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 12 molecular subtypes across 616 patients, 349 significant findings detected with P value < 0.05 and Q value < 0.25.
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1p gain cnv correlated to 'RPPA_CNMF'.
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1q gain cnv correlated to 'CN_CNMF'.
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2p gain cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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2q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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3p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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3q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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4p gain cnv correlated to 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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4q gain cnv correlated to 'CN_CNMF'.
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5p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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5q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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6p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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6q gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.
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7p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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7q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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8p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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8q gain cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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9p gain cnv correlated to 'CN_CNMF'.
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9q gain cnv correlated to 'CN_CNMF'.
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10p gain cnv correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.
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10q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
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11p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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11q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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12p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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12q gain cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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13q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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14q gain cnv correlated to 'CN_CNMF'.
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15q gain cnv correlated to 'MRNA_CHIERARCHICAL'.
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16p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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16q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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17q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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18p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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18q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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19p gain cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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19q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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20p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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20q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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21q gain cnv correlated to 'CN_CNMF'.
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22q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
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xp gain cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CNMF'.
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xq gain cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.
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1p loss cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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1q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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2p loss cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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2q loss cnv correlated to 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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3p loss cnv correlated to 'CN_CNMF'.
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3q loss cnv correlated to 'CN_CNMF'.
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4p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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4q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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5p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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5q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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6p loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'MRNASEQ_CHIERARCHICAL'.
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8p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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8q loss cnv correlated to 'CN_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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9p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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9q loss cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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10p loss cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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10q loss cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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11p loss cnv correlated to 'CN_CNMF'.
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11q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
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12p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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12q loss cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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13q loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.
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14q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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15q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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16p loss cnv correlated to 'CN_CNMF'.
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16q loss cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.
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17p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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17q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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18p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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18q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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19p loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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19q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
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20p loss cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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20q loss cnv correlated to 'RPPA_CNMF'.
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21q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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22q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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xp loss cnv correlated to 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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xq loss cnv correlated to 'RPPA_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 349 significant findings detected.
|
Clinical Features |
MRNA CNMF |
MRNA CHIERARCHICAL |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
||
| nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
| 14q loss | 207 (34%) | 409 |
0.00024 (0.00169) |
3e-05 (0.000278) |
1e-05 (0.000102) |
1e-05 (0.000102) |
0.0961 (0.228) |
0.0313 (0.0957) |
1e-05 (0.000102) |
1e-05 (0.000102) |
0.00183 (0.00995) |
1e-05 (0.000102) |
0.0175 (0.0621) |
0.0183 (0.0629) |
| 7q gain | 312 (51%) | 304 |
0.00021 (0.00151) |
1e-05 (0.000102) |
1e-05 (0.000102) |
0.00988 (0.0389) |
0.0544 (0.149) |
0.00263 (0.0134) |
0.00014 (0.00104) |
1e-05 (0.000102) |
0.00444 (0.0207) |
1e-05 (0.000102) |
0.0482 (0.137) |
0.635 (0.801) |
| 20q gain | 463 (75%) | 153 |
1e-05 (0.000102) |
1e-05 (0.000102) |
1e-05 (0.000102) |
1e-05 (0.000102) |
0.0127 (0.0481) |
0.58 (0.764) |
1e-05 (0.000102) |
1e-05 (0.000102) |
1e-05 (0.000102) |
1e-05 (0.000102) |
9e-05 (0.000708) |
0.126 (0.281) |
| 18p loss | 381 (62%) | 235 |
1e-05 (0.000102) |
1e-05 (0.000102) |
1e-05 (0.000102) |
1e-05 (0.000102) |
0.151 (0.325) |
0.555 (0.747) |
1e-05 (0.000102) |
1e-05 (0.000102) |
1e-05 (0.000102) |
1e-05 (0.000102) |
0.00019 (0.00137) |
8e-05 (0.000645) |
| 18q loss | 408 (66%) | 208 |
1e-05 (0.000102) |
1e-05 (0.000102) |
1e-05 (0.000102) |
1e-05 (0.000102) |
0.146 (0.317) |
0.374 (0.585) |
1e-05 (0.000102) |
1e-05 (0.000102) |
1e-05 (0.000102) |
1e-05 (0.000102) |
0.00224 (0.0117) |
0.00025 (0.00174) |
| 7p gain | 349 (57%) | 267 |
0.00047 (0.0031) |
1e-05 (0.000102) |
1e-05 (0.000102) |
0.00019 (0.00137) |
0.0908 (0.219) |
0.00572 (0.0251) |
2e-05 (0.000193) |
1e-05 (0.000102) |
0.00137 (0.00798) |
1e-05 (0.000102) |
0.0509 (0.143) |
0.264 (0.464) |
| 13q gain | 372 (60%) | 244 |
1e-05 (0.000102) |
1e-05 (0.000102) |
1e-05 (0.000102) |
1e-05 (0.000102) |
0.453 (0.662) |
0.118 (0.269) |
0.00013 (0.000976) |
1e-05 (0.000102) |
1e-05 (0.000102) |
1e-05 (0.000102) |
0.00236 (0.0122) |
0.264 (0.464) |
| 8q gain | 316 (51%) | 300 |
0.146 (0.317) |
0.0385 (0.113) |
1e-05 (0.000102) |
0.00119 (0.00714) |
0.238 (0.435) |
0.0326 (0.0995) |
0.00167 (0.00928) |
0.0168 (0.0606) |
0.306 (0.507) |
0.0127 (0.0481) |
0.00266 (0.0135) |
0.662 (0.824) |
| 17q gain | 113 (18%) | 503 |
0.0047 (0.0214) |
0.0036 (0.0173) |
1e-05 (0.000102) |
0.00957 (0.0381) |
0.264 (0.464) |
0.00746 (0.0308) |
1e-05 (0.000102) |
1e-05 (0.000102) |
0.181 (0.366) |
0.00852 (0.0342) |
0.177 (0.362) |
0.862 (0.951) |
| 20p gain | 353 (57%) | 263 |
0.00031 (0.00213) |
1e-05 (0.000102) |
1e-05 (0.000102) |
0.00724 (0.0302) |
0.063 (0.167) |
0.292 (0.497) |
0.025 (0.0807) |
1e-05 (0.000102) |
0.0621 (0.166) |
1e-05 (0.000102) |
0.0463 (0.132) |
0.451 (0.66) |
| 15q loss | 230 (37%) | 386 |
0.0001 (0.000769) |
3e-05 (0.000278) |
1e-05 (0.000102) |
0.0001 (0.000769) |
0.225 (0.423) |
0.548 (0.745) |
1e-05 (0.000102) |
1e-05 (0.000102) |
0.00155 (0.00872) |
0.00022 (0.00157) |
0.166 (0.346) |
0.259 (0.46) |
| 17p loss | 340 (55%) | 276 |
3e-05 (0.000278) |
2e-05 (0.000193) |
1e-05 (0.000102) |
1e-05 (0.000102) |
0.596 (0.77) |
0.948 (1.00) |
1e-05 (0.000102) |
1e-05 (0.000102) |
0.00065 (0.00418) |
1e-05 (0.000102) |
0.0714 (0.184) |
0.0817 (0.204) |
| 2q gain | 122 (20%) | 494 |
0.045 (0.129) |
0.00104 (0.0064) |
1e-05 (0.000102) |
0.00595 (0.0259) |
0.742 (0.868) |
0.481 (0.682) |
5e-05 (0.000432) |
1e-05 (0.000102) |
0.0896 (0.218) |
0.0243 (0.0787) |
0.426 (0.639) |
0.824 (0.918) |
| 3q gain | 98 (16%) | 518 |
0.0221 (0.0735) |
0.0027 (0.0136) |
1e-05 (0.000102) |
0.0243 (0.0787) |
0.438 (0.647) |
0.591 (0.769) |
0.0841 (0.208) |
0.00333 (0.0161) |
0.0237 (0.0777) |
0.107 (0.249) |
0.0199 (0.0675) |
0.563 (0.747) |
| 11p gain | 85 (14%) | 531 |
0.0065 (0.0278) |
0.00185 (0.01) |
1e-05 (0.000102) |
0.00013 (0.000976) |
0.432 (0.644) |
0.257 (0.457) |
0.00096 (0.00598) |
0.0001 (0.000769) |
0.197 (0.387) |
0.00204 (0.0108) |
0.507 (0.708) |
0.933 (0.997) |
| 11q gain | 78 (13%) | 538 |
0.00697 (0.0292) |
0.00046 (0.00306) |
1e-05 (0.000102) |
2e-05 (0.000193) |
0.314 (0.516) |
0.255 (0.456) |
7e-05 (0.000574) |
1e-05 (0.000102) |
0.773 (0.885) |
0.00142 (0.00817) |
0.0515 (0.144) |
0.462 (0.668) |
| 19q gain | 113 (18%) | 503 |
0.0228 (0.0757) |
0.00299 (0.0148) |
5e-05 (0.000432) |
0.706 (0.85) |
0.0486 (0.138) |
0.51 (0.708) |
0.293 (0.497) |
0.00107 (0.0065) |
0.0417 (0.12) |
0.0123 (0.0475) |
0.055 (0.15) |
0.672 (0.828) |
| 1p loss | 139 (23%) | 477 |
0.155 (0.331) |
0.00686 (0.029) |
1e-05 (0.000102) |
0.0174 (0.0621) |
0.9 (0.975) |
0.978 (1.00) |
9e-05 (0.000708) |
5e-05 (0.000432) |
0.0372 (0.109) |
0.00113 (0.00682) |
0.386 (0.599) |
0.458 (0.666) |
| 4p loss | 197 (32%) | 419 |
0.0409 (0.118) |
0.00194 (0.0103) |
1e-05 (0.000102) |
0.0112 (0.0435) |
0.555 (0.747) |
0.463 (0.668) |
0.00148 (0.00847) |
8e-05 (0.000645) |
0.204 (0.398) |
0.00464 (0.0213) |
0.673 (0.828) |
0.593 (0.769) |
| 4q loss | 191 (31%) | 425 |
0.018 (0.0624) |
0.0158 (0.0577) |
1e-05 (0.000102) |
0.0205 (0.0692) |
0.901 (0.975) |
0.534 (0.733) |
0.00476 (0.0216) |
1e-05 (0.000102) |
0.179 (0.364) |
0.00727 (0.0302) |
0.467 (0.671) |
0.786 (0.895) |
| 5q loss | 120 (19%) | 496 |
0.00435 (0.0205) |
0.00459 (0.0212) |
1e-05 (0.000102) |
0.0163 (0.0593) |
0.407 (0.618) |
0.9 (0.975) |
0.0209 (0.0703) |
0.00155 (0.00872) |
0.243 (0.439) |
0.00235 (0.0122) |
0.924 (0.992) |
0.608 (0.779) |
| 8p loss | 217 (35%) | 399 |
0.0047 (0.0214) |
0.00107 (0.0065) |
1e-05 (0.000102) |
0.0007 (0.00442) |
0.404 (0.616) |
0.974 (1.00) |
0.00353 (0.017) |
6e-05 (0.000505) |
0.181 (0.366) |
0.0299 (0.0921) |
0.0847 (0.208) |
0.673 (0.828) |
| 2p gain | 123 (20%) | 493 |
0.0822 (0.205) |
0.00321 (0.0156) |
1e-05 (0.000102) |
0.00278 (0.0139) |
0.571 (0.755) |
0.763 (0.883) |
1e-05 (0.000102) |
1e-05 (0.000102) |
0.076 (0.194) |
0.00435 (0.0205) |
0.697 (0.847) |
0.991 (1.00) |
| 3p gain | 75 (12%) | 541 |
0.0243 (0.0787) |
