This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.
Testing the association between copy number variation 81 arm-level events and 10 molecular subtypes across 184 patients, 253 significant findings detected with P value < 0.05 and Q value < 0.25.
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1p gain cnv correlated to 'RPPA_CNMF'.
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1q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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2p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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2q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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3p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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3q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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4p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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4q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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5p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
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5q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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6p gain cnv correlated to 'CN_CNMF'.
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6q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
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7p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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7q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
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8p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
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8q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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9p gain cnv correlated to 'CN_CNMF'.
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9q gain cnv correlated to 'CN_CNMF'.
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10p gain cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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10q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
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11p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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11q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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12p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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12q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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13q gain cnv correlated to 'CN_CNMF'.
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14q gain cnv correlated to 'CN_CNMF'.
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16p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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16q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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17p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', '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', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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18q gain cnv correlated to 'CN_CNMF'.
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19p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
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19q gain cnv correlated to 'CN_CNMF'.
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20p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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20q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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xp gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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xq gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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1p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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1q loss cnv correlated to 'CN_CNMF'.
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2p loss cnv correlated to 'CN_CNMF'.
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2q loss cnv correlated to 'CN_CNMF'.
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3p loss cnv correlated to 'CN_CNMF'.
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3q loss cnv correlated to 'CN_CNMF', 'RPPA_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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4p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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4q loss cnv correlated to 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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5p loss cnv correlated to 'CN_CNMF'.
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5q loss cnv correlated to 'CN_CNMF'.
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6p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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6q 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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8p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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8q loss cnv correlated to 'CN_CNMF'.
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9p 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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10p loss cnv correlated to 'CN_CNMF'.
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10q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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11p loss cnv correlated to 'CN_CNMF'.
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11q loss cnv correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.
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12p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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12q loss cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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13q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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14q loss cnv correlated to 'METHLYATION_CNMF'.
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15q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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16p loss cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.
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16q loss cnv correlated to 'CN_CNMF'.
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17p 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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17q loss cnv correlated to 'CN_CNMF', 'RPPA_CNMF', and 'RPPA_CHIERARCHICAL'.
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18q 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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19p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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19q loss cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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20p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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21q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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22q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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xp loss cnv correlated to 'CN_CNMF'.
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xq loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 81 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, 253 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 | |
6q loss | 83 (45%) | 101 |
1e-05 (0.000279) |
1e-05 (0.000279) |
0.0429 (0.142) |
0.374 (0.571) |
0.00038 (0.0054) |
0.00038 (0.0054) |
0.00112 (0.0105) |
1e-05 (0.000279) |
1e-05 (0.000279) |
1e-05 (0.000279) |
9p loss | 75 (41%) | 109 |
1e-05 (0.000279) |
0.0061 (0.0383) |
0.0218 (0.0916) |
0.31 (0.506) |
0.00332 (0.024) |
0.038 (0.131) |
0.0172 (0.0768) |
0.0134 (0.0653) |
0.00803 (0.0455) |
0.00718 (0.0421) |
17p loss | 80 (43%) | 104 |
1e-05 (0.000279) |
1e-05 (0.000279) |
0.0114 (0.0595) |
0.191 (0.385) |
1e-05 (0.000279) |
1e-05 (0.000279) |
1e-05 (0.000279) |
5e-05 (0.00101) |
1e-05 (0.000279) |
1e-05 (0.000279) |
18q loss | 106 (58%) | 78 |
1e-05 (0.000279) |
0.00029 (0.00467) |
0.0358 (0.128) |
0.592 (0.754) |
0.0021 (0.0172) |
0.00505 (0.0333) |
0.015 (0.0708) |
0.00311 (0.0231) |
0.0469 (0.151) |
5e-05 (0.00101) |
1q gain | 50 (27%) | 134 |
0.00798 (0.0455) |
6e-05 (0.00116) |
0.328 (0.526) |
0.28 (0.473) |
0.0121 (0.0623) |
0.0639 (0.188) |
0.00551 (0.036) |
0.0376 (0.13) |
0.0003 (0.00467) |
0.0117 (0.061) |
17p gain | 9 (5%) | 175 |
4e-05 (0.000876) |
0.0188 (0.082) |
0.453 (0.637) |
0.423 (0.626) |
0.00246 (0.0192) |
0.0007 (0.00777) |
0.00103 (0.0101) |
0.00254 (0.0194) |
0.222 (0.419) |
0.00956 (0.0516) |
1p loss | 36 (20%) | 148 |
3e-05 (0.000675) |
1e-05 (0.000279) |
0.00191 (0.0161) |
0.00397 (0.027) |
0.0097 (0.052) |
0.0637 (0.188) |
0.164 (0.348) |
0.0505 (0.161) |
0.0289 (0.109) |
0.0237 (0.0943) |
8p loss | 41 (22%) | 143 |
0.00102 (0.0101) |
0.00346 (0.0246) |
0.523 (0.701) |
0.34 (0.537) |
0.146 (0.326) |
0.0047 (0.0315) |
0.0155 (0.0723) |
0.0124 (0.0623) |
0.00686 (0.0407) |
0.00231 (0.0184) |
12p loss | 20 (11%) | 164 |
0.0002 (0.00337) |
0.0371 (0.129) |
0.00073 (0.00799) |
0.00098 (0.0098) |
0.0616 (0.187) |
0.00824 (0.0463) |
0.0845 (0.229) |
0.00098 (0.0098) |
0.343 (0.54) |
0.00166 (0.0145) |
20p loss | 20 (11%) | 164 |
0.00033 (0.00486) |
0.0451 (0.146) |
0.689 (0.825) |
0.686 (0.825) |
0.00651 (0.0398) |
0.0919 (0.244) |
0.0369 (0.129) |
0.0395 (0.135) |
0.00188 (0.0161) |
0.0139 (0.0672) |
16p gain | 22 (12%) | 162 |
2e-05 (0.000523) |
0.00074 (0.00799) |
0.0252 (0.0977) |
0.0904 (0.241) |
0.155 (0.338) |
0.0585 (0.18) |
0.0686 (0.197) |
0.014 (0.0672) |
0.00201 (0.0166) |
0.0297 (0.111) |
16q gain | 23 (12%) | 161 |
1e-05 (0.000279) |
0.00027 (0.00446) |
0.37 (0.567) |
0.577 (0.742) |
0.106 (0.265) |
0.0551 (0.172) |
0.0139 (0.0672) |
0.00078 (0.00831) |
0.00252 (0.0194) |
0.00323 (0.0238) |
6p loss | 64 (35%) | 120 |
3e-05 (0.000675) |
0.00011 (0.00194) |
