This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.
Testing the association between copy number variation 80 arm-level events and 10 molecular subtypes across 492 patients, 330 significant findings detected with P value < 0.05 and Q value < 0.25.
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1p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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1q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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2p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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2q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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3p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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3q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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5p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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6p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
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6q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
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7p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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7q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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8p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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8q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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9p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', and 'MRNASEQ_CNMF'.
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9q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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10p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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10q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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11p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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11q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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12p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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12q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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13q gain cnv correlated to 'METHLYATION_CNMF'.
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14q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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16p gain cnv correlated to 'CN_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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16q gain cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
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17p gain cnv correlated to 'MIRSEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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17q gain cnv correlated to 'CN_CNMF'.
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18p gain cnv correlated to 'CN_CNMF'.
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19p gain cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.
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19q gain cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.
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20p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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20q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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21q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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xp gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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xq gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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1p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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1q loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.
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2p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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2q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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3p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CNMF'.
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3q loss cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
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4p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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4q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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5p loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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5q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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6p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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6q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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8p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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8q loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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9p loss cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.
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9q loss cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.
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10p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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10q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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11p loss cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.
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11q loss cnv correlated to 'RPPA_CNMF'.
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12p loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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12q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
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13q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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14q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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15q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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16p loss cnv correlated to 'CN_CNMF'.
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16q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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17p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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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', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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18q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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19p loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
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19q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
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20p loss cnv correlated to 'METHLYATION_CNMF'.
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20q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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21q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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22q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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xp loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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xq loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 330 significant findings detected.
|
Clinical Features |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
||
| nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
| 8p gain | 68 (14%) | 424 |
1e-05 (0.000163) |
1e-05 (0.000163) |
1e-05 (0.000163) |
0.00031 (0.00256) |
2e-05 (0.000281) |
0.0003 (0.00255) |
0.00039 (0.003) |
0.00518 (0.0222) |
6e-05 (0.000696) |
0.00619 (0.0248) |
| 8q gain | 126 (26%) | 366 |
1e-05 (0.000163) |
1e-05 (0.000163) |
0.00024 (0.00216) |
0.00017 (0.0016) |
1e-05 (0.000163) |
3e-05 (0.000387) |
8e-05 (0.000877) |
1e-05 (0.000163) |
2e-05 (0.000281) |
0.00018 (0.00167) |
| 18q loss | 100 (20%) | 392 |
1e-05 (0.000163) |
0.00157 (0.00916) |
0.0368 (0.0988) |
0.00097 (0.00636) |
0.00311 (0.0152) |
0.0304 (0.0874) |
0.00137 (0.00837) |
0.00304 (0.015) |
0.00077 (0.00522) |
0.00125 (0.00775) |
| 7p gain | 101 (21%) | 391 |
1e-05 (0.000163) |
1e-05 (0.000163) |
0.00293 (0.0147) |
0.404 (0.508) |
1e-05 (0.000163) |
3e-05 (0.000387) |
0.00036 (0.00282) |
6e-05 (0.000696) |
0.00109 (0.00692) |
0.00025 (0.0022) |
| 7q gain | 94 (19%) | 398 |
1e-05 (0.000163) |
1e-05 (0.000163) |
0.00954 (0.0357) |
0.754 (0.814) |
1e-05 (0.000163) |
8e-05 (0.000877) |
0.00031 (0.00256) |
6e-05 (0.000696) |
0.00056 (0.00411) |
0.00029 (0.00249) |
| 15q loss | 35 (7%) | 457 |
1e-05 (0.000163) |
0.0035 (0.0163) |
0.00183 (0.0102) |
0.41 (0.511) |
0.00187 (0.0104) |
0.0107 (0.039) |
0.00486 (0.021) |
0.0124 (0.0434) |
0.00315 (0.0152) |
0.034 (0.0945) |
| 3p gain | 40 (8%) | 452 |
1e-05 (0.000163) |
0.0129 (0.045) |
0.159 (0.265) |
0.0273 (0.0809) |
3e-05 (0.000387) |
0.00033 (0.00267) |
0.0532 (0.125) |
0.00496 (0.0213) |
0.00458 (0.02) |
0.00082 (0.00551) |
| 3q gain | 54 (11%) | 438 |
1e-05 (0.000163) |
0.00261 (0.0136) |
0.101 (0.192) |
0.0204 (0.0633) |
6e-05 (0.000696) |
0.00192 (0.0105) |
0.105 (0.197) |
0.0111 (0.04) |
0.00286 (0.0145) |
0.00063 (0.00458) |
| 1p loss | 22 (4%) | 470 |
1e-05 (0.000163) |
0.00094 (0.00621) |
0.35 (0.46) |
0.868 (0.91) |
0.0121 (0.0427) |
0.0002 (0.00184) |
0.00973 (0.0362) |
0.00355 (0.0164) |
0.028 (0.0825) |
0.00304 (0.015) |
| 4p loss | 23 (5%) | 469 |
1e-05 (0.000163) |
0.0427 (0.109) |
0.0806 (0.167) |
0.187 (0.296) |
0.00108 (0.00692) |
0.0404 (0.105) |
2e-05 (0.000281) |
0.00287 (0.0145) |
0.00377 (0.0169) |
0.00015 (0.00148) |
| 10p loss | 41 (8%) | 451 |
1e-05 (0.000163) |
1e-05 (0.000163) |
0.18 (0.291) |
0.314 (0.425) |
7e-05 (0.000789) |
0.00013 (0.00135) |
1e-05 (0.000163) |
5e-05 (0.000625) |
0.0115 (0.041) |
0.00124 (0.00775) |
| 10q loss | 43 (9%) | 449 |
1e-05 (0.000163) |
3e-05 (0.000387) |
0.0692 (0.151) |
0.162 (0.267) |
0.00071 (0.00498) |
0.00046 (0.00347) |
3e-05 (0.000387) |
0.00124 (0.00775) |
0.00246 (0.013) |
0.00395 (0.0177) |
| 13q loss | 78 (16%) | 414 |
1e-05 (0.000163) |
0.0166 (0.0535) |
0.00251 (0.0131) |
0.0102 (0.0376) |
0.236 (0.349) |
0.0555 (0.129) |
0.0134 (0.0461) |
0.0263 (0.0784) |
0.0297 (0.086) |
0.00342 (0.0161) |
| xp loss | 38 (8%) | 454 |
1e-05 (0.000163) |
0.00017 (0.0016) |
0.375 (0.482) |
0.0563 (0.13) |
2e-05 (0.000281) |
4e-05 (0.000508) |
1e-05 (0.000163) |
0.0352 (0.0959) |
0.00575 (0.0235) |
0.00483 (0.021) |
| xq loss | 38 (8%) | 454 |
1e-05 (0.000163) |
0.00017 (0.0016) |
0.375 (0.482) |
0.0571 (0.132) |
1e-05 (0.000163) |
7e-05 (0.000789) |
1e-05 (0.000163) |
0.0352 (0.0959) |
0.00575 (0.0235) |
0.00533 (0.0226) |
| 5p gain | 23 (5%) | 469 |
6e-05 (0.000696) |
0.00051 (0.00381) |
0.0375 (0.0999) |
0.192 (0.301) |
0.00285 (0.0145) |
0.0607 (0.137) |
0.228 (0.343) |
0.0018 (0.0101) |
0.0075 (0.0296) |
0.00179 (0.0101) |
| 6q loss | 41 (8%) | 451 |
1e-05 (0.000163) |
0.0143 (0.0487) |
0.0853 (0.174) |
0.028 (0.0825) |
0.00952 (0.0357) |
0.0007 (0.00496) |
0.0521 (0.124) |
0.0957 (0.185) |
0.0153 (0.0504) |
0.00612 (0.0246) |
| 16q loss | 107 (22%) | 385 |
1e-05 (0.000163) |
1e-05 (0.000163) |
0.0952 (0.185) |
0.978 (0.991) |
0.0036 (0.0165) |
0.0292 (0.085) |
0.00546 (0.0227) |
0.00041 (0.00312) |
0.00233 (0.0125) |
0.418 (0.517) |
| 18p loss | 67 (14%) | 425 |
1e-05 (0.000163) |
0.00914 (0.0346) |
0.256 (0.369) |
0.00212 (0.0115) |
0.00107 (0.00692) |
0.0518 (0.124) |
0.0639 (0.143) |
0.0349 (0.0959) |
0.00076 (0.00522) |
0.0396 (0.103) |
| 20p gain | 26 (5%) | 466 |
1e-05 (0.000163) |
0.0385 (0.101) |
0.317 (0.427) |
0.147 (0.249) |
0.00148 (0.00877) |
0.036 (0.0975) |
0.0148 (0.0496) |
0.00434 (0.0192) |
0.12 (0.214) |
0.118 (0.211) |
| 21q gain | 21 (4%) | 471 |
1e-05 (0.000163) |
0.00862 (0.033) |
0.68 (0.75) |
0.842 (0.89) |
0.0675 (0.148) |
0.027 (0.0802) |
0.0569 (0.131) |
0.00318 (0.0152) |
0.0184 (0.0585) |
0.0205 (0.0634) |
| 5q loss | 23 (5%) | 469 |
1e-05 (0.000163) |
0.018 (0.0578) |
0.183 (0.293) |
0.253 (0.367) |
0.0311 (0.0892) |
0.00191 (0.0105) |
0.0112 (0.0403) |
0.00053 (0.00393) |
0.654 (0.73) |
0.277 (0.39) |
| 17p loss | 76 (15%) | 416 |
1e-05 (0.000163) |
1e-05 (0.000163) |
0.24 (0.353) |
0.155 (0.262) |
0.00017 (0.0016) |
0.00145 (0.00866) |
0.294 (0.406) |
0.0329 (0.0927) |
0.015 (0.0497) |
0.233 (0.346) |
| 17q loss | 20 (4%) | 472 |
0.00037 (0.00287) |
0.00164 (0.00937) |
0.497 (0.59) |
0.526 (0.617) |
0.00194 (0.0106) |
0.0361 (0.0975) |
0.00985 (0.0365) |
0.0457 (0.114) |
0.0557 (0.13) |
0.473 (0.568) |
| 9q gain | 48 (10%) | 444 |
1e-05 (0.000163) |
0.00015 (0.00148) |
0.00782 (0.0305) |
0.107 (0.199) |
0.00031 (0.00256) |
0.246 (0.359) |
0.405 (0.508) |
0.0139 (0.0477) |
0.127 (0.221) |
0.317 (0.427) |
| 10p gain | 15 (3%) | 477 |
0.00246 (0.013) |
0.0009 (0.006) |
0.599 (0.676) |
0.806 (0.859) |
0.123 (0.216) |
0.0343 (0.0945) |
0.00433 (0.0192) |
0.0131 (0.0455) |
0.163 (0.268) |
0.143 (0.244) |
| 11p gain | 27 (5%) | 465 |
1e-05 (0.000163) |
0.0164 (0.0532) |
0.139 (0.237) |
0.405 (0.508) |
0.121 (0.214) |
0.0207 (0.0636) |
0.192 (0.301) |
0.0341 (0.0945) |
0.0232 (0.0699) |
0.202 (0.315) |
