67 | 45 | 49 | 47 | 18 | 51 |
Figure S12. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.04
Table S13. Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
3Q GAIN MUTATED | 47 | 23 | 22 |
3Q GAIN WILD-TYPE | 144 | 206 | 73 |
Figure S13. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.1
Table S14. Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 125 | 108 | 116 |
3Q GAIN MUTATED | 4 | 31 | 23 | 22 |
3Q GAIN WILD-TYPE | 92 | 94 | 85 | 94 |
Figure S14. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S15. Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
3Q GAIN MUTATED | 35 | 2 | 16 | 23 | 10 |
3Q GAIN WILD-TYPE | 103 | 110 | 60 | 83 | 44 |
Figure S15. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S16. Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
3Q GAIN MUTATED | 17 | 2 | 10 | 35 | 2 | 6 | 8 | 2 | 4 |
3Q GAIN WILD-TYPE | 66 | 55 | 34 | 49 | 44 | 45 | 41 | 16 | 50 |
Figure S16. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.017
Table S17. Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
4P GAIN MUTATED | 50 | 20 | 13 |
4P GAIN WILD-TYPE | 141 | 209 | 82 |
Figure S17. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S18. Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
5P GAIN MUTATED | 136 | 93 | 45 |
5P GAIN WILD-TYPE | 55 | 136 | 50 |
Figure S18. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S19. Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
5P GAIN MUTATED | 57 | 29 | 17 | 55 | 16 | 31 | 25 | 0 | 30 |
5P GAIN WILD-TYPE | 26 | 28 | 27 | 29 | 30 | 20 | 24 | 18 | 24 |
Figure S19. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.12
Table S20. Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 248 | 83 |
5P GAIN MUTATED | 37 | 149 | 49 |
5P GAIN WILD-TYPE | 66 | 99 | 34 |
Figure S20. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.063
Table S21. Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 125 | 108 | 116 |
5Q GAIN MUTATED | 43 | 27 | 21 | 23 |
5Q GAIN WILD-TYPE | 53 | 98 | 87 | 93 |
Figure S21. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S22. Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 125 | 108 | 116 |
6P GAIN MUTATED | 19 | 59 | 29 | 16 |
6P GAIN WILD-TYPE | 77 | 66 | 79 | 100 |
Figure S22. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S23. Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
7P GAIN MUTATED | 140 | 84 | 40 |
7P GAIN WILD-TYPE | 51 | 145 | 55 |
Figure S23. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S24. Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
7P GAIN MUTATED | 103 | 32 | 38 | 47 | 27 |
7P GAIN WILD-TYPE | 35 | 80 | 38 | 59 | 27 |
Figure S24. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S25. Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
7P GAIN MUTATED | 53 | 20 | 35 | 51 | 9 | 21 | 27 | 2 | 29 |
7P GAIN WILD-TYPE | 30 | 37 | 9 | 33 | 37 | 30 | 22 | 16 | 25 |
Figure S25. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S26. Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 189 | 228 | 93 |
7P GAIN MUTATED | 71 | 128 | 62 |
7P GAIN WILD-TYPE | 118 | 100 | 31 |
Figure S26. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.12
Table S27. Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 145 | 198 | 91 |
7P GAIN MUTATED | 61 | 102 | 63 |
7P GAIN WILD-TYPE | 84 | 96 | 28 |
Figure S27. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S28. Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 248 | 83 |
7P GAIN MUTATED | 29 | 147 | 50 |
7P GAIN WILD-TYPE | 74 | 101 | 33 |
Figure S28. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S29. Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
7Q GAIN MUTATED | 114 | 65 | 38 |
7Q GAIN WILD-TYPE | 77 | 164 | 57 |
Figure S29. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S30. Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
7Q GAIN MUTATED | 87 | 27 | 33 | 34 | 22 |
7Q GAIN WILD-TYPE | 51 | 85 | 43 | 72 | 32 |
Figure S30. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S31. Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
7Q GAIN MUTATED | 47 | 17 | 30 | 38 | 7 | 16 | 24 | 2 | 22 |
7Q GAIN WILD-TYPE | 36 | 40 | 14 | 46 | 39 | 35 | 25 | 16 | 32 |
Figure S31. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.017
Table S32. Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 248 | 83 |
7Q GAIN MUTATED | 22 | 120 | 40 |
7Q GAIN WILD-TYPE | 81 | 128 | 43 |
Figure S32. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S33. Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
8P GAIN MUTATED | 38 | 39 | 49 |
8P GAIN WILD-TYPE | 153 | 190 | 46 |
Figure S33. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.071
Table S34. Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
8P GAIN MUTATED | 21 | 6 | 8 | 17 | 14 | 24 | 16 | 0 | 12 |
8P GAIN WILD-TYPE | 62 | 51 | 36 | 67 | 32 | 27 | 33 | 18 | 42 |
Figure S34. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S35. Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
8Q GAIN MUTATED | 98 | 68 | 80 |
8Q GAIN WILD-TYPE | 93 | 161 | 15 |
Figure S35. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S36. Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 125 | 108 | 116 |
