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 10 molecular subtypes across 408 patients, 281 significant findings detected with P value < 0.05 and Q value < 0.25.
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1p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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1q gain cnv correlated to 'CN_CNMF'.
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2p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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2q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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3p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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3q gain cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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4p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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4q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
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5p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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5q gain cnv correlated to 'CN_CNMF', 'RPPA_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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6p gain cnv correlated to 'CN_CNMF'.
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6q gain cnv correlated to 'RPPA_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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7p gain cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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7q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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8p gain cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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8q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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9p gain cnv correlated to 'CN_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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9q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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10p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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10q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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11p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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11q gain cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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12p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
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12q gain cnv correlated to 'RPPA_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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13q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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14q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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15q gain cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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16p gain cnv correlated to 'CN_CNMF'.
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16q gain cnv correlated to 'CN_CNMF'.
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17p gain cnv correlated to 'CN_CNMF'.
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17q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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18p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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18q gain cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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19p gain cnv correlated to 'CN_CNMF'.
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19q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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20p gain cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.
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20q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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21q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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22q gain cnv correlated to 'MRNASEQ_CNMF'.
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xp gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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1p loss cnv correlated to 'METHLYATION_CNMF'.
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2p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
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2q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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3p loss cnv correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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3q loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.
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4p loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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4q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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5p loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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5q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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6p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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6q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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7p loss cnv correlated to 'MIRSEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CNMF'.
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7q loss cnv correlated to 'CN_CNMF'.
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8p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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8q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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9p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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9q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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10p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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10q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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11p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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11q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CNMF'.
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12p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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12q loss cnv correlated to 'CN_CNMF'.
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13q loss cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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14q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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15q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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16p loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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16q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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17p loss cnv correlated to 'CN_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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17q loss cnv correlated to 'CN_CNMF'.
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18p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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18q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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19p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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19q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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20p loss cnv correlated to 'RPPA_CHIERARCHICAL'.
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21q loss cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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22q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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xp loss cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.
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xq loss cnv correlated to 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 281 significant findings detected.
Clinical Features |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
||
nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
9q loss | 170 (42%) | 238 |
1e-05 (0.000178) |
1e-05 (0.000178) |
0.0149 (0.0669) |
0.00499 (0.0286) |
3e-05 (0.000424) |
1e-05 (0.000178) |
0.0193 (0.0807) |
0.00059 (0.00532) |
1e-05 (0.000178) |
1e-05 (0.000178) |
14q loss | 122 (30%) | 286 |
1e-05 (0.000178) |
2e-05 (0.000309) |
0.0497 (0.145) |
0.0153 (0.068) |
0.155 (0.304) |
0.00015 (0.00162) |
0.00063 (0.00562) |
0.0241 (0.0912) |
0.00237 (0.0166) |
2e-05 (0.000309) |
9p loss | 175 (43%) | 233 |
1e-05 (0.000178) |
9e-05 (0.00105) |
0.201 (0.363) |
0.0518 (0.15) |
0.0009 (0.00769) |
2e-05 (0.000309) |
0.0295 (0.104) |
0.00101 (0.00828) |
3e-05 (0.000424) |
1e-05 (0.000178) |
3p gain | 142 (35%) | 266 |
8e-05 (0.000965) |
0.0485 (0.142) |
0.158 (0.308) |
0.464 (0.625) |
0.00869 (0.0439) |
0.0199 (0.0807) |
0.0305 (0.106) |
0.0664 (0.175) |
0.0222 (0.0859) |
0.00037 (0.00357) |
9q gain | 56 (14%) | 352 |
0.00021 (0.00224) |
0.0212 (0.0838) |
0.762 (0.84) |
0.00682 (0.0368) |
0.00229 (0.0162) |
0.0003 (0.003) |
0.866 (0.911) |
0.375 (0.549) |
0.00032 (0.00316) |
1e-05 (0.000178) |
3p loss | 53 (13%) | 355 |
0.168 (0.322) |
0.0332 (0.112) |
0.0455 (0.137) |
0.145 (0.289) |
1e-05 (0.000178) |
2e-05 (0.000309) |
0.638 (0.762) |
0.00424 (0.0254) |
0.00038 (0.00362) |
0.0015 (0.0116) |
22q loss | 159 (39%) | 249 |
1e-05 (0.000178) |
0.0196 (0.0807) |
0.636 (0.762) |
0.0166 (0.0727) |
0.00879 (0.0439) |
0.00103 (0.00836) |
0.234 (0.402) |
0.00397 (0.0241) |
0.0671 (0.176) |
1e-05 (0.000178) |
5p gain | 166 (41%) | 242 |
1e-05 (0.000178) |
0.0398 (0.127) |
0.0354 (0.117) |
0.201 (0.363) |
0.105 (0.234) |
0.00042 (0.00396) |
0.835 (0.889) |
0.00281 (0.0186) |
0.0912 (0.217) |
0.00462 (0.0269) |
21q gain | 115 (28%) | 293 |
1e-05 (0.000178) |
1e-05 (0.000178) |
0.432 (0.596) |
0.173 (0.328) |
0.00263 (0.0178) |
0.00164 (0.0125) |
0.00754 (0.0399) |
0.00783 (0.041) |
0.0589 (0.164) |
0.257 (0.431) |
4p loss | 143 (35%) | 265 |
1e-05 (0.000178) |
0.114 (0.249) |
0.581 (0.718) |
0.659 (0.778) |
0.00615 (0.0338) |
9e-05 (0.00105) |
0.0337 (0.113) |
0.00945 (0.0459) |
0.014 (0.0637) |
0.0627 (0.171) |
4q loss | 136 (33%) | 272 |
1e-05 (0.000178) |
0.0624 (0.171) |
0.143 (0.288) |
0.229 (0.397) |
0.038 (0.122) |
0.00099 (0.00828) |
0.389 (0.556) |
0.04 (0.127) |
0.00197 (0.0142) |
0.00287 (0.0187) |
6p loss | 100 (25%) | 308 |
5e-05 (0.000651) |
0.0185 (0.0792) |
0.632 (0.76) |
0.691 (0.791) |
0.185 (0.342) |
0.0363 (0.118) |
0.0471 (0.14) |
0.00463 (0.0269) |
0.086 (0.207) |
8e-05 (0.000965) |
11p loss | 181 (44%) | 227 |
1e-05 (0.000178) |
1e-05 (0.000178) |
0.17 (0.324) |
0.694 (0.793) |
4e-05 (0.000538) |
2e-05 (0.000309) |
0.101 (0.23) |
0.095 (0.223) |
0.00013 (0.00142) |
0.0005 (0.00461) |
13q loss | 86 (21%) | 322 |
1e-05 (0.000178) |
0.631 (0.76) |
0.0144 (0.0649) |
0.106 (0.235) |
0.0186 (0.0792) |