0.151 (0.332) |
0.357 (0.557) |
0.135 (0.309) |
0.0142 (0.0678) |
0.22 (0.419) |
0.00108 (0.0103) |
0.00333 (0.024) |
0.00012 (0.00207) |
13q loss | 20 (11%) | 164 |
0.00046 (0.00591) |
0.009 (0.0493) |
0.83 (0.911) |
0.823 (0.907) |
0.00305 (0.0229) |
0.156 (0.338) |
0.0229 (0.0929) |
0.013 (0.0642) |
0.00191 (0.0161) |
0.0638 (0.188) |
15q loss | 30 (16%) | 154 |
5e-05 (0.00101) |
0.00879 (0.0484) |
0.401 (0.597) |
0.358 (0.557) |
0.0211 (0.09) |
0.00197 (0.0165) |
0.0794 (0.218) |
0.00611 (0.0383) |
0.106 (0.265) |
0.00372 (0.0257) |
19p loss | 19 (10%) | 165 |
0.00128 (0.0118) |
0.0223 (0.0928) |
0.29 (0.485) |
0.809 (0.905) |
0.0622 (0.187) |
0.0247 (0.0972) |
0.389 (0.583) |
0.00614 (0.0383) |
0.00033 (0.00486) |
0.0194 (0.0838) |
21q loss | 58 (32%) | 126 |
1e-05 (0.000279) |
0.0225 (0.0929) |
0.348 (0.547) |
0.459 (0.641) |
0.0219 (0.0916) |
0.0938 (0.248) |
0.389 (0.583) |
0.032 (0.118) |
0.00044 (0.00588) |
0.0362 (0.128) |
4p gain | 11 (6%) | 173 |
0.0156 (0.0723) |
0.578 (0.742) |
0.754 (0.876) |
0.304 (0.498) |
0.00138 (0.0126) |
0.0101 (0.0533) |
0.0352 (0.126) |
0.0207 (0.0888) |
0.779 (0.888) |
0.208 (0.408) |
4q gain | 8 (4%) | 176 |
0.0006 (0.00715) |
0.223 (0.42) |
0.755 (0.876) |
0.302 (0.496) |
0.0218 (0.0916) |
0.0348 (0.125) |
0.0227 (0.0929) |
0.039 (0.134) |
0.52 (0.697) |
0.151 (0.332) |
18p gain | 28 (15%) | 156 |
1e-05 (0.000279) |
0.0188 (0.082) |
0.165 (0.348) |
0.128 (0.302) |
0.026 (0.1) |
0.198 (0.395) |
0.147 (0.326) |
0.0227 (0.0929) |
0.0341 (0.124) |
0.103 (0.262) |
22q loss | 46 (25%) | 138 |
1e-05 (0.000279) |
0.0056 (0.0363) |
0.764 (0.879) |
0.687 (0.825) |
0.22 (0.419) |
0.375 (0.571) |
0.31 (0.506) |
0.0407 (0.137) |
0.00105 (0.0101) |
0.0285 (0.108) |
2q gain | 16 (9%) | 168 |
0.0361 (0.128) |
0.00152 (0.0136) |
0.178 (0.366) |
0.0967 (0.252) |
0.464 (0.646) |
0.181 (0.373) |
0.514 (0.692) |
0.00476 (0.0316) |
0.197 (0.394) |
0.0407 (0.137) |
7p gain | 52 (28%) | 132 |
1e-05 (0.000279) |
0.0161 (0.0735) |
0.0583 (0.18) |
0.378 (0.573) |
0.352 (0.551) |
0.268 (0.463) |
0.279 (0.473) |
0.0471 (0.151) |
0.006 (0.0383) |
0.165 (0.348) |
10p gain | 10 (5%) | 174 |
0.036 (0.128) |
0.201 (0.398) |
0.0269 (0.103) |
0.0274 (0.104) |
0.214 (0.415) |
0.814 (0.906) |
0.473 (0.654) |
0.901 (0.959) |
0.00079 (0.00831) |
1 (1.00) |
12q gain | 22 (12%) | 162 |
1e-05 (0.000279) |
0.0169 (0.0756) |
0.0654 (0.19) |
0.721 (0.851) |
0.586 (0.749) |
0.113 (0.278) |
0.207 (0.407) |
0.0419 (0.14) |
0.00417 (0.0281) |
0.155 (0.338) |
20p gain | 34 (18%) | 150 |
1e-05 (0.000279) |
0.0177 (0.0782) |
0.135 (0.309) |
0.221 (0.419) |
0.229 (0.428) |
0.156 (0.338) |
0.221 (0.419) |
0.0165 (0.0752) |
0.00622 (0.0385) |
0.254 (0.456) |
20q gain | 45 (24%) | 139 |
1e-05 (0.000279) |
0.0313 (0.116) |
0.425 (0.627) |
0.159 (0.34) |
0.543 (0.717) |
0.176 (0.365) |
0.333 (0.531) |
0.0236 (0.0943) |
0.0004 (0.00559) |
0.209 (0.408) |
xp gain | 8 (4%) | 176 |
3e-05 (0.000675) |
0.222 (0.419) |
0.294 (0.49) |
0.0721 (0.202) |
0.124 (0.297) |
0.0344 (0.125) |
0.0429 (0.142) |
0.0405 (0.137) |
0.722 (0.851) |
0.0711 (0.201) |
4p loss | 25 (14%) | 159 |
0.0432 (0.142) |
0.00667 (0.0403) |
0.339 (0.537) |
0.767 (0.881) |
0.104 (0.264) |
0.102 (0.261) |
0.578 (0.742) |
0.0126 (0.0629) |
0.957 (0.994) |
0.00354 (0.0249) |
12q loss | 28 (15%) | 156 |
1e-05 (0.000279) |
0.0611 (0.186) |
0.00689 (0.0407) |
0.0834 (0.227) |
0.156 (0.338) |
0.00236 (0.0186) |
0.121 (0.293) |
0.12 (0.291) |
0.241 (0.443) |
0.0244 (0.0963) |
19q loss | 12 (7%) | 172 |
0.00653 (0.0398) |
0.132 (0.307) |
0.00232 (0.0184) |
0.156 (0.338) |
0.0399 (0.136) |
0.0145 (0.0685) |
0.489 (0.665) |
0.0522 (0.165) |
0.096 (0.252) |
0.0743 (0.207) |
2p gain | 14 (8%) | 170 |
0.0214 (0.0907) |
0.00069 (0.00776) |
0.175 (0.364) |
0.0968 (0.252) |
0.633 (0.791) |
0.188 (0.382) |
0.441 (0.634) |
0.0156 (0.0723) |
0.128 (0.302) |
0.0999 (0.258) |
5q gain | 20 (11%) | 164 |
1e-05 (0.000279) |
0.486 (0.664) |
0.834 (0.912) |
0.672 (0.818) |
0.326 (0.524) |
0.00987 (0.0526) |
0.111 (0.273) |
0.0346 (0.125) |
0.114 (0.28) |
0.145 (0.326) |
8q gain | 48 (26%) | 136 |
3e-05 (0.000675) |
0.00828 (0.0463) |
0.72 (0.851) |
0.623 (0.781) |
0.297 (0.491) |
0.546 (0.718) |
0.397 (0.593) |
0.0794 (0.218) |
0.00114 (0.0106) |
0.0676 (0.196) |
12p gain | 30 (16%) | 154 |
1e-05 (0.000279) |
0.00091 (0.00945) |
0.142 (0.32) |
0.727 (0.855) |
0.675 (0.821) |
0.257 (0.459) |
0.109 (0.269) |
0.0698 (0.199) |
0.00221 (0.0179) |
0.459 (0.641) |
xq gain | 13 (7%) | 171 |
0.0003 (0.00467) |
0.69 (0.826) |
0.222 (0.419) |
0.711 (0.843) |
0.127 (0.301) |
0.00944 (0.0513) |
0.162 (0.344) |
0.0369 (0.129) |
0.812 (0.905) |
0.0867 (0.233) |
3q loss | 19 (10%) | 165 |
0.0329 (0.121) |
0.425 (0.627) |
0.0131 (0.0643) |
0.0681 (0.196) |
0.533 (0.707) |
0.672 (0.818) |
0.786 (0.891) |
1 (1.00) |
0.00733 (0.0427) |
0.854 (0.922) |
4q loss | 25 (14%) | 159 |
0.248 (0.45) |
0.0192 (0.0834) |
0.553 (0.725) |
0.27 (0.464) |
0.0549 (0.172) |
0.182 (0.373) |
0.201 (0.398) |
0.00285 (0.0216) |
0.71 (0.843) |
0.00097 (0.0098) |
17q loss | 22 (12%) | 162 |
0.00061 (0.00716) |
0.221 (0.419) |
0.0438 (0.144) |
0.025 (0.0976) |
0.157 (0.338) |
0.387 (0.583) |
0.518 (0.695) |
0.313 (0.507) |
0.177 (0.365) |
0.318 (0.514) |
3p gain | 10 (5%) | 174 |
0.0123 (0.0623) |
0.00802 (0.0455) |
0.268 (0.463) |
0.245 (0.446) |
0.539 (0.712) |
0.614 (0.775) |
0.839 (0.914) |
0.445 (0.637) |
0.529 (0.704) |
0.528 (0.704) |
3q gain | 20 (11%) | 164 |
0.00044 (0.00588) |
3e-05 (0.000675) |
0.201 (0.398) |
0.322 (0.519) |
0.265 (0.462) |
0.279 (0.473) |
0.773 (0.885) |
0.0607 (0.186) |
0.174 (0.364) |
0.264 (0.462) |
5p gain | 28 (15%) | 156 |
1e-05 (0.000279) |
0.36 (0.558) |
0.677 (0.822) |
0.776 (0.887) |
0.669 (0.818) |
0.158 (0.34) |
0.241 (0.443) |
0.126 (0.299) |
0.00683 (0.0407) |
0.455 (0.638) |
6q gain | 5 (3%) | 179 |
0.016 (0.0735) |
0.654 (0.809) |
0.853 (0.922) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.031 (0.115) |
0.451 (0.637) |
||
7q gain | 48 (26%) | 136 |
2e-05 (0.000523) |
0.0838 (0.228) |
0.169 (0.354) |
0.491 (0.666) |
0.755 (0.876) |
0.261 (0.462) |
0.669 (0.818) |
0.342 (0.538) |
0.0237 (0.0943) |
0.448 (0.637) |
8p gain | 26 (14%) | 158 |
0.00357 (0.0249) |
0.0961 (0.252) |
0.823 (0.907) |
0.353 (0.551) |
0.757 (0.876) |
0.958 (0.994) |
0.223 (0.419) |
0.555 (0.727) |
0.0123 (0.0623) |
0.662 (0.814) |
10q gain | 13 (7%) | 171 |
0.0272 (0.104) |
0.0571 (0.178) |
0.0581 (0.18) |
0.133 (0.308) |
0.147 (0.326) |
0.378 (0.573) |
0.296 (0.491) |
0.913 (0.966) |
0.00045 (0.00588) |
1 (1.00) |
11p gain | 13 (7%) | 171 |
0.00063 (0.00729) |
0.0451 (0.146) |
0.144 (0.326) |
0.821 (0.907) |
0.756 (0.876) |
1 (1.00) |
0.729 (0.855) |
0.791 (0.892) |
0.428 (0.628) |
0.754 (0.876) |
11q gain | 15 (8%) | 169 |
0.0059 (0.0379) |
0.0124 (0.0623) |
0.0644 (0.189) |
0.225 (0.421) |
0.939 (0.982) |
0.937 (0.981) |
0.501 (0.677) |
0.532 (0.707) |
0.284 (0.477) |
0.182 (0.373) |
19p gain | 17 (9%) | 167 |
0.00067 (0.00764) |
0.691 (0.826) |
0.553 (0.725) |
0.109 (0.269) |
0.681 (0.824) |
0.62 (0.78) |
0.0128 (0.0636) |
0.335 (0.532) |
0.382 (0.578) |
0.598 (0.759) |
10q loss | 30 (16%) | 154 |
8e-05 (0.00147) |
0.898 (0.958) |
0.758 (0.876) |
0.756 (0.876) |
0.184 (0.375) |
0.0167 (0.0753) |
0.53 (0.704) |
0.334 (0.531) |
0.228 (0.426) |
0.0991 (0.256) |
11q loss | 16 (9%) | 168 |
0.0006 (0.00715) |
0.658 (0.811) |
0.133 (0.308) |
0.0463 (0.15) |
0.783 (0.89) |
0.819 (0.907) |
0.929 (0.976) |
0.574 (0.742) |
0.399 (0.595) |
0.821 (0.907) |
16p loss | 11 (6%) | 173 |
0.00843 (0.0468) |
0.574 (0.742) |
0.0232 (0.0936) |
0.151 (0.332) |
0.671 (0.818) |
0.489 (0.665) |
0.634 (0.791) |
0.426 (0.627) |
0.278 (0.473) |
0.836 (0.913) |
xq loss | 18 (10%) | 166 |
1e-05 (0.000279) |
0.0448 (0.146) |
0.471 (0.653) |
0.101 (0.26) |
0.367 (0.565) |
0.33 (0.528) |
0.266 (0.462) |
0.833 (0.912) |
0.493 (0.667) |
0.588 (0.75) |
1p gain | 18 (10%) | 166 |
0.428 (0.628) |
0.078 (0.216) |
0.031 (0.115) |
0.0711 (0.201) |
0.759 (0.876) |
0.736 (0.863) |
1 (1.00) |
0.938 (0.981) |
0.134 (0.309) |
0.893 (0.955) |
6p gain | 7 (4%) | 177 |
0.00054 (0.00673) |
0.528 (0.704) |
0.485 (0.664) |
0.24 (0.442) |
0.888 (0.953) |
1 (1.00) |
0.907 (0.962) |
0.875 (0.94) |
0.0602 (0.185) |
1 (1.00) |
9p gain | 8 (4%) | 176 |
0.0109 (0.0572) |
1 (1.00) |
0.791 (0.892) |
0.211 (0.412) |
0.593 (0.754) |
0.638 (0.795) |
0.681 (0.824) |
0.789 (0.892) |
0.578 (0.742) |
0.448 (0.637) |
9q gain | 12 (7%) | 172 |
8e-05 (0.00147) |
0.659 (0.811) |
0.962 (0.996) |
0.834 (0.912) |
0.927 (0.975) |
0.613 (0.774) |
0.63 (0.789) |
0.263 (0.462) |
0.264 (0.462) |
0.284 (0.477) |
13q gain | 29 (16%) | 155 |
0.0167 (0.0753) |
0.787 (0.891) |
0.464 (0.646) |
0.453 (0.637) |
0.212 (0.412) |
0.474 (0.655) |
0.218 (0.419) |
0.126 (0.299) |
0.434 (0.63) |
0.793 (0.893) |
14q gain | 26 (14%) | 158 |
1e-05 (0.000279) |
0.222 (0.419) |
0.824 (0.907) |
0.844 (0.918) |
0.276 (0.471) |
0.574 (0.742) |
0.171 (0.359) |
0.265 (0.462) |
0.105 (0.265) |
0.924 (0.974) |
17q gain | 17 (9%) | 167 |
0.00045 (0.00588) |
0.248 (0.45) |
0.987 (1.00) |
0.864 (0.93) |
0.19 (0.384) |
0.0624 (0.187) |
0.0975 (0.253) |
0.0718 (0.202) |
0.122 (0.293) |
0.244 (0.446) |
18q gain | 12 (7%) | 172 |
6e-05 (0.00116) |
0.684 (0.825) |
0.443 (0.636) |
0.244 (0.446) |
0.378 (0.573) |
0.49 (0.665) |
0.479 (0.659) |
0.125 (0.299) |
0.361 (0.559) |
0.0863 (0.233) |
19q gain | 28 (15%) | 156 |
0.00053 (0.00671) |
0.316 (0.511) |
0.583 (0.746) |
0.0769 (0.213) |
0.896 (0.957) |
0.889 (0.953) |
0.0689 (0.197) |
0.688 (0.825) |
0.106 (0.265) |
1 (1.00) |
1q loss | 8 (4%) | 176 |
0.0413 (0.138) |
0.411 (0.609) |
0.812 (0.905) |
0.233 (0.433) |
1 (1.00) |
0.511 (0.689) |
0.759 (0.876) |
0.697 (0.831) |
0.103 (0.262) |
0.783 (0.89) |
2p loss | 11 (6%) | 173 |
0.0076 (0.044) |
0.577 (0.742) |
0.679 (0.824) |
0.815 (0.906) |
0.67 (0.818) |
0.193 (0.386) |
0.92 (0.972) |
0.761 (0.877) |
0.266 (0.462) |
0.849 (0.921) |
2q loss | 5 (3%) | 179 |
0.00056 (0.00687) |
0.759 (0.876) |
0.453 (0.637) |
0.0895 (0.239) |
0.45 (0.637) |
0.292 (0.487) |
0.159 (0.34) |
0.362 (0.559) |
||
3p loss | 36 (20%) | 148 |
0.00163 (0.0144) |
0.0504 (0.161) |
0.453 (0.637) |
0.305 (0.499) |
0.651 (0.807) |
0.906 (0.962) |
0.208 (0.408) |
0.3 (0.494) |
0.106 (0.265) |
0.556 (0.727) |
5p loss | 9 (5%) | 175 |
0.00335 (0.024) |
0.855 (0.922) |
0.813 (0.905) |
0.853 (0.922) |
0.91 (0.965) |
0.239 (0.442) |
0.844 (0.918) |
1 (1.00) |
0.159 (0.34) |
0.805 (0.903) |
5q loss | 13 (7%) | 171 |
0.00375 (0.0257) |
0.261 (0.462) |
0.409 (0.608) |
0.451 (0.637) |
0.935 (0.981) |
0.251 (0.451) |
0.622 (0.781) |
0.448 (0.637) |
0.137 (0.311) |
0.604 (0.765) |