8Q GAIN MUTATED | 31 | 82 | 56 | 47 |
8Q GAIN WILD-TYPE | 65 | 43 | 52 | 69 |
Figure S36. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S37. Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
8Q GAIN MUTATED | 69 | 33 | 32 | 73 | 21 |
8Q GAIN WILD-TYPE | 69 | 79 | 44 | 33 | 33 |
Figure S37. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S38. Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
8Q GAIN MUTATED | 35 | 17 | 28 | 43 | 19 | 40 | 25 | 0 | 21 |
8Q GAIN WILD-TYPE | 48 | 40 | 16 | 41 | 27 | 11 | 24 | 18 | 33 |
Figure S38. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S39. Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 189 | 228 | 93 |
8Q GAIN MUTATED | 63 | 131 | 50 |
8Q GAIN WILD-TYPE | 126 | 97 | 43 |
Figure S39. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.048
Table S40. Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 248 | 83 |
8Q GAIN MUTATED | 32 | 142 | 37 |
8Q GAIN WILD-TYPE | 71 | 106 | 46 |
Figure S40. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.18
Table S41. Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
9P GAIN MUTATED | 14 | 4 | 0 | 16 | 7 |
9P GAIN WILD-TYPE | 124 | 108 | 76 | 90 | 47 |
Figure S41. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S42. Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
10P GAIN MUTATED | 44 | 31 | 37 |
10P GAIN WILD-TYPE | 147 | 198 | 58 |
Figure S42. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S43. Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 125 | 108 | 116 |
10P GAIN MUTATED | 5 | 44 | 34 | 16 |
10P GAIN WILD-TYPE | 91 | 81 | 74 | 100 |
Figure S43. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.04
Table S44. Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
10P GAIN MUTATED | 28 | 10 | 21 | 37 | 9 |
10P GAIN WILD-TYPE | 110 | 102 | 55 | 69 | 45 |
Figure S44. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S45. Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
10P GAIN MUTATED | 13 | 3 | 10 | 16 | 13 | 22 | 17 | 0 | 11 |
10P GAIN WILD-TYPE | 70 | 54 | 34 | 68 | 33 | 29 | 32 | 18 | 43 |
Figure S45. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.14
Table S46. Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 71 | 198 | 141 | 100 |
10P GAIN MUTATED | 12 | 58 | 15 | 25 |
10P GAIN WILD-TYPE | 59 | 140 | 126 | 75 |
Figure S46. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.017
Table S47. Gene #20: '10q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 125 | 108 | 116 |
10Q GAIN MUTATED | 4 | 33 | 23 | 10 |
10Q GAIN WILD-TYPE | 92 | 92 | 85 | 106 |
Figure S47. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025
Table S48. Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
10Q GAIN MUTATED | 10 | 2 | 7 | 7 | 13 | 16 | 13 | 0 | 7 |
10Q GAIN WILD-TYPE | 73 | 55 | 37 | 77 | 33 | 35 | 36 | 18 | 47 |
Figure S48. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.017
Table S49. Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
11P GAIN MUTATED | 48 | 23 | 25 |
11P GAIN WILD-TYPE | 143 | 206 | 70 |
Figure S49. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S50. Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 71 | 198 | 141 | 100 |
11P GAIN MUTATED | 4 | 40 | 17 | 34 |
11P GAIN WILD-TYPE | 67 | 158 | 124 | 66 |
Figure S50. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S51. Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
11Q GAIN MUTATED | 68 | 25 | 25 |
11Q GAIN WILD-TYPE | 123 | 204 | 70 |
Figure S51. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.24
Table S52. Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
11Q GAIN MUTATED | 22 | 15 | 11 | 27 | 1 | 18 | 9 | 1 | 9 |
11Q GAIN WILD-TYPE | 61 | 42 | 33 | 57 | 45 | 33 | 40 | 17 | 45 |
Figure S52. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.1
Table S53. Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 189 | 228 | 93 |
11Q GAIN MUTATED | 24 | 63 | 28 |
11Q GAIN WILD-TYPE | 165 | 165 | 65 |
Figure S53. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025
Table S54. Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 71 | 198 | 141 | 100 |
11Q GAIN MUTATED | 5 | 52 | 23 | 35 |
11Q GAIN WILD-TYPE | 66 | 146 | 118 | 65 |
Figure S54. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S55. Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
12P GAIN MUTATED | 56 | 37 | 44 |
12P GAIN WILD-TYPE | 135 | 192 | 51 |
Figure S55. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017
Table S56. Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 125 | 108 | 116 |
12P GAIN MUTATED | 10 | 52 | 28 | 30 |
12P GAIN WILD-TYPE | 86 | 73 | 80 | 86 |
Figure S56. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S57. Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
12P GAIN MUTATED | 41 | 5 | 30 | 42 | 12 |
12P GAIN WILD-TYPE | 97 | 107 | 46 | 64 | 42 |
Figure S57. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S58. Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
12P GAIN MUTATED | 17 | 5 | 16 | 26 | 3 | 27 | 24 | 2 | 10 |
12P GAIN WILD-TYPE | 66 | 52 | 28 | 58 | 43 | 24 | 25 | 16 | 44 |