0.0253 (0.0814) |
1e-05 (0.000102) |
0.0581 (0.157) |
0.124 (0.277) |
0.676 (0.83) |
0.589 (0.769) |
0.0124 (0.0475) |
0.0185 (0.0632) |
0.022 (0.0735) |
0.0777 (0.197) |
0.586 (0.769) |
| 16p gain | 148 (24%) | 468 |
0.0344 (0.103) |
0.00188 (0.0101) |
1e-05 (0.000102) |
0.0847 (0.208) |
0.0531 (0.146) |
0.289 (0.496) |
0.00068 (0.00434) |
4e-05 (0.000355) |
0.703 (0.847) |
0.0015 (0.00853) |
0.161 (0.34) |
0.236 (0.433) |
| 16q gain | 145 (24%) | 471 |
0.0295 (0.0915) |
0.00046 (0.00306) |
1e-05 (0.000102) |
0.154 (0.328) |
0.12 (0.271) |
0.726 (0.86) |
0.00178 (0.00978) |
4e-05 (0.000355) |
0.444 (0.654) |
0.00183 (0.00995) |
0.171 (0.351) |
0.17 (0.351) |
| 9q loss | 78 (13%) | 538 |
0.124 (0.277) |
0.0238 (0.0777) |
1e-05 (0.000102) |
0.00014 (0.00104) |
0.756 (0.881) |
0.249 (0.448) |
7e-05 (0.000574) |
0.00124 (0.00739) |
0.364 (0.573) |
0.0179 (0.0624) |
0.123 (0.277) |
0.318 (0.521) |
| 20p loss | 65 (11%) | 551 |
0.103 (0.24) |
0.00963 (0.0381) |
1e-05 (0.000102) |
0.00082 (0.00514) |
0.965 (1.00) |
0.561 (0.747) |
0.101 (0.236) |
0.00035 (0.00236) |
0.235 (0.431) |
0.0656 (0.172) |
0.0288 (0.0908) |
0.0405 (0.118) |
| 21q loss | 193 (31%) | 423 |
0.0111 (0.0434) |
0.00253 (0.013) |
1e-05 (0.000102) |
0.105 (0.244) |
0.423 (0.637) |
0.195 (0.385) |
6e-05 (0.000505) |
0.00218 (0.0114) |
0.0844 (0.208) |
0.00798 (0.0326) |
0.167 (0.347) |
0.119 (0.269) |
| 22q loss | 203 (33%) | 413 |
0.00689 (0.029) |
2e-05 (0.000193) |
1e-05 (0.000102) |
0.232 (0.43) |
0.243 (0.439) |
0.58 (0.764) |
0.0489 (0.138) |
1e-05 (0.000102) |
0.178 (0.362) |
0.00139 (0.00805) |
0.454 (0.663) |
0.256 (0.456) |
| 12q gain | 114 (19%) | 502 |
0.0434 (0.124) |
0.168 (0.348) |
0.00837 (0.0338) |
0.0174 (0.0621) |
0.891 (0.97) |
0.397 (0.611) |
0.36 (0.57) |
0.00818 (0.0332) |
0.0183 (0.0629) |
0.379 (0.59) |
0.89 (0.97) |
0.687 (0.837) |
| 19p gain | 105 (17%) | 511 |
0.377 (0.588) |
0.00821 (0.0332) |
4e-05 (0.000355) |
0.242 (0.439) |
0.0934 (0.223) |
0.14 (0.305) |
0.309 (0.509) |
3e-05 (0.000278) |
0.0172 (0.0616) |
0.00633 (0.0274) |
0.0777 (0.197) |
0.447 (0.657) |
| 10q loss | 111 (18%) | 505 |
0.00897 (0.0359) |
0.278 (0.483) |
1e-05 (0.000102) |
0.0149 (0.0546) |
0.672 (0.828) |
0.432 (0.645) |
0.00318 (0.0156) |
2e-05 (0.000193) |
0.308 (0.509) |
0.299 (0.503) |
0.0895 (0.218) |
0.332 (0.536) |
| 12p loss | 71 (12%) | 545 |
0.0298 (0.092) |
0.00292 (0.0145) |
1e-05 (0.000102) |
0.079 (0.198) |
0.787 (0.896) |
0.398 (0.612) |
0.0283 (0.0898) |
9e-05 (0.000708) |
0.136 (0.3) |
0.514 (0.71) |
0.942 (1.00) |
0.121 (0.272) |
| 12q loss | 71 (12%) | 545 |
0.0582 (0.157) |
0.0076 (0.0313) |
1e-05 (0.000102) |
0.241 (0.439) |
0.396 (0.61) |
0.115 (0.264) |
0.0128 (0.0482) |
4e-05 (0.000355) |
0.037 (0.109) |
0.289 (0.496) |
1 (1.00) |
0.305 (0.507) |
| 6p gain | 122 (20%) | 494 |
0.0155 (0.0567) |
0.00064 (0.00414) |
1e-05 (0.000102) |
0.449 (0.659) |
0.0764 (0.195) |
0.774 (0.885) |
0.706 (0.85) |
0.0363 (0.108) |
0.56 (0.747) |
0.29 (0.496) |
0.654 (0.818) |
0.434 (0.645) |
| 18q gain | 19 (3%) | 597 |
0.217 (0.414) |
0.456 (0.665) |
0.00404 (0.0192) |
0.0136 (0.0508) |
0.274 (0.48) |
0.816 (0.913) |
0.0519 (0.145) |
0.00192 (0.0103) |
0.767 (0.885) |
0.00643 (0.0276) |
1 (1.00) |
0.798 (0.904) |
| xp gain | 100 (16%) | 516 |
0.0167 (0.0605) |
0.0772 (0.196) |
0.00018 (0.00132) |
0.0389 (0.113) |
0.0278 (0.089) |
0.227 (0.424) |
0.114 (0.262) |
0.212 (0.409) |
0.301 (0.504) |
0.753 (0.88) |
0.513 (0.71) |
0.678 (0.83) |
| 1q loss | 82 (13%) | 534 |
0.22 (0.417) |
0.0849 (0.208) |
1e-05 (0.000102) |
0.0111 (0.0434) |
0.953 (1.00) |
0.59 (0.769) |
4e-05 (0.000355) |
0.00101 (0.00625) |
0.411 (0.625) |
0.0624 (0.166) |
0.231 (0.429) |
0.127 (0.282) |
| 2p loss | 17 (3%) | 599 |
0.914 (0.985) |
0.807 (0.908) |
0.029 (0.0909) |
0.0783 (0.198) |
0.421 (0.634) |
0.0125 (0.0478) |
0.0529 (0.146) |
0.00781 (0.032) |
0.0178 (0.0624) |
0.798 (0.904) |
||
| 9p loss | 76 (12%) | 540 |
0.48 (0.682) |
0.193 (0.383) |
1e-05 (0.000102) |
0.00134 (0.00785) |
0.951 (1.00) |
0.355 (0.564) |
0.00035 (0.00236) |
0.0177 (0.0622) |
0.324 (0.524) |
0.0556 (0.151) |
0.808 (0.908) |
0.351 (0.559) |
| 10p loss | 102 (17%) | 514 |
0.00445 (0.0207) |
0.172 (0.352) |
1e-05 (0.000102) |
0.0525 (0.146) |
0.754 (0.88) |
0.731 (0.861) |
0.0031 (0.0153) |
0.00035 (0.00236) |
0.298 (0.503) |
0.317 (0.521) |
0.163 (0.343) |
0.338 (0.543) |
| 19p loss | 62 (10%) | 554 |
0.589 (0.769) |
0.185 (0.371) |
2e-05 (0.000193) |
0.142 (0.31) |
0.727 (0.86) |
0.597 (0.77) |
0.0136 (0.0508) |
0.0215 (0.072) |
0.168 (0.347) |
0.0341 (0.103) |
0.342 (0.548) |
0.148 (0.32) |
| 4p gain | 20 (3%) | 596 |
0.819 (0.915) |
0.293 (0.497) |
0.0523 (0.145) |
0.227 (0.424) |
0.0096 (0.0381) |
0.29 (0.496) |
0.0186 (0.0632) |
0.157 (0.333) |
0.128 (0.284) |
0.463 (0.668) |
0.0048 (0.0217) |
0.0552 (0.151) |
| 5q gain | 67 (11%) | 549 |
0.614 (0.783) |
0.5 (0.703) |
6e-05 (0.000505) |
0.801 (0.905) |
0.663 (0.824) |
0.868 (0.954) |
0.334 (0.537) |
0.0344 (0.103) |
0.316 (0.52) |
0.00575 (0.0251) |
0.571 (0.755) |
0.978 (1.00) |
| 18p gain | 31 (5%) | 585 |
0.355 (0.564) |
0.222 (0.42) |
0.00133 (0.00784) |
0.00364 (0.0174) |
0.462 (0.668) |
0.726 (0.86) |
0.0705 (0.182) |
0.00211 (0.0111) |
0.701 (0.847) |
0.0664 (0.172) |
0.613 (0.783) |
0.495 (0.697) |
| 2q loss | 14 (2%) | 602 |
0.299 (0.503) |
0.67 (0.828) |
0.261 (0.461) |
0.0626 (0.166) |
0.136 (0.3) |
0.0127 (0.0481) |
0.0963 (0.228) |
0.00554 (0.0244) |
0.0176 (0.0622) |
0.437 (0.647) |
||
| 5p loss | 84 (14%) | 532 |
0.293 (0.497) |
0.505 (0.707) |
1e-05 (0.000102) |
0.0237 (0.0777) |
0.415 (0.628) |
0.23 (0.429) |
0.683 (0.832) |
0.00668 (0.0285) |
0.728 (0.86) |
0.109 (0.252) |
0.301 (0.504) |
0.635 (0.801) |
| 8q loss | 36 (6%) | 580 |
0.774 (0.885) |
0.831 (0.923) |
1e-05 (0.000102) |
0.514 (0.71) |
0.225 (0.423) |
0.19 (0.379) |
0.598 (0.77) |
0.664 (0.824) |
0.307 (0.509) |
0.0337 (0.102) |
0.0236 (0.0777) |
0.0908 (0.219) |
| xp loss | 91 (15%) | 525 |
0.964 (1.00) |
0.722 (0.86) |
0.112 (0.257) |
0.734 (0.861) |
0.0134 (0.0502) |
0.0146 (0.0537) |
0.708 (0.85) |
0.957 (1.00) |
0.231 (0.429) |
0.0757 (0.194) |
0.334 (0.537) |
0.0292 (0.0911) |
| xq loss | 79 (13%) | 537 |
0.941 (1.00) |
0.773 (0.885) |
0.0924 (0.222) |
0.553 (0.747) |
0.0657 (0.172) |
0.0334 (0.101) |
0.419 (0.632) |
0.436 (0.646) |
0.199 (0.389) |
0.0487 (0.138) |
0.208 (0.402) |
0.00529 (0.0236) |
| 5p gain | 108 (18%) | 508 |
0.509 (0.708) |
0.0644 (0.169) |
1e-05 (0.000102) |
1 (1.00) |
0.066 (0.172) |
0.395 (0.61) |
0.0289 (0.0908) |
0.079 (0.198) |
0.652 (0.818) |
0.592 (0.769) |
0.509 (0.708) |
0.956 (1.00) |
| 6q gain | 111 (18%) | 505 |
0.138 (0.303) |
0.00132 (0.00782) |
1e-05 (0.000102) |
0.473 (0.677) |
0.215 (0.412) |
0.987 (1.00) |
0.562 (0.747) |
0.198 (0.388) |
0.19 (0.379) |
0.562 (0.747) |
0.727 (0.86) |
0.417 (0.631) |
| 8p gain | 169 (27%) | 447 |
0.414 (0.627) |
0.627 (0.794) |
0.00166 (0.00928) |
0.643 (0.809) |
0.45 (0.66) |
0.579 (0.764) |
0.00679 (0.0288) |
0.163 (0.343) |
0.656 (0.819) |
0.314 (0.516) |
0.0757 (0.194) |
0.398 (0.611) |
| 10p gain | 49 (8%) | 567 |
0.137 (0.302) |
0.18 (0.365) |
0.00052 (0.00339) |
0.82 (0.915) |
0.682 (0.832) |
0.037 (0.109) |
0.559 (0.747) |
0.809 (0.908) |
0.559 (0.747) |
0.575 (0.759) |
0.283 (0.491) |
0.774 (0.885) |
| 10q gain | 29 (5%) | 587 |
0.872 (0.955) |
0.3 (0.503) |
0.00538 (0.0238) |
0.159 (0.337) |
0.304 (0.507) |
0.458 (0.666) |
0.66 (0.824) |
0.604 (0.776) |
0.597 (0.77) |
0.623 (0.792) |
0.0282 (0.0898) |
0.76 (0.882) |
| 12p gain | 128 (21%) | 488 |
0.051 (0.143) |
0.332 (0.536) |
0.0298 (0.092) |
0.0975 (0.23) |
0.935 (0.997) |
0.536 (0.734) |
0.597 (0.77) |
0.0181 (0.0629) |
0.0933 (0.223) |
0.32 (0.521) |
0.869 (0.955) |
0.559 (0.747) |
| 22q gain | 23 (4%) | 593 |
0.11 (0.254) |
0.0937 (0.223) |
0.0143 (0.0528) |
0.489 (0.691) |
0.0855 (0.209) |
0.51 (0.708) |
0.184 (0.37) |
0.277 (0.482) |
0.00446 (0.0207) |
0.603 (0.775) |
0.757 (0.882) |
1 (1.00) |
| xq gain | 109 (18%) | 507 |
0.0931 (0.223) |
0.34 (0.546) |
0.00272 (0.0137) |
0.0594 (0.16) |
0.0185 (0.0632) |
0.194 (0.384) |
0.702 (0.847) |
0.318 (0.521) |
0.487 (0.69) |
0.896 (0.975) |
0.535 (0.734) |
0.762 (0.883) |
| 6p loss | 47 (8%) | 569 |
0.504 (0.707) |
0.0112 (0.0434) |
0.146 (0.317) |
1 (1.00) |
0.772 (0.885) |
0.734 (0.861) |
0.555 (0.747) |
0.0289 (0.0908) |
0.276 (0.482) |
0.319 (0.521) |
0.234 (0.431) |
0.205 (0.398) |
| 11q loss | 92 (15%) | 524 |
0.865 (0.953) |
0.475 (0.677) |
0.00531 (0.0236) |
0.258 (0.458) |
0.404 (0.616) |
0.97 (1.00) |
0.924 (0.992) |
0.164 (0.343) |
0.164 (0.343) |
0.0425 (0.122) |
0.478 (0.679) |
0.62 (0.789) |
| 13q loss | 18 (3%) | 598 |
0.217 (0.414) |
0.00508 (0.0228) |
0.00026 (0.0018) |
0.596 (0.77) |
0.771 (0.885) |
0.866 (0.953) |
0.758 (0.882) |
0.171 (0.351) |
1 (1.00) |
0.971 (1.00) |
0.76 (0.882) |
0.349 (0.557) |
| 16q loss | 44 (7%) | 572 |
0.0341 (0.103) |
0.404 (0.616) |
0.00069 (0.00438) |
0.363 (0.572) |
0.403 (0.616) |
0.731 (0.861) |
0.726 (0.86) |
0.553 (0.747) |
0.161 (0.34) |
0.203 (0.397) |
0.969 (1.00) |
0.734 (0.861) |
| 17q loss | 93 (15%) | 523 |
0.926 (0.992) |
0.784 (0.894) |
1e-05 (0.000102) |
0.952 (1.00) |
0.426 (0.639) |
0.541 (0.738) |
0.891 (0.97) |
0.0293 (0.0914) |
0.122 (0.274) |
0.605 (0.777) |
0.807 (0.908) |
0.654 (0.818) |
| 19q loss | 56 (9%) | 560 |
0.724 (0.86) |
0.0839 (0.208) |
7e-05 (0.000574) |
0.171 (0.351) |
0.283 (0.491) |
0.85 (0.939) |
0.152 (0.327) |
0.0596 (0.16) |
0.215 (0.412) |
0.0262 (0.0841) |
0.518 (0.713) |
0.162 (0.342) |
| 1p gain | 50 (8%) | 566 |
0.247 (0.444) |
0.265 (0.465) |
0.0835 (0.207) |
0.32 (0.521) |
0.0361 (0.107) |
0.217 (0.414) |
0.991 (1.00) |
0.613 (0.783) |
0.518 (0.713) |
0.558 (0.747) |
0.251 (0.45) |
0.289 (0.496) |
| 1q gain | 113 (18%) | 503 |
0.918 (0.987) |
0.737 (0.863) |
0.0138 (0.0512) |
1 (1.00) |
0.0544 (0.149) |
0.225 (0.423) |
0.936 (0.997) |
0.425 (0.638) |
0.218 (0.415) |
0.431 (0.644) |
0.0599 (0.161) |
0.324 (0.524) |
| 4q gain | 21 (3%) | 595 |
0.196 (0.386) |
0.0609 (0.163) |
0.00173 (0.00956) |
0.637 (0.803) |
0.241 (0.439) |
0.446 (0.657) |
0.358 (0.567) |
0.288 (0.496) |
0.0905 (0.219) |
0.361 (0.571) |
0.559 (0.747) |
0.835 (0.926) |
| 9p gain | 124 (20%) | 492 |
0.588 (0.769) |
0.156 (0.332) |
0.00011 (0.000839) |
0.372 (0.583) |
0.464 (0.668) |
0.244 (0.44) |
0.902 (0.975) |
0.388 (0.6) |
0.664 (0.824) |
0.903 (0.975) |
0.109 (0.252) |
0.7 (0.847) |
| 9q gain | 103 (17%) | 513 |
0.721 (0.86) |
0.33 (0.534) |
0.00051 (0.00335) |
0.505 (0.707) |
0.47 (0.674) |
0.0672 (0.174) |
0.915 (0.985) |
0.843 (0.933) |
0.967 (1.00) |
0.791 (0.898) |
0.402 (0.616) |
0.767 (0.885) |
| 14q gain | 43 (7%) | 573 |
0.825 (0.918) |
0.434 (0.645) |
1e-05 (0.000102) |
0.364 (0.573) |
0.734 (0.861) |
0.877 (0.958) |
0.79 (0.897) |
0.612 (0.783) |
0.907 (0.979) |
0.474 (0.677) |
0.217 (0.414) |
0.26 (0.46) |
| 15q gain | 15 (2%) | 601 |
0.365 (0.573) |
0.0354 (0.106) |
0.0797 (0.2) |
0.435 (0.646) |
0.651 (0.817) |
1 (1.00) |
0.954 (1.00) |
0.929 (0.994) |
0.939 (1) |
0.717 (0.86) |
||
| 21q gain | 34 (6%) | 582 |
0.209 (0.404) |
0.206 (0.4) |
0.00024 (0.00169) |
0.195 (0.385) |
0.816 (0.913) |
0.183 (0.369) |
0.806 (0.908) |
0.104 (0.242) |
0.474 (0.677) |
0.725 (0.86) |
0.509 (0.708) |
0.702 (0.847) |
| 3p loss | 68 (11%) | 548 |
0.512 (0.709) |
0.846 (0.935) |
0.0207 (0.0698) |
0.556 (0.747) |
0.0955 (0.227) |
0.586 (0.769) |
0.673 (0.828) |
0.717 (0.86) |
0.673 (0.828) |
0.675 (0.829) |
0.541 (0.738) |
0.727 (0.86) |
| 3q loss | 45 (7%) | 571 |
0.295 (0.498) |
0.116 (0.266) |
0.0409 (0.118) |
0.384 (0.596) |
0.167 (0.347) |
0.771 (0.885) |
0.678 (0.83) |
0.234 (0.431) |
0.461 (0.668) |
0.774 (0.885) |
0.699 (0.847) |
0.635 (0.801) |
| 11p loss | 75 (12%) | 541 |
0.955 (1.00) |
0.934 (0.997) |
0.00639 (0.0276) |
0.475 (0.677) |
0.376 (0.588) |
0.963 (1.00) |
0.803 (0.906) |
0.133 (0.295) |
0.252 (0.45) |
0.0984 (0.231) |
0.557 (0.747) |
0.902 (0.975) |
| 16p loss | 40 (6%) | 576 |
0.12 (0.271) |
0.293 (0.497) |
0.0177 (0.0622) |
0.243 (0.439) |
0.235 (0.431) |
0.494 (0.697) |
0.54 (0.738) |
0.189 (0.378) |
0.226 (0.423) |
0.303 (0.506) |
1 (1.00) |
0.947 (1.00) |
| 20q loss | 8 (1%) | 608 |
1 (1.00) |
0.779 (0.889) |
0.0304 (0.0931) |
0.681 (0.832) |
0.646 (0.812) |
0.886 (0.967) |
0.94 (1.00) |
1 (1.00) |
||||
| 17p gain | 39 (6%) | 577 |
0.498 (0.701) |
0.24 (0.438) |
0.348 (0.556) |
0.626 (0.794) |
0.59 (0.769) |
0.223 (0.421) |
0.294 (0.497) |
0.0664 (0.172) |
0.837 (0.928) |
0.151 (0.326) |
0.464 (0.668) |
0.872 (0.955) |
| 6q loss | 69 (11%) | 547 |
0.568 (0.753) |
0.235 (0.431) |
0.3 (0.503) |
0.799 (0.904) |
0.184 (0.37) |
0.378 (0.588) |
0.136 (0.3) |
0.0642 (0.169) |
0.192 (0.383) |
0.728 (0.86) |
0.0975 (0.23) |
0.286 (0.494) |
| 7p loss | 3 (0%) | 613 |
0.818 (0.915) |
0.626 (0.794) |
0.153 (0.327) |
|||||||||
| 7q loss | 5 (1%) | 611 |
0.873 (0.956) |
0.211 (0.408) |
0.276 (0.482) |
0.523 (0.718) |
0.826 (0.918) |
0.702 (0.847) |
1 (1.00) |
0.543 (0.739) |
P value = 0.0361 (Fisher's exact test), Q value = 0.11
Table S1. Gene #1: '1p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 108 | 197 | 177 |
| 1P GAIN MUTATED | 10 | 21 | 7 |
| 1P GAIN WILD-TYPE | 98 | 176 | 170 |
Figure S1. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 0.0138 (Fisher's exact test), Q value = 0.051
Table S2. Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 1Q GAIN MUTATED | 26 | 50 | 33 | 4 |
| 1Q GAIN WILD-TYPE | 189 | 197 | 99 | 18 |
Figure S2. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00321 (Fisher's exact test), Q value = 0.016
Table S3. Gene #3: '2p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 2P GAIN MUTATED | 3 | 22 | 7 |
| 2P GAIN WILD-TYPE | 47 | 67 | 70 |
Figure S3. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S4. Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 2P GAIN MUTATED | 20 | 63 | 29 | 11 |
| 2P GAIN WILD-TYPE | 195 | 184 | 103 | 11 |
Figure S4. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00278 (Fisher's exact test), Q value = 0.014
Table S5. Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 2P GAIN MUTATED | 22 | 43 | 24 |
| 2P GAIN WILD-TYPE | 95 | 86 | 120 |
Figure S5. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S6. Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 2P GAIN MUTATED | 56 | 14 | 25 | 27 |
| 2P GAIN WILD-TYPE | 100 | 114 | 106 | 171 |
Figure S6. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S7. Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 2P GAIN MUTATED | 25 | 14 | 8 | 12 | 28 | 30 | 5 |
| 2P GAIN WILD-TYPE | 55 | 72 | 56 | 45 | 62 | 108 | 93 |
Figure S7. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00435 (Fisher's exact test), Q value = 0.02