8q loss | 16 (9%) | 168 |
0.0183 (0.0806) |
0.28 (0.473) |
0.395 (0.591) |
0.655 (0.809) |
0.794 (0.893) |
0.437 (0.633) |
0.333 (0.531) |
0.452 (0.637) |
0.0511 (0.162) |
0.169 (0.354) |
10p loss | 36 (20%) | 148 |
0.00031 (0.00474) |
0.297 (0.491) |
0.574 (0.742) |
0.996 (1.00) |
0.159 (0.34) |
0.192 (0.386) |
0.37 (0.567) |
0.148 (0.328) |
0.0621 (0.187) |
0.0955 (0.252) |
11p loss | 17 (9%) | 167 |
0.00153 (0.0136) |
0.13 (0.306) |
0.471 (0.653) |
0.457 (0.64) |
0.943 (0.983) |
0.685 (0.825) |
0.476 (0.655) |
0.482 (0.662) |
0.475 (0.655) |
0.727 (0.855) |
14q loss | 16 (9%) | 168 |
0.237 (0.44) |
0.0229 (0.0929) |
0.19 (0.384) |
0.571 (0.742) |
0.494 (0.668) |
0.0739 (0.206) |
0.375 (0.571) |
0.219 (0.419) |
0.77 (0.883) |
0.583 (0.746) |
16q loss | 13 (7%) | 171 |
0.0251 (0.0976) |
0.941 (0.982) |
0.485 (0.664) |
0.922 (0.972) |
0.708 (0.842) |
0.121 (0.293) |
0.431 (0.63) |
0.245 (0.446) |
0.132 (0.307) |
0.281 (0.474) |
xp loss | 27 (15%) | 157 |
9e-05 (0.00162) |
0.135 (0.309) |
0.104 (0.264) |
0.3 (0.494) |
0.438 (0.633) |
0.288 (0.482) |
0.136 (0.31) |
0.957 (0.994) |
0.25 (0.45) |
0.694 (0.828) |
15q gain | 14 (8%) | 170 |
0.0883 (0.237) |
0.0632 (0.188) |
0.185 (0.377) |
0.784 (0.891) |
0.341 (0.538) |
0.131 (0.306) |
0.249 (0.45) |
1 (1.00) |
0.253 (0.454) |
0.867 (0.933) |
22q gain | 8 (4%) | 176 |
0.352 (0.551) |
0.063 (0.188) |
0.438 (0.633) |
0.644 (0.8) |
0.108 (0.268) |
0.0799 (0.219) |
0.366 (0.563) |
0.0653 (0.19) |
0.146 (0.326) |
0.27 (0.464) |
7p loss | 3 (2%) | 181 |
0.175 (0.364) |
0.617 (0.778) |
0.798 (0.896) |
0.773 (0.885) |
0.427 (0.628) |
1 (1.00) |
0.433 (0.63) |
0.315 (0.511) |
||
7q loss | 4 (2%) | 180 |
0.0712 (0.201) |
0.238 (0.441) |
0.433 (0.63) |
0.713 (0.844) |
0.807 (0.904) |
1 (1.00) |
0.539 (0.712) |
1 (1.00) |
0.261 (0.462) |
0.562 (0.733) |
9q loss | 43 (23%) | 141 |
0.116 (0.282) |
0.545 (0.718) |
0.257 (0.459) |
0.432 (0.63) |
0.272 (0.466) |
0.44 (0.634) |
0.199 (0.396) |
0.265 (0.462) |
0.218 (0.419) |
0.311 (0.506) |
18p loss | 55 (30%) | 129 |
0.13 (0.304) |
0.268 (0.463) |
0.822 (0.907) |
0.95 (0.989) |
0.645 (0.8) |
0.639 (0.795) |
0.365 (0.562) |
0.901 (0.959) |
0.27 (0.464) |
0.274 (0.468) |
20q loss | 5 (3%) | 179 |
0.265 (0.462) |
0.0673 (0.195) |
0.384 (0.579) |
0.846 (0.918) |
0.92 (0.972) |
0.825 (0.907) |
0.129 (0.303) |
0.605 (0.765) |
P value = 0.031 (Fisher's exact test), Q value = 0.12
Table S1. Gene #1: '1p gain' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 35 | 20 | 16 | 18 | 16 |
1P GAIN MUTATED | 1 | 3 | 5 | 1 | 1 |
1P GAIN WILD-TYPE | 34 | 17 | 11 | 17 | 15 |
Figure S1. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

P value = 0.00798 (Fisher's exact test), Q value = 0.045
Table S2. Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
1Q GAIN MUTATED | 14 | 28 | 8 |
1Q GAIN WILD-TYPE | 71 | 47 | 16 |
Figure S2. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0012
Table S3. Gene #2: '1q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
1Q GAIN MUTATED | 23 | 5 | 16 | 6 |
1Q GAIN WILD-TYPE | 22 | 42 | 34 | 35 |
Figure S3. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.062
Table S4. Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 83 | 48 | 46 |
1Q GAIN MUTATED | 28 | 14 | 5 |
1Q GAIN WILD-TYPE | 55 | 34 | 41 |
Figure S4. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 0.00551 (Fisher's exact test), Q value = 0.036
Table S5. Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 69 | 40 | 35 | 33 |
1Q GAIN MUTATED | 27 | 11 | 6 | 3 |
1Q GAIN WILD-TYPE | 42 | 29 | 29 | 30 |
Figure S5. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 0.0376 (Fisher's exact test), Q value = 0.13
Table S6. Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
1Q GAIN MUTATED | 34 | 9 | 4 |
1Q GAIN WILD-TYPE | 68 | 33 | 29 |
Figure S6. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0047
Table S7. Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 67 | 37 |
1Q GAIN MUTATED | 29 | 8 | 9 |
1Q GAIN WILD-TYPE | 40 | 59 | 28 |
Figure S7. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 0.061
Table S8. Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 86 | 47 | 40 |
1Q GAIN MUTATED | 25 | 17 | 4 |
1Q GAIN WILD-TYPE | 61 | 30 | 36 |
Figure S8. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0214 (Fisher's exact test), Q value = 0.091
Table S9. Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
2P GAIN MUTATED | 2 | 10 | 2 |
2P GAIN WILD-TYPE | 83 | 65 | 22 |
Figure S9. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0078
Table S10. Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
2P GAIN MUTATED | 6 | 0 | 8 | 0 |
2P GAIN WILD-TYPE | 39 | 47 | 42 | 41 |
Figure S10. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.072
Table S11. Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
2P GAIN MUTATED | 13 | 0 | 1 |
2P GAIN WILD-TYPE | 89 | 42 | 32 |
Figure S11. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.0361 (Fisher's exact test), Q value = 0.13
Table S12. Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
2Q GAIN MUTATED | 3 | 11 | 2 |
2Q GAIN WILD-TYPE | 82 | 64 | 22 |
Figure S12. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00152 (Fisher's exact test), Q value = 0.014
Table S13. Gene #4: '2q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
2Q GAIN MUTATED | 6 | 0 | 9 | 1 |
2Q GAIN WILD-TYPE | 39 | 47 | 41 | 40 |
Figure S13. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00476 (Fisher's exact test), Q value = 0.032
Table S14. Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
2Q GAIN MUTATED | 15 | 0 | 1 |
2Q GAIN WILD-TYPE | 87 | 42 | 32 |
Figure S14. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.0407 (Fisher's exact test), Q value = 0.14
Table S15. Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 86 | 47 | 40 |
2Q GAIN MUTATED | 13 | 2 | 1 |
2Q GAIN WILD-TYPE | 73 | 45 | 39 |
Figure S15. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0123 (Fisher's exact test), Q value = 0.062
Table S16. Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
3P GAIN MUTATED | 1 | 5 | 4 |
3P GAIN WILD-TYPE | 84 | 70 | 20 |
Figure S16. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00802 (Fisher's exact test), Q value = 0.045
Table S17. Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
3P GAIN MUTATED | 5 | 0 | 5 | 0 |
3P GAIN WILD-TYPE | 40 | 47 | 45 | 41 |
Figure S17. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0059
Table S18. Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
3Q GAIN MUTATED | 3 | 9 | 8 |
3Q GAIN WILD-TYPE | 82 | 66 | 16 |
Figure S18. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00067
Table S19. Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
3Q GAIN MUTATED | 9 | 0 | 11 | 0 |
3Q GAIN WILD-TYPE | 36 | 47 | 39 | 41 |
Figure S19. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.072
Table S20. Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
4P GAIN MUTATED | 3 | 3 | 5 |
4P GAIN WILD-TYPE | 82 | 72 | 19 |
Figure S20. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00138 (Fisher's exact test), Q value = 0.013
Table S21. Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 83 | 48 | 46 |
4P GAIN MUTATED | 3 | 0 | 8 |
4P GAIN WILD-TYPE | 80 | 48 | 38 |
Figure S21. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.053
Table S22. Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 74 | 75 | 28 |
4P GAIN MUTATED | 1 | 5 | 5 |
4P GAIN WILD-TYPE | 73 | 70 | 23 |
Figure S22. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.0352 (Fisher's exact test), Q value = 0.13
Table S23. Gene #7: '4p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 69 | 40 | 35 | 33 |
4P GAIN MUTATED | 3 | 1 | 1 | 6 |
4P GAIN WILD-TYPE | 66 | 39 | 34 | 27 |
Figure S23. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.089
Table S24. Gene #7: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
4P GAIN MUTATED | 6 | 0 | 5 |
4P GAIN WILD-TYPE | 96 | 42 | 28 |
Figure S24. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.0071
Table S25. Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
4Q GAIN MUTATED | 1 | 2 | 5 |
4Q GAIN WILD-TYPE | 84 | 73 | 19 |
Figure S25. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.092
Table S26. Gene #8: '4q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 83 | 48 | 46 |
4Q GAIN MUTATED | 3 | 0 | 5 |
4Q GAIN WILD-TYPE | 80 | 48 | 41 |
Figure S26. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 0.0348 (Fisher's exact test), Q value = 0.13
Table S27. Gene #8: '4q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 74 | 75 | 28 |
4Q GAIN MUTATED | 1 | 3 | 4 |
4Q GAIN WILD-TYPE | 73 | 72 | 24 |
Figure S27. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.0227 (Fisher's exact test), Q value = 0.093
Table S28. Gene #8: '4q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 69 | 40 | 35 | 33 |
4Q GAIN MUTATED | 2 | 1 | 0 | 5 |
4Q GAIN WILD-TYPE | 67 | 39 | 35 | 28 |
Figure S28. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 0.039 (Fisher's exact test), Q value = 0.13
Table S29. Gene #8: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
4Q GAIN MUTATED | 4 | 0 | 4 |
4Q GAIN WILD-TYPE | 98 | 42 | 29 |
Figure S29. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028
Table S30. Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
5P GAIN MUTATED | 3 | 11 | 14 |
5P GAIN WILD-TYPE | 82 | 64 | 10 |
Figure S30. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00683 (Fisher's exact test), Q value = 0.041
Table S31. Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 67 | 37 |
5P GAIN MUTATED | 14 | 4 | 10 |
5P GAIN WILD-TYPE | 55 | 63 | 27 |
Figure S31. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028
Table S32. Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
5Q GAIN MUTATED | 2 | 7 | 11 |
5Q GAIN WILD-TYPE | 83 | 68 | 13 |
Figure S32. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00987 (Fisher's exact test), Q value = 0.053
Table S33. Gene #10: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 74 | 75 | 28 |
5Q GAIN MUTATED | 7 | 5 | 8 |
5Q GAIN WILD-TYPE | 67 | 70 | 20 |
Figure S33. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.0346 (Fisher's exact test), Q value = 0.13
Table S34. Gene #10: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
5Q GAIN MUTATED | 10 | 2 | 8 |
5Q GAIN WILD-TYPE | 92 | 40 | 25 |
Figure S34. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.0067
Table S35. Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
6P GAIN MUTATED | 1 | 1 | 5 |
6P GAIN WILD-TYPE | 84 | 74 | 19 |
Figure S35. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.074
Table S36. Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
6Q GAIN MUTATED | 1 | 1 | 3 |
6Q GAIN WILD-TYPE | 84 | 74 | 21 |