0.264 (0.44) |
0.201 (0.363) |
3e-05 (0.000424) |
0.0108 (0.0507) |
0.00083 (0.00716) |
15q loss | 145 (36%) | 263 |
1e-05 (0.000178) |
1e-05 (0.000178) |
0.0843 (0.204) |
0.414 (0.582) |
0.421 (0.586) |
0.305 (0.479) |
0.00899 (0.0441) |
1e-05 (0.000178) |
0.00646 (0.0353) |
0.00012 (0.00133) |
2p gain | 111 (27%) | 297 |
1e-05 (0.000178) |
1e-05 (0.000178) |
0.327 (0.503) |
0.736 (0.824) |
0.354 (0.529) |
0.0201 (0.081) |
0.117 (0.252) |
0.00812 (0.0416) |
0.228 (0.397) |
0.00146 (0.0114) |
3q gain | 178 (44%) | 230 |
1e-05 (0.000178) |
0.284 (0.458) |
0.68 (0.789) |
0.852 (0.904) |
0.759 (0.838) |
0.082 (0.201) |
0.0341 (0.114) |
0.0287 (0.104) |
0.0329 (0.112) |
3e-05 (0.000424) |
4p gain | 38 (9%) | 370 |
0.00241 (0.0166) |
0.00873 (0.0439) |
0.341 (0.517) |
0.488 (0.637) |
0.00797 (0.0414) |
0.0101 (0.0481) |
0.0122 (0.0566) |
0.456 (0.617) |
0.246 (0.42) |
0.466 (0.626) |
8q gain | 203 (50%) | 205 |
1e-05 (0.000178) |
0.00926 (0.0452) |
0.0275 (0.102) |
0.257 (0.431) |
0.452 (0.615) |
0.818 (0.877) |
0.28 (0.455) |
0.0358 (0.118) |
0.69 (0.791) |
0.042 (0.13) |
2q loss | 91 (22%) | 317 |
0.00118 (0.00939) |
0.0235 (0.0898) |
0.843 (0.897) |
0.747 (0.829) |
0.0635 (0.172) |
0.0314 (0.108) |
0.745 (0.829) |
0.891 (0.929) |
0.0109 (0.0508) |
0.00519 (0.0294) |
5q loss | 159 (39%) | 249 |
1e-05 (0.000178) |
0.00135 (0.0106) |
0.853 (0.904) |
0.173 (0.328) |
0.212 (0.375) |
0.0168 (0.0733) |
0.213 (0.376) |
0.0188 (0.0796) |
0.221 (0.387) |
0.00785 (0.041) |
6q loss | 159 (39%) | 249 |
1e-05 (0.000178) |
0.0135 (0.0614) |
0.746 (0.829) |
0.344 (0.517) |
0.384 (0.552) |
0.0472 (0.14) |
0.0946 (0.222) |
0.00286 (0.0187) |
0.443 (0.606) |
5e-05 (0.000651) |
8p loss | 188 (46%) | 220 |
1e-05 (0.000178) |
0.00596 (0.033) |
0.103 (0.232) |
0.0706 (0.179) |
0.152 (0.3) |
0.0219 (0.0855) |
0.1 (0.23) |
0.0294 (0.104) |
0.308 (0.48) |
0.00342 (0.0214) |
18q loss | 146 (36%) | 262 |
0.00179 (0.0133) |
0.556 (0.696) |
0.808 (0.871) |
0.885 (0.926) |
0.592 (0.727) |
0.0465 (0.139) |
0.00028 (0.00287) |
0.00047 (0.00438) |
0.033 (0.112) |
0.163 (0.315) |
7p gain | 171 (42%) | 237 |
1e-05 (0.000178) |
0.0607 (0.167) |
0.0339 (0.114) |
0.357 (0.531) |
0.663 (0.779) |
0.102 (0.231) |
0.368 (0.543) |
0.0402 (0.127) |
0.2 (0.363) |
0.00012 (0.00133) |
10p gain | 116 (28%) | 292 |
1e-05 (0.000178) |
0.00503 (0.0286) |
0.902 (0.935) |
0.773 (0.847) |
0.749 (0.83) |
0.00245 (0.0167) |
0.862 (0.911) |
0.899 (0.935) |
0.807 (0.871) |
0.0101 (0.0481) |
11p gain | 28 (7%) | 380 |
6e-05 (0.000757) |
0.182 (0.339) |
0.284 (0.458) |
0.0688 (0.177) |
0.0634 (0.172) |
0.00662 (0.0359) |
0.937 (0.958) |
0.571 (0.708) |
0.00224 (0.016) |
0.0175 (0.076) |
14q gain | 58 (14%) | 350 |
7e-05 (0.00087) |
0.0464 (0.139) |
0.422 (0.586) |
0.0658 (0.174) |
0.0433 (0.133) |
0.0424 (0.131) |
0.596 (0.73) |
0.18 (0.338) |
0.37 (0.545) |
0.361 (0.535) |
17q gain | 136 (33%) | 272 |
0.00311 (0.0199) |
0.0313 (0.108) |
0.468 (0.627) |
0.688 (0.791) |
0.0406 (0.128) |
0.305 (0.479) |
0.28 (0.455) |
0.205 (0.367) |
0.294 (0.469) |
0.00279 (0.0186) |
18p gain | 117 (29%) | 291 |
1e-05 (0.000178) |
0.00384 (0.0235) |
0.953 (0.965) |
0.912 (0.941) |
0.289 (0.463) |
0.0204 (0.0816) |
0.329 (0.504) |
0.108 (0.238) |
0.0601 (0.166) |
4e-05 (0.000538) |
xp gain | 66 (16%) | 342 |
0.00054 (0.00492) |
0.00101 (0.00828) |
0.122 (0.257) |
0.0641 (0.172) |
0.00804 (0.0415) |
0.0552 (0.158) |
0.0707 (0.179) |
0.131 (0.27) |
0.0215 (0.0846) |
0.111 (0.243) |
5p loss | 56 (14%) | 352 |
0.0581 (0.162) |
0.00011 (0.00125) |
0.474 (0.631) |
0.537 (0.675) |
0.144 (0.289) |
0.0003 (0.003) |
0.637 (0.762) |
0.736 (0.824) |
0.0176 (0.0762) |
0.01 (0.0481) |
12p loss | 56 (14%) | 352 |
0.00466 (0.0269) |
0.00317 (0.0201) |
0.988 (0.989) |
0.901 (0.935) |
0.0767 (0.19) |
0.016 (0.0706) |
0.259 (0.434) |
0.279 (0.455) |
0.0287 (0.104) |
0.192 (0.35) |
21q loss | 79 (19%) | 329 |
0.209 (0.37) |
0.0897 (0.214) |
0.0685 (0.177) |
0.59 (0.727) |
0.00189 (0.0137) |
0.0106 (0.0499) |
0.383 (0.552) |
0.145 (0.289) |
0.00824 (0.042) |
0.0268 (0.0999) |
xq loss | 80 (20%) | 328 |
0.133 (0.272) |
6e-05 (0.000757) |
0.978 (0.982) |
0.938 (0.958) |
0.387 (0.555) |
0.3 (0.475) |
0.036 (0.118) |
0.116 (0.251) |
0.00171 (0.0129) |
0.01 (0.0481) |
1p gain | 90 (22%) | 318 |
1e-05 (0.000178) |
0.0225 (0.0865) |
0.571 (0.708) |
0.492 (0.64) |
0.85 (0.903) |
0.685 (0.791) |
0.894 (0.931) |
0.382 (0.552) |
0.751 (0.831) |
0.0286 (0.104) |
5q gain | 53 (13%) | 355 |
0.00557 (0.0313) |
0.0833 (0.203) |
0.00894 (0.0441) |
0.119 (0.254) |
0.401 (0.568) |
0.268 (0.443) |
0.344 (0.517) |
0.123 (0.257) |
0.486 (0.637) |
0.0362 (0.118) |
6q gain | 41 (10%) | 367 |
0.184 (0.341) |
0.863 (0.911) |
0.975 (0.982) |
0.0414 (0.129) |
0.39 (0.557) |
0.393 (0.561) |
0.508 (0.654) |
0.505 (0.652) |
0.0442 (0.135) |
0.0242 (0.0912) |
8p gain | 90 (22%) | 318 |
1e-05 (0.000178) |
0.283 (0.458) |
0.0683 (0.177) |
0.0194 (0.0807) |
0.334 (0.511) |
0.952 (0.965) |
0.119 (0.254) |
0.016 (0.0706) |
0.35 (0.525) |
0.177 (0.334) |
9p gain | 68 (17%) | 340 |
1e-05 (0.000178) |
0.116 (0.251) |
0.933 (0.958) |
0.423 (0.586) |
0.101 (0.23) |
0.0638 (0.172) |
0.321 (0.496) |
0.219 (0.384) |
4e-05 (0.000538) |
1e-05 (0.000178) |
10q gain | 45 (11%) | 363 |
0.00037 (0.00357) |
0.0522 (0.151) |
0.482 (0.634) |
0.432 (0.596) |
0.521 (0.661) |
0.0298 (0.104) |
0.44 (0.605) |
0.974 (0.982) |
0.255 (0.429) |
0.0291 (0.104) |
11q gain | 48 (12%) | 360 |
0.00592 (0.033) |
0.319 (0.494) |
0.171 (0.327) |
0.0297 (0.104) |
0.278 (0.455) |
0.141 (0.285) |
0.94 (0.959) |
0.905 (0.937) |
0.0326 (0.111) |
0.154 (0.302) |
18q gain | 63 (15%) | 345 |
0.00428 (0.0254) |
0.246 (0.42) |
0.123 (0.257) |
0.134 (0.273) |
0.585 (0.721) |
0.366 (0.542) |
0.0386 (0.123) |
0.426 (0.59) |
0.325 (0.5) |
0.00704 (0.0377) |
19q gain | 134 (33%) | 274 |
1e-05 (0.000178) |
0.00401 (0.0242) |
0.484 (0.636) |
0.681 (0.789) |
0.301 (0.477) |
0.29 (0.463) |
0.48 (0.634) |
0.0205 (0.0818) |
0.163 (0.315) |
0.183 (0.34) |
20p gain | 201 (49%) | 207 |
1e-05 (0.000178) |
0.063 (0.172) |
0.535 (0.675) |
0.0134 (0.0612) |
0.604 (0.738) |
0.0428 (0.132) |
0.51 (0.656) |
0.138 (0.28) |
0.0641 (0.172) |
0.0553 (0.158) |
20q gain | 229 (56%) | 179 |
2e-05 (0.000309) |
0.0294 (0.104) |
0.471 (0.629) |
0.0759 (0.189) |
0.497 (0.644) |
0.108 (0.238) |
0.376 (0.549) |
0.191 (0.35) |
0.518 (0.661) |
0.0239 (0.0908) |
10q loss | 128 (31%) | 280 |
1e-05 (0.000178) |
0.00025 (0.00259) |
0.561 (0.699) |
0.687 (0.791) |
0.0123 (0.0567) |
0.722 (0.814) |
0.122 (0.257) |
0.0535 (0.154) |
0.288 (0.463) |
0.0646 (0.172) |
11q loss | 131 (32%) | 277 |
1e-05 (0.000178) |
0.022 (0.0855) |
0.0285 (0.104) |
0.118 (0.253) |
0.336 (0.511) |
0.253 (0.428) |
0.701 (0.8) |
0.536 (0.675) |
0.663 (0.779) |
0.284 (0.458) |
16q loss | 103 (25%) | 305 |
1e-05 (0.000178) |
0.0201 (0.081) |
0.702 (0.801) |
0.987 (0.989) |
0.612 (0.743) |
0.356 (0.531) |
0.709 (0.806) |
0.1 (0.23) |
0.453 (0.616) |
0.00354 (0.022) |
17p loss | 180 (44%) | 228 |
0.00024 (0.00252) |
0.265 (0.441) |
0.831 (0.887) |
0.886 (0.926) |
0.305 (0.479) |
0.0696 (0.178) |
0.763 (0.84) |
0.036 (0.118) |
0.162 (0.315) |
0.00384 (0.0235) |
19p loss | 94 (23%) | 314 |
3e-05 (0.000424) |
0.046 (0.138) |
0.641 (0.764) |
0.491 (0.639) |
0.0961 (0.223) |
0.00723 (0.0385) |
0.255 (0.429) |
0.304 (0.479) |
0.342 (0.517) |
0.068 (0.177) |
2q gain | 57 (14%) | 351 |
1e-05 (0.000178) |
0.00184 (0.0136) |
0.306 (0.48) |
0.353 (0.529) |
0.654 (0.776) |
0.243 (0.416) |
0.0646 (0.172) |
0.249 (0.423) |
0.501 (0.649) |
0.277 (0.455) |
4q gain | 26 (6%) | 382 |
0.00187 (0.0137) |
0.101 (0.23) |
0.46 (0.622) |
0.163 (0.315) |
0.0946 (0.222) |
0.112 (0.244) |
0.0199 (0.0807) |
0.494 (0.641) |
0.323 (0.499) |
0.412 (0.579) |
7q gain | 150 (37%) | 258 |
1e-05 (0.000178) |
0.12 (0.255) |
0.279 (0.455) |
0.815 (0.876) |
0.931 (0.958) |
0.662 (0.779) |
0.234 (0.402) |
0.208 (0.37) |
0.803 (0.869) |
0.0024 (0.0166) |
12p gain | 115 (28%) | 293 |
0.00466 (0.0269) |
0.0647 (0.172) |
0.757 (0.837) |
0.53 (0.67) |
0.705 (0.803) |
0.828 (0.884) |
0.728 (0.819) |
0.0235 (0.0898) |
0.303 (0.479) |
0.129 (0.268) |
12q gain | 92 (23%) | 316 |
0.0707 (0.179) |
0.227 (0.397) |
0.0737 (0.185) |
0.0218 (0.0854) |
0.382 (0.552) |
0.127 (0.265) |
0.674 (0.786) |
0.0885 (0.212) |
0.964 (0.974) |
0.0304 (0.106) |
13q gain | 100 (25%) | 308 |
0.0298 (0.104) |
0.658 (0.777) |
0.951 (0.965) |
0.812 (0.873) |
0.319 (0.494) |
0.469 (0.627) |
0.775 (0.847) |
0.824 (0.881) |
0.376 (0.549) |
0.025 (0.0936) |
15q gain | 35 (9%) | 373 |
0.0579 (0.162) |
0.00011 (0.00125) |
0.707 (0.804) |
0.579 (0.716) |
0.336 (0.511) |
0.0318 (0.109) |
0.0743 (0.186) |
0.616 (0.748) |
0.146 (0.29) |
0.0557 (0.159) |
7p loss | 21 (5%) | 387 |
0.0862 (0.207) |
0.464 (0.625) |
0.685 (0.791) |
0.637 (0.762) |
0.409 (0.578) |
0.157 (0.308) |
0.0981 (0.227) |
0.0436 (0.133) |
0.0477 (0.141) |
0.0685 (0.177) |
8q loss | 38 (9%) | 370 |
0.00282 (0.0186) |
0.617 (0.748) |
0.52 (0.661) |
0.276 (0.455) |
0.0366 (0.118) |
0.782 (0.852) |
0.12 (0.255) |
0.28 (0.455) |
0.368 (0.543) |
0.384 (0.552) |
10p loss | 74 (18%) | 334 |
0.0199 (0.0807) |
0.069 (0.177) |
0.867 (0.912) |
0.443 (0.606) |
0.00319 (0.0201) |
0.204 (0.366) |
0.409 (0.578) |
0.108 (0.238) |
0.193 (0.351) |
0.398 (0.565) |
16p loss | 107 (26%) | 301 |
1e-05 (0.000178) |
0.0569 (0.16) |
0.73 (0.821) |
0.817 (0.876) |
0.254 (0.429) |
0.201 (0.363) |
0.518 (0.661) |
0.137 (0.278) |
0.0776 (0.191) |
0.0196 (0.0807) |
18p loss | 99 (24%) | 309 |
0.0183 (0.0786) |
0.0899 (0.214) |
0.344 (0.517) |
0.297 (0.471) |
0.978 (0.982) |
0.028 (0.103) |
0.0747 (0.186) |
0.655 (0.776) |
0.0698 (0.178) |
0.175 (0.331) |
19q loss | 57 (14%) | 351 |
0.00075 (0.00654) |
0.336 (0.511) |
0.204 (0.366) |
0.0936 (0.221) |
0.416 (0.583) |
0.137 (0.278) |
0.0729 (0.184) |
0.628 (0.759) |
0.266 (0.442) |
0.019 (0.0801) |
1q gain | 128 (31%) | 280 |
1e-05 (0.000178) |
0.687 (0.791) |
0.644 (0.767) |
0.909 (0.94) |
0.782 (0.852) |
0.863 (0.911) |
0.375 (0.549) |
0.77 (0.846) |
0.49 (0.639) |
0.538 (0.675) |
6p gain | 78 (19%) | 330 |
0.00065 (0.00573) |
0.481 (0.634) |
0.807 (0.871) |
0.335 (0.511) |
0.871 (0.915) |
0.638 (0.762) |
0.786 (0.854) |
0.881 (0.923) |
0.19 (0.349) |
0.172 (0.327) |
16p gain | 74 (18%) | 334 |
0.0488 (0.143) |
0.129 (0.267) |
0.609 (0.742) |
0.14 (0.282) |
0.396 (0.564) |
0.153 (0.302) |
0.514 (0.66) |
0.206 (0.368) |
0.675 (0.786) |
0.384 (0.552) |
16q gain | 83 (20%) | 325 |
0.0363 (0.118) |
0.0518 (0.15) |
0.478 (0.634) |
0.096 (0.223) |
0.377 (0.549) |
0.111 (0.243) |
0.147 (0.292) |
0.0745 (0.186) |
0.453 (0.616) |
0.125 (0.263) |
17p gain | 58 (14%) | 350 |
0.00096 (0.00812) |
0.0559 (0.159) |
0.429 (0.593) |
0.417 (0.583) |
0.629 (0.759) |
0.163 (0.315) |
0.324 (0.499) |
0.71 (0.806) |
0.532 (0.672) |
0.181 (0.339) |
19p gain | 87 (21%) | 321 |
0.00295 (0.019) |
0.0969 (0.224) |
0.543 (0.68) |
0.599 (0.732) |
0.107 (0.238) |
0.0955 (0.223) |
0.508 (0.654) |
0.378 (0.55) |
0.182 (0.34) |
0.864 (0.911) |
22q gain | 49 (12%) | 359 |
0.102 (0.232) |
0.0571 (0.16) |
0.488 (0.637) |
0.524 (0.665) |
0.00884 (0.0439) |
0.132 (0.272) |
0.146 (0.29) |
0.572 (0.708) |
0.18 (0.338) |
0.235 (0.404) |
1p loss | 34 (8%) | 374 |
0.132 (0.272) |
0.0449 (0.136) |
0.516 (0.661) |
0.733 (0.823) |
0.444 (0.607) |
0.168 (0.322) |
0.233 (0.402) |
0.666 (0.779) |
0.29 (0.463) |
0.481 (0.634) |
2p loss | 45 (11%) | 363 |
0.0769 (0.19) |
0.0861 (0.207) |
1 (1.00) |
0.888 (0.928) |
0.292 (0.465) |
0.0279 (0.103) |
0.519 (0.661) |
0.933 (0.958) |
0.191 (0.35) |
0.214 (0.376) |
3q loss | 24 (6%) | 384 |
0.101 (0.23) |
0.263 (0.44) |
0.28 (0.455) |
0.418 (0.583) |
0.376 (0.549) |
0.48 (0.634) |
0.767 (0.843) |
0.13 (0.269) |
0.00112 (0.009) |
0.117 (0.252) |
7q loss | 27 (7%) | 381 |
0.00154 (0.0118) |
0.479 (0.634) |
0.632 (0.76) |
0.611 (0.743) |
0.937 (0.958) |
0.82 (0.878) |
0.103 (0.232) |
