This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and subtypes.
Testing the association between copy number variation 79 arm-level results and 10 molecular subtypes across 492 patients, 236 significant findings detected with Q value < 0.25.
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1q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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2p gain cnv correlated to 'CN_CNMF'.
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2q gain cnv correlated to 'CN_CNMF'.
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3p gain cnv correlated to 'CN_CNMF'.
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3q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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5p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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6p gain cnv correlated to 'CN_CNMF'.
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6q gain cnv correlated to 'CN_CNMF'.
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7p gain cnv correlated to 'CN_CNMF'.
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7q gain cnv correlated to 'CN_CNMF'.
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8p gain cnv correlated to 'CN_CNMF'.
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8q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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10q gain cnv correlated to 'CN_CNMF'.
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12p gain cnv correlated to 'CN_CNMF'.
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12q gain cnv correlated to 'CN_CNMF'.
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13q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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14q gain cnv correlated to 'CN_CNMF'.
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17p gain cnv correlated to 'CN_CNMF'.
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18p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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18q gain cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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19p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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19q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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20p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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20q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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21q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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22q gain cnv correlated to 'METHLYATION_CNMF'.
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Xq gain cnv correlated to 'CN_CNMF'.
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1p loss cnv correlated to 'CN_CNMF'.
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3p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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3q loss cnv correlated to 'CN_CNMF'.
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4p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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4q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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5p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.
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5q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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6q loss cnv correlated to 'CN_CNMF'.
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7p loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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7q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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8p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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8q loss cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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9p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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9q loss cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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10p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
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10q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
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11p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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11q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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12p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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12q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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13q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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14q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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15q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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16p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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16q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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17p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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17q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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18p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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18q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_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', 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', and 'MIRSEQ_CHIERARCHICAL'.
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22q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Xq loss cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 79 arm-level results and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 236 significant findings detected.
Molecular subtypes |
MRNA CNMF |
MRNA CHIERARCHICAL |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
||
nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
3p loss | 0 (0%) | 461 |
1.34e-14 (8.84e-12) |
0.000141 (0.0699) |
0.000526 (0.244) |
0.028 (1.00) |
1.79e-07 (0.000103) |
8.63e-08 (5.04e-05) |
4.21e-05 (0.0216) |
2.37e-05 (0.0124) |
||
9q loss | 0 (0%) | 399 |
0.0015 (0.657) |
0.000248 (0.119) |
1.53e-37 (1.07e-34) |
5.86e-07 (0.000332) |
0.00601 (1.00) |
0.378 (1.00) |
2.56e-13 (1.68e-10) |
2.82e-16 (1.88e-13) |
2.09e-12 (1.36e-09) |
3.83e-10 (2.38e-07) |
3q gain | 0 (0%) | 442 |
0.176 (1.00) |
0.0543 (1.00) |
3.41e-22 (2.34e-19) |
2.49e-05 (0.013) |
0.388 (1.00) |
0.301 (1.00) |
1.19e-06 (0.000666) |
5.14e-05 (0.0261) |
2.07e-05 (0.0109) |
0.000263 (0.126) |
5p gain | 0 (0%) | 460 |
0.86 (1.00) |
0.623 (1.00) |
3.01e-09 (1.83e-06) |
0.000136 (0.0674) |
0.0311 (1.00) |
0.712 (1.00) |
3.95e-06 (0.00215) |
0.00042 (0.197) |
1.66e-05 (0.00884) |
5.29e-05 (0.0268) |
18p gain | 0 (0%) | 455 |
0.0591 (1.00) |
0.133 (1.00) |
4.94e-14 (3.26e-11) |
6.64e-05 (0.0336) |
0.093 (1.00) |
0.429 (1.00) |
3.34e-05 (0.0173) |
7.28e-07 (0.000411) |
4.26e-09 (2.58e-06) |
6.47e-09 (3.9e-06) |
4p loss | 0 (0%) | 426 |
0.0729 (1.00) |
0.0133 (1.00) |
4.79e-25 (3.3e-22) |
7.08e-11 (4.47e-08) |
0.0339 (1.00) |
0.393 (1.00) |
2.45e-09 (1.49e-06) |
1.29e-07 (7.48e-05) |
1.88e-13 (1.23e-10) |
4.44e-12 (2.88e-09) |
4q loss | 0 (0%) | 428 |
0.683 (1.00) |
0.371 (1.00) |
1.36e-26 (9.39e-24) |
2.66e-11 (1.69e-08) |
0.131 (1.00) |
0.776 (1.00) |
2.64e-08 (1.57e-05) |
2.45e-08 (1.45e-05) |
1.04e-10 (6.55e-08) |
1.39e-10 (8.69e-08) |
5q loss | 0 (0%) | 447 |
0.0729 (1.00) |
0.0133 (1.00) |
1.18e-18 (7.99e-16) |
7.26e-09 (4.37e-06) |
0.0481 (1.00) |
0.153 (1.00) |
6.28e-08 (3.69e-05) |
2.96e-08 (1.76e-05) |
2.83e-09 (1.72e-06) |
7.58e-08 (4.44e-05) |
7q loss | 0 (0%) | 465 |
4.91e-14 (3.24e-11) |
0.00018 (0.0884) |
0.197 (1.00) |
0.0121 (1.00) |
1.32e-07 (7.64e-05) |
1.59e-06 (0.000886) |
1.77e-05 (0.00942) |
1.25e-05 (0.0067) |
||
8p loss | 0 (0%) | 439 |
0.0191 (1.00) |
0.00403 (1.00) |
4.01e-24 (2.75e-21) |
1.08e-11 (6.92e-09) |
0.165 (1.00) |
0.181 (1.00) |
4.84e-12 (3.13e-09) |
6.9e-10 (4.28e-07) |
4.01e-15 (2.67e-12) |
7.17e-17 (4.82e-14) |
9p loss | 0 (0%) | 416 |
0.0227 (1.00) |
0.00379 (1.00) |
2.63e-29 (1.82e-26) |
2.34e-06 (0.00129) |
0.0117 (1.00) |
0.244 (1.00) |
2.12e-12 (1.38e-09) |
7.6e-15 (5.04e-12) |
1.37e-09 (8.42e-07) |
1.19e-08 (7.13e-06) |
11p loss | 0 (0%) | 439 |
1.44e-21 (9.89e-19) |
7.44e-07 (0.000419) |
0.182 (1.00) |
0.75 (1.00) |
4.46e-08 (2.63e-05) |
2.6e-07 (0.000149) |
1.99e-08 (1.18e-05) |
1.99e-06 (0.0011) |
||
11q loss | 0 (0%) | 447 |
1.15e-15 (7.67e-13) |
7.53e-05 (0.0379) |
0.925 (1.00) |
0.713 (1.00) |
0.000397 (0.187) |
8.07e-06 (0.00436) |
2.54e-06 (0.0014) |
0.000184 (0.09) |
||
13q loss | 0 (0%) | 432 |
0.683 (1.00) |
0.371 (1.00) |
2.43e-18 (1.64e-15) |
0.000113 (0.056) |
0.161 (1.00) |
0.393 (1.00) |
0.000395 (0.187) |
3.89e-06 (0.00212) |
7.27e-05 (0.0366) |
0.000188 (0.0919) |
14q loss | 0 (0%) | 450 |
0.0191 (1.00) |
0.00403 (1.00) |
8.94e-17 (6e-14) |
1.48e-09 (9.03e-07) |
0.0847 (1.00) |
0.0052 (1.00) |
3.38e-08 (2e-05) |
1.95e-07 (0.000112) |
3.34e-09 (2.02e-06) |
9.82e-12 (6.33e-09) |
15q loss | 0 (0%) | 411 |
0.00677 (1.00) |
0.00103 (0.456) |
4.68e-35 (3.25e-32) |
1.61e-13 (1.06e-10) |
0.00259 (1.00) |
0.267 (1.00) |
7.92e-10 (4.9e-07) |
1.07e-10 (6.71e-08) |
5.22e-15 (3.46e-12) |
1.07e-16 (7.19e-14) |
16p loss | 0 (0%) | 423 |
0.0191 (1.00) |
0.00403 (1.00) |
2.82e-31 (1.95e-28) |
2.77e-09 (1.69e-06) |
0.193 (1.00) |
0.796 (1.00) |
7.52e-10 (4.65e-07) |
1.47e-09 (9.03e-07) |
1.47e-09 (9.03e-07) |
1.36e-10 (8.51e-08) |
16q loss | 0 (0%) | 382 |
0.00686 (1.00) |
0.00173 (0.751) |
5.94e-40 (4.14e-37) |
2.86e-11 (1.82e-08) |
0.237 (1.00) |
1 (1.00) |
1.01e-11 (6.48e-09) |
2.34e-10 (1.46e-07) |
1.07e-11 (6.87e-09) |
1.9e-11 (1.22e-08) |
17p loss | 0 (0%) | 387 |
0.00686 (1.00) |
0.00173 (0.751) |
8.66e-53 (6.05e-50) |
8.14e-13 (5.31e-10) |
0.000571 (0.263) |
0.665 (1.00) |
1.6e-20 (1.09e-17) |
2.15e-21 (1.47e-18) |
4.87e-17 (3.28e-14) |
2.92e-15 (1.95e-12) |
17q loss | 0 (0%) | 424 |
0.0191 (1.00) |
0.00403 (1.00) |
1.48e-29 (1.02e-26) |
3.41e-05 (0.0176) |
0.0924 (1.00) |
0.612 (1.00) |
4.28e-09 (2.58e-06) |
1.95e-11 (1.24e-08) |
2.71e-07 (0.000156) |
5.5e-07 (0.000313) |
18q loss | 0 (0%) | 443 |
9.75e-18 (6.57e-15) |
1.98e-06 (0.00109) |
0.725 (1.00) |
1 (1.00) |
3.87e-06 (0.00212) |
5.65e-07 (0.00032) |
3.04e-06 (0.00167) |
2.59e-07 (0.000149) |
||
19p loss | 0 (0%) | 458 |
4.63e-12 (3e-09) |
1.07e-07 (6.19e-05) |
0.331 (1.00) |
1 (1.00) |
1.84e-05 (0.00979) |
