This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.
Testing the association between copy number variation 82 arm-level events and 14 molecular subtypes across 579 patients, 264 significant findings detected with P value < 0.05 and Q value < 0.25.
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1p gain cnv correlated to 'CN_CNMF'.
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1q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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2p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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2q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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3p gain cnv correlated to 'CN_CNMF'.
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3q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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4p gain cnv correlated to 'MIR_CNMF', 'CN_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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4q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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5p gain cnv correlated to 'CN_CNMF'.
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6p gain cnv correlated to 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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6q gain cnv correlated to 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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7p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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7q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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8p gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'RPPA_CHIERARCHICAL'.
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8q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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9p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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9q gain cnv correlated to 'RPPA_CHIERARCHICAL'.
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10p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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10q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', and 'CN_CNMF'.
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11p gain cnv correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.
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11q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.
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12p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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12q gain cnv correlated to 'MRNA_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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13q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', and 'METHLYATION_CNMF'.
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16p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.
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16q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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17p gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
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17q gain cnv correlated to 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.
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18p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CNMF'.
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18q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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19p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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19q gain cnv correlated to 'CN_CNMF'.
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20p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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20q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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21q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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xp gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
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xq gain cnv correlated to 'CN_CNMF'.
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1p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', and 'RPPA_CNMF'.
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1q loss cnv correlated to 'MRNA_CHIERARCHICAL'.
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2p loss cnv correlated to 'MRNA_CHIERARCHICAL'.
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3p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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3q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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4p loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.
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4q loss cnv correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.
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5p loss cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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5q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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6p loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'MRNASEQ_CHIERARCHICAL'.
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6q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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8p loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
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8q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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9p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', and 'CN_CNMF'.
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9q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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10q loss cnv correlated to 'MIR_CNMF', 'CN_CNMF', and 'METHLYATION_CNMF'.
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11p loss cnv correlated to 'MRNA_CHIERARCHICAL', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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11q loss cnv correlated to 'CN_CNMF'.
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12p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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12q loss cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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13q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'METHLYATION_CNMF', and 'RPPA_CNMF'.
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14q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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15q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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16p loss cnv correlated to 'MIR_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
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16q loss cnv correlated to 'MIR_CNMF' and 'CN_CNMF'.
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17q loss cnv correlated to 'MRNA_CHIERARCHICAL', 'MIR_CNMF', and 'MIR_CHIERARCHICAL'.
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18p loss cnv correlated to 'MIR_CHIERARCHICAL', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.
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18q loss cnv correlated to 'RPPA_CHIERARCHICAL' and 'MRNASEQ_CNMF'.
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19p loss cnv correlated to 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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19q loss cnv correlated to 'MIR_CHIERARCHICAL', 'CN_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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20p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CNMF'.
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20q loss cnv correlated to 'MIR_CNMF', 'RPPA_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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22q loss cnv correlated to 'MRNA_CNMF', 'MIR_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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xp loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.
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xq loss cnv correlated to 'CN_CNMF'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 14 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 264 significant findings detected.
|
Clinical Features |
MRNA CNMF |
MRNA CHIERARCHICAL |
MIR CNMF |
MIR 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 | Fisher's exact test | Fisher's exact test | |
| 2p gain | 186 (32%) | 393 |
1e-05 (0.000425) |
1e-05 (0.000425) |
0.888 (0.983) |
0.00044 (0.00902) |
1e-05 (0.000425) |
1e-05 (0.000425) |
0.0366 (0.173) |
0.0769 (0.289) |
0.0001 (0.00287) |
0.00166 (0.0232) |
0.822 (0.94) |
0.027 (0.144) |
0.675 (0.855) |
0.612 (0.829) |
| 15q loss | 280 (48%) | 299 |
0.00044 (0.00902) |
0.0175 (0.111) |
9e-05 (0.00265) |
0.00022 (0.00537) |
1e-05 (0.000425) |
2e-05 (0.000765) |
0.379 (0.678) |
0.815 (0.939) |
0.0659 (0.26) |
0.613 (0.829) |
0.00795 (0.0629) |
0.00054 (0.01) |
0.0427 (0.192) |
0.626 (0.833) |
| 2q gain | 155 (27%) | 424 |
0.00045 (0.00906) |
6e-05 (0.00191) |
1 (1.00) |
0.00775 (0.0622) |
1e-05 (0.000425) |
0.00022 (0.00537) |
0.108 (0.341) |
0.322 (0.624) |
0.00361 (0.0401) |
0.0187 (0.117) |
0.611 (0.829) |
0.00652 (0.0554) |
1 (1.00) |
0.745 (0.893) |
| 12p gain | 255 (44%) | 324 |
0.00011 (0.00308) |
0.00174 (0.0241) |
0.745 (0.893) |
0.00081 (0.0139) |
1e-05 (0.000425) |
1e-05 (0.000425) |
0.306 (0.606) |
0.318 (0.618) |
0.0006 (0.0109) |
0.00408 (0.0422) |
0.227 (0.516) |
0.00022 (0.00537) |
0.415 (0.699) |
0.255 (0.544) |
| 12q gain | 177 (31%) | 402 |
0.00489 (0.0456) |
0.0565 (0.237) |
0.626 (0.833) |
0.0344 (0.169) |
1e-05 (0.000425) |
1e-05 (0.000425) |
0.0197 (0.121) |
0.223 (0.514) |
0.00209 (0.0273) |
0.00925 (0.0699) |
0.102 (0.335) |
0.0108 (0.0793) |
0.0743 (0.282) |
0.287 (0.587) |
| 5q loss | 223 (39%) | 356 |
0.00032 (0.00765) |
0.00199 (0.0263) |
0.707 (0.871) |
0.0126 (0.0869) |
0.00048 (0.00934) |
1e-05 (0.000425) |
0.0339 (0.168) |
0.0935 (0.319) |
0.00092 (0.0149) |
0.147 (0.403) |
0.62 (0.833) |
0.00737 (0.06) |
0.378 (0.678) |
0.719 (0.877) |
| 10p gain | 188 (32%) | 391 |
0.0044 (0.0436) |
0.0211 (0.126) |
0.68 (0.857) |
0.378 (0.678) |
1e-05 (0.000425) |
0.00016 (0.00427) |
0.979 (1.00) |
0.00986 (0.0726) |
0.0114 (0.0817) |
0.127 (0.368) |
0.559 (0.804) |
0.00078 (0.0138) |
1 (1.00) |
0.94 (1.00) |
| 20p gain | 289 (50%) | 290 |
0.00129 (0.019) |
0.00099 (0.0156) |
0.725 (0.881) |
0.00036 (0.0081) |
1e-05 (0.000425) |
1e-05 (0.000425) |
0.333 (0.636) |
0.375 (0.677) |
0.00373 (0.0401) |
0.164 (0.435) |
0.222 (0.514) |
0.00368 (0.0401) |
0.391 (0.685) |
0.522 (0.776) |
| 20q gain | 328 (57%) | 251 |
1e-05 (0.000425) |
0.00035 (0.00804) |
0.672 (0.854) |
7e-05 (0.00217) |
1e-05 (0.000425) |
1e-05 (0.000425) |
0.66 (0.849) |
0.081 (0.297) |
0.00889 (0.068) |
0.137 (0.383) |
0.257 (0.546) |
0.00468 (0.0442) |
1 (1.00) |
0.493 (0.756) |
| 8q loss | 90 (16%) | 489 |
0.00718 (0.0593) |
0.00494 (0.0457) |
0.522 (0.776) |
0.262 (0.554) |
0.00109 (0.0165) |
0.0357 (0.172) |
0.0231 (0.132) |
0.229 (0.516) |
0.00099 (0.0156) |
0.0287 (0.151) |
0.663 (0.85) |
0.122 (0.359) |
1 (1.00) |
0.903 (0.989) |
| 6q gain | 97 (17%) | 482 |
0.657 (0.849) |
0.0505 (0.219) |
0.82 (0.94) |
0.0217 (0.127) |
1e-05 (0.000425) |
2e-05 (0.000765) |
0.79 (0.923) |
0.997 (1.00) |
0.00463 (0.0442) |
0.0217 (0.127) |
0.198 (0.488) |
0.0282 (0.149) |
0.381 (0.678) |
0.576 (0.813) |
| 3p loss | 95 (16%) | 484 |
0.0227 (0.131) |
0.00104 (0.0159) |
0.816 (0.939) |
0.00568 (0.0504) |
0.0004 (0.0085) |
0.00229 (0.0292) |
0.648 (0.845) |
0.269 (0.559) |
0.0624 (0.25) |
0.00643 (0.0552) |
0.125 (0.364) |
0.0912 (0.315) |
1 (1.00) |
0.121 (0.359) |
| 3q loss | 43 (7%) | 536 |
0.0125 (0.0868) |
0.0387 (0.179) |
0.285 (0.584) |
0.0573 (0.237) |
0.0309 (0.157) |
0.00303 (0.0355) |
0.932 (1.00) |
0.363 (0.67) |
0.233 (0.517) |
0.0909 (0.315) |
0.304 (0.606) |
0.00104 (0.0159) |
0.594 (0.818) |
0.0336 (0.167) |
| 5p loss | 133 (23%) | 446 |
0.0737 (0.281) |
0.0311 (0.157) |
0.542 (0.791) |
0.0897 (0.312) |
0.0119 (0.0825) |
0.00698 (0.0585) |
0.0894 (0.312) |
0.057 (0.237) |
8e-05 (0.00242) |
0.047 (0.207) |
0.573 (0.811) |
0.0493 (0.214) |
1 (1.00) |
0.906 (0.99) |
| 9q loss | 286 (49%) | 293 |
0.00713 (0.0593) |
0.0128 (0.0873) |
0.221 (0.514) |
0.0334 (0.167) |
1e-05 (0.000425) |
0.00552 (0.0495) |
0.606 (0.828) |
0.684 (0.859) |
0.00816 (0.0641) |
0.0509 (0.219) |
0.224 (0.514) |
0.0581 (0.239) |
1 (1.00) |
0.624 (0.833) |
| 12p loss | 79 (14%) | 500 |
0.00291 (0.0352) |
0.011 (0.0798) |
0.66 (0.849) |
0.00627 (0.0549) |
0.00087 (0.0143) |
0.254 (0.544) |
0.871 (0.971) |
0.15 (0.407) |
0.316 (0.616) |
0.201 (0.492) |
0.0094 (0.0705) |
0.00637 (0.0552) |
0.293 (0.595) |
0.722 (0.878) |