0.084 (0.204) |
0.36 (0.535) |
0.119 (0.254) |
12q loss | 60 (15%) | 348 |
2e-05 (0.000309) |
0.566 (0.704) |
0.684 (0.791) |
0.775 (0.847) |
0.667 (0.779) |
0.52 (0.661) |
0.803 (0.869) |
0.547 (0.685) |
0.667 (0.779) |
0.127 (0.265) |
17q loss | 43 (11%) | 365 |
0.0407 (0.128) |
0.487 (0.637) |
0.952 (0.965) |
0.979 (0.982) |
0.731 (0.821) |
0.937 (0.958) |
0.746 (0.829) |
0.912 (0.941) |
0.646 (0.767) |
0.56 (0.699) |
20p loss | 33 (8%) | 375 |
0.209 (0.37) |
0.103 (0.232) |
0.251 (0.426) |
0.0365 (0.118) |
0.945 (0.961) |
0.718 (0.81) |
0.797 (0.864) |
0.956 (0.967) |
0.4 (0.568) |
0.308 (0.48) |
xp loss | 71 (17%) | 337 |
0.186 (0.344) |
0.0607 (0.167) |
0.655 (0.776) |
0.675 (0.786) |
0.107 (0.238) |
0.717 (0.81) |
0.311 (0.484) |
0.447 (0.61) |
0.278 (0.455) |
0.0454 (0.137) |
xq gain | 47 (12%) | 361 |
0.068 (0.177) |
0.381 (0.552) |
0.691 (0.791) |
0.599 (0.732) |
0.0561 (0.159) |
0.784 (0.853) |
0.228 (0.397) |
0.192 (0.35) |
0.411 (0.579) |
0.421 (0.586) |
1q loss | 34 (8%) | 374 |
0.233 (0.402) |
0.0797 (0.196) |
0.665 (0.779) |
0.744 (0.829) |
0.441 (0.605) |
0.221 (0.387) |
0.894 (0.931) |
0.209 (0.37) |
0.712 (0.807) |
0.165 (0.317) |
20q loss | 14 (3%) | 394 |
0.0919 (0.218) |
0.474 (0.631) |
0.739 (0.825) |
0.462 (0.625) |
0.783 (0.853) |
0.941 (0.959) |
0.466 (0.626) |
0.343 (0.517) |
0.595 (0.73) |
0.937 (0.958) |
P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S1. Gene #1: '1p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
1P GAIN MUTATED | 15 | 50 | 13 | 12 |
1P GAIN WILD-TYPE | 154 | 90 | 46 | 28 |
Figure S1. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0225 (Fisher's exact test), Q value = 0.087
Table S2. Gene #1: '1p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
1P GAIN MUTATED | 27 | 35 | 8 | 20 |
1P GAIN WILD-TYPE | 111 | 81 | 61 | 65 |
Figure S2. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0286 (Fisher's exact test), Q value = 0.1
Table S3. Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
1P GAIN MUTATED | 16 | 11 | 28 | 12 | 1 | 22 |
1P GAIN WILD-TYPE | 58 | 35 | 65 | 54 | 30 | 62 |
Figure S3. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S4. Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
1Q GAIN MUTATED | 32 | 62 | 16 | 18 |
1Q GAIN WILD-TYPE | 137 | 78 | 43 | 22 |
Figure S4. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S5. Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
2P GAIN MUTATED | 14 | 64 | 12 | 21 |
2P GAIN WILD-TYPE | 155 | 76 | 47 | 19 |
Figure S5. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S6. Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
2P GAIN MUTATED | 27 | 56 | 11 | 17 |
2P GAIN WILD-TYPE | 111 | 60 | 58 | 68 |
Figure S6. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.081
Table S7. Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
2P GAIN MUTATED | 44 | 26 | 41 |
2P GAIN WILD-TYPE | 74 | 86 | 133 |
Figure S7. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00812 (Fisher's exact test), Q value = 0.042
Table S8. Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 89 | 99 | 93 | 70 | 54 |
2P GAIN MUTATED | 23 | 32 | 15 | 28 | 12 |
2P GAIN WILD-TYPE | 66 | 67 | 78 | 42 | 42 |
Figure S8. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00146 (Fisher's exact test), Q value = 0.011
Table S9. Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
2P GAIN MUTATED | 17 | 19 | 35 | 18 | 2 | 17 |
2P GAIN WILD-TYPE | 57 | 27 | 58 | 48 | 29 | 67 |
Figure S9. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S10. Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
2Q GAIN MUTATED | 9 | 31 | 5 | 12 |
2Q GAIN WILD-TYPE | 160 | 109 | 54 | 28 |
Figure S10. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00184 (Fisher's exact test), Q value = 0.014
Table S11. Gene #4: '2q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
2Q GAIN MUTATED | 12 | 29 | 7 | 9 |
2Q GAIN WILD-TYPE | 126 | 87 | 62 | 76 |
Figure S11. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00096
Table S12. Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
3P GAIN MUTATED | 40 | 63 | 18 | 21 |
3P GAIN WILD-TYPE | 129 | 77 | 41 | 19 |
Figure S12. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0485 (Fisher's exact test), Q value = 0.14
Table S13. Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
3P GAIN MUTATED | 39 | 52 | 24 | 27 |
3P GAIN WILD-TYPE | 99 | 64 | 45 | 58 |
Figure S13. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00869 (Fisher's exact test), Q value = 0.044
Table S14. Gene #5: '3p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 180 | 108 |
3P GAIN MUTATED | 42 | 73 | 25 |
3P GAIN WILD-TYPE | 74 | 107 | 83 |
Figure S14. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.081
Table S15. Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
3P GAIN MUTATED | 51 | 41 | 48 |
3P GAIN WILD-TYPE | 67 | 71 | 126 |
Figure S15. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.0305 (Fisher's exact test), Q value = 0.11
Table S16. Gene #5: '3p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 120 | 96 | 189 |
3P GAIN MUTATED | 40 | 44 | 57 |
3P GAIN WILD-TYPE | 80 | 52 | 132 |
Figure S16. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 0.086
Table S17. Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 98 | 43 | 134 | 119 |
3P GAIN MUTATED | 28 | 23 | 41 | 45 |
3P GAIN WILD-TYPE | 70 | 20 | 93 | 74 |
Figure S17. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0036
Table S18. Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
3P GAIN MUTATED | 27 | 24 | 37 | 24 | 2 | 23 |
3P GAIN WILD-TYPE | 47 | 22 | 56 | 42 | 29 | 61 |
Figure S18. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S19. Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
3Q GAIN MUTATED | 50 | 81 | 22 | 25 |
3Q GAIN WILD-TYPE | 119 | 59 | 37 | 15 |
Figure S19. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0341 (Fisher's exact test), Q value = 0.11
Table S20. Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 120 | 96 | 189 |
3Q GAIN MUTATED | 49 | 53 | 75 |
3Q GAIN WILD-TYPE | 71 | 43 | 114 |
Figure S20. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 0.0287 (Fisher's exact test), Q value = 0.1
Table S21. Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 89 | 99 | 93 | 70 | 54 |
3Q GAIN MUTATED | 39 | 52 | 28 | 32 | 26 |
3Q GAIN WILD-TYPE | 50 | 47 | 65 | 38 | 28 |
Figure S21. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.0329 (Fisher's exact test), Q value = 0.11
Table S22. Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 98 | 43 | 134 | 119 |
3Q GAIN MUTATED | 37 | 27 | 53 | 54 |
3Q GAIN WILD-TYPE | 61 | 16 | 81 | 65 |
Figure S22. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00042
Table S23. Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
3Q GAIN MUTATED | 30 | 28 | 49 | 32 | 3 | 29 |
3Q GAIN WILD-TYPE | 44 | 18 | 44 | 34 | 28 | 55 |
Figure S23. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00241 (Fisher's exact test), Q value = 0.017
Table S24. Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
4P GAIN MUTATED | 7 | 23 | 4 | 4 |
4P GAIN WILD-TYPE | 162 | 117 | 55 | 36 |
Figure S24. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00873 (Fisher's exact test), Q value = 0.044
Table S25. Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
4P GAIN MUTATED | 7 | 20 | 4 | 7 |
4P GAIN WILD-TYPE | 131 | 96 | 65 | 78 |
Figure S25. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00797 (Fisher's exact test), Q value = 0.041
Table S26. Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 180 | 108 |
4P GAIN MUTATED | 7 | 26 | 5 |
4P GAIN WILD-TYPE | 109 | 154 | 103 |
Figure S26. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.048
Table S27. Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
4P GAIN MUTATED | 11 | 18 | 9 |
4P GAIN WILD-TYPE | 107 | 94 | 165 |
Figure S27. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.0122 (Fisher's exact test), Q value = 0.057
Table S28. Gene #7: '4p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 120 | 96 | 189 |
4P GAIN MUTATED | 4 | 13 | 21 |
4P GAIN WILD-TYPE | 116 | 83 | 168 |
Figure S28. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 0.00187 (Fisher's exact test), Q value = 0.014
Table S29. Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
4Q GAIN MUTATED | 6 | 17 | 0 | 3 |
4Q GAIN WILD-TYPE | 163 | 123 | 59 | 37 |
Figure S29. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.081
Table S30. Gene #8: '4q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 120 | 96 | 189 |
4Q GAIN MUTATED | 2 | 9 | 15 |
4Q GAIN WILD-TYPE | 118 | 87 | 174 |
Figure S30. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S31. Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
5P GAIN MUTATED | 36 | 73 | 36 | 21 |
5P GAIN WILD-TYPE | 133 | 67 | 23 | 19 |
Figure S31. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0398 (Fisher's exact test), Q value = 0.13
Table S32. Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
5P GAIN MUTATED | 65 | 44 | 19 | 38 |
5P GAIN WILD-TYPE | 73 | 72 | 50 | 47 |
Figure S32. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0354 (Fisher's exact test), Q value = 0.12
Table S33. Gene #9: '5p gain' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 37 | 29 | 34 | 5 | 19 |
5P GAIN MUTATED | 11 | 7 | 18 | 0 | 9 |
5P GAIN WILD-TYPE | 26 | 22 | 16 | 5 | 10 |
Figure S33. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.004
Table S34. Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
5P GAIN MUTATED | 34 | 41 | 89 |
5P GAIN WILD-TYPE | 84 | 71 | 85 |
Figure S34. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00281 (Fisher's exact test), Q value = 0.019
Table S35. Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 89 | 99 | 93 | 70 | 54 |
5P GAIN MUTATED | 40 | 49 | 22 | 32 | 22 |
5P GAIN WILD-TYPE | 49 | 50 | 71 | 38 | 32 |
Figure S35. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00462 (Fisher's exact test), Q value = 0.027
Table S36. Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
5P GAIN MUTATED | 23 | 20 | 39 | 31 | 5 | 44 |
5P GAIN WILD-TYPE | 51 | 26 | 54 | 35 | 26 | 40 |
Figure S36. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00557 (Fisher's exact test), Q value = 0.031
Table S37. Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
5Q GAIN MUTATED | 12 | 20 | 11 | 10 |
5Q GAIN WILD-TYPE | 157 | 120 | 48 | 30 |
Figure S37. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00894 (Fisher's exact test), Q value = 0.044
Table S38. Gene #10: '5q gain' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 37 | 29 | 34 | 5 | 19 |
5Q GAIN MUTATED | 4 | 1 | 10 | 0 | 0 |
5Q GAIN WILD-TYPE | 33 | 28 | 24 | 5 | 19 |
Figure S38. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

P value = 0.0362 (Fisher's exact test), Q value = 0.12
Table S39. Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
5Q GAIN MUTATED | 7 | 5 | 11 | 13 | 0 | 16 |
5Q GAIN WILD-TYPE | 67 | 41 | 82 | 53 | 31 | 68 |
Figure S39. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00065 (Fisher's exact test), Q value = 0.0057
Table S40. Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
6P GAIN MUTATED | 17 | 35 | 17 | 9 |
6P GAIN WILD-TYPE | 152 | 105 | 42 | 31 |
Figure S40. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0414 (Fisher's exact test), Q value = 0.13
Table S41. Gene #12: '6q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 42 | 38 | 26 | 18 |
6Q GAIN MUTATED | 1 | 1 | 4 | 3 |
6Q GAIN WILD-TYPE | 41 | 37 | 22 | 15 |
Figure S41. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

P value = 0.0442 (Fisher's exact test), Q value = 0.13
Table S42. Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 98 | 43 | 134 | 119 |
6Q GAIN MUTATED | 13 | 4 | 18 | 5 |
6Q GAIN WILD-TYPE | 85 | 39 | 116 | 114 |
Figure S42. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.0242 (Fisher's exact test), Q value = 0.091
Table S43. Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