Table S8. Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 2P GAIN MUTATED | 7 | 16 | 4 | 20 | 5 | 20 | 12 | 6 | 13 |
| 2P GAIN WILD-TYPE | 42 | 58 | 25 | 66 | 72 | 34 | 45 | 26 | 68 |
Figure S8. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.045 (Fisher's exact test), Q value = 0.13
Table S9. Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 2Q GAIN MUTATED | 5 | 14 | 13 | 2 |
| 2Q GAIN WILD-TYPE | 40 | 49 | 52 | 41 |
Figure S9. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00104 (Fisher's exact test), Q value = 0.0064
Table S10. Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 2Q GAIN MUTATED | 3 | 24 | 7 |
| 2Q GAIN WILD-TYPE | 47 | 65 | 70 |
Figure S10. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S11. Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 2Q GAIN MUTATED | 19 | 64 | 28 | 11 |
| 2Q GAIN WILD-TYPE | 196 | 183 | 104 | 11 |
Figure S11. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00595 (Fisher's exact test), Q value = 0.026
Table S12. Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 2Q GAIN MUTATED | 20 | 41 | 25 |
| 2Q GAIN WILD-TYPE | 97 | 88 | 119 |
Figure S12. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 5e-05 (Fisher's exact test), Q value = 0.00043
Table S13. Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 2Q GAIN MUTATED | 51 | 15 | 25 | 30 |
| 2Q GAIN WILD-TYPE | 105 | 113 | 106 | 168 |
Figure S13. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S14. Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 2Q GAIN MUTATED | 23 | 15 | 5 | 12 | 29 | 31 | 6 |
| 2Q GAIN WILD-TYPE | 57 | 71 | 59 | 45 | 61 | 107 | 92 |
Figure S14. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0243 (Fisher's exact test), Q value = 0.079
Table S15. Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 2Q GAIN MUTATED | 7 | 15 | 4 | 21 | 5 | 17 | 12 | 5 | 15 |
| 2Q GAIN WILD-TYPE | 42 | 59 | 25 | 65 | 72 | 37 | 45 | 27 | 66 |
Figure S15. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0243 (Fisher's exact test), Q value = 0.079
Table S16. Gene #5: '3p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 3P GAIN MUTATED | 2 | 10 | 11 | 1 |
| 3P GAIN WILD-TYPE | 43 | 53 | 54 | 42 |
Figure S16. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.0253 (Fisher's exact test), Q value = 0.081
Table S17. Gene #5: '3p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 3P GAIN MUTATED | 2 | 16 | 6 |
| 3P GAIN WILD-TYPE | 48 | 73 | 71 |
Figure S17. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S18. Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 3P GAIN MUTATED | 8 | 47 | 15 | 5 |
| 3P GAIN WILD-TYPE | 207 | 200 | 117 | 17 |
Figure S18. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0124 (Fisher's exact test), Q value = 0.048
Table S19. Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 3P GAIN MUTATED | 7 | 14 | 3 | 6 | 19 | 20 | 6 |
| 3P GAIN WILD-TYPE | 73 | 72 | 61 | 51 | 71 | 118 | 92 |
Figure S19. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0185 (Fisher's exact test), Q value = 0.063
Table S20. Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 153 | 95 | 86 | 205 |
| 3P GAIN MUTATED | 17 | 15 | 18 | 17 |
| 3P GAIN WILD-TYPE | 136 | 80 | 68 | 188 |
Figure S20. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 0.022 (Fisher's exact test), Q value = 0.073
Table S21. Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 3P GAIN MUTATED | 5 | 12 | 2 | 8 | 3 | 7 | 15 | 5 | 10 |
| 3P GAIN WILD-TYPE | 44 | 62 | 27 | 78 | 74 | 47 | 42 | 27 | 71 |
Figure S21. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0221 (Fisher's exact test), Q value = 0.074
Table S22. Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 3Q GAIN MUTATED | 3 | 12 | 14 | 2 |
| 3Q GAIN WILD-TYPE | 42 | 51 | 51 | 41 |
Figure S22. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.0027 (Fisher's exact test), Q value = 0.014
Table S23. Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 3Q GAIN MUTATED | 2 | 21 | 8 |
| 3Q GAIN WILD-TYPE | 48 | 68 | 69 |
Figure S23. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S24. Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 3Q GAIN MUTATED | 9 | 60 | 24 | 5 |
| 3Q GAIN WILD-TYPE | 206 | 187 | 108 | 17 |
Figure S24. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0243 (Fisher's exact test), Q value = 0.079
Table S25. Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 3Q GAIN MUTATED | 15 | 32 | 20 |
| 3Q GAIN WILD-TYPE | 102 | 97 | 124 |
Figure S25. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00333 (Fisher's exact test), Q value = 0.016
Table S26. Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 3Q GAIN MUTATED | 10 | 17 | 4 | 9 | 24 | 26 | 8 |
| 3Q GAIN WILD-TYPE | 70 | 69 | 60 | 48 | 66 | 112 | 90 |
Figure S26. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0237 (Fisher's exact test), Q value = 0.078
Table S27. Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 153 | 95 | 86 | 205 |
| 3Q GAIN MUTATED | 23 | 19 | 22 | 24 |
| 3Q GAIN WILD-TYPE | 130 | 76 | 64 | 181 |
Figure S27. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 0.0199 (Fisher's exact test), Q value = 0.067
Table S28. Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 40 | 38 | 22 |
| 3Q GAIN MUTATED | 8 | 12 | 9 | 0 |
| 3Q GAIN WILD-TYPE | 27 | 28 | 29 | 22 |
Figure S28. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
P value = 0.0096 (Fisher's exact test), Q value = 0.038
Table S29. Gene #7: '4p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 108 | 197 | 177 |
| 4P GAIN MUTATED | 8 | 2 | 7 |
| 4P GAIN WILD-TYPE | 100 | 195 | 170 |
Figure S29. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 0.0186 (Fisher's exact test), Q value = 0.063
Table S30. Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 4P GAIN MUTATED | 11 | 2 | 1 | 6 |
| 4P GAIN WILD-TYPE | 145 | 126 | 130 | 192 |
Figure S30. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 0.0048 (Fisher's exact test), Q value = 0.022
Table S31. Gene #7: '4p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 40 | 38 | 22 |
| 4P GAIN MUTATED | 0 | 0 | 5 | 0 |
| 4P GAIN WILD-TYPE | 35 | 40 | 33 | 22 |
Figure S31. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
P value = 0.00173 (Fisher's exact test), Q value = 0.0096
Table S32. Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 4Q GAIN MUTATED | 1 | 9 | 9 | 2 |
| 4Q GAIN WILD-TYPE | 214 | 238 | 123 | 20 |
Figure S32. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S33. Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 5P GAIN MUTATED | 19 | 59 | 22 | 8 |
| 5P GAIN WILD-TYPE | 196 | 188 | 110 | 14 |
Figure S33. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0289 (Fisher's exact test), Q value = 0.091
Table S34. Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 5P GAIN MUTATED | 33 | 12 | 27 | 36 |
| 5P GAIN WILD-TYPE | 123 | 116 | 104 | 162 |
Figure S34. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 6e-05 (Fisher's exact test), Q value = 5e-04
Table S35. Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 5Q GAIN MUTATED | 16 | 42 | 5 | 4 |
| 5Q GAIN WILD-TYPE | 199 | 205 | 127 | 18 |
Figure S35. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0344 (Fisher's exact test), Q value = 0.1
Table S36. Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 5Q GAIN MUTATED | 9 | 11 | 1 | 3 | 13 | 21 | 9 |
| 5Q GAIN WILD-TYPE | 71 | 75 | 63 | 54 | 77 | 117 | 89 |
Figure S36. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00575 (Fisher's exact test), Q value = 0.025
Table S37. Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 5Q GAIN MUTATED | 4 | 10 | 1 | 2 | 5 | 4 | 9 | 5 | 16 |
| 5Q GAIN WILD-TYPE | 45 | 64 | 28 | 84 | 72 | 50 | 48 | 27 | 65 |
Figure S37. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0155 (Fisher's exact test), Q value = 0.057
Table S38. Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 6P GAIN MUTATED | 10 | 11 | 18 | 2 |
| 6P GAIN WILD-TYPE | 35 | 52 | 47 | 41 |
Figure S38. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00064 (Fisher's exact test), Q value = 0.0041
Table S39. Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 6P GAIN MUTATED | 5 | 28 | 8 |
| 6P GAIN WILD-TYPE | 45 | 61 | 69 |
Figure S39. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S40. Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 6P GAIN MUTATED | 10 | 75 | 27 | 10 |
| 6P GAIN WILD-TYPE | 205 | 172 | 105 | 12 |
Figure S40. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0363 (Fisher's exact test), Q value = 0.11
Table S41. Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 6P GAIN MUTATED | 14 | 15 | 6 | 16 | 23 | 34 | 14 |
| 6P GAIN WILD-TYPE | 66 | 71 | 58 | 41 | 67 | 104 | 84 |
Figure S41. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00132 (Fisher's exact test), Q value = 0.0078
Table S42. Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 6Q GAIN MUTATED | 5 | 23 | 5 |
| 6Q GAIN WILD-TYPE | 45 | 66 | 72 |
Figure S42. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S43. Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 6Q GAIN MUTATED | 9 | 66 | 27 | 9 |
| 6Q GAIN WILD-TYPE | 206 | 181 | 105 | 13 |
Figure S43. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00047 (Fisher's exact test), Q value = 0.0031
Table S44. Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 7P GAIN MUTATED | 15 | 42 | 35 | 14 |
| 7P GAIN WILD-TYPE | 30 | 21 | 30 | 29 |
Figure S44. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S45. Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 7P GAIN MUTATED | 12 | 64 | 30 |
| 7P GAIN WILD-TYPE | 38 | 25 | 47 |
Figure S45. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S46. Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 7P GAIN MUTATED | 57 | 185 | 86 | 21 |
| 7P GAIN WILD-TYPE | 158 | 62 | 46 | 1 |
Figure S46. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00019 (Fisher's exact test), Q value = 0.0014
Table S47. Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 7P GAIN MUTATED | 65 | 97 | 76 |
| 7P GAIN WILD-TYPE | 52 | 32 | 68 |
Figure S47. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00572 (Fisher's exact test), Q value = 0.025
Table S48. Gene #13: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 228 | 168 | 86 |
| 7P GAIN MUTATED | 135 | 78 | 56 |
| 7P GAIN WILD-TYPE | 93 | 90 | 30 |
Figure S48. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 2e-05 (Fisher's exact test), Q value = 0.00019
Table S49. Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 7P GAIN MUTATED | 113 | 59 | 76 | 99 |
| 7P GAIN WILD-TYPE | 43 | 69 | 55 | 99 |
Figure S49. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S50. Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 7P GAIN MUTATED | 50 | 50 | 14 | 41 | 72 | 90 | 30 |
| 7P GAIN WILD-TYPE | 30 | 36 | 50 | 16 | 18 | 48 | 68 |
Figure S50. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00137 (Fisher's exact test), Q value = 0.008
Table S51. Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 153 | 95 | 86 | 205 |
| 7P GAIN MUTATED | 92 | 61 | 59 | 96 |
| 7P GAIN WILD-TYPE | 61 | 34 | 27 | 109 |
Figure S51. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S52. Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 7P GAIN MUTATED | 32 | 47 | 16 | 57 | 20 | 25 | 39 | 16 | 56 |
| 7P GAIN WILD-TYPE | 17 | 27 | 13 | 29 | 57 | 29 | 18 | 16 | 25 |
Figure S52. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00021 (Fisher's exact test), Q value = 0.0015
Table S53. Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 7Q GAIN MUTATED | 10 | 37 | 33 | 13 |
| 7Q GAIN WILD-TYPE | 35 | 26 | 32 | 30 |
Figure S53. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S54. Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 7Q GAIN MUTATED | 9 | 57 | 27 |
| 7Q GAIN WILD-TYPE | 41 | 32 | 50 |
Figure S54. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S55. Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 7Q GAIN MUTATED | 54 | 161 | 77 | 20 |
| 7Q GAIN WILD-TYPE | 161 | 86 | 55 | 2 |
Figure S55. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00988 (Fisher's exact test), Q value = 0.039
Table S56. Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 7Q GAIN MUTATED | 59 | 84 | 69 |
| 7Q GAIN WILD-TYPE | 58 | 45 | 75 |
Figure S56. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00263 (Fisher's exact test), Q value = 0.013
Table S57. Gene #14: '7q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 228 | 168 | 86 |
| 7Q GAIN MUTATED | 126 | 65 | 47 |
| 7Q GAIN WILD-TYPE | 102 | 103 | 39 |
Figure S57. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 0.00014 (Fisher's exact test), Q value = 0.001
Table S58. Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 7Q GAIN MUTATED | 103 | 54 | 64 | 89 |
| 7Q GAIN WILD-TYPE | 53 | 74 | 67 | 109 |
Figure S58. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S59. Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 7Q GAIN MUTATED | 46 | 46 | 13 | 36 | 63 | 80 | 26 |
| 7Q GAIN WILD-TYPE | 34 | 40 | 51 | 21 | 27 | 58 | 72 |
Figure S59. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00444 (Fisher's exact test), Q value = 0.021
Table S60. Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 153 | 95 | 86 | 205 |
| 7Q GAIN MUTATED | 85 | 54 | 52 | 85 |
| 7Q GAIN WILD-TYPE | 68 | 41 | 34 | 120 |
Figure S60. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S61. Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 7Q GAIN MUTATED | 32 | 41 | 15 | 47 | 18 | 23 | 34 | 14 | 52 |
| 7Q GAIN WILD-TYPE | 17 | 33 | 14 | 39 | 59 | 31 | 23 | 18 | 29 |
Figure S61. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0482 (Fisher's exact test), Q value = 0.14
Table S62. Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 40 | 38 | 22 |
| 7Q GAIN MUTATED | 24 | 28 | 21 | 8 |
| 7Q GAIN WILD-TYPE | 11 | 12 | 17 | 14 |
Figure S62. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
P value = 0.00166 (Fisher's exact test), Q value = 0.0093
Table S63. Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 8P GAIN MUTATED | 43 | 67 | 50 | 9 |
| 8P GAIN WILD-TYPE | 172 | 180 | 82 | 13 |
Figure S63. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00679 (Fisher's exact test), Q value = 0.029
Table S64. Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 8P GAIN MUTATED | 57 | 32 | 38 | 40 |
| 8P GAIN WILD-TYPE | 99 | 96 | 93 | 158 |
Figure S64. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 0.0385 (Fisher's exact test), Q value = 0.11
Table S65. Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 8Q GAIN MUTATED | 17 | 50 | 35 |
| 8Q GAIN WILD-TYPE | 33 | 39 | 42 |
Figure S65. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S66. Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 8Q GAIN MUTATED | 59 | 130 | 114 | 13 |