| 22q loss | 430 (74%) | 149 |
0.00217 (0.028) |
0.0925 (0.317) |
0.0346 (0.169) |
0.129 (0.372) |
4e-05 (0.00143) |
0.00182 (0.0246) |
0.0869 (0.308) |
0.0236 (0.132) |
0.0852 (0.305) |
0.13 (0.372) |
0.0416 (0.188) |
0.576 (0.813) |
0.135 (0.381) |
0.106 (0.34) |
| 6p gain | 170 (29%) | 409 |
0.514 (0.77) |
0.00438 (0.0436) |
0.901 (0.989) |
0.0134 (0.091) |
1e-05 (0.000425) |
6e-05 (0.00191) |
0.864 (0.969) |
0.23 (0.516) |
0.159 (0.424) |
0.00725 (0.0594) |
0.365 (0.671) |
0.0655 (0.26) |
0.415 (0.699) |
0.763 (0.905) |
| 13q gain | 60 (10%) | 519 |
0.00783 (0.0624) |
0.0004 (0.0085) |
0.585 (0.817) |
0.0234 (0.132) |
5e-05 (0.00174) |
1e-05 (0.000425) |
0.493 (0.756) |
0.412 (0.698) |
0.231 (0.516) |
0.427 (0.711) |
0.147 (0.403) |
0.0988 (0.328) |
0.455 (0.737) |
|
| 16p gain | 59 (10%) | 520 |
0.00297 (0.0355) |
0.00441 (0.0436) |
0.401 (0.692) |
0.176 (0.456) |
0.0303 (0.155) |
0.0174 (0.111) |
0.349 (0.654) |
0.0348 (0.169) |
0.648 (0.845) |
0.798 (0.927) |
0.125 (0.364) |
0.0809 (0.297) |
0.481 (0.748) |
|
| 16q gain | 31 (5%) | 548 |
0.00084 (0.014) |
0.0443 (0.197) |
0.161 (0.43) |
0.223 (0.514) |
0.267 (0.559) |
0.00353 (0.0401) |
0.454 (0.737) |
0.0263 (0.142) |
1 (1.00) |
0.361 (0.669) |
0.0008 (0.0139) |
0.106 (0.34) |
1 (1.00) |
|
| 13q loss | 310 (54%) | 269 |
0.0292 (0.152) |
0.00861 (0.0668) |
0.803 (0.931) |
0.0163 (0.105) |
0.051 (0.219) |
1e-05 (0.000425) |
0.00531 (0.0483) |
0.349 (0.654) |
0.467 (0.747) |
0.416 (0.701) |
0.216 (0.512) |
0.532 (0.784) |
0.666 (0.851) |
0.149 (0.405) |
| 19p loss | 185 (32%) | 394 |
0.979 (1.00) |
0.453 (0.737) |
0.329 (0.632) |
0.0444 (0.197) |
0.00522 (0.0479) |
0.0197 (0.121) |
0.00975 (0.0726) |
0.888 (0.983) |
0.67 (0.853) |
0.31 (0.61) |
0.676 (0.855) |
0.117 (0.353) |
0.0115 (0.0818) |
0.125 (0.364) |
| 8q gain | 242 (42%) | 337 |
0.0202 (0.122) |
0.0007 (0.0126) |
0.0788 (0.292) |
0.14 (0.391) |
0.26 (0.551) |
0.448 (0.735) |
0.318 (0.618) |
0.269 (0.559) |
0.0298 (0.154) |
0.0859 (0.305) |
0.557 (0.804) |
0.865 (0.969) |
0.031 (0.157) |
0.688 (0.86) |
| 11p gain | 77 (13%) | 502 |
0.709 (0.871) |
0.102 (0.335) |
0.64 (0.842) |
0.467 (0.747) |
0.133 (0.379) |
0.0144 (0.0962) |
0.0268 (0.144) |
0.0259 (0.141) |
0.0591 (0.24) |
0.0352 (0.171) |
0.562 (0.806) |
0.838 (0.952) |
1 (1.00) |
|
| 21q gain | 109 (19%) | 470 |
0.294 (0.596) |
0.879 (0.977) |
0.961 (1.00) |
0.585 (0.817) |
0.00163 (0.0231) |
0.0168 (0.108) |
0.457 (0.739) |
0.396 (0.69) |
0.333 (0.636) |
0.843 (0.956) |
0.0238 (0.133) |
0.0441 (0.197) |
1 (1.00) |
|
| 12q loss | 105 (18%) | 474 |
0.0825 (0.301) |
0.0835 (0.302) |
0.73 (0.883) |
0.171 (0.449) |
0.0234 (0.132) |
0.227 (0.516) |
0.268 (0.559) |
0.558 (0.804) |
0.174 (0.456) |
0.149 (0.405) |
0.0254 (0.139) |
0.0309 (0.157) |
0.135 (0.381) |
0.0404 (0.184) |
| 14q loss | 215 (37%) | 364 |
0.249 (0.54) |
0.192 (0.483) |
0.968 (1.00) |
0.399 (0.692) |
1e-05 (0.000425) |
0.00374 (0.0401) |
0.98 (1.00) |
0.608 (0.828) |
0.00389 (0.0409) |
0.0468 (0.207) |
0.858 (0.964) |
0.403 (0.694) |
0.381 (0.678) |
0.224 (0.514) |
| 18p loss | 235 (41%) | 344 |
0.408 (0.696) |
0.95 (1.00) |
0.472 (0.748) |
0.0203 (0.122) |
0.544 (0.793) |
0.00254 (0.0317) |
0.314 (0.613) |
0.00693 (0.0585) |
0.0242 (0.133) |
0.113 (0.347) |
0.838 (0.952) |
0.541 (0.791) |
0.666 (0.851) |
0.581 (0.815) |
| 4p gain | 60 (10%) | 519 |
0.245 (0.537) |
0.191 (0.481) |
0.0047 (0.0442) |
0.0604 (0.245) |
0.0158 (0.104) |
0.122 (0.359) |
0.458 (0.739) |
0.396 (0.69) |
0.605 (0.828) |
0.84 (0.953) |
0.323 (0.624) |
0.018 (0.113) |
1 (1.00) |
0.571 (0.811) |
| 10q gain | 111 (19%) | 468 |
0.0038 (0.0404) |
0.00889 (0.068) |
0.245 (0.537) |
0.116 (0.351) |
0.0036 (0.0401) |
0.0929 (0.317) |
0.767 (0.906) |
0.0614 (0.247) |
0.105 (0.34) |
0.22 (0.514) |
0.73 (0.883) |
0.246 (0.538) |
0.646 (0.845) |
0.659 (0.849) |
| 11q gain | 115 (20%) | 464 |
0.393 (0.687) |
0.25 (0.54) |
0.883 (0.979) |
0.179 (0.462) |
0.00467 (0.0442) |
0.00181 (0.0246) |
0.205 (0.498) |
0.00054 (0.01) |
0.306 (0.606) |
0.155 (0.416) |
0.406 (0.695) |
0.78 (0.916) |
0.323 (0.624) |
0.107 (0.341) |
| 17q gain | 47 (8%) | 532 |
0.418 (0.702) |
0.0379 (0.176) |
0.756 (0.901) |
0.0364 (0.173) |
0.524 (0.777) |
0.388 (0.683) |
0.588 (0.818) |
0.373 (0.677) |
0.904 (0.989) |
0.0223 (0.13) |
0.825 (0.943) |
0.879 (0.977) |
1 (1.00) |
|
| 18p gain | 120 (21%) | 459 |
0.183 (0.468) |
0.0987 (0.328) |
0.871 (0.971) |
0.388 (0.683) |
0.00127 (0.0189) |
0.00034 (0.00797) |
0.0231 (0.132) |
0.11 (0.344) |
0.81 (0.937) |
0.687 (0.86) |
0.352 (0.656) |
0.233 (0.517) |
0.646 (0.845) |
0.814 (0.939) |
| 1p loss | 65 (11%) | 514 |
0.0316 (0.159) |
0.00039 (0.0085) |
0.465 (0.747) |
0.196 (0.486) |
0.47 (0.748) |
0.291 (0.593) |
0.0207 (0.124) |
0.211 (0.507) |
0.631 (0.838) |
0.512 (0.767) |
0.445 (0.731) |
0.307 (0.606) |
1 (1.00) |
|
| 6q loss | 242 (42%) | 337 |
0.962 (1.00) |
0.0769 (0.289) |
0.434 (0.721) |
0.0979 (0.328) |
0.0348 (0.169) |
0.0723 (0.278) |
0.626 (0.833) |
0.656 (0.849) |
0.0194 (0.12) |
0.0215 (0.127) |
0.793 (0.925) |
0.569 (0.811) |
0.594 (0.818) |
0.902 (0.989) |
| 9p loss | 262 (45%) | 317 |
0.00323 (0.0375) |
0.00571 (0.0504) |
0.51 (0.766) |
0.184 (0.469) |
0.0162 (0.105) |
0.0685 (0.268) |
0.791 (0.923) |
0.542 (0.791) |
0.9 (0.989) |
0.108 (0.341) |
0.0543 (0.229) |
0.255 (0.544) |
0.391 (0.685) |
0.152 (0.407) |
| 10q loss | 124 (21%) | 455 |
0.939 (1.00) |
0.828 (0.945) |
0.00438 (0.0436) |
0.296 (0.598) |
0.0227 (0.131) |
0.00189 (0.0252) |
0.3 (0.601) |
0.403 (0.694) |
0.773 (0.91) |
0.74 (0.891) |
0.695 (0.863) |
0.374 (0.677) |
0.381 (0.678) |
0.694 (0.863) |
| 11p loss | 198 (34%) | 381 |
0.241 (0.53) |
0.0115 (0.0818) |
0.54 (0.791) |
0.31 (0.61) |
0.202 (0.492) |
0.0365 (0.173) |
0.0988 (0.328) |
0.612 (0.829) |
0.04 (0.184) |
0.112 (0.346) |
0.47 (0.748) |
0.144 (0.396) |
0.323 (0.624) |
0.801 (0.93) |
| 16p loss | 334 (58%) | 245 |
0.38 (0.678) |
0.845 (0.956) |
0.0405 (0.184) |
0.352 (0.656) |
0.218 (0.513) |
0.114 (0.349) |
0.765 (0.906) |
0.23 (0.516) |
0.0397 (0.183) |
0.244 (0.537) |
0.0477 (0.209) |
0.0686 (0.268) |
0.675 (0.855) |
0.369 (0.672) |
| 17q loss | 383 (66%) | 196 |
0.0848 (0.304) |
0.0289 (0.151) |
0.016 (0.105) |
0.0117 (0.0825) |
0.943 (1.00) |
0.559 (0.804) |
0.571 (0.811) |
0.293 (0.594) |
0.534 (0.787) |
0.0973 (0.327) |
0.0777 (0.29) |
0.714 (0.875) |
0.624 (0.833) |
0.278 (0.571) |
| 19q loss | 178 (31%) | 401 |
0.695 (0.863) |
0.248 (0.54) |
0.252 (0.542) |
0.0158 (0.104) |
0.00459 (0.0442) |
0.0731 (0.28) |
0.0607 (0.246) |
0.68 (0.857) |
0.926 (1.00) |
0.718 (0.877) |
0.301 (0.601) |
0.0532 (0.226) |
0.00535 (0.0483) |
0.425 (0.71) |
| 20q loss | 32 (6%) | 547 |
0.117 (0.351) |
0.5 (0.757) |
0.0377 (0.176) |
0.505 (0.76) |
0.442 (0.726) |
0.638 (0.842) |
0.0481 (0.21) |
0.0989 (0.328) |
0.131 (0.375) |
0.0141 (0.095) |
0.135 (0.381) |
0.381 (0.678) |
0.481 (0.748) |
|
| xp loss | 325 (56%) | 254 |
0.143 (0.396) |
0.251 (0.541) |
0.202 (0.492) |
0.668 (0.853) |
0.00644 (0.0552) |
0.0406 (0.184) |
0.174 (0.456) |
0.0362 (0.173) |
0.481 (0.748) |
0.881 (0.978) |
0.214 (0.51) |
0.454 (0.737) |
1 (1.00) |
0.305 (0.606) |
| 1q gain | 221 (38%) | 358 |
0.833 (0.95) |
0.27 (0.559) |
0.704 (0.869) |
0.227 (0.516) |
1e-05 (0.000425) |
0.00906 (0.0689) |
0.501 (0.757) |
0.548 (0.797) |
0.436 (0.721) |
0.276 (0.567) |
0.229 (0.516) |
0.107 (0.341) |
0.198 (0.489) |
0.562 (0.806) |
| 3q gain | 275 (47%) | 304 |
0.934 (1.00) |
0.867 (0.97) |
0.343 (0.647) |
0.428 (0.712) |
1e-05 (0.000425) |
0.0163 (0.105) |
0.639 (0.842) |
0.26 (0.551) |
0.697 (0.863) |
0.925 (1.00) |
0.253 (0.542) |
0.0882 (0.311) |
1 (1.00) |
0.634 (0.839) |
| 4q gain | 32 (6%) | 547 |
0.498 (0.757) |
0.763 (0.905) |
0.211 (0.507) |
0.0787 (0.292) |
0.00454 (0.0442) |
0.00767 (0.062) |
0.353 (0.656) |
0.227 (0.516) |
0.766 (0.906) |
0.855 (0.963) |
0.227 (0.516) |
0.0631 (0.252) |
||
| 7p gain | 181 (31%) | 398 |
0.589 (0.818) |
0.474 (0.748) |
0.0854 (0.305) |
0.109 (0.342) |
1e-05 (0.000425) |
0.00013 (0.00355) |
0.646 (0.845) |
0.498 (0.757) |
0.531 (0.784) |
0.681 (0.857) |
0.966 (1.00) |
0.12 (0.359) |
1 (1.00) |
0.759 (0.903) |
| 7q gain | 203 (35%) | 376 |
0.649 (0.845) |
0.0835 (0.302) |
0.298 (0.599) |
0.377 (0.678) |
1e-05 (0.000425) |
0.00158 (0.0227) |
0.461 (0.743) |
0.25 (0.54) |
0.924 (1.00) |
0.64 (0.842) |
0.151 (0.407) |
0.631 (0.838) |
0.646 (0.845) |
0.365 (0.671) |
| 8p gain | 119 (21%) | 460 |
0.0706 (0.273) |
0.00392 (0.0409) |
0.4 (0.692) |
0.418 (0.702) |
0.692 (0.863) |
0.806 (0.934) |
0.136 (0.383) |
0.003 (0.0355) |
0.618 (0.833) |
1 (1.00) |
0.13 (0.372) |
0.495 (0.756) |
0.221 (0.514) |
0.103 (0.336) |
| 9p gain | 92 (16%) | 487 |
0.111 (0.345) |
0.423 (0.706) |
0.236 (0.521) |
0.867 (0.97) |
0.00276 (0.0337) |
0.00821 (0.0641) |
0.397 (0.691) |
0.728 (0.882) |
0.692 (0.863) |
0.413 (0.698) |
0.185 (0.47) |
0.186 (0.472) |
0.624 (0.833) |
0.606 (0.828) |
| 18q gain | 72 (12%) | 507 |
0.644 (0.845) |
0.165 (0.437) |
0.227 (0.516) |
0.39 (0.685) |
0.0235 (0.132) |
0.024 (0.133) |
0.516 (0.77) |
0.399 (0.692) |
0.485 (0.75) |
0.268 (0.559) |
0.106 (0.34) |
0.196 (0.486) |
1 (1.00) |
1 (1.00) |
| 19p gain | 171 (30%) | 408 |
0.0757 (0.286) |
0.455 (0.737) |
0.52 (0.775) |
0.114 (0.349) |
2e-05 (0.000765) |
0.0264 (0.143) |
0.0551 (0.232) |
0.325 (0.625) |
0.19 (0.479) |
0.577 (0.813) |
0.269 (0.559) |
0.311 (0.611) |
1 (1.00) |
0.746 (0.893) |
| xp gain | 78 (13%) | 501 |
0.45 (0.735) |
0.636 (0.841) |
0.902 (0.989) |
0.593 (0.818) |
0.0302 (0.155) |
0.495 (0.756) |
0.52 (0.775) |
0.765 (0.906) |
0.874 (0.973) |
0.684 (0.859) |
0.0375 (0.176) |
0.0658 (0.26) |
1 (1.00) |
|
| 4p loss | 316 (55%) | 263 |
0.367 (0.672) |
0.0214 (0.127) |
0.281 (0.576) |
0.614 (0.829) |
0.00436 (0.0436) |
0.483 (0.748) |
0.151 (0.407) |
0.132 (0.375) |
0.422 (0.706) |
0.44 (0.726) |
0.121 (0.359) |
0.196 (0.486) |
1 (1.00) |
0.624 (0.833) |
| 4q loss | 362 (63%) | 217 |
0.208 (0.502) |
0.083 (0.302) |
0.502 (0.757) |
0.718 (0.877) |
0.00132 (0.0192) |
0.556 (0.804) |
0.121 (0.359) |
0.0183 (0.115) |
0.268 (0.559) |
0.351 (0.656) |
0.215 (0.51) |
0.179 (0.462) |
1 (1.00) |
0.368 (0.672) |
| 6p loss | 165 (28%) | 414 |
0.97 (1.00) |
0.0196 (0.121) |
0.45 (0.735) |
0.509 (0.765) |
0.149 (0.405) |
0.121 (0.359) |
0.782 (0.917) |
0.849 (0.959) |
0.411 (0.698) |
0.0428 (0.192) |
0.481 (0.748) |
0.102 (0.335) |
0.571 (0.811) |
0.573 (0.811) |
| 8p loss | 277 (48%) | 302 |
0.741 (0.891) |
0.891 (0.984) |
0.239 (0.527) |
0.947 (1.00) |
0.00263 (0.0325) |
0.109 (0.342) |
0.116 (0.351) |
0.296 (0.598) |
0.482 (0.748) |
0.705 (0.869) |
0.703 (0.869) |
0.0374 (0.176) |
1 (1.00) |
0.94 (1.00) |
| 16q loss | 413 (71%) | 166 |
0.581 (0.815) |
0.871 (0.971) |
0.00235 (0.0296) |
0.0779 (0.29) |
0.0277 (0.146) |
0.0652 (0.26) |
0.91 (0.992) |
0.312 (0.612) |
0.195 (0.486) |
0.369 (0.672) |
0.0534 (0.226) |
0.129 (0.372) |
0.624 (0.833) |
0.607 (0.828) |
| 18q loss | 293 (51%) | 286 |
0.344 (0.648) |
0.972 (1.00) |
0.299 (0.6) |
0.957 (1.00) |
0.858 (0.964) |
0.105 (0.34) |
0.714 (0.875) |
0.036 (0.173) |
0.0109 (0.0795) |
0.0917 (0.316) |
0.978 (1.00) |
0.776 (0.912) |
0.67 (0.853) |
0.247 (0.539) |
| 20p loss | 50 (9%) | 529 |
0.355 (0.659) |
0.726 (0.881) |
0.221 (0.514) |
0.621 (0.833) |
0.112 (0.346) |
0.468 (0.747) |
0.103 (0.336) |
0.199 (0.49) |
0.0758 (0.286) |
0.00338 (0.0388) |
0.00083 (0.014) |
0.271 (0.559) |
0.481 (0.748) |
|
| 1p gain | 168 (29%) | 411 |
0.0791 (0.292) |
0.35 (0.655) |
0.121 (0.359) |
0.733 (0.884) |
0.00047 (0.0093) |
0.184 (0.469) |
0.104 (0.337) |
0.265 (0.559) |
0.611 (0.829) |
0.95 (1.00) |
0.255 (0.544) |
0.681 (0.857) |
0.231 (0.516) |
0.523 (0.776) |
| 3p gain | 160 (28%) | 419 |
0.437 (0.722) |
0.449 (0.735) |
0.0699 (0.271) |
0.53 (0.784) |
0.0118 (0.0825) |
0.783 (0.918) |
1 (1.00) |
0.387 (0.683) |
0.658 (0.849) |
0.686 (0.86) |
0.99 (1.00) |
0.817 (0.939) |
1 (1.00) |
0.81 (0.937) |
| 5p gain | 199 (34%) | 380 |
0.565 (0.808) |
0.71 (0.871) |
0.855 (0.963) |
0.761 (0.905) |
0.00052 (0.00995) |
0.196 (0.486) |
0.496 (0.757) |
0.0708 (0.273) |
0.13 (0.372) |
0.541 (0.791) |
0.182 (0.467) |
0.574 (0.812) |
0.666 (0.851) |
0.216 (0.512) |
| 9q gain | 45 (8%) | 534 |
0.253 (0.542) |
0.305 (0.606) |
0.0927 (0.317) |
0.532 (0.784) |
0.141 (0.392) |
0.222 (0.514) |
0.582 (0.815) |
0.0274 (0.146) |
0.48 (0.748) |
0.0939 (0.319) |
0.499 (0.757) |
0.753 (0.899) |
0.455 (0.737) |
|
| 17p gain | 22 (4%) | 557 |
0.435 (0.721) |
0.115 (0.349) |
0.0583 (0.239) |
0.0517 (0.221) |
0.153 (0.409) |
0.233 (0.517) |
0.5 (0.757) |
0.406 (0.695) |
0.21 (0.507) |
0.00373 (0.0401) |
0.175 (0.456) |
0.837 (0.952) |
||
| 19q gain | 161 (28%) | 418 |
0.258 (0.547) |
0.753 (0.899) |
0.906 (0.99) |
0.169 (0.446) |
3e-05 (0.00111) |
0.13 (0.372) |
0.479 (0.748) |
0.463 (0.745) |
0.205 (0.498) |
0.435 (0.721) |
0.271 (0.559) |
0.674 (0.855) |
0.594 (0.818) |
0.722 (0.878) |
| xq gain | 108 (19%) | 471 |
0.654 (0.847) |
0.91 (0.992) |
0.652 (0.846) |
0.215 (0.51) |
6e-05 (0.00191) |
0.866 (0.97) |
0.341 (0.645) |
0.661 (0.849) |
0.903 (0.989) |
0.976 (1.00) |
0.491 (0.756) |
0.483 (0.748) |
0.594 (0.818) |
0.515 (0.77) |
| 1q loss | 43 (7%) | 536 |
0.116 (0.351) |
0.0142 (0.0955) |
0.0573 (0.237) |
0.597 (0.821) |
0.689 (0.861) |
0.384 (0.682) |
0.217 (0.512) |
0.622 (0.833) |
0.466 (0.747) |