7.84e-06 (0.00424) |
1.01e-05 (0.00546) |
6.41e-07 (0.000362) |
||
22q loss | 0 (0%) | 405 |
0.0191 (1.00) |
0.00403 (1.00) |
1.41e-36 (9.78e-34) |
4.23e-08 (2.5e-05) |
0.0721 (1.00) |
1 (1.00) |
4.88e-11 (3.09e-08) |
3.29e-14 (2.17e-11) |
9.64e-11 (6.08e-08) |
1.01e-09 (6.24e-07) |
13q gain | 0 (0%) | 472 |
9.55e-08 (5.56e-05) |
0.00556 (1.00) |
0.735 (1.00) |
0.367 (1.00) |
7.14e-05 (0.036) |
0.000462 (0.216) |
3.45e-05 (0.0178) |
4.23e-05 (0.0217) |
||
19p gain | 0 (0%) | 461 |
0.0591 (1.00) |
0.0151 (1.00) |
2.4e-13 (1.57e-10) |
0.00429 (1.00) |
0.528 (1.00) |
0.151 (1.00) |
4.73e-06 (0.00257) |
1.84e-05 (0.00979) |
9.18e-07 (0.000515) |
3.24e-05 (0.0168) |
19q gain | 0 (0%) | 464 |
4.28e-13 (2.8e-10) |
0.00147 (0.644) |
0.085 (1.00) |
1 (1.00) |
4.73e-06 (0.00257) |
1.59e-06 (0.000886) |
8.12e-07 (0.000456) |
2.17e-05 (0.0114) |
||
20p gain | 0 (0%) | 427 |
0.176 (1.00) |
0.0543 (1.00) |
2.28e-18 (1.54e-15) |
3.47e-05 (0.0179) |
0.291 (1.00) |
1 (1.00) |
9.04e-05 (0.0454) |
0.0119 (1.00) |
1.84e-08 (1.1e-05) |
4.4e-07 (0.00025) |
20q gain | 0 (0%) | 414 |
0.0591 (1.00) |
0.0151 (1.00) |
3.62e-24 (2.49e-21) |
8.6e-08 (5.03e-05) |
0.192 (1.00) |
0.58 (1.00) |
1.75e-06 (0.000967) |
0.000621 (0.285) |
1.63e-11 (1.05e-08) |
3.65e-10 (2.27e-07) |
12p loss | 0 (0%) | 467 |
3.86e-11 (2.46e-08) |
0.000192 (0.0939) |
0.0577 (1.00) |
1 (1.00) |
3.62e-05 (0.0186) |
0.0057 (1.00) |
9.52e-08 (5.55e-05) |
4.34e-06 (0.00236) |
||
1q gain | 0 (0%) | 354 |
0.111 (1.00) |
0.637 (1.00) |
3.04e-07 (0.000174) |
0.00534 (1.00) |
0.00123 (0.54) |
0.000715 (0.325) |
3.31e-06 (0.00182) |
9.23e-07 (0.000517) |
3.74e-07 (0.000213) |
0.0178 (1.00) |
21q gain | 0 (0%) | 467 |
1.13e-08 (6.82e-06) |
0.0794 (1.00) |
0.237 (1.00) |
0.558 (1.00) |
0.000204 (0.0992) |
0.0095 (1.00) |
0.000414 (0.195) |
0.000375 (0.178) |
||
10p loss | 0 (0%) | 469 |
0.176 (1.00) |
0.0543 (1.00) |
4e-11 (2.54e-08) |
0.000334 (0.159) |
0.474 (1.00) |
0.633 (1.00) |
0.000469 (0.218) |
0.0016 (0.696) |
1.25e-05 (0.0067) |
0.00108 (0.477) |
10q loss | 0 (0%) | 468 |
2.94e-10 (1.83e-07) |
0.000192 (0.0939) |
0.451 (1.00) |
1 (1.00) |
0.000469 (0.218) |
0.0057 (1.00) |
0.000214 (0.104) |
0.00195 (0.841) |
||
12q loss | 0 (0%) | 474 |
1.23e-09 (7.56e-07) |
0.0001 (0.0501) |
0.31 (1.00) |
0.429 (1.00) |
0.00106 (0.467) |
0.0067 (1.00) |
1.25e-06 (0.000698) |
1.67e-06 (0.000925) |
||
8q gain | 0 (0%) | 374 |
0.00461 (1.00) |
0.0424 (1.00) |
1.65e-21 (1.13e-18) |
0.368 (1.00) |
0.00495 (1.00) |
1 (1.00) |
0.00591 (1.00) |
0.000299 (0.143) |
0.0018 (0.778) |
3.27e-05 (0.017) |
18q gain | 0 (0%) | 472 |
0.176 (1.00) |
0.0543 (1.00) |
8.26e-06 (0.00445) |
0.00562 (1.00) |
1 (1.00) |
0.0173 (1.00) |
0.00565 (1.00) |
0.000111 (0.0553) |
0.000436 (0.205) |
|
5p loss | 0 (0%) | 465 |
0.352 (1.00) |
0.133 (1.00) |
1.16e-10 (7.29e-08) |
0.000334 (0.159) |
0.162 (1.00) |
0.181 (1.00) |
0.000782 (0.353) |
0.000672 (0.307) |
0.000216 (0.105) |
0.00281 (1.00) |
7p loss | 0 (0%) | 463 |
0.176 (1.00) |
0.0543 (1.00) |
9.88e-10 (6.09e-07) |
0.00656 (1.00) |
0.158 (1.00) |
0.201 (1.00) |
0.000162 (0.0798) |
2.27e-05 (0.0119) |
0.000783 (0.353) |
0.00338 (1.00) |
8q loss | 0 (0%) | 480 |
2.23e-05 (0.0117) |
0.000955 (0.427) |
1 (1.00) |
0.0396 (1.00) |
0.154 (1.00) |
0.000302 (0.144) |
0.000443 (0.207) |
|||
18p loss | 0 (0%) | 456 |
3.15e-12 (2.05e-09) |
2.09e-05 (0.0111) |
0.326 (1.00) |
0.746 (1.00) |
0.00066 (0.302) |
0.000172 (0.0844) |
0.00472 (1.00) |
0.000594 (0.273) |
||
19q loss | 0 (0%) | 464 |
1.79e-08 (1.07e-05) |
4.65e-05 (0.0237) |
0.734 (1.00) |
0.713 (1.00) |
0.000719 (0.326) |
0.00283 (1.00) |
0.000676 (0.308) |
1.46e-05 (0.00783) |
||
21q loss | 0 (0%) | 460 |
0.0591 (1.00) |
0.0151 (1.00) |
6.47e-08 (3.8e-05) |
0.00252 (1.00) |
0.095 (1.00) |
0.75 (1.00) |
0.000148 (0.0732) |
0.00136 (0.598) |
0.00097 (0.432) |
4.43e-05 (0.0226) |
Xq loss | 0 (0%) | 474 |
2.97e-07 (0.00017) |
0.000569 (0.263) |
0.617 (1.00) |
0.633 (1.00) |
0.016 (1.00) |
0.0067 (1.00) |
0.000233 (0.113) |
2.27e-05 (0.0119) |
||
2p gain | 0 (0%) | 441 |
0.233 (1.00) |
0.298 (1.00) |
5.41e-11 (3.42e-08) |
0.0588 (1.00) |
0.177 (1.00) |
0.802 (1.00) |
0.238 (1.00) |
0.434 (1.00) |
0.0184 (1.00) |
0.162 (1.00) |
2q gain | 0 (0%) | 452 |
0.518 (1.00) |
0.769 (1.00) |
4.83e-11 (3.06e-08) |
0.175 (1.00) |
0.0653 (1.00) |
0.575 (1.00) |
0.3 (1.00) |
0.624 (1.00) |
0.015 (1.00) |
0.117 (1.00) |
3p gain | 0 (0%) | 464 |
4.15e-19 (2.82e-16) |
0.121 (1.00) |
0.525 (1.00) |
0.652 (1.00) |
0.0149 (1.00) |
0.0429 (1.00) |
0.338 (1.00) |
0.225 (1.00) |
||
6p gain | 0 (0%) | 454 |
0.43 (1.00) |
0.243 (1.00) |
1.52e-16 (1.02e-13) |
0.0347 (1.00) |
0.661 (1.00) |
1 (1.00) |
0.00665 (1.00) |
0.0075 (1.00) |
0.0121 (1.00) |
0.0302 (1.00) |
6q gain | 0 (0%) | 462 |
0.43 (1.00) |
0.243 (1.00) |
1.58e-13 (1.04e-10) |
0.331 (1.00) |
0.401 (1.00) |
1 (1.00) |
0.00839 (1.00) |
0.00793 (1.00) |
0.168 (1.00) |
0.278 (1.00) |
7p gain | 0 (0%) | 449 |
1 (1.00) |
0.867 (1.00) |
8.62e-19 (5.85e-16) |
0.0118 (1.00) |
0.733 (1.00) |
0.217 (1.00) |
1 (1.00) |
0.475 (1.00) |
0.244 (1.00) |
0.609 (1.00) |
7q gain | 0 (0%) | 449 |
0.944 (1.00) |
0.776 (1.00) |
2.4e-19 (1.63e-16) |
0.0244 (1.00) |
0.889 (1.00) |
0.0552 (1.00) |
0.385 (1.00) |
0.0331 (1.00) |
0.44 (1.00) |
0.425 (1.00) |
8p gain | 0 (0%) | 406 |
0.395 (1.00) |
1 (1.00) |
7.48e-18 (5.05e-15) |
0.913 (1.00) |
0.133 (1.00) |
1 (1.00) |
0.474 (1.00) |
0.434 (1.00) |
0.38 (1.00) |
0.0022 (0.947) |
10q gain | 0 (0%) | 413 |
0.0015 (0.657) |
0.0303 (1.00) |
9.34e-05 (0.0468) |
0.176 (1.00) |
0.388 (1.00) |
0.252 (1.00) |
0.0262 (1.00) |
0.256 (1.00) |
0.0128 (1.00) |
0.00257 (1.00) |
12p gain | 0 (0%) | 455 |
0.815 (1.00) |
0.825 (1.00) |
4.78e-08 (2.82e-05) |
0.00909 (1.00) |
0.937 (1.00) |
1 (1.00) |
0.0455 (1.00) |
0.0906 (1.00) |
0.0241 (1.00) |
0.0169 (1.00) |
12q gain | 0 (0%) | 464 |
0.815 (1.00) |
0.825 (1.00) |
3.68e-07 (0.00021) |
0.121 (1.00) |
0.901 (1.00) |
1 (1.00) |
0.0811 (1.00) |
0.227 (1.00) |
0.126 (1.00) |
0.311 (1.00) |
14q gain | 0 (0%) | 472 |
1 (1.00) |
1 (1.00) |
2.16e-05 (0.0114) |
0.227 (1.00) |
0.239 (1.00) |
0.292 (1.00) |
0.401 (1.00) |
0.0737 (1.00) |
0.0486 (1.00) |
0.0281 (1.00) |
17p gain | 0 (0%) | 485 |
2.6e-05 (0.0136) |
0.244 (1.00) |
1 (1.00) |
0.316 (1.00) |
0.315 (1.00) |
0.0701 (1.00) |
0.145 (1.00) |
|||
22q gain | 0 (0%) | 483 |
0.00473 (1.00) |
0.000537 (0.249) |
0.376 (1.00) |
0.115 (1.00) |
0.361 (1.00) |
0.00132 (0.581) |
0.00259 (1.00) |
|||
Xq gain | 0 (0%) | 480 |
0.000257 (0.123) |
0.322 (1.00) |
0.376 (1.00) |
0.157 (1.00) |
0.447 (1.00) |
0.00871 (1.00) |
0.0888 (1.00) |
|||
1p loss | 0 (0%) | 479 |
1.82e-08 (1.09e-05) |
0.000955 (0.427) |
1 (1.00) |
0.0403 (1.00) |
0.0884 (1.00) |
0.0517 (1.00) |
0.00318 (1.00) |
|||
3q loss | 0 (0%) | 480 |
4.31e-05 (0.022) |
0.0584 (1.00) |
0.024 (1.00) |
0.558 (1.00) |
0.00479 (1.00) |
0.00274 (1.00) |
0.0347 (1.00) |
0.0739 (1.00) |
||
6q loss | 0 (0%) | 480 |
0.683 (1.00) |
0.371 (1.00) |
0.000236 (0.114) |
0.0354 (1.00) |
0.858 (1.00) |
0.558 (1.00) |
0.016 (1.00) |
0.0384 (1.00) |
0.133 (1.00) |
0.0103 (1.00) |
20p loss | 0 (0%) | 477 |
0.000122 (0.0608) |
0.107 (1.00) |
0.243 (1.00) |
0.633 (1.00) |
0.0368 (1.00) |
0.0465 (1.00) |
0.00635 (1.00) |
0.0702 (1.00) |
||
1p gain | 0 (0%) | 471 |
0.683 (1.00) |
0.184 (1.00) |
0.035 (1.00) |
0.661 (1.00) |
0.401 (1.00) |
1 (1.00) |
0.182 (1.00) |
0.29 (1.00) |
0.00743 (1.00) |
0.0758 (1.00) |
4p gain | 0 (0%) | 486 |
0.0039 (1.00) |
0.125 (1.00) |
0.14 (1.00) |
0.0396 (1.00) |
0.154 (1.00) |
0.0229 (1.00) |
0.0281 (1.00) |
|||
5q gain | 0 (0%) | 483 |
0.00286 (1.00) |
0.423 (1.00) |
1 (1.00) |
0.0679 (1.00) |
0.286 (1.00) |
0.052 (1.00) |
0.203 (1.00) |
|||
9p gain | 0 (0%) | 478 |
0.0484 (1.00) |
0.0786 (1.00) |
1 (1.00) |
0.822 (1.00) |
0.0787 (1.00) |
0.0699 (1.00) |
0.0294 (1.00) |
|||
9q gain | 0 (0%) | 488 |
0.352 (1.00) |
0.363 (1.00) |
0.781 (1.00) |
0.361 (1.00) |
0.387 (1.00) |
0.127 (1.00) |
||||
10p gain | 0 (0%) | 405 |
0.00355 (1.00) |
0.064 (1.00) |
0.0007 (0.318) |
0.204 (1.00) |
0.284 (1.00) |
0.136 (1.00) |
0.0155 (1.00) |
0.255 (1.00) |
0.0639 (1.00) |
0.0178 (1.00) |
11p gain | 0 (0%) | 484 |
0.176 (1.00) |
0.0543 (1.00) |
0.0099 (1.00) |
0.0373 (1.00) |
0.109 (1.00) |
1 (1.00) |
0.157 (1.00) |
0.447 (1.00) |
0.13 (1.00) |
0.238 (1.00) |
11q gain | 0 (0%) | 484 |
0.0111 (1.00) |
0.462 (1.00) |
0.109 (1.00) |
0.299 (1.00) |
0.194 (1.00) |
0.396 (1.00) |
0.242 (1.00) |
0.361 (1.00) |
||
15q gain | 0 (0%) | 486 |
0.00416 (1.00) |
0.846 (1.00) |
1 (1.00) |
0.828 (1.00) |
0.699 (1.00) |
0.884 (1.00) |
1 (1.00) |
|||
16p gain | 0 (0%) | 480 |
0.000794 (0.357) |
0.0313 (1.00) |
0.243 (1.00) |
1 (1.00) |
0.0679 (1.00) |
0.0787 (1.00) |
0.0831 (1.00) |
0.336 (1.00) |
||
16q gain | 0 (0%) | 488 |
0.046 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.861 (1.00) |
|||||
17q gain | 0 (0%) | 479 |
0.000727 (0.329) |
0.00357 (1.00) |
0.0531 (1.00) |
1 (1.00) |
0.0276 (1.00) |
0.284 (1.00) |
0.00887 (1.00) |
0.011 (1.00) |
||
1q loss | 0 (0%) | 488 |
0.0365 (1.00) |
0.0574 (1.00) |
0.115 (1.00) |
0.361 (1.00) |
0.0991 (1.00) |
0.127 (1.00) |
||||
2p loss | 0 (0%) | 486 |
0.019 (1.00) |
0.518 (1.00) |
0.14 (1.00) |
0.157 (1.00) |
0.0878 (1.00) |
0.773 (1.00) |
0.199 (1.00) |
|||
2q loss | 0 (0%) | 484 |
0.00637 (1.00) |
0.199 (1.00) |
0.14 (1.00) |
0.157 (1.00) |
0.0878 (1.00) |
0.493 (1.00) |
0.192 (1.00) |
|||
6p loss | 0 (0%) | 482 |
0.683 (1.00) |
0.371 (1.00) |
0.000862 (0.386) |
0.0962 (1.00) |
0.858 (1.00) |
0.558 (1.00) |
0.194 (1.00) |
0.249 (1.00) |
0.172 (1.00) |
0.0171 (1.00) |
20q loss | 0 (0%) | 485 |
0.0106 (1.00) |
0.054 (1.00) |
0.528 (1.00) |
0.391 (1.00) |
0.474 (1.00) |
0.164 (1.00) |
0.078 (1.00) |
P value = 3.04e-07 (Chi-square test), Q value = 0.00017
Table S1. Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
1Q GAIN CNV | 85 | 18 | 21 | 8 | 6 |
1Q GAIN WILD-TYPE | 205 | 22 | 118 | 9 | 0 |
Figure S1. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D2V3.png)
P value = 3.31e-06 (Fisher's exact test), Q value = 0.0018
Table S2. Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
1Q GAIN CNV | 24 | 26 | 51 |
1Q GAIN WILD-TYPE | 118 | 81 | 62 |
Figure S2. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D2V7.png)
P value = 9.23e-07 (Fisher's exact test), Q value = 0.00052
Table S3. Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 65 | 92 | 65 | 140 |
1Q GAIN CNV | 26 | 24 | 31 | 20 |
1Q GAIN WILD-TYPE | 39 | 68 | 34 | 120 |
Figure S3. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D2V8.png)
P value = 3.74e-07 (Fisher's exact test), Q value = 0.00021
Table S4. Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
1Q GAIN CNV | 41 | 35 | 62 |
1Q GAIN WILD-TYPE | 166 | 109 | 70 |
Figure S4. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D2V9.png)
P value = 5.41e-11 (Chi-square test), Q value = 3.4e-08
Table S5. Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
2P GAIN CNV | 9 | 14 | 22 | 5 | 1 |
2P GAIN WILD-TYPE | 281 | 26 | 117 | 12 | 5 |
Figure S5. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D3V3.png)
P value = 4.83e-11 (Chi-square test), Q value = 3.1e-08
Table S6. Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