6Q GAIN MUTATED | 3 | 5 | 15 | 2 | 3 | 12 |
6Q GAIN WILD-TYPE | 71 | 41 | 78 | 64 | 28 | 72 |
Figure S43. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S44. Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
7P GAIN MUTATED | 36 | 76 | 32 | 27 |
7P GAIN WILD-TYPE | 133 | 64 | 27 | 13 |
Figure S44. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0339 (Fisher's exact test), Q value = 0.11
Table S45. Gene #13: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 37 | 29 | 34 | 5 | 19 |
7P GAIN MUTATED | 19 | 6 | 17 | 1 | 5 |
7P GAIN WILD-TYPE | 18 | 23 | 17 | 4 | 14 |
Figure S45. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

P value = 0.0402 (Fisher's exact test), Q value = 0.13
Table S46. Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 89 | 99 | 93 | 70 | 54 |
7P GAIN MUTATED | 43 | 44 | 28 | 35 | 19 |
7P GAIN WILD-TYPE | 46 | 55 | 65 | 35 | 35 |
Figure S46. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.0013
Table S47. Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
7P GAIN MUTATED | 24 | 16 | 45 | 32 | 3 | 44 |
7P GAIN WILD-TYPE | 50 | 30 | 48 | 34 | 28 | 40 |
Figure S47. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S48. Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
7Q GAIN MUTATED | 39 | 63 | 23 | 25 |
7Q GAIN WILD-TYPE | 130 | 77 | 36 | 15 |
Figure S48. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0024 (Fisher's exact test), Q value = 0.017
Table S49. Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
7Q GAIN MUTATED | 21 | 15 | 42 | 28 | 3 | 35 |
7Q GAIN WILD-TYPE | 53 | 31 | 51 | 38 | 28 | 49 |
Figure S49. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S50. Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
8P GAIN MUTATED | 28 | 27 | 11 | 24 |
8P GAIN WILD-TYPE | 141 | 113 | 48 | 16 |
Figure S50. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0194 (Fisher's exact test), Q value = 0.081
Table S51. Gene #15: '8p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 42 | 38 | 26 | 18 |
8P GAIN MUTATED | 9 | 4 | 11 | 2 |
8P GAIN WILD-TYPE | 33 | 34 | 15 | 16 |
Figure S51. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

P value = 0.016 (Fisher's exact test), Q value = 0.071
Table S52. Gene #15: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 89 | 99 | 93 | 70 | 54 |
8P GAIN MUTATED | 26 | 16 | 19 | 22 | 6 |
8P GAIN WILD-TYPE | 63 | 83 | 74 | 48 | 48 |
Figure S52. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S53. Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
8Q GAIN MUTATED | 64 | 73 | 31 | 35 |
8Q GAIN WILD-TYPE | 105 | 67 | 28 | 5 |
Figure S53. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00926 (Fisher's exact test), Q value = 0.045
Table S54. Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
8Q GAIN MUTATED | 67 | 70 | 24 | 42 |
8Q GAIN WILD-TYPE | 71 | 46 | 45 | 43 |
Figure S54. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0275 (Fisher's exact test), Q value = 0.1
Table S55. Gene #16: '8q gain' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 37 | 29 | 34 | 5 | 19 |
8Q GAIN MUTATED | 17 | 6 | 18 | 4 | 7 |
8Q GAIN WILD-TYPE | 20 | 23 | 16 | 1 | 12 |
Figure S55. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

P value = 0.0358 (Fisher's exact test), Q value = 0.12
Table S56. Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 89 | 99 | 93 | 70 | 54 |
8Q GAIN MUTATED | 47 | 47 | 43 | 45 | 20 |
8Q GAIN WILD-TYPE | 42 | 52 | 50 | 25 | 34 |
Figure S56. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.042 (Fisher's exact test), Q value = 0.13
Table S57. Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
8Q GAIN MUTATED | 31 | 21 | 54 | 36 | 9 | 46 |
8Q GAIN WILD-TYPE | 43 | 25 | 39 | 30 | 22 | 38 |
Figure S57. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S58. Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
9P GAIN MUTATED | 11 | 24 | 25 | 8 |
9P GAIN WILD-TYPE | 158 | 116 | 34 | 32 |
Figure S58. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00054
Table S59. Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 98 | 43 | 134 | 119 |
9P GAIN MUTATED | 32 | 4 | 14 | 15 |
9P GAIN WILD-TYPE | 66 | 39 | 120 | 104 |
Figure S59. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S60. Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
9P GAIN MUTATED | 14 | 5 | 13 | 2 | 1 | 30 |
9P GAIN WILD-TYPE | 60 | 41 | 80 | 64 | 30 | 54 |
Figure S60. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.0022
Table S61. Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
9Q GAIN MUTATED | 12 | 21 | 18 | 5 |
9Q GAIN WILD-TYPE | 157 | 119 | 41 | 35 |
Figure S61. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.084
Table S62. Gene #18: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
9Q GAIN MUTATED | 28 | 12 | 4 | 12 |
9Q GAIN WILD-TYPE | 110 | 104 | 65 | 73 |
Figure S62. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00682 (Fisher's exact test), Q value = 0.037
Table S63. Gene #18: '9q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 42 | 38 | 26 | 18 |
9Q GAIN MUTATED | 1 | 6 | 5 | 6 |
9Q GAIN WILD-TYPE | 41 | 32 | 21 | 12 |
Figure S63. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

P value = 0.00229 (Fisher's exact test), Q value = 0.016
Table S64. Gene #18: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 180 | 108 |
9Q GAIN MUTATED | 16 | 14 | 24 |
9Q GAIN WILD-TYPE | 100 | 166 | 84 |
Figure S64. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.003
Table S65. Gene #18: '9q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
9Q GAIN MUTATED | 7 | 10 | 37 |
9Q GAIN WILD-TYPE | 111 | 102 | 137 |
Figure S65. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.0032
Table S66. Gene #18: '9q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 98 | 43 | 134 | 119 |
9Q GAIN MUTATED | 26 | 3 | 10 | 14 |
9Q GAIN WILD-TYPE | 72 | 40 | 124 | 105 |
Figure S66. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S67. Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
9Q GAIN MUTATED | 10 | 5 | 10 | 2 | 0 | 26 |
9Q GAIN WILD-TYPE | 64 | 41 | 83 | 64 | 31 | 58 |
Figure S67. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S68. Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
10P GAIN MUTATED | 15 | 60 | 19 | 22 |
10P GAIN WILD-TYPE | 154 | 80 | 40 | 18 |
Figure S68. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00503 (Fisher's exact test), Q value = 0.029
Table S69. Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
10P GAIN MUTATED | 34 | 48 | 15 | 19 |
10P GAIN WILD-TYPE | 104 | 68 | 54 | 66 |
Figure S69. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00245 (Fisher's exact test), Q value = 0.017
Table S70. Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
10P GAIN MUTATED | 48 | 24 | 44 |
10P GAIN WILD-TYPE | 70 | 88 | 130 |
Figure S70. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.048
Table S71. Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
10P GAIN MUTATED | 23 | 14 | 30 | 23 | 1 | 21 |
10P GAIN WILD-TYPE | 51 | 32 | 63 | 43 | 30 | 63 |
Figure S71. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.0036
Table S72. Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
10Q GAIN MUTATED | 7 | 24 | 6 | 8 |
10Q GAIN WILD-TYPE | 162 | 116 | 53 | 32 |
Figure S72. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.1
Table S73. Gene #20: '10q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
10Q GAIN MUTATED | 21 | 10 | 14 |
10Q GAIN WILD-TYPE | 97 | 102 | 160 |
Figure S73. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.0291 (Fisher's exact test), Q value = 0.1
Table S74. Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
10Q GAIN MUTATED | 9 | 7 | 13 | 11 | 0 | 4 |
10Q GAIN WILD-TYPE | 65 | 39 | 80 | 55 | 31 | 80 |
Figure S74. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00076
Table S75. Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
11P GAIN MUTATED | 6 | 5 | 12 | 5 |
11P GAIN WILD-TYPE | 163 | 135 | 47 | 35 |
Figure S75. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00662 (Fisher's exact test), Q value = 0.036
Table S76. Gene #21: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
11P GAIN MUTATED | 5 | 3 | 20 |
11P GAIN WILD-TYPE | 113 | 109 | 154 |
Figure S76. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00224 (Fisher's exact test), Q value = 0.016
Table S77. Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 98 | 43 | 134 | 119 |
11P GAIN MUTATED | 16 | 1 | 6 | 5 |
11P GAIN WILD-TYPE | 82 | 42 | 128 | 114 |
Figure S77. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 0.076
Table S78. Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
11P GAIN MUTATED | 3 | 1 | 4 | 5 | 1 | 14 |
11P GAIN WILD-TYPE | 71 | 45 | 89 | 61 | 30 | 70 |
Figure S78. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00592 (Fisher's exact test), Q value = 0.033
Table S79. Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
11Q GAIN MUTATED | 10 | 19 | 11 | 8 |
11Q GAIN WILD-TYPE | 159 | 121 | 48 | 32 |
Figure S79. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.1
Table S80. Gene #22: '11q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 42 | 38 | 26 | 18 |
11Q GAIN MUTATED | 4 | 2 | 2 | 6 |
11Q GAIN WILD-TYPE | 38 | 36 | 24 | 12 |
Figure S80. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

P value = 0.0326 (Fisher's exact test), Q value = 0.11
Table S81. Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 98 | 43 | 134 | 119 |
11Q GAIN MUTATED | 20 | 6 | 11 | 11 |
11Q GAIN WILD-TYPE | 78 | 37 | 123 | 108 |
Figure S81. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.00466 (Fisher's exact test), Q value = 0.027
Table S82. Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
12P GAIN MUTATED | 32 | 50 | 19 | 14 |
12P GAIN WILD-TYPE | 137 | 90 | 40 | 26 |
Figure S82. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 0.09
Table S83. Gene #23: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 89 | 99 | 93 | 70 | 54 |
12P GAIN MUTATED | 27 | 29 | 17 | 29 | 13 |
12P GAIN WILD-TYPE | 62 | 70 | 76 | 41 | 41 |
Figure S83. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 0.085
Table S84. Gene #24: '12q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 42 | 38 | 26 | 18 |
12Q GAIN MUTATED | 15 | 3 | 7 | 5 |
12Q GAIN WILD-TYPE | 27 | 35 | 19 | 13 |
Figure S84. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

P value = 0.0304 (Fisher's exact test), Q value = 0.11
Table S85. Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
12Q GAIN MUTATED | 11 | 12 | 26 | 23 | 6 | 13 |
12Q GAIN WILD-TYPE | 63 | 34 | 67 | 43 | 25 | 71 |
Figure S85. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0298 (Fisher's exact test), Q value = 0.1
Table S86. Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
13Q GAIN MUTATED | 29 | 41 | 18 | 12 |
13Q GAIN WILD-TYPE | 140 | 99 | 41 | 28 |
Figure S86. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 0.094
Table S87. Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
13Q GAIN MUTATED | 20 | 10 | 32 | 18 | 2 | 16 |
13Q GAIN WILD-TYPE | 54 | 36 | 61 | 48 | 29 | 68 |
Figure S87. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00087
Table S88. Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
14Q GAIN MUTATED | 14 | 16 | 14 | 14 |
14Q GAIN WILD-TYPE | 155 | 124 | 45 | 26 |
Figure S88. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0464 (Fisher's exact test), Q value = 0.14
Table S89. Gene #26: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
14Q GAIN MUTATED | 21 | 20 | 3 | 14 |
14Q GAIN WILD-TYPE | 117 | 96 | 66 | 71 |
Figure S89. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0433 (Fisher's exact test), Q value = 0.13
Table S90. Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 180 | 108 |
14Q GAIN MUTATED | 18 | 17 | 21 |
14Q GAIN WILD-TYPE | 98 | 163 | 87 |
Figure S90. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 0.0424 (Fisher's exact test), Q value = 0.13
Table S91. Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