Figure S58. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S59. Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 189 | 228 | 93 |
12P GAIN MUTATED | 29 | 82 | 24 |
12P GAIN WILD-TYPE | 160 | 146 | 69 |
Figure S59. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S60. Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 71 | 198 | 141 | 100 |
12P GAIN MUTATED | 10 | 58 | 20 | 47 |
12P GAIN WILD-TYPE | 61 | 140 | 121 | 53 |
Figure S60. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.017
Table S61. Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 248 | 83 |
12P GAIN MUTATED | 10 | 89 | 18 |
12P GAIN WILD-TYPE | 93 | 159 | 65 |
Figure S61. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S62. Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
12Q GAIN MUTATED | 46 | 36 | 48 |
12Q GAIN WILD-TYPE | 145 | 193 | 47 |
Figure S62. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S63. Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 125 | 108 | 116 |
12Q GAIN MUTATED | 7 | 50 | 28 | 29 |
12Q GAIN WILD-TYPE | 89 | 75 | 80 | 87 |
Figure S63. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S64. Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
12Q GAIN MUTATED | 32 | 6 | 29 | 49 | 9 |
12Q GAIN WILD-TYPE | 106 | 106 | 47 | 57 | 45 |
Figure S64. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S65. Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
12Q GAIN MUTATED | 16 | 6 | 15 | 20 | 3 | 32 | 25 | 2 | 6 |
12Q GAIN WILD-TYPE | 67 | 51 | 29 | 64 | 43 | 19 | 24 | 16 | 48 |
Figure S65. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S66. Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 189 | 228 | 93 |
12Q GAIN MUTATED | 27 | 82 | 19 |
12Q GAIN WILD-TYPE | 162 | 146 | 74 |
Figure S66. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S67. Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 71 | 198 | 141 | 100 |
12Q GAIN MUTATED | 13 | 58 | 14 | 43 |
12Q GAIN WILD-TYPE | 58 | 140 | 127 | 57 |
Figure S67. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S68. Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 248 | 83 |
12Q GAIN MUTATED | 8 | 84 | 19 |
12Q GAIN WILD-TYPE | 95 | 164 | 64 |
Figure S68. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S69. Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
14Q GAIN MUTATED | 50 | 34 | 42 |
14Q GAIN WILD-TYPE | 141 | 195 | 53 |
Figure S69. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.12
Table S70. Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
14Q GAIN MUTATED | 37 | 19 | 9 | 42 | 11 |
14Q GAIN WILD-TYPE | 101 | 93 | 67 | 64 | 43 |
Figure S70. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.04
Table S71. Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
14Q GAIN MUTATED | 14 | 12 | 11 | 38 | 8 | 19 | 8 | 0 | 8 |
14Q GAIN WILD-TYPE | 69 | 45 | 33 | 46 | 38 | 32 | 41 | 18 | 46 |
Figure S71. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.056
Table S72. Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 189 | 228 | 93 |
14Q GAIN MUTATED | 27 | 62 | 34 |
14Q GAIN WILD-TYPE | 162 | 166 | 59 |
Figure S72. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S73. Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
15Q GAIN MUTATED | 3 | 5 | 19 | 6 | 2 |
15Q GAIN WILD-TYPE | 135 | 107 | 57 | 100 | 52 |
Figure S73. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S74. Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
15Q GAIN MUTATED | 2 | 1 | 0 | 3 | 3 | 4 | 15 | 3 | 4 |
15Q GAIN WILD-TYPE | 81 | 56 | 44 | 81 | 43 | 47 | 34 | 15 | 50 |
Figure S74. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.025
Table S75. Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
17P GAIN MUTATED | 33 | 22 | 30 |
17P GAIN WILD-TYPE | 158 | 207 | 65 |
Figure S75. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S76. Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
17Q GAIN MUTATED | 99 | 47 | 45 |
17Q GAIN WILD-TYPE | 92 | 182 | 50 |
Figure S76. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.033
Table S77. Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 125 | 108 | 116 |
17Q GAIN MUTATED | 20 | 55 | 56 | 35 |
17Q GAIN WILD-TYPE | 76 | 70 | 52 | 81 |
Figure S77. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.033
Table S78. Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
17Q GAIN MUTATED | 72 | 28 | 20 | 44 | 18 |
17Q GAIN WILD-TYPE | 66 | 84 | 56 | 62 | 36 |
Figure S78. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S79. Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
17Q GAIN MUTATED | 40 | 19 | 21 | 41 | 5 | 26 | 14 | 0 | 16 |
17Q GAIN WILD-TYPE | 43 | 38 | 23 | 43 | 41 | 25 | 35 | 18 | 38 |
Figure S79. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.093
Table S80. Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 189 | 228 | 93 |
17Q GAIN MUTATED | 49 | 104 | 36 |
17Q GAIN WILD-TYPE | 140 | 124 | 57 |
Figure S80. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.033
Table S81. Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 71 | 198 | 141 | 100 |
17Q GAIN MUTATED | 19 | 87 | 34 | 49 |
17Q GAIN WILD-TYPE | 52 | 111 | 107 | 51 |
Figure S81. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.22