2Q GAIN CNV | 6 | 13 | 16 | 4 | 1 |
2Q GAIN WILD-TYPE | 284 | 27 | 123 | 13 | 5 |
Figure S6. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D4V3.png)
P value = 4.15e-19 (Chi-square test), Q value = 2.8e-16
Table S7. Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
3P GAIN CNV | 1 | 4 | 13 | 9 | 1 |
3P GAIN WILD-TYPE | 289 | 36 | 126 | 8 | 5 |
Figure S7. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D5V3.png)
P value = 3.41e-22 (Chi-square test), Q value = 2.3e-19
Table S8. Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
3Q GAIN CNV | 2 | 5 | 31 | 11 | 1 |
3Q GAIN WILD-TYPE | 288 | 35 | 108 | 6 | 5 |
Figure S8. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D6V3.png)
P value = 2.49e-05 (Fisher's exact test), Q value = 0.013
Table S9. Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
3Q GAIN CNV | 29 | 6 | 6 |
3Q GAIN WILD-TYPE | 114 | 79 | 143 |
Figure S9. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D6V4.png)
P value = 1.19e-06 (Fisher's exact test), Q value = 0.00067
Table S10. Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
3Q GAIN CNV | 26 | 6 | 1 |
3Q GAIN WILD-TYPE | 116 | 101 | 112 |
Figure S10. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D6V7.png)
P value = 5.14e-05 (Fisher's exact test), Q value = 0.026
Table S11. Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 65 | 92 | 65 | 140 |
3Q GAIN CNV | 0 | 3 | 7 | 23 |
3Q GAIN WILD-TYPE | 65 | 89 | 58 | 117 |
Figure S11. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D6V8.png)
P value = 2.07e-05 (Fisher's exact test), Q value = 0.011
Table S12. Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
3Q GAIN CNV | 37 | 7 | 6 |
3Q GAIN WILD-TYPE | 170 | 137 | 126 |
Figure S12. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D6V9.png)
P value = 0.000263 (Fisher's exact test), Q value = 0.13
Table S13. Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
3Q GAIN CNV | 9 | 5 | 4 | 32 |
3Q GAIN WILD-TYPE | 184 | 74 | 23 | 152 |
Figure S13. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D6V10.png)
P value = 3.01e-09 (Chi-square test), Q value = 1.8e-06
Table S14. Gene #8: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
5P GAIN CNV | 3 | 2 | 25 | 1 | 1 |
5P GAIN WILD-TYPE | 287 | 38 | 114 | 16 | 5 |
Figure S14. Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D8V3.png)
P value = 0.000136 (Fisher's exact test), Q value = 0.067
Table S15. Gene #8: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
5P GAIN CNV | 20 | 3 | 3 |
5P GAIN WILD-TYPE | 123 | 82 | 146 |
Figure S15. Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D8V4.png)
P value = 3.95e-06 (Fisher's exact test), Q value = 0.0022
Table S16. Gene #8: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
5P GAIN CNV | 19 | 0 | 3 |
5P GAIN WILD-TYPE | 123 | 107 | 110 |
Figure S16. Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D8V7.png)
P value = 0.00042 (Fisher's exact test), Q value = 0.2
Table S17. Gene #8: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 65 | 92 | 65 | 140 |
5P GAIN CNV | 2 | 0 | 3 | 17 |
5P GAIN WILD-TYPE | 63 | 92 | 62 | 123 |
Figure S17. Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D8V8.png)
P value = 1.66e-05 (Fisher's exact test), Q value = 0.0088
Table S18. Gene #8: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
5P GAIN CNV | 25 | 1 | 5 |
5P GAIN WILD-TYPE | 182 | 143 | 127 |
Figure S18. Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D8V9.png)
P value = 5.29e-05 (Fisher's exact test), Q value = 0.027
Table S19. Gene #8: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
5P GAIN CNV | 3 | 3 | 1 | 24 |
5P GAIN WILD-TYPE | 190 | 76 | 26 | 160 |
Figure S19. Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D8V10.png)
P value = 1.52e-16 (Chi-square test), Q value = 1e-13
Table S20. Gene #10: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
6P GAIN CNV | 1 | 3 | 25 | 8 | 1 |
6P GAIN WILD-TYPE | 289 | 37 | 114 | 9 | 5 |
Figure S20. Get High-res Image Gene #10: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D10V3.png)
P value = 1.58e-13 (Chi-square test), Q value = 1e-10
Table S21. Gene #11: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
6Q GAIN CNV | 1 | 3 | 18 | 7 | 1 |
6Q GAIN WILD-TYPE | 289 | 37 | 121 | 10 | 5 |
Figure S21. Get High-res Image Gene #11: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D11V3.png)
P value = 8.62e-19 (Chi-square test), Q value = 5.9e-16
Table S22. Gene #12: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
7P GAIN CNV | 5 | 17 | 14 | 6 | 1 |
7P GAIN WILD-TYPE | 285 | 23 | 125 | 11 | 5 |
Figure S22. Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D12V3.png)
P value = 2.4e-19 (Chi-square test), Q value = 1.6e-16
Table S23. Gene #13: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
7Q GAIN CNV | 8 | 17 | 10 | 7 | 1 |
7Q GAIN WILD-TYPE | 282 | 23 | 129 | 10 | 5 |
Figure S23. Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D13V3.png)
P value = 7.48e-18 (Chi-square test), Q value = 5.1e-15
Table S24. Gene #14: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
8P GAIN CNV | 28 | 16 | 25 | 15 | 2 |
8P GAIN WILD-TYPE | 262 | 24 | 114 | 2 | 4 |
Figure S24. Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D14V3.png)
P value = 1.65e-21 (Chi-square test), Q value = 1.1e-18
Table S25. Gene #15: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
8Q GAIN CNV | 29 | 19 | 51 | 16 | 3 |
8Q GAIN WILD-TYPE | 261 | 21 | 88 | 1 | 3 |
Figure S25. Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D15V3.png)
P value = 0.000299 (Fisher's exact test), Q value = 0.14
Table S26. Gene #15: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 65 | 92 | 65 | 140 |
8Q GAIN CNV | 10 | 12 | 9 | 47 |
8Q GAIN WILD-TYPE | 55 | 80 | 56 | 93 |
Figure S26. Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D15V8.png)
P value = 3.27e-05 (Fisher's exact test), Q value = 0.017
Table S27. Gene #15: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
8Q GAIN CNV | 28 | 17 | 13 | 57 |
8Q GAIN WILD-TYPE | 165 | 62 | 14 | 127 |
Figure S27. Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D15V10.png)
P value = 9.34e-05 (Chi-square test), Q value = 0.047
Table S28. Gene #19: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
10Q GAIN CNV | 44 | 12 | 13 | 7 | 3 |
10Q GAIN WILD-TYPE | 246 | 28 | 126 | 10 | 3 |
Figure S28. Get High-res Image Gene #19: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D19V3.png)
P value = 4.78e-08 (Chi-square test), Q value = 2.8e-05
Table S29. Gene #22: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
12P GAIN CNV | 7 | 7 | 19 | 1 | 3 |
12P GAIN WILD-TYPE | 283 | 33 | 120 | 16 | 3 |
Figure S29. Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D22V3.png)
P value = 3.68e-07 (Chi-square test), Q value = 0.00021
Table S30. Gene #23: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
12Q GAIN CNV | 7 | 6 | 11 | 1 | 3 |
12Q GAIN WILD-TYPE | 283 | 34 | 128 | 16 | 3 |
Figure S30. Get High-res Image Gene #23: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D23V3.png)
P value = 9.55e-08 (Chi-square test), Q value = 5.6e-05
Table S31. Gene #24: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
13Q GAIN CNV | 1 | 0 | 17 | 1 | 1 |
13Q GAIN WILD-TYPE | 289 | 40 | 122 | 16 | 5 |
Figure S31. Get High-res Image Gene #24: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D24V3.png)
P value = 7.14e-05 (Fisher's exact test), Q value = 0.036
Table S32. Gene #24: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
13Q GAIN CNV | 13 | 1 | 0 |
13Q GAIN WILD-TYPE | 129 | 106 | 113 |
Figure S32. Get High-res Image Gene #24: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D24V7.png)
P value = 0.000462 (Fisher's exact test), Q value = 0.22
Table S33. Gene #24: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 65 | 92 | 65 | 140 |
13Q GAIN CNV | 0 | 1 | 0 | 13 |
13Q GAIN WILD-TYPE | 65 | 91 | 65 | 127 |
Figure S33. Get High-res Image Gene #24: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D24V8.png)
P value = 3.45e-05 (Fisher's exact test), Q value = 0.018
Table S34. Gene #24: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
13Q GAIN CNV | 18 | 2 | 0 |
13Q GAIN WILD-TYPE | 189 | 142 | 132 |
Figure S34. Get High-res Image Gene #24: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D24V9.png)
P value = 4.23e-05 (Fisher's exact test), Q value = 0.022
Table S35. Gene #24: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
13Q GAIN CNV | 2 | 0 | 0 | 18 |
13Q GAIN WILD-TYPE | 191 | 79 | 27 | 166 |
Figure S35. Get High-res Image Gene #24: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D24V10.png)
P value = 2.16e-05 (Chi-square test), Q value = 0.011
Table S36. Gene #25: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
14Q GAIN CNV | 2 | 2 | 13 | 3 | 0 |
14Q GAIN WILD-TYPE | 288 | 38 | 126 | 14 | 6 |
Figure S36. Get High-res Image Gene #25: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D25V3.png)
P value = 2.6e-05 (Chi-square test), Q value = 0.014
Table S37. Gene #29: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
17P GAIN CNV | 1 | 0 | 3 | 2 | 1 |
17P GAIN WILD-TYPE | 289 | 40 | 136 | 15 | 5 |
Figure S37. Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D29V3.png)
P value = 4.94e-14 (Chi-square test), Q value = 3.3e-11
Table S38. Gene #31: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
18P GAIN CNV | 2 | 2 | 32 | 1 | 0 |
18P GAIN WILD-TYPE | 288 | 38 | 107 | 16 | 6 |
Figure S38. Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D31V3.png)
P value = 6.64e-05 (Fisher's exact test), Q value = 0.034
Table S39. Gene #31: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
18P GAIN CNV | 20 | 8 | 2 |
18P GAIN WILD-TYPE | 123 | 77 | 147 |
Figure S39. Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D31V4.png)
P value = 3.34e-05 (Fisher's exact test), Q value = 0.017
Table S40. Gene #31: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
18P GAIN CNV | 18 | 2 | 1 |
18P GAIN WILD-TYPE | 124 | 105 | 112 |
Figure S40. Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D31V7.png)
P value = 7.28e-07 (Fisher's exact test), Q value = 0.00041
Table S41. Gene #31: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 65 | 92 | 65 | 140 |
18P GAIN CNV | 0 | 1 | 0 | 20 |
18P GAIN WILD-TYPE | 65 | 91 | 65 | 120 |
Figure S41. Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D31V8.png)
P value = 4.26e-09 (Fisher's exact test), Q value = 2.6e-06
Table S42. Gene #31: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
18P GAIN CNV | 33 | 1 | 3 |
18P GAIN WILD-TYPE | 174 | 143 | 129 |
Figure S42. Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D31V9.png)
P value = 6.47e-09 (Fisher's exact test), Q value = 3.9e-06
Table S43. Gene #31: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
18P GAIN CNV | 2 | 3 | 0 | 32 |
18P GAIN WILD-TYPE | 191 | 76 | 27 | 152 |
Figure S43. Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D31V10.png)
P value = 8.26e-06 (Chi-square test), Q value = 0.0045
Table S44. Gene #32: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
18Q GAIN CNV | 2 | 1 | 16 | 1 | 0 |
18Q GAIN WILD-TYPE | 288 | 39 | 123 | 16 | 6 |
Figure S44. Get High-res Image Gene #32: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D32V3.png)