14Q GAIN MUTATED | 12 | 11 | 33 |
14Q GAIN WILD-TYPE | 106 | 101 | 141 |
Figure S91. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.0013
Table S92. Gene #27: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
15Q GAIN MUTATED | 4 | 6 | 14 | 11 |
15Q GAIN WILD-TYPE | 134 | 110 | 55 | 74 |
Figure S92. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0318 (Fisher's exact test), Q value = 0.11
Table S93. Gene #27: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
15Q GAIN MUTATED | 14 | 13 | 8 |
15Q GAIN WILD-TYPE | 104 | 99 | 166 |
Figure S93. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.0488 (Fisher's exact test), Q value = 0.14
Table S94. Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
16P GAIN MUTATED | 24 | 36 | 9 | 5 |
16P GAIN WILD-TYPE | 145 | 104 | 50 | 35 |
Figure S94. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.12
Table S95. Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
16Q GAIN MUTATED | 27 | 40 | 10 | 6 |
16Q GAIN WILD-TYPE | 142 | 100 | 49 | 34 |
Figure S95. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.0081
Table S96. Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
17P GAIN MUTATED | 12 | 31 | 11 | 4 |
17P GAIN WILD-TYPE | 157 | 109 | 48 | 36 |
Figure S96. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00311 (Fisher's exact test), Q value = 0.02
Table S97. Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
17Q GAIN MUTATED | 42 | 58 | 17 | 19 |
17Q GAIN WILD-TYPE | 127 | 82 | 42 | 21 |
Figure S97. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.11
Table S98. Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
17Q GAIN MUTATED | 36 | 50 | 20 | 30 |
17Q GAIN WILD-TYPE | 102 | 66 | 49 | 55 |
Figure S98. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0406 (Fisher's exact test), Q value = 0.13
Table S99. Gene #31: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 180 | 108 |
17Q GAIN MUTATED | 31 | 72 | 32 |
17Q GAIN WILD-TYPE | 85 | 108 | 76 |
Figure S99. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 0.00279 (Fisher's exact test), Q value = 0.019
Table S100. Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
17Q GAIN MUTATED | 18 | 21 | 42 | 22 | 4 | 25 |
17Q GAIN WILD-TYPE | 56 | 25 | 51 | 44 | 27 | 59 |
Figure S100. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S101. Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
18P GAIN MUTATED | 16 | 54 | 31 | 16 |
18P GAIN WILD-TYPE | 153 | 86 | 28 | 24 |
Figure S101. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00384 (Fisher's exact test), Q value = 0.023
Table S102. Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
18P GAIN MUTATED | 42 | 43 | 9 | 23 |
18P GAIN WILD-TYPE | 96 | 73 | 60 | 62 |
Figure S102. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0204 (Fisher's exact test), Q value = 0.082
Table S103. Gene #32: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
18P GAIN MUTATED | 29 | 25 | 63 |
18P GAIN WILD-TYPE | 89 | 87 | 111 |
Figure S103. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00054
Table S104. Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
18P GAIN MUTATED | 15 | 10 | 36 | 21 | 0 | 30 |
18P GAIN WILD-TYPE | 59 | 36 | 57 | 45 | 31 | 54 |
Figure S104. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00428 (Fisher's exact test), Q value = 0.025
Table S105. Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
18Q GAIN MUTATED | 14 | 26 | 14 | 9 |
18Q GAIN WILD-TYPE | 155 | 114 | 45 | 31 |
Figure S105. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0386 (Fisher's exact test), Q value = 0.12
Table S106. Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 120 | 96 | 189 |
18Q GAIN MUTATED | 15 | 9 | 38 |
18Q GAIN WILD-TYPE | 105 | 87 | 151 |
Figure S106. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 0.00704 (Fisher's exact test), Q value = 0.038
Table S107. Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
18Q GAIN MUTATED | 7 | 4 | 17 | 16 | 0 | 15 |
18Q GAIN WILD-TYPE | 67 | 42 | 76 | 50 | 31 | 69 |
Figure S107. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00295 (Fisher's exact test), Q value = 0.019
Table S108. Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
19P GAIN MUTATED | 24 | 44 | 11 | 8 |
19P GAIN WILD-TYPE | 145 | 96 | 48 | 32 |
Figure S108. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S109. Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
19Q GAIN MUTATED | 34 | 68 | 15 | 17 |
19Q GAIN WILD-TYPE | 135 | 72 | 44 | 23 |
Figure S109. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00401 (Fisher's exact test), Q value = 0.024
Table S110. Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
19Q GAIN MUTATED | 32 | 52 | 23 | 27 |
19Q GAIN WILD-TYPE | 106 | 64 | 46 | 58 |
Figure S110. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0205 (Fisher's exact test), Q value = 0.082
Table S111. Gene #35: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 89 | 99 | 93 | 70 | 54 |
19Q GAIN MUTATED | 27 | 34 | 20 | 31 | 22 |
19Q GAIN WILD-TYPE | 62 | 65 | 73 | 39 | 32 |
Figure S111. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S112. Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
20P GAIN MUTATED | 59 | 79 | 36 | 27 |
20P GAIN WILD-TYPE | 110 | 61 | 23 | 13 |
Figure S112. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.061
Table S113. Gene #36: '20p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 42 | 38 | 26 | 18 |
20P GAIN MUTATED | 14 | 26 | 14 | 11 |
20P GAIN WILD-TYPE | 28 | 12 | 12 | 7 |
Figure S113. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

P value = 0.0428 (Fisher's exact test), Q value = 0.13
Table S114. Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
20P GAIN MUTATED | 69 | 47 | 84 |
20P GAIN WILD-TYPE | 49 | 65 | 90 |
Figure S114. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031
Table S115. Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
20Q GAIN MUTATED | 69 | 92 | 39 | 29 |
20Q GAIN WILD-TYPE | 100 | 48 | 20 | 11 |
Figure S115. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 0.1
Table S116. Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
20Q GAIN MUTATED | 71 | 77 | 32 | 49 |
20Q GAIN WILD-TYPE | 67 | 39 | 37 | 36 |
Figure S116. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0239 (Fisher's exact test), Q value = 0.091
Table S117. Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
20Q GAIN MUTATED | 42 | 28 | 61 | 38 | 9 | 47 |
20Q GAIN WILD-TYPE | 32 | 18 | 32 | 28 | 22 | 37 |
Figure S117. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S118. Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
21Q GAIN MUTATED | 19 | 70 | 15 | 11 |
21Q GAIN WILD-TYPE | 150 | 70 | 44 | 29 |
Figure S118. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S119. Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
21Q GAIN MUTATED | 25 | 54 | 16 | 20 |
21Q GAIN WILD-TYPE | 113 | 62 | 53 | 65 |
Figure S119. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00263 (Fisher's exact test), Q value = 0.018
Table S120. Gene #38: '21q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 180 | 108 |
21Q GAIN MUTATED | 31 | 65 | 19 |
21Q GAIN WILD-TYPE | 85 | 115 | 89 |
Figure S120. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 0.00164 (Fisher's exact test), Q value = 0.012
Table S121. Gene #38: '21q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
21Q GAIN MUTATED | 48 | 30 | 37 |
21Q GAIN WILD-TYPE | 70 | 82 | 137 |
Figure S121. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00754 (Fisher's exact test), Q value = 0.04
Table S122. Gene #38: '21q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 120 | 96 | 189 |
21Q GAIN MUTATED | 28 | 39 | 46 |
21Q GAIN WILD-TYPE | 92 | 57 | 143 |
Figure S122. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 0.00783 (Fisher's exact test), Q value = 0.041
Table S123. Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 89 | 99 | 93 | 70 | 54 |
21Q GAIN MUTATED | 15 | 34 | 20 | 27 | 17 |
21Q GAIN WILD-TYPE | 74 | 65 | 73 | 43 | 37 |
Figure S123. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00884 (Fisher's exact test), Q value = 0.044
Table S124. Gene #39: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 180 | 108 |
22Q GAIN MUTATED | 9 | 32 | 8 |
22Q GAIN WILD-TYPE | 107 | 148 | 100 |
Figure S124. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.0049
Table S125. Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
XP GAIN MUTATED | 16 | 37 | 6 | 7 |
XP GAIN WILD-TYPE | 153 | 103 | 53 | 33 |
Figure S125. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00101 (Fisher's exact test), Q value = 0.0083
Table S126. Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
XP GAIN MUTATED | 10 | 29 | 10 | 17 |
XP GAIN WILD-TYPE | 128 | 87 | 59 | 68 |
Figure S126. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00804 (Fisher's exact test), Q value = 0.041
Table S127. Gene #40: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 180 | 108 |
XP GAIN MUTATED | 12 | 41 | 13 |
XP GAIN WILD-TYPE | 104 | 139 | 95 |
Figure S127. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.085
Table S128. Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 98 | 43 | 134 | 119 |
XP GAIN MUTATED | 12 | 9 | 32 | 13 |
XP GAIN WILD-TYPE | 86 | 34 | 102 | 106 |
Figure S128. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.0449 (Fisher's exact test), Q value = 0.14
Table S129. Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
1P LOSS MUTATED | 8 | 15 | 8 | 3 |
1P LOSS WILD-TYPE | 130 | 101 | 61 | 82 |
Figure S129. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0279 (Fisher's exact test), Q value = 0.1
Table S130. Gene #44: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
2P LOSS MUTATED | 14 | 18 | 11 |
2P LOSS WILD-TYPE | 104 | 94 | 163 |
Figure S130. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00118 (Fisher's exact test), Q value = 0.0094
Table S131. Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
2Q LOSS MUTATED | 22 | 40 | 19 | 10 |
2Q LOSS WILD-TYPE | 147 | 100 | 40 | 30 |
Figure S131. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 0.09
Table S132. Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
2Q LOSS MUTATED | 22 | 36 | 12 | 21 |
2Q LOSS WILD-TYPE | 116 | 80 | 57 | 64 |
Figure S132. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0314 (Fisher's exact test), Q value = 0.11
Table S133. Gene #45: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
2Q LOSS MUTATED | 29 | 32 | 28 |
2Q LOSS WILD-TYPE | 89 | 80 | 146 |
Figure S133. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.051
Table S134. Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 98 | 43 | 134 | 119 |
2Q LOSS MUTATED | 12 | 13 | 38 | 23 |
2Q LOSS WILD-TYPE | 86 | 30 | 96 | 96 |
Figure S134. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.00519 (Fisher's exact test), Q value = 0.029
Table S135. Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
2Q LOSS MUTATED | 14 | 15 | 30 | 13 | 2 | 12 |
2Q LOSS WILD-TYPE | 60 | 31 | 63 | 53 | 29 | 72 |
Figure S135. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0332 (Fisher's exact test), Q value = 0.11
Table S136. Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
3P LOSS MUTATED | 27 | 10 | 5 | 11 |
3P LOSS WILD-TYPE | 111 | 106 | 64 | 74 |
Figure S136. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0455 (Fisher's exact test), Q value = 0.14
Table S137. Gene #46: '3p loss' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 37 | 29 | 34 | 5 | 19 |
3P LOSS MUTATED | 2 | 4 | 10 | 0 | 5 |
3P LOSS WILD-TYPE | 35 | 25 | 24 | 5 | 14 |
Figure S137. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S138. Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 180 | 108 |
3P LOSS MUTATED | 5 | 13 | 34 |
3P LOSS WILD-TYPE | 111 | 167 | 74 |
Figure S138. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031
Table S139. Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
3P LOSS MUTATED | 5 | 8 | 39 |
3P LOSS WILD-TYPE | 113 | 104 | 135 |
