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 12 molecular subtypes across 450 patients, 311 significant findings detected with P value < 0.05 and Q value < 0.25.
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1p gain cnv correlated to 'CN_CNMF', 'RPPA_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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1q gain cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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2p gain cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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2q gain cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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3p gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.
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3q gain cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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4q gain cnv correlated to 'RPPA_CNMF' and 'MRNASEQ_CNMF'.
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5p gain cnv correlated to 'CN_CNMF'.
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5q gain cnv correlated to 'CN_CNMF'.
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6p gain cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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6q gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.
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7p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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7q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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8p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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8q gain cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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9p gain cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.
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9q gain cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.
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10p gain cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.
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10q gain cnv correlated to 'METHLYATION_CNMF'.
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11p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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11q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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12p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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12q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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13q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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16p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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16q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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17q gain cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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18p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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18q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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19p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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19q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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20p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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20q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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21q gain cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.
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22q gain cnv correlated to 'METHLYATION_CNMF'.
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xp gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
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xq gain cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.
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1p loss cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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1q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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4p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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4q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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5p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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5q loss cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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6p loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.
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7q loss cnv correlated to 'CN_CNMF'.
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8p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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8q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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9p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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9q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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10p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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10q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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11p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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11q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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12p loss cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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12q loss cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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13q loss cnv correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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14q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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15q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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16p loss cnv correlated to 'RPPA_CHIERARCHICAL'.
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16q loss cnv correlated to 'RPPA_CHIERARCHICAL'.
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17p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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17q loss cnv correlated to 'CN_CNMF'.
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18p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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18q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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19p loss cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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19q loss cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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20p loss cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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21q loss cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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22q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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xp loss cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.
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xq loss cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 81 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 311 significant findings detected.
|
Clinical Features |
MRNA CNMF |
MRNA CHIERARCHICAL |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
||
| nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
| 20q gain | 321 (71%) | 129 |
1e-05 (0.000121) |
1e-05 (0.000121) |
1e-05 (0.000121) |
1e-05 (0.000121) |
0.00034 (0.00252) |
0.00044 (0.0031) |
1e-05 (0.000121) |
1e-05 (0.000121) |
0.797 (0.931) |
0.00116 (0.00692) |
0.894 (0.988) |
0.00603 (0.027) |
| 14q loss | 139 (31%) | 311 |
1e-05 (0.000121) |
9e-05 (0.000818) |
1e-05 (0.000121) |
1e-05 (0.000121) |
0.00184 (0.0103) |
0.0244 (0.0866) |
1e-05 (0.000121) |
1e-05 (0.000121) |
0.296 (0.533) |
0.0214 (0.079) |
0.0828 (0.221) |
0.00538 (0.025) |
| 18p loss | 254 (56%) | 196 |
1e-05 (0.000121) |
1e-05 (0.000121) |
1e-05 (0.000121) |
1e-05 (0.000121) |
0.0014 (0.00805) |
0.00388 (0.0191) |
1e-05 (0.000121) |
1e-05 (0.000121) |
0.991 (1.00) |
0.0198 (0.075) |
0.464 (0.698) |
0.00046 (0.00313) |
| 18q loss | 271 (60%) | 179 |
1e-05 (0.000121) |
1e-05 (0.000121) |
1e-05 (0.000121) |
1e-05 (0.000121) |
0.00575 (0.0262) |
0.00299 (0.0154) |
1e-05 (0.000121) |
1e-05 (0.000121) |
0.747 (0.901) |
0.0131 (0.0532) |
0.26 (0.486) |
0.00048 (0.00324) |
| 7p gain | 246 (55%) | 204 |
0.00563 (0.0258) |
1e-05 (0.000121) |
1e-05 (0.000121) |
0.00026 (0.00205) |
0.00036 (0.00261) |
0.00211 (0.0115) |
3e-05 (0.000317) |
1e-05 (0.000121) |
0.537 (0.761) |
0.48 (0.714) |
0.96 (1.00) |
0.0173 (0.0672) |
| 7q gain | 223 (50%) | 227 |
0.00407 (0.02) |
1e-05 (0.000121) |
1e-05 (0.000121) |
0.0115 (0.0476) |
0.006 (0.027) |
0.00966 (0.0408) |
0.00112 (0.0068) |
1e-05 (0.000121) |
0.469 (0.704) |
0.659 (0.835) |
0.82 (0.941) |
0.0103 (0.0432) |
| 11q gain | 51 (11%) | 399 |
0.00016 (0.00134) |
1e-05 (0.000121) |
1e-05 (0.000121) |
0.00482 (0.0229) |
0.0287 (0.0985) |
0.602 (0.81) |
4e-05 (0.000418) |
1e-05 (0.000121) |
0.63 (0.821) |
0.00596 (0.0269) |
1 (1.00) |
0.0343 (0.115) |
| 8p loss | 142 (32%) | 308 |
0.0158 (0.0624) |
0.00084 (0.0053) |
1e-05 (0.000121) |
0.0056 (0.0258) |
0.0148 (0.059) |
0.0118 (0.0484) |
8e-05 (0.000748) |
1e-05 (0.000121) |
0.626 (0.82) |
0.134 (0.317) |
0.809 (0.936) |
0.0215 (0.0791) |
| 17p loss | 236 (52%) | 214 |
1e-05 (0.000121) |
1e-05 (0.000121) |
1e-05 (0.000121) |
1e-05 (0.000121) |
0.0249 (0.0879) |
0.00717 (0.0317) |
1e-05 (0.000121) |
1e-05 (0.000121) |
0.804 (0.935) |
0.0643 (0.188) |
0.607 (0.814) |
0.00115 (0.0069) |
| 11p gain | 53 (12%) | 397 |
0.00061 (0.00395) |
0.0001 (0.000892) |
1e-05 (0.000121) |
0.00094 (0.00578) |
0.0753 (0.206) |
0.404 (0.64) |
0.00033 (0.00249) |
1e-05 (0.000121) |
0.896 (0.988) |
0.00202 (0.0111) |
0.927 (1.00) |
0.0886 (0.233) |
| 13q gain | 256 (57%) | 194 |
7e-05 (0.000687) |
1e-05 (0.000121) |
1e-05 (0.000121) |
0.00034 (0.00252) |
0.0372 (0.123) |
0.117 (0.286) |
1e-05 (0.000121) |
1e-05 (0.000121) |
0.441 (0.678) |
0.792 (0.928) |
0.138 (0.322) |
0.165 (0.362) |
| 17q gain | 81 (18%) | 369 |
0.0672 (0.193) |
0.0398 (0.131) |
1e-05 (0.000121) |
0.0001 (0.000892) |
0.366 (0.612) |
0.0281 (0.0968) |
1e-05 (0.000121) |
0.00072 (0.0046) |
0.00878 (0.0376) |
0.0649 (0.188) |
0.519 (0.745) |
0.699 (0.865) |
| 20p gain | 243 (54%) | 207 |
0.00291 (0.0151) |
2e-05 (0.000226) |
1e-05 (0.000121) |
0.0003 (0.0023) |
0.0435 (0.139) |
0.233 (0.453) |
0.00027 (0.00212) |
1e-05 (0.000121) |
0.705 (0.868) |
0.0695 (0.198) |
0.148 (0.335) |
0.246 (0.467) |
| 4p loss | 138 (31%) | 312 |
7e-05 (0.000687) |
0.00139 (0.00804) |
1e-05 (0.000121) |
0.00086 (0.00536) |
0.105 (0.263) |
0.365 (0.612) |
1e-05 (0.000121) |
1e-05 (0.000121) |
0.464 (0.698) |
0.38 (0.624) |
0.0614 (0.182) |
0.0235 (0.0847) |
| 10p loss | 69 (15%) | 381 |
0.0202 (0.076) |
0.0249 (0.0879) |
1e-05 (0.000121) |
0.00078 (0.00496) |
0.0132 (0.0534) |
0.354 (0.6) |
8e-05 (0.000748) |
0.00011 (0.000963) |
0.498 (0.726) |
0.234 (0.454) |
0.502 (0.731) |
0.0912 (0.237) |
| 10q loss | 73 (16%) | 377 |
0.0243 (0.0866) |
0.0414 (0.134) |
1e-05 (0.000121) |
0.00033 (0.00249) |
0.0113 (0.0469) |
0.176 (0.379) |
1e-05 (0.000121) |
1e-05 (0.000121) |
0.611 (0.814) |
0.392 (0.629) |
0.0722 (0.201) |
0.449 (0.682) |
| 15q loss | 157 (35%) | 293 |
0.00202 (0.0111) |
0.00135 (0.0079) |
1e-05 (0.000121) |
0.00038 (0.00274) |
0.0139 (0.0557) |
0.0504 (0.157) |
1e-05 (0.000121) |
1e-05 (0.000121) |
0.9 (0.989) |
0.841 (0.953) |
0.142 (0.329) |
0.0646 (0.188) |
| 2p gain | 82 (18%) | 368 |
0.0713 (0.2) |
0.0217 (0.0797) |
0.00465 (0.0225) |
0.00217 (0.0118) |
0.111 (0.274) |
0.131 (0.311) |
8e-05 (0.000748) |
0.00343 (0.0171) |
0.404 (0.64) |
0.0152 (0.0603) |
0.899 (0.988) |
0.809 (0.936) |
| 8q gain | 227 (50%) | 223 |
0.882 (0.979) |
0.0206 (0.0775) |
1e-05 (0.000121) |
0.102 (0.257) |
0.0736 (0.203) |
0.0347 (0.116) |
0.00276 (0.0144) |
0.00045 (0.00312) |
0.653 (0.833) |
0.014 (0.0559) |
0.408 (0.642) |
0.0726 (0.201) |
| 1p loss | 95 (21%) | 355 |
0.0275 (0.0954) |
0.193 (0.398) |
1e-05 (0.000121) |
0.00318 (0.0161) |
0.645 (0.828) |
0.747 (0.901) |
8e-05 (0.000748) |
3e-05 (0.000317) |
0.882 (0.979) |