Table S82. Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 248 | 83 |
17Q GAIN MUTATED | 22 | 107 | 35 |
17Q GAIN WILD-TYPE | 81 | 141 | 48 |
Figure S82. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.033
Table S83. Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
18P GAIN MUTATED | 45 | 22 | 26 |
18P GAIN WILD-TYPE | 146 | 207 | 69 |
Figure S83. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S84. Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 125 | 108 | 116 |
18P GAIN MUTATED | 7 | 40 | 23 | 11 |
18P GAIN WILD-TYPE | 89 | 85 | 85 | 105 |
Figure S84. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.19
Table S85. Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 248 | 83 |
18P GAIN MUTATED | 6 | 57 | 16 |
18P GAIN WILD-TYPE | 97 | 191 | 67 |
Figure S85. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S86. Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
18Q GAIN MUTATED | 30 | 14 | 27 |
18Q GAIN WILD-TYPE | 161 | 215 | 68 |
Figure S86. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S87. Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 125 | 108 | 116 |
18Q GAIN MUTATED | 4 | 37 | 14 | 6 |
18Q GAIN WILD-TYPE | 92 | 88 | 94 | 110 |
Figure S87. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017
Table S88. Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
18Q GAIN MUTATED | 13 | 8 | 9 | 31 | 4 |
18Q GAIN WILD-TYPE | 125 | 104 | 67 | 75 | 50 |
Figure S88. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.093
Table S89. Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 125 | 108 | 116 |
20P GAIN MUTATED | 22 | 61 | 27 | 38 |
20P GAIN WILD-TYPE | 74 | 64 | 81 | 78 |
Figure S89. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S90. Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
20P GAIN MUTATED | 18 | 10 | 19 | 45 | 14 | 25 | 15 | 1 | 13 |
20P GAIN WILD-TYPE | 65 | 47 | 25 | 39 | 32 | 26 | 34 | 17 | 41 |
Figure S90. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.048
Table S91. Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 189 | 228 | 93 |
20P GAIN MUTATED | 41 | 90 | 40 |
20P GAIN WILD-TYPE | 148 | 138 | 53 |
Figure S91. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S92. Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
20Q GAIN MUTATED | 87 | 60 | 52 |
20Q GAIN WILD-TYPE | 104 | 169 | 43 |
Figure S92. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S93. Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 125 | 108 | 116 |
20Q GAIN MUTATED | 22 | 71 | 39 | 39 |
20Q GAIN WILD-TYPE | 74 | 54 | 69 | 77 |
Figure S93. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017
Table S94. Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
20Q GAIN MUTATED | 58 | 24 | 27 | 60 | 17 |
20Q GAIN WILD-TYPE | 80 | 88 | 49 | 46 | 37 |
Figure S94. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S95. Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
20Q GAIN MUTATED | 26 | 10 | 24 | 52 | 14 | 27 | 18 | 1 | 14 |
20Q GAIN WILD-TYPE | 57 | 47 | 20 | 32 | 32 | 24 | 31 | 17 | 40 |
Figure S95. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.017
Table S96. Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 189 | 228 | 93 |
20Q GAIN MUTATED | 47 | 107 | 41 |
20Q GAIN WILD-TYPE | 142 | 121 | 52 |
Figure S96. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.093
Table S97. Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 71 | 198 | 141 | 100 |
20Q GAIN MUTATED | 16 | 85 | 42 | 52 |
20Q GAIN WILD-TYPE | 55 | 113 | 99 | 48 |
Figure S97. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S98. Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 248 | 83 |
20Q GAIN MUTATED | 19 | 121 | 31 |
20Q GAIN WILD-TYPE | 84 | 127 | 52 |
Figure S98. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.056
Table S99. Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
21Q GAIN MUTATED | 25 | 17 | 5 | 24 | 3 | 4 | 7 | 0 | 8 |
21Q GAIN WILD-TYPE | 58 | 40 | 39 | 60 | 43 | 47 | 42 | 18 | 46 |
Figure S99. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S100. Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
1P LOSS MUTATED | 17 | 31 | 34 |
1P LOSS WILD-TYPE | 174 | 198 | 61 |
Figure S100. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.12
Table S101. Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
1P LOSS MUTATED | 19 | 10 | 15 | 29 | 2 |
1P LOSS WILD-TYPE | 119 | 102 | 61 | 77 | 52 |
Figure S101. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S102. Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
1P LOSS MUTATED | 7 | 7 | 10 | 5 | 10 | 20 | 12 | 1 | 3 |
1P LOSS WILD-TYPE | 76 | 50 | 34 | 79 | 36 | 31 | 37 | 17 | 51 |
Figure S102. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.033
Table S103. Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
3P LOSS MUTATED | 89 | 71 | 53 |
3P LOSS WILD-TYPE | 102 | 158 | 42 |
Figure S103. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.048
Table S104. Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 125 | 108 | 116 |
3P LOSS MUTATED | 33 | 73 | 41 | 38 |
3P LOSS WILD-TYPE | 63 | 52 | 67 | 78 |
Figure S104. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S105. Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