Figure S139. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00424 (Fisher's exact test), Q value = 0.025
Table S140. Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 89 | 99 | 93 | 70 | 54 |
3P LOSS MUTATED | 22 | 9 | 7 | 11 | 4 |
3P LOSS WILD-TYPE | 67 | 90 | 86 | 59 | 50 |
Figure S140. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.0036
Table S141. Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 98 | 43 | 134 | 119 |
3P LOSS MUTATED | 25 | 3 | 15 | 8 |
3P LOSS WILD-TYPE | 73 | 40 | 119 | 111 |
Figure S141. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.0015 (Fisher's exact test), Q value = 0.012
Table S142. Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
3P LOSS MUTATED | 2 | 4 | 15 | 10 | 1 | 19 |
3P LOSS WILD-TYPE | 72 | 42 | 78 | 56 | 30 | 65 |
Figure S142. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00112 (Fisher's exact test), Q value = 0.009
Table S143. Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 98 | 43 | 134 | 119 |
3Q LOSS MUTATED | 13 | 3 | 7 | 1 |
3Q LOSS WILD-TYPE | 85 | 40 | 127 | 118 |
Figure S143. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S144. Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
4P LOSS MUTATED | 28 | 60 | 33 | 22 |
4P LOSS WILD-TYPE | 141 | 80 | 26 | 18 |
Figure S144. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00615 (Fisher's exact test), Q value = 0.034
Table S145. Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 180 | 108 |
4P LOSS MUTATED | 46 | 48 | 47 |
4P LOSS WILD-TYPE | 70 | 132 | 61 |
Figure S145. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.0011
Table S146. Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
4P LOSS MUTATED | 49 | 21 | 71 |
4P LOSS WILD-TYPE | 69 | 91 | 103 |
Figure S146. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.0337 (Fisher's exact test), Q value = 0.11
Table S147. Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 120 | 96 | 189 |
4P LOSS MUTATED | 48 | 40 | 54 |
4P LOSS WILD-TYPE | 72 | 56 | 135 |
Figure S147. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 0.00945 (Fisher's exact test), Q value = 0.046
Table S148. Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 89 | 99 | 93 | 70 | 54 |
4P LOSS MUTATED | 37 | 42 | 19 | 25 | 19 |
4P LOSS WILD-TYPE | 52 | 57 | 74 | 45 | 35 |
Figure S148. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 0.064
Table S149. Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 98 | 43 | 134 | 119 |
4P LOSS MUTATED | 42 | 18 | 33 | 45 |
4P LOSS WILD-TYPE | 56 | 25 | 101 | 74 |
Figure S149. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S150. Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
4Q LOSS MUTATED | 25 | 57 | 35 | 19 |
4Q LOSS WILD-TYPE | 144 | 83 | 24 | 21 |
Figure S150. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.038 (Fisher's exact test), Q value = 0.12
Table S151. Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 180 | 108 |
4Q LOSS MUTATED | 40 | 49 | 45 |
4Q LOSS WILD-TYPE | 76 | 131 | 63 |
Figure S151. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 0.00099 (Fisher's exact test), Q value = 0.0083
Table S152. Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
4Q LOSS MUTATED | 46 | 22 | 66 |
4Q LOSS WILD-TYPE | 72 | 90 | 108 |
Figure S152. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.04 (Fisher's exact test), Q value = 0.13
Table S153. Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 89 | 99 | 93 | 70 | 54 |
4Q LOSS MUTATED | 37 | 35 | 20 | 27 | 17 |
4Q LOSS WILD-TYPE | 52 | 64 | 73 | 43 | 37 |
Figure S153. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00197 (Fisher's exact test), Q value = 0.014
Table S154. Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 98 | 43 | 134 | 119 |
4Q LOSS MUTATED | 43 | 13 | 29 | 45 |
4Q LOSS WILD-TYPE | 55 | 30 | 105 | 74 |
Figure S154. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.00287 (Fisher's exact test), Q value = 0.019
Table S155. Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
4Q LOSS MUTATED | 22 | 15 | 28 | 28 | 2 | 35 |
4Q LOSS WILD-TYPE | 52 | 31 | 65 | 38 | 29 | 49 |
Figure S155. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.0013
Table S156. Gene #50: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
5P LOSS MUTATED | 15 | 29 | 9 | 3 |
5P LOSS WILD-TYPE | 123 | 87 | 60 | 82 |
Figure S156. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.003
Table S157. Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
5P LOSS MUTATED | 29 | 14 | 13 |
5P LOSS WILD-TYPE | 89 | 98 | 161 |
Figure S157. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.0176 (Fisher's exact test), Q value = 0.076
Table S158. Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 98 | 43 | 134 | 119 |
5P LOSS MUTATED | 8 | 11 | 14 | 21 |
5P LOSS WILD-TYPE | 90 | 32 | 120 | 98 |
Figure S158. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.01 (Fisher's exact test), Q value = 0.048
Table S159. Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
5P LOSS MUTATED | 15 | 11 | 13 | 8 | 0 | 7 |
5P LOSS WILD-TYPE | 59 | 35 | 80 | 58 | 31 | 77 |
Figure S159. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S160. Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
5Q LOSS MUTATED | 37 | 77 | 26 | 19 |
5Q LOSS WILD-TYPE | 132 | 63 | 33 | 21 |
Figure S160. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.011
Table S161. Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
5Q LOSS MUTATED | 52 | 61 | 17 | 29 |
5Q LOSS WILD-TYPE | 86 | 55 | 52 | 56 |
Figure S161. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0168 (Fisher's exact test), Q value = 0.073
Table S162. Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
5Q LOSS MUTATED | 59 | 39 | 60 |
5Q LOSS WILD-TYPE | 59 | 73 | 114 |
Figure S162. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.0188 (Fisher's exact test), Q value = 0.08
Table S163. Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 89 | 99 | 93 | 70 | 54 |
5Q LOSS MUTATED | 33 | 44 | 24 | 34 | 24 |
5Q LOSS WILD-TYPE | 56 | 55 | 69 | 36 | 30 |
Figure S163. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00785 (Fisher's exact test), Q value = 0.041
Table S164. Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
5Q LOSS MUTATED | 27 | 24 | 42 | 31 | 5 | 27 |
5Q LOSS WILD-TYPE | 47 | 22 | 51 | 35 | 26 | 57 |
Figure S164. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00065
Table S165. Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
6P LOSS MUTATED | 24 | 51 | 12 | 13 |
6P LOSS WILD-TYPE | 145 | 89 | 47 | 27 |
Figure S165. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.079
Table S166. Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
6P LOSS MUTATED | 23 | 39 | 18 | 20 |
6P LOSS WILD-TYPE | 115 | 77 | 51 | 65 |
Figure S166. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.12
Table S167. Gene #52: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
6P LOSS MUTATED | 36 | 31 | 32 |
6P LOSS WILD-TYPE | 82 | 81 | 142 |
Figure S167. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.0471 (Fisher's exact test), Q value = 0.14
Table S168. Gene #52: '6p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 120 | 96 | 189 |
6P LOSS MUTATED | 26 | 33 | 41 |
6P LOSS WILD-TYPE | 94 | 63 | 148 |
Figure S168. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 0.00463 (Fisher's exact test), Q value = 0.027
Table S169. Gene #52: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 89 | 99 | 93 | 70 | 54 |
6P LOSS MUTATED | 17 | 32 | 13 | 25 | 13 |
6P LOSS WILD-TYPE | 72 | 67 | 80 | 45 | 41 |
Figure S169. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00096
Table S170. Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
6P LOSS MUTATED | 15 | 19 | 32 | 19 | 1 | 12 |
6P LOSS WILD-TYPE | 59 | 27 | 61 | 47 | 30 | 72 |
Figure S170. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S171. Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
6Q LOSS MUTATED | 34 | 83 | 20 | 22 |
6Q LOSS WILD-TYPE | 135 | 57 | 39 | 18 |
Figure S171. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.061
Table S172. Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
6Q LOSS MUTATED | 43 | 59 | 25 | 32 |
6Q LOSS WILD-TYPE | 95 | 57 | 44 | 53 |
Figure S172. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0472 (Fisher's exact test), Q value = 0.14
Table S173. Gene #53: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
6Q LOSS MUTATED | 57 | 42 | 59 |
6Q LOSS WILD-TYPE | 61 | 70 | 115 |
Figure S173. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00286 (Fisher's exact test), Q value = 0.019
Table S174. Gene #53: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 89 | 99 | 93 | 70 | 54 |
6Q LOSS MUTATED | 30 | 48 | 23 | 34 | 23 |
6Q LOSS WILD-TYPE | 59 | 51 | 70 | 36 | 31 |
Figure S174. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00065
Table S175. Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
6Q LOSS MUTATED | 26 | 25 | 46 | 31 | 2 | 26 |
6Q LOSS WILD-TYPE | 48 | 21 | 47 | 35 | 29 | 58 |
Figure S175. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0436 (Fisher's exact test), Q value = 0.13
Table S176. Gene #54: '7p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 89 | 99 | 93 | 70 | 54 |
7P LOSS MUTATED | 2 | 9 | 4 | 6 | 0 |
7P LOSS WILD-TYPE | 87 | 90 | 89 | 64 | 54 |
Figure S176. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.0477 (Fisher's exact test), Q value = 0.14
Table S177. Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 98 | 43 | 134 | 119 |
7P LOSS MUTATED | 4 | 6 | 8 | 3 |
7P LOSS WILD-TYPE | 94 | 37 | 126 | 116 |
Figure S177. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.00154 (Fisher's exact test), Q value = 0.012
Table S178. Gene #55: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
7Q LOSS MUTATED | 3 | 16 | 6 | 2 |
7Q LOSS WILD-TYPE | 166 | 124 | 53 | 38 |
Figure S178. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S179. Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
8P LOSS MUTATED | 48 | 94 | 38 | 8 |
8P LOSS WILD-TYPE | 121 | 46 | 21 | 32 |
Figure S179. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00596 (Fisher's exact test), Q value = 0.033
Table S180. Gene #56: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
8P LOSS MUTATED | 67 | 66 | 24 | 31 |
8P LOSS WILD-TYPE | 71 | 50 | 45 | 54 |
Figure S180. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0219 (Fisher's exact test), Q value = 0.085
Table S181. Gene #56: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
8P LOSS MUTATED | 62 | 40 | 86 |
8P LOSS WILD-TYPE | 56 | 72 | 88 |
Figure S181. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.0294 (Fisher's exact test), Q value = 0.1
Table S182. Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 89 | 99 | 93 | 70 | 54 |
8P LOSS MUTATED | 35 | 57 | 34 | 33 | 27 |
8P LOSS WILD-TYPE | 54 | 42 | 59 | 37 | 27 |
Figure S182. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00342 (Fisher's exact test), Q value = 0.021
Table S183. Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
8P LOSS MUTATED | 34 | 27 | 48 | 26 | 5 | 42 |
8P LOSS WILD-TYPE | 40 | 19 | 45 | 40 | 26 | 42 |
Figure S183. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00282 (Fisher's exact test), Q value = 0.019
Table S184. Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
8Q LOSS MUTATED | 10 | 22 | 6 | 0 |
8Q LOSS WILD-TYPE | 159 | 118 | 53 | 40 |
Figure S184. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0366 (Fisher's exact test), Q value = 0.12
Table S185. Gene #57: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 180 | 108 |
8Q LOSS MUTATED | 18 | 13 | 7 |
8Q LOSS WILD-TYPE | 98 | 167 | 101 |
Figure S185. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S186. Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
9P LOSS MUTATED | 79 | 73 | 3 | 20 |
9P LOSS WILD-TYPE | 90 | 67 | 56 | 20 |
Figure S186. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.0011
Table S187. Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