Figure S36. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.031 (Fisher's exact test), Q value = 0.12
Table S37. Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 67 | 37 |
6Q GAIN MUTATED | 1 | 0 | 3 |
6Q GAIN WILD-TYPE | 68 | 67 | 34 |
Figure S37. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028
Table S38. Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
7P GAIN MUTATED | 12 | 23 | 17 |
7P GAIN WILD-TYPE | 73 | 52 | 7 |
Figure S38. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.074
Table S39. Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
7P GAIN MUTATED | 18 | 9 | 18 | 6 |
7P GAIN WILD-TYPE | 27 | 38 | 32 | 35 |
Figure S39. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0471 (Fisher's exact test), Q value = 0.15
Table S40. Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
7P GAIN MUTATED | 36 | 7 | 7 |
7P GAIN WILD-TYPE | 66 | 35 | 26 |
Figure S40. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.006 (Fisher's exact test), Q value = 0.038
Table S41. Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 67 | 37 |
7P GAIN MUTATED | 26 | 10 | 13 |
7P GAIN WILD-TYPE | 43 | 57 | 24 |
Figure S41. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00052
Table S42. Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
7Q GAIN MUTATED | 12 | 20 | 16 |
7Q GAIN WILD-TYPE | 73 | 55 | 8 |
Figure S42. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 0.094
Table S43. Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 67 | 37 |
7Q GAIN MUTATED | 22 | 10 | 13 |
7Q GAIN WILD-TYPE | 47 | 57 | 24 |
Figure S43. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.00357 (Fisher's exact test), Q value = 0.025
Table S44. Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
8P GAIN MUTATED | 5 | 14 | 7 |
8P GAIN WILD-TYPE | 80 | 61 | 17 |
Figure S44. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.062
Table S45. Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 67 | 37 |
8P GAIN MUTATED | 11 | 4 | 10 |
8P GAIN WILD-TYPE | 58 | 63 | 27 |
Figure S45. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00067
Table S46. Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
8Q GAIN MUTATED | 10 | 25 | 13 |
8Q GAIN WILD-TYPE | 75 | 50 | 11 |
Figure S46. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00828 (Fisher's exact test), Q value = 0.046
Table S47. Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
8Q GAIN MUTATED | 18 | 8 | 16 | 5 |
8Q GAIN WILD-TYPE | 27 | 39 | 34 | 36 |
Figure S47. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00114 (Fisher's exact test), Q value = 0.011
Table S48. Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 67 | 37 |
8Q GAIN MUTATED | 23 | 8 | 15 |
8Q GAIN WILD-TYPE | 46 | 59 | 22 |
Figure S48. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.057
Table S49. Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
9P GAIN MUTATED | 1 | 3 | 4 |
9P GAIN WILD-TYPE | 84 | 72 | 20 |
Figure S49. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0015
Table S50. Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
9Q GAIN MUTATED | 0 | 6 | 6 |
9Q GAIN WILD-TYPE | 85 | 69 | 18 |
Figure S50. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.036 (Fisher's exact test), Q value = 0.13
Table S51. Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
10P GAIN MUTATED | 1 | 7 | 2 |
10P GAIN WILD-TYPE | 84 | 68 | 22 |
Figure S51. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0269 (Fisher's exact test), Q value = 0.1
Table S52. Gene #19: '10p gain' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 35 | 20 | 16 | 18 | 16 |
10P GAIN MUTATED | 6 | 0 | 0 | 0 | 0 |
10P GAIN WILD-TYPE | 29 | 20 | 16 | 18 | 16 |
Figure S52. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

P value = 0.0274 (Fisher's exact test), Q value = 0.1
Table S53. Gene #19: '10p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 12 | 20 | 22 | 15 | 11 | 18 | 7 |
10P GAIN MUTATED | 1 | 0 | 3 | 0 | 0 | 0 | 2 |
10P GAIN WILD-TYPE | 11 | 20 | 19 | 15 | 11 | 18 | 5 |
Figure S53. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.0083
Table S54. Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 67 | 37 |
10P GAIN MUTATED | 2 | 0 | 6 |
10P GAIN WILD-TYPE | 67 | 67 | 31 |
Figure S54. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.0272 (Fisher's exact test), Q value = 0.1
Table S55. Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
10Q GAIN MUTATED | 2 | 7 | 4 |
10Q GAIN WILD-TYPE | 83 | 68 | 20 |
Figure S55. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0059
Table S56. Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 67 | 37 |
10Q GAIN MUTATED | 3 | 0 | 7 |
10Q GAIN WILD-TYPE | 66 | 67 | 30 |
Figure S56. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.0073
Table S57. Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
11P GAIN MUTATED | 1 | 6 | 6 |
11P GAIN WILD-TYPE | 84 | 69 | 18 |
Figure S57. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0451 (Fisher's exact test), Q value = 0.15
Table S58. Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
11P GAIN MUTATED | 5 | 0 | 6 | 2 |
11P GAIN WILD-TYPE | 40 | 47 | 44 | 39 |
Figure S58. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0059 (Fisher's exact test), Q value = 0.038
Table S59. Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
11Q GAIN MUTATED | 2 | 8 | 5 |
11Q GAIN WILD-TYPE | 83 | 67 | 19 |
Figure S59. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.062
Table S60. Gene #22: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
11Q GAIN MUTATED | 5 | 0 | 8 | 2 |
11Q GAIN WILD-TYPE | 40 | 47 | 42 | 39 |
Figure S60. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028
Table S61. Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
12P GAIN MUTATED | 1 | 10 | 19 |
12P GAIN WILD-TYPE | 84 | 65 | 5 |
Figure S61. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.0094
Table S62. Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
12P GAIN MUTATED | 12 | 7 | 11 | 0 |
12P GAIN WILD-TYPE | 33 | 40 | 39 | 41 |
Figure S62. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00221 (Fisher's exact test), Q value = 0.018
Table S63. Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 67 | 37 |
12P GAIN MUTATED | 12 | 4 | 12 |
12P GAIN WILD-TYPE | 57 | 63 | 25 |
Figure S63. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028
Table S64. Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
12Q GAIN MUTATED | 1 | 4 | 17 |
12Q GAIN WILD-TYPE | 84 | 71 | 7 |
Figure S64. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.076
Table S65. Gene #24: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
12Q GAIN MUTATED | 8 | 6 | 8 | 0 |
12Q GAIN WILD-TYPE | 37 | 41 | 42 | 41 |
Figure S65. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0419 (Fisher's exact test), Q value = 0.14
Table S66. Gene #24: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
12Q GAIN MUTATED | 12 | 2 | 8 |
12Q GAIN WILD-TYPE | 90 | 40 | 25 |
Figure S66. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00417 (Fisher's exact test), Q value = 0.028
Table S67. Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 67 | 37 |
12Q GAIN MUTATED | 8 | 3 | 10 |
12Q GAIN WILD-TYPE | 61 | 64 | 27 |
Figure S67. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.075
Table S68. Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
13Q GAIN MUTATED | 7 | 15 | 7 |
13Q GAIN WILD-TYPE | 78 | 60 | 17 |
Figure S68. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028
Table S69. Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
14Q GAIN MUTATED | 3 | 12 | 11 |
14Q GAIN WILD-TYPE | 82 | 63 | 13 |
Figure S69. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00052
Table S70. Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
16P GAIN MUTATED | 1 | 13 | 8 |
16P GAIN WILD-TYPE | 84 | 62 | 16 |
Figure S70. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.008
Table S71. Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
16P GAIN MUTATED | 10 | 1 | 10 | 1 |
16P GAIN WILD-TYPE | 35 | 46 | 40 | 40 |
Figure S71. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0252 (Fisher's exact test), Q value = 0.098
Table S72. Gene #28: '16p gain' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 35 | 20 | 16 | 18 | 16 |
16P GAIN MUTATED | 9 | 2 | 0 | 1 | 0 |
16P GAIN WILD-TYPE | 26 | 18 | 16 | 17 | 16 |
Figure S72. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 0.067
Table S73. Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
16P GAIN MUTATED | 19 | 2 | 1 |
16P GAIN WILD-TYPE | 83 | 40 | 32 |
Figure S73. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00201 (Fisher's exact test), Q value = 0.017
Table S74. Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 67 | 37 |
16P GAIN MUTATED | 11 | 2 | 9 |
16P GAIN WILD-TYPE | 58 | 65 | 28 |
Figure S74. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.11
Table S75. Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 86 | 47 | 40 |
16P GAIN MUTATED | 16 | 5 | 1 |
16P GAIN WILD-TYPE | 70 | 42 | 39 |
Figure S75. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028
Table S76. Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
16Q GAIN MUTATED | 1 | 14 | 8 |
16Q GAIN WILD-TYPE | 84 | 61 | 16 |
Figure S76. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0045
Table S77. Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
16Q GAIN MUTATED | 9 | 1 | 12 | 1 |
16Q GAIN WILD-TYPE | 36 | 46 | 38 | 40 |
Figure S77. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0139 (Fisher's exact test), Q value = 0.067
Table S78. Gene #29: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 69 | 40 | 35 | 33 |
16Q GAIN MUTATED | 16 | 4 | 1 | 2 |
16Q GAIN WILD-TYPE | 53 | 36 | 34 | 31 |
Figure S78. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 0.00078 (Fisher's exact test), Q value = 0.0083
Table S79. Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
16Q GAIN MUTATED | 21 | 2 | 0 |
16Q GAIN WILD-TYPE | 81 | 40 | 33 |
Figure S79. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00252 (Fisher's exact test), Q value = 0.019
Table S80. Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 67 | 37 |
16Q GAIN MUTATED | 13 | 2 | 8 |
16Q GAIN WILD-TYPE | 56 | 65 | 29 |
Figure S80. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.00323 (Fisher's exact test), Q value = 0.024
Table S81. Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 86 | 47 | 40 |
16Q GAIN MUTATED | 17 | 6 | 0 |
16Q GAIN WILD-TYPE | 69 | 41 | 40 |
Figure S81. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00088
Table S82. Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
17P GAIN MUTATED | 3 | 0 | 6 |
17P GAIN WILD-TYPE | 82 | 75 | 18 |
Figure S82. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.082