3P LOSS MUTATED | 28 | 25 | 14 | 42 | 17 | 34 | 26 | 0 | 18 |
3P LOSS WILD-TYPE | 55 | 32 | 30 | 42 | 29 | 17 | 23 | 18 | 36 |
Figure S105. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.025
Table S106. Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
4P LOSS MUTATED | 55 | 31 | 34 |
4P LOSS WILD-TYPE | 136 | 198 | 61 |
Figure S106. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S107. Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 125 | 108 | 116 |
4P LOSS MUTATED | 6 | 44 | 22 | 28 |
4P LOSS WILD-TYPE | 90 | 81 | 86 | 88 |
Figure S107. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.079
Table S108. Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
4P LOSS MUTATED | 30 | 12 | 22 | 40 | 11 |
4P LOSS WILD-TYPE | 108 | 100 | 54 | 66 | 43 |
Figure S108. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017
Table S109. Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
4P LOSS MUTATED | 16 | 9 | 7 | 35 | 2 | 20 | 14 | 2 | 10 |
4P LOSS WILD-TYPE | 67 | 48 | 37 | 49 | 44 | 31 | 35 | 16 | 44 |
Figure S109. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.017
Table S110. Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 189 | 228 | 93 |
4P LOSS MUTATED | 22 | 75 | 22 |
4P LOSS WILD-TYPE | 167 | 153 | 71 |
Figure S110. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S111. Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 71 | 198 | 141 | 100 |
4P LOSS MUTATED | 6 | 54 | 22 | 37 |
4P LOSS WILD-TYPE | 65 | 144 | 119 | 63 |
Figure S111. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.079
Table S112. Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 248 | 83 |
4P LOSS MUTATED | 12 | 75 | 12 |
4P LOSS WILD-TYPE | 91 | 173 | 71 |
Figure S112. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S113. Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
4Q LOSS MUTATED | 61 | 35 | 40 |
4Q LOSS WILD-TYPE | 130 | 194 | 55 |
Figure S113. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S114. Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 125 | 108 | 116 |
4Q LOSS MUTATED | 6 | 56 | 20 | 32 |
4Q LOSS WILD-TYPE | 90 | 69 | 88 | 84 |
Figure S114. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S115. Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
4Q LOSS MUTATED | 33 | 12 | 25 | 49 | 11 |
4Q LOSS WILD-TYPE | 105 | 100 | 51 | 57 | 43 |
Figure S115. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S116. Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
4Q LOSS MUTATED | 17 | 6 | 6 | 38 | 5 | 28 | 19 | 1 | 10 |
4Q LOSS WILD-TYPE | 66 | 51 | 38 | 46 | 41 | 23 | 30 | 17 | 44 |
Figure S116. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S117. Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 189 | 228 | 93 |
4Q LOSS MUTATED | 25 | 85 | 25 |
4Q LOSS WILD-TYPE | 164 | 143 | 68 |
Figure S117. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S118. Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 71 | 198 | 141 | 100 |
4Q LOSS MUTATED | 8 | 61 | 20 | 46 |
4Q LOSS WILD-TYPE | 63 | 137 | 121 | 54 |
Figure S118. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.017
Table S119. Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 248 | 83 |
4Q LOSS MUTATED | 13 | 84 | 16 |
4Q LOSS WILD-TYPE | 90 | 164 | 67 |
Figure S119. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S120. Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
5Q LOSS MUTATED | 68 | 34 | 39 |
5Q LOSS WILD-TYPE | 123 | 195 | 56 |
Figure S120. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S121. Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 125 | 108 | 116 |
5Q LOSS MUTATED | 9 | 50 | 34 | 26 |
5Q LOSS WILD-TYPE | 87 | 75 | 74 | 90 |
Figure S121. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017
Table S122. Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
5Q LOSS MUTATED | 44 | 12 | 22 | 44 | 9 |
5Q LOSS WILD-TYPE | 94 | 100 | 54 | 62 | 45 |
Figure S122. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.079
Table S123. Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
5Q LOSS MUTATED | 24 | 5 | 11 | 32 | 7 | 20 | 18 | 1 | 13 |
5Q LOSS WILD-TYPE | 59 | 52 | 33 | 52 | 39 | 31 | 31 | 17 | 41 |
Figure S123. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S124. Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 189 | 228 | 93 |
5Q LOSS MUTATED | 29 | 87 | 23 |
5Q LOSS WILD-TYPE | 160 | 141 | 70 |
Figure S124. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S125. Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 71 | 198 | 141 | 100 |
5Q LOSS MUTATED | 9 | 62 | 21 | 47 |
5Q LOSS WILD-TYPE | 62 | 136 | 120 | 53 |
Figure S125. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.017
Table S126. Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 248 | 83 |
5Q LOSS MUTATED | 12 | 91 | 18 |
5Q LOSS WILD-TYPE | 91 | 157 | 65 |
Figure S126. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.086
Table S127. Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 125 | 108 | 116 |
6Q LOSS MUTATED | 47 | 56 | 57 | 29 |
6Q LOSS WILD-TYPE | 49 | 69 | 51 | 87 |
Figure S127. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.17