| 8Q GAIN WILD-TYPE | 156 | 117 | 18 | 9 |
Figure S66. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00119 (Fisher's exact test), Q value = 0.0071
Table S67. Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 8Q GAIN MUTATED | 59 | 87 | 67 |
| 8Q GAIN WILD-TYPE | 58 | 42 | 77 |
Figure S67. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.0326 (Fisher's exact test), Q value = 0.099
Table S68. Gene #16: '8q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 228 | 168 | 86 |
| 8Q GAIN MUTATED | 129 | 73 | 42 |
| 8Q GAIN WILD-TYPE | 99 | 95 | 44 |
Figure S68. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 0.00167 (Fisher's exact test), Q value = 0.0093
Table S69. Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 8Q GAIN MUTATED | 94 | 50 | 74 | 95 |
| 8Q GAIN WILD-TYPE | 62 | 78 | 57 | 103 |
Figure S69. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 0.0168 (Fisher's exact test), Q value = 0.061
Table S70. Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 8Q GAIN MUTATED | 46 | 39 | 28 | 30 | 58 | 73 | 39 |
| 8Q GAIN WILD-TYPE | 34 | 47 | 36 | 27 | 32 | 65 | 59 |
Figure S70. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0127 (Fisher's exact test), Q value = 0.048
Table S71. Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 8Q GAIN MUTATED | 18 | 43 | 15 | 58 | 30 | 28 | 29 | 17 | 40 |
| 8Q GAIN WILD-TYPE | 31 | 31 | 14 | 28 | 47 | 26 | 28 | 15 | 41 |
Figure S71. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00266 (Fisher's exact test), Q value = 0.013
Table S72. Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 40 | 38 | 22 |
| 8Q GAIN MUTATED | 13 | 30 | 27 | 11 |
| 8Q GAIN WILD-TYPE | 22 | 10 | 11 | 11 |
Figure S72. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
P value = 0.00011 (Fisher's exact test), Q value = 0.00084
Table S73. Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 9P GAIN MUTATED | 26 | 56 | 31 | 11 |
| 9P GAIN WILD-TYPE | 189 | 191 | 101 | 11 |
Figure S73. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00051 (Fisher's exact test), Q value = 0.0033
Table S74. Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 9Q GAIN MUTATED | 23 | 46 | 24 | 10 |
| 9Q GAIN WILD-TYPE | 192 | 201 | 108 | 12 |
Figure S74. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00052 (Fisher's exact test), Q value = 0.0034
Table S75. Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 10P GAIN MUTATED | 5 | 27 | 14 | 3 |
| 10P GAIN WILD-TYPE | 210 | 220 | 118 | 19 |
Figure S75. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.037 (Fisher's exact test), Q value = 0.11
Table S76. Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 228 | 168 | 86 |
| 10P GAIN MUTATED | 25 | 14 | 2 |
| 10P GAIN WILD-TYPE | 203 | 154 | 84 |
Figure S76. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 0.00538 (Fisher's exact test), Q value = 0.024
Table S77. Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 10Q GAIN MUTATED | 3 | 14 | 9 | 3 |
| 10Q GAIN WILD-TYPE | 212 | 233 | 123 | 19 |
Figure S77. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0282 (Fisher's exact test), Q value = 0.09
Table S78. Gene #20: '10q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 40 | 38 | 22 |
| 10Q GAIN MUTATED | 5 | 1 | 0 | 2 |
| 10Q GAIN WILD-TYPE | 30 | 39 | 38 | 20 |
Figure S78. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
P value = 0.0065 (Fisher's exact test), Q value = 0.028
Table S79. Gene #21: '11p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 11P GAIN MUTATED | 2 | 11 | 13 | 1 |
| 11P GAIN WILD-TYPE | 43 | 52 | 52 | 42 |
Figure S79. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00185 (Fisher's exact test), Q value = 0.01
Table S80. Gene #21: '11p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 11P GAIN MUTATED | 1 | 19 | 7 |
| 11P GAIN WILD-TYPE | 49 | 70 | 70 |
Figure S80. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S81. Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 11P GAIN MUTATED | 6 | 49 | 24 | 6 |
| 11P GAIN WILD-TYPE | 209 | 198 | 108 | 16 |
Figure S81. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00013 (Fisher's exact test), Q value = 0.00098
Table S82. Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 11P GAIN MUTATED | 17 | 32 | 9 |
| 11P GAIN WILD-TYPE | 100 | 97 | 135 |
Figure S82. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00096 (Fisher's exact test), Q value = 0.006
Table S83. Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 11P GAIN MUTATED | 34 | 7 | 18 | 26 |
| 11P GAIN WILD-TYPE | 122 | 121 | 113 | 172 |
Figure S83. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-04 (Fisher's exact test), Q value = 0.00077
Table S84. Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 11P GAIN MUTATED | 17 | 8 | 1 | 9 | 18 | 26 | 6 |
| 11P GAIN WILD-TYPE | 63 | 78 | 63 | 48 | 72 | 112 | 92 |
Figure S84. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00204 (Fisher's exact test), Q value = 0.011
Table S85. Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 11P GAIN MUTATED | 4 | 12 | 1 | 16 | 2 | 8 | 12 | 2 | 17 |
| 11P GAIN WILD-TYPE | 45 | 62 | 28 | 70 | 75 | 46 | 45 | 30 | 64 |
Figure S85. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00697 (Fisher's exact test), Q value = 0.029
Table S86. Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 11Q GAIN MUTATED | 3 | 8 | 15 | 1 |
| 11Q GAIN WILD-TYPE | 42 | 55 | 50 | 42 |
Figure S86. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00046 (Fisher's exact test), Q value = 0.0031
Table S87. Gene #22: '11q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 11Q GAIN MUTATED | 1 | 20 | 6 |
| 11Q GAIN WILD-TYPE | 49 | 69 | 71 |
Figure S87. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S88. Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 11Q GAIN MUTATED | 3 | 45 | 26 | 4 |
| 11Q GAIN WILD-TYPE | 212 | 202 | 106 | 18 |
Figure S88. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 2e-05 (Fisher's exact test), Q value = 0.00019
Table S89. Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 11Q GAIN MUTATED | 13 | 31 | 7 |
| 11Q GAIN WILD-TYPE | 104 | 98 | 137 |
Figure S89. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 7e-05 (Fisher's exact test), Q value = 0.00057
Table S90. Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 11Q GAIN MUTATED | 35 | 5 | 14 | 24 |
| 11Q GAIN WILD-TYPE | 121 | 123 | 117 | 174 |
Figure S90. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S91. Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 11Q GAIN MUTATED | 17 | 6 | 0 | 7 | 19 | 24 | 5 |
| 11Q GAIN WILD-TYPE | 63 | 80 | 64 | 50 | 71 | 114 | 93 |
Figure S91. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00142 (Fisher's exact test), Q value = 0.0082
Table S92. Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 11Q GAIN MUTATED | 2 | 11 | 2 | 18 | 2 | 7 | 8 | 1 | 16 |
| 11Q GAIN WILD-TYPE | 47 | 63 | 27 | 68 | 75 | 47 | 49 | 31 | 65 |
Figure S92. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0298 (Fisher's exact test), Q value = 0.092
Table S93. Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 12P GAIN MUTATED | 54 | 37 | 32 | 5 |
| 12P GAIN WILD-TYPE | 161 | 210 | 100 | 17 |
Figure S93. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0181 (Fisher's exact test), Q value = 0.063
Table S94. Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 12P GAIN MUTATED | 13 | 24 | 15 | 7 | 15 | 23 | 31 |
| 12P GAIN WILD-TYPE | 67 | 62 | 49 | 50 | 75 | 115 | 67 |
Figure S94. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0434 (Fisher's exact test), Q value = 0.12
Table S95. Gene #24: '12q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 12Q GAIN MUTATED | 14 | 10 | 8 | 12 |
| 12Q GAIN WILD-TYPE | 31 | 53 | 57 | 31 |
Figure S95. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00837 (Fisher's exact test), Q value = 0.034
Table S96. Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 12Q GAIN MUTATED | 54 | 33 | 25 | 2 |
| 12Q GAIN WILD-TYPE | 161 | 214 | 107 | 20 |
Figure S96. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0174 (Fisher's exact test), Q value = 0.062
Table S97. Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 12Q GAIN MUTATED | 18 | 14 | 34 |
| 12Q GAIN WILD-TYPE | 99 | 115 | 110 |
Figure S97. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00818 (Fisher's exact test), Q value = 0.033
Table S98. Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 12Q GAIN MUTATED | 13 | 23 | 13 | 5 | 11 | 21 | 28 |
| 12Q GAIN WILD-TYPE | 67 | 63 | 51 | 52 | 79 | 117 | 70 |
Figure S98. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0183 (Fisher's exact test), Q value = 0.063
Table S99. Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 153 | 95 | 86 | 205 |
| 12Q GAIN MUTATED | 30 | 11 | 11 | 51 |
| 12Q GAIN WILD-TYPE | 123 | 84 | 75 | 154 |
Figure S99. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S100. Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 13Q GAIN MUTATED | 17 | 47 | 49 | 17 |
| 13Q GAIN WILD-TYPE | 28 | 16 | 16 | 26 |
Figure S100. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S101. Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 13Q GAIN MUTATED | 13 | 70 | 47 |
| 13Q GAIN WILD-TYPE | 37 | 19 | 30 |
Figure S101. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S102. Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 13Q GAIN MUTATED | 64 | 221 | 74 | 13 |
| 13Q GAIN WILD-TYPE | 151 | 26 | 58 | 9 |
Figure S102. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S103. Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 13Q GAIN MUTATED | 65 | 103 | 72 |
| 13Q GAIN WILD-TYPE | 52 | 26 | 72 |
Figure S103. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00013 (Fisher's exact test), Q value = 0.00098
Table S104. Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 13Q GAIN MUTATED | 115 | 61 | 73 | 120 |
| 13Q GAIN WILD-TYPE | 41 | 67 | 58 | 78 |
Figure S104. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S105. Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 13Q GAIN MUTATED | 56 | 48 | 14 | 44 | 67 | 105 | 35 |
| 13Q GAIN WILD-TYPE | 24 | 38 | 50 | 13 | 23 | 33 | 63 |
Figure S105. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S106. Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 153 | 95 | 86 | 205 |
| 13Q GAIN MUTATED | 92 | 60 | 72 | 107 |
| 13Q GAIN WILD-TYPE | 61 | 35 | 14 | 98 |
Figure S106. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S107. Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 13Q GAIN MUTATED | 30 | 45 | 17 | 58 | 27 | 29 | 45 | 19 | 61 |
| 13Q GAIN WILD-TYPE | 19 | 29 | 12 | 28 | 50 | 25 | 12 | 13 | 20 |
Figure S107. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00236 (Fisher's exact test), Q value = 0.012
Table S108. Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 40 | 38 | 22 |
| 13Q GAIN MUTATED | 23 | 30 | 34 | 10 |
| 13Q GAIN WILD-TYPE | 12 | 10 | 4 | 12 |
Figure S108. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S109. Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 14Q GAIN MUTATED | 6 | 12 | 21 | 4 |
| 14Q GAIN WILD-TYPE | 209 | 235 | 111 | 18 |
Figure S109. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0354 (Fisher's exact test), Q value = 0.11
Table S110. Gene #27: '15q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 15Q GAIN MUTATED | 3 | 0 | 1 |
| 15Q GAIN WILD-TYPE | 47 | 89 | 76 |
Figure S110. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.0344 (Fisher's exact test), Q value = 0.1
Table S111. Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 16P GAIN MUTATED | 8 | 21 | 22 | 6 |
| 16P GAIN WILD-TYPE | 37 | 42 | 43 | 37 |
Figure S111. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00188 (Fisher's exact test), Q value = 0.01
Table S112. Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 16P GAIN MUTATED | 6 | 34 | 17 |
| 16P GAIN WILD-TYPE | 44 | 55 | 60 |
Figure S112. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S113. Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 16P GAIN MUTATED | 8 | 103 | 28 | 9 |
| 16P GAIN WILD-TYPE | 207 | 144 | 104 | 13 |
Figure S113. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00068 (Fisher's exact test), Q value = 0.0043
Table S114. Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 16P GAIN MUTATED | 49 | 17 | 25 | 56 |
| 16P GAIN WILD-TYPE | 107 | 111 | 106 | 142 |
Figure S114. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 4e-05 (Fisher's exact test), Q value = 0.00035
Table S115. Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 16P GAIN MUTATED | 15 | 19 | 4 | 14 | 30 | 49 | 16 |
| 16P GAIN WILD-TYPE | 65 | 67 | 60 | 43 | 60 | 89 | 82 |
Figure S115. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0015 (Fisher's exact test), Q value = 0.0085
Table S116. Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 16P GAIN MUTATED | 11 | 21 | 4 | 22 | 7 | 10 | 16 | 12 | 30 |
| 16P GAIN WILD-TYPE | 38 | 53 | 25 | 64 | 70 | 44 | 41 | 20 | 51 |
Figure S116. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0295 (Fisher's exact test), Q value = 0.091
Table S117. Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 16Q GAIN MUTATED | 6 | 19 | 21 | 6 |
| 16Q GAIN WILD-TYPE | 39 | 44 | 44 | 37 |
Figure S117. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00046 (Fisher's exact test), Q value = 0.0031
Table S118. Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 16Q GAIN MUTATED | 4 | 32 | 16 |
| 16Q GAIN WILD-TYPE | 46 | 57 | 61 |
Figure S118. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S119. Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 16Q GAIN MUTATED | 7 | 103 | 26 | 9 |
| 16Q GAIN WILD-TYPE | 208 | 144 | 106 | 13 |
Figure S119. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00178 (Fisher's exact test), Q value = 0.0098
Table S120. Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 16Q GAIN MUTATED | 49 | 17 | 26 | 52 |
| 16Q GAIN WILD-TYPE | 107 | 111 | 105 | 146 |
Figure S120. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 4e-05 (Fisher's exact test), Q value = 0.00035
Table S121. Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 16Q GAIN MUTATED | 16 | 19 | 4 | 13 | 32 | 46 | 14 |
| 16Q GAIN WILD-TYPE | 64 | 67 | 60 | 44 | 58 | 92 | 84 |
Figure S121. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00183 (Fisher's exact test), Q value = 0.0099
Table S122. Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 16Q GAIN MUTATED | 11 | 23 | 3 | 20 | 7 | 11 | 15 | 11 | 29 |
| 16Q GAIN WILD-TYPE | 38 | 51 | 26 | 66 | 70 | 43 | 42 | 21 | 52 |
Figure S122. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0047 (Fisher's exact test), Q value = 0.021