P value = 0.000111 (Fisher's exact test), Q value = 0.055
Table S45. Gene #32: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
18Q GAIN CNV | 17 | 0 | 3 |
18Q GAIN WILD-TYPE | 190 | 144 | 129 |
Figure S45. Get High-res Image Gene #32: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D32V9.png)
P value = 0.000436 (Fisher's exact test), Q value = 0.2
Table S46. Gene #32: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
18Q GAIN CNV | 1 | 3 | 0 | 16 |
18Q GAIN WILD-TYPE | 192 | 76 | 27 | 168 |
Figure S46. Get High-res Image Gene #32: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D32V10.png)
P value = 2.4e-13 (Chi-square test), Q value = 1.6e-10
Table S47. Gene #33: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
19P GAIN CNV | 0 | 1 | 27 | 3 | 0 |
19P GAIN WILD-TYPE | 290 | 39 | 112 | 14 | 6 |
Figure S47. Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D33V3.png)
P value = 4.73e-06 (Fisher's exact test), Q value = 0.0026
Table S48. Gene #33: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
19P GAIN CNV | 16 | 1 | 0 |
19P GAIN WILD-TYPE | 126 | 106 | 113 |
Figure S48. Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D33V7.png)
P value = 1.84e-05 (Fisher's exact test), Q value = 0.0098
Table S49. Gene #33: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 65 | 92 | 65 | 140 |
19P GAIN CNV | 0 | 0 | 1 | 16 |
19P GAIN WILD-TYPE | 65 | 92 | 64 | 124 |
Figure S49. Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D33V8.png)
P value = 9.18e-07 (Fisher's exact test), Q value = 0.00052
Table S50. Gene #33: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
19P GAIN CNV | 27 | 3 | 1 |
19P GAIN WILD-TYPE | 180 | 141 | 131 |
Figure S50. Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D33V9.png)
P value = 3.24e-05 (Fisher's exact test), Q value = 0.017
Table S51. Gene #33: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
19P GAIN CNV | 4 | 1 | 2 | 24 |
19P GAIN WILD-TYPE | 189 | 78 | 25 | 160 |
Figure S51. Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D33V10.png)
P value = 4.28e-13 (Chi-square test), Q value = 2.8e-10
Table S52. Gene #34: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
19Q GAIN CNV | 0 | 0 | 25 | 3 | 0 |
19Q GAIN WILD-TYPE | 290 | 40 | 114 | 14 | 6 |
Figure S52. Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D34V3.png)
P value = 4.73e-06 (Fisher's exact test), Q value = 0.0026
Table S53. Gene #34: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
19Q GAIN CNV | 16 | 1 | 0 |
19Q GAIN WILD-TYPE | 126 | 106 | 113 |
Figure S53. Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D34V7.png)
P value = 1.59e-06 (Fisher's exact test), Q value = 0.00089
Table S54. Gene #34: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 65 | 92 | 65 | 140 |
19Q GAIN CNV | 0 | 0 | 0 | 17 |
19Q GAIN WILD-TYPE | 65 | 92 | 65 | 123 |
Figure S54. Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D34V8.png)
P value = 8.12e-07 (Fisher's exact test), Q value = 0.00046
Table S55. Gene #34: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
19Q GAIN CNV | 25 | 2 | 1 |
19Q GAIN WILD-TYPE | 182 | 142 | 131 |
Figure S55. Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D34V9.png)
P value = 2.17e-05 (Fisher's exact test), Q value = 0.011
Table S56. Gene #34: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
19Q GAIN CNV | 3 | 1 | 1 | 23 |
19Q GAIN WILD-TYPE | 190 | 78 | 26 | 161 |
Figure S56. Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D34V10.png)
P value = 2.28e-18 (Chi-square test), Q value = 1.5e-15
Table S57. Gene #35: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
20P GAIN CNV | 4 | 13 | 43 | 3 | 2 |
20P GAIN WILD-TYPE | 286 | 27 | 96 | 14 | 4 |
Figure S57. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D35V3.png)
P value = 3.47e-05 (Fisher's exact test), Q value = 0.018
Table S58. Gene #35: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
20P GAIN CNV | 37 | 9 | 11 |
20P GAIN WILD-TYPE | 106 | 76 | 138 |
Figure S58. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D35V4.png)
P value = 9.04e-05 (Fisher's exact test), Q value = 0.045
Table S59. Gene #35: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
20P GAIN CNV | 27 | 5 | 5 |
20P GAIN WILD-TYPE | 115 | 102 | 108 |
Figure S59. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D35V7.png)
P value = 1.84e-08 (Fisher's exact test), Q value = 1.1e-05
Table S60. Gene #35: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
20P GAIN CNV | 50 | 7 | 8 |
20P GAIN WILD-TYPE | 157 | 137 | 124 |
Figure S60. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D35V9.png)
P value = 4.4e-07 (Fisher's exact test), Q value = 0.00025
Table S61. Gene #35: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
20P GAIN CNV | 11 | 10 | 0 | 44 |
20P GAIN WILD-TYPE | 182 | 69 | 27 | 140 |
Figure S61. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D35V10.png)
P value = 3.62e-24 (Chi-square test), Q value = 2.5e-21
Table S62. Gene #36: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
20Q GAIN CNV | 4 | 15 | 54 | 3 | 2 |
20Q GAIN WILD-TYPE | 286 | 25 | 85 | 14 | 4 |
Figure S62. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D36V3.png)
P value = 8.6e-08 (Fisher's exact test), Q value = 5e-05
Table S63. Gene #36: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
20Q GAIN CNV | 47 | 10 | 12 |
20Q GAIN WILD-TYPE | 96 | 75 | 137 |
Figure S63. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D36V4.png)
P value = 1.75e-06 (Fisher's exact test), Q value = 0.00097
Table S64. Gene #36: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
20Q GAIN CNV | 32 | 5 | 5 |
20Q GAIN WILD-TYPE | 110 | 102 | 108 |
Figure S64. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D36V7.png)
P value = 1.63e-11 (Fisher's exact test), Q value = 1e-08
Table S65. Gene #36: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
20Q GAIN CNV | 61 | 8 | 8 |
20Q GAIN WILD-TYPE | 146 | 136 | 124 |
Figure S65. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D36V9.png)
P value = 3.65e-10 (Fisher's exact test), Q value = 2.3e-07
Table S66. Gene #36: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
20Q GAIN CNV | 12 | 10 | 0 | 55 |
20Q GAIN WILD-TYPE | 181 | 69 | 27 | 129 |
Figure S66. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D36V10.png)
P value = 1.13e-08 (Chi-square test), Q value = 6.8e-06
Table S67. Gene #37: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
21Q GAIN CNV | 1 | 2 | 21 | 1 | 0 |
21Q GAIN WILD-TYPE | 289 | 38 | 118 | 16 | 6 |
Figure S67. Get High-res Image Gene #37: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D37V3.png)
P value = 0.000204 (Fisher's exact test), Q value = 0.099
Table S68. Gene #37: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
21Q GAIN CNV | 12 | 1 | 0 |
21Q GAIN WILD-TYPE | 130 | 106 | 113 |
Figure S68. Get High-res Image Gene #37: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D37V7.png)
P value = 0.000414 (Fisher's exact test), Q value = 0.19
Table S69. Gene #37: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
21Q GAIN CNV | 20 | 4 | 1 |
21Q GAIN WILD-TYPE | 187 | 140 | 131 |
Figure S69. Get High-res Image Gene #37: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D37V9.png)
P value = 0.000375 (Fisher's exact test), Q value = 0.18
Table S70. Gene #37: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
21Q GAIN CNV | 4 | 1 | 0 | 20 |
21Q GAIN WILD-TYPE | 189 | 78 | 27 | 164 |
Figure S70. Get High-res Image Gene #37: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D37V10.png)
P value = 0.000537 (Fisher's exact test), Q value = 0.25
Table S71. Gene #38: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
22Q GAIN CNV | 8 | 0 | 0 |
22Q GAIN WILD-TYPE | 135 | 85 | 149 |
Figure S71. Get High-res Image Gene #38: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D38V4.png)
P value = 0.000257 (Chi-square test), Q value = 0.12
Table S72. Gene #39: 'Xq gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
XQ GAIN CNV | 0 | 1 | 10 | 1 | 0 |
XQ GAIN WILD-TYPE | 290 | 39 | 129 | 16 | 6 |
Figure S72. Get High-res Image Gene #39: 'Xq gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D39V3.png)
P value = 1.82e-08 (Chi-square test), Q value = 1.1e-05
Table S73. Gene #40: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
1P LOSS CNV | 0 | 4 | 7 | 0 | 2 |
1P LOSS WILD-TYPE | 290 | 36 | 132 | 17 | 4 |
Figure S73. Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D40V3.png)
P value = 1.34e-14 (Chi-square test), Q value = 8.8e-12
Table S74. Gene #44: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
3P LOSS CNV | 0 | 2 | 29 | 0 | 0 |
3P LOSS WILD-TYPE | 290 | 38 | 110 | 17 | 6 |
Figure S74. Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D44V3.png)
P value = 0.000141 (Fisher's exact test), Q value = 0.07
Table S75. Gene #44: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
3P LOSS CNV | 19 | 6 | 2 |
3P LOSS WILD-TYPE | 124 | 79 | 147 |
Figure S75. Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D44V4.png)
P value = 0.000526 (Chi-square test), Q value = 0.24
Table S76. Gene #44: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 41 | 37 | 39 | 12 | 41 | 24 |
3P LOSS CNV | 1 | 7 | 0 | 0 | 0 | 1 |
3P LOSS WILD-TYPE | 40 | 30 | 39 | 12 | 41 | 23 |
Figure S76. Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D44V5.png)
P value = 1.79e-07 (Fisher's exact test), Q value = 1e-04
Table S77. Gene #44: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
3P LOSS CNV | 19 | 1 | 0 |
3P LOSS WILD-TYPE | 123 | 106 | 113 |
Figure S77. Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D44V7.png)
P value = 8.63e-08 (Fisher's exact test), Q value = 5e-05
Table S78. Gene #44: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 65 | 92 | 65 | 140 |
3P LOSS CNV | 0 | 0 | 0 | 20 |
3P LOSS WILD-TYPE | 65 | 92 | 65 | 120 |
Figure S78. Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D44V8.png)
P value = 4.21e-05 (Fisher's exact test), Q value = 0.022
Table S79. Gene #44: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
3P LOSS CNV | 24 | 2 | 3 |
3P LOSS WILD-TYPE | 183 | 142 | 129 |
Figure S79. Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D44V9.png)
P value = 2.37e-05 (Fisher's exact test), Q value = 0.012
Table S80. Gene #44: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
3P LOSS CNV | 2 | 3 | 1 | 23 |
3P LOSS WILD-TYPE | 191 | 76 | 26 | 161 |
Figure S80. Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D44V10.png)
P value = 4.31e-05 (Chi-square test), Q value = 0.022
Table S81. Gene #45: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
3Q LOSS CNV | 0 | 1 | 11 | 0 | 0 |
3Q LOSS WILD-TYPE | 290 | 39 | 128 | 17 | 6 |
Figure S81. Get High-res Image Gene #45: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D45V3.png)
P value = 4.79e-25 (Chi-square test), Q value = 3.3e-22
Table S82. Gene #46: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
4P LOSS CNV | 2 | 8 | 54 | 1 | 1 |
4P LOSS WILD-TYPE | 288 | 32 | 85 | 16 | 5 |
Figure S82. Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D46V3.png)
P value = 7.08e-11 (Fisher's exact test), Q value = 4.5e-08
Table S83. Gene #46: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