| 12q gain | 18 (4%) | 474 |
0.00144 (0.00866) |
0.0032 (0.0152) |
0.00898 (0.0342) |
0.427 (0.524) |
0.103 (0.193) |
0.0602 (0.137) |
0.871 (0.912) |
0.0321 (0.0915) |
0.113 (0.205) |
0.00437 (0.0192) |
| 20q gain | 29 (6%) | 463 |
1e-05 (0.000163) |
0.00776 (0.0304) |
0.00917 (0.0346) |
0.0763 (0.162) |
0.0394 (0.103) |
0.0873 (0.175) |
0.0789 (0.165) |
0.00664 (0.0264) |
0.261 (0.374) |
0.204 (0.316) |
| 6p loss | 26 (5%) | 466 |
1e-05 (0.000163) |
0.012 (0.0427) |
0.0864 (0.174) |
0.0619 (0.139) |
0.117 (0.21) |
0.0028 (0.0145) |
0.192 (0.301) |
0.0838 (0.172) |
0.0435 (0.11) |
0.0164 (0.0532) |
| 8p loss | 171 (35%) | 321 |
1e-05 (0.000163) |
1e-05 (0.000163) |
0.918 (0.945) |
0.345 (0.456) |
2e-05 (0.000281) |
2e-05 (0.000281) |
0.0129 (0.045) |
0.0672 (0.148) |
0.187 (0.296) |
0.338 (0.448) |
| 12p loss | 47 (10%) | 445 |
0.0001 (0.00108) |
0.17 (0.278) |
0.744 (0.807) |
0.699 (0.765) |
0.0336 (0.0942) |
0.436 (0.535) |
0.041 (0.106) |
0.0145 (0.0493) |
0.0147 (0.0495) |
0.304 (0.415) |
| 22q loss | 47 (10%) | 445 |
1e-05 (0.000163) |
0.244 (0.357) |
0.471 (0.566) |
0.371 (0.481) |
0.0149 (0.0496) |
0.0479 (0.118) |
0.256 (0.369) |
0.0285 (0.0833) |
0.0769 (0.163) |
0.0377 (0.1) |
| 2p gain | 11 (2%) | 481 |
0.00596 (0.0242) |
0.0342 (0.0945) |
0.0795 (0.166) |
0.445 (0.542) |
0.00348 (0.0163) |
0.0925 (0.183) |
0.159 (0.265) |
0.0203 (0.0632) |
0.189 (0.298) |
0.25 (0.363) |
| 9p gain | 34 (7%) | 458 |
1e-05 (0.000163) |
0.00014 (0.00142) |
0.0496 (0.121) |
0.126 (0.219) |
0.00612 (0.0246) |
0.0952 (0.185) |
0.646 (0.723) |
0.112 (0.205) |
0.35 (0.46) |
0.232 (0.346) |
| 10q gain | 14 (3%) | 478 |
0.00546 (0.0227) |
0.00576 (0.0235) |
0.132 (0.229) |
0.0928 (0.183) |
0.0716 (0.155) |
0.0328 (0.0927) |
0.0118 (0.0419) |
0.087 (0.174) |
0.352 (0.462) |
0.216 (0.329) |
| 11q gain | 30 (6%) | 462 |
1e-05 (0.000163) |
0.0368 (0.0988) |
0.0826 (0.17) |
0.341 (0.452) |
0.134 (0.23) |
0.0531 (0.125) |
0.216 (0.329) |
0.0325 (0.0923) |
0.0433 (0.11) |
0.273 (0.386) |
| 12p gain | 15 (3%) | 477 |
0.00251 (0.0131) |
0.00298 (0.0149) |
0.0112 (0.0403) |
0.832 (0.884) |
0.124 (0.218) |
0.0643 (0.143) |
0.883 (0.92) |
0.00376 (0.0169) |
0.238 (0.352) |
0.0604 (0.137) |
| 2q loss | 18 (4%) | 474 |
0.00013 (0.00135) |
0.0219 (0.0671) |
0.763 (0.823) |
0.885 (0.921) |
0.363 (0.473) |
0.484 (0.577) |
0.0639 (0.143) |
0.0352 (0.0959) |
0.00708 (0.028) |
0.18 (0.291) |
| 4q loss | 16 (3%) | 476 |
0.00013 (0.00135) |
0.125 (0.219) |
0.541 (0.629) |
0.865 (0.908) |
0.00161 (0.00927) |
0.133 (0.229) |
0.0694 (0.151) |
0.0468 (0.116) |
0.0814 (0.168) |
0.0422 (0.108) |
| 5p loss | 12 (2%) | 480 |
0.0037 (0.0168) |
0.201 (0.314) |
0.555 (0.64) |
0.549 (0.636) |
0.416 (0.516) |
0.00575 (0.0235) |
0.318 (0.427) |
0.00329 (0.0156) |
0.481 (0.575) |
0.0491 (0.12) |
| 1q gain | 26 (5%) | 466 |
0.00014 (0.00142) |
0.145 (0.246) |
0.0704 (0.153) |
0.214 (0.328) |
0.102 (0.193) |
0.00067 (0.00483) |
0.0994 (0.189) |
0.0337 (0.0944) |
0.688 (0.757) |
0.13 (0.226) |
| 16p gain | 32 (7%) | 460 |
1e-05 (0.000163) |
0.256 (0.369) |
0.119 (0.212) |
0.862 (0.906) |
0.175 (0.284) |
0.231 (0.346) |
0.469 (0.565) |
0.00531 (0.0226) |
0.0409 (0.106) |
0.0784 (0.165) |
| xp gain | 7 (1%) | 485 |
0.0184 (0.0585) |
0.00848 (0.0327) |
0.156 (0.262) |
0.84 (0.889) |
0.0835 (0.172) |
0.0922 (0.182) |
0.121 (0.214) |
0.0456 (0.114) |
0.283 (0.397) |
0.369 (0.479) |
| xq gain | 7 (1%) | 485 |
0.0199 (0.0621) |
0.00849 (0.0327) |
0.156 (0.262) |
0.84 (0.889) |
0.0841 (0.172) |
0.0933 (0.183) |
0.123 (0.216) |
0.0455 (0.114) |
0.283 (0.397) |
0.374 (0.482) |
| 2p loss | 14 (3%) | 478 |
0.0007 (0.00496) |
0.00839 (0.0326) |
0.589 (0.666) |
0.577 (0.659) |
0.494 (0.587) |
0.611 (0.687) |
0.0501 (0.121) |
0.264 (0.375) |
0.0153 (0.0504) |
0.406 (0.508) |
| 8q loss | 21 (4%) | 471 |
0.0514 (0.123) |
0.00022 (0.002) |
0.718 (0.783) |
0.634 (0.712) |
0.00036 (0.00282) |
0.00073 (0.00508) |
0.0538 (0.126) |
0.397 (0.504) |
0.444 (0.541) |
0.0861 (0.174) |
| 9p loss | 21 (4%) | 471 |
0.00025 (0.0022) |
0.312 (0.424) |
0.089 (0.178) |
0.00541 (0.0227) |
0.42 (0.518) |
0.0221 (0.0671) |
0.18 (0.291) |
0.246 (0.359) |
0.0753 (0.161) |
0.527 (0.617) |
| 20q loss | 8 (2%) | 484 |
0.0489 (0.12) |
0.00158 (0.00916) |
0.78 (0.836) |
0.373 (0.482) |
0.351 (0.46) |
0.0428 (0.109) |
0.232 (0.346) |
0.0785 (0.165) |
0.726 (0.789) |
0.912 (0.941) |
| 1p gain | 15 (3%) | 477 |
0.00109 (0.00692) |
0.514 (0.605) |
0.0733 (0.158) |
0.464 (0.562) |
0.112 (0.205) |
0.00151 (0.00888) |
0.33 (0.441) |
0.0775 (0.164) |
0.72 (0.783) |
0.501 (0.594) |
| 2q gain | 7 (1%) | 485 |
0.0188 (0.0592) |
0.418 (0.517) |
0.227 (0.342) |
0.689 (0.757) |
0.0189 (0.0592) |
0.554 (0.64) |
0.123 (0.216) |
0.063 (0.141) |
0.444 (0.541) |
0.513 (0.604) |
| 6p gain | 10 (2%) | 482 |
0.0148 (0.0496) |
0.222 (0.337) |
0.303 (0.415) |
0.405 (0.508) |
0.353 (0.462) |
0.274 (0.387) |
0.581 (0.659) |
0.104 (0.195) |
0.037 (0.0991) |
0.317 (0.427) |
| 6q gain | 6 (1%) | 486 |
0.0493 (0.12) |
0.461 (0.559) |
0.478 (0.573) |
0.913 (0.941) |
0.944 (0.967) |
0.581 (0.659) |
0.51 (0.602) |
0.0382 (0.101) |
0.16 (0.266) |
0.208 (0.32) |
| 14q gain | 10 (2%) | 482 |
0.0014 (0.00848) |
0.0907 (0.18) |
0.522 (0.614) |
0.778 (0.835) |
0.0103 (0.0377) |
0.229 (0.344) |
0.0994 (0.189) |
0.257 (0.369) |
0.289 (0.4) |
0.0547 (0.128) |
| 16q gain | 7 (1%) | 485 |
0.109 (0.202) |
0.0251 (0.0751) |
0.883 (0.92) |
0.928 (0.952) |
0.561 (0.643) |
1 (1.00) |
0.862 (0.906) |
0.0303 (0.0874) |
0.285 (0.398) |
0.365 (0.474) |
| 17p gain | 8 (2%) | 484 |
0.29 (0.401) |
0.922 (0.948) |
0.358 (0.468) |
1 (1.00) |
0.383 (0.489) |
0.661 (0.734) |
0.511 (0.603) |
0.0158 (0.0516) |
1 (1.00) |
0.0107 (0.039) |
| 19p gain | 12 (2%) | 480 |
0.00032 (0.00261) |
0.103 (0.193) |
0.00362 (0.0165) |
0.302 (0.413) |
0.637 (0.714) |
0.342 (0.452) |
0.112 (0.205) |
0.0848 (0.173) |
0.375 (0.482) |
0.361 (0.471) |
| 19q gain | 12 (2%) | 480 |
0.00036 (0.00282) |
0.111 (0.205) |
0.0411 (0.106) |
0.108 (0.201) |
0.581 (0.659) |
0.367 (0.476) |
0.0955 (0.185) |
0.0613 (0.139) |
0.405 (0.508) |
0.284 (0.397) |
| 3p loss | 9 (2%) | 483 |
0.114 (0.206) |
0.134 (0.23) |
0.468 (0.565) |
0.205 (0.317) |
0.192 (0.301) |
0.038 (0.101) |
0.0184 (0.0585) |
0.408 (0.509) |
0.117 (0.21) |
0.181 (0.292) |
| 3q loss | 5 (1%) | 487 |
0.423 (0.521) |
0.66 (0.734) |
0.491 (0.584) |
0.25 (0.363) |
0.0221 (0.0671) |
0.032 (0.0915) |
||||
| 9q loss | 11 (2%) | 481 |
0.0476 (0.118) |
0.264 (0.375) |
0.0154 (0.0504) |
0.232 (0.346) |
0.175 (0.285) |
0.187 (0.296) |
0.116 (0.21) |
0.507 (0.599) |
0.332 (0.442) |
0.604 (0.682) |
| 12q loss | 20 (4%) | 472 |
0.00137 (0.00837) |
0.296 (0.407) |
0.287 (0.399) |
0.331 (0.441) |
0.294 (0.406) |
0.262 (0.374) |
0.0738 (0.158) |
0.05 (0.121) |
0.0779 (0.164) |
0.555 (0.64) |
| 14q loss | 25 (5%) | 467 |
0.00028 (0.00243) |
0.0239 (0.0718) |
0.241 (0.354) |
0.84 (0.889) |
0.196 (0.306) |
0.0983 (0.189) |
0.067 (0.148) |
0.0646 (0.143) |
0.0506 (0.121) |
0.306 (0.417) |
| 19p loss | 19 (4%) | 473 |
2e-05 (0.000281) |
0.318 (0.427) |
0.387 (0.492) |
0.121 (0.214) |
0.0956 (0.185) |
0.113 (0.205) |
0.0143 (0.0487) |
0.13 (0.226) |
0.0808 (0.167) |
0.277 (0.391) |
| 19q loss | 18 (4%) | 474 |
2e-05 (0.000281) |
0.308 (0.419) |
0.482 (0.576) |
0.252 (0.365) |
0.0657 (0.145) |
0.0957 (0.185) |
0.0221 (0.0671) |
0.203 (0.315) |
0.155 (0.262) |
0.44 (0.54) |
| 21q loss | 24 (5%) | 468 |
0.0032 (0.0152) |
0.0573 (0.132) |
0.0971 (0.187) |
0.159 (0.265) |
0.0188 (0.0592) |
0.328 (0.439) |
0.0991 (0.189) |
0.102 (0.193) |
0.259 (0.371) |
0.453 (0.55) |
| 13q gain | 8 (2%) | 484 |
0.0588 (0.135) |
0.0439 (0.111) |
0.135 (0.232) |
0.851 (0.897) |
0.546 (0.634) |
0.66 (0.734) |
0.568 (0.649) |
0.561 (0.643) |
0.539 (0.628) |
0.908 (0.939) |
| 17q gain | 11 (2%) | 481 |
0.0473 (0.117) |
0.535 (0.625) |
0.0728 (0.157) |
0.957 (0.975) |
0.125 (0.219) |
0.217 (0.329) |
0.465 (0.562) |
0.111 (0.205) |
0.746 (0.807) |
0.376 (0.482) |
| 18p gain | 19 (4%) | 473 |
0.00077 (0.00522) |
0.234 (0.347) |
0.0905 (0.18) |
1 (1.00) |
0.442 (0.54) |
0.792 (0.848) |
0.925 (0.95) |
0.675 (0.747) |
1 (1.00) |
0.972 (0.987) |
| 1q loss | 6 (1%) | 486 |
0.0501 (0.121) |
0.111 (0.205) |
0.158 (0.264) |
0.474 (0.569) |
0.0631 (0.141) |
0.0963 (0.186) |
0.0743 (0.159) |
0.102 (0.193) |
0.0284 (0.0833) |
0.207 (0.32) |
| 11p loss | 8 (2%) | 484 |
0.0519 (0.124) |
0.284 (0.397) |
0.541 (0.629) |
0.702 (0.767) |
0.0594 (0.136) |
0.117 (0.21) |
0.114 (0.206) |
0.262 (0.374) |
0.611 (0.687) |
0.0463 (0.115) |
| 11q loss | 5 (1%) | 487 |
0.295 (0.407) |
0.206 (0.318) |
0.0395 (0.103) |
0.888 (0.921) |
0.078 (0.164) |
0.301 (0.413) |
0.237 (0.351) |
0.188 (0.298) |
0.187 (0.296) |
0.172 (0.282) |
| 16p loss | 31 (6%) | 461 |
1e-05 (0.000163) |
0.267 (0.378) |
0.968 (0.984) |
0.137 (0.234) |
0.242 (0.355) |
0.442 (0.54) |
0.387 (0.492) |
0.325 (0.435) |
0.156 (0.262) |
0.955 (0.975) |
| 20p loss | 19 (4%) | 473 |
0.0528 (0.125) |
0.0032 (0.0152) |
0.984 (0.997) |
0.954 (0.975) |
0.876 (0.916) |
0.184 (0.294) |
0.379 (0.485) |
0.185 (0.295) |
0.536 (0.626) |
0.793 (0.848) |
| 4p gain | 9 (2%) | 483 |
0.165 (0.272) |
0.698 (0.765) |
0.806 (0.859) |
0.42 (0.518) |
0.881 (0.92) |
0.769 (0.828) |
0.657 (0.733) |
0.413 (0.513) |
0.554 (0.64) |
0.581 (0.659) |
| 4q gain | 10 (2%) | 482 |
0.0864 (0.174) |
0.678 (0.749) |
0.608 (0.685) |
0.404 (0.508) |
0.279 (0.393) |
0.558 (0.642) |
0.831 (0.884) |
0.174 (0.284) |
0.401 (0.508) |
0.215 (0.329) |
| 5q gain | 12 (2%) | 480 |
0.0867 (0.174) |
0.113 (0.205) |
0.0707 (0.153) |
0.578 (0.659) |
0.097 (0.187) |
0.229 (0.344) |
0.386 (0.492) |
0.159 (0.265) |
0.166 (0.272) |
0.255 (0.369) |
| 15q gain | 6 (1%) | 486 |
0.175 (0.284) |
0.896 (0.927) |
0.213 (0.326) |
0.89 (0.922) |
0.705 (0.769) |
0.666 (0.738) |
0.746 (0.807) |
0.182 (0.293) |
0.844 (0.891) |
0.803 (0.857) |
| 18q gain | 10 (2%) | 482 |
0.0863 (0.174) |
0.744 (0.807) |
0.411 (0.512) |
0.966 (0.983) |
0.683 (0.752) |
0.776 (0.835) |
1 (1.00) |
0.336 (0.447) |
0.955 (0.975) |
0.223 (0.337) |
| 22q gain | 4 (1%) | 488 |
0.692 (0.76) |
0.311 (0.422) |
0.287 (0.399) |
0.888 (0.921) |
0.562 (0.643) |
0.222 (0.337) |
0.392 (0.498) |
0.407 (0.509) |
0.56 (0.643) |
0.651 (0.728) |
P value = 0.00109 (Fisher's exact test), Q value = 0.0069
Table S1. Gene #1: '1p gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 1P GAIN MUTATED | 0 | 0 | 2 | 13 |
| 1P GAIN WILD-TYPE | 108 | 91 | 96 | 182 |
Figure S1. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00151 (Fisher's exact test), Q value = 0.0089
Table S2. Gene #1: '1p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 1P GAIN MUTATED | 0 | 12 | 3 |
| 1P GAIN WILD-TYPE | 171 | 193 | 112 |
Figure S2. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00014 (Fisher's exact test), Q value = 0.0014
Table S3. Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 1Q GAIN MUTATED | 3 | 0 | 2 | 21 |
| 1Q GAIN WILD-TYPE | 105 | 91 | 96 | 174 |
Figure S3. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00067 (Fisher's exact test), Q value = 0.0048
Table S4. Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 1Q GAIN MUTATED | 1 | 15 | 10 |
| 1Q GAIN WILD-TYPE | 170 | 190 | 105 |
Figure S4. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0337 (Fisher's exact test), Q value = 0.094
Table S5. Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 1Q GAIN MUTATED | 4 | 4 | 3 | 14 | 1 |
| 1Q GAIN WILD-TYPE | 143 | 94 | 56 | 114 | 55 |
Figure S5. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00596 (Fisher's exact test), Q value = 0.024
Table S6. Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 2P GAIN MUTATED | 0 | 1 | 0 | 10 |
| 2P GAIN WILD-TYPE | 108 | 90 | 98 | 185 |
Figure S6. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.0342 (Fisher's exact test), Q value = 0.095
Table S7. Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 2P GAIN MUTATED | 1 | 5 | 1 | 4 |
| 2P GAIN WILD-TYPE | 160 | 132 | 123 | 66 |
Figure S7. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.00348 (Fisher's exact test), Q value = 0.016
Table S8. Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 2P GAIN MUTATED | 1 | 1 | 9 | 0 |
| 2P GAIN WILD-TYPE | 94 | 140 | 138 | 108 |
Figure S8. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.0203 (Fisher's exact test), Q value = 0.063
Table S9. Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 2P GAIN MUTATED | 0 | 4 | 0 | 6 | 1 |
| 2P GAIN WILD-TYPE | 147 | 94 | 59 | 122 | 55 |
Figure S9. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0188 (Fisher's exact test), Q value = 0.059
Table S10. Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 2Q GAIN MUTATED | 0 | 0 | 0 | 7 |
| 2Q GAIN WILD-TYPE | 108 | 91 | 98 | 188 |
Figure S10. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.0189 (Fisher's exact test), Q value = 0.059
Table S11. Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 2Q GAIN MUTATED | 0 | 1 | 6 | 0 |
| 2Q GAIN WILD-TYPE | 95 | 140 | 141 | 108 |
Figure S11. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S12. Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 3P GAIN MUTATED | 0 | 1 | 1 | 38 |
| 3P GAIN WILD-TYPE | 108 | 90 | 97 | 157 |
Figure S12. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.0129 (Fisher's exact test), Q value = 0.045
Table S13. Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 3P GAIN MUTATED | 7 | 13 | 8 | 12 |
| 3P GAIN WILD-TYPE | 154 | 124 | 116 | 58 |
Figure S13. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.0273 (Fisher's exact test), Q value = 0.081
Table S14. Gene #5: '3p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 74 | 113 | 92 | 68 |
| 3P GAIN MUTATED | 2 | 13 | 4 | 9 |
| 3P GAIN WILD-TYPE | 72 | 100 | 88 | 59 |
Figure S14. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
P value = 3e-05 (Fisher's exact test), Q value = 0.00039
Table S15. Gene #5: '3p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 3P GAIN MUTATED | 3 | 7 | 26 | 4 |
| 3P GAIN WILD-TYPE | 92 | 134 | 121 | 104 |
Figure S15. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.00033 (Fisher's exact test), Q value = 0.0027
Table S16. Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 3P GAIN MUTATED | 4 | 27 | 9 |
