This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and subtypes.
Testing the association between copy number variation 80 arm-level results and 10 molecular subtypes across 913 patients, 374 significant findings detected with Q value < 0.25.
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1p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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1q gain cnv correlated to 'MRNA_CNMF', 'CN_CNMF', and 'METHLYATION_CNMF'.
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2p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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2q gain cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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3p gain cnv correlated to 'CN_CNMF'.
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3q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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4p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.
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4q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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5p gain cnv correlated to 'CN_CNMF'.
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5q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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6p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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6q gain cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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7q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
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8p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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8q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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9p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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9q gain cnv correlated to 'CN_CNMF'.
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10p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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10q gain cnv correlated to 'CN_CNMF'.
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11q gain cnv correlated to 'CN_CNMF'.
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12p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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12q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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14q gain cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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16p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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17q gain cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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18p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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18q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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19p gain cnv correlated to 'CN_CNMF'.
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19q gain cnv correlated to 'CN_CNMF'.
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20p gain cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.
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20q gain cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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21q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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22q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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Xq gain cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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1p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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2p loss cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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2q loss cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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3p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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4p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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4q 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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5p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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5q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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6p loss cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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6q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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7p loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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7q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
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8p loss cnv correlated to 'MRNA_CNMF', 'CN_CNMF', and 'METHLYATION_CNMF'.
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9p loss cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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9q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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10p loss cnv correlated to 'CN_CNMF'.
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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', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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11q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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12p loss cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
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12q loss cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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13q loss cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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14q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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15q loss cnv correlated to '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', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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16q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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17p loss cnv correlated to 'MRNA_CNMF', 'CN_CNMF', and 'METHLYATION_CNMF'.
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17q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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18p loss cnv correlated to 'MRNA_CNMF', 'CN_CNMF', and 'METHLYATION_CNMF'.
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18q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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19p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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19q loss cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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20p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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20q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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21q loss cnv correlated to 'CN_CNMF'.
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22q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Xq loss cnv correlated to 'MIRSEQ_CHIERARCHICAL'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 80 arm-level results and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 374 significant findings detected.
Molecular subtypes |
MRNA CNMF |
MRNA CHIERARCHICAL |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
||
nCNV (%) | nWild-Type | Chi-square test | Fisher's exact test | Chi-square test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
2p gain | 0 (0%) | 865 |
1.06e-08 (7.28e-06) |
3.56e-11 (2.57e-08) |
3.7e-10 (2.62e-07) |
4.62e-05 (0.0247) |
1.97e-08 (1.33e-05) |
3.14e-08 (2.1e-05) |
7.82e-12 (5.7e-09) |
7.35e-14 (5.5e-11) |
7.96e-11 (5.7e-08) |
3.26e-08 (2.18e-05) |
10p gain | 0 (0%) | 803 |
7.38e-11 (5.3e-08) |
9.62e-08 (6.31e-05) |
5.04e-15 (3.85e-12) |
3.37e-15 (2.58e-12) |
2.39e-05 (0.0133) |
1.42e-06 (0.000878) |
1.15e-15 (8.85e-13) |
2.46e-16 (1.9e-13) |
2.44e-12 (1.8e-09) |
2.15e-14 (1.62e-11) |
4p loss | 0 (0%) | 728 |
4.5e-12 (3.29e-09) |
1.24e-12 (9.11e-10) |
9.98e-28 (7.93e-25) |
3.87e-14 (2.91e-11) |
0.00014 (0.0692) |
7.57e-06 (0.0044) |
2.85e-17 (2.21e-14) |
9.21e-18 (7.18e-15) |
6.76e-14 (5.07e-11) |
5.98e-15 (4.56e-12) |
5p loss | 0 (0%) | 840 |
1.49e-08 (1.01e-05) |
4.14e-06 (0.00244) |
8.97e-21 (7.04e-18) |
4.03e-12 (2.95e-09) |
4.28e-05 (0.0229) |
6.72e-06 (0.00391) |
1.79e-08 (1.21e-05) |
3.4e-08 (2.27e-05) |
1.86e-14 (1.41e-11) |
1.1e-16 (8.48e-14) |
5q loss | 0 (0%) | 789 |
4.14e-19 (3.24e-16) |
9.95e-15 (7.55e-12) |
4.59e-45 (3.67e-42) |
1.21e-32 (9.64e-30) |
1.86e-09 (1.29e-06) |
6.93e-11 (4.98e-08) |
4.87e-22 (3.83e-19) |
9.55e-24 (7.56e-21) |
1.06e-27 (8.39e-25) |
1.15e-33 (9.17e-31) |
14q loss | 0 (0%) | 777 |
1.09e-10 (7.8e-08) |
8.5e-08 (5.6e-05) |
2.6e-22 (2.05e-19) |
6.83e-16 (5.27e-13) |
0.000185 (0.0897) |
8.52e-05 (0.0438) |
2.46e-11 (1.78e-08) |
1.53e-11 (1.11e-08) |
5.57e-13 (4.13e-10) |
1.18e-13 (8.81e-11) |
16q loss | 0 (0%) | 523 |
7.08e-08 (4.68e-05) |
1.75e-13 (1.3e-10) |
9.63e-12 (7.01e-09) |
6.1e-17 (4.73e-14) |
8.18e-06 (0.00473) |
1.02e-09 (7.12e-07) |
1.01e-16 (7.81e-14) |
8.02e-20 (6.29e-17) |
9.39e-15 (7.14e-12) |
4.4e-18 (3.43e-15) |
17q loss | 0 (0%) | 770 |
1.08e-10 (7.74e-08) |
1.72e-06 (0.00106) |
8.88e-11 (6.35e-08) |
7.48e-05 (0.0388) |
9.69e-10 (6.78e-07) |
6.4e-07 (0.000404) |
1.9e-10 (1.35e-07) |
4.84e-08 (3.22e-05) |