Table S128. Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
6Q LOSS MUTATED | 43 | 20 | 22 | 23 | 28 | 29 | 16 | 4 | 21 |
6Q LOSS WILD-TYPE | 40 | 37 | 22 | 61 | 18 | 22 | 33 | 14 | 33 |
Figure S128. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S129. Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
8P LOSS MUTATED | 114 | 58 | 30 |
8P LOSS WILD-TYPE | 77 | 171 | 65 |
Figure S129. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.048
Table S130. Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
8P LOSS MUTATED | 77 | 36 | 23 | 40 | 14 |
8P LOSS WILD-TYPE | 61 | 76 | 53 | 66 | 40 |
Figure S130. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S131. Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
8P LOSS MUTATED | 39 | 23 | 25 | 46 | 8 | 15 | 14 | 2 | 18 |
8P LOSS WILD-TYPE | 44 | 34 | 19 | 38 | 38 | 36 | 35 | 16 | 36 |
Figure S131. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.048
Table S132. Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
9P LOSS MUTATED | 36 | 30 | 18 | 51 | 19 | 24 | 41 | 8 | 23 |
9P LOSS WILD-TYPE | 47 | 27 | 26 | 33 | 27 | 27 | 8 | 10 | 31 |
Figure S132. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.086
Table S133. Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
9Q LOSS MUTATED | 108 | 87 | 53 |
9Q LOSS WILD-TYPE | 83 | 142 | 42 |
Figure S133. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.17
Table S134. Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 125 | 108 | 116 |
9Q LOSS MUTATED | 36 | 79 | 44 | 48 |
9Q LOSS WILD-TYPE | 60 | 46 | 64 | 68 |
Figure S134. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017
Table S135. Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 71 | 198 | 141 | 100 |
9Q LOSS MUTATED | 29 | 92 | 54 | 70 |
9Q LOSS WILD-TYPE | 42 | 106 | 87 | 30 |
Figure S135. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S136. Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
10P LOSS MUTATED | 67 | 29 | 14 |
10P LOSS WILD-TYPE | 124 | 200 | 81 |
Figure S136. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.048
Table S137. Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
10P LOSS MUTATED | 46 | 18 | 5 | 23 | 15 |
10P LOSS WILD-TYPE | 92 | 94 | 71 | 83 | 39 |
Figure S137. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S138. Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
10P LOSS MUTATED | 18 | 16 | 10 | 36 | 0 | 10 | 4 | 2 | 11 |
10P LOSS WILD-TYPE | 65 | 41 | 34 | 48 | 46 | 41 | 45 | 16 | 43 |
Figure S138. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.033
Table S139. Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
10Q LOSS MUTATED | 70 | 39 | 23 |
10Q LOSS WILD-TYPE | 121 | 190 | 72 |
Figure S139. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S140. Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
10Q LOSS MUTATED | 23 | 16 | 12 | 44 | 0 | 10 | 9 | 2 | 11 |
10Q LOSS WILD-TYPE | 60 | 41 | 32 | 40 | 46 | 41 | 40 | 16 | 43 |
Figure S140. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S141. Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
11P LOSS MUTATED | 55 | 28 | 29 |
11P LOSS WILD-TYPE | 136 | 201 | 66 |
Figure S141. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.15
Table S142. Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
12P LOSS MUTATED | 22 | 17 | 5 | 28 | 11 | 3 | 4 | 2 | 14 |
12P LOSS WILD-TYPE | 61 | 40 | 39 | 56 | 35 | 48 | 45 | 16 | 40 |
Figure S142. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.033
Table S143. Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
12Q LOSS MUTATED | 55 | 36 | 8 |
12Q LOSS WILD-TYPE | 136 | 193 | 87 |
Figure S143. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.063
Table S144. Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
12Q LOSS MUTATED | 23 | 12 | 4 | 24 | 10 | 1 | 3 | 2 | 14 |
12Q LOSS WILD-TYPE | 60 | 45 | 40 | 60 | 36 | 50 | 46 | 16 | 40 |
Figure S144. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S145. Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
13Q LOSS MUTATED | 125 | 66 | 61 |
13Q LOSS WILD-TYPE | 66 | 163 | 34 |
Figure S145. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S146. Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
13Q LOSS MUTATED | 86 | 40 | 24 | 66 | 23 |
13Q LOSS WILD-TYPE | 52 | 72 | 52 | 40 | 31 |
Figure S146. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S147. Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
13Q LOSS MUTATED | 52 | 22 | 25 | 48 | 10 | 36 | 19 | 1 | 26 |
13Q LOSS WILD-TYPE | 31 | 35 | 19 | 36 | 36 | 15 | 30 | 17 | 28 |
Figure S147. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S148. Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
15Q LOSS MUTATED | 113 | 73 | 56 |
15Q LOSS WILD-TYPE | 78 | 156 | 39 |
Figure S148. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.1
Table S149. Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 125 | 108 | 116 |
15Q LOSS MUTATED | 27 | 65 | 63 | 53 |
15Q LOSS WILD-TYPE | 69 | 60 | 45 | 63 |
Figure S149. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S150. Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
15Q LOSS MUTATED | 92 | 37 | 13 | 61 | 26 |