9P LOSS MUTATED | 37 | 61 | 34 | 43 |
9P LOSS WILD-TYPE | 101 | 55 | 35 | 42 |
Figure S187. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 9e-04 (Fisher's exact test), Q value = 0.0077
Table S188. Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 180 | 108 |
9P LOSS MUTATED | 44 | 96 | 35 |
9P LOSS WILD-TYPE | 72 | 84 | 73 |
Figure S188. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031
Table S189. Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
9P LOSS MUTATED | 63 | 60 | 52 |
9P LOSS WILD-TYPE | 55 | 52 | 122 |
Figure S189. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.0295 (Fisher's exact test), Q value = 0.1
Table S190. Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 120 | 96 | 189 |
9P LOSS MUTATED | 42 | 51 | 82 |
9P LOSS WILD-TYPE | 78 | 45 | 107 |
Figure S190. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 0.00101 (Fisher's exact test), Q value = 0.0083
Table S191. Gene #58: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 89 | 99 | 93 | 70 | 54 |
9P LOSS MUTATED | 26 | 48 | 37 | 43 | 21 |
9P LOSS WILD-TYPE | 63 | 51 | 56 | 27 | 33 |
Figure S191. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00042
Table S192. Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 98 | 43 | 134 | 119 |
9P LOSS MUTATED | 23 | 25 | 70 | 53 |
9P LOSS WILD-TYPE | 75 | 18 | 64 | 66 |
Figure S192. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S193. Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
9P LOSS MUTATED | 24 | 25 | 43 | 39 | 21 | 19 |
9P LOSS WILD-TYPE | 50 | 21 | 50 | 27 | 10 | 65 |
Figure S193. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S194. Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
9Q LOSS MUTATED | 79 | 65 | 4 | 22 |
9Q LOSS WILD-TYPE | 90 | 75 | 55 | 18 |
Figure S194. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S195. Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
9Q LOSS MUTATED | 33 | 57 | 37 | 43 |
9Q LOSS WILD-TYPE | 105 | 59 | 32 | 42 |
Figure S195. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.067
Table S196. Gene #59: '9q loss' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 37 | 29 | 34 | 5 | 19 |
9Q LOSS MUTATED | 21 | 12 | 8 | 3 | 4 |
9Q LOSS WILD-TYPE | 16 | 17 | 26 | 2 | 15 |
Figure S196. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

P value = 0.00499 (Fisher's exact test), Q value = 0.029
Table S197. Gene #59: '9q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 42 | 38 | 26 | 18 |
9Q LOSS MUTATED | 24 | 14 | 8 | 2 |
9Q LOSS WILD-TYPE | 18 | 24 | 18 | 16 |
Figure S197. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00042
Table S198. Gene #59: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 180 | 108 |
9Q LOSS MUTATED | 39 | 100 | 31 |
9Q LOSS WILD-TYPE | 77 | 80 | 77 |
Figure S198. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S199. Gene #59: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
9Q LOSS MUTATED | 62 | 65 | 43 |
9Q LOSS WILD-TYPE | 56 | 47 | 131 |
Figure S199. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.0193 (Fisher's exact test), Q value = 0.081
Table S200. Gene #59: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 120 | 96 | 189 |
9Q LOSS MUTATED | 39 | 49 | 82 |
9Q LOSS WILD-TYPE | 81 | 47 | 107 |
Figure S200. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.0053
Table S201. Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 89 | 99 | 93 | 70 | 54 |
9Q LOSS MUTATED | 22 | 43 | 40 | 41 | 24 |
9Q LOSS WILD-TYPE | 67 | 56 | 53 | 29 | 30 |
Figure S201. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S202. Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 98 | 43 | 134 | 119 |
9Q LOSS MUTATED | 17 | 25 | 76 | 49 |
9Q LOSS WILD-TYPE | 81 | 18 | 58 | 70 |
Figure S202. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S203. Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
9Q LOSS MUTATED | 28 | 24 | 43 | 35 | 25 | 12 |
9Q LOSS WILD-TYPE | 46 | 22 | 50 | 31 | 6 | 72 |
Figure S203. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0199 (Fisher's exact test), Q value = 0.081
Table S204. Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
10P LOSS MUTATED | 20 | 34 | 14 | 6 |
10P LOSS WILD-TYPE | 149 | 106 | 45 | 34 |
Figure S204. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00319 (Fisher's exact test), Q value = 0.02
Table S205. Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 180 | 108 |
10P LOSS MUTATED | 10 | 35 | 27 |
10P LOSS WILD-TYPE | 106 | 145 | 81 |
Figure S205. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S206. Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
10Q LOSS MUTATED | 23 | 68 | 24 | 13 |
10Q LOSS WILD-TYPE | 146 | 72 | 35 | 27 |
Figure S206. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0026
Table S207. Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
10Q LOSS MUTATED | 30 | 52 | 16 | 30 |
10Q LOSS WILD-TYPE | 108 | 64 | 53 | 55 |
Figure S207. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.057
Table S208. Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 180 | 108 |
10Q LOSS MUTATED | 24 | 66 | 35 |
10Q LOSS WILD-TYPE | 92 | 114 | 73 |
Figure S208. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S209. Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
11P LOSS MUTATED | 58 | 90 | 11 | 22 |
11P LOSS WILD-TYPE | 111 | 50 | 48 | 18 |
Figure S209. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S210. Gene #62: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
11P LOSS MUTATED | 33 | 67 | 39 | 42 |
11P LOSS WILD-TYPE | 105 | 49 | 30 | 43 |
Figure S210. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00054
Table S211. Gene #62: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 180 | 108 |
11P LOSS MUTATED | 41 | 101 | 37 |
11P LOSS WILD-TYPE | 75 | 79 | 71 |
Figure S211. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031
Table S212. Gene #62: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
11P LOSS MUTATED | 64 | 62 | 53 |
11P LOSS WILD-TYPE | 54 | 50 | 121 |
Figure S212. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.0014
Table S213. Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 98 | 43 | 134 | 119 |
11P LOSS MUTATED | 25 | 23 | 70 | 57 |
11P LOSS WILD-TYPE | 73 | 20 | 64 | 62 |
Figure S213. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0046
Table S214. Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
11P LOSS MUTATED | 29 | 24 | 49 | 37 | 15 | 21 |
11P LOSS WILD-TYPE | 45 | 22 | 44 | 29 | 16 | 63 |
Figure S214. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S215. Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
11Q LOSS MUTATED | 36 | 63 | 12 | 20 |
11Q LOSS WILD-TYPE | 133 | 77 | 47 | 20 |
Figure S215. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.022 (Fisher's exact test), Q value = 0.086
Table S216. Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
11Q LOSS MUTATED | 32 | 44 | 21 | 34 |
11Q LOSS WILD-TYPE | 106 | 72 | 48 | 51 |
Figure S216. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0285 (Fisher's exact test), Q value = 0.1
Table S217. Gene #63: '11q loss' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 37 | 29 | 34 | 5 | 19 |
11Q LOSS MUTATED | 16 | 6 | 15 | 1 | 2 |
11Q LOSS WILD-TYPE | 21 | 23 | 19 | 4 | 17 |
Figure S217. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

P value = 0.00466 (Fisher's exact test), Q value = 0.027
Table S218. Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
12P LOSS MUTATED | 12 | 29 | 9 | 6 |
12P LOSS WILD-TYPE | 157 | 111 | 50 | 34 |
Figure S218. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00317 (Fisher's exact test), Q value = 0.02
Table S219. Gene #64: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
12P LOSS MUTATED | 10 | 25 | 13 | 8 |
12P LOSS WILD-TYPE | 128 | 91 | 56 | 77 |
Figure S219. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.071
Table S220. Gene #64: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
12P LOSS MUTATED | 25 | 14 | 16 |
12P LOSS WILD-TYPE | 93 | 98 | 158 |
Figure S220. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.0287 (Fisher's exact test), Q value = 0.1
Table S221. Gene #64: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 98 | 43 | 134 | 119 |
12P LOSS MUTATED | 7 | 11 | 21 | 16 |
12P LOSS WILD-TYPE | 91 | 32 | 113 | 103 |
Figure S221. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031
Table S222. Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
12Q LOSS MUTATED | 10 | 25 | 16 | 9 |
12Q LOSS WILD-TYPE | 159 | 115 | 43 | 31 |
Figure S222. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S223. Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
13Q LOSS MUTATED | 15 | 42 | 17 | 12 |
13Q LOSS WILD-TYPE | 154 | 98 | 42 | 28 |
Figure S223. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.065
Table S224. Gene #66: '13q loss' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 37 | 29 | 34 | 5 | 19 |
13Q LOSS MUTATED | 8 | 5 | 16 | 0 | 2 |
13Q LOSS WILD-TYPE | 29 | 24 | 18 | 5 | 17 |
Figure S224. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.079
Table S225. Gene #66: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 180 | 108 |
13Q LOSS MUTATED | 20 | 31 | 33 |
13Q LOSS WILD-TYPE | 96 | 149 | 75 |
Figure S225. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00042
Table S226. Gene #66: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 89 | 99 | 93 | 70 | 54 |
13Q LOSS MUTATED | 28 | 29 | 8 | 18 | 3 |
13Q LOSS WILD-TYPE | 61 | 70 | 85 | 52 | 51 |
Figure S226. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.0108 (Fisher's exact test), Q value = 0.051
Table S227. Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 98 | 43 | 134 | 119 |
13Q LOSS MUTATED | 32 | 11 | 24 | 18 |
13Q LOSS WILD-TYPE | 66 | 32 | 110 | 101 |
Figure S227. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.0072
Table S228. Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
13Q LOSS MUTATED | 6 | 14 | 21 | 13 | 3 | 28 |
13Q LOSS WILD-TYPE | 68 | 32 | 72 | 53 | 28 | 56 |
Figure S228. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S229. Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
14Q LOSS MUTATED | 29 | 75 | 11 | 7 |
14Q LOSS WILD-TYPE | 140 | 65 | 48 | 33 |
Figure S229. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031
Table S230. Gene #67: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
14Q LOSS MUTATED | 34 | 53 | 24 | 11 |
14Q LOSS WILD-TYPE | 104 | 63 | 45 | 74 |
Figure S230. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0497 (Fisher's exact test), Q value = 0.15
Table S231. Gene #67: '14q loss' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 37 | 29 | 34 | 5 | 19 |
14Q LOSS MUTATED | 13 | 2 | 9 | 2 | 6 |
14Q LOSS WILD-TYPE | 24 | 27 | 25 | 3 | 13 |
Figure S231. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.068
Table S232. Gene #67: '14q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 42 | 38 | 26 | 18 |
14Q LOSS MUTATED | 16 | 4 | 5 | 7 |
14Q LOSS WILD-TYPE | 26 | 34 | 21 | 11 |
Figure S232. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.0016
Table S233. Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
14Q LOSS MUTATED | 53 | 31 | 37 |
14Q LOSS WILD-TYPE | 65 | 81 | 137 |
Figure S233. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00063 (Fisher's exact test), Q value = 0.0056
Table S234. Gene #67: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 120 | 96 | 189 |
14Q LOSS MUTATED | 32 | 44 | 45 |
14Q LOSS WILD-TYPE | 88 | 52 | 144 |
Figure S234. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.091
Table S235. Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 89 | 99 | 93 | 70 | 54 |
14Q LOSS MUTATED | 21 | 39 | 19 | 25 | 17 |
14Q LOSS WILD-TYPE | 68 | 60 | 74 | 45 | 37 |
Figure S235. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00237 (Fisher's exact test), Q value = 0.017
Table S236. Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 98 | 43 | 134 | 119 |
14Q LOSS MUTATED | 23 | 22 | 32 | 42 |