Table S123. Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 17Q GAIN MUTATED | 3 | 18 | 13 | 3 |
| 17Q GAIN WILD-TYPE | 42 | 45 | 52 | 40 |
Figure S123. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.0036 (Fisher's exact test), Q value = 0.017
Table S124. Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 17Q GAIN MUTATED | 3 | 24 | 10 |
| 17Q GAIN WILD-TYPE | 47 | 65 | 67 |
Figure S124. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S125. Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 17Q GAIN MUTATED | 15 | 61 | 34 | 3 |
| 17Q GAIN WILD-TYPE | 200 | 186 | 98 | 19 |
Figure S125. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00957 (Fisher's exact test), Q value = 0.038
Table S126. Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 17Q GAIN MUTATED | 18 | 37 | 22 |
| 17Q GAIN WILD-TYPE | 99 | 92 | 122 |
Figure S126. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00746 (Fisher's exact test), Q value = 0.031
Table S127. Gene #31: '17q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 228 | 168 | 86 |
| 17Q GAIN MUTATED | 42 | 20 | 24 |
| 17Q GAIN WILD-TYPE | 186 | 148 | 62 |
Figure S127. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S128. Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 17Q GAIN MUTATED | 53 | 15 | 14 | 31 |
| 17Q GAIN WILD-TYPE | 103 | 113 | 117 | 167 |
Figure S128. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S129. Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 17Q GAIN MUTATED | 27 | 17 | 3 | 7 | 18 | 35 | 6 |
| 17Q GAIN WILD-TYPE | 53 | 69 | 61 | 50 | 72 | 103 | 92 |
Figure S129. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00852 (Fisher's exact test), Q value = 0.034
Table S130. Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 17Q GAIN MUTATED | 12 | 11 | 3 | 25 | 4 | 10 | 12 | 5 | 15 |
| 17Q GAIN WILD-TYPE | 37 | 63 | 26 | 61 | 73 | 44 | 45 | 27 | 66 |
Figure S130. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00133 (Fisher's exact test), Q value = 0.0078
Table S131. Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 18P GAIN MUTATED | 12 | 4 | 12 | 3 |
| 18P GAIN WILD-TYPE | 203 | 243 | 120 | 19 |
Figure S131. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00364 (Fisher's exact test), Q value = 0.017
Table S132. Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 18P GAIN MUTATED | 8 | 1 | 13 |
| 18P GAIN WILD-TYPE | 109 | 128 | 131 |
Figure S132. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00211 (Fisher's exact test), Q value = 0.011
Table S133. Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 18P GAIN MUTATED | 1 | 3 | 10 | 3 | 5 | 2 | 7 |
| 18P GAIN WILD-TYPE | 79 | 83 | 54 | 54 | 85 | 136 | 91 |
Figure S133. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00404 (Fisher's exact test), Q value = 0.019
Table S134. Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 18Q GAIN MUTATED | 9 | 2 | 5 | 3 |
| 18Q GAIN WILD-TYPE | 206 | 245 | 127 | 19 |
Figure S134. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0136 (Fisher's exact test), Q value = 0.051
Table S135. Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 18Q GAIN MUTATED | 6 | 0 | 7 |
| 18Q GAIN WILD-TYPE | 111 | 129 | 137 |
Figure S135. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00192 (Fisher's exact test), Q value = 0.01
Table S136. Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 18Q GAIN MUTATED | 0 | 1 | 7 | 1 | 4 | 1 | 5 |
| 18Q GAIN WILD-TYPE | 80 | 85 | 57 | 56 | 86 | 137 | 93 |
Figure S136. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00643 (Fisher's exact test), Q value = 0.028
Table S137. Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 18Q GAIN MUTATED | 1 | 6 | 1 | 0 | 8 | 1 | 1 | 0 | 1 |
| 18Q GAIN WILD-TYPE | 48 | 68 | 28 | 86 | 69 | 53 | 56 | 32 | 80 |
Figure S137. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00821 (Fisher's exact test), Q value = 0.033
Table S138. Gene #34: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 19P GAIN MUTATED | 2 | 20 | 9 |
| 19P GAIN WILD-TYPE | 48 | 69 | 68 |
Figure S138. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 4e-05 (Fisher's exact test), Q value = 0.00035
Table S139. Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 19P GAIN MUTATED | 16 | 60 | 24 | 5 |
| 19P GAIN WILD-TYPE | 199 | 187 | 108 | 17 |
Figure S139. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.00028
Table S140. Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 19P GAIN MUTATED | 11 | 20 | 3 | 13 | 23 | 29 | 5 |
| 19P GAIN WILD-TYPE | 69 | 66 | 61 | 44 | 67 | 109 | 93 |
Figure S140. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0172 (Fisher's exact test), Q value = 0.062
Table S141. Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 153 | 95 | 86 | 205 |
| 19P GAIN MUTATED | 28 | 24 | 12 | 23 |
| 19P GAIN WILD-TYPE | 125 | 71 | 74 | 182 |
Figure S141. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 0.00633 (Fisher's exact test), Q value = 0.027
Table S142. Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 19P GAIN MUTATED | 11 | 14 | 6 | 13 | 3 | 8 | 7 | 11 | 14 |
| 19P GAIN WILD-TYPE | 38 | 60 | 23 | 73 | 74 | 46 | 50 | 21 | 67 |
Figure S142. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0228 (Fisher's exact test), Q value = 0.076
Table S143. Gene #35: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 19Q GAIN MUTATED | 3 | 16 | 6 | 8 |
| 19Q GAIN WILD-TYPE | 42 | 47 | 59 | 35 |
Figure S143. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00299 (Fisher's exact test), Q value = 0.015
Table S144. Gene #35: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 19Q GAIN MUTATED | 1 | 19 | 13 |
| 19Q GAIN WILD-TYPE | 49 | 70 | 64 |
Figure S144. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 5e-05 (Fisher's exact test), Q value = 0.00043
Table S145. Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 19Q GAIN MUTATED | 22 | 63 | 21 | 7 |
| 19Q GAIN WILD-TYPE | 193 | 184 | 111 | 15 |
Figure S145. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0486 (Fisher's exact test), Q value = 0.14
Table S146. Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 108 | 197 | 177 |
| 19Q GAIN MUTATED | 26 | 42 | 24 |
| 19Q GAIN WILD-TYPE | 82 | 155 | 153 |
Figure S146. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 0.00107 (Fisher's exact test), Q value = 0.0065
Table S147. Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 19Q GAIN MUTATED | 14 | 21 | 4 | 12 | 23 | 30 | 8 |
| 19Q GAIN WILD-TYPE | 66 | 65 | 60 | 45 | 67 | 108 | 90 |
Figure S147. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0417 (Fisher's exact test), Q value = 0.12
Table S148. Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 153 | 95 | 86 | 205 |
| 19Q GAIN MUTATED | 29 | 25 | 10 | 30 |
| 19Q GAIN WILD-TYPE | 124 | 70 | 76 | 175 |
Figure S148. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 0.0123 (Fisher's exact test), Q value = 0.048
Table S149. Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 19Q GAIN MUTATED | 14 | 13 | 5 | 16 | 5 | 9 | 6 | 11 | 15 |
| 19Q GAIN WILD-TYPE | 35 | 61 | 24 | 70 | 72 | 45 | 51 | 21 | 66 |
Figure S149. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00031 (Fisher's exact test), Q value = 0.0021
Table S150. Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 20P GAIN MUTATED | 16 | 41 | 48 | 21 |
| 20P GAIN WILD-TYPE | 29 | 22 | 17 | 22 |
Figure S150. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S151. Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 20P GAIN MUTATED | 13 | 60 | 53 |
| 20P GAIN WILD-TYPE | 37 | 29 | 24 |
Figure S151. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S152. Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 20P GAIN MUTATED | 82 | 174 | 76 | 21 |
| 20P GAIN WILD-TYPE | 133 | 73 | 56 | 1 |
Figure S152. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00724 (Fisher's exact test), Q value = 0.03
Table S153. Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 20P GAIN MUTATED | 68 | 86 | 69 |
| 20P GAIN WILD-TYPE | 49 | 43 | 75 |
Figure S153. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.025 (Fisher's exact test), Q value = 0.081
Table S154. Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 20P GAIN MUTATED | 102 | 61 | 72 | 115 |
| 20P GAIN WILD-TYPE | 54 | 67 | 59 | 83 |
Figure S154. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S155. Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 20P GAIN MUTATED | 52 | 46 | 16 | 45 | 56 | 97 | 38 |
| 20P GAIN WILD-TYPE | 28 | 40 | 48 | 12 | 34 | 41 | 60 |
Figure S155. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S156. Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 20P GAIN MUTATED | 26 | 41 | 16 | 52 | 19 | 37 | 41 | 17 | 61 |
| 20P GAIN WILD-TYPE | 23 | 33 | 13 | 34 | 58 | 17 | 16 | 15 | 20 |
Figure S156. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0463 (Fisher's exact test), Q value = 0.13
Table S157. Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 40 | 38 | 22 |
| 20P GAIN MUTATED | 25 | 29 | 21 | 9 |
| 20P GAIN WILD-TYPE | 10 | 11 | 17 | 13 |
Figure S157. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S158. Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 20Q GAIN MUTATED | 19 | 61 | 59 | 24 |
| 20Q GAIN WILD-TYPE | 26 | 2 | 6 | 19 |
Figure S158. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S159. Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 20Q GAIN MUTATED | 15 | 86 | 62 |
| 20Q GAIN WILD-TYPE | 35 | 3 | 15 |
Figure S159. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S160. Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 20Q GAIN MUTATED | 91 | 241 | 109 | 22 |
| 20Q GAIN WILD-TYPE | 124 | 6 | 23 | 0 |
Figure S160. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S161. Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 20Q GAIN MUTATED | 82 | 126 | 86 |
| 20Q GAIN WILD-TYPE | 35 | 3 | 58 |
Figure S161. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.0127 (Fisher's exact test), Q value = 0.048
Table S162. Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 108 | 197 | 177 |
| 20Q GAIN MUTATED | 86 | 155 | 118 |
| 20Q GAIN WILD-TYPE | 22 | 42 | 59 |
Figure S162. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S163. Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 20Q GAIN MUTATED | 150 | 73 | 91 | 146 |
| 20Q GAIN WILD-TYPE | 6 | 55 | 40 | 52 |
Figure S163. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S164. Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 20Q GAIN MUTATED | 71 | 62 | 18 | 50 | 83 | 131 | 45 |
| 20Q GAIN WILD-TYPE | 9 | 24 | 46 | 7 | 7 | 7 | 53 |
Figure S164. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S165. Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 153 | 95 | 86 | 205 |
| 20Q GAIN MUTATED | 110 | 78 | 82 | 135 |
| 20Q GAIN WILD-TYPE | 43 | 17 | 4 | 70 |
Figure S165. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S166. Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 20Q GAIN MUTATED | 36 | 56 | 20 | 72 | 28 | 47 | 50 | 20 | 76 |
| 20Q GAIN WILD-TYPE | 13 | 18 | 9 | 14 | 49 | 7 | 7 | 12 | 5 |
Figure S166. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 9e-05 (Fisher's exact test), Q value = 0.00071
Table S167. Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 40 | 38 | 22 |
| 20Q GAIN MUTATED | 29 | 37 | 36 | 11 |
| 20Q GAIN WILD-TYPE | 6 | 3 | 2 | 11 |
Figure S167. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
P value = 0.00024 (Fisher's exact test), Q value = 0.0017
Table S168. Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 21Q GAIN MUTATED | 2 | 17 | 13 | 2 |
| 21Q GAIN WILD-TYPE | 213 | 230 | 119 | 20 |
Figure S168. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0143 (Fisher's exact test), Q value = 0.053
Table S169. Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 22Q GAIN MUTATED | 2 | 12 | 9 | 0 |
| 22Q GAIN WILD-TYPE | 213 | 235 | 123 | 22 |
Figure S169. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00446 (Fisher's exact test), Q value = 0.021
Table S170. Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 153 | 95 | 86 | 205 |
| 22Q GAIN MUTATED | 1 | 5 | 8 | 6 |
| 22Q GAIN WILD-TYPE | 152 | 90 | 78 | 199 |
Figure S170. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 0.0167 (Fisher's exact test), Q value = 0.06
Table S171. Gene #40: 'xp gain' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| XP GAIN MUTATED | 3 | 16 | 6 | 9 |
| XP GAIN WILD-TYPE | 42 | 47 | 59 | 34 |
Figure S171. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00018 (Fisher's exact test), Q value = 0.0013
Table S172. Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| XP GAIN MUTATED | 18 | 57 | 22 | 3 |
| XP GAIN WILD-TYPE | 197 | 190 | 110 | 19 |
Figure S172. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0389 (Fisher's exact test), Q value = 0.11
Table S173. Gene #40: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| XP GAIN MUTATED | 11 | 27 | 25 |
| XP GAIN WILD-TYPE | 106 | 102 | 119 |
Figure S173. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.0278 (Fisher's exact test), Q value = 0.089
Table S174. Gene #40: 'xp gain' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 108 | 197 | 177 |
| XP GAIN MUTATED | 19 | 44 | 21 |
| XP GAIN WILD-TYPE | 89 | 153 | 156 |
Figure S174. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 0.00272 (Fisher's exact test), Q value = 0.014
Table S175. Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| XQ GAIN MUTATED | 22 | 55 | 28 | 4 |
| XQ GAIN WILD-TYPE | 193 | 192 | 104 | 18 |
Figure S175. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0185 (Fisher's exact test), Q value = 0.063
Table S176. Gene #41: 'xq gain' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 108 | 197 | 177 |
| XQ GAIN MUTATED | 22 | 46 | 22 |
| XQ GAIN WILD-TYPE | 86 | 151 | 155 |
Figure S176. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 0.00686 (Fisher's exact test), Q value = 0.029
Table S177. Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 1P LOSS MUTATED | 6 | 28 | 11 |
| 1P LOSS WILD-TYPE | 44 | 61 | 66 |
Figure S177. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S178. Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 1P LOSS MUTATED | 14 | 78 | 33 | 14 |
| 1P LOSS WILD-TYPE | 201 | 169 | 99 | 8 |
Figure S178. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0174 (Fisher's exact test), Q value = 0.062
Table S179. Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 1P LOSS MUTATED | 29 | 39 | 23 |
| 1P LOSS WILD-TYPE | 88 | 90 | 121 |
Figure S179. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 9e-05 (Fisher's exact test), Q value = 0.00071
Table S180. Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 1P LOSS MUTATED | 51 | 14 | 33 | 40 |
| 1P LOSS WILD-TYPE | 105 | 114 | 98 | 158 |