| 3P GAIN WILD-TYPE | 167 | 178 | 106 |
Figure S16. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00496 (Fisher's exact test), Q value = 0.021
Table S17. Gene #5: '3p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 3P GAIN MUTATED | 7 | 6 | 2 | 21 | 3 |
| 3P GAIN WILD-TYPE | 140 | 92 | 57 | 107 | 53 |
Figure S17. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00458 (Fisher's exact test), Q value = 0.02
Table S18. Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 65 | 91 | 78 | 84 |
| 3P GAIN MUTATED | 0 | 13 | 6 | 5 |
| 3P GAIN WILD-TYPE | 65 | 78 | 72 | 79 |
Figure S18. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.00082 (Fisher's exact test), Q value = 0.0055
Table S19. Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 75 | 86 | 69 | 23 | 65 |
| 3P GAIN MUTATED | 2 | 16 | 4 | 0 | 2 |
| 3P GAIN WILD-TYPE | 73 | 70 | 65 | 23 | 63 |
Figure S19. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S20. Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 3Q GAIN MUTATED | 3 | 1 | 2 | 48 |
| 3Q GAIN WILD-TYPE | 105 | 90 | 96 | 147 |
Figure S20. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00261 (Fisher's exact test), Q value = 0.014
Table S21. Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 3Q GAIN MUTATED | 8 | 17 | 14 | 15 |
| 3Q GAIN WILD-TYPE | 153 | 120 | 110 | 55 |
Figure S21. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.0204 (Fisher's exact test), Q value = 0.063
Table S22. Gene #6: '3q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 74 | 113 | 92 | 68 |
| 3Q GAIN MUTATED | 3 | 17 | 7 | 12 |
| 3Q GAIN WILD-TYPE | 71 | 96 | 85 | 56 |
Figure S22. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
P value = 6e-05 (Fisher's exact test), Q value = 7e-04
Table S23. Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 3Q GAIN MUTATED | 3 | 14 | 31 | 6 |
| 3Q GAIN WILD-TYPE | 92 | 127 | 116 | 102 |
Figure S23. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.00192 (Fisher's exact test), Q value = 0.011
Table S24. Gene #6: '3q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 3Q GAIN MUTATED | 8 | 32 | 14 |
| 3Q GAIN WILD-TYPE | 163 | 173 | 101 |
Figure S24. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0111 (Fisher's exact test), Q value = 0.04
Table S25. Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 3Q GAIN MUTATED | 11 | 10 | 4 | 25 | 3 |
| 3Q GAIN WILD-TYPE | 136 | 88 | 55 | 103 | 53 |
Figure S25. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00286 (Fisher's exact test), Q value = 0.015
Table S26. Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 65 | 91 | 78 | 84 |
| 3Q GAIN MUTATED | 1 | 17 | 8 | 6 |
| 3Q GAIN WILD-TYPE | 64 | 74 | 70 | 78 |
Figure S26. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.00063 (Fisher's exact test), Q value = 0.0046
Table S27. Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 75 | 86 | 69 | 23 | 65 |
| 3Q GAIN MUTATED | 3 | 19 | 7 | 1 | 2 |
| 3Q GAIN WILD-TYPE | 72 | 67 | 62 | 22 | 63 |
Figure S27. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 6e-05 (Fisher's exact test), Q value = 7e-04
Table S28. Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 5P GAIN MUTATED | 2 | 0 | 1 | 20 |
| 5P GAIN WILD-TYPE | 106 | 91 | 97 | 175 |
Figure S28. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00051 (Fisher's exact test), Q value = 0.0038
Table S29. Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 5P GAIN MUTATED | 3 | 5 | 4 | 11 |
| 5P GAIN WILD-TYPE | 158 | 132 | 120 | 59 |
Figure S29. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.0375 (Fisher's exact test), Q value = 0.1
Table S30. Gene #9: '5p gain' versus Molecular Subtype #3: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 105 | 51 | 44 | 51 | 58 | 38 |
| 5P GAIN MUTATED | 1 | 4 | 2 | 1 | 5 | 4 |
| 5P GAIN WILD-TYPE | 104 | 47 | 42 | 50 | 53 | 34 |
Figure S30. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'RPPA_CNMF'
P value = 0.00285 (Fisher's exact test), Q value = 0.015
Table S31. Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 5P GAIN MUTATED | 1 | 7 | 14 | 1 |
| 5P GAIN WILD-TYPE | 94 | 134 | 133 | 107 |
Figure S31. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.0018 (Fisher's exact test), Q value = 0.01
Table S32. Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 5P GAIN MUTATED | 4 | 3 | 0 | 15 | 1 |
| 5P GAIN WILD-TYPE | 143 | 95 | 59 | 113 | 55 |
Figure S32. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0075 (Fisher's exact test), Q value = 0.03
Table S33. Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 65 | 91 | 78 | 84 |
| 5P GAIN MUTATED | 0 | 10 | 2 | 3 |
| 5P GAIN WILD-TYPE | 65 | 81 | 76 | 81 |
Figure S33. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.00179 (Fisher's exact test), Q value = 0.01
Table S34. Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 75 | 86 | 69 | 23 | 65 |
| 5P GAIN MUTATED | 3 | 11 | 1 | 0 | 0 |
| 5P GAIN WILD-TYPE | 72 | 75 | 68 | 23 | 65 |
Figure S34. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.0148 (Fisher's exact test), Q value = 0.05
Table S35. Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 6P GAIN MUTATED | 0 | 0 | 1 | 9 |
| 6P GAIN WILD-TYPE | 108 | 91 | 97 | 186 |
Figure S35. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.037 (Fisher's exact test), Q value = 0.099
Table S36. Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 65 | 91 | 78 | 84 |
| 6P GAIN MUTATED | 0 | 4 | 4 | 0 |
| 6P GAIN WILD-TYPE | 65 | 87 | 74 | 84 |
Figure S36. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.0493 (Fisher's exact test), Q value = 0.12
Table S37. Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 6Q GAIN MUTATED | 0 | 0 | 0 | 6 |
| 6Q GAIN WILD-TYPE | 108 | 91 | 98 | 189 |
Figure S37. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.0382 (Fisher's exact test), Q value = 0.1
Table S38. Gene #12: '6q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 6Q GAIN MUTATED | 0 | 1 | 0 | 5 | 0 |
| 6Q GAIN WILD-TYPE | 147 | 97 | 59 | 123 | 56 |
Figure S38. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S39. Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 7P GAIN MUTATED | 7 | 6 | 12 | 76 |
| 7P GAIN WILD-TYPE | 101 | 85 | 86 | 119 |
Figure S39. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S40. Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 7P GAIN MUTATED | 13 | 47 | 19 | 22 |
| 7P GAIN WILD-TYPE | 148 | 90 | 105 | 48 |
Figure S40. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.00293 (Fisher's exact test), Q value = 0.015
Table S41. Gene #13: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 105 | 51 | 44 | 51 | 58 | 38 |
| 7P GAIN MUTATED | 18 | 12 | 9 | 4 | 23 | 8 |
| 7P GAIN WILD-TYPE | 87 | 39 | 35 | 47 | 35 | 30 |
Figure S41. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S42. Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 7P GAIN MUTATED | 14 | 20 | 59 | 8 |
| 7P GAIN WILD-TYPE | 81 | 121 | 88 | 100 |
Figure S42. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.00039
Table S43. Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 7P GAIN MUTATED | 21 | 63 | 17 |
| 7P GAIN WILD-TYPE | 150 | 142 | 98 |
Figure S43. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00036 (Fisher's exact test), Q value = 0.0028
Table S44. Gene #13: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 208 | 71 | 123 | 86 |
| 7P GAIN MUTATED | 57 | 17 | 11 | 15 |
| 7P GAIN WILD-TYPE | 151 | 54 | 112 | 71 |
Figure S44. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 6e-05 (Fisher's exact test), Q value = 7e-04
Table S45. Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 7P GAIN MUTATED | 16 | 27 | 15 | 38 | 4 |
| 7P GAIN WILD-TYPE | 131 | 71 | 44 | 90 | 52 |
Figure S45. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00109 (Fisher's exact test), Q value = 0.0069
Table S46. Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 65 | 91 | 78 | 84 |
| 7P GAIN MUTATED | 4 | 28 | 20 | 17 |
| 7P GAIN WILD-TYPE | 61 | 63 | 58 | 67 |
Figure S46. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.00025 (Fisher's exact test), Q value = 0.0022
Table S47. Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 75 | 86 | 69 | 23 | 65 |
| 7P GAIN MUTATED | 9 | 31 | 19 | 1 | 9 |
| 7P GAIN WILD-TYPE | 66 | 55 | 50 | 22 | 56 |
Figure S47. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S48. Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 7Q GAIN MUTATED | 7 | 6 | 11 | 70 |
| 7Q GAIN WILD-TYPE | 101 | 85 | 87 | 125 |
Figure S48. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S49. Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 7Q GAIN MUTATED | 11 | 44 | 17 | 22 |
| 7Q GAIN WILD-TYPE | 150 | 93 | 107 | 48 |
Figure S49. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.00954 (Fisher's exact test), Q value = 0.036
Table S50. Gene #14: '7q gain' versus Molecular Subtype #3: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 105 | 51 | 44 | 51 | 58 | 38 |
| 7Q GAIN MUTATED | 17 | 12 | 8 | 4 | 21 | 7 |
| 7Q GAIN WILD-TYPE | 88 | 39 | 36 | 47 | 37 | 31 |
Figure S50. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'RPPA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S51. Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 7Q GAIN MUTATED | 13 | 19 | 55 | 7 |
| 7Q GAIN WILD-TYPE | 82 | 122 | 92 | 101 |
Figure S51. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 8e-05 (Fisher's exact test), Q value = 0.00088
Table S52. Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 7Q GAIN MUTATED | 20 | 58 | 16 |
| 7Q GAIN WILD-TYPE | 151 | 147 | 99 |
Figure S52. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00031 (Fisher's exact test), Q value = 0.0026
Table S53. Gene #14: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 208 | 71 | 123 | 86 |
| 7Q GAIN MUTATED | 53 | 17 | 10 | 13 |
| 7Q GAIN WILD-TYPE | 155 | 54 | 113 | 73 |
Figure S53. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 6e-05 (Fisher's exact test), Q value = 7e-04
Table S54. Gene #14: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 7Q GAIN MUTATED | 14 | 26 | 14 | 35 | 4 |
| 7Q GAIN WILD-TYPE | 133 | 72 | 45 | 93 | 52 |
Figure S54. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00056 (Fisher's exact test), Q value = 0.0041
Table S55. Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 65 | 91 | 78 | 84 |
| 7Q GAIN MUTATED | 4 | 28 | 20 | 14 |
| 7Q GAIN WILD-TYPE | 61 | 63 | 58 | 70 |
Figure S55. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.00029 (Fisher's exact test), Q value = 0.0025
Table S56. Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 75 | 86 | 69 | 23 | 65 |
| 7Q GAIN MUTATED | 9 | 29 | 19 | 1 | 8 |
| 7Q GAIN WILD-TYPE | 66 | 57 | 50 | 22 | 57 |
Figure S56. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S57. Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 8P GAIN MUTATED | 3 | 4 | 3 | 58 |
| 8P GAIN WILD-TYPE | 105 | 87 | 95 | 137 |
Figure S57. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S58. Gene #15: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 8P GAIN MUTATED | 7 | 32 | 10 | 19 |
| 8P GAIN WILD-TYPE | 154 | 105 | 114 | 51 |
Figure S58. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S59. Gene #15: '8p gain' versus Molecular Subtype #3: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 105 | 51 | 44 | 51 | 58 | 38 |
| 8P GAIN MUTATED | 4 | 9 | 2 | 7 | 18 | 10 |
| 8P GAIN WILD-TYPE | 101 | 42 | 42 | 44 | 40 | 28 |
Figure S59. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'RPPA_CNMF'
P value = 0.00031 (Fisher's exact test), Q value = 0.0026
Table S60. Gene #15: '8p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 74 | 113 | 92 | 68 |
| 8P GAIN MUTATED | 7 | 13 | 8 | 22 |
| 8P GAIN WILD-TYPE | 67 | 100 | 84 | 46 |
Figure S60. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
P value = 2e-05 (Fisher's exact test), Q value = 0.00028
Table S61. Gene #15: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 8P GAIN MUTATED | 6 | 12 | 40 | 10 |
| 8P GAIN WILD-TYPE | 89 | 129 | 107 | 98 |
Figure S61. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 3e-04 (Fisher's exact test), Q value = 0.0026
Table S62. Gene #15: '8p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 8P GAIN MUTATED | 13 | 44 | 11 |
| 8P GAIN WILD-TYPE | 158 | 161 | 104 |
Figure S62. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00039 (Fisher's exact test), Q value = 0.003
Table S63. Gene #15: '8p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 208 | 71 | 123 | 86 |
| 8P GAIN MUTATED | 44 | 7 | 7 | 9 |
| 8P GAIN WILD-TYPE | 164 | 64 | 116 | 77 |
Figure S63. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.00518 (Fisher's exact test), Q value = 0.022
Table S64. Gene #15: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 8P GAIN MUTATED | 11 | 14 | 10 | 28 | 4 |
| 8P GAIN WILD-TYPE | 136 | 84 | 49 | 100 | 52 |
Figure S64. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 6e-05 (Fisher's exact test), Q value = 7e-04
Table S65. Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 65 | 91 | 78 | 84 |
| 8P GAIN MUTATED | 1 | 24 | 7 | 13 |
| 8P GAIN WILD-TYPE | 64 | 67 | 71 | 71 |
Figure S65. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.00619 (Fisher's exact test), Q value = 0.025
Table S66. Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 75 | 86 | 69 | 23 | 65 |
| 8P GAIN MUTATED | 4 | 22 | 9 | 2 | 8 |
| 8P GAIN WILD-TYPE | 71 | 64 | 60 | 21 | 57 |
Figure S66. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S67. Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 8Q GAIN MUTATED | 12 | 8 | 7 | 99 |
| 8Q GAIN WILD-TYPE | 96 | 83 | 91 | 96 |
Figure S67. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S68. Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 8Q GAIN MUTATED | 18 | 49 | 27 | 32 |
| 8Q GAIN WILD-TYPE | 143 | 88 | 97 | 38 |
Figure S68. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.00024 (Fisher's exact test), Q value = 0.0022
Table S69. Gene #16: '8q gain' versus Molecular Subtype #3: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 105 | 51 | 44 | 51 | 58 | 38 |
| 8Q GAIN MUTATED | 16 | 14 | 5 | 13 | 24 | 16 |
| 8Q GAIN WILD-TYPE | 89 | 37 | 39 | 38 | 34 | 22 |
Figure S69. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'RPPA_CNMF'