1 (1.00) |
0.969 (1.00) |
0.934 (1.00) |
||
| 2p loss | 53 (9%) | 526 |
0.932 (1.00) |
0.0239 (0.133) |
0.618 (0.833) |
0.491 (0.756) |
0.58 (0.815) |
0.773 (0.91) |
0.485 (0.75) |
0.894 (0.986) |
0.336 (0.638) |
0.816 (0.939) |
0.722 (0.878) |
0.399 (0.692) |
0.481 (0.748) |
|
| 11q loss | 148 (26%) | 431 |
0.297 (0.599) |
0.904 (0.989) |
0.213 (0.509) |
0.565 (0.808) |
0.00981 (0.0726) |
0.0698 (0.271) |
0.419 (0.702) |
0.767 (0.906) |
0.271 (0.559) |
0.798 (0.927) |
0.5 (0.757) |
0.179 (0.462) |
0.594 (0.818) |
0.385 (0.683) |
| xq loss | 280 (48%) | 299 |
0.196 (0.486) |
0.352 (0.656) |
0.404 (0.695) |
0.96 (1.00) |
0.00019 (0.00496) |
0.113 (0.348) |
0.55 (0.8) |
0.0844 (0.304) |
0.748 (0.895) |
1 (1.00) |
0.647 (0.845) |
0.67 (0.853) |
1 (1.00) |
0.288 (0.588) |
| 5q gain | 60 (10%) | 519 |
0.059 (0.24) |
0.196 (0.486) |
0.823 (0.941) |
0.895 (0.987) |
0.845 (0.956) |
0.493 (0.756) |
0.467 (0.747) |
0.366 (0.672) |
0.709 (0.871) |
0.41 (0.698) |
0.379 (0.678) |
0.795 (0.927) |
0.481 (0.748) |
|
| 14q gain | 59 (10%) | 520 |
0.142 (0.393) |
0.192 (0.483) |
0.407 (0.695) |
0.7 (0.866) |
0.412 (0.698) |
0.742 (0.891) |
0.33 (0.632) |
0.172 (0.452) |
0.505 (0.76) |
0.572 (0.811) |
0.659 (0.849) |
0.632 (0.838) |
1 (1.00) |
|
| 15q gain | 40 (7%) | 539 |
0.846 (0.956) |
0.481 (0.748) |
0.089 (0.311) |
0.758 (0.902) |
0.0962 (0.326) |
0.607 (0.828) |
0.112 (0.346) |
0.105 (0.34) |
0.736 (0.887) |
0.932 (1.00) |
0.313 (0.612) |
0.2 (0.491) |
1 (1.00) |
|
| 22q gain | 24 (4%) | 555 |
0.365 (0.671) |
0.6 (0.824) |
0.93 (1.00) |
0.605 (0.828) |
0.368 (0.672) |
0.175 (0.456) |
0.39 (0.685) |
0.374 (0.677) |
0.56 (0.804) |
0.613 (0.829) |
0.0973 (0.327) |
0.0822 (0.301) |
0.571 (0.811) |
0.386 (0.683) |
| 2q loss | 59 (10%) | 520 |
0.92 (1.00) |
0.27 (0.559) |
0.697 (0.863) |
0.149 (0.405) |
0.858 (0.964) |
0.681 (0.857) |
0.89 (0.984) |
0.935 (1.00) |
0.499 (0.757) |
0.791 (0.923) |
0.557 (0.804) |
0.23 (0.516) |
0.481 (0.748) |
|
| 7p loss | 121 (21%) | 458 |
0.991 (1.00) |
0.406 (0.695) |
0.477 (0.748) |
0.696 (0.863) |
0.111 (0.345) |
0.149 (0.405) |
0.54 (0.791) |
0.325 (0.625) |
0.773 (0.91) |
0.716 (0.876) |
0.539 (0.791) |
0.796 (0.927) |
0.594 (0.818) |
0.2 (0.491) |
| 7q loss | 81 (14%) | 498 |
0.337 (0.638) |
0.0888 (0.311) |
0.346 (0.652) |
0.3 (0.601) |
0.734 (0.885) |
0.109 (0.342) |
0.82 (0.94) |
0.0686 (0.268) |
0.482 (0.748) |
0.311 (0.611) |
0.123 (0.361) |
0.819 (0.94) |
1 (1.00) |
0.334 (0.638) |
| 10p loss | 97 (17%) | 482 |
0.223 (0.514) |
0.963 (1.00) |
0.219 (0.514) |
0.335 (0.638) |
0.646 (0.845) |
0.232 (0.516) |
0.592 (0.818) |
0.0875 (0.309) |
0.652 (0.846) |
0.553 (0.803) |
0.364 (0.671) |
0.834 (0.95) |
1 (1.00) |
0.223 (0.514) |
| 17p loss | 478 (83%) | 101 |
0.336 (0.638) |
0.228 (0.516) |
0.135 (0.381) |
0.208 (0.502) |
0.59 (0.818) |
0.25 (0.54) |
0.556 (0.804) |
0.186 (0.472) |
0.103 (0.336) |
0.0567 (0.237) |
0.471 (0.748) |
0.473 (0.748) |
1 (1.00) |
|
| 21q loss | 199 (34%) | 380 |
0.819 (0.94) |
0.0517 (0.221) |
0.383 (0.68) |
0.179 (0.462) |
0.493 (0.756) |
0.142 (0.393) |
0.651 (0.846) |
0.441 (0.726) |
0.581 (0.815) |
0.411 (0.698) |
0.687 (0.86) |
0.731 (0.883) |
0.162 (0.43) |
0.584 (0.816) |
P value = 0.00047 (Fisher's exact test), Q value = 0.0093
Table S1. Gene #1: '1p gain' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 1P GAIN MUTATED | 37 | 52 | 79 |
| 1P GAIN WILD-TYPE | 134 | 154 | 123 |
Figure S1. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #5: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
Table S2. Gene #2: '1q gain' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 1Q GAIN MUTATED | 56 | 55 | 110 |
| 1Q GAIN WILD-TYPE | 115 | 151 | 92 |
Figure S2. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.00906 (Fisher's exact test), Q value = 0.069
Table S3. Gene #2: '1q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 1Q GAIN MUTATED | 82 | 57 | 78 |
| 1Q GAIN WILD-TYPE | 90 | 118 | 143 |
Figure S3. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
Table S4. Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 216 | 126 |
| 2P GAIN MUTATED | 93 | 45 | 36 |
| 2P GAIN WILD-TYPE | 122 | 171 | 90 |
Figure S4. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
Table S5. Gene #3: '2p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 2P GAIN MUTATED | 77 | 48 | 49 |
| 2P GAIN WILD-TYPE | 233 | 110 | 40 |
Figure S5. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.00044 (Fisher's exact test), Q value = 0.009
Table S6. Gene #3: '2p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_10 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|---|
| ALL | 85 | 57 | 58 | 82 | 34 | 75 | 34 | 36 | 52 | 42 |
| 2P GAIN MUTATED | 21 | 16 | 22 | 21 | 10 | 20 | 17 | 9 | 30 | 8 |
| 2P GAIN WILD-TYPE | 64 | 41 | 36 | 61 | 24 | 55 | 17 | 27 | 22 | 34 |
Figure S6. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
Table S7. Gene #3: '2p gain' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 2P GAIN MUTATED | 37 | 47 | 102 |
| 2P GAIN WILD-TYPE | 134 | 159 | 100 |
Figure S7. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
Table S8. Gene #3: '2p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 2P GAIN MUTATED | 83 | 44 | 52 |
| 2P GAIN WILD-TYPE | 89 | 131 | 169 |
Figure S8. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.0366 (Fisher's exact test), Q value = 0.17
Table S9. Gene #3: '2p gain' versus Molecular Subtype #7: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 120 | 196 | 82 |
| 2P GAIN MUTATED | 39 | 71 | 17 |
| 2P GAIN WILD-TYPE | 81 | 125 | 65 |
Figure S9. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'RPPA_CNMF'
P value = 1e-04 (Fisher's exact test), Q value = 0.0029
Table S10. Gene #3: '2p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 100 | 67 | 91 |
| 2P GAIN MUTATED | 31 | 12 | 45 |
| 2P GAIN WILD-TYPE | 69 | 55 | 46 |
Figure S10. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
P value = 0.00166 (Fisher's exact test), Q value = 0.023
Table S11. Gene #3: '2p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 106 | 116 | 36 |
| 2P GAIN MUTATED | 32 | 34 | 22 |
| 2P GAIN WILD-TYPE | 74 | 82 | 14 |
Figure S11. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
P value = 0.027 (Fisher's exact test), Q value = 0.14
Table S12. Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 105 | 71 | 165 | 106 |
| 2P GAIN MUTATED | 23 | 27 | 63 | 32 |
| 2P GAIN WILD-TYPE | 82 | 44 | 102 | 74 |
Figure S12. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00045 (Fisher's exact test), Q value = 0.0091
Table S13. Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 216 | 126 |
| 2Q GAIN MUTATED | 76 | 42 | 29 |
| 2Q GAIN WILD-TYPE | 139 | 174 | 97 |
Figure S13. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 6e-05 (Fisher's exact test), Q value = 0.0019
Table S14. Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 2Q GAIN MUTATED | 70 | 36 | 41 |
| 2Q GAIN WILD-TYPE | 240 | 122 | 48 |
Figure S14. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.00775 (Fisher's exact test), Q value = 0.062
Table S15. Gene #4: '2q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_10 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|---|
| ALL | 85 | 57 | 58 | 82 | 34 | 75 | 34 | 36 | 52 | 42 |
| 2Q GAIN MUTATED | 16 | 12 | 18 | 18 | 9 | 20 | 15 | 6 | 24 | 8 |
| 2Q GAIN WILD-TYPE | 69 | 45 | 40 | 64 | 25 | 55 | 19 | 30 | 28 | 34 |
Figure S15. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
Table S16. Gene #4: '2q gain' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 2Q GAIN MUTATED | 31 | 40 | 84 |
| 2Q GAIN WILD-TYPE | 140 | 166 | 118 |
Figure S16. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.00022 (Fisher's exact test), Q value = 0.0054
Table S17. Gene #4: '2q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 2Q GAIN MUTATED | 66 | 36 | 49 |
| 2Q GAIN WILD-TYPE | 106 | 139 | 172 |
Figure S17. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.00361 (Fisher's exact test), Q value = 0.04
Table S18. Gene #4: '2q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 100 | 67 | 91 |
| 2Q GAIN MUTATED | 24 | 11 | 36 |
| 2Q GAIN WILD-TYPE | 76 | 56 | 55 |
Figure S18. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
P value = 0.0187 (Fisher's exact test), Q value = 0.12
Table S19. Gene #4: '2q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 106 | 116 | 36 |
| 2Q GAIN MUTATED | 24 | 30 | 17 |
| 2Q GAIN WILD-TYPE | 82 | 86 | 19 |
Figure S19. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00652 (Fisher's exact test), Q value = 0.055
Table S20. Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 105 | 71 | 165 | 106 |
| 2Q GAIN MUTATED | 16 | 23 | 55 | 28 |
| 2Q GAIN WILD-TYPE | 89 | 48 | 110 | 78 |
Figure S20. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0118 (Fisher's exact test), Q value = 0.083
Table S21. Gene #5: '3p gain' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 3P GAIN MUTATED | 38 | 51 | 71 |
| 3P GAIN WILD-TYPE | 133 | 155 | 131 |
Figure S21. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #5: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
Table S22. Gene #6: '3q gain' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 3Q GAIN MUTATED | 58 | 90 | 127 |
| 3Q GAIN WILD-TYPE | 113 | 116 | 75 |
Figure S22. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.0163 (Fisher's exact test), Q value = 0.11
Table S23. Gene #6: '3q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 3Q GAIN MUTATED | 96 | 72 | 99 |
| 3Q GAIN WILD-TYPE | 76 | 103 | 122 |
Figure S23. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.0047 (Fisher's exact test), Q value = 0.044
Table S24. Gene #7: '4p gain' versus Molecular Subtype #3: 'MIR_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 159 | 164 | 232 |
| 4P GAIN MUTATED | 7 | 16 | 33 |
| 4P GAIN WILD-TYPE | 152 | 148 | 199 |
Figure S24. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'MIR_CNMF'
P value = 0.0158 (Fisher's exact test), Q value = 0.1
Table S25. Gene #7: '4p gain' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 4P GAIN MUTATED | 9 | 23 | 28 |
| 4P GAIN WILD-TYPE | 162 | 183 | 174 |
Figure S25. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.018 (Fisher's exact test), Q value = 0.11
Table S26. Gene #7: '4p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 105 | 71 | 165 | 106 |
| 4P GAIN MUTATED | 8 | 13 | 24 | 6 |
| 4P GAIN WILD-TYPE | 97 | 58 | 141 | 100 |
Figure S26. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00454 (Fisher's exact test), Q value = 0.044
Table S27. Gene #8: '4q gain' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 4Q GAIN MUTATED | 2 | 15 | 15 |
| 4Q GAIN WILD-TYPE | 169 | 191 | 187 |
Figure S27. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.00767 (Fisher's exact test), Q value = 0.062
Table S28. Gene #8: '4q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 4Q GAIN MUTATED | 17 | 8 | 6 |
| 4Q GAIN WILD-TYPE | 155 | 167 | 215 |
Figure S28. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.00052 (Fisher's exact test), Q value = 0.0099
Table S29. Gene #9: '5p gain' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 5P GAIN MUTATED | 39 | 77 | 83 |
| 5P GAIN WILD-TYPE | 132 | 129 | 119 |
Figure S29. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.00438 (Fisher's exact test), Q value = 0.044
Table S30. Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 6P GAIN MUTATED | 79 | 44 | 39 |
| 6P GAIN WILD-TYPE | 231 | 114 | 50 |
Figure S30. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.0134 (Fisher's exact test), Q value = 0.091
Table S31. Gene #11: '6p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_10 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|---|
| ALL | 85 | 57 | 58 | 82 | 34 | 75 | 34 | 36 | 52 | 42 |
| 6P GAIN MUTATED | 20 | 13 | 14 | 20 | 11 | 28 | 11 | 13 | 25 | 6 |
| 6P GAIN WILD-TYPE | 65 | 44 | 44 | 62 | 23 | 47 | 23 | 23 | 27 | 36 |
Figure S31. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
Table S32. Gene #11: '6p gain' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 6P GAIN MUTATED | 29 | 56 | 85 |
| 6P GAIN WILD-TYPE | 142 | 150 | 117 |
Figure S32. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'CN_CNMF'
P value = 6e-05 (Fisher's exact test), Q value = 0.0019
Table S33. Gene #11: '6p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 6P GAIN MUTATED | 72 | 39 | 55 |
| 6P GAIN WILD-TYPE | 100 | 136 | 166 |
Figure S33. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.00725 (Fisher's exact test), Q value = 0.059
Table S34. Gene #11: '6p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 106 | 116 | 36 |
| 6P GAIN MUTATED | 32 | 32 | 20 |
| 6P GAIN WILD-TYPE | 74 | 84 | 16 |
Figure S34. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0217 (Fisher's exact test), Q value = 0.13
Table S35. Gene #12: '6q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_10 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|---|
| ALL | 85 | 57 | 58 | 82 | 34 | 75 | 34 | 36 | 52 | 42 |
| 6Q GAIN MUTATED | 11 | 5 | 9 | 14 | 7 | 9 | 10 | 8 | 16 | 3 |
| 6Q GAIN WILD-TYPE | 74 | 52 | 49 | 68 | 27 | 66 | 24 | 28 | 36 | 39 |
Figure S35. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
Table S36. Gene #12: '6q gain' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 6Q GAIN MUTATED | 12 | 30 | 55 |