0.02 (0.0756) |
0.852 (0.96) |
0.572 (0.789) |
| 4q loss | 127 (28%) | 323 |
0.00011 (0.000963) |
0.00949 (0.0403) |
1e-05 (0.000121) |
9e-05 (0.000818) |
0.105 (0.263) |
0.247 (0.467) |
1e-05 (0.000121) |
1e-05 (0.000121) |
0.217 (0.43) |
0.288 (0.523) |
0.251 (0.474) |
0.204 (0.41) |
| 12p loss | 47 (10%) | 403 |
0.0626 (0.185) |
0.00813 (0.0351) |
1e-05 (0.000121) |
0.00471 (0.0226) |
0.41 (0.642) |
0.799 (0.933) |
0.00092 (0.0057) |
6e-05 (0.000601) |
0.881 (0.979) |
0.41 (0.642) |
0.44 (0.677) |
0.0208 (0.0778) |
| 12q loss | 49 (11%) | 401 |
0.11 (0.273) |
0.00777 (0.034) |
1e-05 (0.000121) |
0.00807 (0.035) |
0.524 (0.749) |
0.687 (0.856) |
0.00029 (0.00226) |
0.00013 (0.00111) |
0.955 (1.00) |
0.68 (0.85) |
0.914 (0.995) |
0.0213 (0.079) |
| 20p loss | 44 (10%) | 406 |
0.0895 (0.233) |
0.00066 (0.00425) |
9e-05 (0.000818) |
0.0351 (0.117) |
0.908 (0.993) |
0.26 (0.487) |
0.0189 (0.0724) |
0.00971 (0.0409) |
0.831 (0.946) |
0.0443 (0.14) |
0.483 (0.715) |
0.625 (0.819) |
| 22q loss | 146 (32%) | 304 |
0.00051 (0.00342) |
0.00043 (0.00305) |
1e-05 (0.000121) |
0.00302 (0.0154) |
0.177 (0.379) |
0.305 (0.541) |
2e-05 (0.000226) |
1e-05 (0.000121) |
0.186 (0.389) |
0.399 (0.636) |
0.616 (0.816) |
0.445 (0.68) |
| 2q gain | 78 (17%) | 372 |
0.0703 (0.199) |
0.0218 (0.0797) |
0.00152 (0.00869) |
0.00113 (0.00682) |
0.284 (0.517) |
0.144 (0.331) |
0.00035 (0.00256) |
0.00138 (0.00803) |
0.492 (0.721) |
0.0733 (0.202) |
1 (1.00) |
0.558 (0.779) |
| 16p gain | 107 (24%) | 343 |
3e-05 (0.000317) |
1e-05 (0.000121) |
1e-05 (0.000121) |
0.0987 (0.251) |
0.158 (0.352) |
0.105 (0.263) |
0.00161 (0.0091) |
1e-05 (0.000121) |
0.575 (0.79) |
0.189 (0.394) |
0.905 (0.992) |
0.14 (0.325) |
| 16q gain | 105 (23%) | 345 |
6e-05 (0.000601) |
1e-05 (0.000121) |
1e-05 (0.000121) |
0.143 (0.33) |
0.182 (0.384) |
0.156 (0.349) |
0.00243 (0.0129) |
1e-05 (0.000121) |
0.804 (0.935) |
0.182 (0.384) |
1 (1.00) |
0.177 (0.379) |
| 11q loss | 63 (14%) | 387 |
0.0413 (0.134) |
0.0159 (0.0625) |
0.00356 (0.0177) |
0.00503 (0.0237) |
0.602 (0.81) |
0.931 (1.00) |
0.237 (0.457) |
0.00236 (0.0126) |
0.84 (0.953) |
0.68 (0.85) |
0.779 (0.919) |
0.837 (0.952) |
| 21q loss | 124 (28%) | 326 |
0.00992 (0.0416) |
0.0852 (0.226) |
1e-05 (0.000121) |
0.0433 (0.139) |
0.226 (0.441) |
0.6 (0.81) |
1e-05 (0.000121) |
0.00892 (0.038) |
0.459 (0.694) |
0.0514 (0.159) |
0.814 (0.937) |
0.381 (0.624) |
| 6p gain | 85 (19%) | 365 |
0.212 (0.422) |
3e-05 (0.000317) |
1e-05 (0.000121) |
0.214 (0.425) |
0.598 (0.81) |
0.993 (1.00) |
0.043 (0.138) |
0.0171 (0.0665) |
0.549 (0.77) |
0.934 (1.00) |
0.264 (0.492) |
0.162 (0.36) |
| 18p gain | 22 (5%) | 428 |
0.0921 (0.239) |
0.673 (0.845) |
5e-05 (0.000517) |
0.00103 (0.0063) |
0.83 (0.946) |
0.894 (0.988) |
0.0334 (0.113) |
3e-05 (0.000317) |
0.271 (0.5) |
0.177 (0.379) |
0.911 (0.994) |
0.484 (0.715) |
| 18q gain | 13 (3%) | 437 |
0.144 (0.331) |
1 (1.00) |
0.00449 (0.0219) |
0.013 (0.0529) |
0.677 (0.849) |
0.475 (0.71) |
0.0189 (0.0724) |
3e-05 (0.000317) |
0.559 (0.779) |
0.183 (0.386) |
0.449 (0.682) |
0.194 (0.398) |
| 19q gain | 84 (19%) | 366 |
0.29 (0.524) |
0.193 (0.398) |
0.00261 (0.0138) |
0.294 (0.53) |
0.0711 (0.2) |
0.0609 (0.182) |
0.494 (0.723) |
0.00012 (0.00103) |
0.165 (0.362) |
0.72 (0.88) |
0.0406 (0.133) |
0.00035 (0.00256) |
| 1q loss | 56 (12%) | 394 |
0.412 (0.643) |
0.696 (0.862) |
2e-05 (0.000226) |
0.161 (0.358) |
0.44 (0.677) |
0.587 (0.802) |
0.00195 (0.0108) |
0.00578 (0.0263) |
0.641 (0.827) |
0.00536 (0.025) |
0.172 (0.374) |
0.819 (0.941) |
| 5q loss | 78 (17%) | 372 |
0.164 (0.362) |
0.305 (0.541) |
2e-05 (0.000226) |
0.208 (0.415) |
0.0227 (0.0822) |
0.143 (0.331) |
0.00015 (0.00127) |
0.00025 (0.00199) |
0.902 (0.989) |
0.696 (0.862) |
0.755 (0.906) |
0.353 (0.6) |
| 9p loss | 54 (12%) | 396 |
0.57 (0.789) |
0.0657 (0.19) |
0.00054 (0.0036) |
0.00292 (0.0151) |
0.907 (0.993) |
0.359 (0.605) |
8e-05 (0.000748) |
0.0006 (0.00394) |
0.371 (0.614) |
0.278 (0.51) |
0.41 (0.642) |
0.318 (0.557) |
| 9q loss | 53 (12%) | 397 |
0.119 (0.288) |
0.0614 (0.182) |
0.00022 (0.00178) |
0.00058 (0.00384) |
0.986 (1.00) |
0.544 (0.769) |
0.00017 (0.00141) |
0.00122 (0.00723) |
0.541 (0.766) |
0.189 (0.393) |
0.221 (0.434) |
0.373 (0.616) |
| 19p loss | 40 (9%) | 410 |
1 (1.00) |
0.345 (0.593) |
0.0504 (0.157) |
0.326 (0.568) |
0.571 (0.789) |
0.352 (0.6) |
0.00328 (0.0164) |
0.0224 (0.0812) |
0.0424 (0.137) |
0.00454 (0.0221) |
0.652 (0.833) |
0.629 (0.821) |
| 1p gain | 35 (8%) | 415 |
0.639 (0.826) |
0.443 (0.678) |
0.0309 (0.106) |
0.611 (0.814) |
0.00849 (0.0365) |
0.059 (0.179) |
0.773 (0.919) |
0.0323 (0.11) |
0.389 (0.629) |
0.145 (0.332) |
0.258 (0.485) |
0.149 (0.335) |
| 1q gain | 80 (18%) | 370 |
0.871 (0.975) |
0.692 (0.859) |
0.0113 (0.0469) |
0.106 (0.265) |
0.195 (0.399) |
0.00469 (0.0226) |
0.486 (0.717) |
0.0944 (0.242) |
0.734 (0.889) |
0.137 (0.322) |
0.0456 (0.144) |
0.471 (0.706) |
| 3q gain | 65 (14%) | 385 |
0.0926 (0.239) |
0.00012 (0.00103) |
1e-05 (0.000121) |
0.083 (0.221) |
0.0942 (0.242) |
0.284 (0.517) |
0.234 (0.453) |
0.0265 (0.0927) |
0.667 (0.842) |
0.635 (0.825) |
0.789 (0.927) |
0.0568 (0.173) |
| 19p gain | 74 (16%) | 376 |
0.351 (0.6) |
0.272 (0.5) |
6e-05 (0.000601) |
0.11 (0.273) |
0.257 (0.485) |
0.229 (0.447) |
0.392 (0.629) |
0.00022 (0.00178) |
0.0892 (0.233) |
0.331 (0.574) |
0.179 (0.381) |
0.0194 (0.0738) |
| 13q loss | 12 (3%) | 438 |
0.873 (0.976) |
0.438 (0.676) |
0.246 (0.467) |
0.043 (0.138) |
0.00161 (0.0091) |
0.093 (0.24) |
0.459 (0.694) |
0.92 (0.999) |
0.6 (0.81) |
0.107 (0.266) |
0.0342 (0.115) |
0.806 (0.936) |
| 19q loss | 35 (8%) | 415 |
0.732 (0.888) |
0.705 (0.868) |
0.0671 (0.193) |
0.444 (0.679) |
0.209 (0.417) |
0.148 (0.335) |
0.00476 (0.0227) |
0.0171 (0.0665) |
0.299 (0.536) |
0.049 (0.153) |
0.324 (0.565) |
0.462 (0.696) |
| 3p gain | 45 (10%) | 405 |
0.136 (0.32) |
0.00757 (0.0333) |
2e-05 (0.000226) |
0.295 (0.533) |
0.147 (0.335) |
0.124 (0.3) |
0.775 (0.919) |
0.355 (0.6) |
0.688 (0.856) |
0.849 (0.96) |
0.719 (0.88) |
0.391 (0.629) |
| 4q gain | 17 (4%) | 433 |
0.128 (0.305) |
0.121 (0.292) |
0.151 (0.34) |
0.815 (0.938) |
0.00675 (0.03) |
0.122 (0.294) |
0.0349 (0.117) |
0.548 (0.77) |
0.148 (0.335) |
0.134 (0.317) |
||
| 6q gain | 77 (17%) | 373 |
0.185 (0.388) |
2e-05 (0.000226) |
1e-05 (0.000121) |
0.259 (0.486) |
0.932 (1.00) |
0.55 (0.771) |
0.285 (0.517) |
0.173 (0.374) |
0.502 (0.731) |
0.914 (0.995) |
0.613 (0.814) |
0.164 (0.362) |
| 8p gain | 132 (29%) | 318 |
0.974 (1.00) |
0.965 (1.00) |
0.00022 (0.00178) |
0.975 (1.00) |
0.308 (0.542) |
0.386 (0.628) |
0.024 (0.086) |
0.0566 (0.173) |
0.573 (0.789) |
0.186 (0.39) |
0.881 (0.979) |
0.917 (0.997) |
| 9p gain | 81 (18%) | 369 |
0.194 (0.398) |
0.138 (0.322) |
0.00046 (0.00313) |
0.946 (1.00) |
0.00167 (0.00938) |
0.383 (0.625) |
0.931 (1.00) |
0.672 (0.845) |
0.874 (0.976) |
0.923 (1.00) |
0.0707 (0.199) |
0.145 (0.332) |
| 9q gain | 71 (16%) | 379 |
0.165 (0.362) |
0.202 (0.407) |
0.0266 (0.0927) |
0.814 (0.937) |
0.00045 (0.00312) |
0.513 (0.738) |
0.964 (1.00) |
0.939 (1.00) |
0.353 (0.6) |
0.391 (0.629) |
0.307 (0.542) |
0.536 (0.76) |
| 10p gain | 37 (8%) | 413 |
0.598 (0.81) |
1 (1.00) |
0.00264 (0.0139) |
0.371 (0.614) |
0.022 (0.0801) |
0.0686 (0.196) |
0.379 (0.623) |
0.339 (0.584) |
0.426 (0.662) |
0.719 (0.88) |
0.931 (1.00) |
0.354 (0.6) |
| 12p gain | 93 (21%) | 357 |
0.177 (0.379) |
1 (1.00) |
0.00562 (0.0258) |
0.00322 (0.0162) |
0.77 (0.917) |
0.713 (0.876) |
0.938 (1.00) |
0.653 (0.833) |
0.427 (0.662) |
0.547 (0.77) |
0.35 (0.599) |
0.963 (1.00) |
| 12q gain | 87 (19%) | 363 |
0.195 (0.398) |
0.896 (0.988) |
0.00525 (0.0247) |
0.00061 (0.00395) |
0.609 (0.814) |
0.732 (0.888) |
0.773 (0.919) |
0.622 (0.819) |
0.199 (0.404) |
0.181 (0.383) |
0.509 (0.733) |
0.714 (0.877) |
| 21q gain | 24 (5%) | 426 |
0.0355 (0.118) |
0.297 (0.534) |
0.00132 (0.00778) |
0.576 (0.79) |
0.728 (0.885) |
0.972 (1.00) |
0.64 (0.826) |
0.0969 (0.247) |
0.22 (0.434) |
0.266 (0.493) |
||
| xp gain | 67 (15%) | 383 |
0.0995 (0.251) |
0.24 (0.459) |
0.00046 (0.00313) |
0.0777 (0.212) |
0.22 (0.434) |
0.644 (0.828) |
0.776 (0.919) |
0.08 (0.216) |
0.791 (0.927) |
0.967 (1.00) |
0.0434 (0.139) |
0.0607 (0.182) |
| xq gain | 76 (17%) | 374 |
0.0437 (0.139) |
0.237 (0.457) |
0.00023 (0.00185) |
0.267 (0.494) |
0.13 (0.31) |
0.506 (0.731) |
0.802 (0.935) |
0.577 (0.79) |
0.434 (0.673) |
0.957 (1.00) |
0.328 (0.57) |
0.271 (0.499) |
| 5p loss | 59 (13%) | 391 |
0.66 (0.835) |
0.855 (0.961) |
0.0003 (0.0023) |
0.0805 (0.217) |
0.323 (0.565) |
0.679 (0.85) |
0.0724 (0.201) |
0.00086 (0.00536) |
0.751 (0.904) |
0.67 (0.845) |
0.302 (0.54) |
0.396 (0.635) |
| 8q loss | 25 (6%) | 425 |
0.811 (0.936) |
0.399 (0.636) |
0.00218 (0.0118) |
0.376 (0.619) |
0.425 (0.662) |
0.66 (0.835) |
0.356 (0.601) |
0.505 (0.731) |
0.391 (0.629) |
0.746 (0.901) |
0.405 (0.64) |
0.00221 (0.0119) |
| 11p loss | 52 (12%) | 398 |
0.224 (0.439) |
0.193 (0.398) |
0.00801 (0.0349) |
0.0209 (0.0779) |
0.728 (0.885) |
0.872 (0.975) |
0.0799 (0.216) |
0.0849 (0.225) |
0.854 (0.96) |
0.205 (0.412) |
0.635 (0.825) |
0.768 (0.917) |
| xp loss | 65 (14%) | 385 |
0.0278 (0.0962) |
0.237 (0.457) |
0.0176 (0.0679) |
0.794 (0.928) |
0.0676 (0.193) |
0.164 (0.362) |
0.56 (0.779) |
0.519 (0.745) |
0.063 (0.186) |
0.438 (0.676) |
0.631 (0.821) |
0.18 (0.383) |
| xq loss | 54 (12%) | 396 |
0.016 (0.0629) |
0.252 (0.475) |
0.00307 (0.0156) |
0.0992 (0.251) |
0.243 (0.465) |
0.371 (0.614) |
0.191 (0.396) |
0.201 (0.407) |
0.0704 (0.199) |
0.657 (0.835) |
0.483 (0.715) |
0.0675 (0.193) |
| 5p gain | 69 (15%) | 381 |
0.354 (0.6) |
0.119 (0.288) |
0.0244 (0.0866) |
0.589 (0.803) |
0.528 (0.751) |
0.993 (1.00) |
0.119 (0.288) |
0.0756 (0.206) |
0.848 (0.959) |
0.448 (0.682) |
0.722 (0.88) |
0.558 (0.779) |
| 5q gain | 44 (10%) | 406 |
0.875 (0.976) |
0.775 (0.919) |
0.00645 (0.0288) |
0.652 (0.833) |
0.476 (0.711) |
0.646 (0.828) |
0.206 (0.412) |
0.0717 (0.2) |
0.506 (0.731) |
0.0949 (0.243) |
1 (1.00) |
0.854 (0.96) |
| 10q gain | 23 (5%) | 427 |
0.17 (0.37) |
0.443 (0.678) |
0.0551 (0.17) |
0.0482 (0.151) |
0.365 (0.612) |
0.593 (0.807) |
0.78 (0.92) |
0.588 (0.802) |
0.752 (0.904) |
0.862 (0.968) |
0.888 (0.984) |
0.244 (0.465) |
| 22q gain | 13 (3%) | 437 |
1 (1.00) |
0.79 (0.927) |
0.0609 (0.182) |
0.0466 (0.146) |
0.525 (0.749) |
0.621 (0.819) |
0.0565 (0.173) |
0.219 (0.433) |
0.925 (1.00) |
0.645 (0.828) |
0.828 (0.945) |
0.481 (0.714) |
| 6p loss | 34 (8%) | 416 |
1 (1.00) |
0.456 (0.691) |
0.368 (0.612) |
0.527 (0.751) |
0.177 (0.379) |
0.138 (0.322) |
0.303 (0.54) |
0.965 (1.00) |
0.617 (0.816) |
0.786 (0.926) |
0.0262 (0.0919) |
0.082 (0.22) |
| 7q loss | 4 (1%) | 446 |
0.0377 (0.124) |
0.374 (0.616) |
0.672 (0.845) |
0.722 (0.88) |
0.561 (0.781) |
0.63 (0.821) |
||||||
| 16p loss | 31 (7%) | 419 |
0.405 (0.64) |
0.688 (0.856) |
0.912 (0.995) |
0.829 (0.945) |
0.387 (0.628) |
0.0129 (0.0525) |
0.173 (0.374) |
0.198 (0.403) |
0.504 (0.731) |
0.481 (0.714) |
0.623 (0.819) |
1 (1.00) |
| 16q loss | 29 (6%) | 421 |
0.406 (0.641) |
0.688 (0.856) |
0.349 (0.599) |
1 (1.00) |
0.217 (0.43) |
0.0336 (0.114) |
0.147 (0.335) |
0.307 (0.542) |
0.524 (0.749) |
0.756 (0.906) |
0.624 (0.819) |
1 (1.00) |
| 17q loss | 66 (15%) | 384 |
0.265 (0.492) |
0.381 (0.624) |
0.00041 (0.00293) |
0.0891 (0.233) |
0.565 (0.785) |
0.618 (0.816) |
0.166 (0.362) |
0.0579 (0.176) |
0.328 (0.57) |
0.268 (0.496) |
0.705 (0.868) |
0.164 (0.362) |
| 4p gain | 12 (3%) | 438 |
0.0751 (0.206) |
0.155 (0.349) |
0.317 (0.556) |
0.922 (1.00) |
0.107 (0.265) |
0.657 (0.835) |
0.61 (0.814) |
0.577 (0.79) |
||||
| 14q gain | 35 (8%) | 415 |
0.338 (0.584) |
0.64 (0.826) |
0.505 (0.731) |
0.59 (0.804) |
0.408 (0.642) |
0.755 (0.906) |
0.488 (0.717) |
0.571 (0.789) |
0.67 (0.845) |
0.183 (0.386) |
0.238 (0.457) |
0.339 (0.584) |
| 15q gain | 12 (3%) | 438 |
1 (1.00) |
0.81 (0.936) |
0.493 (0.722) |
0.224 (0.439) |
0.081 (0.218) |
0.079 (0.215) |
0.978 (1.00) |
0.852 (0.96) |
0.924 (1.00) |
0.765 (0.915) |
||
| 17p gain | 29 (6%) | 421 |
0.841 (0.953) |
0.566 (0.785) |
0.426 (0.662) |
0.303 (0.54) |
0.114 (0.28) |
0.368 (0.612) |
0.366 (0.612) |
0.115 (0.28) |
0.385 (0.628) |
0.761 (0.911) |
0.548 (0.77) |
0.46 (0.695) |
| 2p loss | 6 (1%) | 444 |
0.898 (0.988) |
0.811 (0.936) |
0.285 (0.517) |
0.705 (0.868) |
0.787 (0.926) |
0.131 (0.311) |
0.127 (0.304) |
0.638 (0.826) |
0.48 (0.714) |
|||
| 2q loss | 7 (2%) | 443 |
1 (1.00) |
0.507 (0.731) |
0.615 (0.816) |
0.31 (0.545) |
0.438 (0.676) |
0.398 (0.636) |
0.0625 (0.185) |
0.389 (0.629) |
0.245 (0.467) |
|||
| 3p loss | 55 (12%) | 395 |
0.778 (0.919) |
0.488 (0.717) |
0.0854 (0.226) |
0.361 (0.607) |
0.6 (0.81) |
0.627 (0.82) |
0.0634 (0.186) |
0.0562 (0.173) |
0.611 (0.814) |
0.607 (0.814) |
0.306 (0.542) |
0.658 (0.835) |
| 3q loss | 34 (8%) | 416 |
0.826 (0.945) |
1 (1.00) |
0.769 (0.917) |
0.613 (0.814) |
0.405 (0.64) |
0.872 (0.975) |
0.0869 (0.229) |
0.199 (0.404) |
0.262 (0.488) |
0.93 (1.00) |
0.897 (0.988) |
0.126 (0.301) |
| 6q loss | 46 (10%) | 404 |
0.821 (0.941) |
1 (1.00) |
0.536 (0.76) |
0.488 (0.717) |
0.201 (0.407) |
0.0967 (0.247) |
0.282 (0.515) |