P value = 0.00017 (Fisher's exact test), Q value = 0.0016
Table S70. Gene #16: '8q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 74 | 113 | 92 | 68 |
| 8Q GAIN MUTATED | 12 | 24 | 20 | 32 |
| 8Q GAIN WILD-TYPE | 62 | 89 | 72 | 36 |
Figure S70. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S71. Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 8Q GAIN MUTATED | 14 | 26 | 67 | 19 |
| 8Q GAIN WILD-TYPE | 81 | 115 | 80 | 89 |
Figure S71. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.00039
Table S72. Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 8Q GAIN MUTATED | 27 | 74 | 25 |
| 8Q GAIN WILD-TYPE | 144 | 131 | 90 |
Figure S72. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 8e-05 (Fisher's exact test), Q value = 0.00088
Table S73. Gene #16: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 208 | 71 | 123 | 86 |
| 8Q GAIN MUTATED | 74 | 17 | 15 | 19 |
| 8Q GAIN WILD-TYPE | 134 | 54 | 108 | 67 |
Figure S73. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S74. Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 8Q GAIN MUTATED | 18 | 26 | 18 | 54 | 9 |
| 8Q GAIN WILD-TYPE | 129 | 72 | 41 | 74 | 47 |
Figure S74. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 2e-05 (Fisher's exact test), Q value = 0.00028
Table S75. Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 65 | 91 | 78 | 84 |
| 8Q GAIN MUTATED | 6 | 41 | 16 | 20 |
| 8Q GAIN WILD-TYPE | 59 | 50 | 62 | 64 |
Figure S75. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.00018 (Fisher's exact test), Q value = 0.0017
Table S76. Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 75 | 86 | 69 | 23 | 65 |
| 8Q GAIN MUTATED | 13 | 39 | 15 | 2 | 14 |
| 8Q GAIN WILD-TYPE | 62 | 47 | 54 | 21 | 51 |
Figure S76. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S77. Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 9P GAIN MUTATED | 3 | 0 | 0 | 31 |
| 9P GAIN WILD-TYPE | 105 | 91 | 98 | 164 |
Figure S77. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00014 (Fisher's exact test), Q value = 0.0014
Table S78. Gene #17: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 9P GAIN MUTATED | 6 | 8 | 5 | 15 |
| 9P GAIN WILD-TYPE | 155 | 129 | 119 | 55 |
Figure S78. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.0496 (Fisher's exact test), Q value = 0.12
Table S79. Gene #17: '9p gain' versus Molecular Subtype #3: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 105 | 51 | 44 | 51 | 58 | 38 |
| 9P GAIN MUTATED | 3 | 5 | 3 | 1 | 7 | 5 |
| 9P GAIN WILD-TYPE | 102 | 46 | 41 | 50 | 51 | 33 |
Figure S79. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'RPPA_CNMF'
P value = 0.00612 (Fisher's exact test), Q value = 0.025
Table S80. Gene #17: '9p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 9P GAIN MUTATED | 1 | 9 | 18 | 6 |
| 9P GAIN WILD-TYPE | 94 | 132 | 129 | 102 |
Figure S80. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S81. Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 9Q GAIN MUTATED | 5 | 1 | 1 | 41 |
| 9Q GAIN WILD-TYPE | 103 | 90 | 97 | 154 |
Figure S81. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00015 (Fisher's exact test), Q value = 0.0015
Table S82. Gene #18: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 9Q GAIN MUTATED | 11 | 7 | 12 | 18 |
| 9Q GAIN WILD-TYPE | 150 | 130 | 112 | 52 |
Figure S82. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.00782 (Fisher's exact test), Q value = 0.031
Table S83. Gene #18: '9q gain' versus Molecular Subtype #3: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 105 | 51 | 44 | 51 | 58 | 38 |
| 9Q GAIN MUTATED | 3 | 7 | 4 | 3 | 8 | 8 |
| 9Q GAIN WILD-TYPE | 102 | 44 | 40 | 48 | 50 | 30 |
Figure S83. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'RPPA_CNMF'
P value = 0.00031 (Fisher's exact test), Q value = 0.0026
Table S84. Gene #18: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 9Q GAIN MUTATED | 1 | 15 | 24 | 8 |
| 9Q GAIN WILD-TYPE | 94 | 126 | 123 | 100 |
Figure S84. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.0139 (Fisher's exact test), Q value = 0.048
Table S85. Gene #18: '9q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 9Q GAIN MUTATED | 10 | 6 | 5 | 23 | 3 |
| 9Q GAIN WILD-TYPE | 137 | 92 | 54 | 105 | 53 |
Figure S85. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00246 (Fisher's exact test), Q value = 0.013
Table S86. Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 10P GAIN MUTATED | 1 | 1 | 0 | 13 |
| 10P GAIN WILD-TYPE | 107 | 90 | 98 | 182 |
Figure S86. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 9e-04 (Fisher's exact test), Q value = 0.006
Table S87. Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 10P GAIN MUTATED | 0 | 9 | 2 | 4 |
| 10P GAIN WILD-TYPE | 161 | 128 | 122 | 66 |
Figure S87. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.0343 (Fisher's exact test), Q value = 0.095
Table S88. Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 10P GAIN MUTATED | 1 | 10 | 4 |
| 10P GAIN WILD-TYPE | 170 | 195 | 111 |
Figure S88. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00433 (Fisher's exact test), Q value = 0.019
Table S89. Gene #19: '10p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 208 | 71 | 123 | 86 |
| 10P GAIN MUTATED | 5 | 3 | 0 | 7 |
| 10P GAIN WILD-TYPE | 203 | 68 | 123 | 79 |
Figure S89. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.0131 (Fisher's exact test), Q value = 0.045
Table S90. Gene #19: '10p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 10P GAIN MUTATED | 1 | 1 | 1 | 8 | 4 |
| 10P GAIN WILD-TYPE | 146 | 97 | 58 | 120 | 52 |
Figure S90. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00546 (Fisher's exact test), Q value = 0.023
Table S91. Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 10Q GAIN MUTATED | 1 | 1 | 0 | 12 |
| 10Q GAIN WILD-TYPE | 107 | 90 | 98 | 183 |
Figure S91. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00576 (Fisher's exact test), Q value = 0.024
Table S92. Gene #20: '10q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 10Q GAIN MUTATED | 0 | 8 | 3 | 3 |
| 10Q GAIN WILD-TYPE | 161 | 129 | 121 | 67 |
Figure S92. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.0328 (Fisher's exact test), Q value = 0.093
Table S93. Gene #20: '10q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 10Q GAIN MUTATED | 1 | 10 | 3 |
| 10Q GAIN WILD-TYPE | 170 | 195 | 112 |
Figure S93. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0118 (Fisher's exact test), Q value = 0.042
Table S94. Gene #20: '10q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 208 | 71 | 123 | 86 |
| 10Q GAIN MUTATED | 5 | 3 | 0 | 6 |
| 10Q GAIN WILD-TYPE | 203 | 68 | 123 | 80 |
Figure S94. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S95. Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 11P GAIN MUTATED | 2 | 0 | 1 | 24 |
| 11P GAIN WILD-TYPE | 106 | 91 | 97 | 171 |
Figure S95. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.0164 (Fisher's exact test), Q value = 0.053
Table S96. Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 11P GAIN MUTATED | 4 | 9 | 5 | 9 |
| 11P GAIN WILD-TYPE | 157 | 128 | 119 | 61 |
Figure S96. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.0207 (Fisher's exact test), Q value = 0.064
Table S97. Gene #21: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 11P GAIN MUTATED | 4 | 18 | 5 |
| 11P GAIN WILD-TYPE | 167 | 187 | 110 |
Figure S97. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0341 (Fisher's exact test), Q value = 0.095
Table S98. Gene #21: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 11P GAIN MUTATED | 4 | 6 | 4 | 12 | 0 |
| 11P GAIN WILD-TYPE | 143 | 92 | 55 | 116 | 56 |
Figure S98. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0232 (Fisher's exact test), Q value = 0.07
Table S99. Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 65 | 91 | 78 | 84 |
| 11P GAIN MUTATED | 1 | 9 | 6 | 1 |
| 11P GAIN WILD-TYPE | 64 | 82 | 72 | 83 |
Figure S99. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S100. Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 11Q GAIN MUTATED | 2 | 0 | 1 | 27 |
| 11Q GAIN WILD-TYPE | 106 | 91 | 97 | 168 |
Figure S100. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.0368 (Fisher's exact test), Q value = 0.099
Table S101. Gene #22: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 11Q GAIN MUTATED | 5 | 10 | 6 | 9 |
| 11Q GAIN WILD-TYPE | 156 | 127 | 118 | 61 |
Figure S101. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.0325 (Fisher's exact test), Q value = 0.092
Table S102. Gene #22: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 11Q GAIN MUTATED | 5 | 7 | 4 | 13 | 0 |
| 11Q GAIN WILD-TYPE | 142 | 91 | 55 | 115 | 56 |
Figure S102. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0433 (Fisher's exact test), Q value = 0.11
Table S103. Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 65 | 91 | 78 | 84 |
| 11Q GAIN MUTATED | 1 | 9 | 7 | 2 |
| 11Q GAIN WILD-TYPE | 64 | 82 | 71 | 82 |
Figure S103. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.00251 (Fisher's exact test), Q value = 0.013
Table S104. Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 12P GAIN MUTATED | 1 | 1 | 0 | 13 |
| 12P GAIN WILD-TYPE | 107 | 90 | 98 | 182 |
Figure S104. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00298 (Fisher's exact test), Q value = 0.015
Table S105. Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 12P GAIN MUTATED | 2 | 5 | 1 | 7 |
| 12P GAIN WILD-TYPE | 159 | 132 | 123 | 63 |
Figure S105. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.0112 (Fisher's exact test), Q value = 0.04
Table S106. Gene #23: '12p gain' versus Molecular Subtype #3: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 105 | 51 | 44 | 51 | 58 | 38 |
| 12P GAIN MUTATED | 0 | 3 | 1 | 0 | 4 | 0 |
| 12P GAIN WILD-TYPE | 105 | 48 | 43 | 51 | 54 | 38 |
Figure S106. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'RPPA_CNMF'
P value = 0.00376 (Fisher's exact test), Q value = 0.017
Table S107. Gene #23: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 12P GAIN MUTATED | 2 | 1 | 1 | 11 | 0 |
| 12P GAIN WILD-TYPE | 145 | 97 | 58 | 117 | 56 |
Figure S107. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00144 (Fisher's exact test), Q value = 0.0087
Table S108. Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 12Q GAIN MUTATED | 2 | 1 | 0 | 15 |
| 12Q GAIN WILD-TYPE | 106 | 90 | 98 | 180 |
Figure S108. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.0032 (Fisher's exact test), Q value = 0.015
Table S109. Gene #24: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 12Q GAIN MUTATED | 6 | 5 | 0 | 7 |
| 12Q GAIN WILD-TYPE | 155 | 132 | 124 | 63 |
Figure S109. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.00898 (Fisher's exact test), Q value = 0.034
Table S110. Gene #24: '12q gain' versus Molecular Subtype #3: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 105 | 51 | 44 | 51 | 58 | 38 |
| 12Q GAIN MUTATED | 0 | 3 | 1 | 1 | 6 | 1 |
| 12Q GAIN WILD-TYPE | 105 | 48 | 43 | 50 | 52 | 37 |
Figure S110. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'RPPA_CNMF'
P value = 0.0321 (Fisher's exact test), Q value = 0.092
Table S111. Gene #24: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 12Q GAIN MUTATED | 4 | 1 | 3 | 10 | 0 |
| 12Q GAIN WILD-TYPE | 143 | 97 | 56 | 118 | 56 |
Figure S111. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00437 (Fisher's exact test), Q value = 0.019
Table S112. Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 75 | 86 | 69 | 23 | 65 |
| 12Q GAIN MUTATED | 2 | 10 | 0 | 1 | 1 |
| 12Q GAIN WILD-TYPE | 73 | 76 | 69 | 22 | 64 |
Figure S112. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.0439 (Fisher's exact test), Q value = 0.11
Table S113. Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 13Q GAIN MUTATED | 0 | 2 | 3 | 3 |
| 13Q GAIN WILD-TYPE | 161 | 135 | 121 | 67 |
Figure S113. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.0014 (Fisher's exact test), Q value = 0.0085
Table S114. Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 14Q GAIN MUTATED | 0 | 0 | 0 | 10 |
| 14Q GAIN WILD-TYPE | 108 | 91 | 98 | 185 |
Figure S114. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.0103 (Fisher's exact test), Q value = 0.038
Table S115. Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 14Q GAIN MUTATED | 0 | 1 | 8 | 1 |
| 14Q GAIN WILD-TYPE | 95 | 140 | 139 | 107 |
Figure S115. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S116. Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 16P GAIN MUTATED | 3 | 1 | 1 | 27 |
| 16P GAIN WILD-TYPE | 105 | 90 | 97 | 168 |
Figure S116. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00531 (Fisher's exact test), Q value = 0.023
Table S117. Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 16P GAIN MUTATED | 2 | 5 | 6 | 14 | 4 |
| 16P GAIN WILD-TYPE | 145 | 93 | 53 | 114 | 52 |
Figure S117. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0409 (Fisher's exact test), Q value = 0.11
Table S118. Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 65 | 91 | 78 | 84 |
| 16P GAIN MUTATED | 0 | 6 | 7 | 8 |
| 16P GAIN WILD-TYPE | 65 | 85 | 71 | 76 |
Figure S118. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.0251 (Fisher's exact test), Q value = 0.075
Table S119. Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 16Q GAIN MUTATED | 1 | 1 | 1 | 4 |
| 16Q GAIN WILD-TYPE | 160 | 136 | 123 | 66 |
Figure S119. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.0303 (Fisher's exact test), Q value = 0.087
Table S120. Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 16Q GAIN MUTATED | 0 | 0 | 1 | 5 | 1 |
| 16Q GAIN WILD-TYPE | 147 | 98 | 58 | 123 | 55 |
Figure S120. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0158 (Fisher's exact test), Q value = 0.052
Table S121. Gene #30: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 17P GAIN MUTATED | 1 | 0 | 4 | 3 | 0 |
| 17P GAIN WILD-TYPE | 146 | 98 | 55 | 125 | 56 |
Figure S121. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0107 (Fisher's exact test), Q value = 0.039
Table S122. Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 75 | 86 | 69 | 23 | 65 |
| 17P GAIN MUTATED | 0 | 5 | 0 | 1 | 0 |
| 17P GAIN WILD-TYPE | 75 | 81 | 69 | 22 | 65 |
Figure S122. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.0473 (Fisher's exact test), Q value = 0.12