Table S83. Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
17P GAIN MUTATED | 2 | 6 | 0 | 1 |
17P GAIN WILD-TYPE | 43 | 41 | 50 | 40 |
Figure S83. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00246 (Fisher's exact test), Q value = 0.019
Table S84. Gene #30: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 83 | 48 | 46 |
17P GAIN MUTATED | 1 | 1 | 7 |
17P GAIN WILD-TYPE | 82 | 47 | 39 |
Figure S84. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 7e-04 (Fisher's exact test), Q value = 0.0078
Table S85. Gene #30: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 74 | 75 | 28 |
17P GAIN MUTATED | 1 | 2 | 6 |
17P GAIN WILD-TYPE | 73 | 73 | 22 |
Figure S85. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00103 (Fisher's exact test), Q value = 0.01
Table S86. Gene #30: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 69 | 40 | 35 | 33 |
17P GAIN MUTATED | 0 | 1 | 2 | 6 |
17P GAIN WILD-TYPE | 69 | 39 | 33 | 27 |
Figure S86. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 0.00254 (Fisher's exact test), Q value = 0.019
Table S87. Gene #30: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
17P GAIN MUTATED | 2 | 1 | 6 |
17P GAIN WILD-TYPE | 100 | 41 | 27 |
Figure S87. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00956 (Fisher's exact test), Q value = 0.052
Table S88. Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 86 | 47 | 40 |
17P GAIN MUTATED | 2 | 1 | 6 |
17P GAIN WILD-TYPE | 84 | 46 | 34 |
Figure S88. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0059
Table S89. Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
17Q GAIN MUTATED | 2 | 8 | 7 |
17Q GAIN WILD-TYPE | 83 | 67 | 17 |
Figure S89. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028
Table S90. Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
18P GAIN MUTATED | 2 | 16 | 10 |
18P GAIN WILD-TYPE | 83 | 59 | 14 |
Figure S90. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.082
Table S91. Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
18P GAIN MUTATED | 8 | 4 | 13 | 2 |
18P GAIN WILD-TYPE | 37 | 43 | 37 | 39 |
Figure S91. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.026 (Fisher's exact test), Q value = 0.1
Table S92. Gene #32: '18p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 83 | 48 | 46 |
18P GAIN MUTATED | 19 | 3 | 5 |
18P GAIN WILD-TYPE | 64 | 45 | 41 |
Figure S92. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.093
Table S93. Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
18P GAIN MUTATED | 22 | 2 | 3 |
18P GAIN WILD-TYPE | 80 | 40 | 30 |
Figure S93. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.0341 (Fisher's exact test), Q value = 0.12
Table S94. Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 67 | 37 |
18P GAIN MUTATED | 16 | 5 | 5 |
18P GAIN WILD-TYPE | 53 | 62 | 32 |
Figure S94. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0012
Table S95. Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
18Q GAIN MUTATED | 1 | 4 | 7 |
18Q GAIN WILD-TYPE | 84 | 71 | 17 |
Figure S95. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0076
Table S96. Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
19P GAIN MUTATED | 4 | 5 | 8 |
19P GAIN WILD-TYPE | 81 | 70 | 16 |
Figure S96. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.064
Table S97. Gene #34: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 69 | 40 | 35 | 33 |
19P GAIN MUTATED | 8 | 2 | 0 | 7 |
19P GAIN WILD-TYPE | 61 | 38 | 35 | 26 |
Figure S97. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.0067
Table S98. Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
19Q GAIN MUTATED | 6 | 12 | 10 |
19Q GAIN WILD-TYPE | 79 | 63 | 14 |
Figure S98. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028
Table S99. Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
20P GAIN MUTATED | 7 | 12 | 15 |
20P GAIN WILD-TYPE | 78 | 63 | 9 |
Figure S99. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.078
Table S100. Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
20P GAIN MUTATED | 15 | 7 | 8 | 3 |
20P GAIN WILD-TYPE | 30 | 40 | 42 | 38 |
Figure S100. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.075
Table S101. Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
20P GAIN MUTATED | 23 | 2 | 8 |
20P GAIN WILD-TYPE | 79 | 40 | 25 |
Figure S101. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00622 (Fisher's exact test), Q value = 0.038
Table S102. Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 67 | 37 |
20P GAIN MUTATED | 16 | 5 | 11 |
20P GAIN WILD-TYPE | 53 | 62 | 26 |
Figure S102. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028
Table S103. Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
20Q GAIN MUTATED | 8 | 21 | 16 |
20Q GAIN WILD-TYPE | 77 | 54 | 8 |
Figure S103. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.12
Table S104. Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
20Q GAIN MUTATED | 16 | 10 | 14 | 4 |
20Q GAIN WILD-TYPE | 29 | 37 | 36 | 37 |
Figure S104. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0236 (Fisher's exact test), Q value = 0.094
Table S105. Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
20Q GAIN MUTATED | 31 | 4 | 8 |
20Q GAIN WILD-TYPE | 71 | 38 | 25 |
Figure S105. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.0056
Table S106. Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 67 | 37 |
20Q GAIN MUTATED | 22 | 6 | 14 |
20Q GAIN WILD-TYPE | 47 | 61 | 23 |
Figure S106. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00067
Table S107. Gene #39: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
XP GAIN MUTATED | 0 | 2 | 6 |
XP GAIN WILD-TYPE | 85 | 73 | 18 |
Figure S107. Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0344 (Fisher's exact test), Q value = 0.12
Table S108. Gene #39: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 74 | 75 | 28 |
XP GAIN MUTATED | 1 | 3 | 4 |
XP GAIN WILD-TYPE | 73 | 72 | 24 |
Figure S108. Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.0429 (Fisher's exact test), Q value = 0.14
Table S109. Gene #39: 'xp gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 69 | 40 | 35 | 33 |
XP GAIN MUTATED | 4 | 0 | 0 | 4 |
XP GAIN WILD-TYPE | 65 | 40 | 35 | 29 |
Figure S109. Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 0.0405 (Fisher's exact test), Q value = 0.14
Table S110. Gene #39: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
XP GAIN MUTATED | 4 | 0 | 4 |
XP GAIN WILD-TYPE | 98 | 42 | 29 |
Figure S110. Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0047
Table S111. Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
XQ GAIN MUTATED | 2 | 4 | 7 |
XQ GAIN WILD-TYPE | 83 | 71 | 17 |
Figure S111. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00944 (Fisher's exact test), Q value = 0.051
Table S112. Gene #40: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 74 | 75 | 28 |
XQ GAIN MUTATED | 2 | 5 | 6 |
XQ GAIN WILD-TYPE | 72 | 70 | 22 |
Figure S112. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.0369 (Fisher's exact test), Q value = 0.13
Table S113. Gene #40: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
XQ GAIN MUTATED | 6 | 1 | 6 |
XQ GAIN WILD-TYPE | 96 | 41 | 27 |
Figure S113. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00067
Table S114. Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
1P LOSS MUTATED | 5 | 24 | 7 |
1P LOSS WILD-TYPE | 80 | 51 | 17 |
Figure S114. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028
Table S115. Gene #41: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
1P LOSS MUTATED | 22 | 6 | 7 | 1 |
1P LOSS WILD-TYPE | 23 | 41 | 43 | 40 |
Figure S115. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00191 (Fisher's exact test), Q value = 0.016
Table S116. Gene #41: '1p loss' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 35 | 20 | 16 | 18 | 16 |
1P LOSS MUTATED | 14 | 2 | 0 | 1 | 3 |
1P LOSS WILD-TYPE | 21 | 18 | 16 | 17 | 13 |
Figure S116. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

P value = 0.00397 (Fisher's exact test), Q value = 0.027
Table S117. Gene #41: '1p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 12 | 20 | 22 | 15 | 11 | 18 | 7 |
1P LOSS MUTATED | 6 | 2 | 4 | 0 | 0 | 5 | 3 |
1P LOSS WILD-TYPE | 6 | 18 | 18 | 15 | 11 | 13 | 4 |
Figure S117. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

P value = 0.0097 (Fisher's exact test), Q value = 0.052
Table S118. Gene #41: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 83 | 48 | 46 |
1P LOSS MUTATED | 23 | 8 | 3 |
1P LOSS WILD-TYPE | 60 | 40 | 43 |
Figure S118. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 0.0289 (Fisher's exact test), Q value = 0.11
Table S119. Gene #41: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 67 | 37 |
1P LOSS MUTATED | 17 | 6 | 9 |
1P LOSS WILD-TYPE | 52 | 61 | 28 |
Figure S119. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 0.094
Table S120. Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 86 | 47 | 40 |
1P LOSS MUTATED | 21 | 9 | 2 |
1P LOSS WILD-TYPE | 65 | 38 | 38 |
Figure S120. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0413 (Fisher's exact test), Q value = 0.14
Table S121. Gene #42: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
1Q LOSS MUTATED | 1 | 4 | 3 |
1Q LOSS WILD-TYPE | 84 | 71 | 21 |
Figure S121. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0076 (Fisher's exact test), Q value = 0.044
Table S122. Gene #43: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
2P LOSS MUTATED | 2 | 4 | 5 |
2P LOSS WILD-TYPE | 83 | 71 | 19 |
Figure S122. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0069
Table S123. Gene #44: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
2Q LOSS MUTATED | 0 | 1 | 4 |
2Q LOSS WILD-TYPE | 85 | 74 | 20 |
Figure S123. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00163 (Fisher's exact test), Q value = 0.014
Table S124. Gene #45: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
3P LOSS MUTATED | 8 | 19 | 9 |
3P LOSS WILD-TYPE | 77 | 56 | 15 |
Figure S124. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0329 (Fisher's exact test), Q value = 0.12
Table S125. Gene #46: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
3Q LOSS MUTATED | 5 | 8 | 6 |
3Q LOSS WILD-TYPE | 80 | 67 | 18 |
Figure S125. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.064
Table S126. Gene #46: '3q loss' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 35 | 20 | 16 | 18 | 16 |
3Q LOSS MUTATED | 9 | 1 | 1 | 0 | 0 |
3Q LOSS WILD-TYPE | 26 | 19 | 15 | 18 | 16 |
Figure S126. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

P value = 0.00733 (Fisher's exact test), Q value = 0.043
Table S127. Gene #46: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 67 | 37 |
3Q LOSS MUTATED | 8 | 2 | 8 |
3Q LOSS WILD-TYPE | 61 | 65 | 29 |