0.725 (0.883) |
0.608 (0.814) |
0.964 (1.00) |
0.0597 (0.18) |
0.0645 (0.188) |
| 20q loss | 4 (1%) | 446 |
0.828 (0.945) |
0.19 (0.394) |
0.548 (0.77) |
0.386 (0.628) |
0.305 (0.541) |
P value = 0.0309 (Fisher's exact test), Q value = 0.11
Table S1. Gene #1: '1p gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 1P GAIN MUTATED | 9 | 20 | 6 |
| 1P GAIN WILD-TYPE | 193 | 150 | 72 |
Figure S1. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00849 (Fisher's exact test), Q value = 0.037
Table S2. Gene #1: '1p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 78 | 127 | 26 | 94 |
| 1P GAIN MUTATED | 6 | 13 | 4 | 1 |
| 1P GAIN WILD-TYPE | 72 | 114 | 22 | 93 |
Figure S2. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 0.0323 (Fisher's exact test), Q value = 0.11
Table S3. Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 1P GAIN MUTATED | 6 | 14 | 2 | 12 | 1 |
| 1P GAIN WILD-TYPE | 73 | 94 | 94 | 117 | 35 |
Figure S3. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0113 (Fisher's exact test), Q value = 0.047
Table S4. Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 1Q GAIN MUTATED | 26 | 42 | 12 |
| 1Q GAIN WILD-TYPE | 176 | 128 | 66 |
Figure S4. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00469 (Fisher's exact test), Q value = 0.023
Table S5. Gene #2: '1q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 59 | 48 | 56 | 68 | 68 | 26 |
| 1Q GAIN MUTATED | 16 | 7 | 17 | 12 | 5 | 2 |
| 1Q GAIN WILD-TYPE | 43 | 41 | 39 | 56 | 63 | 24 |
Figure S5. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 0.0456 (Fisher's exact test), Q value = 0.14
Table S6. Gene #2: '1q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 29 | 32 | 24 |
| 1Q GAIN MUTATED | 1 | 7 | 6 |
| 1Q GAIN WILD-TYPE | 28 | 25 | 18 |
Figure S6. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
P value = 0.0217 (Fisher's exact test), Q value = 0.08
Table S7. Gene #3: '2p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 2P GAIN MUTATED | 2 | 10 | 9 |
| 2P GAIN WILD-TYPE | 40 | 62 | 23 |
Figure S7. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.00465 (Fisher's exact test), Q value = 0.022
Table S8. Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 2P GAIN MUTATED | 26 | 44 | 12 |
| 2P GAIN WILD-TYPE | 176 | 126 | 66 |
Figure S8. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00217 (Fisher's exact test), Q value = 0.012
Table S9. Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 2P GAIN MUTATED | 36 | 12 | 12 |
| 2P GAIN WILD-TYPE | 82 | 87 | 64 |
Figure S9. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 8e-05 (Fisher's exact test), Q value = 0.00075
Table S10. Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 2P GAIN MUTATED | 39 | 9 | 16 | 18 |
| 2P GAIN WILD-TYPE | 82 | 98 | 74 | 112 |
Figure S10. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 0.00343 (Fisher's exact test), Q value = 0.017
Table S11. Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 2P GAIN MUTATED | 16 | 30 | 12 | 23 | 1 |
| 2P GAIN WILD-TYPE | 63 | 78 | 84 | 106 | 35 |
Figure S11. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0152 (Fisher's exact test), Q value = 0.06
Table S12. Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 135 | 50 | 77 | 135 |
| 2P GAIN MUTATED | 20 | 9 | 23 | 17 |
| 2P GAIN WILD-TYPE | 115 | 41 | 54 | 118 |
Figure S12. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0218 (Fisher's exact test), Q value = 0.08
Table S13. Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 2Q GAIN MUTATED | 2 | 10 | 9 |
| 2Q GAIN WILD-TYPE | 40 | 62 | 23 |
Figure S13. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.00152 (Fisher's exact test), Q value = 0.0087
Table S14. Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 2Q GAIN MUTATED | 22 | 43 | 13 |
| 2Q GAIN WILD-TYPE | 180 | 127 | 65 |
Figure S14. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00113 (Fisher's exact test), Q value = 0.0068
Table S15. Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 2Q GAIN MUTATED | 35 | 11 | 10 |
| 2Q GAIN WILD-TYPE | 83 | 88 | 66 |
Figure S15. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00035 (Fisher's exact test), Q value = 0.0026
Table S16. Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 2Q GAIN MUTATED | 36 | 10 | 14 | 18 |
| 2Q GAIN WILD-TYPE | 85 | 97 | 76 | 112 |
Figure S16. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 0.00138 (Fisher's exact test), Q value = 0.008
Table S17. Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 2Q GAIN MUTATED | 16 | 29 | 9 | 23 | 1 |
| 2Q GAIN WILD-TYPE | 63 | 79 | 87 | 106 | 35 |
Figure S17. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00757 (Fisher's exact test), Q value = 0.033
Table S18. Gene #5: '3p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 3P GAIN MUTATED | 2 | 4 | 8 |
| 3P GAIN WILD-TYPE | 40 | 68 | 24 |
Figure S18. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 2e-05 (Fisher's exact test), Q value = 0.00023
Table S19. Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 3P GAIN MUTATED | 9 | 32 | 4 |
| 3P GAIN WILD-TYPE | 193 | 138 | 74 |
Figure S19. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00012 (Fisher's exact test), Q value = 0.001
Table S20. Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 3Q GAIN MUTATED | 2 | 6 | 12 |
| 3Q GAIN WILD-TYPE | 40 | 66 | 20 |
Figure S20. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S21. Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 3Q GAIN MUTATED | 10 | 46 | 9 |
| 3Q GAIN WILD-TYPE | 192 | 124 | 69 |
Figure S21. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0265 (Fisher's exact test), Q value = 0.093
Table S22. Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 3Q GAIN MUTATED | 16 | 19 | 8 | 21 | 1 |
| 3Q GAIN WILD-TYPE | 63 | 89 | 88 | 108 | 35 |
Figure S22. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00675 (Fisher's exact test), Q value = 0.03
Table S23. Gene #8: '4q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 78 | 127 | 26 | 94 |
| 4Q GAIN MUTATED | 7 | 1 | 1 | 1 |
| 4Q GAIN WILD-TYPE | 71 | 126 | 25 | 93 |
Figure S23. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 0.0349 (Fisher's exact test), Q value = 0.12
Table S24. Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 4Q GAIN MUTATED | 8 | 0 | 4 | 5 |
| 4Q GAIN WILD-TYPE | 113 | 107 | 86 | 125 |
Figure S24. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 0.0244 (Fisher's exact test), Q value = 0.087
Table S25. Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 5P GAIN MUTATED | 21 | 34 | 14 |
| 5P GAIN WILD-TYPE | 181 | 136 | 64 |
Figure S25. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00645 (Fisher's exact test), Q value = 0.029
Table S26. Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 5Q GAIN MUTATED | 11 | 26 | 7 |
| 5Q GAIN WILD-TYPE | 191 | 144 | 71 |
Figure S26. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.00032
Table S27. Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 6P GAIN MUTATED | 5 | 7 | 16 |
| 6P GAIN WILD-TYPE | 37 | 65 | 16 |
Figure S27. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S28. Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 6P GAIN MUTATED | 16 | 57 | 12 |
| 6P GAIN WILD-TYPE | 186 | 113 | 66 |
Figure S28. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.043 (Fisher's exact test), Q value = 0.14
Table S29. Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 6P GAIN MUTATED | 24 | 11 | 19 | 31 |
| 6P GAIN WILD-TYPE | 97 | 96 | 71 | 99 |
Figure S29. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 0.0171 (Fisher's exact test), Q value = 0.066
Table S30. Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 6P GAIN MUTATED | 20 | 21 | 9 | 31 | 4 |
| 6P GAIN WILD-TYPE | 59 | 87 | 87 | 98 | 32 |
Figure S30. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 2e-05 (Fisher's exact test), Q value = 0.00023
Table S31. Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 6Q GAIN MUTATED | 5 | 4 | 14 |
| 6Q GAIN WILD-TYPE | 37 | 68 | 18 |
Figure S31. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S32. Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 6Q GAIN MUTATED | 15 | 50 | 12 |
| 6Q GAIN WILD-TYPE | 187 | 120 | 66 |
Figure S32. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00563 (Fisher's exact test), Q value = 0.026
Table S33. Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 61 | 29 | 21 |
| 7P GAIN MUTATED | 11 | 39 | 10 | 9 |
| 7P GAIN WILD-TYPE | 24 | 22 | 19 | 12 |
Figure S33. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S34. Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 7P GAIN MUTATED | 10 | 33 | 26 |
| 7P GAIN WILD-TYPE | 32 | 39 | 6 |
Figure S34. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S35. Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 7P GAIN MUTATED | 66 | 127 | 53 |
| 7P GAIN WILD-TYPE | 136 | 43 | 25 |
Figure S35. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00026 (Fisher's exact test), Q value = 0.0021
Table S36. Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 7P GAIN MUTATED | 86 | 47 | 39 |
| 7P GAIN WILD-TYPE | 32 | 52 | 37 |
Figure S36. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00036 (Fisher's exact test), Q value = 0.0026
Table S37. Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 78 | 127 | 26 | 94 |
| 7P GAIN MUTATED | 53 | 63 | 19 | 37 |
| 7P GAIN WILD-TYPE | 25 | 64 | 7 | 57 |
Figure S37. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 0.00211 (Fisher's exact test), Q value = 0.012
Table S38. Gene #13: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 59 | 48 | 56 | 68 | 68 | 26 |
| 7P GAIN MUTATED | 42 | 31 | 26 | 36 | 26 | 11 |
| 7P GAIN WILD-TYPE | 17 | 17 | 30 | 32 | 42 | 15 |
Figure S38. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 3e-05 (Fisher's exact test), Q value = 0.00032
Table S39. Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 7P GAIN MUTATED | 86 | 43 | 50 | 66 |
| 7P GAIN WILD-TYPE | 35 | 64 | 40 | 64 |
Figure S39. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S40. Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 7P GAIN MUTATED | 58 | 71 | 33 | 75 | 8 |
| 7P GAIN WILD-TYPE | 21 | 37 | 63 | 54 | 28 |
Figure S40. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0173 (Fisher's exact test), Q value = 0.067
Table S41. Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 12 | 22 | 17 | 24 | 10 |
| 7P GAIN MUTATED | 12 | 15 | 11 | 11 | 6 |
| 7P GAIN WILD-TYPE | 0 | 7 | 6 | 13 | 4 |
Figure S41. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.00407 (Fisher's exact test), Q value = 0.02
Table S42. Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 61 | 29 | 21 |
| 7Q GAIN MUTATED | 7 | 34 | 9 | 9 |
| 7Q GAIN WILD-TYPE | 28 | 27 | 20 | 12 |
Figure S42. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S43. Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 7Q GAIN MUTATED | 8 | 27 | 24 |
| 7Q GAIN WILD-TYPE | 34 | 45 | 8 |
Figure S43. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S44. Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 7Q GAIN MUTATED | 65 | 111 | 47 |
| 7Q GAIN WILD-TYPE | 137 | 59 | 31 |
Figure S44. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0115 (Fisher's exact test), Q value = 0.048
Table S45. Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 7Q GAIN MUTATED | 76 | 45 | 37 |
| 7Q GAIN WILD-TYPE | 42 | 54 | 39 |
Figure S45. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.006 (Fisher's exact test), Q value = 0.027
Table S46. Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 78 | 127 | 26 | 94 |
| 7Q GAIN MUTATED | 47 | 55 | 17 | 36 |
| 7Q GAIN WILD-TYPE | 31 | 72 | 9 | 58 |
Figure S46. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 0.00966 (Fisher's exact test), Q value = 0.041
Table S47. Gene #14: '7q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 59 | 48 | 56 | 68 | 68 | 26 |
| 7Q GAIN MUTATED | 40 | 25 | 24 | 31 | 24 | 11 |
| 7Q GAIN WILD-TYPE | 19 | 23 | 32 | 37 | 44 | 15 |
Figure S47. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 0.00112 (Fisher's exact test), Q value = 0.0068
Table S48. Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 7Q GAIN MUTATED | 76 | 40 | 47 | 59 |
| 7Q GAIN WILD-TYPE | 45 | 67 | 43 | 71 |
Figure S48. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S49. Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 7Q GAIN MUTATED | 54 | 64 | 32 | 67 | 5 |
| 7Q GAIN WILD-TYPE | 25 | 44 | 64 | 62 | 31 |
Figure S49. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0103 (Fisher's exact test), Q value = 0.043
Table S50. Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 12 | 22 | 17 | 24 | 10 |
| 7Q GAIN MUTATED | 12 | 13 | 8 | 11 | 7 |
| 7Q GAIN WILD-TYPE | 0 | 9 | 9 | 13 | 3 |
Figure S50. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.00022 (Fisher's exact test), Q value = 0.0018
Table S51. Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 8P GAIN MUTATED | 47 | 47 | 38 |
| 8P GAIN WILD-TYPE | 155 | 123 | 40 |
Figure S51. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.024 (Fisher's exact test), Q value = 0.086
Table S52. Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 8P GAIN MUTATED | 40 | 33 | 32 | 25 |
| 8P GAIN WILD-TYPE | 81 | 74 | 58 | 105 |