9.64e-07 (0.000605) |
2.69e-05 (0.0148) |
22q loss | 0 (0%) | 607 |
4.25e-05 (0.0228) |
1.42e-07 (9.23e-05) |
2.97e-06 (0.00179) |
5.32e-07 (0.000338) |
0.000476 (0.208) |
1.64e-05 (0.0092) |
2.18e-10 (1.55e-07) |
2.62e-11 (1.89e-08) |
1.57e-08 (1.07e-05) |
0.000171 (0.0839) |
1p gain | 0 (0%) | 818 |
1.33e-05 (0.00755) |
6.2e-07 (0.000392) |
3.78e-07 (0.000242) |
0.0198 (1.00) |
2.11e-05 (0.0118) |
0.000125 (0.0622) |
1.32e-07 (8.61e-05) |
2.53e-06 (0.00154) |
3.47e-05 (0.0188) |
2.24e-05 (0.0125) |
6p gain | 0 (0%) | 809 |
0.000185 (0.0897) |
4.92e-05 (0.0261) |
1e-14 (7.58e-12) |
6.04e-11 (4.35e-08) |
0.00785 (1.00) |
0.0427 (1.00) |
1.69e-09 (1.18e-06) |
3.84e-09 (2.66e-06) |
2.95e-09 (2.04e-06) |
3.86e-09 (2.66e-06) |
8q gain | 0 (0%) | 532 |
2.29e-05 (0.0127) |
0.000315 (0.147) |
1.33e-23 (1.05e-20) |
8.16e-13 (6.03e-10) |
0.668 (1.00) |
0.503 (1.00) |
1.36e-08 (9.29e-06) |
1.11e-07 (7.25e-05) |
1.05e-09 (7.32e-07) |
5.51e-06 (0.00322) |
9p gain | 0 (0%) | 845 |
1.38e-08 (9.4e-06) |
1.6e-08 (1.09e-05) |
1.79e-08 (1.21e-05) |
0.000842 (0.347) |
0.00881 (1.00) |
0.000106 (0.0537) |
8.46e-08 (5.58e-05) |
3.98e-09 (2.74e-06) |
1.11e-06 (0.00069) |
1.44e-07 (9.34e-05) |
21q gain | 0 (0%) | 809 |
5.97e-05 (0.0314) |
0.00019 (0.0921) |
7.1e-10 (4.97e-07) |
4.67e-09 (3.21e-06) |
0.0684 (1.00) |
0.00554 (1.00) |
2.05e-11 (1.49e-08) |
1.13e-10 (8.03e-08) |
3.95e-05 (0.0213) |
3.66e-07 (0.000235) |
4q loss | 0 (0%) | 758 |
1.79e-06 (0.0011) |
2.1e-08 (1.42e-05) |
7.17e-21 (5.64e-18) |
1.19e-10 (8.46e-08) |
0.0168 (1.00) |
0.00171 (0.651) |
4.88e-12 (3.56e-09) |
1.13e-12 (8.31e-10) |
4.17e-07 (0.000266) |
4.61e-10 (3.24e-07) |
6q loss | 0 (0%) | 742 |
4.71e-05 (0.0252) |
9.19e-07 (0.000577) |
1.2e-14 (9.07e-12) |
6.48e-08 (4.29e-05) |
0.00055 (0.236) |
0.0052 (1.00) |
2.4e-08 (1.62e-05) |
5.38e-07 (0.000341) |
0.00447 (1.00) |
2.54e-06 (0.00154) |
2q gain | 0 (0%) | 888 |
0.00458 (1.00) |
1.99e-05 (0.0111) |
0.000123 (0.0611) |
0.00625 (1.00) |
1.54e-07 (9.95e-05) |
0.000444 (0.198) |
3.22e-06 (0.00193) |
7.38e-07 (0.000465) |
0.000367 (0.169) |
0.00137 (0.54) |
16p gain | 0 (0%) | 659 |
1.01e-05 (0.00578) |
8.07e-05 (0.0416) |
0.0119 (1.00) |
5.27e-07 (0.000335) |
0.000119 (0.0594) |
6.58e-05 (0.0345) |
1.2e-05 (0.00684) |
2.56e-06 (0.00155) |
0.00235 (0.866) |
0.0184 (1.00) |
1p loss | 0 (0%) | 790 |
0.000228 (0.109) |
3.98e-10 (2.8e-07) |
2.44e-23 (1.93e-20) |
1.84e-06 (0.00113) |
0.702 (1.00) |
0.175 (1.00) |
3.92e-11 (2.83e-08) |
2.18e-13 (1.62e-10) |
0.000899 (0.37) |
0.000177 (0.0863) |
2p loss | 0 (0%) | 838 |
0.0116 (1.00) |
3.09e-05 (0.0169) |
2.58e-12 (1.89e-09) |
1.72e-07 (0.000111) |
0.0361 (1.00) |
0.00428 (1.00) |
2.09e-07 (0.000135) |
7.81e-07 (0.000491) |
0.000265 (0.125) |
0.00057 (0.244) |
2q loss | 0 (0%) | 822 |
0.112 (1.00) |
0.000444 (0.198) |
2.48e-12 (1.82e-09) |
4.01e-06 (0.00237) |
0.0688 (1.00) |
0.0281 (1.00) |
0.000387 (0.176) |
0.000322 (0.15) |
0.000495 (0.215) |
0.000423 (0.189) |
3p loss | 0 (0%) | 821 |
0.000694 (0.29) |
0.000914 (0.374) |
2.58e-09 (1.79e-06) |
3.42e-05 (0.0186) |
0.00233 (0.864) |
5.31e-05 (0.0281) |
3.32e-05 (0.018) |
0.000279 (0.131) |
2.18e-06 (0.00133) |
0.000443 (0.198) |
9p loss | 0 (0%) | 723 |
2.39e-05 (0.0133) |
0.00148 (0.574) |
5.07e-19 (3.97e-16) |
1.08e-13 (8.09e-11) |
0.0381 (1.00) |
0.858 (1.00) |
3.34e-06 (0.00199) |
7.71e-06 (0.00447) |
5.65e-05 (0.0297) |
2.37e-07 (0.000152) |
11q loss | 0 (0%) | 684 |
2.01e-07 (0.000129) |
0.000327 (0.152) |
2.04e-31 (1.62e-28) |
1.5e-11 (1.09e-08) |
0.208 (1.00) |
0.191 (1.00) |
4.03e-06 (0.00238) |
1.26e-05 (0.00716) |
0.00368 (1.00) |
3.01e-05 (0.0165) |
12q loss | 0 (0%) | 861 |
0.000708 (0.295) |
0.000244 (0.116) |
9.88e-05 (0.0504) |
4.1e-09 (2.82e-06) |
0.00486 (1.00) |
0.00265 (0.974) |
4.09e-08 (2.72e-05) |
1.98e-07 (0.000128) |
3.21e-06 (0.00192) |
1.34e-06 (0.000833) |
15q loss | 0 (0%) | 751 |
0.00701 (1.00) |
0.000121 (0.0604) |
3.85e-17 (2.99e-14) |
4.94e-07 (0.000315) |
0.117 (1.00) |
0.00548 (1.00) |
0.000106 (0.0536) |
0.000116 (0.058) |
7.41e-05 (0.0385) |
3.04e-06 (0.00182) |
19p loss | 0 (0%) | 846 |
1.65e-05 (0.00926) |
0.000461 (0.203) |
7.77e-13 (5.75e-10) |
1.43e-08 (9.72e-06) |
0.424 (1.00) |
0.0741 (1.00) |
0.000554 (0.237) |
0.000512 (0.222) |
0.000287 (0.135) |
0.000754 (0.312) |
3q gain | 0 (0%) | 814 |
0.0146 (1.00) |
0.00685 (1.00) |
2.38e-09 (1.65e-06) |
0.000321 (0.15) |
0.0149 (1.00) |
0.11 (1.00) |
0.000357 (0.165) |
0.000108 (0.0544) |
4.79e-06 (0.00282) |
2.53e-06 (0.00154) |
6q gain | 0 (0%) | 852 |
0.00194 (0.73) |
0.0048 (1.00) |
1.72e-14 (1.3e-11) |
0.00131 (0.522) |
0.000535 (0.23) |
0.0271 (1.00) |
4.89e-06 (0.00287) |
3.35e-06 (0.00199) |
6.69e-05 (0.035) |
3.4e-06 (0.00202) |
18p gain | 0 (0%) | 826 |
0.00268 (0.983) |
0.00417 (1.00) |
2.57e-07 (0.000165) |
1.03e-07 (6.74e-05) |
0.0139 (1.00) |
0.0126 (1.00) |
3.57e-06 (0.00211) |
1.42e-07 (9.23e-05) |
1.52e-05 (0.00857) |
0.000104 (0.0528) |
20q gain | 0 (0%) | 637 |
1.44e-05 (0.00815) |
0.00883 (1.00) |
3.32e-29 (2.65e-26) |
2.35e-14 (1.77e-11) |
0.199 (1.00) |
0.792 (1.00) |