Figure S127. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.0432 (Fisher's exact test), Q value = 0.14
Table S128. Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
4P LOSS MUTATED | 6 | 15 | 4 |
4P LOSS WILD-TYPE | 79 | 60 | 20 |
Figure S128. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00667 (Fisher's exact test), Q value = 0.04
Table S129. Gene #47: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
4P LOSS MUTATED | 11 | 1 | 9 | 4 |
4P LOSS WILD-TYPE | 34 | 46 | 41 | 37 |
Figure S129. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.063
Table S130. Gene #47: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
4P LOSS MUTATED | 20 | 1 | 3 |
4P LOSS WILD-TYPE | 82 | 41 | 30 |
Figure S130. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00354 (Fisher's exact test), Q value = 0.025
Table S131. Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 86 | 47 | 40 |
4P LOSS MUTATED | 19 | 2 | 2 |
4P LOSS WILD-TYPE | 67 | 45 | 38 |
Figure S131. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0192 (Fisher's exact test), Q value = 0.083
Table S132. Gene #48: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
4Q LOSS MUTATED | 10 | 1 | 8 | 6 |
4Q LOSS WILD-TYPE | 35 | 46 | 42 | 35 |
Figure S132. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00285 (Fisher's exact test), Q value = 0.022
Table S133. Gene #48: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
4Q LOSS MUTATED | 17 | 0 | 7 |
4Q LOSS WILD-TYPE | 85 | 42 | 26 |
Figure S133. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00097 (Fisher's exact test), Q value = 0.0098
Table S134. Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 86 | 47 | 40 |
4Q LOSS MUTATED | 17 | 0 | 6 |
4Q LOSS WILD-TYPE | 69 | 47 | 34 |
Figure S134. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00335 (Fisher's exact test), Q value = 0.024
Table S135. Gene #49: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
5P LOSS MUTATED | 0 | 8 | 1 |
5P LOSS WILD-TYPE | 85 | 67 | 23 |
Figure S135. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00375 (Fisher's exact test), Q value = 0.026
Table S136. Gene #50: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
5Q LOSS MUTATED | 1 | 8 | 4 |
5Q LOSS WILD-TYPE | 84 | 67 | 20 |
Figure S136. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00067
Table S137. Gene #51: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
6P LOSS MUTATED | 15 | 37 | 12 |
6P LOSS WILD-TYPE | 70 | 38 | 12 |
Figure S137. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0019
Table S138. Gene #51: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
6P LOSS MUTATED | 23 | 8 | 24 | 8 |
6P LOSS WILD-TYPE | 22 | 39 | 26 | 33 |
Figure S138. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.068
Table S139. Gene #51: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 74 | 75 | 28 |
6P LOSS MUTATED | 21 | 34 | 5 |
6P LOSS WILD-TYPE | 53 | 41 | 23 |
Figure S139. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00108 (Fisher's exact test), Q value = 0.01
Table S140. Gene #51: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
6P LOSS MUTATED | 46 | 7 | 7 |
6P LOSS WILD-TYPE | 56 | 35 | 26 |
Figure S140. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00333 (Fisher's exact test), Q value = 0.024
Table S141. Gene #51: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 67 | 37 |
6P LOSS MUTATED | 31 | 13 | 16 |
6P LOSS WILD-TYPE | 38 | 54 | 21 |
Figure S141. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0021
Table S142. Gene #51: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 86 | 47 | 40 |
6P LOSS MUTATED | 43 | 11 | 6 |
6P LOSS WILD-TYPE | 43 | 36 | 34 |
Figure S142. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028
Table S143. Gene #52: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
6Q LOSS MUTATED | 18 | 51 | 14 |
6Q LOSS WILD-TYPE | 67 | 24 | 10 |
Figure S143. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028
Table S144. Gene #52: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
6Q LOSS MUTATED | 27 | 9 | 34 | 12 |
6Q LOSS WILD-TYPE | 18 | 38 | 16 | 29 |
Figure S144. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0429 (Fisher's exact test), Q value = 0.14
Table S145. Gene #52: '6q loss' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 35 | 20 | 16 | 18 | 16 |
6Q LOSS MUTATED | 23 | 8 | 4 | 6 | 8 |
6Q LOSS WILD-TYPE | 12 | 12 | 12 | 12 | 8 |
Figure S145. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0054
Table S146. Gene #52: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 83 | 48 | 46 |
6Q LOSS MUTATED | 49 | 18 | 11 |
6Q LOSS WILD-TYPE | 34 | 30 | 35 |
Figure S146. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0054
Table S147. Gene #52: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 74 | 75 | 28 |
6Q LOSS MUTATED | 29 | 44 | 5 |
6Q LOSS WILD-TYPE | 45 | 31 | 23 |
Figure S147. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00112 (Fisher's exact test), Q value = 0.011
Table S148. Gene #52: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 69 | 40 | 35 | 33 |
6Q LOSS MUTATED | 43 | 14 | 12 | 9 |
6Q LOSS WILD-TYPE | 26 | 26 | 23 | 24 |
Figure S148. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028
Table S149. Gene #52: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
6Q LOSS MUTATED | 61 | 10 | 7 |
6Q LOSS WILD-TYPE | 41 | 32 | 26 |
Figure S149. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028
Table S150. Gene #52: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 67 | 37 |
6Q LOSS MUTATED | 46 | 13 | 19 |
6Q LOSS WILD-TYPE | 23 | 54 | 18 |
Figure S150. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028
Table S151. Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 86 | 47 | 40 |
6Q LOSS MUTATED | 54 | 18 | 6 |
6Q LOSS WILD-TYPE | 32 | 29 | 34 |
Figure S151. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00102 (Fisher's exact test), Q value = 0.01
Table S152. Gene #55: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
8P LOSS MUTATED | 9 | 23 | 9 |
8P LOSS WILD-TYPE | 76 | 52 | 15 |
Figure S152. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00346 (Fisher's exact test), Q value = 0.025
Table S153. Gene #55: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
8P LOSS MUTATED | 10 | 7 | 20 | 4 |
8P LOSS WILD-TYPE | 35 | 40 | 30 | 37 |
Figure S153. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0047 (Fisher's exact test), Q value = 0.031
Table S154. Gene #55: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 74 | 75 | 28 |
8P LOSS MUTATED | 11 | 26 | 3 |
8P LOSS WILD-TYPE | 63 | 49 | 25 |
Figure S154. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.0155 (Fisher's exact test), Q value = 0.072
Table S155. Gene #55: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 69 | 40 | 35 | 33 |
8P LOSS MUTATED | 23 | 3 | 7 | 7 |
8P LOSS WILD-TYPE | 46 | 37 | 28 | 26 |
Figure S155. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.062
Table S156. Gene #55: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
8P LOSS MUTATED | 31 | 4 | 5 |
8P LOSS WILD-TYPE | 71 | 38 | 28 |
Figure S156. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00686 (Fisher's exact test), Q value = 0.041
Table S157. Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 67 | 37 |
8P LOSS MUTATED | 20 | 7 | 12 |
8P LOSS WILD-TYPE | 49 | 60 | 25 |
Figure S157. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.00231 (Fisher's exact test), Q value = 0.018
Table S158. Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 86 | 47 | 40 |
8P LOSS MUTATED | 29 | 6 | 4 |
8P LOSS WILD-TYPE | 57 | 41 | 36 |
Figure S158. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0183 (Fisher's exact test), Q value = 0.081
Table S159. Gene #56: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
8Q LOSS MUTATED | 3 | 8 | 5 |
8Q LOSS WILD-TYPE | 82 | 67 | 19 |
Figure S159. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028
Table S160. Gene #57: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
9P LOSS MUTATED | 18 | 49 | 8 |
9P LOSS WILD-TYPE | 67 | 26 | 16 |
Figure S160. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0061 (Fisher's exact test), Q value = 0.038
Table S161. Gene #57: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
9P LOSS MUTATED | 20 | 12 | 29 | 13 |
9P LOSS WILD-TYPE | 25 | 35 | 21 | 28 |
Figure S161. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.092
Table S162. Gene #57: '9p loss' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 35 | 20 | 16 | 18 | 16 |
9P LOSS MUTATED | 18 | 11 | 2 | 5 | 9 |
9P LOSS WILD-TYPE | 17 | 9 | 14 | 13 | 7 |
Figure S162. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

P value = 0.00332 (Fisher's exact test), Q value = 0.024
Table S163. Gene #57: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 83 | 48 | 46 |
9P LOSS MUTATED | 41 | 19 | 9 |
9P LOSS WILD-TYPE | 42 | 29 | 37 |
Figure S163. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 0.038 (Fisher's exact test), Q value = 0.13
Table S164. Gene #57: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 74 | 75 | 28 |
9P LOSS MUTATED | 31 | 33 | 5 |
9P LOSS WILD-TYPE | 43 | 42 | 23 |
Figure S164. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.0172 (Fisher's exact test), Q value = 0.077
Table S165. Gene #57: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 69 | 40 | 35 | 33 |
9P LOSS MUTATED | 36 | 13 | 13 | 7 |
9P LOSS WILD-TYPE | 33 | 27 | 22 | 26 |
Figure S165. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.065
Table S166. Gene #57: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
9P LOSS MUTATED | 49 | 12 | 8 |
9P LOSS WILD-TYPE | 53 | 30 | 25 |
Figure S166. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00803 (Fisher's exact test), Q value = 0.045
Table S167. Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 67 | 37 |
9P LOSS MUTATED | 35 | 17 | 16 |
9P LOSS WILD-TYPE | 34 | 50 | 21 |
Figure S167. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.00718 (Fisher's exact test), Q value = 0.042
Table S168. Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 86 | 47 | 40 |
9P LOSS MUTATED | 42 | 18 | 8 |
9P LOSS WILD-TYPE | 44 | 29 | 32 |
Figure S168. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.0047
Table S169. Gene #59: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
10P LOSS MUTATED | 8 | 17 | 11 |
10P LOSS WILD-TYPE | 77 | 58 | 13 |
Figure S169. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0015
Table S170. Gene #60: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
10Q LOSS MUTATED | 5 | 15 | 10 |
10Q LOSS WILD-TYPE | 80 | 60 | 14 |
Figure S170. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.075
Table S171. Gene #60: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 74 | 75 | 28 |