Figure S52. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 0.0206 (Fisher's exact test), Q value = 0.077
Table S53. Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 8Q GAIN MUTATED | 14 | 31 | 21 |
| 8Q GAIN WILD-TYPE | 28 | 41 | 11 |
Figure S53. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S54. Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 8Q GAIN MUTATED | 66 | 90 | 71 |
| 8Q GAIN WILD-TYPE | 136 | 80 | 7 |
Figure S54. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0347 (Fisher's exact test), Q value = 0.12
Table S55. Gene #16: '8q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 59 | 48 | 56 | 68 | 68 | 26 |
| 8Q GAIN MUTATED | 38 | 27 | 27 | 26 | 29 | 10 |
| 8Q GAIN WILD-TYPE | 21 | 21 | 29 | 42 | 39 | 16 |
Figure S55. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 0.00276 (Fisher's exact test), Q value = 0.014
Table S56. Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 8Q GAIN MUTATED | 73 | 41 | 52 | 59 |
| 8Q GAIN WILD-TYPE | 48 | 66 | 38 | 71 |
Figure S56. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 0.00045 (Fisher's exact test), Q value = 0.0031
Table S57. Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 8Q GAIN MUTATED | 48 | 61 | 40 | 68 | 8 |
| 8Q GAIN WILD-TYPE | 31 | 47 | 56 | 61 | 28 |
Figure S57. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.014 (Fisher's exact test), Q value = 0.056
Table S58. Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 135 | 50 | 77 | 135 |
| 8Q GAIN MUTATED | 60 | 32 | 47 | 61 |
| 8Q GAIN WILD-TYPE | 75 | 18 | 30 | 74 |
Figure S58. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00046 (Fisher's exact test), Q value = 0.0031
Table S59. Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 9P GAIN MUTATED | 28 | 46 | 7 |
| 9P GAIN WILD-TYPE | 174 | 124 | 71 |
Figure S59. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00167 (Fisher's exact test), Q value = 0.0094
Table S60. Gene #17: '9p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 78 | 127 | 26 | 94 |
| 9P GAIN MUTATED | 16 | 15 | 11 | 11 |
| 9P GAIN WILD-TYPE | 62 | 112 | 15 | 83 |
Figure S60. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 0.0266 (Fisher's exact test), Q value = 0.093
Table S61. Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 9Q GAIN MUTATED | 26 | 37 | 8 |
| 9Q GAIN WILD-TYPE | 176 | 133 | 70 |
Figure S61. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00045 (Fisher's exact test), Q value = 0.0031
Table S62. Gene #18: '9q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 78 | 127 | 26 | 94 |
| 9Q GAIN MUTATED | 11 | 14 | 12 | 10 |
| 9Q GAIN WILD-TYPE | 67 | 113 | 14 | 84 |
Figure S62. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 0.00264 (Fisher's exact test), Q value = 0.014
Table S63. Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 10P GAIN MUTATED | 9 | 24 | 4 |
| 10P GAIN WILD-TYPE | 193 | 146 | 74 |
Figure S63. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.022 (Fisher's exact test), Q value = 0.08
Table S64. Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 78 | 127 | 26 | 94 |
| 10P GAIN MUTATED | 11 | 5 | 0 | 9 |
| 10P GAIN WILD-TYPE | 67 | 122 | 26 | 85 |
Figure S64. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 0.0482 (Fisher's exact test), Q value = 0.15
Table S65. Gene #20: '10q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 10Q GAIN MUTATED | 4 | 11 | 3 |
| 10Q GAIN WILD-TYPE | 114 | 88 | 73 |
Figure S65. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00061 (Fisher's exact test), Q value = 0.004
Table S66. Gene #21: '11p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 61 | 29 | 21 |
| 11P GAIN MUTATED | 1 | 9 | 0 | 7 |
| 11P GAIN WILD-TYPE | 34 | 52 | 29 | 14 |
Figure S66. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 1e-04 (Fisher's exact test), Q value = 0.00089
Table S67. Gene #21: '11p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 11P GAIN MUTATED | 1 | 5 | 11 |
| 11P GAIN WILD-TYPE | 41 | 67 | 21 |
Figure S67. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S68. Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 11P GAIN MUTATED | 6 | 38 | 9 |
| 11P GAIN WILD-TYPE | 196 | 132 | 69 |
Figure S68. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00094 (Fisher's exact test), Q value = 0.0058
Table S69. Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 11P GAIN MUTATED | 24 | 4 | 8 |
| 11P GAIN WILD-TYPE | 94 | 95 | 68 |
Figure S69. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00033 (Fisher's exact test), Q value = 0.0025
Table S70. Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 11P GAIN MUTATED | 24 | 3 | 9 | 17 |
| 11P GAIN WILD-TYPE | 97 | 104 | 81 | 113 |
Figure S70. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S71. Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 11P GAIN MUTATED | 14 | 17 | 0 | 22 | 0 |
| 11P GAIN WILD-TYPE | 65 | 91 | 96 | 107 | 36 |
Figure S71. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00202 (Fisher's exact test), Q value = 0.011
Table S72. Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 135 | 50 | 77 | 135 |
| 11P GAIN MUTATED | 7 | 8 | 17 | 15 |
| 11P GAIN WILD-TYPE | 128 | 42 | 60 | 120 |
Figure S72. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00016 (Fisher's exact test), Q value = 0.0013
Table S73. Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 61 | 29 | 21 |
| 11Q GAIN MUTATED | 1 | 9 | 0 | 8 |
| 11Q GAIN WILD-TYPE | 34 | 52 | 29 | 13 |
Figure S73. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S74. Gene #22: '11q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 11Q GAIN MUTATED | 1 | 4 | 13 |
| 11Q GAIN WILD-TYPE | 41 | 68 | 19 |
Figure S74. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S75. Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 11Q GAIN MUTATED | 3 | 37 | 11 |
| 11Q GAIN WILD-TYPE | 199 | 133 | 67 |
Figure S75. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00482 (Fisher's exact test), Q value = 0.023
Table S76. Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 11Q GAIN MUTATED | 22 | 5 | 6 |
| 11Q GAIN WILD-TYPE | 96 | 94 | 70 |
Figure S76. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.0287 (Fisher's exact test), Q value = 0.098
Table S77. Gene #22: '11q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 78 | 127 | 26 | 94 |
| 11Q GAIN MUTATED | 10 | 9 | 6 | 5 |
| 11Q GAIN WILD-TYPE | 68 | 118 | 20 | 89 |
Figure S77. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 4e-05 (Fisher's exact test), Q value = 0.00042
Table S78. Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 11Q GAIN MUTATED | 25 | 2 | 8 | 16 |
| 11Q GAIN WILD-TYPE | 96 | 105 | 82 | 114 |
Figure S78. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S79. Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 11Q GAIN MUTATED | 13 | 18 | 0 | 20 | 0 |
| 11Q GAIN WILD-TYPE | 66 | 90 | 96 | 109 | 36 |
Figure S79. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00596 (Fisher's exact test), Q value = 0.027
Table S80. Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 135 | 50 | 77 | 135 |
| 11Q GAIN MUTATED | 7 | 7 | 16 | 15 |
| 11Q GAIN WILD-TYPE | 128 | 43 | 61 | 120 |
Figure S80. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0343 (Fisher's exact test), Q value = 0.12
Table S81. Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 12 | 22 | 17 | 24 | 10 |
| 11Q GAIN MUTATED | 3 | 5 | 1 | 0 | 2 |
| 11Q GAIN WILD-TYPE | 9 | 17 | 16 | 24 | 8 |
Figure S81. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.00562 (Fisher's exact test), Q value = 0.026
Table S82. Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 12P GAIN MUTATED | 51 | 22 | 20 |
| 12P GAIN WILD-TYPE | 151 | 148 | 58 |
Figure S82. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00322 (Fisher's exact test), Q value = 0.016
Table S83. Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 12P GAIN MUTATED | 13 | 29 | 16 |
| 12P GAIN WILD-TYPE | 105 | 70 | 60 |
Figure S83. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00525 (Fisher's exact test), Q value = 0.025
Table S84. Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 12Q GAIN MUTATED | 48 | 20 | 19 |
| 12Q GAIN WILD-TYPE | 154 | 150 | 59 |
Figure S84. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00061 (Fisher's exact test), Q value = 0.004
Table S85. Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 12Q GAIN MUTATED | 10 | 28 | 14 |
| 12Q GAIN WILD-TYPE | 108 | 71 | 62 |
Figure S85. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 7e-05 (Fisher's exact test), Q value = 0.00069
Table S86. Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 61 | 29 | 21 |
| 13Q GAIN MUTATED | 14 | 46 | 10 | 15 |
| 13Q GAIN WILD-TYPE | 21 | 15 | 19 | 6 |
Figure S86. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S87. Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 13Q GAIN MUTATED | 12 | 46 | 27 |
| 13Q GAIN WILD-TYPE | 30 | 26 | 5 |
Figure S87. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S88. Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 13Q GAIN MUTATED | 64 | 147 | 45 |
| 13Q GAIN WILD-TYPE | 138 | 23 | 33 |
Figure S88. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00034 (Fisher's exact test), Q value = 0.0025
Table S89. Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 13Q GAIN MUTATED | 84 | 46 | 38 |
| 13Q GAIN WILD-TYPE | 34 | 53 | 38 |
Figure S89. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.0372 (Fisher's exact test), Q value = 0.12
Table S90. Gene #25: '13q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 78 | 127 | 26 | 94 |
| 13Q GAIN MUTATED | 48 | 80 | 16 | 42 |
| 13Q GAIN WILD-TYPE | 30 | 47 | 10 | 52 |
Figure S90. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S91. Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 13Q GAIN MUTATED | 86 | 36 | 50 | 82 |
| 13Q GAIN WILD-TYPE | 35 | 71 | 40 | 48 |
Figure S91. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S92. Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 13Q GAIN MUTATED | 62 | 71 | 26 | 87 | 8 |
| 13Q GAIN WILD-TYPE | 17 | 37 | 70 | 42 | 28 |
Figure S92. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 3e-05 (Fisher's exact test), Q value = 0.00032
Table S93. Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 61 | 29 | 21 |
| 16P GAIN MUTATED | 5 | 21 | 2 | 13 |
| 16P GAIN WILD-TYPE | 30 | 40 | 27 | 8 |
Figure S93. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S94. Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 16P GAIN MUTATED | 4 | 16 | 21 |
| 16P GAIN WILD-TYPE | 38 | 56 | 11 |
Figure S94. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S95. Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 16P GAIN MUTATED | 15 | 79 | 13 |
| 16P GAIN WILD-TYPE | 187 | 91 | 65 |
Figure S95. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00161 (Fisher's exact test), Q value = 0.0091
Table S96. Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 16P GAIN MUTATED | 34 | 14 | 17 | 42 |
| 16P GAIN WILD-TYPE | 87 | 93 | 73 | 88 |
Figure S96. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S97. Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 16P GAIN MUTATED | 25 | 22 | 10 | 50 | 0 |
| 16P GAIN WILD-TYPE | 54 | 86 | 86 | 79 | 36 |
Figure S97. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 6e-05 (Fisher's exact test), Q value = 6e-04
Table S98. Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 61 | 29 | 21 |
| 16Q GAIN MUTATED | 4 | 19 | 2 | 13 |
| 16Q GAIN WILD-TYPE | 31 | 42 | 27 | 8 |
Figure S98. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S99. Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 16Q GAIN MUTATED | 3 | 16 | 19 |
| 16Q GAIN WILD-TYPE | 39 | 56 | 13 |
Figure S99. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S100. Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 16Q GAIN MUTATED | 14 | 78 | 13 |
| 16Q GAIN WILD-TYPE | 188 | 92 | 65 |
Figure S100. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00243 (Fisher's exact test), Q value = 0.013
Table S101. Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 16Q GAIN MUTATED | 35 | 14 | 16 | 40 |
| 16Q GAIN WILD-TYPE | 86 | 93 | 74 | 90 |
Figure S101. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S102. Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 16Q GAIN MUTATED | 25 | 23 | 10 | 47 | 0 |
| 16Q GAIN WILD-TYPE | 54 | 85 | 86 | 82 | 36 |
Figure S102. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0398 (Fisher's exact test), Q value = 0.13
Table S103. Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 17Q GAIN MUTATED | 3 | 10 | 9 |
| 17Q GAIN WILD-TYPE | 39 | 62 | 23 |
Figure S103. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S104. Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 17Q GAIN MUTATED | 18 | 46 | 17 |
| 17Q GAIN WILD-TYPE | 184 | 124 | 61 |
Figure S104. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 1e-04 (Fisher's exact test), Q value = 0.00089
Table S105. Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 17Q GAIN MUTATED | 37 | 17 | 6 |
| 17Q GAIN WILD-TYPE | 81 | 82 | 70 |
Figure S105. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.0281 (Fisher's exact test), Q value = 0.097
Table S106. Gene #31: '17q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 59 | 48 | 56 | 68 | 68 | 26 |