3.01e-05 (0.0165) |
2.95e-06 (0.00178) |
5.37e-06 (0.00314) |
0.0136 (1.00) |
Xq gain | 0 (0%) | 892 |
0.000738 (0.306) |
0.000165 (0.0811) |
0.000166 (0.0817) |
0.0193 (1.00) |
0.0754 (1.00) |
0.00725 (1.00) |
0.000388 (0.176) |
1.47e-05 (0.00831) |
4.83e-05 (0.0257) |
0.000182 (0.0886) |
6p loss | 0 (0%) | 804 |
0.0142 (1.00) |
9.32e-05 (0.0476) |
1.09e-09 (7.57e-07) |
4.96e-05 (0.0263) |
0.0131 (1.00) |
0.00604 (1.00) |
1.23e-05 (0.00703) |
1.85e-05 (0.0104) |
0.0197 (1.00) |
0.000394 (0.178) |
9q loss | 0 (0%) | 766 |
0.0075 (1.00) |
0.000614 (0.259) |
9.61e-16 (7.4e-13) |
1.74e-12 (1.28e-09) |
0.0135 (1.00) |
0.18 (1.00) |
9.07e-08 (5.96e-05) |
8.3e-06 (0.00479) |
4.12e-05 (0.0222) |
2.12e-10 (1.51e-07) |
13q loss | 0 (0%) | 646 |
0.000134 (0.0664) |
0.000611 (0.259) |
1.62e-27 (1.28e-24) |
2.84e-10 (2.01e-07) |
0.727 (1.00) |
0.489 (1.00) |
0.000411 (0.185) |
0.000523 (0.226) |
2.49e-08 (1.67e-05) |
0.00278 (1.00) |
4p gain | 0 (0%) | 884 |
1.38e-06 (0.000858) |
2.66e-05 (0.0147) |
1.12e-06 (7e-04) |
4.15e-05 (0.0224) |
0.0485 (1.00) |
0.0396 (1.00) |
0.0221 (1.00) |
0.00514 (1.00) |
0.000222 (0.107) |
0.00146 (0.569) |
4q gain | 0 (0%) | 886 |
1.38e-06 (0.000858) |
2.66e-05 (0.0147) |
1.27e-08 (8.7e-06) |
0.000389 (0.176) |
0.0551 (1.00) |
0.0126 (1.00) |
0.0159 (1.00) |
0.00313 (1.00) |
0.00394 (1.00) |
0.000218 (0.105) |
12p gain | 0 (0%) | 798 |
0.00691 (1.00) |
0.00154 (0.593) |
9e-14 (6.72e-11) |
4.76e-05 (0.0254) |
0.246 (1.00) |
0.0679 (1.00) |
9.11e-05 (0.0466) |
0.000256 (0.121) |
0.000371 (0.17) |
0.0017 (0.651) |
17q gain | 0 (0%) | 790 |
4.01e-07 (0.000256) |
0.00782 (1.00) |
2.64e-18 (2.06e-15) |
3.27e-06 (0.00196) |
0.464 (1.00) |
0.00912 (1.00) |
0.000108 (0.0542) |
1.19e-06 (0.000741) |
0.0126 (1.00) |
0.00416 (1.00) |
10q loss | 0 (0%) | 802 |
0.000512 (0.222) |
0.00147 (0.571) |
4.34e-14 (3.26e-11) |
9.95e-07 (0.000623) |
0.00524 (1.00) |
0.112 (1.00) |
5.36e-05 (0.0283) |
0.000363 (0.167) |
0.00792 (1.00) |
0.00126 (0.502) |
19q loss | 0 (0%) | 860 |
7.41e-05 (0.0385) |
0.00138 (0.544) |
3.66e-10 (2.59e-07) |
1.62e-05 (0.00912) |
0.101 (1.00) |
0.0767 (1.00) |
0.0017 (0.651) |
8.9e-06 (0.00512) |
0.00554 (1.00) |
0.00046 (0.202) |
20p loss | 0 (0%) | 860 |
0.0561 (1.00) |
0.0463 (1.00) |
1.42e-06 (0.000878) |
2.42e-05 (0.0134) |
0.362 (1.00) |
0.43 (1.00) |
0.00268 (0.983) |
0.000252 (0.12) |
0.000176 (0.0863) |
0.000223 (0.107) |
20q loss | 0 (0%) | 884 |
0.0579 (1.00) |
0.1 (1.00) |
6.97e-05 (0.0364) |
2.82e-06 (0.00171) |
0.496 (1.00) |
0.172 (1.00) |
0.00416 (1.00) |
0.00032 (0.149) |
0.000443 (0.198) |
3.3e-05 (0.018) |
8p gain | 0 (0%) | 738 |
0.0334 (1.00) |
0.0797 (1.00) |
5.71e-15 (4.36e-12) |
0.00037 (0.17) |
0.197 (1.00) |
0.457 (1.00) |
0.00026 (0.123) |
1.18e-05 (0.00679) |
0.00322 (1.00) |
0.2 (1.00) |
20p gain | 0 (0%) | 674 |
3.66e-05 (0.0198) |
0.0269 (1.00) |
3.08e-23 (2.43e-20) |
3.06e-08 (2.05e-05) |
0.0217 (1.00) |
0.133 (1.00) |
0.00296 (1.00) |
0.000719 (0.299) |
0.000293 (0.138) |
0.523 (1.00) |
22q gain | 0 (0%) | 870 |
0.0749 (1.00) |
0.00523 (1.00) |
3.75e-08 (2.5e-05) |
0.000999 (0.403) |
0.0685 (1.00) |
0.153 (1.00) |
4.84e-06 (0.00285) |
1.57e-06 (0.000965) |
0.00134 (0.531) |
1.03e-06 (0.000646) |
16p loss | 0 (0%) | 858 |
0.00385 (1.00) |
0.0204 (1.00) |
1.42e-05 (0.00803) |
2.47e-05 (0.0136) |
0.184 (1.00) |
0.286 (1.00) |
0.00334 (1.00) |
0.00469 (1.00) |
0.000225 (0.108) |
0.000233 (0.111) |
1q gain | 0 (0%) | 426 |
7.04e-05 (0.0367) |
0.714 (1.00) |
3.02e-08 (2.03e-05) |
2.87e-15 (2.2e-12) |
0.103 (1.00) |
0.186 (1.00) |
0.147 (1.00) |
0.12 (1.00) |
0.0467 (1.00) |
0.0154 (1.00) |
5q gain | 0 (0%) | 805 |
0.00552 (1.00) |
0.00581 (1.00) |
7.31e-17 (5.67e-14) |
0.00965 (1.00) |
0.0042 (1.00) |
0.00691 (1.00) |
0.00152 (0.587) |
0.000152 (0.0749) |
0.000236 (0.113) |
0.00172 (0.653) |
14q gain | 0 (0%) | 836 |
0.000674 (0.282) |
0.012 (1.00) |
0.000978 (0.395) |
0.00684 (1.00) |
0.949 (1.00) |
0.316 (1.00) |
5.13e-06 (0.00301) |
0.000453 (0.2) |
8.16e-05 (0.042) |
0.335 (1.00) |
18q gain | 0 (0%) | 836 |
0.00117 (0.469) |
0.03 (1.00) |
6.69e-06 (0.0039) |
0.0127 (1.00) |
0.311 (1.00) |
0.274 (1.00) |
0.000346 (0.16) |
9.95e-05 (0.0506) |
0.00103 (0.413) |
0.00782 (1.00) |
7p loss | 0 (0%) | 865 |
0.167 (1.00) |
0.024 (1.00) |
9.93e-06 (0.00571) |
0.0017 (0.651) |
0.371 (1.00) |
0.438 (1.00) |
0.00268 (0.983) |
0.000451 (0.2) |
0.000601 (0.256) |
0.000466 (0.204) |
8p loss | 0 (0%) | 643 |
0.000103 (0.0525) |
0.178 (1.00) |
2.58e-15 (1.98e-12) |
9.84e-08 (6.44e-05) |
0.647 (1.00) |
0.909 (1.00) |
0.00628 (1.00) |
0.0232 (1.00) |
0.0103 (1.00) |
0.00842 (1.00) |
11p loss | 0 (0%) | 769 |
0.0342 (1.00) |
0.156 (1.00) |
8.5e-15 (6.47e-12) |
8.61e-08 (5.66e-05) |
0.0925 (1.00) |
0.0151 (1.00) |
0.0232 (1.00) |
0.0228 (1.00) |
0.00593 (1.00) |
5.61e-05 (0.0296) |
17p loss | 0 (0%) | 540 |
8.23e-06 (0.00476) |
0.694 (1.00) |
6.2e-14 (4.65e-11) |
5.8e-08 (3.85e-05) |
0.00142 (0.555) |
0.123 (1.00) |
0.193 (1.00) |
0.458 (1.00) |
0.0342 (1.00) |
0.0753 (1.00) |
18p loss | 0 (0%) | 738 |
0.000377 (0.172) |
0.645 (1.00) |