15Q LOSS WILD-TYPE | 46 | 75 | 63 | 45 | 28 |
Figure S150. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S151. Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
15Q LOSS MUTATED | 48 | 23 | 31 | 49 | 7 | 34 | 9 | 0 | 28 |
15Q LOSS WILD-TYPE | 35 | 34 | 13 | 35 | 39 | 17 | 40 | 18 | 26 |
Figure S151. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.025
Table S152. Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 189 | 228 | 93 |
15Q LOSS MUTATED | 63 | 122 | 55 |
15Q LOSS WILD-TYPE | 126 | 106 | 38 |
Figure S152. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S153. Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 248 | 83 |
15Q LOSS MUTATED | 27 | 133 | 46 |
15Q LOSS WILD-TYPE | 76 | 115 | 37 |
Figure S153. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S154. Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
16P LOSS MUTATED | 50 | 28 | 33 |
16P LOSS WILD-TYPE | 141 | 201 | 62 |
Figure S154. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.056
Table S155. Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 125 | 108 | 116 |
16P LOSS MUTATED | 7 | 36 | 35 | 20 |
16P LOSS WILD-TYPE | 89 | 89 | 73 | 96 |
Figure S155. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.063
Table S156. Gene #68: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
16P LOSS MUTATED | 42 | 10 | 14 | 35 | 8 |
16P LOSS WILD-TYPE | 96 | 102 | 62 | 71 | 46 |
Figure S156. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S157. Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
16Q LOSS MUTATED | 62 | 39 | 39 |
16Q LOSS WILD-TYPE | 129 | 190 | 56 |
Figure S157. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025
Table S158. Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 125 | 108 | 116 |
16Q LOSS MUTATED | 12 | 42 | 42 | 24 |
16Q LOSS WILD-TYPE | 84 | 83 | 66 | 92 |
Figure S158. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S159. Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
16Q LOSS MUTATED | 59 | 15 | 16 | 39 | 9 |
16Q LOSS WILD-TYPE | 79 | 97 | 60 | 67 | 45 |
Figure S159. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025
Table S160. Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
16Q LOSS MUTATED | 35 | 7 | 20 | 29 | 9 | 17 | 10 | 0 | 11 |
16Q LOSS WILD-TYPE | 48 | 50 | 24 | 55 | 37 | 34 | 39 | 18 | 43 |
Figure S160. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S161. Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
17P LOSS MUTATED | 117 | 58 | 40 |
17P LOSS WILD-TYPE | 74 | 171 | 55 |
Figure S161. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.079
Table S162. Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 125 | 108 | 116 |
17P LOSS MUTATED | 28 | 53 | 63 | 39 |
17P LOSS WILD-TYPE | 68 | 72 | 45 | 77 |
Figure S162. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S163. Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
18P LOSS MUTATED | 92 | 61 | 28 |
18P LOSS WILD-TYPE | 99 | 168 | 67 |
Figure S163. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S164. Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
18Q LOSS MUTATED | 116 | 74 | 26 |
18Q LOSS WILD-TYPE | 75 | 155 | 69 |
Figure S164. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025
Table S165. Gene #73: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 40 | 33 | 45 | 31 | 32 |
18Q LOSS MUTATED | 17 | 6 | 34 | 15 | 12 |
18Q LOSS WILD-TYPE | 23 | 27 | 11 | 16 | 20 |
Figure S165. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.086
Table S166. Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
18Q LOSS MUTATED | 80 | 39 | 33 | 32 | 20 |
18Q LOSS WILD-TYPE | 58 | 73 | 43 | 74 | 34 |
Figure S166. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.1
Table S167. Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
18Q LOSS MUTATED | 39 | 27 | 25 | 42 | 7 | 14 | 24 | 9 | 17 |
18Q LOSS WILD-TYPE | 44 | 30 | 19 | 42 | 39 | 37 | 25 | 9 | 37 |
Figure S167. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S168. Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
19P LOSS MUTATED | 109 | 72 | 63 |
19P LOSS WILD-TYPE | 82 | 157 | 32 |
Figure S168. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S169. Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 125 | 108 | 116 |
19P LOSS MUTATED | 31 | 87 | 46 | 43 |
19P LOSS WILD-TYPE | 65 | 38 | 62 | 73 |
Figure S169. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S170. Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
19P LOSS MUTATED | 63 | 39 | 42 | 73 | 17 |
19P LOSS WILD-TYPE | 75 | 73 | 34 | 33 | 37 |
Figure S170. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S171. Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
19P LOSS MUTATED | 29 | 17 | 21 | 50 | 31 | 35 | 33 | 4 | 14 |
19P LOSS WILD-TYPE | 54 | 40 | 23 | 34 | 15 | 16 | 16 | 14 | 40 |
Figure S171. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S172. Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 189 | 228 | 93 |
19P LOSS MUTATED | 65 | 135 | 39 |
19P LOSS WILD-TYPE | 124 | 93 | 54 |
Figure S172. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S173. Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 71 | 198 | 141 | 100 |
19P LOSS MUTATED | 31 | 97 | 43 | 68 |