| 17Q GAIN MUTATED | 12 | 14 | 10 | 10 | 10 | 0 |
| 17Q GAIN WILD-TYPE | 47 | 34 | 46 | 58 | 58 | 26 |
Figure S106. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S107. Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 17Q GAIN MUTATED | 43 | 10 | 10 | 18 |
| 17Q GAIN WILD-TYPE | 78 | 97 | 80 | 112 |
Figure S107. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 0.00072 (Fisher's exact test), Q value = 0.0046
Table S108. Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 17Q GAIN MUTATED | 17 | 31 | 7 | 23 | 3 |
| 17Q GAIN WILD-TYPE | 62 | 77 | 89 | 106 | 33 |
Figure S108. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00878 (Fisher's exact test), Q value = 0.038
Table S109. Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 160 | 65 | 172 |
| 17Q GAIN MUTATED | 40 | 6 | 26 |
| 17Q GAIN WILD-TYPE | 120 | 59 | 146 |
Figure S109. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 5e-05 (Fisher's exact test), Q value = 0.00052
Table S110. Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 18P GAIN MUTATED | 14 | 0 | 8 |
| 18P GAIN WILD-TYPE | 188 | 170 | 70 |
Figure S110. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00103 (Fisher's exact test), Q value = 0.0063
Table S111. Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 18P GAIN MUTATED | 1 | 12 | 3 |
| 18P GAIN WILD-TYPE | 117 | 87 | 73 |
Figure S111. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.0334 (Fisher's exact test), Q value = 0.11
Table S112. Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 18P GAIN MUTATED | 2 | 10 | 6 | 4 |
| 18P GAIN WILD-TYPE | 119 | 97 | 84 | 126 |
Figure S112. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.00032
Table S113. Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 18P GAIN MUTATED | 2 | 2 | 13 | 1 | 4 |
| 18P GAIN WILD-TYPE | 77 | 106 | 83 | 128 | 32 |
Figure S113. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00449 (Fisher's exact test), Q value = 0.022
Table S114. Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 18Q GAIN MUTATED | 10 | 0 | 3 |
| 18Q GAIN WILD-TYPE | 192 | 170 | 75 |
Figure S114. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.013 (Fisher's exact test), Q value = 0.053
Table S115. Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 18Q GAIN MUTATED | 0 | 6 | 3 |
| 18Q GAIN WILD-TYPE | 118 | 93 | 73 |
Figure S115. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.0189 (Fisher's exact test), Q value = 0.072
Table S116. Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 18Q GAIN MUTATED | 0 | 4 | 6 | 3 |
| 18Q GAIN WILD-TYPE | 121 | 103 | 84 | 127 |
Figure S116. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.00032
Table S117. Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 18Q GAIN MUTATED | 1 | 0 | 8 | 0 | 4 |
| 18Q GAIN WILD-TYPE | 78 | 108 | 88 | 129 | 32 |
Figure S117. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 6e-05 (Fisher's exact test), Q value = 6e-04
Table S118. Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 19P GAIN MUTATED | 16 | 43 | 15 |
| 19P GAIN WILD-TYPE | 186 | 127 | 63 |
Figure S118. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00022 (Fisher's exact test), Q value = 0.0018
Table S119. Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 19P GAIN MUTATED | 26 | 18 | 9 | 20 | 1 |
| 19P GAIN WILD-TYPE | 53 | 90 | 87 | 109 | 35 |
Figure S119. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0194 (Fisher's exact test), Q value = 0.074
Table S120. Gene #34: '19p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 12 | 22 | 17 | 24 | 10 |
| 19P GAIN MUTATED | 3 | 9 | 2 | 1 | 1 |
| 19P GAIN WILD-TYPE | 9 | 13 | 15 | 23 | 9 |
Figure S120. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.00261 (Fisher's exact test), Q value = 0.014
Table S121. Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 19Q GAIN MUTATED | 25 | 45 | 14 |
| 19Q GAIN WILD-TYPE | 177 | 125 | 64 |
Figure S121. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00012 (Fisher's exact test), Q value = 0.001
Table S122. Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 19Q GAIN MUTATED | 28 | 20 | 12 | 23 | 1 |
| 19Q GAIN WILD-TYPE | 51 | 88 | 84 | 106 | 35 |
Figure S122. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0406 (Fisher's exact test), Q value = 0.13
Table S123. Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 29 | 32 | 24 |
| 19Q GAIN MUTATED | 4 | 11 | 2 |
| 19Q GAIN WILD-TYPE | 25 | 21 | 22 |
Figure S123. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
P value = 0.00035 (Fisher's exact test), Q value = 0.0026
Table S124. Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 12 | 22 | 17 | 24 | 10 |
| 19Q GAIN MUTATED | 4 | 10 | 2 | 0 | 1 |
| 19Q GAIN WILD-TYPE | 8 | 12 | 15 | 24 | 9 |
Figure S124. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.00291 (Fisher's exact test), Q value = 0.015
Table S125. Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 61 | 29 | 21 |
| 20P GAIN MUTATED | 12 | 41 | 14 | 16 |
| 20P GAIN WILD-TYPE | 23 | 20 | 15 | 5 |
Figure S125. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 2e-05 (Fisher's exact test), Q value = 0.00023
Table S126. Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 20P GAIN MUTATED | 11 | 51 | 21 |
| 20P GAIN WILD-TYPE | 31 | 21 | 11 |
Figure S126. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S127. Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 20P GAIN MUTATED | 75 | 125 | 43 |
| 20P GAIN WILD-TYPE | 127 | 45 | 35 |
Figure S127. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 3e-04 (Fisher's exact test), Q value = 0.0023
Table S128. Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 20P GAIN MUTATED | 80 | 43 | 34 |
| 20P GAIN WILD-TYPE | 38 | 56 | 42 |
Figure S128. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.0435 (Fisher's exact test), Q value = 0.14
Table S129. Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 78 | 127 | 26 | 94 |
| 20P GAIN MUTATED | 48 | 63 | 16 | 39 |
| 20P GAIN WILD-TYPE | 30 | 64 | 10 | 55 |
Figure S129. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 0.00027 (Fisher's exact test), Q value = 0.0021
Table S130. Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 20P GAIN MUTATED | 79 | 41 | 44 | 77 |
| 20P GAIN WILD-TYPE | 42 | 66 | 46 | 53 |
Figure S130. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S131. Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 20P GAIN MUTATED | 47 | 71 | 30 | 87 | 6 |
| 20P GAIN WILD-TYPE | 32 | 37 | 66 | 42 | 30 |
Figure S131. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S132. Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 61 | 29 | 21 |
| 20Q GAIN MUTATED | 13 | 58 | 15 | 18 |
| 20Q GAIN WILD-TYPE | 22 | 3 | 14 | 3 |
Figure S132. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S133. Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 20Q GAIN MUTATED | 12 | 61 | 31 |
| 20Q GAIN WILD-TYPE | 30 | 11 | 1 |
Figure S133. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S134. Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 20Q GAIN MUTATED | 88 | 168 | 65 |
| 20Q GAIN WILD-TYPE | 114 | 2 | 13 |
Figure S134. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S135. Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 20Q GAIN MUTATED | 113 | 51 | 47 |
| 20Q GAIN WILD-TYPE | 5 | 48 | 29 |
Figure S135. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00034 (Fisher's exact test), Q value = 0.0025
Table S136. Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 78 | 127 | 26 | 94 |
| 20Q GAIN MUTATED | 63 | 93 | 21 | 50 |
| 20Q GAIN WILD-TYPE | 15 | 34 | 5 | 44 |
Figure S136. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 0.00044 (Fisher's exact test), Q value = 0.0031
Table S137. Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 59 | 48 | 56 | 68 | 68 | 26 |
| 20Q GAIN MUTATED | 51 | 37 | 40 | 49 | 36 | 14 |
| 20Q GAIN WILD-TYPE | 8 | 11 | 16 | 19 | 32 | 12 |
Figure S137. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S138. Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 20Q GAIN MUTATED | 116 | 46 | 64 | 93 |
| 20Q GAIN WILD-TYPE | 5 | 61 | 26 | 37 |
Figure S138. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S139. Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 20Q GAIN MUTATED | 73 | 95 | 34 | 111 | 6 |
| 20Q GAIN WILD-TYPE | 6 | 13 | 62 | 18 | 30 |
Figure S139. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00116 (Fisher's exact test), Q value = 0.0069
Table S140. Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 135 | 50 | 77 | 135 |
| 20Q GAIN MUTATED | 92 | 36 | 68 | 87 |
| 20Q GAIN WILD-TYPE | 43 | 14 | 9 | 48 |
Figure S140. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00603 (Fisher's exact test), Q value = 0.027
Table S141. Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 12 | 22 | 17 | 24 | 10 |
| 20Q GAIN MUTATED | 12 | 20 | 13 | 13 | 9 |
| 20Q GAIN WILD-TYPE | 0 | 2 | 4 | 11 | 1 |
Figure S141. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.0355 (Fisher's exact test), Q value = 0.12
Table S142. Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 61 | 29 | 21 |
| 21Q GAIN MUTATED | 0 | 2 | 0 | 3 |
| 21Q GAIN WILD-TYPE | 35 | 59 | 29 | 18 |
Figure S142. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00132 (Fisher's exact test), Q value = 0.0078
Table S143. Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 21Q GAIN MUTATED | 3 | 14 | 7 |
| 21Q GAIN WILD-TYPE | 199 | 156 | 71 |
Figure S143. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0466 (Fisher's exact test), Q value = 0.15
Table S144. Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 22Q GAIN MUTATED | 8 | 1 | 1 |
| 22Q GAIN WILD-TYPE | 110 | 98 | 75 |
Figure S144. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00046 (Fisher's exact test), Q value = 0.0031
Table S145. Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| XP GAIN MUTATED | 16 | 33 | 18 |
| XP GAIN WILD-TYPE | 186 | 137 | 60 |
Figure S145. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0434 (Fisher's exact test), Q value = 0.14
Table S146. Gene #40: 'xp gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 29 | 32 | 24 |
| XP GAIN MUTATED | 1 | 8 | 5 |
| XP GAIN WILD-TYPE | 28 | 24 | 19 |
Figure S146. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
P value = 0.0437 (Fisher's exact test), Q value = 0.14
Table S147. Gene #41: 'xq gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 61 | 29 | 21 |
| XQ GAIN MUTATED | 2 | 9 | 9 | 2 |
| XQ GAIN WILD-TYPE | 33 | 52 | 20 | 19 |
Figure S147. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00023 (Fisher's exact test), Q value = 0.0018
Table S148. Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| XQ GAIN MUTATED | 21 | 31 | 24 |
| XQ GAIN WILD-TYPE | 181 | 139 | 54 |
Figure S148. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0275 (Fisher's exact test), Q value = 0.095
Table S149. Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 61 | 29 | 21 |
| 1P LOSS MUTATED | 7 | 18 | 1 | 4 |
| 1P LOSS WILD-TYPE | 28 | 43 | 28 | 17 |
Figure S149. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S150. Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 1P LOSS MUTATED | 22 | 64 | 9 |
| 1P LOSS WILD-TYPE | 180 | 106 | 69 |
Figure S150. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00318 (Fisher's exact test), Q value = 0.016
Table S151. Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 1P LOSS MUTATED | 37 | 13 | 13 |
| 1P LOSS WILD-TYPE | 81 | 86 | 63 |
Figure S151. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 8e-05 (Fisher's exact test), Q value = 0.00075
Table S152. Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 1P LOSS MUTATED | 38 | 8 | 20 | 28 |
| 1P LOSS WILD-TYPE | 83 | 99 | 70 | 102 |
Figure S152. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.00032
Table S153. Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 1P LOSS MUTATED | 29 | 23 | 8 | 31 | 3 |
| 1P LOSS WILD-TYPE | 50 | 85 | 88 | 98 | 33 |
Figure S153. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.02 (Fisher's exact test), Q value = 0.076
Table S154. Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 135 | 50 | 77 | 135 |
| 1P LOSS MUTATED | 27 | 9 | 26 | 21 |
| 1P LOSS WILD-TYPE | 108 | 41 | 51 | 114 |
Figure S154. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 2e-05 (Fisher's exact test), Q value = 0.00023
Table S155. Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 1Q LOSS MUTATED | 11 | 37 | 8 |
| 1Q LOSS WILD-TYPE | 191 | 133 | 70 |
Figure S155. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00195 (Fisher's exact test), Q value = 0.011
Table S156. Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 1Q LOSS MUTATED | 23 | 4 | 14 | 14 |
| 1Q LOSS WILD-TYPE | 98 | 103 | 76 | 116 |
Figure S156. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 0.00578 (Fisher's exact test), Q value = 0.026
Table S157. Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 1Q LOSS MUTATED | 17 | 15 | 4 | 17 | 2 |
| 1Q LOSS WILD-TYPE | 62 | 93 | 92 | 112 | 34 |
Figure S157. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00536 (Fisher's exact test), Q value = 0.025
Table S158. Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 135 | 50 | 77 | 135 |