6.18e-10 (4.34e-07) |
3.32e-06 (0.00198) |
0.892 (1.00) |
0.962 (1.00) |
0.0193 (1.00) |
0.267 (1.00) |
0.0262 (1.00) |
0.0095 (1.00) |
12q gain | 0 (0%) | 826 |
0.0372 (1.00) |
0.0631 (1.00) |
1.81e-15 (1.39e-12) |
8.74e-05 (0.0448) |
0.275 (1.00) |
0.4 (1.00) |
0.00218 (0.813) |
0.0257 (1.00) |
0.0379 (1.00) |
0.191 (1.00) |
7q loss | 0 (0%) | 849 |
0.327 (1.00) |
0.0996 (1.00) |
0.000443 (0.198) |
0.206 (1.00) |
0.236 (1.00) |
0.421 (1.00) |
0.0227 (1.00) |
0.00459 (1.00) |
0.00423 (1.00) |
1.37e-05 (0.00778) |
12p loss | 0 (0%) | 846 |
0.305 (1.00) |
0.0978 (1.00) |
0.0158 (1.00) |
1.57e-06 (0.000965) |
0.149 (1.00) |
0.274 (1.00) |
7.88e-05 (0.0407) |
0.000909 (0.373) |
0.000958 (0.388) |
0.000669 (0.281) |
18q loss | 0 (0%) | 736 |
0.00133 (0.527) |
0.644 (1.00) |
6.11e-13 (4.52e-10) |
7.01e-08 (4.64e-05) |
0.535 (1.00) |
0.828 (1.00) |
0.00179 (0.679) |
0.166 (1.00) |
0.0377 (1.00) |
0.0618 (1.00) |
3p gain | 0 (0%) | 856 |
0.346 (1.00) |
0.153 (1.00) |
6.6e-07 (0.000417) |
0.532 (1.00) |
0.315 (1.00) |
0.151 (1.00) |
0.277 (1.00) |
0.0321 (1.00) |
0.132 (1.00) |
0.0196 (1.00) |
5p gain | 0 (0%) | 741 |
0.156 (1.00) |
0.421 (1.00) |
4.56e-10 (3.21e-07) |
0.153 (1.00) |
0.593 (1.00) |
0.459 (1.00) |
0.837 (1.00) |
0.123 (1.00) |
0.185 (1.00) |
0.853 (1.00) |
7q gain | 0 (0%) | 795 |
0.00273 (0.994) |
0.0094 (1.00) |
0.00892 (1.00) |
0.00182 (0.689) |
0.404 (1.00) |
0.271 (1.00) |
0.0199 (1.00) |
0.000482 (0.21) |
0.0577 (1.00) |
0.02 (1.00) |
9q gain | 0 (0%) | 857 |
0.455 (1.00) |
0.0805 (1.00) |
0.000148 (0.0732) |
0.161 (1.00) |
1 (1.00) |
0.488 (1.00) |
0.0493 (1.00) |
0.0033 (1.00) |
0.0115 (1.00) |
0.0346 (1.00) |
10q gain | 0 (0%) | 868 |
0.0114 (1.00) |
0.0144 (1.00) |
0.000533 (0.23) |
0.0159 (1.00) |
0.073 (1.00) |
0.0476 (1.00) |
0.00418 (1.00) |
0.00196 (0.736) |
0.0125 (1.00) |
0.0113 (1.00) |
11q gain | 0 (0%) | 867 |
0.537 (1.00) |
0.77 (1.00) |
0.000131 (0.0649) |
0.153 (1.00) |
0.909 (1.00) |
0.745 (1.00) |
0.316 (1.00) |
0.539 (1.00) |
0.0417 (1.00) |
0.0232 (1.00) |
19p gain | 0 (0%) | 844 |
0.125 (1.00) |
0.0293 (1.00) |
0.000382 (0.174) |
0.141 (1.00) |
0.0373 (1.00) |
0.114 (1.00) |
0.00646 (1.00) |
0.000944 (0.383) |
0.00148 (0.576) |
0.000918 (0.374) |
19q gain | 0 (0%) | 827 |
0.142 (1.00) |
0.0376 (1.00) |
0.000415 (0.186) |
0.111 (1.00) |
0.154 (1.00) |
0.251 (1.00) |
0.0256 (1.00) |
0.0021 (0.783) |
0.00371 (1.00) |
0.0145 (1.00) |
10p loss | 0 (0%) | 838 |
0.025 (1.00) |
0.0119 (1.00) |
2.55e-06 (0.00154) |
0.0213 (1.00) |
0.716 (1.00) |
0.46 (1.00) |
0.0016 (0.618) |
0.0272 (1.00) |
0.0912 (1.00) |
0.0987 (1.00) |
21q loss | 0 (0%) | 827 |
0.0238 (1.00) |
0.269 (1.00) |
1.67e-06 (0.00102) |
0.0576 (1.00) |
1 (1.00) |
0.812 (1.00) |
0.615 (1.00) |
0.622 (1.00) |
0.0408 (1.00) |
0.364 (1.00) |
Xq loss | 0 (0%) | 882 |
0.668 (1.00) |
0.0736 (1.00) |
0.000611 (0.259) |
0.00451 (1.00) |
0.0154 (1.00) |
0.2 (1.00) |
0.00209 (0.781) |
0.000923 (0.376) |
0.00233 (0.864) |
0.000357 (0.165) |
7p gain | 0 (0%) | 755 |
0.151 (1.00) |
0.257 (1.00) |
0.0621 (1.00) |
0.0146 (1.00) |
0.947 (1.00) |
0.52 (1.00) |
0.1 (1.00) |
0.0459 (1.00) |
0.51 (1.00) |
0.469 (1.00) |
11p gain | 0 (0%) | 846 |
0.943 (1.00) |
0.606 (1.00) |
0.00507 (1.00) |
0.0342 (1.00) |
0.318 (1.00) |
0.155 (1.00) |
0.336 (1.00) |
0.705 (1.00) |
0.0255 (1.00) |
0.0604 (1.00) |
13q gain | 0 (0%) | 866 |
0.525 (1.00) |
0.619 (1.00) |
0.0284 (1.00) |
0.0306 (1.00) |
0.0642 (1.00) |
0.258 (1.00) |
0.000625 (0.263) |
0.0245 (1.00) |
0.0529 (1.00) |
0.0245 (1.00) |
15q gain | 0 (0%) | 868 |
0.727 (1.00) |
0.474 (1.00) |
0.682 (1.00) |
0.145 (1.00) |
0.817 (1.00) |
0.561 (1.00) |
0.0548 (1.00) |
0.141 (1.00) |
0.391 (1.00) |
0.428 (1.00) |
16q gain | 0 (0%) | 857 |
0.531 (1.00) |
0.215 (1.00) |
0.000841 (0.347) |
0.0705 (1.00) |
0.134 (1.00) |
0.775 (1.00) |
0.134 (1.00) |
0.0146 (1.00) |
0.00434 (1.00) |
0.000609 (0.259) |
17p gain | 0 (0%) | 866 |
0.0217 (1.00) |
0.396 (1.00) |
0.00182 (0.689) |
0.619 (1.00) |
0.18 (1.00) |
0.2 (1.00) |
0.633 (1.00) |
0.641 (1.00) |
0.89 (1.00) |
0.842 (1.00) |
1q loss | 0 (0%) | 891 |
0.243 (1.00) |
0.0336 (1.00) |
0.00419 (1.00) |
0.211 (1.00) |
0.272 (1.00) |
0.739 (1.00) |
0.0172 (1.00) |
0.0102 (1.00) |
0.185 (1.00) |
0.15 (1.00) |
3q loss | 0 (0%) | 869 |
0.0197 (1.00) |
0.00585 (1.00) |
0.00104 (0.415) |
0.00415 (1.00) |
0.185 (1.00) |
0.0657 (1.00) |
0.00925 (1.00) |
0.0314 (1.00) |
0.00134 (0.531) |
0.0279 (1.00) |
8q loss | 0 (0%) | 867 |
0.507 (1.00) |
0.526 (1.00) |
0.203 (1.00) |
0.103 (1.00) |
0.688 (1.00) |
0.566 (1.00) |
0.0317 (1.00) |
0.26 (1.00) |
0.316 (1.00) |
0.398 (1.00) |
P value = 1.33e-05 (Chi-square test), Q value = 0.0075
Table S1. Gene #1: '1p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
1P GAIN CNV | 11 | 2 | 1 | 27 | 11 | 4 | 4 | 5 |
1P GAIN WILD-TYPE | 113 | 34 | 22 | 68 | 61 | 16 | 99 | 35 |
Figure S1. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D1V1.png)
P value = 6.2e-07 (Fisher's exact test), Q value = 0.00039
Table S2. Gene #1: '1p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 140 | 125 | 248 |