Table S123. Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 17Q GAIN MUTATED | 1 | 0 | 1 | 9 |
| 17Q GAIN WILD-TYPE | 107 | 91 | 97 | 186 |
Figure S123. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00077 (Fisher's exact test), Q value = 0.0052
Table S124. Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 18P GAIN MUTATED | 2 | 0 | 1 | 16 |
| 18P GAIN WILD-TYPE | 106 | 91 | 97 | 179 |
Figure S124. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00032 (Fisher's exact test), Q value = 0.0026
Table S125. Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 19P GAIN MUTATED | 0 | 0 | 0 | 12 |
| 19P GAIN WILD-TYPE | 108 | 91 | 98 | 183 |
Figure S125. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00362 (Fisher's exact test), Q value = 0.017
Table S126. Gene #34: '19p gain' versus Molecular Subtype #3: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 105 | 51 | 44 | 51 | 58 | 38 |
| 19P GAIN MUTATED | 0 | 3 | 1 | 0 | 1 | 4 |
| 19P GAIN WILD-TYPE | 105 | 48 | 43 | 51 | 57 | 34 |
Figure S126. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'RPPA_CNMF'
P value = 0.00036 (Fisher's exact test), Q value = 0.0028
Table S127. Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 19Q GAIN MUTATED | 0 | 0 | 0 | 12 |
| 19Q GAIN WILD-TYPE | 108 | 91 | 98 | 183 |
Figure S127. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.0411 (Fisher's exact test), Q value = 0.11
Table S128. Gene #35: '19q gain' versus Molecular Subtype #3: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 105 | 51 | 44 | 51 | 58 | 38 |
| 19Q GAIN MUTATED | 1 | 2 | 1 | 0 | 1 | 4 |
| 19Q GAIN WILD-TYPE | 104 | 49 | 43 | 51 | 57 | 34 |
Figure S128. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'RPPA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S129. Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 20P GAIN MUTATED | 1 | 0 | 2 | 23 |
| 20P GAIN WILD-TYPE | 107 | 91 | 96 | 172 |
Figure S129. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.0385 (Fisher's exact test), Q value = 0.1
Table S130. Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 20P GAIN MUTATED | 3 | 12 | 6 | 5 |
| 20P GAIN WILD-TYPE | 158 | 125 | 118 | 65 |
Figure S130. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.00148 (Fisher's exact test), Q value = 0.0088
Table S131. Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 20P GAIN MUTATED | 1 | 5 | 17 | 3 |
| 20P GAIN WILD-TYPE | 94 | 136 | 130 | 105 |
Figure S131. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.036 (Fisher's exact test), Q value = 0.097
Table S132. Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 20P GAIN MUTATED | 4 | 17 | 5 |
| 20P GAIN WILD-TYPE | 167 | 188 | 110 |
Figure S132. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0148 (Fisher's exact test), Q value = 0.05
Table S133. Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 208 | 71 | 123 | 86 |
| 20P GAIN MUTATED | 18 | 1 | 2 | 4 |
| 20P GAIN WILD-TYPE | 190 | 70 | 121 | 82 |
Figure S133. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.00434 (Fisher's exact test), Q value = 0.019
Table S134. Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 20P GAIN MUTATED | 3 | 5 | 1 | 15 | 1 |
| 20P GAIN WILD-TYPE | 144 | 93 | 58 | 113 | 55 |
Figure S134. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S135. Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 20Q GAIN MUTATED | 1 | 0 | 2 | 26 |
| 20Q GAIN WILD-TYPE | 107 | 91 | 96 | 169 |
Figure S135. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00776 (Fisher's exact test), Q value = 0.03
Table S136. Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 20Q GAIN MUTATED | 4 | 14 | 4 | 7 |
| 20Q GAIN WILD-TYPE | 157 | 123 | 120 | 63 |
Figure S136. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.00917 (Fisher's exact test), Q value = 0.035
Table S137. Gene #37: '20q gain' versus Molecular Subtype #3: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 105 | 51 | 44 | 51 | 58 | 38 |
| 20Q GAIN MUTATED | 5 | 2 | 4 | 0 | 10 | 3 |
| 20Q GAIN WILD-TYPE | 100 | 49 | 40 | 51 | 48 | 35 |
Figure S137. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'RPPA_CNMF'
P value = 0.0394 (Fisher's exact test), Q value = 0.1
Table S138. Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 20Q GAIN MUTATED | 3 | 6 | 16 | 4 |
| 20Q GAIN WILD-TYPE | 92 | 135 | 131 | 104 |
Figure S138. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.00664 (Fisher's exact test), Q value = 0.026
Table S139. Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 20Q GAIN MUTATED | 4 | 8 | 1 | 15 | 1 |
| 20Q GAIN WILD-TYPE | 143 | 90 | 58 | 113 | 55 |
Figure S139. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S140. Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 21Q GAIN MUTATED | 0 | 0 | 1 | 20 |
| 21Q GAIN WILD-TYPE | 108 | 91 | 97 | 175 |
Figure S140. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00862 (Fisher's exact test), Q value = 0.033
Table S141. Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 21Q GAIN MUTATED | 2 | 6 | 5 | 8 |
| 21Q GAIN WILD-TYPE | 159 | 131 | 119 | 62 |
Figure S141. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.027 (Fisher's exact test), Q value = 0.08
Table S142. Gene #38: '21q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 21Q GAIN MUTATED | 2 | 13 | 6 |
| 21Q GAIN WILD-TYPE | 169 | 192 | 109 |
Figure S142. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00318 (Fisher's exact test), Q value = 0.015
Table S143. Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 21Q GAIN MUTATED | 1 | 3 | 2 | 13 | 2 |
| 21Q GAIN WILD-TYPE | 146 | 95 | 57 | 115 | 54 |
Figure S143. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0184 (Fisher's exact test), Q value = 0.058
Table S144. Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 65 | 91 | 78 | 84 |
| 21Q GAIN MUTATED | 0 | 10 | 3 | 4 |
| 21Q GAIN WILD-TYPE | 65 | 81 | 75 | 80 |
Figure S144. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.0205 (Fisher's exact test), Q value = 0.063
Table S145. Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 75 | 86 | 69 | 23 | 65 |
| 21Q GAIN MUTATED | 2 | 11 | 3 | 0 | 1 |
| 21Q GAIN WILD-TYPE | 73 | 75 | 66 | 23 | 64 |
Figure S145. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.0184 (Fisher's exact test), Q value = 0.058
Table S146. Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| XP GAIN MUTATED | 0 | 0 | 0 | 7 |
| XP GAIN WILD-TYPE | 108 | 91 | 98 | 188 |
Figure S146. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00848 (Fisher's exact test), Q value = 0.033
Table S147. Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| XP GAIN MUTATED | 0 | 2 | 1 | 4 |
| XP GAIN WILD-TYPE | 161 | 135 | 123 | 66 |
Figure S147. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.0456 (Fisher's exact test), Q value = 0.11
Table S148. Gene #40: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| XP GAIN MUTATED | 0 | 2 | 0 | 5 | 0 |
| XP GAIN WILD-TYPE | 147 | 96 | 59 | 123 | 56 |
Figure S148. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0199 (Fisher's exact test), Q value = 0.062
Table S149. Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| XQ GAIN MUTATED | 0 | 0 | 0 | 7 |
| XQ GAIN WILD-TYPE | 108 | 91 | 98 | 188 |
Figure S149. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00849 (Fisher's exact test), Q value = 0.033
Table S150. Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| XQ GAIN MUTATED | 0 | 2 | 1 | 4 |
| XQ GAIN WILD-TYPE | 161 | 135 | 123 | 66 |
Figure S150. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.0455 (Fisher's exact test), Q value = 0.11
Table S151. Gene #41: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| XQ GAIN MUTATED | 0 | 2 | 0 | 5 | 0 |
| XQ GAIN WILD-TYPE | 147 | 96 | 59 | 123 | 56 |
Figure S151. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S152. Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 1P LOSS MUTATED | 0 | 0 | 0 | 22 |
| 1P LOSS WILD-TYPE | 108 | 91 | 98 | 173 |
Figure S152. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00094 (Fisher's exact test), Q value = 0.0062
Table S153. Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 1P LOSS MUTATED | 0 | 9 | 9 | 4 |
| 1P LOSS WILD-TYPE | 161 | 128 | 115 | 66 |
Figure S153. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.0121 (Fisher's exact test), Q value = 0.043
Table S154. Gene #42: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 1P LOSS MUTATED | 1 | 9 | 11 | 1 |
| 1P LOSS WILD-TYPE | 94 | 132 | 136 | 107 |
Figure S154. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 2e-04 (Fisher's exact test), Q value = 0.0018
Table S155. Gene #42: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 1P LOSS MUTATED | 0 | 13 | 9 |
| 1P LOSS WILD-TYPE | 171 | 192 | 106 |
Figure S155. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00973 (Fisher's exact test), Q value = 0.036
Table S156. Gene #42: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 208 | 71 | 123 | 86 |
| 1P LOSS MUTATED | 14 | 3 | 0 | 4 |
| 1P LOSS WILD-TYPE | 194 | 68 | 123 | 82 |
Figure S156. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.00355 (Fisher's exact test), Q value = 0.016
Table S157. Gene #42: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 1P LOSS MUTATED | 1 | 3 | 4 | 12 | 1 |
| 1P LOSS WILD-TYPE | 146 | 95 | 55 | 116 | 55 |
Figure S157. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.028 (Fisher's exact test), Q value = 0.082
Table S158. Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 65 | 91 | 78 | 84 |
| 1P LOSS MUTATED | 0 | 8 | 7 | 3 |
| 1P LOSS WILD-TYPE | 65 | 83 | 71 | 81 |
Figure S158. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.00304 (Fisher's exact test), Q value = 0.015
Table S159. Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 75 | 86 | 69 | 23 | 65 |
| 1P LOSS MUTATED | 0 | 11 | 5 | 0 | 2 |
| 1P LOSS WILD-TYPE | 75 | 75 | 64 | 23 | 63 |
Figure S159. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.0284 (Fisher's exact test), Q value = 0.083
Table S160. Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 65 | 91 | 78 | 84 |
| 1Q LOSS MUTATED | 0 | 1 | 4 | 0 |
| 1Q LOSS WILD-TYPE | 65 | 90 | 74 | 84 |
Figure S160. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 7e-04 (Fisher's exact test), Q value = 0.005
Table S161. Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 2P LOSS MUTATED | 1 | 0 | 0 | 13 |
| 2P LOSS WILD-TYPE | 107 | 91 | 98 | 182 |
Figure S161. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00839 (Fisher's exact test), Q value = 0.033
Table S162. Gene #44: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 2P LOSS MUTATED | 0 | 4 | 6 | 4 |
| 2P LOSS WILD-TYPE | 161 | 133 | 118 | 66 |
Figure S162. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.0153 (Fisher's exact test), Q value = 0.05
Table S163. Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 65 | 91 | 78 | 84 |
| 2P LOSS MUTATED | 0 | 8 | 3 | 1 |
| 2P LOSS WILD-TYPE | 65 | 83 | 75 | 83 |
Figure S163. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.00013 (Fisher's exact test), Q value = 0.0014
Table S164. Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 2Q LOSS MUTATED | 2 | 0 | 0 | 16 |
| 2Q LOSS WILD-TYPE | 106 | 91 | 98 | 179 |
Figure S164. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.0219 (Fisher's exact test), Q value = 0.067
Table S165. Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 2Q LOSS MUTATED | 1 | 5 | 7 | 5 |
| 2Q LOSS WILD-TYPE | 160 | 132 | 117 | 65 |
Figure S165. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.0352 (Fisher's exact test), Q value = 0.096
Table S166. Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 2Q LOSS MUTATED | 3 | 2 | 0 | 10 | 3 |
| 2Q LOSS WILD-TYPE | 144 | 96 | 59 | 118 | 53 |
Figure S166. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00708 (Fisher's exact test), Q value = 0.028
Table S167. Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 65 | 91 | 78 | 84 |
| 2Q LOSS MUTATED | 0 | 10 | 3 | 2 |
| 2Q LOSS WILD-TYPE | 65 | 81 | 75 | 82 |
Figure S167. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.038 (Fisher's exact test), Q value = 0.1
Table S168. Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 3P LOSS MUTATED | 0 | 5 | 4 |
| 3P LOSS WILD-TYPE | 171 | 200 | 111 |
Figure S168. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0184 (Fisher's exact test), Q value = 0.058
Table S169. Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 208 | 71 | 123 | 86 |
| 3P LOSS MUTATED | 4 | 4 | 0 | 0 |
| 3P LOSS WILD-TYPE | 204 | 67 | 123 | 86 |
Figure S169. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.0221 (Fisher's exact test), Q value = 0.067
Table S170. Gene #47: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 208 | 71 | 123 | 86 |
| 3Q LOSS MUTATED | 1 | 3 | 0 | 0 |
| 3Q LOSS WILD-TYPE | 207 | 68 | 123 | 86 |
Figure S170. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.032 (Fisher's exact test), Q value = 0.092
Table S171. Gene #47: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 3Q LOSS MUTATED | 0 | 3 | 1 | 0 | 0 |
| 3Q LOSS WILD-TYPE | 147 | 95 | 58 | 128 | 56 |
Figure S171. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S172. Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 4P LOSS MUTATED | 1 | 0 | 0 | 22 |
| 4P LOSS WILD-TYPE | 107 | 91 | 98 | 173 |
Figure S172. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.0427 (Fisher's exact test), Q value = 0.11
Table S173. Gene #48: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 4P LOSS MUTATED | 2 | 9 | 7 | 5 |
| 4P LOSS WILD-TYPE | 159 | 128 | 117 | 65 |
Figure S173. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.00108 (Fisher's exact test), Q value = 0.0069
Table S174. Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 4P LOSS MUTATED | 0 | 11 | 11 | 1 |
| 4P LOSS WILD-TYPE | 95 | 130 | 136 | 107 |
Figure S174. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.0404 (Fisher's exact test), Q value = 0.1
Table S175. Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 4P LOSS MUTATED | 3 | 11 | 9 |
| 4P LOSS WILD-TYPE | 168 | 194 | 106 |
Figure S175. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 2e-05 (Fisher's exact test), Q value = 0.00028
Table S176. Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 208 | 71 | 123 | 86 |