4P LOSS CNV | 41 | 15 | 3 |
4P LOSS WILD-TYPE | 102 | 70 | 146 |
Figure S83. Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D46V4.png)
P value = 2.45e-09 (Fisher's exact test), Q value = 1.5e-06
Table S84. Gene #46: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
4P LOSS CNV | 30 | 1 | 3 |
4P LOSS WILD-TYPE | 112 | 106 | 110 |
Figure S84. Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D46V7.png)
P value = 1.29e-07 (Fisher's exact test), Q value = 7.5e-05
Table S85. Gene #46: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 65 | 92 | 65 | 140 |
4P LOSS CNV | 2 | 1 | 2 | 29 |
4P LOSS WILD-TYPE | 63 | 91 | 63 | 111 |
Figure S85. Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D46V8.png)
P value = 1.88e-13 (Fisher's exact test), Q value = 1.2e-10
Table S86. Gene #46: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
4P LOSS CNV | 55 | 4 | 5 |
4P LOSS WILD-TYPE | 152 | 140 | 127 |
Figure S86. Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D46V9.png)
P value = 4.44e-12 (Fisher's exact test), Q value = 2.9e-09
Table S87. Gene #46: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
4P LOSS CNV | 4 | 7 | 4 | 49 |
4P LOSS WILD-TYPE | 189 | 72 | 23 | 135 |
Figure S87. Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D46V10.png)
P value = 1.36e-26 (Chi-square test), Q value = 9.4e-24
Table S88. Gene #47: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
4Q LOSS CNV | 1 | 8 | 54 | 0 | 1 |
4Q LOSS WILD-TYPE | 289 | 32 | 85 | 17 | 5 |
Figure S88. Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D47V3.png)
P value = 2.66e-11 (Fisher's exact test), Q value = 1.7e-08
Table S89. Gene #47: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
4Q LOSS CNV | 39 | 16 | 2 |
4Q LOSS WILD-TYPE | 104 | 69 | 147 |
Figure S89. Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D47V4.png)
P value = 2.64e-08 (Fisher's exact test), Q value = 1.6e-05
Table S90. Gene #47: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
4Q LOSS CNV | 27 | 0 | 5 |
4Q LOSS WILD-TYPE | 115 | 107 | 108 |
Figure S90. Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D47V7.png)
P value = 2.45e-08 (Fisher's exact test), Q value = 1.5e-05
Table S91. Gene #47: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 65 | 92 | 65 | 140 |
4Q LOSS CNV | 2 | 0 | 2 | 28 |
4Q LOSS WILD-TYPE | 63 | 92 | 63 | 112 |
Figure S91. Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D47V8.png)
P value = 1.04e-10 (Fisher's exact test), Q value = 6.6e-08
Table S92. Gene #47: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
4Q LOSS CNV | 51 | 6 | 5 |
4Q LOSS WILD-TYPE | 156 | 138 | 127 |
Figure S92. Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D47V9.png)
P value = 1.39e-10 (Fisher's exact test), Q value = 8.7e-08
Table S93. Gene #47: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
4Q LOSS CNV | 5 | 6 | 5 | 46 |
4Q LOSS WILD-TYPE | 188 | 73 | 22 | 138 |
Figure S93. Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D47V10.png)
P value = 1.16e-10 (Chi-square test), Q value = 7.3e-08
Table S94. Gene #48: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
5P LOSS CNV | 0 | 8 | 19 | 0 | 0 |
5P LOSS WILD-TYPE | 290 | 32 | 120 | 17 | 6 |
Figure S94. Get High-res Image Gene #48: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D48V3.png)
P value = 0.000334 (Fisher's exact test), Q value = 0.16
Table S95. Gene #48: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
5P LOSS CNV | 15 | 4 | 1 |
5P LOSS WILD-TYPE | 128 | 81 | 148 |
Figure S95. Get High-res Image Gene #48: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D48V4.png)
P value = 0.000216 (Fisher's exact test), Q value = 0.1
Table S96. Gene #48: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
5P LOSS CNV | 22 | 3 | 2 |
5P LOSS WILD-TYPE | 185 | 141 | 130 |
Figure S96. Get High-res Image Gene #48: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D48V9.png)
P value = 1.18e-18 (Chi-square test), Q value = 8e-16
Table S97. Gene #49: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
5Q LOSS CNV | 0 | 7 | 38 | 0 | 0 |
5Q LOSS WILD-TYPE | 290 | 33 | 101 | 17 | 6 |
Figure S97. Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D49V3.png)
P value = 7.26e-09 (Fisher's exact test), Q value = 4.4e-06
Table S98. Gene #49: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
5Q LOSS CNV | 29 | 6 | 1 |
5Q LOSS WILD-TYPE | 114 | 79 | 148 |
Figure S98. Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D49V4.png)
P value = 6.28e-08 (Fisher's exact test), Q value = 3.7e-05
Table S99. Gene #49: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
5Q LOSS CNV | 25 | 1 | 2 |
5Q LOSS WILD-TYPE | 117 | 106 | 111 |
Figure S99. Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D49V7.png)
P value = 2.96e-08 (Fisher's exact test), Q value = 1.8e-05
Table S100. Gene #49: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 65 | 92 | 65 | 140 |
5Q LOSS CNV | 0 | 0 | 3 | 25 |
5Q LOSS WILD-TYPE | 65 | 92 | 62 | 115 |
Figure S100. Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D49V8.png)
P value = 2.83e-09 (Fisher's exact test), Q value = 1.7e-06
Table S101. Gene #49: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
5Q LOSS CNV | 38 | 4 | 2 |
5Q LOSS WILD-TYPE | 169 | 140 | 130 |
Figure S101. Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D49V9.png)
P value = 7.58e-08 (Fisher's exact test), Q value = 4.4e-05
Table S102. Gene #49: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
5Q LOSS CNV | 4 | 4 | 1 | 35 |
5Q LOSS WILD-TYPE | 189 | 75 | 26 | 149 |
Figure S102. Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D49V10.png)
P value = 0.000236 (Chi-square test), Q value = 0.11
Table S103. Gene #51: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
6Q LOSS CNV | 0 | 3 | 9 | 0 | 0 |
6Q LOSS WILD-TYPE | 290 | 37 | 130 | 17 | 6 |
Figure S103. Get High-res Image Gene #51: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D51V3.png)
P value = 9.88e-10 (Chi-square test), Q value = 6.1e-07
Table S104. Gene #52: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
7P LOSS CNV | 3 | 1 | 24 | 0 | 1 |
7P LOSS WILD-TYPE | 287 | 39 | 115 | 17 | 5 |
Figure S104. Get High-res Image Gene #52: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D52V3.png)
P value = 0.000162 (Fisher's exact test), Q value = 0.08
Table S105. Gene #52: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
7P LOSS CNV | 18 | 2 | 2 |
7P LOSS WILD-TYPE | 124 | 105 | 111 |
Figure S105. Get High-res Image Gene #52: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D52V7.png)
P value = 2.27e-05 (Fisher's exact test), Q value = 0.012
Table S106. Gene #52: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 65 | 92 | 65 | 140 |
7P LOSS CNV | 2 | 0 | 1 | 19 |
7P LOSS WILD-TYPE | 63 | 92 | 64 | 121 |
Figure S106. Get High-res Image Gene #52: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D52V8.png)
P value = 4.91e-14 (Chi-square test), Q value = 3.2e-11
Table S107. Gene #53: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
7Q LOSS CNV | 0 | 0 | 26 | 0 | 1 |
7Q LOSS WILD-TYPE | 290 | 40 | 113 | 17 | 5 |
Figure S107. Get High-res Image Gene #53: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D53V3.png)
P value = 0.00018 (Fisher's exact test), Q value = 0.088
Table S108. Gene #53: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
7Q LOSS CNV | 16 | 6 | 1 |
7Q LOSS WILD-TYPE | 127 | 79 | 148 |
Figure S108. Get High-res Image Gene #53: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D53V4.png)
P value = 1.32e-07 (Fisher's exact test), Q value = 7.6e-05
Table S109. Gene #53: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
7Q LOSS CNV | 17 | 0 | 0 |
7Q LOSS WILD-TYPE | 125 | 107 | 113 |
Figure S109. Get High-res Image Gene #53: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D53V7.png)
P value = 1.59e-06 (Fisher's exact test), Q value = 0.00089
Table S110. Gene #53: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 65 | 92 | 65 | 140 |
7Q LOSS CNV | 0 | 0 | 0 | 17 |
7Q LOSS WILD-TYPE | 65 | 92 | 65 | 123 |
Figure S110. Get High-res Image Gene #53: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D53V8.png)
P value = 1.77e-05 (Fisher's exact test), Q value = 0.0094
Table S111. Gene #53: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
7Q LOSS CNV | 23 | 3 | 1 |
7Q LOSS WILD-TYPE | 184 | 141 | 131 |
Figure S111. Get High-res Image Gene #53: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D53V9.png)
P value = 1.25e-05 (Fisher's exact test), Q value = 0.0067
Table S112. Gene #53: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
7Q LOSS CNV | 3 | 1 | 0 | 23 |
7Q LOSS WILD-TYPE | 190 | 78 | 27 | 161 |
Figure S112. Get High-res Image Gene #53: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D53V10.png)
P value = 4.01e-24 (Chi-square test), Q value = 2.8e-21
Table S113. Gene #54: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
8P LOSS CNV | 2 | 1 | 48 | 2 | 0 |
8P LOSS WILD-TYPE | 288 | 39 | 91 | 15 | 6 |
Figure S113. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D54V3.png)
P value = 1.08e-11 (Fisher's exact test), Q value = 6.9e-09
Table S114. Gene #54: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
8P LOSS CNV | 37 | 8 | 1 |
8P LOSS WILD-TYPE | 106 | 77 | 148 |
Figure S114. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D54V4.png)
P value = 4.84e-12 (Fisher's exact test), Q value = 3.1e-09
Table S115. Gene #54: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
8P LOSS CNV | 30 | 0 | 1 |
8P LOSS WILD-TYPE | 112 | 107 | 112 |
Figure S115. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D54V7.png)
P value = 6.9e-10 (Fisher's exact test), Q value = 4.3e-07
Table S116. Gene #54: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 65 | 92 | 65 | 140 |
8P LOSS CNV | 1 | 0 | 1 | 29 |
8P LOSS WILD-TYPE | 64 | 92 | 64 | 111 |
Figure S116. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D54V8.png)
P value = 4.01e-15 (Fisher's exact test), Q value = 2.7e-12
Table S117. Gene #54: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
8P LOSS CNV | 47 | 1 | 2 |
8P LOSS WILD-TYPE | 160 | 143 | 130 |
Figure S117. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D54V9.png)
P value = 7.17e-17 (Fisher's exact test), Q value = 4.8e-14
Table S118. Gene #54: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
8P LOSS CNV | 1 | 2 | 0 | 47 |
8P LOSS WILD-TYPE | 192 | 77 | 27 | 137 |
Figure S118. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D54V10.png)
P value = 2.23e-05 (Chi-square test), Q value = 0.012
Table S119. Gene #55: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
8Q LOSS CNV | 0 | 0 | 11 | 1 | 0 |
8Q LOSS WILD-TYPE | 290 | 40 | 128 | 16 | 6 |
Figure S119. Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D55V3.png)
P value = 0.000302 (Fisher's exact test), Q value = 0.14
Table S120. Gene #55: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
8Q LOSS CNV | 11 | 0 | 0 |
8Q LOSS WILD-TYPE | 196 | 144 | 132 |
Figure S120. Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D55V9.png)
P value = 0.000443 (Fisher's exact test), Q value = 0.21
Table S121. Gene #55: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