10Q LOSS MUTATED | 6 | 19 | 4 |
10Q LOSS WILD-TYPE | 68 | 56 | 24 |
Figure S171. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00153 (Fisher's exact test), Q value = 0.014
Table S172. Gene #61: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
11P LOSS MUTATED | 2 | 9 | 6 |
11P LOSS WILD-TYPE | 83 | 66 | 18 |
Figure S172. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0071
Table S173. Gene #62: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
11Q LOSS MUTATED | 2 | 7 | 7 |
11Q LOSS WILD-TYPE | 83 | 68 | 17 |
Figure S173. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0463 (Fisher's exact test), Q value = 0.15
Table S174. Gene #62: '11q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 12 | 20 | 22 | 15 | 11 | 18 | 7 |
11Q LOSS MUTATED | 0 | 0 | 1 | 4 | 0 | 1 | 0 |
11Q LOSS WILD-TYPE | 12 | 20 | 21 | 11 | 11 | 17 | 7 |
Figure S174. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.0034
Table S175. Gene #63: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
12P LOSS MUTATED | 3 | 17 | 0 |
12P LOSS WILD-TYPE | 82 | 58 | 24 |
Figure S175. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0371 (Fisher's exact test), Q value = 0.13
Table S176. Gene #63: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
12P LOSS MUTATED | 7 | 1 | 9 | 3 |
12P LOSS WILD-TYPE | 38 | 46 | 41 | 38 |
Figure S176. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.008
Table S177. Gene #63: '12p loss' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 35 | 20 | 16 | 18 | 16 |
12P LOSS MUTATED | 9 | 0 | 0 | 0 | 0 |
12P LOSS WILD-TYPE | 26 | 20 | 16 | 18 | 16 |
Figure S177. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

P value = 0.00098 (Fisher's exact test), Q value = 0.0098
Table S178. Gene #63: '12p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 12 | 20 | 22 | 15 | 11 | 18 | 7 |
12P LOSS MUTATED | 3 | 0 | 3 | 0 | 0 | 0 | 3 |
12P LOSS WILD-TYPE | 9 | 20 | 19 | 15 | 11 | 18 | 4 |
Figure S178. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

P value = 0.00824 (Fisher's exact test), Q value = 0.046
Table S179. Gene #63: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 74 | 75 | 28 |
12P LOSS MUTATED | 5 | 14 | 0 |
12P LOSS WILD-TYPE | 69 | 61 | 28 |
Figure S179. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00098 (Fisher's exact test), Q value = 0.0098
Table S180. Gene #63: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
12P LOSS MUTATED | 18 | 0 | 1 |
12P LOSS WILD-TYPE | 84 | 42 | 32 |
Figure S180. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00166 (Fisher's exact test), Q value = 0.014
Table S181. Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 86 | 47 | 40 |
12P LOSS MUTATED | 16 | 1 | 1 |
12P LOSS WILD-TYPE | 70 | 46 | 39 |
Figure S181. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028
Table S182. Gene #64: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
12Q LOSS MUTATED | 2 | 25 | 1 |
12Q LOSS WILD-TYPE | 83 | 50 | 23 |
Figure S182. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00689 (Fisher's exact test), Q value = 0.041
Table S183. Gene #64: '12q loss' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 35 | 20 | 16 | 18 | 16 |
12Q LOSS MUTATED | 10 | 1 | 0 | 0 | 2 |
12Q LOSS WILD-TYPE | 25 | 19 | 16 | 18 | 14 |
Figure S183. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

P value = 0.00236 (Fisher's exact test), Q value = 0.019
Table S184. Gene #64: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 74 | 75 | 28 |
12Q LOSS MUTATED | 8 | 18 | 0 |
12Q LOSS WILD-TYPE | 66 | 57 | 28 |
Figure S184. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.0244 (Fisher's exact test), Q value = 0.096
Table S185. Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 86 | 47 | 40 |
12Q LOSS MUTATED | 17 | 7 | 1 |
12Q LOSS WILD-TYPE | 69 | 40 | 39 |
Figure S185. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.0059
Table S186. Gene #65: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
13Q LOSS MUTATED | 2 | 12 | 6 |
13Q LOSS WILD-TYPE | 83 | 63 | 18 |
Figure S186. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.009 (Fisher's exact test), Q value = 0.049
Table S187. Gene #65: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
13Q LOSS MUTATED | 6 | 2 | 11 | 1 |
13Q LOSS WILD-TYPE | 39 | 45 | 39 | 40 |
Figure S187. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00305 (Fisher's exact test), Q value = 0.023
Table S188. Gene #65: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 83 | 48 | 46 |
13Q LOSS MUTATED | 16 | 2 | 1 |
13Q LOSS WILD-TYPE | 67 | 46 | 45 |
Figure S188. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 0.0229 (Fisher's exact test), Q value = 0.093
Table S189. Gene #65: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 69 | 40 | 35 | 33 |
13Q LOSS MUTATED | 13 | 1 | 4 | 1 |
13Q LOSS WILD-TYPE | 56 | 39 | 31 | 32 |
Figure S189. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.064
Table S190. Gene #65: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
13Q LOSS MUTATED | 17 | 1 | 1 |
13Q LOSS WILD-TYPE | 85 | 41 | 32 |
Figure S190. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00191 (Fisher's exact test), Q value = 0.016
Table S191. Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 67 | 37 |
13Q LOSS MUTATED | 13 | 1 | 5 |
13Q LOSS WILD-TYPE | 56 | 66 | 32 |
Figure S191. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.0229 (Fisher's exact test), Q value = 0.093
Table S192. Gene #66: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
14Q LOSS MUTATED | 9 | 1 | 4 | 2 |
14Q LOSS WILD-TYPE | 36 | 46 | 46 | 39 |
Figure S192. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.001
Table S193. Gene #67: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
15Q LOSS MUTATED | 3 | 20 | 7 |
15Q LOSS WILD-TYPE | 82 | 55 | 17 |
Figure S193. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00879 (Fisher's exact test), Q value = 0.048
Table S194. Gene #67: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
15Q LOSS MUTATED | 9 | 2 | 14 | 5 |
15Q LOSS WILD-TYPE | 36 | 45 | 36 | 36 |
Figure S194. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0211 (Fisher's exact test), Q value = 0.09
Table S195. Gene #67: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 83 | 48 | 46 |
15Q LOSS MUTATED | 21 | 4 | 5 |
15Q LOSS WILD-TYPE | 62 | 44 | 41 |
Figure S195. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 0.00197 (Fisher's exact test), Q value = 0.016
Table S196. Gene #67: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 74 | 75 | 28 |
15Q LOSS MUTATED | 8 | 21 | 1 |
15Q LOSS WILD-TYPE | 66 | 54 | 27 |
Figure S196. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00611 (Fisher's exact test), Q value = 0.038
Table S197. Gene #67: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
15Q LOSS MUTATED | 25 | 2 | 3 |
15Q LOSS WILD-TYPE | 77 | 40 | 30 |
Figure S197. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00372 (Fisher's exact test), Q value = 0.026
Table S198. Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 86 | 47 | 40 |
15Q LOSS MUTATED | 22 | 4 | 2 |
15Q LOSS WILD-TYPE | 64 | 43 | 38 |
Figure S198. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00843 (Fisher's exact test), Q value = 0.047
Table S199. Gene #68: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
16P LOSS MUTATED | 2 | 4 | 5 |
16P LOSS WILD-TYPE | 83 | 71 | 19 |
Figure S199. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0232 (Fisher's exact test), Q value = 0.094
Table S200. Gene #68: '16p loss' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 35 | 20 | 16 | 18 | 16 |
16P LOSS MUTATED | 0 | 0 | 2 | 0 | 2 |
16P LOSS WILD-TYPE | 35 | 20 | 14 | 18 | 14 |
Figure S200. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

P value = 0.0251 (Fisher's exact test), Q value = 0.098
Table S201. Gene #69: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
16Q LOSS MUTATED | 3 | 5 | 5 |
16Q LOSS WILD-TYPE | 82 | 70 | 19 |
Figure S201. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028
Table S202. Gene #70: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
17P LOSS MUTATED | 7 | 65 | 8 |
17P LOSS WILD-TYPE | 78 | 10 | 16 |
Figure S202. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028
Table S203. Gene #70: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
17P LOSS MUTATED | 28 | 7 | 37 | 8 |
17P LOSS WILD-TYPE | 17 | 40 | 13 | 33 |
Figure S203. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.059
Table S204. Gene #70: '17p loss' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 35 | 20 | 16 | 18 | 16 |
17P LOSS MUTATED | 24 | 10 | 4 | 5 | 6 |
17P LOSS WILD-TYPE | 11 | 10 | 12 | 13 | 10 |
Figure S204. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028
Table S205. Gene #70: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 83 | 48 | 46 |
17P LOSS MUTATED | 49 | 22 | 6 |
17P LOSS WILD-TYPE | 34 | 26 | 40 |
Figure S205. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028
Table S206. Gene #70: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 74 | 75 | 28 |
17P LOSS MUTATED | 37 | 39 | 1 |
17P LOSS WILD-TYPE | 37 | 36 | 27 |
Figure S206. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028
Table S207. Gene #70: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 69 | 40 | 35 | 33 |
17P LOSS MUTATED | 47 | 16 | 8 | 6 |
17P LOSS WILD-TYPE | 22 | 24 | 27 | 27 |
Figure S207. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.001
Table S208. Gene #70: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
17P LOSS MUTATED | 58 | 14 | 5 |
17P LOSS WILD-TYPE | 44 | 28 | 28 |
Figure S208. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028
Table S209. Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 67 | 37 |
17P LOSS MUTATED | 46 | 13 | 17 |
17P LOSS WILD-TYPE | 23 | 54 | 20 |
Figure S209. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028
Table S210. Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 86 | 47 | 40 |
17P LOSS MUTATED | 49 | 22 | 5 |
17P LOSS WILD-TYPE | 37 | 25 | 35 |
Figure S210. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.0072
Table S211. Gene #71: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
17Q LOSS MUTATED | 3 | 17 | 2 |
17Q LOSS WILD-TYPE | 82 | 58 | 22 |
Figure S211. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0438 (Fisher's exact test), Q value = 0.14
Table S212. Gene #71: '17q loss' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 35 | 20 | 16 | 18 | 16 |
17Q LOSS MUTATED | 10 | 2 | 2 | 0 | 1 |
17Q LOSS WILD-TYPE | 25 | 18 | 14 | 18 | 15 |
Figure S212. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 0.098
Table S213. Gene #71: '17q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 12 | 20 | 22 | 15 | 11 | 18 | 7 |