| 4P LOSS MUTATED | 21 | 1 | 1 | 0 |
| 4P LOSS WILD-TYPE | 187 | 70 | 122 | 86 |
Figure S176. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.00287 (Fisher's exact test), Q value = 0.015
Table S177. Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 4P LOSS MUTATED | 6 | 1 | 2 | 14 | 0 |
| 4P LOSS WILD-TYPE | 141 | 97 | 57 | 114 | 56 |
Figure S177. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00377 (Fisher's exact test), Q value = 0.017
Table S178. Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 65 | 91 | 78 | 84 |
| 4P LOSS MUTATED | 0 | 11 | 4 | 2 |
| 4P LOSS WILD-TYPE | 65 | 80 | 74 | 82 |
Figure S178. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.00015 (Fisher's exact test), Q value = 0.0015
Table S179. Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 75 | 86 | 69 | 23 | 65 |
| 4P LOSS MUTATED | 1 | 13 | 3 | 0 | 0 |
| 4P LOSS WILD-TYPE | 74 | 73 | 66 | 23 | 65 |
Figure S179. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.00013 (Fisher's exact test), Q value = 0.0014
Table S180. Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 4Q LOSS MUTATED | 1 | 0 | 0 | 15 |
| 4Q LOSS WILD-TYPE | 107 | 91 | 98 | 180 |
Figure S180. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00161 (Fisher's exact test), Q value = 0.0093
Table S181. Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 4Q LOSS MUTATED | 0 | 6 | 10 | 0 |
| 4Q LOSS WILD-TYPE | 95 | 135 | 137 | 108 |
Figure S181. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.0468 (Fisher's exact test), Q value = 0.12
Table S182. Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 4Q LOSS MUTATED | 3 | 1 | 1 | 10 | 1 |
| 4Q LOSS WILD-TYPE | 144 | 97 | 58 | 118 | 55 |
Figure S182. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0422 (Fisher's exact test), Q value = 0.11
Table S183. Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 75 | 86 | 69 | 23 | 65 |
| 4Q LOSS MUTATED | 2 | 8 | 2 | 0 | 0 |
| 4Q LOSS WILD-TYPE | 73 | 78 | 67 | 23 | 65 |
Figure S183. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.0037 (Fisher's exact test), Q value = 0.017
Table S184. Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 5P LOSS MUTATED | 1 | 0 | 0 | 11 |
| 5P LOSS WILD-TYPE | 107 | 91 | 98 | 184 |
Figure S184. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00575 (Fisher's exact test), Q value = 0.024
Table S185. Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 5P LOSS MUTATED | 0 | 6 | 6 |
| 5P LOSS WILD-TYPE | 171 | 199 | 109 |
Figure S185. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00329 (Fisher's exact test), Q value = 0.016
Table S186. Gene #50: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 5P LOSS MUTATED | 0 | 1 | 4 | 6 | 0 |
| 5P LOSS WILD-TYPE | 147 | 97 | 55 | 122 | 56 |
Figure S186. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0491 (Fisher's exact test), Q value = 0.12
Table S187. Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 75 | 86 | 69 | 23 | 65 |
| 5P LOSS MUTATED | 0 | 5 | 3 | 1 | 0 |
| 5P LOSS WILD-TYPE | 75 | 81 | 66 | 22 | 65 |
Figure S187. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S188. Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 5Q LOSS MUTATED | 1 | 0 | 0 | 22 |
| 5Q LOSS WILD-TYPE | 107 | 91 | 98 | 173 |
Figure S188. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.018 (Fisher's exact test), Q value = 0.058
Table S189. Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 5Q LOSS MUTATED | 2 | 7 | 7 | 7 |
| 5Q LOSS WILD-TYPE | 159 | 130 | 117 | 63 |
Figure S189. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.0311 (Fisher's exact test), Q value = 0.089
Table S190. Gene #51: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 5Q LOSS MUTATED | 1 | 6 | 13 | 3 |
| 5Q LOSS WILD-TYPE | 94 | 135 | 134 | 105 |
Figure S190. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.00191 (Fisher's exact test), Q value = 0.011
Table S191. Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 5Q LOSS MUTATED | 1 | 15 | 7 |
| 5Q LOSS WILD-TYPE | 170 | 190 | 108 |
Figure S191. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0112 (Fisher's exact test), Q value = 0.04
Table S192. Gene #51: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 208 | 71 | 123 | 86 |
| 5Q LOSS MUTATED | 17 | 2 | 2 | 1 |
| 5Q LOSS WILD-TYPE | 191 | 69 | 121 | 85 |
Figure S192. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.00053 (Fisher's exact test), Q value = 0.0039
Table S193. Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 5Q LOSS MUTATED | 1 | 2 | 6 | 12 | 1 |
| 5Q LOSS WILD-TYPE | 146 | 96 | 53 | 116 | 55 |
Figure S193. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S194. Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 6P LOSS MUTATED | 2 | 0 | 1 | 23 |
| 6P LOSS WILD-TYPE | 106 | 91 | 97 | 172 |
Figure S194. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.012 (Fisher's exact test), Q value = 0.043
Table S195. Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 6P LOSS MUTATED | 2 | 9 | 8 | 7 |
| 6P LOSS WILD-TYPE | 159 | 128 | 116 | 63 |
Figure S195. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.0028 (Fisher's exact test), Q value = 0.014
Table S196. Gene #52: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 6P LOSS MUTATED | 2 | 13 | 11 |
| 6P LOSS WILD-TYPE | 169 | 192 | 104 |
Figure S196. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0435 (Fisher's exact test), Q value = 0.11
Table S197. Gene #52: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 65 | 91 | 78 | 84 |
| 6P LOSS MUTATED | 0 | 9 | 4 | 4 |
| 6P LOSS WILD-TYPE | 65 | 82 | 74 | 80 |
Figure S197. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.0164 (Fisher's exact test), Q value = 0.053
Table S198. Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 75 | 86 | 69 | 23 | 65 |
| 6P LOSS MUTATED | 1 | 11 | 2 | 0 | 3 |
| 6P LOSS WILD-TYPE | 74 | 75 | 67 | 23 | 62 |
Figure S198. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S199. Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 6Q LOSS MUTATED | 2 | 0 | 5 | 34 |
| 6Q LOSS WILD-TYPE | 106 | 91 | 93 | 161 |
Figure S199. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.0143 (Fisher's exact test), Q value = 0.049
Table S200. Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 6Q LOSS MUTATED | 5 | 15 | 12 | 9 |
| 6Q LOSS WILD-TYPE | 156 | 122 | 112 | 61 |
Figure S200. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.028 (Fisher's exact test), Q value = 0.082
Table S201. Gene #53: '6q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 74 | 113 | 92 | 68 |
| 6Q LOSS MUTATED | 4 | 9 | 3 | 11 |
| 6Q LOSS WILD-TYPE | 70 | 104 | 89 | 57 |
Figure S201. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
P value = 0.00952 (Fisher's exact test), Q value = 0.036
Table S202. Gene #53: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 6Q LOSS MUTATED | 4 | 12 | 21 | 4 |
| 6Q LOSS WILD-TYPE | 91 | 129 | 126 | 104 |
Figure S202. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 7e-04 (Fisher's exact test), Q value = 0.005
Table S203. Gene #53: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 6Q LOSS MUTATED | 4 | 25 | 12 |
| 6Q LOSS WILD-TYPE | 167 | 180 | 103 |
Figure S203. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0153 (Fisher's exact test), Q value = 0.05
Table S204. Gene #53: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 65 | 91 | 78 | 84 |
| 6Q LOSS MUTATED | 1 | 14 | 5 | 9 |
| 6Q LOSS WILD-TYPE | 64 | 77 | 73 | 75 |
Figure S204. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.00612 (Fisher's exact test), Q value = 0.025
Table S205. Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 75 | 86 | 69 | 23 | 65 |
| 6Q LOSS MUTATED | 5 | 16 | 2 | 0 | 6 |
| 6Q LOSS WILD-TYPE | 70 | 70 | 67 | 23 | 59 |
Figure S205. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S206. Gene #54: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 8P LOSS MUTATED | 53 | 7 | 27 | 84 |
| 8P LOSS WILD-TYPE | 55 | 84 | 71 | 111 |
Figure S206. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S207. Gene #54: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 8P LOSS MUTATED | 29 | 48 | 62 | 32 |
| 8P LOSS WILD-TYPE | 132 | 89 | 62 | 38 |
Figure S207. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 2e-05 (Fisher's exact test), Q value = 0.00028
Table S208. Gene #54: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 8P LOSS MUTATED | 22 | 72 | 49 | 28 |
| 8P LOSS WILD-TYPE | 73 | 69 | 98 | 80 |
Figure S208. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 2e-05 (Fisher's exact test), Q value = 0.00028
Table S209. Gene #54: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 8P LOSS MUTATED | 41 | 69 | 61 |
| 8P LOSS WILD-TYPE | 130 | 136 | 54 |
Figure S209. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0129 (Fisher's exact test), Q value = 0.045
Table S210. Gene #54: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 208 | 71 | 123 | 86 |
| 8P LOSS MUTATED | 83 | 17 | 34 | 36 |
| 8P LOSS WILD-TYPE | 125 | 54 | 89 | 50 |
Figure S210. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.00022 (Fisher's exact test), Q value = 0.002
Table S211. Gene #55: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 8Q LOSS MUTATED | 0 | 6 | 12 | 3 |
| 8Q LOSS WILD-TYPE | 161 | 131 | 112 | 67 |
Figure S211. Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.00036 (Fisher's exact test), Q value = 0.0028
Table S212. Gene #55: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 8Q LOSS MUTATED | 1 | 15 | 4 | 1 |
| 8Q LOSS WILD-TYPE | 94 | 126 | 143 | 107 |
Figure S212. Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.00073 (Fisher's exact test), Q value = 0.0051
Table S213. Gene #55: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 8Q LOSS MUTATED | 2 | 7 | 12 |
| 8Q LOSS WILD-TYPE | 169 | 198 | 103 |
Figure S213. Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00025 (Fisher's exact test), Q value = 0.0022
Table S214. Gene #56: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 9P LOSS MUTATED | 1 | 1 | 1 | 18 |
| 9P LOSS WILD-TYPE | 107 | 90 | 97 | 177 |
Figure S214. Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00541 (Fisher's exact test), Q value = 0.023
Table S215. Gene #56: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 74 | 113 | 92 | 68 |
| 9P LOSS MUTATED | 2 | 1 | 3 | 8 |
| 9P LOSS WILD-TYPE | 72 | 112 | 89 | 60 |
Figure S215. Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
P value = 0.0221 (Fisher's exact test), Q value = 0.067
Table S216. Gene #56: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 9P LOSS MUTATED | 3 | 8 | 10 |
| 9P LOSS WILD-TYPE | 168 | 197 | 105 |
Figure S216. Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0476 (Fisher's exact test), Q value = 0.12
Table S217. Gene #57: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 9Q LOSS MUTATED | 1 | 0 | 1 | 9 |
| 9Q LOSS WILD-TYPE | 107 | 91 | 97 | 186 |
Figure S217. Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.0154 (Fisher's exact test), Q value = 0.05
Table S218. Gene #57: '9q loss' versus Molecular Subtype #3: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 105 | 51 | 44 | 51 | 58 | 38 |
| 9Q LOSS MUTATED | 2 | 4 | 0 | 0 | 0 | 3 |
| 9Q LOSS WILD-TYPE | 103 | 47 | 44 | 51 | 58 | 35 |
Figure S218. Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #3: 'RPPA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S219. Gene #58: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 10P LOSS MUTATED | 7 | 0 | 1 | 33 |
| 10P LOSS WILD-TYPE | 101 | 91 | 97 | 162 |
Figure S219. Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S220. Gene #58: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 10P LOSS MUTATED | 2 | 10 | 20 | 9 |
| 10P LOSS WILD-TYPE | 159 | 127 | 104 | 61 |
Figure S220. Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 7e-05 (Fisher's exact test), Q value = 0.00079
Table S221. Gene #58: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 10P LOSS MUTATED | 2 | 20 | 17 | 2 |
| 10P LOSS WILD-TYPE | 93 | 121 | 130 | 106 |
Figure S221. Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.00013 (Fisher's exact test), Q value = 0.0014
Table S222. Gene #58: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 10P LOSS MUTATED | 3 | 22 | 16 |
| 10P LOSS WILD-TYPE | 168 | 183 | 99 |
Figure S222. Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S223. Gene #58: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 208 | 71 | 123 | 86 |
| 10P LOSS MUTATED | 26 | 4 | 0 | 9 |
| 10P LOSS WILD-TYPE | 182 | 67 | 123 | 77 |
Figure S223. Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 5e-05 (Fisher's exact test), Q value = 0.00062
Table S224. Gene #58: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 10P LOSS MUTATED | 3 | 5 | 7 | 22 | 2 |
| 10P LOSS WILD-TYPE | 144 | 93 | 52 | 106 | 54 |
Figure S224. Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0115 (Fisher's exact test), Q value = 0.041
Table S225. Gene #58: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 65 | 91 | 78 | 84 |
| 10P LOSS MUTATED | 0 | 8 | 6 | 11 |
| 10P LOSS WILD-TYPE | 65 | 83 | 72 | 73 |
Figure S225. Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.00124 (Fisher's exact test), Q value = 0.0077
Table S226. Gene #58: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 75 | 86 | 69 | 23 | 65 |
| 10P LOSS MUTATED | 0 | 13 | 6 | 0 | 6 |
| 10P LOSS WILD-TYPE | 75 | 73 | 63 | 23 | 59 |
Figure S226. Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S227. Gene #59: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 10Q LOSS MUTATED | 6 | 0 | 3 | 34 |
| 10Q LOSS WILD-TYPE | 102 | 91 | 95 | 161 |
Figure S227. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.00039
Table S228. Gene #59: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 10Q LOSS MUTATED | 3 | 11 | 18 | 11 |
| 10Q LOSS WILD-TYPE | 158 | 126 | 106 | 59 |
Figure S228. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.00071 (Fisher's exact test), Q value = 0.005
Table S229. Gene #59: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 10Q LOSS MUTATED | 2 | 21 | 16 | 4 |
| 10Q LOSS WILD-TYPE | 93 | 120 | 131 | 104 |
Figure S229. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.00046 (Fisher's exact test), Q value = 0.0035