8Q LOSS CNV | 0 | 0 | 0 | 11 |
8Q LOSS WILD-TYPE | 193 | 79 | 27 | 173 |
Figure S121. Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D55V10.png)
P value = 2.63e-29 (Chi-square test), Q value = 1.8e-26
Table S122. Gene #56: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
9P LOSS CNV | 2 | 11 | 61 | 2 | 0 |
9P LOSS WILD-TYPE | 288 | 29 | 78 | 15 | 6 |
Figure S122. Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D56V3.png)
P value = 2.34e-06 (Fisher's exact test), Q value = 0.0013
Table S123. Gene #56: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
9P LOSS CNV | 36 | 19 | 8 |
9P LOSS WILD-TYPE | 107 | 66 | 141 |
Figure S123. Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D56V4.png)
P value = 2.12e-12 (Fisher's exact test), Q value = 1.4e-09
Table S124. Gene #56: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
9P LOSS CNV | 41 | 3 | 3 |
9P LOSS WILD-TYPE | 101 | 104 | 110 |
Figure S124. Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D56V7.png)
P value = 7.6e-15 (Fisher's exact test), Q value = 5e-12
Table S125. Gene #56: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 65 | 92 | 65 | 140 |
9P LOSS CNV | 0 | 1 | 3 | 43 |
9P LOSS WILD-TYPE | 65 | 91 | 62 | 97 |
Figure S125. Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D56V8.png)
P value = 1.37e-09 (Fisher's exact test), Q value = 8.4e-07
Table S126. Gene #56: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
9P LOSS CNV | 55 | 15 | 4 |
9P LOSS WILD-TYPE | 152 | 129 | 128 |
Figure S126. Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D56V9.png)
P value = 1.19e-08 (Fisher's exact test), Q value = 7.1e-06
Table S127. Gene #56: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
9P LOSS CNV | 14 | 4 | 4 | 52 |
9P LOSS WILD-TYPE | 179 | 75 | 23 | 132 |
Figure S127. Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D56V10.png)
P value = 0.000248 (Fisher's exact test), Q value = 0.12
Table S128. Gene #57: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 20 | 15 | 18 |
9Q LOSS CNV | 0 | 0 | 7 |
9Q LOSS WILD-TYPE | 20 | 15 | 11 |
Figure S128. Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D57V2.png)
P value = 1.53e-37 (Chi-square test), Q value = 1.1e-34
Table S129. Gene #57: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
9Q LOSS CNV | 3 | 13 | 75 | 1 | 1 |
9Q LOSS WILD-TYPE | 287 | 27 | 64 | 16 | 5 |
Figure S129. Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D57V3.png)
P value = 5.86e-07 (Fisher's exact test), Q value = 0.00033
Table S130. Gene #57: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
9Q LOSS CNV | 46 | 21 | 12 |
9Q LOSS WILD-TYPE | 97 | 64 | 137 |
Figure S130. Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D57V4.png)
P value = 2.56e-13 (Fisher's exact test), Q value = 1.7e-10
Table S131. Gene #57: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
9Q LOSS CNV | 48 | 4 | 5 |
9Q LOSS WILD-TYPE | 94 | 103 | 108 |
Figure S131. Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D57V7.png)
P value = 2.82e-16 (Fisher's exact test), Q value = 1.9e-13
Table S132. Gene #57: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 65 | 92 | 65 | 140 |
9Q LOSS CNV | 0 | 2 | 5 | 50 |
9Q LOSS WILD-TYPE | 65 | 90 | 60 | 90 |
Figure S132. Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D57V8.png)
P value = 2.09e-12 (Fisher's exact test), Q value = 1.4e-09
Table S133. Gene #57: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
9Q LOSS CNV | 69 | 16 | 6 |
9Q LOSS WILD-TYPE | 138 | 128 | 126 |
Figure S133. Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D57V9.png)
P value = 3.83e-10 (Fisher's exact test), Q value = 2.4e-07
Table S134. Gene #57: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
9Q LOSS CNV | 15 | 8 | 6 | 62 |
9Q LOSS WILD-TYPE | 178 | 71 | 21 | 122 |
Figure S134. Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D57V10.png)
P value = 4e-11 (Chi-square test), Q value = 2.5e-08
Table S135. Gene #58: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
10P LOSS CNV | 0 | 1 | 22 | 0 | 0 |
10P LOSS WILD-TYPE | 290 | 39 | 117 | 17 | 6 |
Figure S135. Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D58V3.png)
P value = 0.000334 (Fisher's exact test), Q value = 0.16
Table S136. Gene #58: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
10P LOSS CNV | 15 | 4 | 1 |
10P LOSS WILD-TYPE | 128 | 81 | 148 |
Figure S136. Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D58V4.png)
P value = 0.000469 (Fisher's exact test), Q value = 0.22
Table S137. Gene #58: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
10P LOSS CNV | 11 | 1 | 0 |
10P LOSS WILD-TYPE | 131 | 106 | 113 |
Figure S137. Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D58V7.png)
P value = 1.25e-05 (Fisher's exact test), Q value = 0.0067
Table S138. Gene #58: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
10P LOSS CNV | 20 | 1 | 1 |
10P LOSS WILD-TYPE | 187 | 143 | 131 |
Figure S138. Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D58V9.png)
P value = 2.94e-10 (Chi-square test), Q value = 1.8e-07
Table S139. Gene #59: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
10Q LOSS CNV | 1 | 1 | 22 | 0 | 0 |
10Q LOSS WILD-TYPE | 289 | 39 | 117 | 17 | 6 |
Figure S139. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D59V3.png)
P value = 0.000192 (Fisher's exact test), Q value = 0.094
Table S140. Gene #59: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
10Q LOSS CNV | 16 | 5 | 1 |
10Q LOSS WILD-TYPE | 127 | 80 | 148 |
Figure S140. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D59V4.png)
P value = 0.000469 (Fisher's exact test), Q value = 0.22
Table S141. Gene #59: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
10Q LOSS CNV | 11 | 1 | 0 |
10Q LOSS WILD-TYPE | 131 | 106 | 113 |
Figure S141. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D59V7.png)
P value = 0.000214 (Fisher's exact test), Q value = 0.1
Table S142. Gene #59: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
10Q LOSS CNV | 20 | 2 | 2 |
10Q LOSS WILD-TYPE | 187 | 142 | 130 |
Figure S142. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D59V9.png)
P value = 1.44e-21 (Chi-square test), Q value = 9.9e-19
Table S143. Gene #60: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
11P LOSS CNV | 1 | 4 | 45 | 1 | 2 |
11P LOSS WILD-TYPE | 289 | 36 | 94 | 16 | 4 |
Figure S143. Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D60V3.png)
P value = 7.44e-07 (Fisher's exact test), Q value = 0.00042
Table S144. Gene #60: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
11P LOSS CNV | 31 | 13 | 4 |
11P LOSS WILD-TYPE | 112 | 72 | 145 |
Figure S144. Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D60V4.png)
P value = 4.46e-08 (Fisher's exact test), Q value = 2.6e-05
Table S145. Gene #60: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
11P LOSS CNV | 24 | 0 | 3 |
11P LOSS WILD-TYPE | 118 | 107 | 110 |
Figure S145. Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D60V7.png)
P value = 2.6e-07 (Fisher's exact test), Q value = 0.00015
Table S146. Gene #60: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 65 | 92 | 65 | 140 |
11P LOSS CNV | 1 | 0 | 2 | 24 |
11P LOSS WILD-TYPE | 64 | 92 | 63 | 116 |
Figure S146. Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D60V8.png)
P value = 1.99e-08 (Fisher's exact test), Q value = 1.2e-05
Table S147. Gene #60: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
11P LOSS CNV | 42 | 7 | 3 |
11P LOSS WILD-TYPE | 165 | 137 | 129 |
Figure S147. Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D60V9.png)
P value = 1.99e-06 (Fisher's exact test), Q value = 0.0011
Table S148. Gene #60: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
11P LOSS CNV | 7 | 5 | 3 | 37 |
11P LOSS WILD-TYPE | 186 | 74 | 24 | 147 |
Figure S148. Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D60V10.png)
P value = 1.15e-15 (Chi-square test), Q value = 7.7e-13
Table S149. Gene #61: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
11Q LOSS CNV | 1 | 6 | 35 | 1 | 2 |
11Q LOSS WILD-TYPE | 289 | 34 | 104 | 16 | 4 |
Figure S149. Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D61V3.png)
P value = 7.53e-05 (Fisher's exact test), Q value = 0.038
Table S150. Gene #61: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
11Q LOSS CNV | 26 | 12 | 5 |
11Q LOSS WILD-TYPE | 117 | 73 | 144 |
Figure S150. Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D61V4.png)
P value = 0.000397 (Fisher's exact test), Q value = 0.19
Table S151. Gene #61: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
11Q LOSS CNV | 17 | 2 | 2 |
11Q LOSS WILD-TYPE | 125 | 105 | 111 |
Figure S151. Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D61V7.png)
P value = 8.07e-06 (Fisher's exact test), Q value = 0.0044
Table S152. Gene #61: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 65 | 92 | 65 | 140 |
11Q LOSS CNV | 1 | 0 | 1 | 19 |
11Q LOSS WILD-TYPE | 64 | 92 | 64 | 121 |
Figure S152. Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D61V8.png)
P value = 2.54e-06 (Fisher's exact test), Q value = 0.0014
Table S153. Gene #61: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
11Q LOSS CNV | 35 | 7 | 3 |
11Q LOSS WILD-TYPE | 172 | 137 | 129 |
Figure S153. Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D61V9.png)
P value = 0.000184 (Fisher's exact test), Q value = 0.09
Table S154. Gene #61: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
11Q LOSS CNV | 8 | 4 | 2 | 31 |
11Q LOSS WILD-TYPE | 185 | 75 | 25 | 153 |
Figure S154. Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D61V10.png)
P value = 3.86e-11 (Chi-square test), Q value = 2.5e-08
Table S155. Gene #62: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
12P LOSS CNV | 0 | 2 | 23 | 0 | 0 |
12P LOSS WILD-TYPE | 290 | 38 | 116 | 17 | 6 |
Figure S155. Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D62V3.png)
P value = 0.000192 (Fisher's exact test), Q value = 0.094
Table S156. Gene #62: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
12P LOSS CNV | 16 | 5 | 1 |
12P LOSS WILD-TYPE | 127 | 80 | 148 |
Figure S156. Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D62V4.png)
P value = 3.62e-05 (Fisher's exact test), Q value = 0.019
Table S157. Gene #62: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
12P LOSS CNV | 12 | 0 | 0 |
12P LOSS WILD-TYPE | 130 | 107 | 113 |
Figure S157. Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D62V7.png)
P value = 9.52e-08 (Fisher's exact test), Q value = 5.6e-05
Table S158. Gene #62: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
12P LOSS CNV | 23 | 1 | 0 |
12P LOSS WILD-TYPE | 184 | 143 | 132 |
Figure S158. Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D62V9.png)
P value = 4.34e-06 (Fisher's exact test), Q value = 0.0024
Table S159. Gene #62: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
12P LOSS CNV | 1 | 1 | 1 | 21 |
12P LOSS WILD-TYPE | 192 | 78 | 26 | 163 |
Figure S159. Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D62V10.png)
P value = 1.23e-09 (Chi-square test), Q value = 7.6e-07
Table S160. Gene #63: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
12Q LOSS CNV | 0 | 0 | 18 | 0 | 0 |
12Q LOSS WILD-TYPE | 290 | 40 | 121 | 17 | 6 |
Figure S160. Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D63V3.png)