| 6Q GAIN WILD-TYPE | 159 | 176 | 147 |
Figure S36. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'CN_CNMF'
P value = 2e-05 (Fisher's exact test), Q value = 0.00077
Table S37. Gene #12: '6q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 6Q GAIN MUTATED | 48 | 16 | 32 |
| 6Q GAIN WILD-TYPE | 124 | 159 | 189 |
Figure S37. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.00463 (Fisher's exact test), Q value = 0.044
Table S38. Gene #12: '6q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 100 | 67 | 91 |
| 6Q GAIN MUTATED | 19 | 5 | 25 |
| 6Q GAIN WILD-TYPE | 81 | 62 | 66 |
Figure S38. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
P value = 0.0217 (Fisher's exact test), Q value = 0.13
Table S39. Gene #12: '6q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 106 | 116 | 36 |
| 6Q GAIN MUTATED | 19 | 17 | 13 |
| 6Q GAIN WILD-TYPE | 87 | 99 | 23 |
Figure S39. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0282 (Fisher's exact test), Q value = 0.15
Table S40. Gene #12: '6q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 105 | 71 | 165 | 106 |
| 6Q GAIN MUTATED | 15 | 19 | 35 | 12 |
| 6Q GAIN WILD-TYPE | 90 | 52 | 130 | 94 |
Figure S40. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
Table S41. Gene #13: '7p gain' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 7P GAIN MUTATED | 43 | 44 | 94 |
| 7P GAIN WILD-TYPE | 128 | 162 | 108 |
Figure S41. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.00013 (Fisher's exact test), Q value = 0.0036
Table S42. Gene #13: '7p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 7P GAIN MUTATED | 75 | 41 | 63 |
| 7P GAIN WILD-TYPE | 97 | 134 | 158 |
Figure S42. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
Table S43. Gene #14: '7q gain' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 7Q GAIN MUTATED | 46 | 57 | 100 |
| 7Q GAIN WILD-TYPE | 125 | 149 | 102 |
Figure S43. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.00158 (Fisher's exact test), Q value = 0.023
Table S44. Gene #14: '7q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 7Q GAIN MUTATED | 76 | 45 | 77 |
| 7Q GAIN WILD-TYPE | 96 | 130 | 144 |
Figure S44. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.00392 (Fisher's exact test), Q value = 0.041
Table S45. Gene #15: '8p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 8P GAIN MUTATED | 49 | 45 | 22 |
| 8P GAIN WILD-TYPE | 261 | 113 | 67 |
Figure S45. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.003 (Fisher's exact test), Q value = 0.035
Table S46. Gene #15: '8p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 116 | 96 | 128 | 58 |
| 8P GAIN MUTATED | 36 | 12 | 20 | 9 |
| 8P GAIN WILD-TYPE | 80 | 84 | 108 | 49 |
Figure S46. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'
P value = 0.0202 (Fisher's exact test), Q value = 0.12
Table S47. Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 216 | 126 |
| 8Q GAIN MUTATED | 83 | 86 | 67 |
| 8Q GAIN WILD-TYPE | 132 | 130 | 59 |
Figure S47. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 7e-04 (Fisher's exact test), Q value = 0.013
Table S48. Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 8Q GAIN MUTATED | 115 | 87 | 34 |
| 8Q GAIN WILD-TYPE | 195 | 71 | 55 |
Figure S48. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.0298 (Fisher's exact test), Q value = 0.15
Table S49. Gene #16: '8q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 100 | 67 | 91 |
| 8Q GAIN MUTATED | 48 | 35 | 30 |
| 8Q GAIN WILD-TYPE | 52 | 32 | 61 |
Figure S49. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
P value = 0.031 (Fisher's exact test), Q value = 0.16
Table S50. Gene #16: '8q gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 |
|---|---|---|
| ALL | 12 | 10 |
| 8Q GAIN MUTATED | 7 | 1 |
| 8Q GAIN WILD-TYPE | 5 | 9 |
Figure S50. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'
P value = 0.00276 (Fisher's exact test), Q value = 0.034
Table S51. Gene #17: '9p gain' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 9P GAIN MUTATED | 17 | 29 | 46 |
| 9P GAIN WILD-TYPE | 154 | 177 | 156 |
Figure S51. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.00821 (Fisher's exact test), Q value = 0.064
Table S52. Gene #17: '9p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 9P GAIN MUTATED | 33 | 16 | 42 |
| 9P GAIN WILD-TYPE | 139 | 159 | 179 |
Figure S52. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.0274 (Fisher's exact test), Q value = 0.15
Table S53. Gene #18: '9q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 116 | 96 | 128 | 58 |
| 9Q GAIN MUTATED | 8 | 4 | 18 | 2 |
| 9Q GAIN WILD-TYPE | 108 | 92 | 110 | 56 |
Figure S53. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'
P value = 0.0044 (Fisher's exact test), Q value = 0.044
Table S54. Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 216 | 126 |
| 10P GAIN MUTATED | 81 | 53 | 48 |
| 10P GAIN WILD-TYPE | 134 | 163 | 78 |
Figure S54. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.0211 (Fisher's exact test), Q value = 0.13
Table S55. Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 10P GAIN MUTATED | 90 | 52 | 40 |
| 10P GAIN WILD-TYPE | 220 | 106 | 49 |
Figure S55. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
Table S56. Gene #19: '10p gain' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 10P GAIN MUTATED | 41 | 45 | 102 |
| 10P GAIN WILD-TYPE | 130 | 161 | 100 |
Figure S56. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.00016 (Fisher's exact test), Q value = 0.0043
Table S57. Gene #19: '10p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 10P GAIN MUTATED | 77 | 44 | 63 |
| 10P GAIN WILD-TYPE | 95 | 131 | 158 |
Figure S57. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.00986 (Fisher's exact test), Q value = 0.073
Table S58. Gene #19: '10p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 116 | 96 | 128 | 58 |
| 10P GAIN MUTATED | 44 | 35 | 36 | 9 |
| 10P GAIN WILD-TYPE | 72 | 61 | 92 | 49 |
Figure S58. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'
P value = 0.0114 (Fisher's exact test), Q value = 0.082
Table S59. Gene #19: '10p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 100 | 67 | 91 |
| 10P GAIN MUTATED | 32 | 13 | 38 |
| 10P GAIN WILD-TYPE | 68 | 54 | 53 |
Figure S59. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
P value = 0.00078 (Fisher's exact test), Q value = 0.014
Table S60. Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 105 | 71 | 165 | 106 |
| 10P GAIN MUTATED | 22 | 27 | 70 | 27 |
| 10P GAIN WILD-TYPE | 83 | 44 | 95 | 79 |
Figure S60. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0038 (Fisher's exact test), Q value = 0.04
Table S61. Gene #20: '10q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 216 | 126 |
| 10Q GAIN MUTATED | 55 | 28 | 24 |
| 10Q GAIN WILD-TYPE | 160 | 188 | 102 |
Figure S61. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00889 (Fisher's exact test), Q value = 0.068
Table S62. Gene #20: '10q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 10Q GAIN MUTATED | 52 | 27 | 28 |
| 10Q GAIN WILD-TYPE | 258 | 131 | 61 |
Figure S62. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.0036 (Fisher's exact test), Q value = 0.04
Table S63. Gene #20: '10q gain' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 10Q GAIN MUTATED | 24 | 33 | 54 |
| 10Q GAIN WILD-TYPE | 147 | 173 | 148 |
Figure S63. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.0144 (Fisher's exact test), Q value = 0.096
Table S64. Gene #21: '11p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 11P GAIN MUTATED | 26 | 13 | 37 |
| 11P GAIN WILD-TYPE | 146 | 162 | 184 |
Figure S64. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.0268 (Fisher's exact test), Q value = 0.14
Table S65. Gene #21: '11p gain' versus Molecular Subtype #7: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 120 | 196 | 82 |
| 11P GAIN MUTATED | 8 | 33 | 10 |
| 11P GAIN WILD-TYPE | 112 | 163 | 72 |
Figure S65. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'RPPA_CNMF'
P value = 0.0259 (Fisher's exact test), Q value = 0.14
Table S66. Gene #21: '11p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 116 | 96 | 128 | 58 |
| 11P GAIN MUTATED | 11 | 21 | 15 | 4 |
| 11P GAIN WILD-TYPE | 105 | 75 | 113 | 54 |
Figure S66. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'
P value = 0.0352 (Fisher's exact test), Q value = 0.17
Table S67. Gene #21: '11p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 106 | 116 | 36 |
| 11P GAIN MUTATED | 21 | 17 | 1 |
| 11P GAIN WILD-TYPE | 85 | 99 | 35 |
Figure S67. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00467 (Fisher's exact test), Q value = 0.044
Table S68. Gene #22: '11q gain' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 11Q GAIN MUTATED | 20 | 48 | 47 |
| 11Q GAIN WILD-TYPE | 151 | 158 | 155 |
Figure S68. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.00181 (Fisher's exact test), Q value = 0.025
Table S69. Gene #22: '11q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 11Q GAIN MUTATED | 38 | 20 | 55 |
| 11Q GAIN WILD-TYPE | 134 | 155 | 166 |
Figure S69. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.00054 (Fisher's exact test), Q value = 0.01
Table S70. Gene #22: '11q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 116 | 96 | 128 | 58 |
| 11Q GAIN MUTATED | 19 | 27 | 27 | 2 |
| 11Q GAIN WILD-TYPE | 97 | 69 | 101 | 56 |
Figure S70. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'
P value = 0.00011 (Fisher's exact test), Q value = 0.0031
Table S71. Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 216 | 126 |
| 12P GAIN MUTATED | 118 | 75 | 49 |
| 12P GAIN WILD-TYPE | 97 | 141 | 77 |
Figure S71. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00174 (Fisher's exact test), Q value = 0.024
Table S72. Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 12P GAIN MUTATED | 132 | 57 | 53 |
| 12P GAIN WILD-TYPE | 178 | 101 | 36 |
Figure S72. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.00081 (Fisher's exact test), Q value = 0.014
Table S73. Gene #23: '12p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_10 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|---|
| ALL | 85 | 57 | 58 | 82 | 34 | 75 | 34 | 36 | 52 | 42 |
| 12P GAIN MUTATED | 33 | 20 | 28 | 36 | 15 | 30 | 19 | 11 | 37 | 12 |
| 12P GAIN WILD-TYPE | 52 | 37 | 30 | 46 | 19 | 45 | 15 | 25 | 15 | 30 |
Figure S73. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
Table S74. Gene #23: '12p gain' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 12P GAIN MUTATED | 54 | 68 | 133 |
| 12P GAIN WILD-TYPE | 117 | 138 | 69 |
Figure S74. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
Table S75. Gene #23: '12p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 12P GAIN MUTATED | 104 | 71 | 74 |
| 12P GAIN WILD-TYPE | 68 | 104 | 147 |
Figure S75. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 6e-04 (Fisher's exact test), Q value = 0.011
Table S76. Gene #23: '12p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 100 | 67 | 91 |
| 12P GAIN MUTATED | 31 | 24 | 52 |
| 12P GAIN WILD-TYPE | 69 | 43 | 39 |
Figure S76. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
P value = 0.00408 (Fisher's exact test), Q value = 0.042
Table S77. Gene #23: '12p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 106 | 116 | 36 |
| 12P GAIN MUTATED | 32 | 54 | 21 |
| 12P GAIN WILD-TYPE | 74 | 62 | 15 |
Figure S77. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00022 (Fisher's exact test), Q value = 0.0054
Table S78. Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 105 | 71 | 165 | 106 |
| 12P GAIN MUTATED | 27 | 38 | 81 | 46 |
| 12P GAIN WILD-TYPE | 78 | 33 | 84 | 60 |
Figure S78. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00489 (Fisher's exact test), Q value = 0.046
Table S79. Gene #24: '12q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 216 | 126 |
| 12Q GAIN MUTATED | 81 | 50 | 38 |
| 12Q GAIN WILD-TYPE | 134 | 166 | 88 |
Figure S79. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.0344 (Fisher's exact test), Q value = 0.17
Table S80. Gene #24: '12q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_10 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|---|
| ALL | 85 | 57 | 58 | 82 | 34 | 75 | 34 | 36 | 52 | 42 |
| 12Q GAIN MUTATED | 27 | 16 | 21 | 21 | 11 | 20 | 15 | 9 | 23 | 5 |
| 12Q GAIN WILD-TYPE | 58 | 41 | 37 | 61 | 23 | 55 | 19 | 27 | 29 | 37 |
Figure S80. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
Table S81. Gene #24: '12q gain' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 12Q GAIN MUTATED | 40 | 38 | 99 |
| 12Q GAIN WILD-TYPE | 131 | 168 | 103 |
Figure S81. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
Table S82. Gene #24: '12q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 12Q GAIN MUTATED | 78 | 43 | 54 |
| 12Q GAIN WILD-TYPE | 94 | 132 | 167 |
Figure S82. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.0197 (Fisher's exact test), Q value = 0.12
Table S83. Gene #24: '12q gain' versus Molecular Subtype #7: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 120 | 196 | 82 |
| 12Q GAIN MUTATED | 33 | 68 | 15 |
| 12Q GAIN WILD-TYPE | 87 | 128 | 67 |
Figure S83. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'RPPA_CNMF'
P value = 0.00209 (Fisher's exact test), Q value = 0.027
Table S84. Gene #24: '12q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 100 | 67 | 91 |