Figure S180. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 5e-05 (Fisher's exact test), Q value = 0.00043
Table S181. Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 1P LOSS MUTATED | 24 | 14 | 5 | 15 | 30 | 39 | 11 |
| 1P LOSS WILD-TYPE | 56 | 72 | 59 | 42 | 60 | 99 | 87 |
Figure S181. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0372 (Fisher's exact test), Q value = 0.11
Table S182. Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 153 | 95 | 86 | 205 |
| 1P LOSS MUTATED | 33 | 27 | 26 | 35 |
| 1P LOSS WILD-TYPE | 120 | 68 | 60 | 170 |
Figure S182. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 0.00113 (Fisher's exact test), Q value = 0.0068
Table S183. Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 1P LOSS MUTATED | 13 | 14 | 4 | 22 | 5 | 20 | 15 | 5 | 23 |
| 1P LOSS WILD-TYPE | 36 | 60 | 25 | 64 | 72 | 34 | 42 | 27 | 58 |
Figure S183. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S184. Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 1Q LOSS MUTATED | 7 | 42 | 22 | 11 |
| 1Q LOSS WILD-TYPE | 208 | 205 | 110 | 11 |
Figure S184. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0111 (Fisher's exact test), Q value = 0.043
Table S185. Gene #43: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 1Q LOSS MUTATED | 15 | 27 | 12 |
| 1Q LOSS WILD-TYPE | 102 | 102 | 132 |
Figure S185. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 4e-05 (Fisher's exact test), Q value = 0.00035
Table S186. Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 1Q LOSS MUTATED | 34 | 4 | 18 | 25 |
| 1Q LOSS WILD-TYPE | 122 | 124 | 113 | 173 |
Figure S186. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 0.00101 (Fisher's exact test), Q value = 0.0063
Table S187. Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 1Q LOSS MUTATED | 16 | 6 | 3 | 7 | 19 | 24 | 6 |
| 1Q LOSS WILD-TYPE | 64 | 80 | 61 | 50 | 71 | 114 | 92 |
Figure S187. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.029 (Fisher's exact test), Q value = 0.091
Table S188. Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 2P LOSS MUTATED | 1 | 10 | 6 | 0 |
| 2P LOSS WILD-TYPE | 214 | 237 | 126 | 22 |
Figure S188. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0125 (Fisher's exact test), Q value = 0.048
Table S189. Gene #44: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 228 | 168 | 86 |
| 2P LOSS MUTATED | 5 | 1 | 6 |
| 2P LOSS WILD-TYPE | 223 | 167 | 80 |
Figure S189. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 0.00781 (Fisher's exact test), Q value = 0.032
Table S190. Gene #44: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 2P LOSS MUTATED | 0 | 0 | 0 | 2 | 3 | 4 | 8 |
| 2P LOSS WILD-TYPE | 80 | 86 | 64 | 55 | 87 | 134 | 90 |
Figure S190. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0178 (Fisher's exact test), Q value = 0.062
Table S191. Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 153 | 95 | 86 | 205 |
| 2P LOSS MUTATED | 2 | 0 | 6 | 8 |
| 2P LOSS WILD-TYPE | 151 | 95 | 80 | 197 |
Figure S191. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 0.0127 (Fisher's exact test), Q value = 0.048
Table S192. Gene #45: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 228 | 168 | 86 |
| 2Q LOSS MUTATED | 5 | 0 | 4 |
| 2Q LOSS WILD-TYPE | 223 | 168 | 82 |
Figure S192. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 0.00554 (Fisher's exact test), Q value = 0.024
Table S193. Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 2Q LOSS MUTATED | 0 | 0 | 0 | 1 | 2 | 3 | 8 |
| 2Q LOSS WILD-TYPE | 80 | 86 | 64 | 56 | 88 | 135 | 90 |
Figure S193. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0176 (Fisher's exact test), Q value = 0.062
Table S194. Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 153 | 95 | 86 | 205 |
| 2Q LOSS MUTATED | 1 | 0 | 5 | 7 |
| 2Q LOSS WILD-TYPE | 152 | 95 | 81 | 198 |
Figure S194. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 0.0207 (Fisher's exact test), Q value = 0.07
Table S195. Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 3P LOSS MUTATED | 15 | 35 | 13 | 5 |
| 3P LOSS WILD-TYPE | 200 | 212 | 119 | 17 |
Figure S195. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0409 (Fisher's exact test), Q value = 0.12
Table S196. Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 3Q LOSS MUTATED | 11 | 20 | 9 | 5 |
| 3Q LOSS WILD-TYPE | 204 | 227 | 123 | 17 |
Figure S196. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0409 (Fisher's exact test), Q value = 0.12
Table S197. Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 4P LOSS MUTATED | 13 | 24 | 26 | 7 |
| 4P LOSS WILD-TYPE | 32 | 39 | 39 | 36 |
Figure S197. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00194 (Fisher's exact test), Q value = 0.01
Table S198. Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 4P LOSS MUTATED | 11 | 41 | 18 |
| 4P LOSS WILD-TYPE | 39 | 48 | 59 |
Figure S198. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S199. Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 4P LOSS MUTATED | 20 | 108 | 53 | 16 |
| 4P LOSS WILD-TYPE | 195 | 139 | 79 | 6 |
Figure S199. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0112 (Fisher's exact test), Q value = 0.044
Table S200. Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 4P LOSS MUTATED | 33 | 54 | 37 |
| 4P LOSS WILD-TYPE | 84 | 75 | 107 |
Figure S200. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00148 (Fisher's exact test), Q value = 0.0085
Table S201. Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 4P LOSS MUTATED | 64 | 25 | 43 | 64 |
| 4P LOSS WILD-TYPE | 92 | 103 | 88 | 134 |
Figure S201. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 8e-05 (Fisher's exact test), Q value = 0.00065
Table S202. Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 4P LOSS MUTATED | 33 | 22 | 7 | 19 | 37 | 54 | 24 |
| 4P LOSS WILD-TYPE | 47 | 64 | 57 | 38 | 53 | 84 | 74 |
Figure S202. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00464 (Fisher's exact test), Q value = 0.021
Table S203. Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 4P LOSS MUTATED | 16 | 17 | 10 | 33 | 12 | 15 | 22 | 10 | 36 |
| 4P LOSS WILD-TYPE | 33 | 57 | 19 | 53 | 65 | 39 | 35 | 22 | 45 |
Figure S203. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.018 (Fisher's exact test), Q value = 0.062
Table S204. Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 4Q LOSS MUTATED | 12 | 23 | 26 | 6 |
| 4Q LOSS WILD-TYPE | 33 | 40 | 39 | 37 |
Figure S204. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.0158 (Fisher's exact test), Q value = 0.058
Table S205. Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 4Q LOSS MUTATED | 10 | 37 | 20 |
| 4Q LOSS WILD-TYPE | 40 | 52 | 57 |
Figure S205. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S206. Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 4Q LOSS MUTATED | 18 | 110 | 48 | 15 |
| 4Q LOSS WILD-TYPE | 197 | 137 | 84 | 7 |
Figure S206. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0205 (Fisher's exact test), Q value = 0.069
Table S207. Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 4Q LOSS MUTATED | 39 | 49 | 33 |
| 4Q LOSS WILD-TYPE | 78 | 80 | 111 |
Figure S207. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00476 (Fisher's exact test), Q value = 0.022
Table S208. Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 4Q LOSS MUTATED | 61 | 25 | 41 | 63 |
| 4Q LOSS WILD-TYPE | 95 | 103 | 90 | 135 |
Figure S208. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S209. Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 4Q LOSS MUTATED | 32 | 21 | 5 | 21 | 36 | 51 | 24 |
| 4Q LOSS WILD-TYPE | 48 | 65 | 59 | 36 | 54 | 87 | 74 |
Figure S209. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00727 (Fisher's exact test), Q value = 0.03
Table S210. Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 4Q LOSS MUTATED | 17 | 17 | 8 | 34 | 12 | 17 | 19 | 7 | 34 |
| 4Q LOSS WILD-TYPE | 32 | 57 | 21 | 52 | 65 | 37 | 38 | 25 | 47 |
Figure S210. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S211. Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 5P LOSS MUTATED | 6 | 38 | 33 | 7 |
| 5P LOSS WILD-TYPE | 209 | 209 | 99 | 15 |
Figure S211. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0237 (Fisher's exact test), Q value = 0.078
Table S212. Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 5P LOSS MUTATED | 14 | 28 | 15 |
| 5P LOSS WILD-TYPE | 103 | 101 | 129 |
Figure S212. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00668 (Fisher's exact test), Q value = 0.028
Table S213. Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 5P LOSS MUTATED | 14 | 13 | 1 | 14 | 10 | 20 | 12 |
| 5P LOSS WILD-TYPE | 66 | 73 | 63 | 43 | 80 | 118 | 86 |
Figure S213. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00435 (Fisher's exact test), Q value = 0.02
Table S214. Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 5Q LOSS MUTATED | 7 | 14 | 17 | 1 |
| 5Q LOSS WILD-TYPE | 38 | 49 | 48 | 42 |
Figure S214. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00459 (Fisher's exact test), Q value = 0.021
Table S215. Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 5Q LOSS MUTATED | 7 | 25 | 7 |
| 5Q LOSS WILD-TYPE | 43 | 64 | 70 |
Figure S215. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S216. Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 5Q LOSS MUTATED | 6 | 50 | 54 | 10 |
| 5Q LOSS WILD-TYPE | 209 | 197 | 78 | 12 |
Figure S216. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0163 (Fisher's exact test), Q value = 0.059
Table S217. Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 5Q LOSS MUTATED | 24 | 37 | 21 |
| 5Q LOSS WILD-TYPE | 93 | 92 | 123 |
Figure S217. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.0209 (Fisher's exact test), Q value = 0.07
Table S218. Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 5Q LOSS MUTATED | 40 | 15 | 29 | 36 |
| 5Q LOSS WILD-TYPE | 116 | 113 | 102 | 162 |
Figure S218. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 0.00155 (Fisher's exact test), Q value = 0.0087
Table S219. Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 5Q LOSS MUTATED | 19 | 12 | 4 | 18 | 22 | 32 | 13 |
| 5Q LOSS WILD-TYPE | 61 | 74 | 60 | 39 | 68 | 106 | 85 |
Figure S219. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00235 (Fisher's exact test), Q value = 0.012
Table S220. Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 5Q LOSS MUTATED | 9 | 12 | 9 | 26 | 6 | 4 | 12 | 7 | 19 |
| 5Q LOSS WILD-TYPE | 40 | 62 | 20 | 60 | 71 | 50 | 45 | 25 | 62 |
Figure S220. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0112 (Fisher's exact test), Q value = 0.043
Table S221. Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 6P LOSS MUTATED | 5 | 2 | 11 |
| 6P LOSS WILD-TYPE | 45 | 87 | 66 |
Figure S221. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.0289 (Fisher's exact test), Q value = 0.091
Table S222. Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 6P LOSS MUTATED | 8 | 3 | 4 | 1 | 12 | 7 | 12 |
| 6P LOSS WILD-TYPE | 72 | 83 | 60 | 56 | 78 | 131 | 86 |
Figure S222. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0047 (Fisher's exact test), Q value = 0.021
Table S223. Gene #56: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 8P LOSS MUTATED | 12 | 30 | 31 | 9 |
| 8P LOSS WILD-TYPE | 33 | 33 | 34 | 34 |
Figure S223. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00107 (Fisher's exact test), Q value = 0.0065
Table S224. Gene #56: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 8P LOSS MUTATED | 9 | 44 | 29 |
| 8P LOSS WILD-TYPE | 41 | 45 | 48 |
Figure S224. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S225. Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 8P LOSS MUTATED | 17 | 118 | 74 | 8 |
| 8P LOSS WILD-TYPE | 198 | 129 | 58 | 14 |
Figure S225. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 7e-04 (Fisher's exact test), Q value = 0.0044
Table S226. Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 8P LOSS MUTATED | 38 | 61 | 36 |
| 8P LOSS WILD-TYPE | 79 | 68 | 108 |
Figure S226. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00353 (Fisher's exact test), Q value = 0.017
Table S227. Gene #56: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 8P LOSS MUTATED | 61 | 28 | 48 | 79 |
| 8P LOSS WILD-TYPE | 95 | 100 | 83 | 119 |
Figure S227. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 6e-05 (Fisher's exact test), Q value = 5e-04
Table S228. Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 8P LOSS MUTATED | 28 | 25 | 8 | 24 | 40 | 64 | 27 |
| 8P LOSS WILD-TYPE | 52 | 61 | 56 | 33 | 50 | 74 | 71 |
Figure S228. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0299 (Fisher's exact test), Q value = 0.092
Table S229. Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 8P LOSS MUTATED | 17 | 23 | 9 | 37 | 15 | 20 | 26 | 9 | 34 |
| 8P LOSS WILD-TYPE | 32 | 51 | 20 | 49 | 62 | 34 | 31 | 23 | 47 |
Figure S229. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S230. Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 8Q LOSS MUTATED | 2 | 18 | 10 | 6 |
| 8Q LOSS WILD-TYPE | 213 | 229 | 122 | 16 |
Figure S230. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0337 (Fisher's exact test), Q value = 0.1
Table S231. Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 8Q LOSS MUTATED | 5 | 4 | 1 | 3 | 0 | 3 | 5 | 1 | 10 |
| 8Q LOSS WILD-TYPE | 44 | 70 | 28 | 83 | 77 | 51 | 52 | 31 | 71 |
Figure S231. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0236 (Fisher's exact test), Q value = 0.078
Table S232. Gene #57: '8q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 40 | 38 | 22 |
| 8Q LOSS MUTATED | 8 | 2 | 3 | 0 |
| 8Q LOSS WILD-TYPE | 27 | 38 | 35 | 22 |
Figure S232. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S233. Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 9P LOSS MUTATED | 8 | 47 | 17 | 4 |
| 9P LOSS WILD-TYPE | 207 | 200 | 115 | 18 |
Figure S233. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00134 (Fisher's exact test), Q value = 0.0078
Table S234. Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 9P LOSS MUTATED | 17 | 27 | 9 |
| 9P LOSS WILD-TYPE | 100 | 102 | 135 |
Figure S234. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00035 (Fisher's exact test), Q value = 0.0024
Table S235. Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 9P LOSS MUTATED | 32 | 7 | 20 | 17 |
| 9P LOSS WILD-TYPE | 124 | 121 | 111 | 181 |
Figure S235. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 0.0177 (Fisher's exact test), Q value = 0.062
Table S236. Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 9P LOSS MUTATED | 13 | 9 | 2 | 12 | 15 | 18 | 7 |
| 9P LOSS WILD-TYPE | 67 | 77 | 62 | 45 | 75 | 120 | 91 |
Figure S236. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0238 (Fisher's exact test), Q value = 0.078