Table S230. Gene #59: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 10Q LOSS MUTATED | 5 | 20 | 18 |
| 10Q LOSS WILD-TYPE | 166 | 185 | 97 |
Figure S230. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 3e-05 (Fisher's exact test), Q value = 0.00039
Table S231. Gene #59: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 208 | 71 | 123 | 86 |
| 10Q LOSS MUTATED | 26 | 2 | 1 | 12 |
| 10Q LOSS WILD-TYPE | 182 | 69 | 122 | 74 |
Figure S231. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.00124 (Fisher's exact test), Q value = 0.0077
Table S232. Gene #59: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 10Q LOSS MUTATED | 5 | 4 | 6 | 21 | 5 |
| 10Q LOSS WILD-TYPE | 142 | 94 | 53 | 107 | 51 |
Figure S232. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00246 (Fisher's exact test), Q value = 0.013
Table S233. Gene #59: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 65 | 91 | 78 | 84 |
| 10Q LOSS MUTATED | 0 | 11 | 6 | 13 |
| 10Q LOSS WILD-TYPE | 65 | 80 | 72 | 71 |
Figure S233. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.00395 (Fisher's exact test), Q value = 0.018
Table S234. Gene #59: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 75 | 86 | 69 | 23 | 65 |
| 10Q LOSS MUTATED | 1 | 14 | 7 | 0 | 8 |
| 10Q LOSS WILD-TYPE | 74 | 72 | 62 | 23 | 57 |
Figure S234. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.0463 (Fisher's exact test), Q value = 0.12
Table S235. Gene #60: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 75 | 86 | 69 | 23 | 65 |
| 11P LOSS MUTATED | 0 | 5 | 0 | 0 | 1 |
| 11P LOSS WILD-TYPE | 75 | 81 | 69 | 23 | 64 |
Figure S235. Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.0395 (Fisher's exact test), Q value = 0.1
Table S236. Gene #61: '11q loss' versus Molecular Subtype #3: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 105 | 51 | 44 | 51 | 58 | 38 |
| 11Q LOSS MUTATED | 0 | 0 | 0 | 0 | 1 | 2 |
| 11Q LOSS WILD-TYPE | 105 | 51 | 44 | 51 | 57 | 36 |
Figure S236. Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #3: 'RPPA_CNMF'
P value = 1e-04 (Fisher's exact test), Q value = 0.0011
Table S237. Gene #62: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 12P LOSS MUTATED | 8 | 1 | 6 | 32 |
| 12P LOSS WILD-TYPE | 100 | 90 | 92 | 163 |
Figure S237. Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.0336 (Fisher's exact test), Q value = 0.094
Table S238. Gene #62: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 12P LOSS MUTATED | 3 | 20 | 15 | 9 |
| 12P LOSS WILD-TYPE | 92 | 121 | 132 | 99 |
Figure S238. Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.041 (Fisher's exact test), Q value = 0.11
Table S239. Gene #62: '12p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 208 | 71 | 123 | 86 |
| 12P LOSS MUTATED | 27 | 2 | 8 | 7 |
| 12P LOSS WILD-TYPE | 181 | 69 | 115 | 79 |
Figure S239. Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.0145 (Fisher's exact test), Q value = 0.049
Table S240. Gene #62: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 12P LOSS MUTATED | 12 | 4 | 11 | 15 | 2 |
| 12P LOSS WILD-TYPE | 135 | 94 | 48 | 113 | 54 |
Figure S240. Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0147 (Fisher's exact test), Q value = 0.049
Table S241. Gene #62: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 65 | 91 | 78 | 84 |
| 12P LOSS MUTATED | 3 | 17 | 6 | 5 |
| 12P LOSS WILD-TYPE | 62 | 74 | 72 | 79 |
Figure S241. Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.00137 (Fisher's exact test), Q value = 0.0084
Table S242. Gene #63: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 12Q LOSS MUTATED | 3 | 0 | 1 | 16 |
| 12Q LOSS WILD-TYPE | 105 | 91 | 97 | 179 |
Figure S242. Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.05 (Fisher's exact test), Q value = 0.12
Table S243. Gene #63: '12q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 12Q LOSS MUTATED | 3 | 4 | 6 | 5 | 0 |
| 12Q LOSS WILD-TYPE | 144 | 94 | 53 | 123 | 56 |
Figure S243. Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S244. Gene #64: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 13Q LOSS MUTATED | 5 | 2 | 7 | 64 |
| 13Q LOSS WILD-TYPE | 103 | 89 | 91 | 131 |
Figure S244. Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.0166 (Fisher's exact test), Q value = 0.053
Table S245. Gene #64: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 13Q LOSS MUTATED | 18 | 18 | 23 | 19 |
| 13Q LOSS WILD-TYPE | 143 | 119 | 101 | 51 |
Figure S245. Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.00251 (Fisher's exact test), Q value = 0.013
Table S246. Gene #64: '13q loss' versus Molecular Subtype #3: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 105 | 51 | 44 | 51 | 58 | 38 |
| 13Q LOSS MUTATED | 11 | 8 | 6 | 3 | 12 | 14 |
| 13Q LOSS WILD-TYPE | 94 | 43 | 38 | 48 | 46 | 24 |
Figure S246. Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #3: 'RPPA_CNMF'
P value = 0.0102 (Fisher's exact test), Q value = 0.038
Table S247. Gene #64: '13q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 74 | 113 | 92 | 68 |
| 13Q LOSS MUTATED | 10 | 22 | 6 | 16 |
| 13Q LOSS WILD-TYPE | 64 | 91 | 86 | 52 |
Figure S247. Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
P value = 0.0134 (Fisher's exact test), Q value = 0.046
Table S248. Gene #64: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 208 | 71 | 123 | 86 |
| 13Q LOSS MUTATED | 43 | 13 | 13 | 7 |
| 13Q LOSS WILD-TYPE | 165 | 58 | 110 | 79 |
Figure S248. Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.0263 (Fisher's exact test), Q value = 0.078
Table S249. Gene #64: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 13Q LOSS MUTATED | 16 | 15 | 9 | 31 | 5 |
| 13Q LOSS WILD-TYPE | 131 | 83 | 50 | 97 | 51 |
Figure S249. Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0297 (Fisher's exact test), Q value = 0.086
Table S250. Gene #64: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 65 | 91 | 78 | 84 |
| 13Q LOSS MUTATED | 4 | 21 | 12 | 16 |
| 13Q LOSS WILD-TYPE | 61 | 70 | 66 | 68 |
Figure S250. Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.00342 (Fisher's exact test), Q value = 0.016
Table S251. Gene #64: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 75 | 86 | 69 | 23 | 65 |
| 13Q LOSS MUTATED | 6 | 25 | 13 | 2 | 7 |
| 13Q LOSS WILD-TYPE | 69 | 61 | 56 | 21 | 58 |
Figure S251. Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.00028 (Fisher's exact test), Q value = 0.0024
Table S252. Gene #65: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 14Q LOSS MUTATED | 5 | 1 | 0 | 19 |
| 14Q LOSS WILD-TYPE | 103 | 90 | 98 | 176 |
Figure S252. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.0239 (Fisher's exact test), Q value = 0.072
Table S253. Gene #65: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 14Q LOSS MUTATED | 3 | 7 | 7 | 8 |
| 14Q LOSS WILD-TYPE | 158 | 130 | 117 | 62 |
Figure S253. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S254. Gene #66: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 15Q LOSS MUTATED | 3 | 0 | 1 | 31 |
| 15Q LOSS WILD-TYPE | 105 | 91 | 97 | 164 |
Figure S254. Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.0035 (Fisher's exact test), Q value = 0.016
Table S255. Gene #66: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 15Q LOSS MUTATED | 3 | 12 | 11 | 9 |
| 15Q LOSS WILD-TYPE | 158 | 125 | 113 | 61 |
Figure S255. Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.00183 (Fisher's exact test), Q value = 0.01
Table S256. Gene #66: '15q loss' versus Molecular Subtype #3: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 105 | 51 | 44 | 51 | 58 | 38 |
| 15Q LOSS MUTATED | 3 | 7 | 3 | 0 | 5 | 7 |
| 15Q LOSS WILD-TYPE | 102 | 44 | 41 | 51 | 53 | 31 |
Figure S256. Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #3: 'RPPA_CNMF'
P value = 0.00187 (Fisher's exact test), Q value = 0.01
Table S257. Gene #66: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 15Q LOSS MUTATED | 4 | 9 | 20 | 2 |
| 15Q LOSS WILD-TYPE | 91 | 132 | 127 | 106 |
Figure S257. Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.0107 (Fisher's exact test), Q value = 0.039
Table S258. Gene #66: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 15Q LOSS MUTATED | 5 | 22 | 8 |
| 15Q LOSS WILD-TYPE | 166 | 183 | 107 |
Figure S258. Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00486 (Fisher's exact test), Q value = 0.021
Table S259. Gene #66: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 208 | 71 | 123 | 86 |
| 15Q LOSS MUTATED | 20 | 6 | 1 | 7 |
| 15Q LOSS WILD-TYPE | 188 | 65 | 122 | 79 |
Figure S259. Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.0124 (Fisher's exact test), Q value = 0.043
Table S260. Gene #66: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 15Q LOSS MUTATED | 3 | 7 | 3 | 15 | 6 |
| 15Q LOSS WILD-TYPE | 144 | 91 | 56 | 113 | 50 |
Figure S260. Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00315 (Fisher's exact test), Q value = 0.015
Table S261. Gene #66: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 65 | 91 | 78 | 84 |
| 15Q LOSS MUTATED | 0 | 14 | 6 | 7 |
| 15Q LOSS WILD-TYPE | 65 | 77 | 72 | 77 |
Figure S261. Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.034 (Fisher's exact test), Q value = 0.095
Table S262. Gene #66: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 75 | 86 | 69 | 23 | 65 |
| 15Q LOSS MUTATED | 2 | 13 | 6 | 0 | 6 |
| 15Q LOSS WILD-TYPE | 73 | 73 | 63 | 23 | 59 |
Figure S262. Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S263. Gene #67: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 16P LOSS MUTATED | 8 | 0 | 0 | 23 |
| 16P LOSS WILD-TYPE | 100 | 91 | 98 | 172 |
Figure S263. Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S264. Gene #68: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 16Q LOSS MUTATED | 27 | 1 | 6 | 73 |
| 16Q LOSS WILD-TYPE | 81 | 90 | 92 | 122 |
Figure S264. Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S265. Gene #68: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 16Q LOSS MUTATED | 15 | 34 | 32 | 26 |
| 16Q LOSS WILD-TYPE | 146 | 103 | 92 | 44 |
Figure S265. Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.0036 (Fisher's exact test), Q value = 0.017
Table S266. Gene #68: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 16Q LOSS MUTATED | 12 | 38 | 41 | 16 |
| 16Q LOSS WILD-TYPE | 83 | 103 | 106 | 92 |
Figure S266. Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.0292 (Fisher's exact test), Q value = 0.085
Table S267. Gene #68: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 16Q LOSS MUTATED | 26 | 51 | 30 |
| 16Q LOSS WILD-TYPE | 145 | 154 | 85 |
Figure S267. Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00546 (Fisher's exact test), Q value = 0.023
Table S268. Gene #68: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 208 | 71 | 123 | 86 |
| 16Q LOSS MUTATED | 59 | 11 | 16 | 19 |
| 16Q LOSS WILD-TYPE | 149 | 60 | 107 | 67 |
Figure S268. Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.00041 (Fisher's exact test), Q value = 0.0031
Table S269. Gene #68: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 16Q LOSS MUTATED | 20 | 15 | 18 | 42 | 10 |
| 16Q LOSS WILD-TYPE | 127 | 83 | 41 | 86 | 46 |
Figure S269. Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00233 (Fisher's exact test), Q value = 0.013
Table S270. Gene #68: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 65 | 91 | 78 | 84 |
| 16Q LOSS MUTATED | 6 | 31 | 17 | 17 |
| 16Q LOSS WILD-TYPE | 59 | 60 | 61 | 67 |
Figure S270. Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S271. Gene #69: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 17P LOSS MUTATED | 11 | 1 | 3 | 61 |
| 17P LOSS WILD-TYPE | 97 | 90 | 95 | 134 |
Figure S271. Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S272. Gene #69: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 17P LOSS MUTATED | 10 | 19 | 27 | 20 |
| 17P LOSS WILD-TYPE | 151 | 118 | 97 | 50 |
Figure S272. Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.00017 (Fisher's exact test), Q value = 0.0016
Table S273. Gene #69: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 17P LOSS MUTATED | 8 | 34 | 27 | 7 |
| 17P LOSS WILD-TYPE | 87 | 107 | 120 | 101 |
Figure S273. Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.00145 (Fisher's exact test), Q value = 0.0087
Table S274. Gene #69: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 17P LOSS MUTATED | 16 | 31 | 29 |
| 17P LOSS WILD-TYPE | 155 | 174 | 86 |
Figure S274. Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0329 (Fisher's exact test), Q value = 0.093
Table S275. Gene #69: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 17P LOSS MUTATED | 15 | 11 | 10 | 30 | 9 |
| 17P LOSS WILD-TYPE | 132 | 87 | 49 | 98 | 47 |
Figure S275. Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.015 (Fisher's exact test), Q value = 0.05
Table S276. Gene #69: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 65 | 91 | 78 | 84 |
| 17P LOSS MUTATED | 3 | 20 | 13 | 16 |
| 17P LOSS WILD-TYPE | 62 | 71 | 65 | 68 |
Figure S276. Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.00037 (Fisher's exact test), Q value = 0.0029
Table S277. Gene #70: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 17Q LOSS MUTATED | 1 | 0 | 2 | 17 |
| 17Q LOSS WILD-TYPE | 107 | 91 | 96 | 178 |
Figure S277. Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00164 (Fisher's exact test), Q value = 0.0094
Table S278. Gene #70: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 17Q LOSS MUTATED | 0 | 9 | 7 | 4 |
| 17Q LOSS WILD-TYPE | 161 | 128 | 117 | 66 |
Figure S278. Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.00194 (Fisher's exact test), Q value = 0.011
Table S279. Gene #70: '17q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 17Q LOSS MUTATED | 1 | 7 | 12 | 0 |
| 17Q LOSS WILD-TYPE | 94 | 134 | 135 | 108 |
Figure S279. Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.0361 (Fisher's exact test), Q value = 0.097
Table S280. Gene #70: '17q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 17Q LOSS MUTATED | 2 | 11 | 7 |
| 17Q LOSS WILD-TYPE | 169 | 194 | 108 |
Figure S280. Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00985 (Fisher's exact test), Q value = 0.036
Table S281. Gene #70: '17q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 208 | 71 | 123 | 86 |