| 12Q GAIN MUTATED | 22 | 22 | 42 |
| 12Q GAIN WILD-TYPE | 78 | 45 | 49 |
Figure S84. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
P value = 0.00925 (Fisher's exact test), Q value = 0.07
Table S85. Gene #24: '12q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 106 | 116 | 36 |
| 12Q GAIN MUTATED | 24 | 47 | 15 |
| 12Q GAIN WILD-TYPE | 82 | 69 | 21 |
Figure S85. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0108 (Fisher's exact test), Q value = 0.079
Table S86. Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 105 | 71 | 165 | 106 |
| 12Q GAIN MUTATED | 19 | 28 | 53 | 34 |
| 12Q GAIN WILD-TYPE | 86 | 43 | 112 | 72 |
Figure S86. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00783 (Fisher's exact test), Q value = 0.062
Table S87. Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 216 | 126 |
| 13Q GAIN MUTATED | 26 | 12 | 19 |
| 13Q GAIN WILD-TYPE | 189 | 204 | 107 |
Figure S87. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 4e-04 (Fisher's exact test), Q value = 0.0085
Table S88. Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 13Q GAIN MUTATED | 19 | 20 | 18 |
| 13Q GAIN WILD-TYPE | 291 | 138 | 71 |
Figure S88. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.0234 (Fisher's exact test), Q value = 0.13
Table S89. Gene #25: '13q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_10 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|---|
| ALL | 85 | 57 | 58 | 82 | 34 | 75 | 34 | 36 | 52 | 42 |
| 13Q GAIN MUTATED | 6 | 8 | 5 | 6 | 2 | 10 | 9 | 1 | 8 | 1 |
| 13Q GAIN WILD-TYPE | 79 | 49 | 53 | 76 | 32 | 65 | 25 | 35 | 44 | 41 |
Figure S89. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
P value = 5e-05 (Fisher's exact test), Q value = 0.0017
Table S90. Gene #25: '13q gain' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 13Q GAIN MUTATED | 22 | 7 | 31 |
| 13Q GAIN WILD-TYPE | 149 | 199 | 171 |
Figure S90. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #5: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
Table S91. Gene #25: '13q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 13Q GAIN MUTATED | 31 | 20 | 8 |
| 13Q GAIN WILD-TYPE | 141 | 155 | 213 |
Figure S91. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.00297 (Fisher's exact test), Q value = 0.035
Table S92. Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 216 | 126 |
| 16P GAIN MUTATED | 34 | 18 | 6 |
| 16P GAIN WILD-TYPE | 181 | 198 | 120 |
Figure S92. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00441 (Fisher's exact test), Q value = 0.044
Table S93. Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 16P GAIN MUTATED | 34 | 8 | 16 |
| 16P GAIN WILD-TYPE | 276 | 150 | 73 |
Figure S93. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.0303 (Fisher's exact test), Q value = 0.16
Table S94. Gene #28: '16p gain' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 16P GAIN MUTATED | 14 | 15 | 30 |
| 16P GAIN WILD-TYPE | 157 | 191 | 172 |
Figure S94. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.0174 (Fisher's exact test), Q value = 0.11
Table S95. Gene #28: '16p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 16P GAIN MUTATED | 23 | 9 | 26 |
| 16P GAIN WILD-TYPE | 149 | 166 | 195 |
Figure S95. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.0348 (Fisher's exact test), Q value = 0.17
Table S96. Gene #28: '16p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 116 | 96 | 128 | 58 |
| 16P GAIN MUTATED | 6 | 14 | 19 | 4 |
| 16P GAIN WILD-TYPE | 110 | 82 | 109 | 54 |
Figure S96. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'
P value = 0.00084 (Fisher's exact test), Q value = 0.014
Table S97. Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 216 | 126 |
| 16Q GAIN MUTATED | 18 | 12 | 0 |
| 16Q GAIN WILD-TYPE | 197 | 204 | 126 |
Figure S97. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.0443 (Fisher's exact test), Q value = 0.2
Table S98. Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 16Q GAIN MUTATED | 20 | 3 | 7 |
| 16Q GAIN WILD-TYPE | 290 | 155 | 82 |
Figure S98. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.00353 (Fisher's exact test), Q value = 0.04
Table S99. Gene #29: '16q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 16Q GAIN MUTATED | 10 | 2 | 18 |
| 16Q GAIN WILD-TYPE | 162 | 173 | 203 |
Figure S99. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.0263 (Fisher's exact test), Q value = 0.14
Table S100. Gene #29: '16q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 116 | 96 | 128 | 58 |
| 16Q GAIN MUTATED | 2 | 11 | 8 | 3 |
| 16Q GAIN WILD-TYPE | 114 | 85 | 120 | 55 |
Figure S100. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'
P value = 8e-04 (Fisher's exact test), Q value = 0.014
Table S101. Gene #29: '16q gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 121 | 182 | 144 |
| 16Q GAIN MUTATED | 0 | 9 | 13 |
| 16Q GAIN WILD-TYPE | 121 | 173 | 131 |
Figure S101. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'
P value = 0.00373 (Fisher's exact test), Q value = 0.04
Table S102. Gene #30: '17p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 106 | 116 | 36 |
| 17P GAIN MUTATED | 5 | 2 | 6 |
| 17P GAIN WILD-TYPE | 101 | 114 | 30 |
Figure S102. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0379 (Fisher's exact test), Q value = 0.18
Table S103. Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 17Q GAIN MUTATED | 18 | 16 | 12 |
| 17Q GAIN WILD-TYPE | 292 | 142 | 77 |
Figure S103. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.0364 (Fisher's exact test), Q value = 0.17
Table S104. Gene #31: '17q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_10 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|---|
| ALL | 85 | 57 | 58 | 82 | 34 | 75 | 34 | 36 | 52 | 42 |
| 17Q GAIN MUTATED | 8 | 5 | 5 | 4 | 1 | 3 | 0 | 4 | 10 | 6 |
| 17Q GAIN WILD-TYPE | 77 | 52 | 53 | 78 | 33 | 72 | 34 | 32 | 42 | 36 |
Figure S104. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
P value = 0.0223 (Fisher's exact test), Q value = 0.13
Table S105. Gene #31: '17q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 106 | 116 | 36 |
| 17Q GAIN MUTATED | 12 | 7 | 8 |
| 17Q GAIN WILD-TYPE | 94 | 109 | 28 |
Figure S105. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00127 (Fisher's exact test), Q value = 0.019
Table S106. Gene #32: '18p gain' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 18P GAIN MUTATED | 26 | 35 | 59 |
| 18P GAIN WILD-TYPE | 145 | 171 | 143 |
Figure S106. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.00034 (Fisher's exact test), Q value = 0.008
Table S107. Gene #32: '18p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 18P GAIN MUTATED | 54 | 26 | 38 |
| 18P GAIN WILD-TYPE | 118 | 149 | 183 |
Figure S107. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.0231 (Fisher's exact test), Q value = 0.13
Table S108. Gene #32: '18p gain' versus Molecular Subtype #7: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 120 | 196 | 82 |
| 18P GAIN MUTATED | 20 | 48 | 9 |
| 18P GAIN WILD-TYPE | 100 | 148 | 73 |
Figure S108. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'RPPA_CNMF'
P value = 0.0235 (Fisher's exact test), Q value = 0.13
Table S109. Gene #33: '18q gain' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 18Q GAIN MUTATED | 14 | 23 | 35 |
| 18Q GAIN WILD-TYPE | 157 | 183 | 167 |
Figure S109. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.024 (Fisher's exact test), Q value = 0.13
Table S110. Gene #33: '18q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 18Q GAIN MUTATED | 32 | 17 | 23 |
| 18Q GAIN WILD-TYPE | 140 | 158 | 198 |
Figure S110. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 2e-05 (Fisher's exact test), Q value = 0.00077
Table S111. Gene #34: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 19P GAIN MUTATED | 33 | 55 | 83 |
| 19P GAIN WILD-TYPE | 138 | 151 | 119 |
Figure S111. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.0264 (Fisher's exact test), Q value = 0.14
Table S112. Gene #34: '19p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 19P GAIN MUTATED | 60 | 39 | 69 |
| 19P GAIN WILD-TYPE | 112 | 136 | 152 |
Figure S112. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.0011
Table S113. Gene #35: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 19Q GAIN MUTATED | 33 | 49 | 79 |
| 19Q GAIN WILD-TYPE | 138 | 157 | 123 |
Figure S113. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.00129 (Fisher's exact test), Q value = 0.019
Table S114. Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 216 | 126 |
| 20P GAIN MUTATED | 125 | 88 | 64 |
| 20P GAIN WILD-TYPE | 90 | 128 | 62 |
Figure S114. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00099 (Fisher's exact test), Q value = 0.016
Table S115. Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 20P GAIN MUTATED | 147 | 70 | 60 |
| 20P GAIN WILD-TYPE | 163 | 88 | 29 |
Figure S115. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.00036 (Fisher's exact test), Q value = 0.0081
Table S116. Gene #36: '20p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_10 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|---|
| ALL | 85 | 57 | 58 | 82 | 34 | 75 | 34 | 36 | 52 | 42 |
| 20P GAIN MUTATED | 31 | 27 | 33 | 36 | 21 | 41 | 26 | 16 | 32 | 13 |
| 20P GAIN WILD-TYPE | 54 | 30 | 25 | 46 | 13 | 34 | 8 | 20 | 20 | 29 |
Figure S116. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
Table S117. Gene #36: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 20P GAIN MUTATED | 66 | 79 | 144 |
| 20P GAIN WILD-TYPE | 105 | 127 | 58 |
Figure S117. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
Table S118. Gene #36: '20p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 20P GAIN MUTATED | 117 | 79 | 86 |
| 20P GAIN WILD-TYPE | 55 | 96 | 135 |
Figure S118. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.00373 (Fisher's exact test), Q value = 0.04
Table S119. Gene #36: '20p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 100 | 67 | 91 |
| 20P GAIN MUTATED | 44 | 28 | 59 |
| 20P GAIN WILD-TYPE | 56 | 39 | 32 |
Figure S119. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
P value = 0.00368 (Fisher's exact test), Q value = 0.04
Table S120. Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 105 | 71 | 165 | 106 |
| 20P GAIN MUTATED | 40 | 41 | 98 | 50 |
| 20P GAIN WILD-TYPE | 65 | 30 | 67 | 56 |
Figure S120. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
Table S121. Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 216 | 126 |
| 20Q GAIN MUTATED | 143 | 95 | 76 |
| 20Q GAIN WILD-TYPE | 72 | 121 | 50 |
Figure S121. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00035 (Fisher's exact test), Q value = 0.008
Table S122. Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 20Q GAIN MUTATED | 164 | 83 | 67 |
| 20Q GAIN WILD-TYPE | 146 | 75 | 22 |
Figure S122. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 7e-05 (Fisher's exact test), Q value = 0.0022
Table S123. Gene #37: '20q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_10 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|---|
| ALL | 85 | 57 | 58 | 82 | 34 | 75 | 34 | 36 | 52 | 42 |
| 20Q GAIN MUTATED | 35 | 30 | 35 | 40 | 24 | 41 | 26 | 21 | 42 | 19 |
| 20Q GAIN WILD-TYPE | 50 | 27 | 23 | 42 | 10 | 34 | 8 | 15 | 10 | 23 |
Figure S123. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
Table S124. Gene #37: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 20Q GAIN MUTATED | 69 | 98 | 161 |
| 20Q GAIN WILD-TYPE | 102 | 108 | 41 |
Figure S124. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
Table S125. Gene #37: '20q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 20Q GAIN MUTATED | 132 | 87 | 101 |
| 20Q GAIN WILD-TYPE | 40 | 88 | 120 |
Figure S125. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.00889 (Fisher's exact test), Q value = 0.068
Table S126. Gene #37: '20q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 100 | 67 | 91 |
| 20Q GAIN MUTATED | 53 | 31 | 63 |
| 20Q GAIN WILD-TYPE | 47 | 36 | 28 |
Figure S126. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
P value = 0.00468 (Fisher's exact test), Q value = 0.044
Table S127. Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 105 | 71 | 165 | 106 |
| 20Q GAIN MUTATED | 48 | 47 | 108 | 57 |
| 20Q GAIN WILD-TYPE | 57 | 24 | 57 | 49 |
Figure S127. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00163 (Fisher's exact test), Q value = 0.023
Table S128. Gene #38: '21q gain' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 21Q GAIN MUTATED | 22 | 33 | 54 |
| 21Q GAIN WILD-TYPE | 149 | 173 | 148 |
Figure S128. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.0168 (Fisher's exact test), Q value = 0.11
Table S129. Gene #38: '21q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 21Q GAIN MUTATED | 45 | 25 | 39 |
| 21Q GAIN WILD-TYPE | 127 | 150 | 182 |
Figure S129. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.0238 (Fisher's exact test), Q value = 0.13
Table S130. Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 121 | 182 | 144 |
| 21Q GAIN MUTATED | 34 | 30 | 23 |
| 21Q GAIN WILD-TYPE | 87 | 152 | 121 |
Figure S130. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'
P value = 0.0441 (Fisher's exact test), Q value = 0.2
Table S131. Gene #38: '21q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 105 | 71 | 165 | 106 |
| 21Q GAIN MUTATED | 16 | 20 | 37 | 14 |