Table S237. Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 9Q LOSS MUTATED | 2 | 17 | 7 |
| 9Q LOSS WILD-TYPE | 48 | 72 | 70 |
Figure S237. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S238. Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 9Q LOSS MUTATED | 7 | 50 | 17 | 4 |
| 9Q LOSS WILD-TYPE | 208 | 197 | 115 | 18 |
Figure S238. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00014 (Fisher's exact test), Q value = 0.001
Table S239. Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 9Q LOSS MUTATED | 19 | 27 | 7 |
| 9Q LOSS WILD-TYPE | 98 | 102 | 137 |
Figure S239. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 7e-05 (Fisher's exact test), Q value = 0.00057
Table S240. Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 9Q LOSS MUTATED | 33 | 6 | 21 | 18 |
| 9Q LOSS WILD-TYPE | 123 | 122 | 110 | 180 |
Figure S240. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 0.00124 (Fisher's exact test), Q value = 0.0074
Table S241. Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 9Q LOSS MUTATED | 11 | 7 | 2 | 12 | 19 | 21 | 6 |
| 9Q LOSS WILD-TYPE | 69 | 79 | 62 | 45 | 71 | 117 | 92 |
Figure S241. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0179 (Fisher's exact test), Q value = 0.062
Table S242. Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 9Q LOSS MUTATED | 9 | 9 | 3 | 18 | 2 | 9 | 5 | 2 | 11 |
| 9Q LOSS WILD-TYPE | 40 | 65 | 26 | 68 | 75 | 45 | 52 | 30 | 70 |
Figure S242. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00445 (Fisher's exact test), Q value = 0.021
Table S243. Gene #60: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 10P LOSS MUTATED | 3 | 4 | 17 | 4 |
| 10P LOSS WILD-TYPE | 42 | 59 | 48 | 39 |
Figure S243. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S244. Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 10P LOSS MUTATED | 10 | 48 | 35 | 9 |
| 10P LOSS WILD-TYPE | 205 | 199 | 97 | 13 |
Figure S244. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0031 (Fisher's exact test), Q value = 0.015
Table S245. Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 10P LOSS MUTATED | 40 | 13 | 21 | 27 |
| 10P LOSS WILD-TYPE | 116 | 115 | 110 | 171 |
Figure S245. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 0.00035 (Fisher's exact test), Q value = 0.0024
Table S246. Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 10P LOSS MUTATED | 16 | 10 | 3 | 11 | 28 | 23 | 10 |
| 10P LOSS WILD-TYPE | 64 | 76 | 61 | 46 | 62 | 115 | 88 |
Figure S246. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00897 (Fisher's exact test), Q value = 0.036
Table S247. Gene #61: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 10Q LOSS MUTATED | 5 | 6 | 19 | 4 |
| 10Q LOSS WILD-TYPE | 40 | 57 | 46 | 39 |
Figure S247. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S248. Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 10Q LOSS MUTATED | 7 | 55 | 41 | 8 |
| 10Q LOSS WILD-TYPE | 208 | 192 | 91 | 14 |
Figure S248. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0149 (Fisher's exact test), Q value = 0.055
Table S249. Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 10Q LOSS MUTATED | 17 | 36 | 23 |
| 10Q LOSS WILD-TYPE | 100 | 93 | 121 |
Figure S249. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00318 (Fisher's exact test), Q value = 0.016
Table S250. Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 10Q LOSS MUTATED | 42 | 13 | 22 | 33 |
| 10Q LOSS WILD-TYPE | 114 | 115 | 109 | 165 |
Figure S250. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 2e-05 (Fisher's exact test), Q value = 0.00019
Table S251. Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 10Q LOSS MUTATED | 18 | 9 | 1 | 10 | 32 | 26 | 14 |
| 10Q LOSS WILD-TYPE | 62 | 77 | 63 | 47 | 58 | 112 | 84 |
Figure S251. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00639 (Fisher's exact test), Q value = 0.028
Table S252. Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 11P LOSS MUTATED | 14 | 41 | 18 | 2 |
| 11P LOSS WILD-TYPE | 201 | 206 | 114 | 20 |
Figure S252. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00531 (Fisher's exact test), Q value = 0.024
Table S253. Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 11Q LOSS MUTATED | 19 | 50 | 19 | 4 |
| 11Q LOSS WILD-TYPE | 196 | 197 | 113 | 18 |
Figure S253. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0425 (Fisher's exact test), Q value = 0.12
Table S254. Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 11Q LOSS MUTATED | 11 | 9 | 5 | 9 | 5 | 8 | 12 | 5 | 20 |
| 11Q LOSS WILD-TYPE | 38 | 65 | 24 | 77 | 72 | 46 | 45 | 27 | 61 |
Figure S254. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0298 (Fisher's exact test), Q value = 0.092
Table S255. Gene #64: '12p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 12P LOSS MUTATED | 2 | 11 | 9 | 1 |
| 12P LOSS WILD-TYPE | 43 | 52 | 56 | 42 |
Figure S255. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00292 (Fisher's exact test), Q value = 0.015
Table S256. Gene #64: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 12P LOSS MUTATED | 0 | 15 | 8 |
| 12P LOSS WILD-TYPE | 50 | 74 | 69 |
Figure S256. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S257. Gene #64: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 12P LOSS MUTATED | 2 | 50 | 16 | 3 |
| 12P LOSS WILD-TYPE | 213 | 197 | 116 | 19 |
Figure S257. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0283 (Fisher's exact test), Q value = 0.09
Table S258. Gene #64: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 12P LOSS MUTATED | 26 | 7 | 14 | 24 |
| 12P LOSS WILD-TYPE | 130 | 121 | 117 | 174 |
Figure S258. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 9e-05 (Fisher's exact test), Q value = 0.00071
Table S259. Gene #64: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 12P LOSS MUTATED | 16 | 3 | 1 | 8 | 15 | 22 | 6 |
| 12P LOSS WILD-TYPE | 64 | 83 | 63 | 49 | 75 | 116 | 92 |
Figure S259. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0076 (Fisher's exact test), Q value = 0.031
Table S260. Gene #65: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 12Q LOSS MUTATED | 0 | 13 | 8 |
| 12Q LOSS WILD-TYPE | 50 | 76 | 69 |
Figure S260. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S261. Gene #65: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 12Q LOSS MUTATED | 3 | 50 | 14 | 4 |
| 12Q LOSS WILD-TYPE | 212 | 197 | 118 | 18 |
Figure S261. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0128 (Fisher's exact test), Q value = 0.048
Table S262. Gene #65: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 12Q LOSS MUTATED | 28 | 7 | 14 | 22 |
| 12Q LOSS WILD-TYPE | 128 | 121 | 117 | 176 |
Figure S262. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 4e-05 (Fisher's exact test), Q value = 0.00035
Table S263. Gene #65: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 12Q LOSS MUTATED | 18 | 2 | 2 | 8 | 15 | 21 | 5 |
| 12Q LOSS WILD-TYPE | 62 | 84 | 62 | 49 | 75 | 117 | 93 |
Figure S263. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.037 (Fisher's exact test), Q value = 0.11
Table S264. Gene #65: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 153 | 95 | 86 | 205 |
| 12Q LOSS MUTATED | 15 | 18 | 13 | 17 |
| 12Q LOSS WILD-TYPE | 138 | 77 | 73 | 188 |
Figure S264. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 0.00508 (Fisher's exact test), Q value = 0.023
Table S265. Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 13Q LOSS MUTATED | 4 | 0 | 1 |
| 13Q LOSS WILD-TYPE | 46 | 89 | 76 |
Figure S265. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 0.00026 (Fisher's exact test), Q value = 0.0018
Table S266. Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 13Q LOSS MUTATED | 3 | 3 | 8 | 4 |
| 13Q LOSS WILD-TYPE | 212 | 244 | 124 | 18 |
Figure S266. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00024 (Fisher's exact test), Q value = 0.0017
Table S267. Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 14Q LOSS MUTATED | 10 | 30 | 31 | 7 |
| 14Q LOSS WILD-TYPE | 35 | 33 | 34 | 36 |
Figure S267. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.00028
Table S268. Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 14Q LOSS MUTATED | 6 | 45 | 27 |
| 14Q LOSS WILD-TYPE | 44 | 44 | 50 |
Figure S268. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S269. Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 14Q LOSS MUTATED | 18 | 154 | 26 | 9 |
| 14Q LOSS WILD-TYPE | 197 | 93 | 106 | 13 |
Figure S269. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S270. Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 14Q LOSS MUTATED | 33 | 67 | 28 |
| 14Q LOSS WILD-TYPE | 84 | 62 | 116 |
Figure S270. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.0313 (Fisher's exact test), Q value = 0.096
Table S271. Gene #67: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 228 | 168 | 86 |
| 14Q LOSS MUTATED | 70 | 55 | 40 |
| 14Q LOSS WILD-TYPE | 158 | 113 | 46 |
Figure S271. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S272. Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 14Q LOSS MUTATED | 81 | 23 | 30 | 72 |
| 14Q LOSS WILD-TYPE | 75 | 105 | 101 | 126 |
Figure S272. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S273. Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 14Q LOSS MUTATED | 35 | 26 | 3 | 21 | 37 | 65 | 19 |
| 14Q LOSS WILD-TYPE | 45 | 60 | 61 | 36 | 53 | 73 | 79 |
Figure S273. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00183 (Fisher's exact test), Q value = 0.0099
Table S274. Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 153 | 95 | 86 | 205 |
| 14Q LOSS MUTATED | 41 | 34 | 43 | 60 |
| 14Q LOSS WILD-TYPE | 112 | 61 | 43 | 145 |
Figure S274. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S275. Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 14Q LOSS MUTATED | 13 | 20 | 9 | 27 | 6 | 29 | 28 | 12 | 34 |
| 14Q LOSS WILD-TYPE | 36 | 54 | 20 | 59 | 71 | 25 | 29 | 20 | 47 |
Figure S275. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0175 (Fisher's exact test), Q value = 0.062
Table S276. Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 40 | 38 | 22 |
| 14Q LOSS MUTATED | 14 | 13 | 23 | 5 |
| 14Q LOSS WILD-TYPE | 21 | 27 | 15 | 17 |
Figure S276. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
P value = 0.0183 (Fisher's exact test), Q value = 0.063
Table S277. Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 63 | 16 | 34 | 22 |
| 14Q LOSS MUTATED | 18 | 6 | 17 | 14 |
| 14Q LOSS WILD-TYPE | 45 | 10 | 17 | 8 |
Figure S277. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-04 (Fisher's exact test), Q value = 0.00077
Table S278. Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 15Q LOSS MUTATED | 11 | 32 | 35 | 8 |
| 15Q LOSS WILD-TYPE | 34 | 31 | 30 | 35 |
Figure S278. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.00028
Table S279. Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 15Q LOSS MUTATED | 11 | 52 | 23 |
| 15Q LOSS WILD-TYPE | 39 | 37 | 54 |
Figure S279. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S280. Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 15Q LOSS MUTATED | 17 | 136 | 61 | 16 |
| 15Q LOSS WILD-TYPE | 198 | 111 | 71 | 6 |
Figure S280. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 1e-04 (Fisher's exact test), Q value = 0.00077
Table S281. Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 15Q LOSS MUTATED | 39 | 66 | 39 |
| 15Q LOSS WILD-TYPE | 78 | 63 | 105 |
Figure S281. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S282. Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 15Q LOSS MUTATED | 78 | 28 | 47 | 76 |
| 15Q LOSS WILD-TYPE | 78 | 100 | 84 | 122 |
Figure S282. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S283. Gene #68: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 15Q LOSS MUTATED | 36 | 27 | 2 | 23 | 46 | 64 | 31 |
| 15Q LOSS WILD-TYPE | 44 | 59 | 62 | 34 | 44 | 74 | 67 |
Figure S283. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00155 (Fisher's exact test), Q value = 0.0087
Table S284. Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 153 | 95 | 86 | 205 |
| 15Q LOSS MUTATED | 47 | 45 | 43 | 65 |
| 15Q LOSS WILD-TYPE | 106 | 50 | 43 | 140 |
Figure S284. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 0.00022 (Fisher's exact test), Q value = 0.0016
Table S285. Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 15Q LOSS MUTATED | 16 | 31 | 8 | 37 | 11 | 18 | 26 | 14 | 39 |
| 15Q LOSS WILD-TYPE | 33 | 43 | 21 | 49 | 66 | 36 | 31 | 18 | 42 |
Figure S285. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0177 (Fisher's exact test), Q value = 0.062
Table S286. Gene #69: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 16P LOSS MUTATED | 7 | 16 | 14 | 3 |
| 16P LOSS WILD-TYPE | 208 | 231 | 118 | 19 |
Figure S286. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0341 (Fisher's exact test), Q value = 0.1
Table S287. Gene #70: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 16Q LOSS MUTATED | 5 | 7 | 2 | 0 |
| 16Q LOSS WILD-TYPE | 40 | 56 | 63 | 43 |
Figure S287. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00069 (Fisher's exact test), Q value = 0.0044
Table S288. Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 16Q LOSS MUTATED | 7 | 15 | 19 | 3 |
| 16Q LOSS WILD-TYPE | 208 | 232 | 113 | 19 |
Figure S288. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.00028
Table S289. Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 17P LOSS MUTATED | 16 | 45 | 44 | 15 |
| 17P LOSS WILD-TYPE | 29 | 18 | 21 | 28 |
Figure S289. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 2e-05 (Fisher's exact test), Q value = 0.00019
Table S290. Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 17P LOSS MUTATED | 13 | 61 | 46 |
| 17P LOSS WILD-TYPE | 37 | 28 | 31 |
Figure S290. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S291. Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 17P LOSS MUTATED | 43 | 187 | 96 | 14 |
| 17P LOSS WILD-TYPE | 172 | 60 | 36 | 8 |
Figure S291. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S292. Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 17P LOSS MUTATED | 51 | 99 | 67 |
| 17P LOSS WILD-TYPE | 66 | 30 | 77 |
Figure S292. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S293. Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 17P LOSS MUTATED | 109 | 50 | 70 | 109 |
| 17P LOSS WILD-TYPE | 47 | 78 | 61 | 89 |
Figure S293. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S294. Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 17P LOSS MUTATED | 50 | 44 | 8 | 38 | 66 | 93 | 39 |
| 17P LOSS WILD-TYPE | 30 | 42 | 56 | 19 | 24 | 45 | 59 |
Figure S294. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00065 (Fisher's exact test), Q value = 0.0042
Table S295. Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 153 | 95 | 86 | 205 |