P value = 1e-04 (Fisher's exact test), Q value = 0.05
Table S161. Gene #63: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
12Q LOSS CNV | 13 | 3 | 0 |
12Q LOSS WILD-TYPE | 130 | 82 | 149 |
Figure S161. Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D63V4.png)
P value = 1.25e-06 (Fisher's exact test), Q value = 7e-04
Table S162. Gene #63: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
12Q LOSS CNV | 17 | 0 | 0 |
12Q LOSS WILD-TYPE | 190 | 144 | 132 |
Figure S162. Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D63V9.png)
P value = 1.67e-06 (Fisher's exact test), Q value = 0.00092
Table S163. Gene #63: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
12Q LOSS CNV | 0 | 0 | 0 | 17 |
12Q LOSS WILD-TYPE | 193 | 79 | 27 | 167 |
Figure S163. Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D63V10.png)
P value = 2.43e-18 (Chi-square test), Q value = 1.6e-15
Table S164. Gene #64: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
13Q LOSS CNV | 5 | 15 | 39 | 0 | 1 |
13Q LOSS WILD-TYPE | 285 | 25 | 100 | 17 | 5 |
Figure S164. Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D64V3.png)
P value = 0.000113 (Fisher's exact test), Q value = 0.056
Table S165. Gene #64: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
13Q LOSS CNV | 31 | 14 | 8 |
13Q LOSS WILD-TYPE | 112 | 71 | 141 |
Figure S165. Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D64V4.png)
P value = 0.000395 (Fisher's exact test), Q value = 0.19
Table S166. Gene #64: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
13Q LOSS CNV | 23 | 3 | 6 |
13Q LOSS WILD-TYPE | 119 | 104 | 107 |
Figure S166. Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D64V7.png)
P value = 3.89e-06 (Fisher's exact test), Q value = 0.0021
Table S167. Gene #64: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 65 | 92 | 65 | 140 |
13Q LOSS CNV | 3 | 1 | 2 | 26 |
13Q LOSS WILD-TYPE | 62 | 91 | 63 | 114 |
Figure S167. Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D64V8.png)
P value = 7.27e-05 (Fisher's exact test), Q value = 0.037
Table S168. Gene #64: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
13Q LOSS CNV | 41 | 10 | 8 |
13Q LOSS WILD-TYPE | 166 | 134 | 124 |
Figure S168. Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D64V9.png)
P value = 0.000188 (Fisher's exact test), Q value = 0.092
Table S169. Gene #64: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
13Q LOSS CNV | 11 | 7 | 6 | 35 |
13Q LOSS WILD-TYPE | 182 | 72 | 21 | 149 |
Figure S169. Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D64V10.png)
P value = 8.94e-17 (Chi-square test), Q value = 6e-14
Table S170. Gene #65: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
14Q LOSS CNV | 0 | 4 | 35 | 1 | 2 |
14Q LOSS WILD-TYPE | 290 | 36 | 104 | 16 | 4 |
Figure S170. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D65V3.png)
P value = 1.48e-09 (Fisher's exact test), Q value = 9e-07
Table S171. Gene #65: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
14Q LOSS CNV | 27 | 5 | 0 |
14Q LOSS WILD-TYPE | 116 | 80 | 149 |
Figure S171. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D65V4.png)
P value = 3.38e-08 (Fisher's exact test), Q value = 2e-05
Table S172. Gene #65: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
14Q LOSS CNV | 23 | 0 | 2 |
14Q LOSS WILD-TYPE | 119 | 107 | 111 |
Figure S172. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D65V7.png)
P value = 1.95e-07 (Fisher's exact test), Q value = 0.00011
Table S173. Gene #65: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 65 | 92 | 65 | 140 |
14Q LOSS CNV | 1 | 0 | 1 | 23 |
14Q LOSS WILD-TYPE | 64 | 92 | 64 | 117 |
Figure S173. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D65V8.png)
P value = 3.34e-09 (Fisher's exact test), Q value = 2e-06
Table S174. Gene #65: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
14Q LOSS CNV | 35 | 1 | 4 |
14Q LOSS WILD-TYPE | 172 | 143 | 128 |
Figure S174. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D65V9.png)
P value = 9.82e-12 (Fisher's exact test), Q value = 6.3e-09
Table S175. Gene #65: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
14Q LOSS CNV | 0 | 4 | 1 | 35 |
14Q LOSS WILD-TYPE | 193 | 75 | 26 | 149 |
Figure S175. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D65V10.png)
P value = 4.68e-35 (Chi-square test), Q value = 3.2e-32
Table S176. Gene #66: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
15Q LOSS CNV | 1 | 10 | 67 | 0 | 3 |
15Q LOSS WILD-TYPE | 289 | 30 | 72 | 17 | 3 |
Figure S176. Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D66V3.png)
P value = 1.61e-13 (Fisher's exact test), Q value = 1.1e-10
Table S177. Gene #66: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
15Q LOSS CNV | 51 | 16 | 4 |
15Q LOSS WILD-TYPE | 92 | 69 | 145 |
Figure S177. Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D66V4.png)
P value = 7.92e-10 (Fisher's exact test), Q value = 4.9e-07
Table S178. Gene #66: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
15Q LOSS CNV | 36 | 2 | 5 |
15Q LOSS WILD-TYPE | 106 | 105 | 108 |
Figure S178. Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D66V7.png)
P value = 1.07e-10 (Fisher's exact test), Q value = 6.7e-08
Table S179. Gene #66: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 65 | 92 | 65 | 140 |
15Q LOSS CNV | 1 | 1 | 4 | 37 |
15Q LOSS WILD-TYPE | 64 | 91 | 61 | 103 |
Figure S179. Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D66V8.png)
P value = 5.22e-15 (Fisher's exact test), Q value = 3.5e-12
Table S180. Gene #66: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
15Q LOSS CNV | 66 | 7 | 6 |
15Q LOSS WILD-TYPE | 141 | 137 | 126 |
Figure S180. Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D66V9.png)
P value = 1.07e-16 (Fisher's exact test), Q value = 7.2e-14
Table S181. Gene #66: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
15Q LOSS CNV | 4 | 8 | 6 | 61 |
15Q LOSS WILD-TYPE | 189 | 71 | 21 | 123 |
Figure S181. Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D66V10.png)
P value = 2.82e-31 (Chi-square test), Q value = 2e-28
Table S182. Gene #67: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
16P LOSS CNV | 2 | 6 | 61 | 0 | 0 |
16P LOSS WILD-TYPE | 288 | 34 | 78 | 17 | 6 |
Figure S182. Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D67V3.png)
P value = 2.77e-09 (Fisher's exact test), Q value = 1.7e-06
Table S183. Gene #67: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
16P LOSS CNV | 38 | 17 | 4 |
16P LOSS WILD-TYPE | 105 | 68 | 145 |
Figure S183. Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D67V4.png)
P value = 7.52e-10 (Fisher's exact test), Q value = 4.7e-07
Table S184. Gene #67: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
16P LOSS CNV | 35 | 2 | 4 |
16P LOSS WILD-TYPE | 107 | 105 | 109 |
Figure S184. Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D67V7.png)
P value = 1.47e-09 (Fisher's exact test), Q value = 9e-07
Table S185. Gene #67: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 65 | 92 | 65 | 140 |
16P LOSS CNV | 3 | 1 | 2 | 35 |
16P LOSS WILD-TYPE | 62 | 91 | 63 | 105 |
Figure S185. Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D67V8.png)
P value = 1.47e-09 (Fisher's exact test), Q value = 9e-07
Table S186. Gene #67: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
16P LOSS CNV | 52 | 6 | 8 |
16P LOSS WILD-TYPE | 155 | 138 | 124 |
Figure S186. Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D67V9.png)
P value = 1.36e-10 (Fisher's exact test), Q value = 8.5e-08
Table S187. Gene #67: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
16P LOSS CNV | 6 | 7 | 4 | 49 |
16P LOSS WILD-TYPE | 187 | 72 | 23 | 135 |
Figure S187. Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D67V10.png)
P value = 5.94e-40 (Chi-square test), Q value = 4.1e-37
Table S188. Gene #68: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
16Q LOSS CNV | 13 | 10 | 87 | 0 | 0 |
16Q LOSS WILD-TYPE | 277 | 30 | 52 | 17 | 6 |
Figure S188. Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D68V3.png)
P value = 2.86e-11 (Fisher's exact test), Q value = 1.8e-08
Table S189. Gene #68: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
16Q LOSS CNV | 58 | 25 | 11 |
16Q LOSS WILD-TYPE | 85 | 60 | 138 |
Figure S189. Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D68V4.png)
P value = 1.01e-11 (Fisher's exact test), Q value = 6.5e-09
Table S190. Gene #68: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
16Q LOSS CNV | 54 | 6 | 11 |
16Q LOSS WILD-TYPE | 88 | 101 | 102 |
Figure S190. Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D68V7.png)
P value = 2.34e-10 (Fisher's exact test), Q value = 1.5e-07
Table S191. Gene #68: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 65 | 92 | 65 | 140 |
16Q LOSS CNV | 9 | 4 | 6 | 52 |
16Q LOSS WILD-TYPE | 56 | 88 | 59 | 88 |
Figure S191. Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D68V8.png)
P value = 1.07e-11 (Fisher's exact test), Q value = 6.9e-09
Table S192. Gene #68: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
16Q LOSS CNV | 77 | 12 | 17 |
16Q LOSS WILD-TYPE | 130 | 132 | 115 |
Figure S192. Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D68V9.png)
P value = 1.9e-11 (Fisher's exact test), Q value = 1.2e-08
Table S193. Gene #68: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
16Q LOSS CNV | 18 | 11 | 5 | 72 |
16Q LOSS WILD-TYPE | 175 | 68 | 22 | 112 |
Figure S193. Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D68V10.png)
P value = 8.66e-53 (Chi-square test), Q value = 6e-50
Table S194. Gene #69: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
17P LOSS CNV | 3 | 9 | 93 | 0 | 0 |
17P LOSS WILD-TYPE | 287 | 31 | 46 | 17 | 6 |
Figure S194. Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D69V3.png)
P value = 8.14e-13 (Fisher's exact test), Q value = 5.3e-10
Table S195. Gene #69: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
17P LOSS CNV | 61 | 18 | 10 |
17P LOSS WILD-TYPE | 82 | 67 | 139 |
Figure S195. Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D69V4.png)
P value = 1.6e-20 (Fisher's exact test), Q value = 1.1e-17
Table S196. Gene #69: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
17P LOSS CNV | 58 | 2 | 4 |
17P LOSS WILD-TYPE | 84 | 105 | 109 |
Figure S196. Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D69V7.png)
P value = 2.15e-21 (Fisher's exact test), Q value = 1.5e-18
Table S197. Gene #69: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 65 | 92 | 65 | 140 |
17P LOSS CNV | 1 | 0 | 5 | 58 |
17P LOSS WILD-TYPE | 64 | 92 | 60 | 82 |
Figure S197. Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D69V8.png)
P value = 4.87e-17 (Fisher's exact test), Q value = 3.3e-14
Table S198. Gene #69: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
17P LOSS CNV | 81 | 15 | 6 |
17P LOSS WILD-TYPE | 126 | 129 | 126 |
Figure S198. Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D69V9.png)
P value = 2.92e-15 (Fisher's exact test), Q value = 1.9e-12
Table S199. Gene #69: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
17P LOSS CNV | 15 | 7 | 5 | 75 |
17P LOSS WILD-TYPE | 178 | 72 | 22 | 109 |
Figure S199. Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D69V10.png)