| 21Q GAIN WILD-TYPE | 89 | 51 | 128 | 92 |
Figure S131. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0302 (Fisher's exact test), Q value = 0.16
Table S132. Gene #40: 'xp gain' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| XP GAIN MUTATED | 14 | 29 | 35 |
| XP GAIN WILD-TYPE | 157 | 177 | 167 |
Figure S132. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.0375 (Fisher's exact test), Q value = 0.18
Table S133. Gene #40: 'xp gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 121 | 182 | 144 |
| XP GAIN MUTATED | 17 | 31 | 11 |
| XP GAIN WILD-TYPE | 104 | 151 | 133 |
Figure S133. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'
P value = 6e-05 (Fisher's exact test), Q value = 0.0019
Table S134. Gene #41: 'xq gain' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| XQ GAIN MUTATED | 17 | 35 | 56 |
| XQ GAIN WILD-TYPE | 154 | 171 | 146 |
Figure S134. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.0316 (Fisher's exact test), Q value = 0.16
Table S135. Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 216 | 126 |
| 1P LOSS MUTATED | 33 | 16 | 13 |
| 1P LOSS WILD-TYPE | 182 | 200 | 113 |
Figure S135. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00039 (Fisher's exact test), Q value = 0.0085
Table S136. Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 1P LOSS MUTATED | 31 | 10 | 21 |
| 1P LOSS WILD-TYPE | 279 | 148 | 68 |
Figure S136. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.0207 (Fisher's exact test), Q value = 0.12
Table S137. Gene #42: '1p loss' versus Molecular Subtype #7: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 120 | 196 | 82 |
| 1P LOSS MUTATED | 23 | 17 | 8 |
| 1P LOSS WILD-TYPE | 97 | 179 | 74 |
Figure S137. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'RPPA_CNMF'
P value = 0.0142 (Fisher's exact test), Q value = 0.095
Table S138. Gene #43: '1q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 1Q LOSS MUTATED | 20 | 7 | 13 |
| 1Q LOSS WILD-TYPE | 290 | 151 | 76 |
Figure S138. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.0239 (Fisher's exact test), Q value = 0.13
Table S139. Gene #44: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 2P LOSS MUTATED | 39 | 10 | 4 |
| 2P LOSS WILD-TYPE | 271 | 148 | 85 |
Figure S139. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.0227 (Fisher's exact test), Q value = 0.13
Table S140. Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 216 | 126 |
| 3P LOSS MUTATED | 45 | 25 | 24 |
| 3P LOSS WILD-TYPE | 170 | 191 | 102 |
Figure S140. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00104 (Fisher's exact test), Q value = 0.016
Table S141. Gene #46: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 3P LOSS MUTATED | 38 | 30 | 26 |
| 3P LOSS WILD-TYPE | 272 | 128 | 63 |
Figure S141. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.00568 (Fisher's exact test), Q value = 0.05
Table S142. Gene #46: '3p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_10 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|---|
| ALL | 85 | 57 | 58 | 82 | 34 | 75 | 34 | 36 | 52 | 42 |
| 3P LOSS MUTATED | 16 | 4 | 4 | 12 | 5 | 13 | 12 | 8 | 15 | 5 |
| 3P LOSS WILD-TYPE | 69 | 53 | 54 | 70 | 29 | 62 | 22 | 28 | 37 | 37 |
Figure S142. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
P value = 4e-04 (Fisher's exact test), Q value = 0.0085
Table S143. Gene #46: '3p loss' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 3P LOSS MUTATED | 23 | 22 | 50 |
| 3P LOSS WILD-TYPE | 148 | 184 | 152 |
Figure S143. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.00229 (Fisher's exact test), Q value = 0.029
Table S144. Gene #46: '3p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 3P LOSS MUTATED | 42 | 27 | 25 |
| 3P LOSS WILD-TYPE | 130 | 148 | 196 |
Figure S144. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.00643 (Fisher's exact test), Q value = 0.055
Table S145. Gene #46: '3p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 106 | 116 | 36 |
| 3P LOSS MUTATED | 21 | 14 | 13 |
| 3P LOSS WILD-TYPE | 85 | 102 | 23 |
Figure S145. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0125 (Fisher's exact test), Q value = 0.087
Table S146. Gene #47: '3q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 216 | 126 |
| 3Q LOSS MUTATED | 22 | 8 | 13 |
| 3Q LOSS WILD-TYPE | 193 | 208 | 113 |
Figure S146. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.0387 (Fisher's exact test), Q value = 0.18
Table S147. Gene #47: '3q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 3Q LOSS MUTATED | 17 | 14 | 12 |
| 3Q LOSS WILD-TYPE | 293 | 144 | 77 |
Figure S147. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.0309 (Fisher's exact test), Q value = 0.16
Table S148. Gene #47: '3q loss' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 3Q LOSS MUTATED | 14 | 8 | 21 |
| 3Q LOSS WILD-TYPE | 157 | 198 | 181 |
Figure S148. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.00303 (Fisher's exact test), Q value = 0.035
Table S149. Gene #47: '3q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 3Q LOSS MUTATED | 22 | 13 | 8 |
| 3Q LOSS WILD-TYPE | 150 | 162 | 213 |
Figure S149. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.00104 (Fisher's exact test), Q value = 0.016
Table S150. Gene #47: '3q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 105 | 71 | 165 | 106 |
| 3Q LOSS MUTATED | 3 | 7 | 21 | 2 |
| 3Q LOSS WILD-TYPE | 102 | 64 | 144 | 104 |
Figure S150. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0336 (Fisher's exact test), Q value = 0.17
Table S151. Gene #47: '3q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 6 | 2 | 2 | 6 | 4 | 2 |
| 3Q LOSS MUTATED | 1 | 1 | 0 | 0 | 0 | 2 |
| 3Q LOSS WILD-TYPE | 5 | 1 | 2 | 6 | 4 | 0 |
Figure S151. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.0214 (Fisher's exact test), Q value = 0.13
Table S152. Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 4P LOSS MUTATED | 176 | 72 | 55 |
| 4P LOSS WILD-TYPE | 134 | 86 | 34 |
Figure S152. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.00436 (Fisher's exact test), Q value = 0.044
Table S153. Gene #48: '4p loss' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 4P LOSS MUTATED | 93 | 96 | 127 |
| 4P LOSS WILD-TYPE | 78 | 110 | 75 |
Figure S153. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.00132 (Fisher's exact test), Q value = 0.019
Table S154. Gene #49: '4q loss' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 4Q LOSS MUTATED | 107 | 111 | 144 |
| 4Q LOSS WILD-TYPE | 64 | 95 | 58 |
Figure S154. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.0183 (Fisher's exact test), Q value = 0.11
Table S155. Gene #49: '4q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 116 | 96 | 128 | 58 |
| 4Q LOSS MUTATED | 70 | 69 | 82 | 27 |
| 4Q LOSS WILD-TYPE | 46 | 27 | 46 | 31 |
Figure S155. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'
P value = 0.0311 (Fisher's exact test), Q value = 0.16
Table S156. Gene #50: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 5P LOSS MUTATED | 69 | 30 | 30 |
| 5P LOSS WILD-TYPE | 241 | 128 | 59 |
Figure S156. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.0119 (Fisher's exact test), Q value = 0.083
Table S157. Gene #50: '5p loss' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 5P LOSS MUTATED | 33 | 39 | 61 |
| 5P LOSS WILD-TYPE | 138 | 167 | 141 |
Figure S157. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.00698 (Fisher's exact test), Q value = 0.058
Table S158. Gene #50: '5p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 5P LOSS MUTATED | 52 | 28 | 50 |
| 5P LOSS WILD-TYPE | 120 | 147 | 171 |
Figure S158. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 8e-05 (Fisher's exact test), Q value = 0.0024
Table S159. Gene #50: '5p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 100 | 67 | 91 |
| 5P LOSS MUTATED | 21 | 10 | 39 |
| 5P LOSS WILD-TYPE | 79 | 57 | 52 |
Figure S159. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
P value = 0.047 (Fisher's exact test), Q value = 0.21
Table S160. Gene #50: '5p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 106 | 116 | 36 |
| 5P LOSS MUTATED | 25 | 29 | 16 |
| 5P LOSS WILD-TYPE | 81 | 87 | 20 |
Figure S160. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0493 (Fisher's exact test), Q value = 0.21
Table S161. Gene #50: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 105 | 71 | 165 | 106 |
| 5P LOSS MUTATED | 23 | 27 | 38 | 22 |
| 5P LOSS WILD-TYPE | 82 | 44 | 127 | 84 |
Figure S161. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00032 (Fisher's exact test), Q value = 0.0077
Table S162. Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 216 | 126 |
| 5Q LOSS MUTATED | 105 | 68 | 41 |
| 5Q LOSS WILD-TYPE | 110 | 148 | 85 |
Figure S162. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00199 (Fisher's exact test), Q value = 0.026
Table S163. Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 5Q LOSS MUTATED | 113 | 52 | 49 |
| 5Q LOSS WILD-TYPE | 197 | 106 | 40 |
Figure S163. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.0126 (Fisher's exact test), Q value = 0.087
Table S164. Gene #51: '5q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_10 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|---|
| ALL | 85 | 57 | 58 | 82 | 34 | 75 | 34 | 36 | 52 | 42 |
| 5Q LOSS MUTATED | 27 | 20 | 23 | 28 | 14 | 24 | 22 | 14 | 29 | 13 |
| 5Q LOSS WILD-TYPE | 58 | 37 | 35 | 54 | 20 | 51 | 12 | 22 | 23 | 29 |
Figure S164. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
P value = 0.00048 (Fisher's exact test), Q value = 0.0093
Table S165. Gene #51: '5q loss' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 5Q LOSS MUTATED | 54 | 69 | 100 |
| 5Q LOSS WILD-TYPE | 117 | 137 | 102 |
Figure S165. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #5: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
Table S166. Gene #51: '5q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 5Q LOSS MUTATED | 96 | 51 | 72 |
| 5Q LOSS WILD-TYPE | 76 | 124 | 149 |
Figure S166. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.0339 (Fisher's exact test), Q value = 0.17
Table S167. Gene #51: '5q loss' versus Molecular Subtype #7: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 120 | 196 | 82 |
| 5Q LOSS MUTATED | 39 | 84 | 23 |
| 5Q LOSS WILD-TYPE | 81 | 112 | 59 |
Figure S167. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'RPPA_CNMF'
P value = 0.00092 (Fisher's exact test), Q value = 0.015
Table S168. Gene #51: '5q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 100 | 67 | 91 |
| 5Q LOSS MUTATED | 36 | 18 | 50 |
| 5Q LOSS WILD-TYPE | 64 | 49 | 41 |
Figure S168. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
P value = 0.00737 (Fisher's exact test), Q value = 0.06
Table S169. Gene #51: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 105 | 71 | 165 | 106 |
| 5Q LOSS MUTATED | 37 | 36 | 76 | 31 |
| 5Q LOSS WILD-TYPE | 68 | 35 | 89 | 75 |
Figure S169. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0196 (Fisher's exact test), Q value = 0.12
Table S170. Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 6P LOSS MUTATED | 98 | 46 | 15 |
| 6P LOSS WILD-TYPE | 212 | 112 | 74 |
Figure S170. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.0428 (Fisher's exact test), Q value = 0.19
Table S171. Gene #52: '6p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 106 | 116 | 36 |
| 6P LOSS MUTATED | 34 | 30 | 4 |
| 6P LOSS WILD-TYPE | 72 | 86 | 32 |
Figure S171. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0348 (Fisher's exact test), Q value = 0.17
Table S172. Gene #53: '6q loss' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 6Q LOSS MUTATED | 80 | 92 | 70 |
| 6Q LOSS WILD-TYPE | 91 | 114 | 132 |
Figure S172. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.0194 (Fisher's exact test), Q value = 0.12
Table S173. Gene #53: '6q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 100 | 67 | 91 |
| 6Q LOSS MUTATED | 43 | 33 | 26 |
| 6Q LOSS WILD-TYPE | 57 | 34 | 65 |
Figure S173. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
P value = 0.0215 (Fisher's exact test), Q value = 0.13
Table S174. Gene #53: '6q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 106 | 116 | 36 |
| 6Q LOSS MUTATED | 48 | 47 | 7 |
| 6Q LOSS WILD-TYPE | 58 | 69 | 29 |
Figure S174. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00263 (Fisher's exact test), Q value = 0.032
Table S175. Gene #56: '8p loss' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 8P LOSS MUTATED | 66 | 97 | 114 |
| 8P LOSS WILD-TYPE | 105 | 109 | 88 |
Figure S175. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.0374 (Fisher's exact test), Q value = 0.18
Table S176. Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 105 | 71 | 165 | 106 |
| 8P LOSS MUTATED | 37 | 39 | 83 | 51 |
| 8P LOSS WILD-TYPE | 68 | 32 | 82 | 55 |
Figure S176. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00718 (Fisher's exact test), Q value = 0.059
Table S177. Gene #57: '8q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 216 | 126 |
| 8Q LOSS MUTATED | 46 | 25 | 14 |
| 8Q LOSS WILD-TYPE | 169 | 191 | 112 |
Figure S177. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00494 (Fisher's exact test), Q value = 0.046
Table S178. Gene #57: '8q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 8Q LOSS MUTATED | 43 | 18 | 24 |
| 8Q LOSS WILD-TYPE | 267 | 140 | 65 |