| 17P LOSS MUTATED | 77 | 54 | 64 | 103 |
| 17P LOSS WILD-TYPE | 76 | 41 | 22 | 102 |
Figure S295. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S296. Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 17P LOSS MUTATED | 23 | 42 | 16 | 56 | 20 | 35 | 38 | 16 | 52 |
| 17P LOSS WILD-TYPE | 26 | 32 | 13 | 30 | 57 | 19 | 19 | 16 | 29 |
Figure S296. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S297. Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 17Q LOSS MUTATED | 11 | 47 | 25 | 10 |
| 17Q LOSS WILD-TYPE | 204 | 200 | 107 | 12 |
Figure S297. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0293 (Fisher's exact test), Q value = 0.091
Table S298. Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 17Q LOSS MUTATED | 13 | 13 | 2 | 13 | 18 | 18 | 16 |
| 17Q LOSS WILD-TYPE | 67 | 73 | 62 | 44 | 72 | 120 | 82 |
Figure S298. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S299. Gene #73: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 18P LOSS MUTATED | 13 | 53 | 52 | 13 |
| 18P LOSS WILD-TYPE | 32 | 10 | 13 | 30 |
Figure S299. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S300. Gene #73: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 18P LOSS MUTATED | 10 | 77 | 44 |
| 18P LOSS WILD-TYPE | 40 | 12 | 33 |
Figure S300. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S301. Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 18P LOSS MUTATED | 47 | 223 | 94 | 17 |
| 18P LOSS WILD-TYPE | 168 | 24 | 38 | 5 |
Figure S301. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S302. Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 18P LOSS MUTATED | 61 | 122 | 65 |
| 18P LOSS WILD-TYPE | 56 | 7 | 79 |
Figure S302. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S303. Gene #73: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 18P LOSS MUTATED | 141 | 48 | 73 | 117 |
| 18P LOSS WILD-TYPE | 15 | 80 | 58 | 81 |
Figure S303. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S304. Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 18P LOSS MUTATED | 67 | 50 | 7 | 39 | 72 | 108 | 36 |
| 18P LOSS WILD-TYPE | 13 | 36 | 57 | 18 | 18 | 30 | 62 |
Figure S304. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S305. Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 153 | 95 | 86 | 205 |
| 18P LOSS MUTATED | 86 | 64 | 75 | 106 |
| 18P LOSS WILD-TYPE | 67 | 31 | 11 | 99 |
Figure S305. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S306. Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 18P LOSS MUTATED | 27 | 43 | 17 | 59 | 17 | 41 | 45 | 17 | 65 |
| 18P LOSS WILD-TYPE | 22 | 31 | 12 | 27 | 60 | 13 | 12 | 15 | 16 |
Figure S306. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00019 (Fisher's exact test), Q value = 0.0014
Table S307. Gene #73: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 40 | 38 | 22 |
| 18P LOSS MUTATED | 23 | 30 | 34 | 8 |
| 18P LOSS WILD-TYPE | 12 | 10 | 4 | 14 |
Figure S307. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
P value = 8e-05 (Fisher's exact test), Q value = 0.00065
Table S308. Gene #73: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 63 | 16 | 34 | 22 |
| 18P LOSS MUTATED | 33 | 16 | 26 | 20 |
| 18P LOSS WILD-TYPE | 30 | 0 | 8 | 2 |
Figure S308. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S309. Gene #74: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 18Q LOSS MUTATED | 16 | 54 | 54 | 15 |
| 18Q LOSS WILD-TYPE | 29 | 9 | 11 | 28 |
Figure S309. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S310. Gene #74: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 18Q LOSS MUTATED | 13 | 77 | 49 |
| 18Q LOSS WILD-TYPE | 37 | 12 | 28 |
Figure S310. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S311. Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 18Q LOSS MUTATED | 52 | 228 | 111 | 17 |
| 18Q LOSS WILD-TYPE | 163 | 19 | 21 | 5 |
Figure S311. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S312. Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 18Q LOSS MUTATED | 67 | 123 | 76 |
| 18Q LOSS WILD-TYPE | 50 | 6 | 68 |
Figure S312. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S313. Gene #74: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 18Q LOSS MUTATED | 140 | 56 | 82 | 128 |
| 18Q LOSS WILD-TYPE | 16 | 72 | 49 | 70 |
Figure S313. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S314. Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 18Q LOSS MUTATED | 66 | 57 | 10 | 44 | 76 | 111 | 42 |
| 18Q LOSS WILD-TYPE | 14 | 29 | 54 | 13 | 14 | 27 | 56 |
Figure S314. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S315. Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 153 | 95 | 86 | 205 |
| 18Q LOSS MUTATED | 93 | 65 | 79 | 118 |
| 18Q LOSS WILD-TYPE | 60 | 30 | 7 | 87 |
Figure S315. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S316. Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 18Q LOSS MUTATED | 31 | 46 | 18 | 64 | 20 | 42 | 49 | 19 | 66 |
| 18Q LOSS WILD-TYPE | 18 | 28 | 11 | 22 | 57 | 12 | 8 | 13 | 15 |
Figure S316. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00224 (Fisher's exact test), Q value = 0.012
Table S317. Gene #74: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 40 | 38 | 22 |
| 18Q LOSS MUTATED | 25 | 32 | 34 | 10 |
| 18Q LOSS WILD-TYPE | 10 | 8 | 4 | 12 |
Figure S317. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
P value = 0.00025 (Fisher's exact test), Q value = 0.0017
Table S318. Gene #74: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 63 | 16 | 34 | 22 |
| 18Q LOSS MUTATED | 38 | 16 | 26 | 21 |
| 18Q LOSS WILD-TYPE | 25 | 0 | 8 | 1 |
Figure S318. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 2e-05 (Fisher's exact test), Q value = 0.00019
Table S319. Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 19P LOSS MUTATED | 6 | 30 | 23 | 3 |
| 19P LOSS WILD-TYPE | 209 | 217 | 109 | 19 |
Figure S319. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0136 (Fisher's exact test), Q value = 0.051
Table S320. Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 19P LOSS MUTATED | 26 | 7 | 10 | 19 |
| 19P LOSS WILD-TYPE | 130 | 121 | 121 | 179 |
Figure S320. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 0.0215 (Fisher's exact test), Q value = 0.072
Table S321. Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 19P LOSS MUTATED | 16 | 3 | 3 | 5 | 11 | 14 | 10 |
| 19P LOSS WILD-TYPE | 64 | 83 | 61 | 52 | 79 | 124 | 88 |
Figure S321. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0341 (Fisher's exact test), Q value = 0.1
Table S322. Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 19P LOSS MUTATED | 2 | 4 | 3 | 18 | 4 | 4 | 7 | 3 | 10 |
| 19P LOSS WILD-TYPE | 47 | 70 | 26 | 68 | 73 | 50 | 50 | 29 | 71 |
Figure S322. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 7e-05 (Fisher's exact test), Q value = 0.00057
Table S323. Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 19Q LOSS MUTATED | 6 | 25 | 22 | 3 |
| 19Q LOSS WILD-TYPE | 209 | 222 | 110 | 19 |
Figure S323. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0262 (Fisher's exact test), Q value = 0.084
Table S324. Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 19Q LOSS MUTATED | 0 | 6 | 3 | 15 | 3 | 4 | 7 | 3 | 8 |
| 19Q LOSS WILD-TYPE | 49 | 68 | 26 | 71 | 74 | 50 | 50 | 29 | 73 |
Figure S324. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00963 (Fisher's exact test), Q value = 0.038
Table S325. Gene #77: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 20P LOSS MUTATED | 2 | 17 | 5 |
| 20P LOSS WILD-TYPE | 48 | 72 | 72 |
Figure S325. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S326. Gene #77: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 20P LOSS MUTATED | 5 | 38 | 22 | 0 |
| 20P LOSS WILD-TYPE | 210 | 209 | 110 | 22 |
Figure S326. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00082 (Fisher's exact test), Q value = 0.0051
Table S327. Gene #77: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 129 | 144 |
| 20P LOSS MUTATED | 9 | 24 | 7 |
| 20P LOSS WILD-TYPE | 108 | 105 | 137 |
Figure S327. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00035 (Fisher's exact test), Q value = 0.0024
Table S328. Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 20P LOSS MUTATED | 9 | 10 | 0 | 3 | 16 | 22 | 5 |
| 20P LOSS WILD-TYPE | 71 | 76 | 64 | 54 | 74 | 116 | 93 |
Figure S328. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0288 (Fisher's exact test), Q value = 0.091
Table S329. Gene #77: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 35 | 40 | 38 | 22 |
| 20P LOSS MUTATED | 0 | 5 | 7 | 1 |
| 20P LOSS WILD-TYPE | 35 | 35 | 31 | 21 |
Figure S329. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
P value = 0.0405 (Fisher's exact test), Q value = 0.12
Table S330. Gene #77: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 63 | 16 | 34 | 22 |
| 20P LOSS MUTATED | 4 | 5 | 3 | 1 |
| 20P LOSS WILD-TYPE | 59 | 11 | 31 | 21 |
Figure S330. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.0304 (Fisher's exact test), Q value = 0.093
Table S331. Gene #78: '20q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 108 | 197 | 177 |
| 20Q LOSS MUTATED | 0 | 1 | 6 |
| 20Q LOSS WILD-TYPE | 108 | 196 | 171 |
Figure S331. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 0.0111 (Fisher's exact test), Q value = 0.043
Table S332. Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 21Q LOSS MUTATED | 10 | 26 | 22 | 6 |
| 21Q LOSS WILD-TYPE | 35 | 37 | 43 | 37 |
Figure S332. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00253 (Fisher's exact test), Q value = 0.013
Table S333. Gene #79: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 21Q LOSS MUTATED | 10 | 38 | 16 |
| 21Q LOSS WILD-TYPE | 40 | 51 | 61 |
Figure S333. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S334. Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 21Q LOSS MUTATED | 32 | 104 | 43 | 14 |
| 21Q LOSS WILD-TYPE | 183 | 143 | 89 | 8 |
Figure S334. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 6e-05 (Fisher's exact test), Q value = 5e-04
Table S335. Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 21Q LOSS MUTATED | 71 | 28 | 35 | 57 |
| 21Q LOSS WILD-TYPE | 85 | 100 | 96 | 141 |
Figure S335. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 0.00218 (Fisher's exact test), Q value = 0.011
Table S336. Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 21Q LOSS MUTATED | 30 | 24 | 10 | 21 | 35 | 51 | 20 |
| 21Q LOSS WILD-TYPE | 50 | 62 | 54 | 36 | 55 | 87 | 78 |
Figure S336. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00798 (Fisher's exact test), Q value = 0.033
Table S337. Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 21Q LOSS MUTATED | 16 | 17 | 6 | 32 | 13 | 21 | 25 | 8 | 30 |
| 21Q LOSS WILD-TYPE | 33 | 57 | 23 | 54 | 64 | 33 | 32 | 24 | 51 |
Figure S337. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00689 (Fisher's exact test), Q value = 0.029
Table S338. Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 45 | 63 | 65 | 43 |
| 22Q LOSS MUTATED | 12 | 28 | 27 | 7 |
| 22Q LOSS WILD-TYPE | 33 | 35 | 38 | 36 |
Figure S338. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 2e-05 (Fisher's exact test), Q value = 0.00019
Table S339. Gene #80: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 89 | 77 |
| 22Q LOSS MUTATED | 5 | 40 | 29 |
| 22Q LOSS WILD-TYPE | 45 | 49 | 48 |
Figure S339. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S340. Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 215 | 247 | 132 | 22 |
| 22Q LOSS MUTATED | 25 | 120 | 46 | 12 |
| 22Q LOSS WILD-TYPE | 190 | 127 | 86 | 10 |
Figure S340. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0489 (Fisher's exact test), Q value = 0.14
Table S341. Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 156 | 128 | 131 | 198 |
| 22Q LOSS MUTATED | 62 | 31 | 42 | 67 |
| 22Q LOSS WILD-TYPE | 94 | 97 | 89 | 131 |
Figure S341. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 1e-04
Table S342. Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 80 | 86 | 64 | 57 | 90 | 138 | 98 |
| 22Q LOSS MUTATED | 30 | 27 | 5 | 23 | 35 | 59 | 23 |
| 22Q LOSS WILD-TYPE | 50 | 59 | 59 | 34 | 55 | 79 | 75 |
Figure S342. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00139 (Fisher's exact test), Q value = 0.008
Table S343. Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| 22Q LOSS MUTATED | 14 | 23 | 2 | 33 | 15 | 22 | 25 | 11 | 32 |
| 22Q LOSS WILD-TYPE | 35 | 51 | 27 | 53 | 62 | 32 | 32 | 21 | 49 |
Figure S343. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0134 (Fisher's exact test), Q value = 0.05
Table S344. Gene #81: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 108 | 197 | 177 |
| XP LOSS MUTATED | 12 | 41 | 19 |
| XP LOSS WILD-TYPE | 96 | 156 | 158 |
Figure S344. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 0.0146 (Fisher's exact test), Q value = 0.054
Table S345. Gene #81: 'xp loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 228 | 168 | 86 |
| XP LOSS MUTATED | 23 | 33 | 16 |
| XP LOSS WILD-TYPE | 205 | 135 | 70 |
Figure S345. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 0.0292 (Fisher's exact test), Q value = 0.091
Table S346. Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 63 | 16 | 34 | 22 |
| XP LOSS MUTATED | 4 | 5 | 7 | 3 |
| XP LOSS WILD-TYPE | 59 | 11 | 27 | 19 |
Figure S346. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.0334 (Fisher's exact test), Q value = 0.1
Table S347. Gene #82: 'xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 228 | 168 | 86 |
| XQ LOSS MUTATED | 22 | 31 | 9 |
| XQ LOSS WILD-TYPE | 206 | 137 | 77 |
Figure S347. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 0.0487 (Fisher's exact test), Q value = 0.14
Table S348. Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 49 | 74 | 29 | 86 | 77 | 54 | 57 | 32 | 81 |
| XQ LOSS MUTATED | 5 | 5 | 6 | 15 | 6 | 3 | 9 | 1 | 14 |
| XQ LOSS WILD-TYPE | 44 | 69 | 23 | 71 | 71 | 51 | 48 | 31 | 67 |
Figure S348. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00529 (Fisher's exact test), Q value = 0.024
Table S349. Gene #82: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 63 | 16 | 34 | 22 |
| XQ LOSS MUTATED | 3 | 5 | 8 | 2 |
| XQ LOSS WILD-TYPE | 60 | 11 | 26 | 20 |
Figure S349. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #12: '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/COADREAD-TP/22524545/transformed.cor.cli.txt
-
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/COADREAD-TP/22555066/COADREAD-TP.transferedmergedcluster.txt
-
Number of patients = 616
-
Number of significantly arm-level cnvs = 82
-
Number of molecular subtypes = 12
-
Exclude genes that fewer than K tumors have mutations, K = 3
For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.