1P GAIN CNV | 14 | 34 | 17 |
1P GAIN WILD-TYPE | 126 | 91 | 231 |
Figure S2. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D1V2.png)
P value = 3.78e-07 (Chi-square test), Q value = 0.00024
Table S3. Gene #1: '1p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
1P GAIN CNV | 21 | 15 | 7 | 46 | 6 |
1P GAIN WILD-TYPE | 326 | 207 | 65 | 177 | 43 |
Figure S3. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D1V3.png)
P value = 2.11e-05 (Fisher's exact test), Q value = 0.012
Table S4. Gene #1: '1p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 147 | 133 | 117 |
1P GAIN CNV | 35 | 13 | 6 |
1P GAIN WILD-TYPE | 112 | 120 | 111 |
Figure S4. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D1V5.png)
P value = 0.000125 (Fisher's exact test), Q value = 0.062
Table S5. Gene #1: '1p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 110 | 126 |
1P GAIN CNV | 20 | 5 | 29 |
1P GAIN WILD-TYPE | 141 | 105 | 97 |
Figure S5. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D1V6.png)
P value = 1.32e-07 (Fisher's exact test), Q value = 8.6e-05
Table S6. Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
1P GAIN CNV | 48 | 11 | 28 |
1P GAIN WILD-TYPE | 186 | 137 | 418 |
Figure S6. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D1V7.png)
P value = 2.53e-06 (Fisher's exact test), Q value = 0.0015
Table S7. Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
1P GAIN CNV | 15 | 30 | 42 |
1P GAIN WILD-TYPE | 201 | 378 | 162 |
Figure S7. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D1V8.png)
P value = 3.47e-05 (Fisher's exact test), Q value = 0.019
Table S8. Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
1P GAIN CNV | 17 | 27 | 45 |
1P GAIN WILD-TYPE | 217 | 365 | 210 |
Figure S8. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D1V9.png)
P value = 2.24e-05 (Fisher's exact test), Q value = 0.012
Table S9. Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
1P GAIN CNV | 27 | 19 | 43 |
1P GAIN WILD-TYPE | 335 | 265 | 192 |
Figure S9. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D1V10.png)
P value = 7.04e-05 (Chi-square test), Q value = 0.037
Table S10. Gene #2: '1q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
1Q GAIN CNV | 53 | 17 | 13 | 53 | 39 | 10 | 80 | 25 |
1Q GAIN WILD-TYPE | 71 | 19 | 10 | 42 | 33 | 10 | 23 | 15 |
Figure S10. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D2V1.png)
P value = 3.02e-08 (Chi-square test), Q value = 2e-05
Table S11. Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
1Q GAIN CNV | 171 | 124 | 63 | 104 | 25 |
1Q GAIN WILD-TYPE | 176 | 98 | 9 | 119 | 24 |
Figure S11. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D2V3.png)
P value = 2.87e-15 (Chi-square test), Q value = 2.2e-12
Table S12. Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
1Q GAIN CNV | 44 | 108 | 60 | 58 | 16 | 26 |
1Q GAIN WILD-TYPE | 57 | 31 | 33 | 79 | 24 | 71 |
Figure S12. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D2V4.png)
P value = 1.06e-08 (Chi-square test), Q value = 7.3e-06
Table S13. Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
2P GAIN CNV | 3 | 0 | 0 | 18 | 11 | 0 | 1 | 0 |
2P GAIN WILD-TYPE | 121 | 36 | 23 | 77 | 61 | 20 | 102 | 40 |
Figure S13. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D3V1.png)
P value = 3.56e-11 (Fisher's exact test), Q value = 2.6e-08
Table S14. Gene #3: '2p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 140 | 125 | 248 |
2P GAIN CNV | 0 | 25 | 8 |
2P GAIN WILD-TYPE | 140 | 100 | 240 |
Figure S14. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D3V2.png)
P value = 3.7e-10 (Chi-square test), Q value = 2.6e-07
Table S15. Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
2P GAIN CNV | 2 | 11 | 3 | 31 | 1 |
2P GAIN WILD-TYPE | 345 | 211 | 69 | 192 | 48 |
Figure S15. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D3V3.png)
P value = 4.62e-05 (Chi-square test), Q value = 0.025
Table S16. Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
2P GAIN CNV | 14 | 1 | 4 | 5 | 1 | 2 |
2P GAIN WILD-TYPE | 87 | 138 | 89 | 132 | 39 | 95 |
Figure S16. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D3V4.png)
P value = 1.97e-08 (Fisher's exact test), Q value = 1.3e-05
Table S17. Gene #3: '2p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 147 | 133 | 117 |
2P GAIN CNV | 24 | 0 | 4 |
2P GAIN WILD-TYPE | 123 | 133 | 113 |
Figure S17. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D3V5.png)
P value = 3.14e-08 (Fisher's exact test), Q value = 2.1e-05
Table S18. Gene #3: '2p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 110 | 126 |
2P GAIN CNV | 4 | 1 | 23 |
2P GAIN WILD-TYPE | 157 | 109 | 103 |
Figure S18. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D3V6.png)
P value = 7.82e-12 (Fisher's exact test), Q value = 5.7e-09
Table S19. Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
2P GAIN CNV | 35 | 0 | 12 |
2P GAIN WILD-TYPE | 199 | 148 | 434 |
Figure S19. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D3V7.png)
P value = 7.35e-14 (Fisher's exact test), Q value = 5.5e-11
Table S20. Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