Figure S178. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.00109 (Fisher's exact test), Q value = 0.016
Table S179. Gene #57: '8q loss' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 8Q LOSS MUTATED | 18 | 25 | 47 |
| 8Q LOSS WILD-TYPE | 153 | 181 | 155 |
Figure S179. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.0357 (Fisher's exact test), Q value = 0.17
Table S180. Gene #57: '8q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 8Q LOSS MUTATED | 37 | 24 | 27 |
| 8Q LOSS WILD-TYPE | 135 | 151 | 194 |
Figure S180. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.0231 (Fisher's exact test), Q value = 0.13
Table S181. Gene #57: '8q loss' versus Molecular Subtype #7: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 120 | 196 | 82 |
| 8Q LOSS MUTATED | 20 | 36 | 5 |
| 8Q LOSS WILD-TYPE | 100 | 160 | 77 |
Figure S181. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #7: 'RPPA_CNMF'
P value = 0.00099 (Fisher's exact test), Q value = 0.016
Table S182. Gene #57: '8q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 100 | 67 | 91 |
| 8Q LOSS MUTATED | 12 | 6 | 27 |
| 8Q LOSS WILD-TYPE | 88 | 61 | 64 |
Figure S182. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
P value = 0.0287 (Fisher's exact test), Q value = 0.15
Table S183. Gene #57: '8q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 106 | 116 | 36 |
| 8Q LOSS MUTATED | 14 | 19 | 12 |
| 8Q LOSS WILD-TYPE | 92 | 97 | 24 |
Figure S183. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00323 (Fisher's exact test), Q value = 0.037
Table S184. Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 216 | 126 |
| 9P LOSS MUTATED | 106 | 77 | 65 |
| 9P LOSS WILD-TYPE | 109 | 139 | 61 |
Figure S184. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00571 (Fisher's exact test), Q value = 0.05
Table S185. Gene #58: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 9P LOSS MUTATED | 125 | 70 | 53 |
| 9P LOSS WILD-TYPE | 185 | 88 | 36 |
Figure S185. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.0162 (Fisher's exact test), Q value = 0.11
Table S186. Gene #58: '9p loss' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 9P LOSS MUTATED | 79 | 78 | 105 |
| 9P LOSS WILD-TYPE | 92 | 128 | 97 |
Figure S186. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.00713 (Fisher's exact test), Q value = 0.059
Table S187. Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 216 | 126 |
| 9Q LOSS MUTATED | 120 | 88 | 63 |
| 9Q LOSS WILD-TYPE | 95 | 128 | 63 |
Figure S187. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.0128 (Fisher's exact test), Q value = 0.087
Table S188. Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 9Q LOSS MUTATED | 143 | 72 | 56 |
| 9Q LOSS WILD-TYPE | 167 | 86 | 33 |
Figure S188. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.0334 (Fisher's exact test), Q value = 0.17
Table S189. Gene #59: '9q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_10 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|---|
| ALL | 85 | 57 | 58 | 82 | 34 | 75 | 34 | 36 | 52 | 42 |
| 9Q LOSS MUTATED | 31 | 30 | 34 | 33 | 21 | 33 | 21 | 18 | 31 | 19 |
| 9Q LOSS WILD-TYPE | 54 | 27 | 24 | 49 | 13 | 42 | 13 | 18 | 21 | 23 |
Figure S189. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
Table S190. Gene #59: '9q loss' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 9Q LOSS MUTATED | 81 | 68 | 137 |
| 9Q LOSS WILD-TYPE | 90 | 138 | 65 |
Figure S190. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.00552 (Fisher's exact test), Q value = 0.05
Table S191. Gene #59: '9q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 9Q LOSS MUTATED | 102 | 80 | 97 |
| 9Q LOSS WILD-TYPE | 70 | 95 | 124 |
Figure S191. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.00816 (Fisher's exact test), Q value = 0.064
Table S192. Gene #59: '9q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 100 | 67 | 91 |
| 9Q LOSS MUTATED | 42 | 23 | 53 |
| 9Q LOSS WILD-TYPE | 58 | 44 | 38 |
Figure S192. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
P value = 0.00438 (Fisher's exact test), Q value = 0.044
Table S193. Gene #61: '10q loss' versus Molecular Subtype #3: 'MIR_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 159 | 164 | 232 |
| 10Q LOSS MUTATED | 32 | 23 | 64 |
| 10Q LOSS WILD-TYPE | 127 | 141 | 168 |
Figure S193. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #3: 'MIR_CNMF'
P value = 0.0227 (Fisher's exact test), Q value = 0.13
Table S194. Gene #61: '10q loss' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 10Q LOSS MUTATED | 33 | 35 | 56 |
| 10Q LOSS WILD-TYPE | 138 | 171 | 146 |
Figure S194. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.00189 (Fisher's exact test), Q value = 0.025
Table S195. Gene #61: '10q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 10Q LOSS MUTATED | 53 | 27 | 43 |
| 10Q LOSS WILD-TYPE | 119 | 148 | 178 |
Figure S195. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.0115 (Fisher's exact test), Q value = 0.082
Table S196. Gene #62: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 11P LOSS MUTATED | 91 | 57 | 41 |
| 11P LOSS WILD-TYPE | 219 | 101 | 48 |
Figure S196. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.0365 (Fisher's exact test), Q value = 0.17
Table S197. Gene #62: '11p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 11P LOSS MUTATED | 72 | 54 | 67 |
| 11P LOSS WILD-TYPE | 100 | 121 | 154 |
Figure S197. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.04 (Fisher's exact test), Q value = 0.18
Table S198. Gene #62: '11p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 100 | 67 | 91 |
| 11P LOSS MUTATED | 33 | 15 | 38 |
| 11P LOSS WILD-TYPE | 67 | 52 | 53 |
Figure S198. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
P value = 0.00981 (Fisher's exact test), Q value = 0.073
Table S199. Gene #63: '11q loss' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 11Q LOSS MUTATED | 38 | 43 | 67 |
| 11Q LOSS WILD-TYPE | 133 | 163 | 135 |
Figure S199. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.00291 (Fisher's exact test), Q value = 0.035
Table S200. Gene #64: '12p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 216 | 126 |
| 12P LOSS MUTATED | 18 | 32 | 27 |
| 12P LOSS WILD-TYPE | 197 | 184 | 99 |
Figure S200. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.011 (Fisher's exact test), Q value = 0.08
Table S201. Gene #64: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 12P LOSS MUTATED | 42 | 30 | 5 |
| 12P LOSS WILD-TYPE | 268 | 128 | 84 |
Figure S201. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.00627 (Fisher's exact test), Q value = 0.055
Table S202. Gene #64: '12p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_10 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|---|
| ALL | 85 | 57 | 58 | 82 | 34 | 75 | 34 | 36 | 52 | 42 |
| 12P LOSS MUTATED | 12 | 12 | 6 | 11 | 4 | 12 | 1 | 11 | 1 | 7 |
| 12P LOSS WILD-TYPE | 73 | 45 | 52 | 71 | 30 | 63 | 33 | 25 | 51 | 35 |
Figure S202. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
P value = 0.00087 (Fisher's exact test), Q value = 0.014
Table S203. Gene #64: '12p loss' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 12P LOSS MUTATED | 26 | 39 | 14 |
| 12P LOSS WILD-TYPE | 145 | 167 | 188 |
Figure S203. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.0094 (Fisher's exact test), Q value = 0.071
Table S204. Gene #64: '12p loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 121 | 182 | 144 |
| 12P LOSS MUTATED | 18 | 35 | 11 |
| 12P LOSS WILD-TYPE | 103 | 147 | 133 |
Figure S204. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'
P value = 0.00637 (Fisher's exact test), Q value = 0.055
Table S205. Gene #64: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 105 | 71 | 165 | 106 |
| 12P LOSS MUTATED | 24 | 5 | 26 | 9 |
| 12P LOSS WILD-TYPE | 81 | 66 | 139 | 97 |
Figure S205. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0234 (Fisher's exact test), Q value = 0.13
Table S206. Gene #65: '12q loss' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 12Q LOSS MUTATED | 29 | 49 | 27 |
| 12Q LOSS WILD-TYPE | 142 | 157 | 175 |
Figure S206. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.0254 (Fisher's exact test), Q value = 0.14
Table S207. Gene #65: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 121 | 182 | 144 |
| 12Q LOSS MUTATED | 24 | 40 | 16 |
| 12Q LOSS WILD-TYPE | 97 | 142 | 128 |
Figure S207. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'
P value = 0.0309 (Fisher's exact test), Q value = 0.16
Table S208. Gene #65: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 105 | 71 | 165 | 106 |
| 12Q LOSS MUTATED | 27 | 9 | 32 | 12 |
| 12Q LOSS WILD-TYPE | 78 | 62 | 133 | 94 |
Figure S208. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0404 (Fisher's exact test), Q value = 0.18
Table S209. Gene #65: '12q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 6 | 2 | 2 | 6 | 4 | 2 |
| 12Q LOSS MUTATED | 0 | 0 | 1 | 4 | 0 | 0 |
| 12Q LOSS WILD-TYPE | 6 | 2 | 1 | 2 | 4 | 2 |
Figure S209. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.0292 (Fisher's exact test), Q value = 0.15
Table S210. Gene #66: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 216 | 126 |
| 13Q LOSS MUTATED | 111 | 129 | 57 |
| 13Q LOSS WILD-TYPE | 104 | 87 | 69 |
Figure S210. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00861 (Fisher's exact test), Q value = 0.067
Table S211. Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 13Q LOSS MUTATED | 182 | 78 | 37 |
| 13Q LOSS WILD-TYPE | 128 | 80 | 52 |
Figure S211. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.0163 (Fisher's exact test), Q value = 0.11
Table S212. Gene #66: '13q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_10 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|---|
| ALL | 85 | 57 | 58 | 82 | 34 | 75 | 34 | 36 | 52 | 42 |
| 13Q LOSS MUTATED | 46 | 29 | 38 | 50 | 17 | 30 | 13 | 26 | 25 | 24 |
| 13Q LOSS WILD-TYPE | 39 | 28 | 20 | 32 | 17 | 45 | 21 | 10 | 27 | 18 |
Figure S212. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
Table S213. Gene #66: '13q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 13Q LOSS MUTATED | 89 | 72 | 144 |
| 13Q LOSS WILD-TYPE | 83 | 103 | 77 |
Figure S213. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.00531 (Fisher's exact test), Q value = 0.048
Table S214. Gene #66: '13q loss' versus Molecular Subtype #7: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 120 | 196 | 82 |
| 13Q LOSS MUTATED | 55 | 121 | 37 |
| 13Q LOSS WILD-TYPE | 65 | 75 | 45 |
Figure S214. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #7: 'RPPA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
Table S215. Gene #67: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 14Q LOSS MUTATED | 52 | 58 | 105 |
| 14Q LOSS WILD-TYPE | 119 | 148 | 97 |
Figure S215. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.00374 (Fisher's exact test), Q value = 0.04
Table S216. Gene #67: '14q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 14Q LOSS MUTATED | 81 | 58 | 70 |
| 14Q LOSS WILD-TYPE | 91 | 117 | 151 |
Figure S216. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.00389 (Fisher's exact test), Q value = 0.041
Table S217. Gene #67: '14q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 100 | 67 | 91 |
| 14Q LOSS MUTATED | 33 | 14 | 42 |
| 14Q LOSS WILD-TYPE | 67 | 53 | 49 |
Figure S217. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
P value = 0.0468 (Fisher's exact test), Q value = 0.21
Table S218. Gene #67: '14q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 106 | 116 | 36 |
| 14Q LOSS MUTATED | 35 | 35 | 19 |
| 14Q LOSS WILD-TYPE | 71 | 81 | 17 |
Figure S218. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00044 (Fisher's exact test), Q value = 0.009
Table S219. Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 216 | 126 |
| 15Q LOSS MUTATED | 126 | 87 | 57 |
| 15Q LOSS WILD-TYPE | 89 | 129 | 69 |
Figure S219. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.0175 (Fisher's exact test), Q value = 0.11
Table S220. Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 15Q LOSS MUTATED | 150 | 66 | 54 |
| 15Q LOSS WILD-TYPE | 160 | 92 | 35 |
Figure S220. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 9e-05 (Fisher's exact test), Q value = 0.0026
Table S221. Gene #68: '15q loss' versus Molecular Subtype #3: 'MIR_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 159 | 164 | 232 |
| 15Q LOSS MUTATED | 62 | 70 | 138 |
| 15Q LOSS WILD-TYPE | 97 | 94 | 94 |
Figure S221. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #3: 'MIR_CNMF'
P value = 0.00022 (Fisher's exact test), Q value = 0.0054
Table S222. Gene #68: '15q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_10 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|---|
| ALL | 85 | 57 | 58 | 82 | 34 | 75 | 34 | 36 | 52 | 42 |
| 15Q LOSS MUTATED | 26 | 27 | 34 | 41 | 18 | 42 | 23 | 18 | 30 | 11 |
| 15Q LOSS WILD-TYPE | 59 | 30 | 24 | 41 | 16 | 33 | 11 | 18 | 22 | 31 |
Figure S222. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
Table S223. Gene #68: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 15Q LOSS MUTATED | 65 | 74 | 141 |
| 15Q LOSS WILD-TYPE | 106 | 132 | 61 |
Figure S223. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'
P value = 2e-05 (Fisher's exact test), Q value = 0.00077