| 1Q LOSS MUTATED | 14 | 7 | 18 | 9 |
| 1Q LOSS WILD-TYPE | 121 | 43 | 59 | 126 |
Figure S158. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 7e-05 (Fisher's exact test), Q value = 0.00069
Table S159. Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 61 | 29 | 21 |
| 4P LOSS MUTATED | 8 | 28 | 1 | 9 |
| 4P LOSS WILD-TYPE | 27 | 33 | 28 | 12 |
Figure S159. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00139 (Fisher's exact test), Q value = 0.008
Table S160. Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 4P LOSS MUTATED | 7 | 21 | 18 |
| 4P LOSS WILD-TYPE | 35 | 51 | 14 |
Figure S160. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S161. Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 4P LOSS MUTATED | 31 | 88 | 19 |
| 4P LOSS WILD-TYPE | 171 | 82 | 59 |
Figure S161. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00086 (Fisher's exact test), Q value = 0.0054
Table S162. Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 4P LOSS MUTATED | 49 | 18 | 22 |
| 4P LOSS WILD-TYPE | 69 | 81 | 54 |
Figure S162. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S163. Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 4P LOSS MUTATED | 56 | 12 | 28 | 41 |
| 4P LOSS WILD-TYPE | 65 | 95 | 62 | 89 |
Figure S163. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S164. Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 4P LOSS MUTATED | 35 | 41 | 8 | 50 | 3 |
| 4P LOSS WILD-TYPE | 44 | 67 | 88 | 79 | 33 |
Figure S164. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0235 (Fisher's exact test), Q value = 0.085
Table S165. Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 12 | 22 | 17 | 24 | 10 |
| 4P LOSS MUTATED | 8 | 6 | 4 | 4 | 5 |
| 4P LOSS WILD-TYPE | 4 | 16 | 13 | 20 | 5 |
Figure S165. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.00011 (Fisher's exact test), Q value = 0.00096
Table S166. Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 61 | 29 | 21 |
| 4Q LOSS MUTATED | 7 | 26 | 1 | 9 |
| 4Q LOSS WILD-TYPE | 28 | 35 | 28 | 12 |
Figure S166. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00949 (Fisher's exact test), Q value = 0.04
Table S167. Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 4Q LOSS MUTATED | 6 | 22 | 15 |
| 4Q LOSS WILD-TYPE | 36 | 50 | 17 |
Figure S167. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S168. Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 4Q LOSS MUTATED | 26 | 85 | 16 |
| 4Q LOSS WILD-TYPE | 176 | 85 | 62 |
Figure S168. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 9e-05 (Fisher's exact test), Q value = 0.00082
Table S169. Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 4Q LOSS MUTATED | 47 | 14 | 20 |
| 4Q LOSS WILD-TYPE | 71 | 85 | 56 |
Figure S169. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S170. Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 4Q LOSS MUTATED | 51 | 12 | 23 | 40 |
| 4Q LOSS WILD-TYPE | 70 | 95 | 67 | 90 |
Figure S170. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S171. Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 4Q LOSS MUTATED | 33 | 38 | 6 | 46 | 3 |
| 4Q LOSS WILD-TYPE | 46 | 70 | 90 | 83 | 33 |
Figure S171. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 3e-04 (Fisher's exact test), Q value = 0.0023
Table S172. Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 5P LOSS MUTATED | 13 | 34 | 12 |
| 5P LOSS WILD-TYPE | 189 | 136 | 66 |
Figure S172. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00086 (Fisher's exact test), Q value = 0.0054
Table S173. Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 5P LOSS MUTATED | 12 | 21 | 2 | 20 | 4 |
| 5P LOSS WILD-TYPE | 67 | 87 | 94 | 109 | 32 |
Figure S173. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 2e-05 (Fisher's exact test), Q value = 0.00023
Table S174. Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 5Q LOSS MUTATED | 16 | 44 | 18 |
| 5Q LOSS WILD-TYPE | 186 | 126 | 60 |
Figure S174. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0227 (Fisher's exact test), Q value = 0.082
Table S175. Gene #51: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 78 | 127 | 26 | 94 |
| 5Q LOSS MUTATED | 19 | 16 | 5 | 8 |
| 5Q LOSS WILD-TYPE | 59 | 111 | 21 | 86 |
Figure S175. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 0.00015 (Fisher's exact test), Q value = 0.0013
Table S176. Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 5Q LOSS MUTATED | 32 | 6 | 19 | 21 |
| 5Q LOSS WILD-TYPE | 89 | 101 | 71 | 109 |
Figure S176. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 0.00025 (Fisher's exact test), Q value = 0.002
Table S177. Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 5Q LOSS MUTATED | 20 | 26 | 5 | 24 | 3 |
| 5Q LOSS WILD-TYPE | 59 | 82 | 91 | 105 | 33 |
Figure S177. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0262 (Fisher's exact test), Q value = 0.092
Table S178. Gene #52: '6p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 29 | 32 | 24 |
| 6P LOSS MUTATED | 6 | 2 | 0 |
| 6P LOSS WILD-TYPE | 23 | 30 | 24 |
Figure S178. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
P value = 0.0377 (Fisher's exact test), Q value = 0.12
Table S179. Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 7Q LOSS MUTATED | 0 | 4 | 0 |
| 7Q LOSS WILD-TYPE | 202 | 166 | 78 |
Figure S179. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0158 (Fisher's exact test), Q value = 0.062
Table S180. Gene #55: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 61 | 29 | 21 |
| 8P LOSS MUTATED | 7 | 27 | 5 | 9 |
| 8P LOSS WILD-TYPE | 28 | 34 | 24 | 12 |
Figure S180. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00084 (Fisher's exact test), Q value = 0.0053
Table S181. Gene #55: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 8P LOSS MUTATED | 5 | 27 | 16 |
| 8P LOSS WILD-TYPE | 37 | 45 | 16 |
Figure S181. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S182. Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 8P LOSS MUTATED | 25 | 80 | 37 |
| 8P LOSS WILD-TYPE | 177 | 90 | 41 |
Figure S182. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0056 (Fisher's exact test), Q value = 0.026
Table S183. Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 8P LOSS MUTATED | 49 | 21 | 23 |
| 8P LOSS WILD-TYPE | 69 | 78 | 53 |
Figure S183. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.0148 (Fisher's exact test), Q value = 0.059
Table S184. Gene #55: '8p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 78 | 127 | 26 | 94 |
| 8P LOSS MUTATED | 34 | 35 | 7 | 20 |
| 8P LOSS WILD-TYPE | 44 | 92 | 19 | 74 |
Figure S184. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 0.0118 (Fisher's exact test), Q value = 0.048
Table S185. Gene #55: '8p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 59 | 48 | 56 | 68 | 68 | 26 |
| 8P LOSS MUTATED | 24 | 19 | 18 | 20 | 11 | 4 |
| 8P LOSS WILD-TYPE | 35 | 29 | 38 | 48 | 57 | 22 |
Figure S185. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 8e-05 (Fisher's exact test), Q value = 0.00075
Table S186. Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 8P LOSS MUTATED | 50 | 16 | 28 | 48 |
| 8P LOSS WILD-TYPE | 71 | 91 | 62 | 82 |
Figure S186. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S187. Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 8P LOSS MUTATED | 37 | 35 | 13 | 54 | 3 |
| 8P LOSS WILD-TYPE | 42 | 73 | 83 | 75 | 33 |
Figure S187. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0215 (Fisher's exact test), Q value = 0.079
Table S188. Gene #55: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 12 | 22 | 17 | 24 | 10 |
| 8P LOSS MUTATED | 8 | 9 | 6 | 3 | 3 |
| 8P LOSS WILD-TYPE | 4 | 13 | 11 | 21 | 7 |
Figure S188. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.00218 (Fisher's exact test), Q value = 0.012
Table S189. Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 8Q LOSS MUTATED | 5 | 18 | 2 |
| 8Q LOSS WILD-TYPE | 197 | 152 | 76 |
Figure S189. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00221 (Fisher's exact test), Q value = 0.012
Table S190. Gene #56: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 12 | 22 | 17 | 24 | 10 |
| 8Q LOSS MUTATED | 6 | 1 | 1 | 2 | 0 |
| 8Q LOSS WILD-TYPE | 6 | 21 | 16 | 22 | 10 |
Figure S190. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.00054 (Fisher's exact test), Q value = 0.0036
Table S191. Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 9P LOSS MUTATED | 12 | 32 | 10 |
| 9P LOSS WILD-TYPE | 190 | 138 | 68 |
Figure S191. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00292 (Fisher's exact test), Q value = 0.015
Table S192. Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 9P LOSS MUTATED | 24 | 5 | 10 |
| 9P LOSS WILD-TYPE | 94 | 94 | 66 |
Figure S192. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 8e-05 (Fisher's exact test), Q value = 0.00075
Table S193. Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 9P LOSS MUTATED | 26 | 3 | 13 | 12 |
| 9P LOSS WILD-TYPE | 95 | 104 | 77 | 118 |
Figure S193. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 6e-04 (Fisher's exact test), Q value = 0.0039
Table S194. Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 9P LOSS MUTATED | 16 | 18 | 4 | 16 | 0 |
| 9P LOSS WILD-TYPE | 63 | 90 | 92 | 113 | 36 |
Figure S194. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00022 (Fisher's exact test), Q value = 0.0018
Table S195. Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 9Q LOSS MUTATED | 11 | 33 | 9 |
| 9Q LOSS WILD-TYPE | 191 | 137 | 69 |
Figure S195. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00058 (Fisher's exact test), Q value = 0.0038
Table S196. Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 9Q LOSS MUTATED | 25 | 4 | 9 |
| 9Q LOSS WILD-TYPE | 93 | 95 | 67 |
Figure S196. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00017 (Fisher's exact test), Q value = 0.0014
Table S197. Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 9Q LOSS MUTATED | 24 | 3 | 14 | 12 |
| 9Q LOSS WILD-TYPE | 97 | 104 | 76 | 118 |
Figure S197. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 0.00122 (Fisher's exact test), Q value = 0.0072
Table S198. Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 9Q LOSS MUTATED | 18 | 15 | 4 | 15 | 1 |
| 9Q LOSS WILD-TYPE | 61 | 93 | 92 | 114 | 35 |
Figure S198. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0202 (Fisher's exact test), Q value = 0.076
Table S199. Gene #59: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 61 | 29 | 21 |
| 10P LOSS MUTATED | 2 | 11 | 0 | 4 |
| 10P LOSS WILD-TYPE | 33 | 50 | 29 | 17 |
Figure S199. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.0249 (Fisher's exact test), Q value = 0.088
Table S200. Gene #59: '10p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 10P LOSS MUTATED | 1 | 9 | 7 |
| 10P LOSS WILD-TYPE | 41 | 63 | 25 |
Figure S200. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S201. Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 10P LOSS MUTATED | 11 | 44 | 14 |
| 10P LOSS WILD-TYPE | 191 | 126 | 64 |
Figure S201. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00078 (Fisher's exact test), Q value = 0.005
Table S202. Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 10P LOSS MUTATED | 32 | 8 | 11 |
| 10P LOSS WILD-TYPE | 86 | 91 | 65 |
Figure S202. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.0132 (Fisher's exact test), Q value = 0.053
Table S203. Gene #59: '10p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 78 | 127 | 26 | 94 |
| 10P LOSS MUTATED | 15 | 22 | 8 | 7 |
| 10P LOSS WILD-TYPE | 63 | 105 | 18 | 87 |
Figure S203. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 8e-05 (Fisher's exact test), Q value = 0.00075
Table S204. Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 10P LOSS MUTATED | 32 | 5 | 14 | 17 |
| 10P LOSS WILD-TYPE | 89 | 102 | 76 | 113 |
Figure S204. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 0.00011 (Fisher's exact test), Q value = 0.00096
Table S205. Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 10P LOSS MUTATED | 22 | 18 | 7 | 21 | 0 |
| 10P LOSS WILD-TYPE | 57 | 90 | 89 | 108 | 36 |
Figure S205. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0243 (Fisher's exact test), Q value = 0.087
Table S206. Gene #60: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 61 | 29 | 21 |
| 10Q LOSS MUTATED | 3 | 12 | 0 | 4 |
| 10Q LOSS WILD-TYPE | 32 | 49 | 29 | 17 |
Figure S206. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.0414 (Fisher's exact test), Q value = 0.13
Table S207. Gene #60: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 10Q LOSS MUTATED | 2 | 9 | 8 |
| 10Q LOSS WILD-TYPE | 40 | 63 | 24 |
Figure S207. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S208. Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 10Q LOSS MUTATED | 10 | 48 | 15 |
| 10Q LOSS WILD-TYPE | 192 | 122 | 63 |
Figure S208. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00033 (Fisher's exact test), Q value = 0.0025
Table S209. Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 10Q LOSS MUTATED | 34 | 8 | 11 |
| 10Q LOSS WILD-TYPE | 84 | 91 | 65 |
Figure S209. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.0113 (Fisher's exact test), Q value = 0.047
Table S210. Gene #60: '10q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 78 | 127 | 26 | 94 |