17Q LOSS MUTATED | 3 | 2 | 3 | 2 | 1 | 0 | 4 |
17Q LOSS WILD-TYPE | 9 | 18 | 19 | 13 | 10 | 18 | 3 |
Figure S213. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028
Table S214. Gene #73: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
18Q LOSS MUTATED | 36 | 62 | 8 |
18Q LOSS WILD-TYPE | 49 | 13 | 16 |
Figure S214. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0047
Table S215. Gene #73: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
18Q LOSS MUTATED | 31 | 18 | 38 | 19 |
18Q LOSS WILD-TYPE | 14 | 29 | 12 | 22 |
Figure S215. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0358 (Fisher's exact test), Q value = 0.13
Table S216. Gene #73: '18q loss' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 35 | 20 | 16 | 18 | 16 |
18Q LOSS MUTATED | 25 | 12 | 7 | 5 | 9 |
18Q LOSS WILD-TYPE | 10 | 8 | 9 | 13 | 7 |
Figure S216. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

P value = 0.0021 (Fisher's exact test), Q value = 0.017
Table S217. Gene #73: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 83 | 48 | 46 |
18Q LOSS MUTATED | 57 | 29 | 17 |
18Q LOSS WILD-TYPE | 26 | 19 | 29 |
Figure S217. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 0.00505 (Fisher's exact test), Q value = 0.033
Table S218. Gene #73: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 74 | 75 | 28 |
18Q LOSS MUTATED | 43 | 51 | 9 |
18Q LOSS WILD-TYPE | 31 | 24 | 19 |
Figure S218. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.015 (Fisher's exact test), Q value = 0.071
Table S219. Gene #73: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 69 | 40 | 35 | 33 |
18Q LOSS MUTATED | 50 | 21 | 18 | 14 |
18Q LOSS WILD-TYPE | 19 | 19 | 17 | 19 |
Figure S219. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 0.00311 (Fisher's exact test), Q value = 0.023
Table S220. Gene #73: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
18Q LOSS MUTATED | 70 | 20 | 13 |
18Q LOSS WILD-TYPE | 32 | 22 | 20 |
Figure S220. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.0469 (Fisher's exact test), Q value = 0.15
Table S221. Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 67 | 37 |
18Q LOSS MUTATED | 48 | 33 | 20 |
18Q LOSS WILD-TYPE | 21 | 34 | 17 |
Figure S221. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.001
Table S222. Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 86 | 47 | 40 |
18Q LOSS MUTATED | 59 | 31 | 11 |
18Q LOSS WILD-TYPE | 27 | 16 | 29 |
Figure S222. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00128 (Fisher's exact test), Q value = 0.012
Table S223. Gene #74: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
19P LOSS MUTATED | 2 | 12 | 5 |
19P LOSS WILD-TYPE | 83 | 63 | 19 |
Figure S223. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0223 (Fisher's exact test), Q value = 0.093
Table S224. Gene #74: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
19P LOSS MUTATED | 8 | 1 | 8 | 2 |
19P LOSS WILD-TYPE | 37 | 46 | 42 | 39 |
Figure S224. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.097
Table S225. Gene #74: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 74 | 75 | 28 |
19P LOSS MUTATED | 6 | 13 | 0 |
19P LOSS WILD-TYPE | 68 | 62 | 28 |
Figure S225. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00614 (Fisher's exact test), Q value = 0.038
Table S226. Gene #74: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
19P LOSS MUTATED | 17 | 2 | 0 |
19P LOSS WILD-TYPE | 85 | 40 | 33 |
Figure S226. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.0049
Table S227. Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 67 | 37 |
19P LOSS MUTATED | 15 | 1 | 2 |
19P LOSS WILD-TYPE | 54 | 66 | 35 |
Figure S227. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.0194 (Fisher's exact test), Q value = 0.084
Table S228. Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 86 | 47 | 40 |
19P LOSS MUTATED | 12 | 6 | 0 |
19P LOSS WILD-TYPE | 74 | 41 | 40 |
Figure S228. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00653 (Fisher's exact test), Q value = 0.04
Table S229. Gene #75: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
19Q LOSS MUTATED | 1 | 7 | 4 |
19Q LOSS WILD-TYPE | 84 | 68 | 20 |
Figure S229. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00232 (Fisher's exact test), Q value = 0.018
Table S230. Gene #75: '19q loss' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 35 | 20 | 16 | 18 | 16 |
19Q LOSS MUTATED | 0 | 1 | 0 | 0 | 4 |
19Q LOSS WILD-TYPE | 35 | 19 | 16 | 18 | 12 |
Figure S230. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

P value = 0.0399 (Fisher's exact test), Q value = 0.14
Table S231. Gene #75: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 83 | 48 | 46 |
19Q LOSS MUTATED | 10 | 1 | 1 |
19Q LOSS WILD-TYPE | 73 | 47 | 45 |
Figure S231. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.069
Table S232. Gene #75: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 74 | 75 | 28 |
19Q LOSS MUTATED | 2 | 10 | 0 |
19Q LOSS WILD-TYPE | 72 | 65 | 28 |
Figure S232. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.0049
Table S233. Gene #76: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
20P LOSS MUTATED | 2 | 16 | 2 |
20P LOSS WILD-TYPE | 83 | 59 | 22 |
Figure S233. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0451 (Fisher's exact test), Q value = 0.15
Table S234. Gene #76: '20p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
20P LOSS MUTATED | 6 | 2 | 10 | 2 |
20P LOSS WILD-TYPE | 39 | 45 | 40 | 39 |
Figure S234. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00651 (Fisher's exact test), Q value = 0.04
Table S235. Gene #76: '20p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 83 | 48 | 46 |
20P LOSS MUTATED | 11 | 8 | 0 |
20P LOSS WILD-TYPE | 72 | 40 | 46 |
Figure S235. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 0.0369 (Fisher's exact test), Q value = 0.13
Table S236. Gene #76: '20p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 69 | 40 | 35 | 33 |
20P LOSS MUTATED | 11 | 6 | 2 | 0 |
20P LOSS WILD-TYPE | 58 | 34 | 33 | 33 |
Figure S236. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 0.0395 (Fisher's exact test), Q value = 0.13
Table S237. Gene #76: '20p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
20P LOSS MUTATED | 15 | 4 | 0 |
20P LOSS WILD-TYPE | 87 | 38 | 33 |
Figure S237. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00188 (Fisher's exact test), Q value = 0.016
Table S238. Gene #76: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 67 | 37 |
20P LOSS MUTATED | 11 | 1 | 7 |
20P LOSS WILD-TYPE | 58 | 66 | 30 |
Figure S238. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.0139 (Fisher's exact test), Q value = 0.067
Table S239. Gene #76: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 86 | 47 | 40 |
20P LOSS MUTATED | 11 | 8 | 0 |
20P LOSS WILD-TYPE | 75 | 39 | 40 |
Figure S239. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028
Table S240. Gene #78: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
21Q LOSS MUTATED | 11 | 38 | 9 |
21Q LOSS WILD-TYPE | 74 | 37 | 15 |
Figure S240. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0225 (Fisher's exact test), Q value = 0.093
Table S241. Gene #78: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
21Q LOSS MUTATED | 17 | 9 | 22 | 9 |
21Q LOSS WILD-TYPE | 28 | 38 | 28 | 32 |
Figure S241. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0219 (Fisher's exact test), Q value = 0.092
Table S242. Gene #78: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 83 | 48 | 46 |
21Q LOSS MUTATED | 30 | 18 | 7 |
21Q LOSS WILD-TYPE | 53 | 30 | 39 |
Figure S242. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 0.032 (Fisher's exact test), Q value = 0.12
Table S243. Gene #78: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
21Q LOSS MUTATED | 39 | 11 | 5 |
21Q LOSS WILD-TYPE | 63 | 31 | 28 |
Figure S243. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.0059
Table S244. Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 67 | 37 |
21Q LOSS MUTATED | 31 | 10 | 12 |
21Q LOSS WILD-TYPE | 38 | 57 | 25 |
Figure S244. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.0362 (Fisher's exact test), Q value = 0.13
Table S245. Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 86 | 47 | 40 |
21Q LOSS MUTATED | 29 | 18 | 6 |
21Q LOSS WILD-TYPE | 57 | 29 | 34 |
Figure S245. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028
Table S246. Gene #79: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
22Q LOSS MUTATED | 7 | 30 | 9 |
22Q LOSS WILD-TYPE | 78 | 45 | 15 |
Figure S246. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0056 (Fisher's exact test), Q value = 0.036
Table S247. Gene #79: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
22Q LOSS MUTATED | 18 | 7 | 16 | 5 |
22Q LOSS WILD-TYPE | 27 | 40 | 34 | 36 |
Figure S247. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0407 (Fisher's exact test), Q value = 0.14
Table S248. Gene #79: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 42 | 33 |
22Q LOSS MUTATED | 32 | 6 | 5 |
22Q LOSS WILD-TYPE | 70 | 36 | 28 |
Figure S248. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00105 (Fisher's exact test), Q value = 0.01
Table S249. Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 67 | 37 |
22Q LOSS MUTATED | 22 | 7 | 14 |
22Q LOSS WILD-TYPE | 47 | 60 | 23 |
Figure S249. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.0285 (Fisher's exact test), Q value = 0.11
Table S250. Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 86 | 47 | 40 |
22Q LOSS MUTATED | 27 | 12 | 4 |
22Q LOSS WILD-TYPE | 59 | 35 | 36 |
Figure S250. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.0016
Table S251. Gene #80: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
XP LOSS MUTATED | 3 | 18 | 6 |
XP LOSS WILD-TYPE | 82 | 57 | 18 |
Figure S251. Get High-res Image Gene #80: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028
Table S252. Gene #81: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 24 |
XQ LOSS MUTATED | 0 | 13 | 5 |
XQ LOSS WILD-TYPE | 85 | 62 | 19 |
Figure S252. Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0448 (Fisher's exact test), Q value = 0.15
Table S253. Gene #81: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 47 | 50 | 41 |
XQ LOSS MUTATED | 7 | 5 | 6 | 0 |
XQ LOSS WILD-TYPE | 38 | 42 | 44 | 41 |
Figure S253. Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

-
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/PAAD-TP/15096459/transformed.cor.cli.txt
-
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PAAD-TP/15107801/PAAD-TP.transferedmergedcluster.txt
-
Number of patients = 184
-
Number of significantly arm-level cnvs = 81
-
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.