Table S224. Gene #68: '15q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 15Q LOSS MUTATED | 114 | 69 | 94 |
| 15Q LOSS WILD-TYPE | 58 | 106 | 127 |
Figure S224. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.00795 (Fisher's exact test), Q value = 0.063
Table S225. Gene #68: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 121 | 182 | 144 |
| 15Q LOSS MUTATED | 55 | 108 | 63 |
| 15Q LOSS WILD-TYPE | 66 | 74 | 81 |
Figure S225. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'
P value = 0.00054 (Fisher's exact test), Q value = 0.01
Table S226. Gene #68: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 105 | 71 | 165 | 106 |
| 15Q LOSS MUTATED | 43 | 37 | 103 | 43 |
| 15Q LOSS WILD-TYPE | 62 | 34 | 62 | 63 |
Figure S226. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0427 (Fisher's exact test), Q value = 0.19
Table S227. Gene #68: '15q loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 |
|---|---|---|
| ALL | 12 | 10 |
| 15Q LOSS MUTATED | 4 | 8 |
| 15Q LOSS WILD-TYPE | 8 | 2 |
Figure S227. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'
P value = 0.0405 (Fisher's exact test), Q value = 0.18
Table S228. Gene #69: '16p loss' versus Molecular Subtype #3: 'MIR_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 159 | 164 | 232 |
| 16P LOSS MUTATED | 97 | 81 | 142 |
| 16P LOSS WILD-TYPE | 62 | 83 | 90 |
Figure S228. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #3: 'MIR_CNMF'
P value = 0.0397 (Fisher's exact test), Q value = 0.18
Table S229. Gene #69: '16p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 100 | 67 | 91 |
| 16P LOSS MUTATED | 67 | 32 | 57 |
| 16P LOSS WILD-TYPE | 33 | 35 | 34 |
Figure S229. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
P value = 0.0477 (Fisher's exact test), Q value = 0.21
Table S230. Gene #69: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 121 | 182 | 144 |
| 16P LOSS MUTATED | 67 | 120 | 77 |
| 16P LOSS WILD-TYPE | 54 | 62 | 67 |
Figure S230. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'
P value = 0.00235 (Fisher's exact test), Q value = 0.03
Table S231. Gene #70: '16q loss' versus Molecular Subtype #3: 'MIR_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 159 | 164 | 232 |
| 16Q LOSS MUTATED | 117 | 100 | 178 |
| 16Q LOSS WILD-TYPE | 42 | 64 | 54 |
Figure S231. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'MIR_CNMF'
P value = 0.0277 (Fisher's exact test), Q value = 0.15
Table S232. Gene #70: '16q loss' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 16Q LOSS MUTATED | 112 | 144 | 157 |
| 16Q LOSS WILD-TYPE | 59 | 62 | 45 |
Figure S232. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.0289 (Fisher's exact test), Q value = 0.15
Table S233. Gene #72: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 310 | 158 | 89 |
| 17Q LOSS MUTATED | 220 | 94 | 55 |
| 17Q LOSS WILD-TYPE | 90 | 64 | 34 |
Figure S233. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.016 (Fisher's exact test), Q value = 0.11
Table S234. Gene #72: '17q loss' versus Molecular Subtype #3: 'MIR_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 159 | 164 | 232 |
| 17Q LOSS MUTATED | 104 | 96 | 168 |
| 17Q LOSS WILD-TYPE | 55 | 68 | 64 |
Figure S234. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #3: 'MIR_CNMF'
P value = 0.0117 (Fisher's exact test), Q value = 0.083
Table S235. Gene #72: '17q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_10 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|---|
| ALL | 85 | 57 | 58 | 82 | 34 | 75 | 34 | 36 | 52 | 42 |
| 17Q LOSS MUTATED | 50 | 37 | 43 | 59 | 19 | 50 | 30 | 26 | 26 | 28 |
| 17Q LOSS WILD-TYPE | 35 | 20 | 15 | 23 | 15 | 25 | 4 | 10 | 26 | 14 |
Figure S235. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
P value = 0.0203 (Fisher's exact test), Q value = 0.12
Table S236. Gene #73: '18p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_10 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|---|
| ALL | 85 | 57 | 58 | 82 | 34 | 75 | 34 | 36 | 52 | 42 |
| 18P LOSS MUTATED | 37 | 16 | 20 | 27 | 21 | 40 | 12 | 17 | 20 | 19 |
| 18P LOSS WILD-TYPE | 48 | 41 | 38 | 55 | 13 | 35 | 22 | 19 | 32 | 23 |
Figure S236. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
P value = 0.00254 (Fisher's exact test), Q value = 0.032
Table S237. Gene #73: '18p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 18P LOSS MUTATED | 59 | 90 | 83 |
| 18P LOSS WILD-TYPE | 113 | 85 | 138 |
Figure S237. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.00693 (Fisher's exact test), Q value = 0.058
Table S238. Gene #73: '18p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 116 | 96 | 128 | 58 |
| 18P LOSS MUTATED | 57 | 29 | 62 | 19 |
| 18P LOSS WILD-TYPE | 59 | 67 | 66 | 39 |
Figure S238. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'
P value = 0.0242 (Fisher's exact test), Q value = 0.13
Table S239. Gene #73: '18p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 100 | 67 | 91 |
| 18P LOSS MUTATED | 40 | 18 | 44 |
| 18P LOSS WILD-TYPE | 60 | 49 | 47 |
Figure S239. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
P value = 0.036 (Fisher's exact test), Q value = 0.17
Table S240. Gene #74: '18q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 116 | 96 | 128 | 58 |
| 18Q LOSS MUTATED | 61 | 41 | 75 | 23 |
| 18Q LOSS WILD-TYPE | 55 | 55 | 53 | 35 |
Figure S240. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'
P value = 0.0109 (Fisher's exact test), Q value = 0.079
Table S241. Gene #74: '18q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 100 | 67 | 91 |
| 18Q LOSS MUTATED | 44 | 28 | 57 |
| 18Q LOSS WILD-TYPE | 56 | 39 | 34 |
Figure S241. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
P value = 0.0444 (Fisher's exact test), Q value = 0.2
Table S242. Gene #75: '19p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_10 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|---|
| ALL | 85 | 57 | 58 | 82 | 34 | 75 | 34 | 36 | 52 | 42 |
| 19P LOSS MUTATED | 26 | 16 | 20 | 31 | 8 | 20 | 18 | 9 | 11 | 19 |
| 19P LOSS WILD-TYPE | 59 | 41 | 38 | 51 | 26 | 55 | 16 | 27 | 41 | 23 |
Figure S242. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
P value = 0.00522 (Fisher's exact test), Q value = 0.048
Table S243. Gene #75: '19p loss' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 19P LOSS MUTATED | 56 | 50 | 79 |
| 19P LOSS WILD-TYPE | 115 | 156 | 123 |
Figure S243. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.0197 (Fisher's exact test), Q value = 0.12
Table S244. Gene #75: '19p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 19P LOSS MUTATED | 69 | 49 | 62 |
| 19P LOSS WILD-TYPE | 103 | 126 | 159 |
Figure S244. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.00975 (Fisher's exact test), Q value = 0.073
Table S245. Gene #75: '19p loss' versus Molecular Subtype #7: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 120 | 196 | 82 |
| 19P LOSS MUTATED | 27 | 56 | 35 |
| 19P LOSS WILD-TYPE | 93 | 140 | 47 |
Figure S245. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #7: 'RPPA_CNMF'
P value = 0.0115 (Fisher's exact test), Q value = 0.082
Table S246. Gene #75: '19p loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 |
|---|---|---|
| ALL | 12 | 10 |
| 19P LOSS MUTATED | 8 | 1 |
| 19P LOSS WILD-TYPE | 4 | 9 |
Figure S246. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'
P value = 0.0158 (Fisher's exact test), Q value = 0.1
Table S247. Gene #76: '19q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_10 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|---|
| ALL | 85 | 57 | 58 | 82 | 34 | 75 | 34 | 36 | 52 | 42 |
| 19Q LOSS MUTATED | 29 | 16 | 16 | 31 | 7 | 18 | 18 | 9 | 9 | 17 |
| 19Q LOSS WILD-TYPE | 56 | 41 | 42 | 51 | 27 | 57 | 16 | 27 | 43 | 25 |
Figure S247. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
P value = 0.00459 (Fisher's exact test), Q value = 0.044
Table S248. Gene #76: '19q loss' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 19Q LOSS MUTATED | 61 | 46 | 71 |
| 19Q LOSS WILD-TYPE | 110 | 160 | 131 |
Figure S248. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.00535 (Fisher's exact test), Q value = 0.048
Table S249. Gene #76: '19q loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 |
|---|---|---|
| ALL | 12 | 10 |
| 19Q LOSS MUTATED | 7 | 0 |
| 19Q LOSS WILD-TYPE | 5 | 10 |
Figure S249. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'
P value = 0.00338 (Fisher's exact test), Q value = 0.039
Table S250. Gene #77: '20p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 106 | 116 | 36 |
| 20P LOSS MUTATED | 13 | 3 | 6 |
| 20P LOSS WILD-TYPE | 93 | 113 | 30 |
Figure S250. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00083 (Fisher's exact test), Q value = 0.014
Table S251. Gene #77: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 121 | 182 | 144 |
| 20P LOSS MUTATED | 2 | 23 | 15 |
| 20P LOSS WILD-TYPE | 119 | 159 | 129 |
Figure S251. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'
P value = 0.0377 (Fisher's exact test), Q value = 0.18
Table S252. Gene #78: '20q loss' versus Molecular Subtype #3: 'MIR_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 159 | 164 | 232 |
| 20Q LOSS MUTATED | 11 | 3 | 16 |
| 20Q LOSS WILD-TYPE | 148 | 161 | 216 |
Figure S252. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #3: 'MIR_CNMF'
P value = 0.0481 (Fisher's exact test), Q value = 0.21
Table S253. Gene #78: '20q loss' versus Molecular Subtype #7: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 120 | 196 | 82 |
| 20Q LOSS MUTATED | 4 | 15 | 1 |
| 20Q LOSS WILD-TYPE | 116 | 181 | 81 |
Figure S253. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #7: 'RPPA_CNMF'
P value = 0.0141 (Fisher's exact test), Q value = 0.095
Table S254. Gene #78: '20q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 106 | 116 | 36 |
| 20Q LOSS MUTATED | 8 | 1 | 3 |
| 20Q LOSS WILD-TYPE | 98 | 115 | 33 |
Figure S254. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00217 (Fisher's exact test), Q value = 0.028
Table S255. Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 216 | 126 |
| 22Q LOSS MUTATED | 175 | 144 | 93 |
| 22Q LOSS WILD-TYPE | 40 | 72 | 33 |
Figure S255. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.0346 (Fisher's exact test), Q value = 0.17
Table S256. Gene #80: '22q loss' versus Molecular Subtype #3: 'MIR_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 159 | 164 | 232 |
| 22Q LOSS MUTATED | 110 | 117 | 185 |
| 22Q LOSS WILD-TYPE | 49 | 47 | 47 |
Figure S256. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #3: 'MIR_CNMF'
P value = 4e-05 (Fisher's exact test), Q value = 0.0014
Table S257. Gene #80: '22q loss' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| 22Q LOSS MUTATED | 120 | 139 | 171 |
| 22Q LOSS WILD-TYPE | 51 | 67 | 31 |
Figure S257. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.00182 (Fisher's exact test), Q value = 0.025
Table S258. Gene #80: '22q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| 22Q LOSS MUTATED | 140 | 134 | 146 |
| 22Q LOSS WILD-TYPE | 32 | 41 | 75 |
Figure S258. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.0236 (Fisher's exact test), Q value = 0.13
Table S259. Gene #80: '22q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 116 | 96 | 128 | 58 |
| 22Q LOSS MUTATED | 80 | 81 | 96 | 38 |
| 22Q LOSS WILD-TYPE | 36 | 15 | 32 | 20 |
Figure S259. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'
P value = 0.0416 (Fisher's exact test), Q value = 0.19
Table S260. Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 121 | 182 | 144 |
| 22Q LOSS MUTATED | 83 | 148 | 110 |
| 22Q LOSS WILD-TYPE | 38 | 34 | 34 |
Figure S260. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'
P value = 0.00644 (Fisher's exact test), Q value = 0.055
Table S261. Gene #81: 'xp loss' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| XP LOSS MUTATED | 97 | 131 | 97 |
| XP LOSS WILD-TYPE | 74 | 75 | 105 |
Figure S261. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #5: 'CN_CNMF'
P value = 0.0406 (Fisher's exact test), Q value = 0.18
Table S262. Gene #81: 'xp loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 172 | 175 | 221 |
| XP LOSS MUTATED | 84 | 101 | 136 |
| XP LOSS WILD-TYPE | 88 | 74 | 85 |
Figure S262. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
P value = 0.0362 (Fisher's exact test), Q value = 0.17
Table S263. Gene #81: 'xp loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 116 | 96 | 128 | 58 |
| XP LOSS MUTATED | 54 | 62 | 70 | 37 |
| XP LOSS WILD-TYPE | 62 | 34 | 58 | 21 |
Figure S263. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'
P value = 0.00019 (Fisher's exact test), Q value = 0.005
Table S264. Gene #82: 'xq loss' versus Molecular Subtype #5: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 171 | 206 | 202 |
| XQ LOSS MUTATED | 92 | 114 | 74 |
| XQ LOSS WILD-TYPE | 79 | 92 | 128 |
Figure S264. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #5: 'CN_CNMF'
-
Copy number data file = broad_values_by_arm.txt from GISTIC pipeline
-
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/OV-TP/15096464/transformed.cor.cli.txt
-
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/OV-TP/15120653/OV-TP.transferedmergedcluster.txt
-
Number of patients = 579
-
Number of significantly arm-level cnvs = 82
-
Number of molecular subtypes = 14
-
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.