2P GAIN CNV | 0 | 13 | 34 |
2P GAIN WILD-TYPE | 216 | 395 | 170 |
Figure S20. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D3V8.png)
P value = 7.96e-11 (Fisher's exact test), Q value = 5.7e-08
Table S21. Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
2P GAIN CNV | 1 | 9 | 32 |
2P GAIN WILD-TYPE | 233 | 383 | 223 |
Figure S21. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D3V9.png)
P value = 3.26e-08 (Fisher's exact test), Q value = 2.2e-05
Table S22. Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
2P GAIN CNV | 11 | 3 | 28 |
2P GAIN WILD-TYPE | 351 | 281 | 207 |
Figure S22. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D3V10.png)
P value = 1.99e-05 (Fisher's exact test), Q value = 0.011
Table S23. Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 140 | 125 | 248 |
2Q GAIN CNV | 0 | 13 | 6 |
2Q GAIN WILD-TYPE | 140 | 112 | 242 |
Figure S23. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D4V2.png)
P value = 0.000123 (Chi-square test), Q value = 0.061
Table S24. Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
2Q GAIN CNV | 1 | 6 | 3 | 15 | 0 |
2Q GAIN WILD-TYPE | 346 | 216 | 69 | 208 | 49 |
Figure S24. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D4V3.png)
P value = 1.54e-07 (Fisher's exact test), Q value = 1e-04
Table S25. Gene #4: '2q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 147 | 133 | 117 |
2Q GAIN CNV | 16 | 0 | 0 |
2Q GAIN WILD-TYPE | 131 | 133 | 117 |
Figure S25. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D4V5.png)
P value = 0.000444 (Fisher's exact test), Q value = 0.2
Table S26. Gene #4: '2q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 110 | 126 |
2Q GAIN CNV | 4 | 0 | 12 |
2Q GAIN WILD-TYPE | 157 | 110 | 114 |
Figure S26. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D4V6.png)
P value = 3.22e-06 (Fisher's exact test), Q value = 0.0019
Table S27. Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
2Q GAIN CNV | 18 | 0 | 6 |
2Q GAIN WILD-TYPE | 216 | 148 | 440 |
Figure S27. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D4V7.png)
P value = 7.38e-07 (Fisher's exact test), Q value = 0.00047
Table S28. Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
2Q GAIN CNV | 0 | 7 | 17 |
2Q GAIN WILD-TYPE | 216 | 401 | 187 |
Figure S28. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D4V8.png)
P value = 0.000367 (Fisher's exact test), Q value = 0.17
Table S29. Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
2Q GAIN CNV | 1 | 5 | 14 |
2Q GAIN WILD-TYPE | 233 | 387 | 241 |
Figure S29. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D4V9.png)
P value = 6.6e-07 (Chi-square test), Q value = 0.00042
Table S30. Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
3P GAIN CNV | 5 | 19 | 11 | 14 | 8 |
3P GAIN WILD-TYPE | 342 | 203 | 61 | 209 | 41 |
Figure S30. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D5V3.png)
P value = 2.38e-09 (Chi-square test), Q value = 1.7e-06
Table S31. Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
3Q GAIN CNV | 9 | 26 | 13 | 42 | 9 |
3Q GAIN WILD-TYPE | 338 | 196 | 59 | 181 | 40 |
Figure S31. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D6V3.png)
P value = 0.000321 (Chi-square test), Q value = 0.15
Table S32. Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
3Q GAIN CNV | 18 | 5 | 11 | 13 | 2 | 2 |
3Q GAIN WILD-TYPE | 83 | 134 | 82 | 124 | 38 | 95 |
Figure S32. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D6V4.png)
P value = 0.000357 (Fisher's exact test), Q value = 0.16
Table S33. Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
3Q GAIN CNV | 41 | 7 | 46 |
3Q GAIN WILD-TYPE | 193 | 141 | 400 |
Figure S33. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D6V7.png)
P value = 0.000108 (Fisher's exact test), Q value = 0.054
Table S34. Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
3Q GAIN CNV | 11 | 46 | 37 |
3Q GAIN WILD-TYPE | 205 | 362 | 167 |
Figure S34. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D6V8.png)
P value = 4.79e-06 (Fisher's exact test), Q value = 0.0028
Table S35. Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
3Q GAIN CNV | 11 | 38 | 47 |
3Q GAIN WILD-TYPE | 223 | 354 | 208 |
Figure S35. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D6V9.png)
P value = 2.53e-06 (Fisher's exact test), Q value = 0.0015
Table S36. Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
3Q GAIN CNV | 40 | 13 | 43 |
3Q GAIN WILD-TYPE | 322 | 271 | 192 |
Figure S36. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D6V10.png)
P value = 1.38e-06 (Chi-square test), Q value = 0.00086
Table S37. Gene #7: '4p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
4P GAIN CNV | 15 | 0 | 0 | 0 | 1 | 0 | 1 | 0 |
4P GAIN WILD-TYPE | 109 | 36 | 23 | 95 | 71 | 20 | 102 | 40 |
Figure S37. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D7V1.png)
P value = 2.66e-05 (Fisher's exact test), Q value = 0.015
Table S38. Gene #7: '4p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 140 | 125 | 248 |
4P GAIN CNV | 0 | 0 | 17 |
4P GAIN WILD-TYPE | 140 | 125 | 231 |
Figure S38. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D7V2.png)