| 17Q LOSS MUTATED | 12 | 5 | 0 | 3 |
| 17Q LOSS WILD-TYPE | 196 | 66 | 123 | 83 |
Figure S281. Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.0457 (Fisher's exact test), Q value = 0.11
Table S282. Gene #70: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 17Q LOSS MUTATED | 1 | 7 | 2 | 7 | 3 |
| 17Q LOSS WILD-TYPE | 146 | 91 | 57 | 121 | 53 |
Figure S282. Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S283. Gene #71: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 18P LOSS MUTATED | 15 | 1 | 2 | 49 |
| 18P LOSS WILD-TYPE | 93 | 90 | 96 | 146 |
Figure S283. Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00914 (Fisher's exact test), Q value = 0.035
Table S284. Gene #71: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 18P LOSS MUTATED | 11 | 20 | 22 | 14 |
| 18P LOSS WILD-TYPE | 150 | 117 | 102 | 56 |
Figure S284. Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.00212 (Fisher's exact test), Q value = 0.011
Table S285. Gene #71: '18p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 74 | 113 | 92 | 68 |
| 18P LOSS MUTATED | 8 | 11 | 7 | 19 |
| 18P LOSS WILD-TYPE | 66 | 102 | 85 | 49 |
Figure S285. Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
P value = 0.00107 (Fisher's exact test), Q value = 0.0069
Table S286. Gene #71: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 18P LOSS MUTATED | 6 | 21 | 32 | 8 |
| 18P LOSS WILD-TYPE | 89 | 120 | 115 | 100 |
Figure S286. Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.0349 (Fisher's exact test), Q value = 0.096
Table S287. Gene #71: '18p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 18P LOSS MUTATED | 15 | 7 | 12 | 24 | 8 |
| 18P LOSS WILD-TYPE | 132 | 91 | 47 | 104 | 48 |
Figure S287. Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00076 (Fisher's exact test), Q value = 0.0052
Table S288. Gene #71: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 65 | 91 | 78 | 84 |
| 18P LOSS MUTATED | 1 | 21 | 11 | 12 |
| 18P LOSS WILD-TYPE | 64 | 70 | 67 | 72 |
Figure S288. Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.0396 (Fisher's exact test), Q value = 0.1
Table S289. Gene #71: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 75 | 86 | 69 | 23 | 65 |
| 18P LOSS MUTATED | 7 | 19 | 10 | 0 | 9 |
| 18P LOSS WILD-TYPE | 68 | 67 | 59 | 23 | 56 |
Figure S289. Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S290. Gene #72: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 18Q LOSS MUTATED | 22 | 1 | 3 | 74 |
| 18Q LOSS WILD-TYPE | 86 | 90 | 95 | 121 |
Figure S290. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00157 (Fisher's exact test), Q value = 0.0092
Table S291. Gene #72: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 18Q LOSS MUTATED | 18 | 31 | 36 | 15 |
| 18Q LOSS WILD-TYPE | 143 | 106 | 88 | 55 |
Figure S291. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.0368 (Fisher's exact test), Q value = 0.099
Table S292. Gene #72: '18q loss' versus Molecular Subtype #3: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 105 | 51 | 44 | 51 | 58 | 38 |
| 18Q LOSS MUTATED | 12 | 15 | 6 | 10 | 14 | 11 |
| 18Q LOSS WILD-TYPE | 93 | 36 | 38 | 41 | 44 | 27 |
Figure S292. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #3: 'RPPA_CNMF'
P value = 0.00097 (Fisher's exact test), Q value = 0.0064
Table S293. Gene #72: '18q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 74 | 113 | 92 | 68 |
| 18Q LOSS MUTATED | 10 | 22 | 11 | 25 |
| 18Q LOSS WILD-TYPE | 64 | 91 | 81 | 43 |
Figure S293. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
P value = 0.00311 (Fisher's exact test), Q value = 0.015
Table S294. Gene #72: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 18Q LOSS MUTATED | 12 | 32 | 42 | 14 |
| 18Q LOSS WILD-TYPE | 83 | 109 | 105 | 94 |
Figure S294. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.0304 (Fisher's exact test), Q value = 0.087
Table S295. Gene #72: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 18Q LOSS MUTATED | 24 | 47 | 29 |
| 18Q LOSS WILD-TYPE | 147 | 158 | 86 |
Figure S295. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00137 (Fisher's exact test), Q value = 0.0084
Table S296. Gene #72: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 208 | 71 | 123 | 86 |
| 18Q LOSS MUTATED | 55 | 11 | 12 | 20 |
| 18Q LOSS WILD-TYPE | 153 | 60 | 111 | 66 |
Figure S296. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.00304 (Fisher's exact test), Q value = 0.015
Table S297. Gene #72: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 18Q LOSS MUTATED | 21 | 12 | 17 | 37 | 11 |
| 18Q LOSS WILD-TYPE | 126 | 86 | 42 | 91 | 45 |
Figure S297. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00077 (Fisher's exact test), Q value = 0.0052
Table S298. Gene #72: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 65 | 91 | 78 | 84 |
| 18Q LOSS MUTATED | 4 | 29 | 17 | 17 |
| 18Q LOSS WILD-TYPE | 61 | 62 | 61 | 67 |
Figure S298. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.00125 (Fisher's exact test), Q value = 0.0078
Table S299. Gene #72: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 75 | 86 | 69 | 23 | 65 |
| 18Q LOSS MUTATED | 8 | 31 | 13 | 2 | 13 |
| 18Q LOSS WILD-TYPE | 67 | 55 | 56 | 21 | 52 |
Figure S299. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 2e-05 (Fisher's exact test), Q value = 0.00028
Table S300. Gene #73: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 19P LOSS MUTATED | 0 | 0 | 1 | 18 |
| 19P LOSS WILD-TYPE | 108 | 91 | 97 | 177 |
Figure S300. Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.0143 (Fisher's exact test), Q value = 0.049
Table S301. Gene #73: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 208 | 71 | 123 | 86 |
| 19P LOSS MUTATED | 13 | 2 | 0 | 3 |
| 19P LOSS WILD-TYPE | 195 | 69 | 123 | 83 |
Figure S301. Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 2e-05 (Fisher's exact test), Q value = 0.00028
Table S302. Gene #74: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 19Q LOSS MUTATED | 0 | 0 | 1 | 17 |
| 19Q LOSS WILD-TYPE | 108 | 91 | 97 | 178 |
Figure S302. Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.0221 (Fisher's exact test), Q value = 0.067
Table S303. Gene #74: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 208 | 71 | 123 | 86 |
| 19Q LOSS MUTATED | 12 | 2 | 0 | 3 |
| 19Q LOSS WILD-TYPE | 196 | 69 | 123 | 83 |
Figure S303. Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.0032 (Fisher's exact test), Q value = 0.015
Table S304. Gene #75: '20p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 20P LOSS MUTATED | 3 | 4 | 3 | 9 |
| 20P LOSS WILD-TYPE | 158 | 133 | 121 | 61 |
Figure S304. Get High-res Image Gene #75: '20p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.0489 (Fisher's exact test), Q value = 0.12
Table S305. Gene #76: '20q loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 20Q LOSS MUTATED | 0 | 1 | 0 | 7 |
| 20Q LOSS WILD-TYPE | 108 | 90 | 98 | 188 |
Figure S305. Get High-res Image Gene #76: '20q loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00158 (Fisher's exact test), Q value = 0.0092
Table S306. Gene #76: '20q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| 20Q LOSS MUTATED | 0 | 1 | 2 | 5 |
| 20Q LOSS WILD-TYPE | 161 | 136 | 122 | 65 |
Figure S306. Get High-res Image Gene #76: '20q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.0428 (Fisher's exact test), Q value = 0.11
Table S307. Gene #76: '20q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 20Q LOSS MUTATED | 0 | 4 | 4 |
| 20Q LOSS WILD-TYPE | 171 | 201 | 111 |
Figure S307. Get High-res Image Gene #76: '20q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0032 (Fisher's exact test), Q value = 0.015
Table S308. Gene #77: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 21Q LOSS MUTATED | 5 | 0 | 2 | 17 |
| 21Q LOSS WILD-TYPE | 103 | 91 | 96 | 178 |
Figure S308. Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.0188 (Fisher's exact test), Q value = 0.059
Table S309. Gene #77: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 21Q LOSS MUTATED | 2 | 12 | 9 | 1 |
| 21Q LOSS WILD-TYPE | 93 | 129 | 138 | 107 |
Figure S309. Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S310. Gene #78: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| 22Q LOSS MUTATED | 6 | 2 | 2 | 37 |
| 22Q LOSS WILD-TYPE | 102 | 89 | 96 | 158 |
Figure S310. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.0149 (Fisher's exact test), Q value = 0.05
Table S311. Gene #78: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| 22Q LOSS MUTATED | 5 | 11 | 24 | 7 |
| 22Q LOSS WILD-TYPE | 90 | 130 | 123 | 101 |
Figure S311. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.0479 (Fisher's exact test), Q value = 0.12
Table S312. Gene #78: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| 22Q LOSS MUTATED | 9 | 25 | 13 |
| 22Q LOSS WILD-TYPE | 162 | 180 | 102 |
Figure S312. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0285 (Fisher's exact test), Q value = 0.083
Table S313. Gene #78: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| 22Q LOSS MUTATED | 6 | 11 | 7 | 18 | 3 |
| 22Q LOSS WILD-TYPE | 141 | 87 | 52 | 110 | 53 |
Figure S313. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0377 (Fisher's exact test), Q value = 0.1
Table S314. Gene #78: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 75 | 86 | 69 | 23 | 65 |
| 22Q LOSS MUTATED | 2 | 12 | 10 | 1 | 4 |
| 22Q LOSS WILD-TYPE | 73 | 74 | 59 | 22 | 61 |
Figure S314. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S315. Gene #79: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| XP LOSS MUTATED | 5 | 0 | 0 | 33 |
| XP LOSS WILD-TYPE | 103 | 91 | 98 | 162 |
Figure S315. Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00017 (Fisher's exact test), Q value = 0.0016
Table S316. Gene #79: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| XP LOSS MUTATED | 2 | 13 | 13 | 10 |
| XP LOSS WILD-TYPE | 159 | 124 | 111 | 60 |
Figure S316. Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 2e-05 (Fisher's exact test), Q value = 0.00028
Table S317. Gene #79: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| XP LOSS MUTATED | 0 | 13 | 23 | 2 |
| XP LOSS WILD-TYPE | 95 | 128 | 124 | 106 |
Figure S317. Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 4e-05 (Fisher's exact test), Q value = 0.00051
Table S318. Gene #79: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| XP LOSS MUTATED | 2 | 23 | 13 |
| XP LOSS WILD-TYPE | 169 | 182 | 102 |
Figure S318. Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S319. Gene #79: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 208 | 71 | 123 | 86 |
| XP LOSS MUTATED | 30 | 1 | 1 | 6 |
| XP LOSS WILD-TYPE | 178 | 70 | 122 | 80 |
Figure S319. Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.0352 (Fisher's exact test), Q value = 0.096
Table S320. Gene #79: 'xp loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| XP LOSS MUTATED | 6 | 5 | 5 | 18 | 4 |
| XP LOSS WILD-TYPE | 141 | 93 | 54 | 110 | 52 |
Figure S320. Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00575 (Fisher's exact test), Q value = 0.024
Table S321. Gene #79: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 65 | 91 | 78 | 84 |
| XP LOSS MUTATED | 0 | 9 | 2 | 9 |
| XP LOSS WILD-TYPE | 65 | 82 | 76 | 75 |
Figure S321. Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.00483 (Fisher's exact test), Q value = 0.021
Table S322. Gene #79: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 75 | 86 | 69 | 23 | 65 |
| XP LOSS MUTATED | 1 | 13 | 3 | 0 | 3 |
| XP LOSS WILD-TYPE | 74 | 73 | 66 | 23 | 62 |
Figure S322. Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S323. Gene #80: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 108 | 91 | 98 | 195 |
| XQ LOSS MUTATED | 5 | 0 | 0 | 33 |
| XQ LOSS WILD-TYPE | 103 | 91 | 98 | 162 |
Figure S323. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00017 (Fisher's exact test), Q value = 0.0016
Table S324. Gene #80: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 161 | 137 | 124 | 70 |
| XQ LOSS MUTATED | 2 | 13 | 13 | 10 |
| XQ LOSS WILD-TYPE | 159 | 124 | 111 | 60 |
Figure S324. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S325. Gene #80: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 95 | 141 | 147 | 108 |
| XQ LOSS MUTATED | 0 | 13 | 23 | 2 |
| XQ LOSS WILD-TYPE | 95 | 128 | 124 | 106 |
Figure S325. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 7e-05 (Fisher's exact test), Q value = 0.00079
Table S326. Gene #80: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 205 | 115 |
| XQ LOSS MUTATED | 2 | 23 | 13 |
| XQ LOSS WILD-TYPE | 169 | 182 | 102 |
Figure S326. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S327. Gene #80: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 208 | 71 | 123 | 86 |
| XQ LOSS MUTATED | 30 | 1 | 1 | 6 |
| XQ LOSS WILD-TYPE | 178 | 70 | 122 | 80 |
Figure S327. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.0352 (Fisher's exact test), Q value = 0.096
Table S328. Gene #80: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 147 | 98 | 59 | 128 | 56 |
| XQ LOSS MUTATED | 6 | 5 | 5 | 18 | 4 |
| XQ LOSS WILD-TYPE | 141 | 93 | 54 | 110 | 52 |
Figure S328. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00575 (Fisher's exact test), Q value = 0.024
Table S329. Gene #80: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 65 | 91 | 78 | 84 |
| XQ LOSS MUTATED | 0 | 9 | 2 | 9 |
| XQ LOSS WILD-TYPE | 65 | 82 | 76 | 75 |
Figure S329. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.00533 (Fisher's exact test), Q value = 0.023
Table S330. Gene #80: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 75 | 86 | 69 | 23 | 65 |
| XQ LOSS MUTATED | 1 | 13 | 3 | 0 | 3 |
| XQ LOSS WILD-TYPE | 74 | 73 | 66 | 23 | 62 |
Figure S330. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
-
Copy number data file = broad_values_by_arm.txt from GISTIC pipeline
-
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PRAD-TP/22533740/transformed.cor.cli.txt
-
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PRAD-TP/22553796/PRAD-TP.transferedmergedcluster.txt
-
Number of patients = 492
-
Number of significantly arm-level cnvs = 80
-
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 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.