| 10Q LOSS MUTATED | 18 | 20 | 8 | 8 |
| 10Q LOSS WILD-TYPE | 60 | 107 | 18 | 86 |
Figure S210. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S211. Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 10Q LOSS MUTATED | 34 | 4 | 15 | 19 |
| 10Q LOSS WILD-TYPE | 87 | 103 | 75 | 111 |
Figure S211. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S212. Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 10Q LOSS MUTATED | 24 | 19 | 5 | 24 | 0 |
| 10Q LOSS WILD-TYPE | 55 | 89 | 91 | 105 | 36 |
Figure S212. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00801 (Fisher's exact test), Q value = 0.035
Table S213. Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 11P LOSS MUTATED | 17 | 30 | 5 |
| 11P LOSS WILD-TYPE | 185 | 140 | 73 |
Figure S213. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0209 (Fisher's exact test), Q value = 0.078
Table S214. Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 11P LOSS MUTATED | 20 | 5 | 8 |
| 11P LOSS WILD-TYPE | 98 | 94 | 68 |
Figure S214. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.0413 (Fisher's exact test), Q value = 0.13
Table S215. Gene #62: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 61 | 29 | 21 |
| 11Q LOSS MUTATED | 2 | 13 | 1 | 4 |
| 11Q LOSS WILD-TYPE | 33 | 48 | 28 | 17 |
Figure S215. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.0159 (Fisher's exact test), Q value = 0.063
Table S216. Gene #62: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 11Q LOSS MUTATED | 1 | 15 | 4 |
| 11Q LOSS WILD-TYPE | 41 | 57 | 28 |
Figure S216. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.00356 (Fisher's exact test), Q value = 0.018
Table S217. Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 11Q LOSS MUTATED | 20 | 36 | 7 |
| 11Q LOSS WILD-TYPE | 182 | 134 | 71 |
Figure S217. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00503 (Fisher's exact test), Q value = 0.024
Table S218. Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 11Q LOSS MUTATED | 25 | 6 | 11 |
| 11Q LOSS WILD-TYPE | 93 | 93 | 65 |
Figure S218. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00236 (Fisher's exact test), Q value = 0.013
Table S219. Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 11Q LOSS MUTATED | 16 | 16 | 7 | 24 | 0 |
| 11Q LOSS WILD-TYPE | 63 | 92 | 89 | 105 | 36 |
Figure S219. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00813 (Fisher's exact test), Q value = 0.035
Table S220. Gene #63: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 12P LOSS MUTATED | 0 | 8 | 6 |
| 12P LOSS WILD-TYPE | 42 | 64 | 26 |
Figure S220. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S221. Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 12P LOSS MUTATED | 2 | 37 | 8 |
| 12P LOSS WILD-TYPE | 200 | 133 | 70 |
Figure S221. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00471 (Fisher's exact test), Q value = 0.023
Table S222. Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 12P LOSS MUTATED | 22 | 5 | 6 |
| 12P LOSS WILD-TYPE | 96 | 94 | 70 |
Figure S222. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00092 (Fisher's exact test), Q value = 0.0057
Table S223. Gene #63: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 12P LOSS MUTATED | 20 | 2 | 9 | 16 |
| 12P LOSS WILD-TYPE | 101 | 105 | 81 | 114 |
Figure S223. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 6e-05 (Fisher's exact test), Q value = 6e-04
Table S224. Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 12P LOSS MUTATED | 15 | 13 | 1 | 18 | 0 |
| 12P LOSS WILD-TYPE | 64 | 95 | 95 | 111 | 36 |
Figure S224. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0208 (Fisher's exact test), Q value = 0.078
Table S225. Gene #63: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 12 | 22 | 17 | 24 | 10 |
| 12P LOSS MUTATED | 4 | 3 | 1 | 0 | 2 |
| 12P LOSS WILD-TYPE | 8 | 19 | 16 | 24 | 8 |
Figure S225. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.00777 (Fisher's exact test), Q value = 0.034
Table S226. Gene #64: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 12Q LOSS MUTATED | 0 | 7 | 6 |
| 12Q LOSS WILD-TYPE | 42 | 65 | 26 |
Figure S226. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S227. Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 12Q LOSS MUTATED | 5 | 36 | 8 |
| 12Q LOSS WILD-TYPE | 197 | 134 | 70 |
Figure S227. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00807 (Fisher's exact test), Q value = 0.035
Table S228. Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 12Q LOSS MUTATED | 23 | 6 | 7 |
| 12Q LOSS WILD-TYPE | 95 | 93 | 69 |
Figure S228. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00029 (Fisher's exact test), Q value = 0.0023
Table S229. Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 12Q LOSS MUTATED | 22 | 2 | 9 | 16 |
| 12Q LOSS WILD-TYPE | 99 | 105 | 81 | 114 |
Figure S229. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 0.00013 (Fisher's exact test), Q value = 0.0011
Table S230. Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 12Q LOSS MUTATED | 15 | 14 | 2 | 18 | 0 |
| 12Q LOSS WILD-TYPE | 64 | 94 | 94 | 111 | 36 |
Figure S230. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0213 (Fisher's exact test), Q value = 0.079
Table S231. Gene #64: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 12 | 22 | 17 | 24 | 10 |
| 12Q LOSS MUTATED | 4 | 3 | 1 | 0 | 2 |
| 12Q LOSS WILD-TYPE | 8 | 19 | 16 | 24 | 8 |
Figure S231. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.043 (Fisher's exact test), Q value = 0.14
Table S232. Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 13Q LOSS MUTATED | 5 | 0 | 4 |
| 13Q LOSS WILD-TYPE | 113 | 99 | 72 |
Figure S232. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00161 (Fisher's exact test), Q value = 0.0091
Table S233. Gene #65: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 78 | 127 | 26 | 94 |
| 13Q LOSS MUTATED | 5 | 0 | 1 | 0 |
| 13Q LOSS WILD-TYPE | 73 | 127 | 25 | 94 |
Figure S233. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 0.0342 (Fisher's exact test), Q value = 0.12
Table S234. Gene #65: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 29 | 32 | 24 |
| 13Q LOSS MUTATED | 0 | 4 | 0 |
| 13Q LOSS WILD-TYPE | 29 | 28 | 24 |
Figure S234. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S235. Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 61 | 29 | 21 |
| 14Q LOSS MUTATED | 5 | 33 | 2 | 10 |
| 14Q LOSS WILD-TYPE | 30 | 28 | 27 | 11 |
Figure S235. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 9e-05 (Fisher's exact test), Q value = 0.00082
Table S236. Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 14Q LOSS MUTATED | 4 | 29 | 17 |
| 14Q LOSS WILD-TYPE | 38 | 43 | 15 |
Figure S236. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S237. Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 14Q LOSS MUTATED | 23 | 103 | 13 |
| 14Q LOSS WILD-TYPE | 179 | 67 | 65 |
Figure S237. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S238. Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 14Q LOSS MUTATED | 56 | 14 | 17 |
| 14Q LOSS WILD-TYPE | 62 | 85 | 59 |
Figure S238. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00184 (Fisher's exact test), Q value = 0.01
Table S239. Gene #66: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 78 | 127 | 26 | 94 |
| 14Q LOSS MUTATED | 25 | 50 | 8 | 15 |
| 14Q LOSS WILD-TYPE | 53 | 77 | 18 | 79 |
Figure S239. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 0.0244 (Fisher's exact test), Q value = 0.087
Table S240. Gene #66: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 59 | 48 | 56 | 68 | 68 | 26 |
| 14Q LOSS MUTATED | 19 | 21 | 14 | 26 | 12 | 6 |
| 14Q LOSS WILD-TYPE | 40 | 27 | 42 | 42 | 56 | 20 |
Figure S240. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S241. Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 14Q LOSS MUTATED | 60 | 9 | 22 | 48 |
| 14Q LOSS WILD-TYPE | 61 | 98 | 68 | 82 |
Figure S241. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S242. Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 14Q LOSS MUTATED | 33 | 45 | 4 | 55 | 2 |
| 14Q LOSS WILD-TYPE | 46 | 63 | 92 | 74 | 34 |
Figure S242. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0214 (Fisher's exact test), Q value = 0.079
Table S243. Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 135 | 50 | 77 | 135 |
| 14Q LOSS MUTATED | 40 | 8 | 32 | 39 |
| 14Q LOSS WILD-TYPE | 95 | 42 | 45 | 96 |
Figure S243. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00538 (Fisher's exact test), Q value = 0.025
Table S244. Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 12 | 22 | 17 | 24 | 10 |
| 14Q LOSS MUTATED | 4 | 8 | 5 | 3 | 8 |
| 14Q LOSS WILD-TYPE | 8 | 14 | 12 | 21 | 2 |
Figure S244. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.00202 (Fisher's exact test), Q value = 0.011
Table S245. Gene #67: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 61 | 29 | 21 |
| 15Q LOSS MUTATED | 8 | 30 | 4 | 10 |
| 15Q LOSS WILD-TYPE | 27 | 31 | 25 | 11 |
Figure S245. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00135 (Fisher's exact test), Q value = 0.0079
Table S246. Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 15Q LOSS MUTATED | 7 | 27 | 18 |
| 15Q LOSS WILD-TYPE | 35 | 45 | 14 |
Figure S246. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S247. Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 15Q LOSS MUTATED | 28 | 107 | 22 |
| 15Q LOSS WILD-TYPE | 174 | 63 | 56 |
Figure S247. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00038 (Fisher's exact test), Q value = 0.0027
Table S248. Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 15Q LOSS MUTATED | 57 | 22 | 25 |
| 15Q LOSS WILD-TYPE | 61 | 77 | 51 |
Figure S248. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.0139 (Fisher's exact test), Q value = 0.056
Table S249. Gene #67: '15q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 78 | 127 | 26 | 94 |
| 15Q LOSS MUTATED | 35 | 38 | 12 | 23 |
| 15Q LOSS WILD-TYPE | 43 | 89 | 14 | 71 |
Figure S249. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S250. Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 15Q LOSS MUTATED | 59 | 14 | 32 | 51 |
| 15Q LOSS WILD-TYPE | 62 | 93 | 58 | 79 |
Figure S250. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S251. Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 15Q LOSS MUTATED | 40 | 45 | 10 | 57 | 4 |
| 15Q LOSS WILD-TYPE | 39 | 63 | 86 | 72 | 32 |
Figure S251. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0129 (Fisher's exact test), Q value = 0.053
Table S252. Gene #68: '16p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 59 | 48 | 56 | 68 | 68 | 26 |
| 16P LOSS MUTATED | 6 | 0 | 5 | 0 | 4 | 2 |
| 16P LOSS WILD-TYPE | 53 | 48 | 51 | 68 | 64 | 24 |
Figure S252. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 0.0336 (Fisher's exact test), Q value = 0.11
Table S253. Gene #69: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 59 | 48 | 56 | 68 | 68 | 26 |
| 16Q LOSS MUTATED | 5 | 0 | 4 | 0 | 4 | 2 |
| 16Q LOSS WILD-TYPE | 54 | 48 | 52 | 68 | 64 | 24 |
Figure S253. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S254. Gene #70: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 61 | 29 | 21 |
| 17P LOSS MUTATED | 9 | 46 | 8 | 15 |
| 17P LOSS WILD-TYPE | 26 | 15 | 21 | 6 |
Figure S254. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S255. Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 17P LOSS MUTATED | 8 | 46 | 24 |
| 17P LOSS WILD-TYPE | 34 | 26 | 8 |
Figure S255. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S256. Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 17P LOSS MUTATED | 48 | 135 | 53 |
| 17P LOSS WILD-TYPE | 154 | 35 | 25 |
Figure S256. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S257. Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 17P LOSS MUTATED | 89 | 33 | 32 |
| 17P LOSS WILD-TYPE | 29 | 66 | 44 |
Figure S257. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.0249 (Fisher's exact test), Q value = 0.088
Table S258. Gene #70: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 78 | 127 | 26 | 94 |
| 17P LOSS MUTATED | 44 | 71 | 14 | 35 |
| 17P LOSS WILD-TYPE | 34 | 56 | 12 | 59 |
Figure S258. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 0.00717 (Fisher's exact test), Q value = 0.032
Table S259. Gene #70: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 59 | 48 | 56 | 68 | 68 | 26 |
| 17P LOSS MUTATED | 38 | 26 | 30 | 38 | 23 | 9 |
| 17P LOSS WILD-TYPE | 21 | 22 | 26 | 30 | 45 | 17 |
Figure S259. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S260. Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 17P LOSS MUTATED | 91 | 26 | 46 | 72 |
| 17P LOSS WILD-TYPE | 30 | 81 | 44 | 58 |
Figure S260. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S261. Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 17P LOSS MUTATED | 53 | 73 | 19 | 86 | 4 |
| 17P LOSS WILD-TYPE | 26 | 35 | 77 | 43 | 32 |
Figure S261. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00115 (Fisher's exact test), Q value = 0.0069
Table S262. Gene #70: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 12 | 22 | 17 | 24 | 10 |
| 17P LOSS MUTATED | 8 | 17 | 11 | 8 | 10 |
| 17P LOSS WILD-TYPE | 4 | 5 | 6 | 16 | 0 |