19P LOSS WILD-TYPE | 40 | 101 | 98 | 32 |
Figure S173. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S174. Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
19Q LOSS MUTATED | 82 | 38 | 39 |
19Q LOSS WILD-TYPE | 109 | 191 | 56 |
Figure S174. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.093
Table S175. Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 125 | 108 | 116 |
19Q LOSS MUTATED | 17 | 54 | 37 | 26 |
19Q LOSS WILD-TYPE | 79 | 71 | 71 | 90 |
Figure S175. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.12
Table S176. Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
19Q LOSS MUTATED | 47 | 23 | 23 | 50 | 10 |
19Q LOSS WILD-TYPE | 91 | 89 | 53 | 56 | 44 |
Figure S176. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.04
Table S177. Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
19Q LOSS MUTATED | 20 | 13 | 17 | 34 | 17 | 23 | 21 | 0 | 8 |
19Q LOSS WILD-TYPE | 63 | 44 | 27 | 50 | 29 | 28 | 28 | 18 | 46 |
Figure S177. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.04
Table S178. Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 189 | 228 | 93 |
19Q LOSS MUTATED | 38 | 90 | 27 |
19Q LOSS WILD-TYPE | 151 | 138 | 66 |
Figure S178. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017
Table S179. Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 71 | 198 | 141 | 100 |
19Q LOSS MUTATED | 18 | 64 | 25 | 48 |
19Q LOSS WILD-TYPE | 53 | 134 | 116 | 52 |
Figure S179. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.063
Table S180. Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
20P LOSS MUTATED | 62 | 33 | 22 |
20P LOSS WILD-TYPE | 129 | 196 | 73 |
Figure S180. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S181. Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
21Q LOSS MUTATED | 52 | 59 | 54 |
21Q LOSS WILD-TYPE | 139 | 170 | 41 |
Figure S181. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S182. Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
21Q LOSS MUTATED | 40 | 14 | 30 | 58 | 11 |
21Q LOSS WILD-TYPE | 98 | 98 | 46 | 48 | 43 |
Figure S182. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S183. Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
21Q LOSS MUTATED | 14 | 8 | 17 | 31 | 11 | 32 | 24 | 4 | 12 |
21Q LOSS WILD-TYPE | 69 | 49 | 27 | 53 | 35 | 19 | 25 | 14 | 42 |
Figure S183. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.017
Table S184. Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 189 | 228 | 93 |
21Q LOSS MUTATED | 39 | 96 | 27 |
21Q LOSS WILD-TYPE | 150 | 132 | 66 |
Figure S184. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.071
Table S185. Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 71 | 198 | 141 | 100 |
21Q LOSS MUTATED | 15 | 66 | 32 | 49 |
21Q LOSS WILD-TYPE | 56 | 132 | 109 | 51 |
Figure S185. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S186. Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 191 | 229 | 95 |
22Q LOSS MUTATED | 99 | 60 | 61 |
22Q LOSS WILD-TYPE | 92 | 169 | 34 |
Figure S186. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S187. Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 125 | 108 | 116 |
22Q LOSS MUTATED | 24 | 69 | 56 | 41 |
22Q LOSS WILD-TYPE | 72 | 56 | 52 | 75 |
Figure S187. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S188. Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
22Q LOSS MUTATED | 70 | 30 | 34 | 62 | 11 |
22Q LOSS WILD-TYPE | 68 | 82 | 42 | 44 | 43 |
Figure S188. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095
Table S189. Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 83 | 57 | 44 | 84 | 46 | 51 | 49 | 18 | 54 |
22Q LOSS MUTATED | 47 | 14 | 20 | 40 | 14 | 33 | 24 | 4 | 11 |
22Q LOSS WILD-TYPE | 36 | 43 | 24 | 44 | 32 | 18 | 25 | 14 | 43 |
Figure S189. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.056
Table S190. Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 189 | 228 | 93 |
22Q LOSS MUTATED | 58 | 119 | 39 |
22Q LOSS WILD-TYPE | 131 | 109 | 54 |
Figure S190. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025
Table S191. Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 71 | 198 | 141 | 100 |
22Q LOSS MUTATED | 21 | 100 | 41 | 54 |
22Q LOSS WILD-TYPE | 50 | 98 | 100 | 46 |
Figure S191. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.12
Table S192. Gene #79: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 248 | 83 |
22Q LOSS MUTATED | 28 | 128 | 31 |
22Q LOSS WILD-TYPE | 75 | 120 | 52 |
Figure S192. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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Copy number data file = transformed.cor.cli.txt
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Molecular subtypes file = LUAD-TP.transferedmergedcluster.txt
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Number of patients = 515
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Number of significantly arm-level cnvs = 80
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Number of molecular subtypes = 12
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Exclude genes that fewer than K tumors have mutations, 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.