14Q LOSS WILD-TYPE | 75 | 21 | 102 | 77 |
Figure S236. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031
Table S237. Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
14Q LOSS MUTATED | 19 | 22 | 33 | 28 | 1 | 16 |
14Q LOSS WILD-TYPE | 55 | 24 | 60 | 38 | 30 | 68 |
Figure S237. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S238. Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
15Q LOSS MUTATED | 23 | 76 | 32 | 14 |
15Q LOSS WILD-TYPE | 146 | 64 | 27 | 26 |
Figure S238. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S239. Gene #68: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
15Q LOSS MUTATED | 59 | 57 | 9 | 20 |
15Q LOSS WILD-TYPE | 79 | 59 | 60 | 65 |
Figure S239. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00899 (Fisher's exact test), Q value = 0.044
Table S240. Gene #68: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 120 | 96 | 189 |
15Q LOSS MUTATED | 40 | 47 | 58 |
15Q LOSS WILD-TYPE | 80 | 49 | 131 |
Figure S240. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S241. Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 89 | 99 | 93 | 70 | 54 |
15Q LOSS MUTATED | 29 | 50 | 17 | 34 | 15 |
15Q LOSS WILD-TYPE | 60 | 49 | 76 | 36 | 39 |
Figure S241. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00646 (Fisher's exact test), Q value = 0.035
Table S242. Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 98 | 43 | 134 | 119 |
15Q LOSS MUTATED | 41 | 24 | 40 | 36 |
15Q LOSS WILD-TYPE | 57 | 19 | 94 | 83 |
Figure S242. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0013
Table S243. Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
15Q LOSS MUTATED | 23 | 24 | 37 | 21 | 1 | 35 |
15Q LOSS WILD-TYPE | 51 | 22 | 56 | 45 | 30 | 49 |
Figure S243. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S244. Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
16P LOSS MUTATED | 16 | 41 | 36 | 14 |
16P LOSS WILD-TYPE | 153 | 99 | 23 | 26 |
Figure S244. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.081
Table S245. Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
16P LOSS MUTATED | 16 | 11 | 25 | 14 | 3 | 33 |
16P LOSS WILD-TYPE | 58 | 35 | 68 | 52 | 28 | 51 |
Figure S245. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S246. Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
16Q LOSS MUTATED | 9 | 44 | 32 | 18 |
16Q LOSS WILD-TYPE | 160 | 96 | 27 | 22 |
Figure S246. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.081
Table S247. Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
16Q LOSS MUTATED | 31 | 41 | 11 | 20 |
16Q LOSS WILD-TYPE | 107 | 75 | 58 | 65 |
Figure S247. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00354 (Fisher's exact test), Q value = 0.022
Table S248. Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
16Q LOSS MUTATED | 11 | 14 | 29 | 13 | 2 | 28 |
16Q LOSS WILD-TYPE | 63 | 32 | 64 | 53 | 29 | 56 |
Figure S248. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0025
Table S249. Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
17P LOSS MUTATED | 58 | 72 | 23 | 27 |
17P LOSS WILD-TYPE | 111 | 68 | 36 | 13 |
Figure S249. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.036 (Fisher's exact test), Q value = 0.12
Table S250. Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 89 | 99 | 93 | 70 | 54 |
17P LOSS MUTATED | 44 | 40 | 30 | 38 | 26 |
17P LOSS WILD-TYPE | 45 | 59 | 63 | 32 | 28 |
Figure S250. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00384 (Fisher's exact test), Q value = 0.023
Table S251. Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
17P LOSS MUTATED | 28 | 20 | 45 | 40 | 6 | 35 |
17P LOSS WILD-TYPE | 46 | 26 | 48 | 26 | 25 | 49 |
Figure S251. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0407 (Fisher's exact test), Q value = 0.13
Table S252. Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
17Q LOSS MUTATED | 10 | 22 | 7 | 4 |
17Q LOSS WILD-TYPE | 159 | 118 | 52 | 36 |
Figure S252. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0183 (Fisher's exact test), Q value = 0.079
Table S253. Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
18P LOSS MUTATED | 36 | 46 | 8 | 9 |
18P LOSS WILD-TYPE | 133 | 94 | 51 | 31 |
Figure S253. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.1
Table S254. Gene #73: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
18P LOSS MUTATED | 38 | 27 | 32 |
18P LOSS WILD-TYPE | 80 | 85 | 142 |
Figure S254. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00179 (Fisher's exact test), Q value = 0.013
Table S255. Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
18Q LOSS MUTATED | 44 | 66 | 21 | 15 |
18Q LOSS WILD-TYPE | 125 | 74 | 38 | 25 |
Figure S255. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0465 (Fisher's exact test), Q value = 0.14
Table S256. Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
18Q LOSS MUTATED | 53 | 37 | 54 |
18Q LOSS WILD-TYPE | 65 | 75 | 120 |
Figure S256. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.0029
Table S257. Gene #74: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 120 | 96 | 189 |
18Q LOSS MUTATED | 42 | 51 | 53 |
18Q LOSS WILD-TYPE | 78 | 45 | 136 |
Figure S257. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0044
Table S258. Gene #74: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 89 | 99 | 93 | 70 | 54 |
18Q LOSS MUTATED | 24 | 53 | 26 | 27 | 16 |
18Q LOSS WILD-TYPE | 65 | 46 | 67 | 43 | 38 |
Figure S258. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.033 (Fisher's exact test), Q value = 0.11
Table S259. Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 98 | 43 | 134 | 119 |
18Q LOSS MUTATED | 29 | 23 | 45 | 49 |
18Q LOSS WILD-TYPE | 69 | 20 | 89 | 70 |
Figure S259. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00042
Table S260. Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
19P LOSS MUTATED | 22 | 44 | 10 | 18 |
19P LOSS WILD-TYPE | 147 | 96 | 49 | 22 |
Figure S260. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.046 (Fisher's exact test), Q value = 0.14
Table S261. Gene #75: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
19P LOSS MUTATED | 35 | 33 | 8 | 18 |
19P LOSS WILD-TYPE | 103 | 83 | 61 | 67 |
Figure S261. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00723 (Fisher's exact test), Q value = 0.038
Table S262. Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
19P LOSS MUTATED | 32 | 14 | 46 |
19P LOSS WILD-TYPE | 86 | 98 | 128 |
Figure S262. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00075 (Fisher's exact test), Q value = 0.0065
Table S263. Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
19Q LOSS MUTATED | 11 | 25 | 10 | 11 |
19Q LOSS WILD-TYPE | 158 | 115 | 49 | 29 |
Figure S263. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.019 (Fisher's exact test), Q value = 0.08
Table S264. Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
19Q LOSS MUTATED | 8 | 6 | 17 | 5 | 0 | 17 |
19Q LOSS WILD-TYPE | 66 | 40 | 76 | 61 | 31 | 67 |
Figure S264. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0365 (Fisher's exact test), Q value = 0.12
Table S265. Gene #77: '20p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 42 | 38 | 26 | 18 |
20P LOSS MUTATED | 6 | 0 | 2 | 3 |
20P LOSS WILD-TYPE | 36 | 38 | 24 | 15 |
Figure S265. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

P value = 0.00189 (Fisher's exact test), Q value = 0.014
Table S266. Gene #79: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 180 | 108 |
21Q LOSS MUTATED | 17 | 28 | 34 |
21Q LOSS WILD-TYPE | 99 | 152 | 74 |
Figure S266. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.05
Table S267. Gene #79: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
21Q LOSS MUTATED | 14 | 20 | 45 |
21Q LOSS WILD-TYPE | 104 | 92 | 129 |
Figure S267. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00824 (Fisher's exact test), Q value = 0.042
Table S268. Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 98 | 43 | 134 | 119 |
21Q LOSS MUTATED | 31 | 6 | 21 | 18 |
21Q LOSS WILD-TYPE | 67 | 37 | 113 | 101 |
Figure S268. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.0268 (Fisher's exact test), Q value = 0.1
Table S269. Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
21Q LOSS MUTATED | 12 | 8 | 15 | 12 | 2 | 27 |
21Q LOSS WILD-TYPE | 62 | 38 | 78 | 54 | 29 | 57 |
Figure S269. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S270. Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 169 | 140 | 59 | 40 |
22Q LOSS MUTATED | 24 | 73 | 44 | 18 |
22Q LOSS WILD-TYPE | 145 | 67 | 15 | 22 |
Figure S270. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.081
Table S271. Gene #80: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
22Q LOSS MUTATED | 62 | 48 | 16 | 33 |
22Q LOSS WILD-TYPE | 76 | 68 | 53 | 52 |
Figure S271. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.073
Table S272. Gene #80: '22q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 42 | 38 | 26 | 18 |
22Q LOSS MUTATED | 12 | 22 | 6 | 7 |
22Q LOSS WILD-TYPE | 30 | 16 | 20 | 11 |
Figure S272. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

P value = 0.00879 (Fisher's exact test), Q value = 0.044
Table S273. Gene #80: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 180 | 108 |
22Q LOSS MUTATED | 50 | 55 | 51 |
22Q LOSS WILD-TYPE | 66 | 125 | 57 |
Figure S273. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.0084
Table S274. Gene #80: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 112 | 174 |
22Q LOSS MUTATED | 44 | 29 | 83 |
22Q LOSS WILD-TYPE | 74 | 83 | 91 |
Figure S274. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00397 (Fisher's exact test), Q value = 0.024
Table S275. Gene #80: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 89 | 99 | 93 | 70 | 54 |
22Q LOSS MUTATED | 39 | 47 | 21 | 29 | 22 |
22Q LOSS WILD-TYPE | 50 | 52 | 72 | 41 | 32 |
Figure S275. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018
Table S276. Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
22Q LOSS MUTATED | 23 | 13 | 45 | 30 | 1 | 42 |
22Q LOSS WILD-TYPE | 51 | 33 | 48 | 36 | 30 | 42 |
Figure S276. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0454 (Fisher's exact test), Q value = 0.14
Table S277. Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
XP LOSS MUTATED | 8 | 4 | 21 | 16 | 8 | 11 |
XP LOSS WILD-TYPE | 66 | 42 | 72 | 50 | 23 | 73 |
Figure S277. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00076
Table S278. Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 138 | 116 | 69 | 85 |
XQ LOSS MUTATED | 12 | 32 | 12 | 24 |
XQ LOSS WILD-TYPE | 126 | 84 | 57 | 61 |
Figure S278. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.036 (Fisher's exact test), Q value = 0.12
Table S279. Gene #82: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 120 | 96 | 189 |
XQ LOSS MUTATED | 15 | 19 | 46 |
XQ LOSS WILD-TYPE | 105 | 77 | 143 |
Figure S279. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 0.00171 (Fisher's exact test), Q value = 0.013
Table S280. Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 98 | 43 | 134 | 119 |
XQ LOSS MUTATED | 10 | 10 | 39 | 18 |
XQ LOSS WILD-TYPE | 88 | 33 | 95 | 101 |
Figure S280. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.01 (Fisher's exact test), Q value = 0.048
Table S281. Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 74 | 46 | 93 | 66 | 31 | 84 |
XQ LOSS MUTATED | 8 | 9 | 28 | 13 | 9 | 10 |
XQ LOSS WILD-TYPE | 66 | 37 | 65 | 53 | 22 | 74 |
Figure S281. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

-
Copy number data file = broad_values_by_arm.txt from GISTIC pipeline
-
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BLCA-TP/15082909/transformed.cor.cli.txt
-
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BLCA-TP/15111049/BLCA-TP.transferedmergedcluster.txt
-
Number of patients = 408
-
Number of significantly arm-level cnvs = 82
-
Number of molecular subtypes = 10
-
Exclude genes that fewer than K tumors have mutations, K = 3
For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.