P value = 1.48e-29 (Chi-square test), Q value = 1e-26
Table S200. Gene #70: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
17Q LOSS CNV | 1 | 9 | 58 | 0 | 0 |
17Q LOSS WILD-TYPE | 289 | 31 | 81 | 17 | 6 |
Figure S200. Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D70V3.png)
P value = 3.41e-05 (Fisher's exact test), Q value = 0.018
Table S201. Gene #70: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
17Q LOSS CNV | 35 | 14 | 9 |
17Q LOSS WILD-TYPE | 108 | 71 | 140 |
Figure S201. Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D70V4.png)
P value = 4.28e-09 (Fisher's exact test), Q value = 2.6e-06
Table S202. Gene #70: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
17Q LOSS CNV | 33 | 2 | 4 |
17Q LOSS WILD-TYPE | 109 | 105 | 109 |
Figure S202. Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D70V7.png)
P value = 1.95e-11 (Fisher's exact test), Q value = 1.2e-08
Table S203. Gene #70: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 65 | 92 | 65 | 140 |
17Q LOSS CNV | 1 | 0 | 3 | 35 |
17Q LOSS WILD-TYPE | 64 | 92 | 62 | 105 |
Figure S203. Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D70V8.png)
P value = 2.71e-07 (Fisher's exact test), Q value = 0.00016
Table S204. Gene #70: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
17Q LOSS CNV | 48 | 11 | 6 |
17Q LOSS WILD-TYPE | 159 | 133 | 126 |
Figure S204. Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D70V9.png)
P value = 5.5e-07 (Fisher's exact test), Q value = 0.00031
Table S205. Gene #70: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
17Q LOSS CNV | 11 | 5 | 5 | 44 |
17Q LOSS WILD-TYPE | 182 | 74 | 22 | 140 |
Figure S205. Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D70V10.png)
P value = 3.15e-12 (Chi-square test), Q value = 2e-09
Table S206. Gene #71: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
18P LOSS CNV | 1 | 9 | 25 | 0 | 1 |
18P LOSS WILD-TYPE | 289 | 31 | 114 | 17 | 5 |
Figure S206. Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D71V3.png)
P value = 2.09e-05 (Fisher's exact test), Q value = 0.011
Table S207. Gene #71: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
18P LOSS CNV | 22 | 6 | 2 |
18P LOSS WILD-TYPE | 121 | 79 | 147 |
Figure S207. Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D71V4.png)
P value = 0.000172 (Fisher's exact test), Q value = 0.084
Table S208. Gene #71: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 65 | 92 | 65 | 140 |
18P LOSS CNV | 1 | 0 | 4 | 17 |
18P LOSS WILD-TYPE | 64 | 92 | 61 | 123 |
Figure S208. Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D71V8.png)
P value = 9.75e-18 (Chi-square test), Q value = 6.6e-15
Table S209. Gene #72: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
18Q LOSS CNV | 1 | 9 | 38 | 0 | 1 |
18Q LOSS WILD-TYPE | 289 | 31 | 101 | 17 | 5 |
Figure S209. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D72V3.png)
P value = 1.98e-06 (Fisher's exact test), Q value = 0.0011
Table S210. Gene #72: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
18Q LOSS CNV | 30 | 10 | 4 |
18Q LOSS WILD-TYPE | 113 | 75 | 145 |
Figure S210. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D72V4.png)
P value = 3.87e-06 (Fisher's exact test), Q value = 0.0021
Table S211. Gene #72: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
18Q LOSS CNV | 23 | 1 | 4 |
18Q LOSS WILD-TYPE | 119 | 106 | 109 |
Figure S211. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D72V7.png)
P value = 5.65e-07 (Fisher's exact test), Q value = 0.00032
Table S212. Gene #72: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 65 | 92 | 65 | 140 |
18Q LOSS CNV | 1 | 0 | 3 | 24 |
18Q LOSS WILD-TYPE | 64 | 92 | 62 | 116 |
Figure S212. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D72V8.png)
P value = 3.04e-06 (Fisher's exact test), Q value = 0.0017
Table S213. Gene #72: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
18Q LOSS CNV | 37 | 5 | 6 |
18Q LOSS WILD-TYPE | 170 | 139 | 126 |
Figure S213. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D72V9.png)
P value = 2.59e-07 (Fisher's exact test), Q value = 0.00015
Table S214. Gene #72: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
18Q LOSS CNV | 4 | 6 | 6 | 32 |
18Q LOSS WILD-TYPE | 189 | 73 | 21 | 152 |
Figure S214. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D72V10.png)
P value = 4.63e-12 (Chi-square test), Q value = 3e-09
Table S215. Gene #73: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
19P LOSS CNV | 0 | 7 | 26 | 1 | 0 |
19P LOSS WILD-TYPE | 290 | 33 | 113 | 16 | 6 |
Figure S215. Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D73V3.png)
P value = 1.07e-07 (Fisher's exact test), Q value = 6.2e-05
Table S216. Gene #73: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
19P LOSS CNV | 25 | 4 | 1 |
19P LOSS WILD-TYPE | 118 | 81 | 148 |
Figure S216. Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D73V4.png)
P value = 1.84e-05 (Fisher's exact test), Q value = 0.0098
Table S217. Gene #73: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
19P LOSS CNV | 16 | 0 | 2 |
19P LOSS WILD-TYPE | 126 | 107 | 111 |
Figure S217. Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D73V7.png)
P value = 7.84e-06 (Fisher's exact test), Q value = 0.0042
Table S218. Gene #73: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 65 | 92 | 65 | 140 |
19P LOSS CNV | 1 | 0 | 0 | 17 |
19P LOSS WILD-TYPE | 64 | 92 | 65 | 123 |
Figure S218. Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D73V8.png)
P value = 1.01e-05 (Fisher's exact test), Q value = 0.0055
Table S219. Gene #73: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
19P LOSS CNV | 27 | 2 | 4 |
19P LOSS WILD-TYPE | 180 | 142 | 128 |
Figure S219. Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D73V9.png)
P value = 6.41e-07 (Fisher's exact test), Q value = 0.00036
Table S220. Gene #73: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
19P LOSS CNV | 1 | 4 | 3 | 25 |
19P LOSS WILD-TYPE | 192 | 75 | 24 | 159 |
Figure S220. Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D73V10.png)
P value = 1.79e-08 (Chi-square test), Q value = 1.1e-05
Table S221. Gene #74: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
19Q LOSS CNV | 1 | 6 | 20 | 1 | 0 |
19Q LOSS WILD-TYPE | 289 | 34 | 119 | 16 | 6 |
Figure S221. Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D74V3.png)
P value = 4.65e-05 (Fisher's exact test), Q value = 0.024
Table S222. Gene #74: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
19Q LOSS CNV | 18 | 5 | 1 |
19Q LOSS WILD-TYPE | 125 | 80 | 148 |
Figure S222. Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D74V4.png)
P value = 1.46e-05 (Fisher's exact test), Q value = 0.0078
Table S223. Gene #74: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
19Q LOSS CNV | 1 | 3 | 3 | 20 |
19Q LOSS WILD-TYPE | 192 | 76 | 24 | 164 |
Figure S223. Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D74V10.png)
P value = 0.000122 (Chi-square test), Q value = 0.061
Table S224. Gene #75: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
20P LOSS CNV | 1 | 2 | 12 | 0 | 0 |
20P LOSS WILD-TYPE | 289 | 38 | 127 | 17 | 6 |
Figure S224. Get High-res Image Gene #75: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D75V3.png)
P value = 6.47e-08 (Chi-square test), Q value = 3.8e-05
Table S225. Gene #77: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
21Q LOSS CNV | 3 | 4 | 23 | 1 | 1 |
21Q LOSS WILD-TYPE | 287 | 36 | 116 | 16 | 5 |
Figure S225. Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D77V3.png)
P value = 0.000148 (Fisher's exact test), Q value = 0.073
Table S226. Gene #77: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
21Q LOSS CNV | 15 | 0 | 3 |
21Q LOSS WILD-TYPE | 127 | 107 | 110 |
Figure S226. Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D77V7.png)
P value = 4.43e-05 (Fisher's exact test), Q value = 0.023
Table S227. Gene #77: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
21Q LOSS CNV | 2 | 7 | 0 | 21 |
21Q LOSS WILD-TYPE | 191 | 72 | 27 | 163 |
Figure S227. Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D77V10.png)
P value = 1.41e-36 (Chi-square test), Q value = 9.8e-34
Table S228. Gene #78: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
22Q LOSS CNV | 1 | 13 | 71 | 1 | 1 |
22Q LOSS WILD-TYPE | 289 | 27 | 68 | 16 | 5 |
Figure S228. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D78V3.png)
P value = 4.23e-08 (Fisher's exact test), Q value = 2.5e-05
Table S229. Gene #78: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 85 | 149 |
22Q LOSS CNV | 46 | 22 | 10 |
22Q LOSS WILD-TYPE | 97 | 63 | 139 |
Figure S229. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D78V4.png)
P value = 4.88e-11 (Fisher's exact test), Q value = 3.1e-08
Table S230. Gene #78: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 142 | 107 | 113 |
22Q LOSS CNV | 41 | 3 | 5 |
22Q LOSS WILD-TYPE | 101 | 104 | 108 |
Figure S230. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D78V7.png)
P value = 3.29e-14 (Fisher's exact test), Q value = 2.2e-11
Table S231. Gene #78: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 65 | 92 | 65 | 140 |
22Q LOSS CNV | 1 | 1 | 3 | 44 |
22Q LOSS WILD-TYPE | 64 | 91 | 62 | 96 |
Figure S231. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D78V8.png)
P value = 9.64e-11 (Fisher's exact test), Q value = 6.1e-08
Table S232. Gene #78: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
22Q LOSS CNV | 64 | 14 | 7 |
22Q LOSS WILD-TYPE | 143 | 130 | 125 |
Figure S232. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D78V9.png)
P value = 1.01e-09 (Fisher's exact test), Q value = 6.2e-07
Table S233. Gene #78: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
22Q LOSS CNV | 13 | 8 | 6 | 58 |
22Q LOSS WILD-TYPE | 180 | 71 | 21 | 126 |
Figure S233. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D78V10.png)
P value = 2.97e-07 (Chi-square test), Q value = 0.00017
Table S234. Gene #79: 'Xq loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 290 | 40 | 139 | 17 | 6 |
XQ LOSS CNV | 0 | 1 | 16 | 1 | 0 |
XQ LOSS WILD-TYPE | 290 | 39 | 123 | 16 | 6 |
Figure S234. Get High-res Image Gene #79: 'Xq loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D79V3.png)
P value = 0.000233 (Fisher's exact test), Q value = 0.11
Table S235. Gene #79: 'Xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 207 | 144 | 132 |
XQ LOSS CNV | 16 | 1 | 1 |
XQ LOSS WILD-TYPE | 191 | 143 | 131 |
Figure S235. Get High-res Image Gene #79: 'Xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D79V9.png)
P value = 2.27e-05 (Fisher's exact test), Q value = 0.012
Table S236. Gene #79: 'Xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 193 | 79 | 27 | 184 |
XQ LOSS CNV | 0 | 1 | 1 | 16 |
XQ LOSS WILD-TYPE | 193 | 78 | 26 | 168 |
Figure S236. Get High-res Image Gene #79: 'Xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D79V10.png)
-
Mutation data file = broad_values_by_arm.mutsig.cluster.txt
-
Molecular subtypes file = UCEC-TP.transferedmergedcluster.txt
-
Number of patients = 492
-
Number of significantly arm-level cnvs = 79
-
Number of molecular subtypes = 10
-
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 multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.