Figure S262. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.00041 (Fisher's exact test), Q value = 0.0029
Table S263. Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 17Q LOSS MUTATED | 16 | 38 | 12 |
| 17Q LOSS WILD-TYPE | 186 | 132 | 66 |
Figure S263. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S264. Gene #72: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 61 | 29 | 21 |
| 18P LOSS MUTATED | 7 | 51 | 6 | 16 |
| 18P LOSS WILD-TYPE | 28 | 10 | 23 | 5 |
Figure S264. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S265. Gene #72: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 18P LOSS MUTATED | 6 | 46 | 28 |
| 18P LOSS WILD-TYPE | 36 | 26 | 4 |
Figure S265. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S266. Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 18P LOSS MUTATED | 50 | 157 | 47 |
| 18P LOSS WILD-TYPE | 152 | 13 | 31 |
Figure S266. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S267. Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 18P LOSS MUTATED | 105 | 31 | 35 |
| 18P LOSS WILD-TYPE | 13 | 68 | 41 |
Figure S267. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.0014 (Fisher's exact test), Q value = 0.0081
Table S268. Gene #72: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 78 | 127 | 26 | 94 |
| 18P LOSS MUTATED | 47 | 79 | 15 | 35 |
| 18P LOSS WILD-TYPE | 31 | 48 | 11 | 59 |
Figure S268. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 0.00388 (Fisher's exact test), Q value = 0.019
Table S269. Gene #72: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 59 | 48 | 56 | 68 | 68 | 26 |
| 18P LOSS MUTATED | 36 | 31 | 37 | 37 | 26 | 9 |
| 18P LOSS WILD-TYPE | 23 | 17 | 19 | 31 | 42 | 17 |
Figure S269. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S270. Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 18P LOSS MUTATED | 107 | 25 | 48 | 73 |
| 18P LOSS WILD-TYPE | 14 | 82 | 42 | 57 |
Figure S270. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S271. Gene #72: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 18P LOSS MUTATED | 62 | 83 | 15 | 91 | 2 |
| 18P LOSS WILD-TYPE | 17 | 25 | 81 | 38 | 34 |
Figure S271. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0198 (Fisher's exact test), Q value = 0.075
Table S272. Gene #72: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 135 | 50 | 77 | 135 |
| 18P LOSS MUTATED | 71 | 25 | 55 | 70 |
| 18P LOSS WILD-TYPE | 64 | 25 | 22 | 65 |
Figure S272. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00046 (Fisher's exact test), Q value = 0.0031
Table S273. Gene #72: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 12 | 22 | 17 | 24 | 10 |
| 18P LOSS MUTATED | 10 | 15 | 12 | 6 | 9 |
| 18P LOSS WILD-TYPE | 2 | 7 | 5 | 18 | 1 |
Figure S273. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S274. Gene #73: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 61 | 29 | 21 |
| 18Q LOSS MUTATED | 8 | 52 | 7 | 16 |
| 18Q LOSS WILD-TYPE | 27 | 9 | 22 | 5 |
Figure S274. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S275. Gene #73: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 18Q LOSS MUTATED | 7 | 48 | 28 |
| 18Q LOSS WILD-TYPE | 35 | 24 | 4 |
Figure S275. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S276. Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 18Q LOSS MUTATED | 57 | 157 | 57 |
| 18Q LOSS WILD-TYPE | 145 | 13 | 21 |
Figure S276. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S277. Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 18Q LOSS MUTATED | 106 | 39 | 39 |
| 18Q LOSS WILD-TYPE | 12 | 60 | 37 |
Figure S277. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00575 (Fisher's exact test), Q value = 0.026
Table S278. Gene #73: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 78 | 127 | 26 | 94 |
| 18Q LOSS MUTATED | 51 | 81 | 15 | 40 |
| 18Q LOSS WILD-TYPE | 27 | 46 | 11 | 54 |
Figure S278. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 0.00299 (Fisher's exact test), Q value = 0.015
Table S279. Gene #73: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 59 | 48 | 56 | 68 | 68 | 26 |
| 18Q LOSS MUTATED | 39 | 33 | 38 | 39 | 28 | 10 |
| 18Q LOSS WILD-TYPE | 20 | 15 | 18 | 29 | 40 | 16 |
Figure S279. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S280. Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 18Q LOSS MUTATED | 107 | 31 | 54 | 78 |
| 18Q LOSS WILD-TYPE | 14 | 76 | 36 | 52 |
Figure S280. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S281. Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 18Q LOSS MUTATED | 67 | 86 | 21 | 94 | 2 |
| 18Q LOSS WILD-TYPE | 12 | 22 | 75 | 35 | 34 |
Figure S281. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0131 (Fisher's exact test), Q value = 0.053
Table S282. Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 135 | 50 | 77 | 135 |
| 18Q LOSS MUTATED | 79 | 28 | 58 | 72 |
| 18Q LOSS WILD-TYPE | 56 | 22 | 19 | 63 |
Figure S282. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00048 (Fisher's exact test), Q value = 0.0032
Table S283. Gene #73: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 12 | 22 | 17 | 24 | 10 |
| 18Q LOSS MUTATED | 10 | 17 | 12 | 8 | 10 |
| 18Q LOSS WILD-TYPE | 2 | 5 | 5 | 16 | 0 |
Figure S283. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.00328 (Fisher's exact test), Q value = 0.016
Table S284. Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 19P LOSS MUTATED | 20 | 4 | 4 | 12 |
| 19P LOSS WILD-TYPE | 101 | 103 | 86 | 118 |
Figure S284. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 0.0224 (Fisher's exact test), Q value = 0.081
Table S285. Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 19P LOSS MUTATED | 4 | 15 | 3 | 16 | 2 |
| 19P LOSS WILD-TYPE | 75 | 93 | 93 | 113 | 34 |
Figure S285. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0424 (Fisher's exact test), Q value = 0.14
Table S286. Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 160 | 65 | 172 |
| 19P LOSS MUTATED | 15 | 1 | 19 |
| 19P LOSS WILD-TYPE | 145 | 64 | 153 |
Figure S286. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 0.00454 (Fisher's exact test), Q value = 0.022
Table S287. Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 135 | 50 | 77 | 135 |
| 19P LOSS MUTATED | 9 | 0 | 13 | 13 |
| 19P LOSS WILD-TYPE | 126 | 50 | 64 | 122 |
Figure S287. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00476 (Fisher's exact test), Q value = 0.023
Table S288. Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 19Q LOSS MUTATED | 17 | 3 | 3 | 12 |
| 19Q LOSS WILD-TYPE | 104 | 104 | 87 | 118 |
Figure S288. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 0.0171 (Fisher's exact test), Q value = 0.066
Table S289. Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 19Q LOSS MUTATED | 2 | 12 | 3 | 16 | 2 |
| 19Q LOSS WILD-TYPE | 77 | 96 | 93 | 113 | 34 |
Figure S289. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.049 (Fisher's exact test), Q value = 0.15
Table S290. Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 135 | 50 | 77 | 135 |
| 19Q LOSS MUTATED | 7 | 1 | 11 | 11 |
| 19Q LOSS WILD-TYPE | 128 | 49 | 66 | 124 |
Figure S290. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00066 (Fisher's exact test), Q value = 0.0042
Table S291. Gene #76: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 20P LOSS MUTATED | 0 | 5 | 8 |
| 20P LOSS WILD-TYPE | 42 | 67 | 24 |
Figure S291. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 9e-05 (Fisher's exact test), Q value = 0.00082
Table S292. Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 20P LOSS MUTATED | 7 | 23 | 14 |
| 20P LOSS WILD-TYPE | 195 | 147 | 64 |
Figure S292. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0351 (Fisher's exact test), Q value = 0.12
Table S293. Gene #76: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 20P LOSS MUTATED | 18 | 5 | 6 |
| 20P LOSS WILD-TYPE | 100 | 94 | 70 |
Figure S293. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.0189 (Fisher's exact test), Q value = 0.072
Table S294. Gene #76: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 20P LOSS MUTATED | 19 | 4 | 10 | 11 |
| 20P LOSS WILD-TYPE | 102 | 103 | 80 | 119 |
Figure S294. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 0.00971 (Fisher's exact test), Q value = 0.041
Table S295. Gene #76: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 20P LOSS MUTATED | 14 | 12 | 3 | 14 | 1 |
| 20P LOSS WILD-TYPE | 65 | 96 | 93 | 115 | 35 |
Figure S295. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0443 (Fisher's exact test), Q value = 0.14
Table S296. Gene #76: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 135 | 50 | 77 | 135 |
| 20P LOSS MUTATED | 10 | 10 | 9 | 9 |
| 20P LOSS WILD-TYPE | 125 | 40 | 68 | 126 |
Figure S296. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00992 (Fisher's exact test), Q value = 0.042
Table S297. Gene #78: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 61 | 29 | 21 |
| 21Q LOSS MUTATED | 7 | 25 | 3 | 4 |
| 21Q LOSS WILD-TYPE | 28 | 36 | 26 | 17 |
Figure S297. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S298. Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 21Q LOSS MUTATED | 37 | 74 | 13 |
| 21Q LOSS WILD-TYPE | 165 | 96 | 65 |
Figure S298. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0433 (Fisher's exact test), Q value = 0.14
Table S299. Gene #78: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 21Q LOSS MUTATED | 42 | 20 | 21 |
| 21Q LOSS WILD-TYPE | 76 | 79 | 55 |
Figure S299. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S300. Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 21Q LOSS MUTATED | 55 | 15 | 21 | 32 |
| 21Q LOSS WILD-TYPE | 66 | 92 | 69 | 98 |
Figure S300. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 0.00892 (Fisher's exact test), Q value = 0.038
Table S301. Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 21Q LOSS MUTATED | 29 | 33 | 18 | 39 | 4 |
| 21Q LOSS WILD-TYPE | 50 | 75 | 78 | 90 | 32 |
Figure S301. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00051 (Fisher's exact test), Q value = 0.0034
Table S302. Gene #79: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 61 | 29 | 21 |
| 22Q LOSS MUTATED | 7 | 32 | 4 | 9 |
| 22Q LOSS WILD-TYPE | 28 | 29 | 25 | 12 |
Figure S302. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00043 (Fisher's exact test), Q value = 0.0031
Table S303. Gene #79: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 72 | 32 |
| 22Q LOSS MUTATED | 5 | 33 | 14 |
| 22Q LOSS WILD-TYPE | 37 | 39 | 18 |
Figure S303. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S304. Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| 22Q LOSS MUTATED | 37 | 94 | 15 |
| 22Q LOSS WILD-TYPE | 165 | 76 | 63 |
Figure S304. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00302 (Fisher's exact test), Q value = 0.015
Table S305. Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 118 | 99 | 76 |
| 22Q LOSS MUTATED | 44 | 18 | 28 |
| 22Q LOSS WILD-TYPE | 74 | 81 | 48 |
Figure S305. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 2e-05 (Fisher's exact test), Q value = 0.00023
Table S306. Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 121 | 107 | 90 | 130 |
| 22Q LOSS MUTATED | 52 | 16 | 28 | 49 |
| 22Q LOSS WILD-TYPE | 69 | 91 | 62 | 81 |
Figure S306. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S307. Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 79 | 108 | 96 | 129 | 36 |
| 22Q LOSS MUTATED | 35 | 41 | 10 | 57 | 2 |
| 22Q LOSS WILD-TYPE | 44 | 67 | 86 | 72 | 34 |
Figure S307. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0278 (Fisher's exact test), Q value = 0.096
Table S308. Gene #80: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 61 | 29 | 21 |
| XP LOSS MUTATED | 4 | 15 | 3 | 0 |
| XP LOSS WILD-TYPE | 31 | 46 | 26 | 21 |
Figure S308. Get High-res Image Gene #80: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.0176 (Fisher's exact test), Q value = 0.068
Table S309. Gene #80: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| XP LOSS MUTATED | 19 | 33 | 13 |
| XP LOSS WILD-TYPE | 183 | 137 | 65 |
Figure S309. Get High-res Image Gene #80: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.016 (Fisher's exact test), Q value = 0.063
Table S310. Gene #81: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 61 | 29 | 21 |
| XQ LOSS MUTATED | 4 | 15 | 2 | 0 |
| XQ LOSS WILD-TYPE | 31 | 46 | 27 | 21 |
Figure S310. Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00307 (Fisher's exact test), Q value = 0.016
Table S311. Gene #81: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 202 | 170 | 78 |
| XQ LOSS MUTATED | 15 | 32 | 7 |
| XQ LOSS WILD-TYPE | 187 | 138 | 71 |
Figure S311. Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'
-
Copy number data file = broad_values_by_arm.txt from GISTIC pipeline
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Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/COAD-TP/15082917/transformed.cor.cli.txt
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Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/COAD-TP/15098885/COAD-TP.transferedmergedcluster.txt
-
Number of patients = 450
-
Number of significantly arm-level cnvs = 81
-
Number of molecular subtypes = 12
-
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.