P value = 1.12e-06 (Chi-square test), Q value = 7e-04
Table S39. Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
4P GAIN CNV | 1 | 19 | 2 | 4 | 3 |
4P GAIN WILD-TYPE | 346 | 203 | 70 | 219 | 46 |
Figure S39. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D7V3.png)
P value = 4.15e-05 (Chi-square test), Q value = 0.022
Table S40. Gene #7: '4p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
4P GAIN CNV | 0 | 1 | 4 | 12 | 0 | 0 |
4P GAIN WILD-TYPE | 101 | 138 | 89 | 125 | 40 | 97 |
Figure S40. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D7V4.png)
P value = 0.000222 (Fisher's exact test), Q value = 0.11
Table S41. Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
4P GAIN CNV | 3 | 23 | 2 |
4P GAIN WILD-TYPE | 231 | 369 | 253 |
Figure S41. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D7V9.png)
P value = 1.38e-06 (Chi-square test), Q value = 0.00086
Table S42. Gene #8: '4q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
4Q GAIN CNV | 15 | 0 | 0 | 0 | 1 | 0 | 1 | 0 |
4Q GAIN WILD-TYPE | 109 | 36 | 23 | 95 | 71 | 20 | 102 | 40 |
Figure S42. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D8V1.png)
P value = 2.66e-05 (Fisher's exact test), Q value = 0.015
Table S43. Gene #8: '4q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 140 | 125 | 248 |
4Q GAIN CNV | 0 | 0 | 17 |
4Q GAIN WILD-TYPE | 140 | 125 | 231 |
Figure S43. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D8V2.png)
P value = 1.27e-08 (Chi-square test), Q value = 8.7e-06
Table S44. Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
4Q GAIN CNV | 1 | 20 | 1 | 2 | 3 |
4Q GAIN WILD-TYPE | 346 | 202 | 71 | 221 | 46 |
Figure S44. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D8V3.png)
P value = 0.000389 (Chi-square test), Q value = 0.18
Table S45. Gene #8: '4q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
4Q GAIN CNV | 0 | 1 | 3 | 10 | 0 | 0 |
4Q GAIN WILD-TYPE | 101 | 138 | 90 | 127 | 40 | 97 |
Figure S45. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D8V4.png)
P value = 0.000218 (Fisher's exact test), Q value = 0.11
Table S46. Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
4Q GAIN CNV | 21 | 3 | 2 |
4Q GAIN WILD-TYPE | 341 | 281 | 233 |
Figure S46. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D8V10.png)
P value = 4.56e-10 (Chi-square test), Q value = 3.2e-07
Table S47. Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
5P GAIN CNV | 30 | 61 | 26 | 43 | 12 |
5P GAIN WILD-TYPE | 317 | 161 | 46 | 180 | 37 |
Figure S47. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D9V3.png)
P value = 7.31e-17 (Chi-square test), Q value = 5.7e-14
Table S48. Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
5Q GAIN CNV | 20 | 46 | 25 | 8 | 9 |
5Q GAIN WILD-TYPE | 327 | 176 | 47 | 215 | 40 |
Figure S48. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D10V3.png)
P value = 0.000152 (Fisher's exact test), Q value = 0.075
Table S49. Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
5Q GAIN CNV | 23 | 65 | 10 |
5Q GAIN WILD-TYPE | 193 | 343 | 194 |
Figure S49. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D10V8.png)
P value = 0.000236 (Fisher's exact test), Q value = 0.11
Table S50. Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
5Q GAIN CNV | 22 | 64 | 16 |
5Q GAIN WILD-TYPE | 212 | 328 | 239 |
Figure S50. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D10V9.png)
P value = 0.000185 (Chi-square test), Q value = 0.09
Table S51. Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
6P GAIN CNV | 11 | 0 | 0 | 20 | 12 | 5 | 10 | 0 |
6P GAIN WILD-TYPE | 113 | 36 | 23 | 75 | 60 | 15 | 93 | 40 |
Figure S51. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D11V1.png)
P value = 4.92e-05 (Fisher's exact test), Q value = 0.026
Table S52. Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 140 | 125 | 248 |
6P GAIN CNV | 4 | 24 | 30 |
6P GAIN WILD-TYPE | 136 | 101 | 218 |
Figure S52. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D11V2.png)
P value = 1e-14 (Chi-square test), Q value = 7.6e-12
Table S53. Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
6P GAIN CNV | 11 | 15 | 15 | 52 | 11 |
6P GAIN WILD-TYPE | 336 | 207 | 57 | 171 | 38 |
Figure S53. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D11V3.png)
P value = 6.04e-11 (Chi-square test), Q value = 4.3e-08
Table S54. Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
6P GAIN CNV | 31 | 8 | 14 | 14 | 1 | 1 |
6P GAIN WILD-TYPE | 70 | 131 | 79 | 123 | 39 | 96 |
Figure S54. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D11V4.png)
P value = 1.69e-09 (Fisher's exact test), Q value = 1.2e-06
Table S55. Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
6P GAIN CNV | 50 | 3 | 39 |
6P GAIN WILD-TYPE | 184 | 145 | 407 |
Figure S55. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D11V7.png)
P value = 3.84e-09 (Fisher's exact test), Q value = 2.7e-06
Table S56. Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
6P GAIN CNV | 5 | 45 | 42 |
6P GAIN WILD-TYPE | 211 | 363 | 162 |
Figure S56. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D11V8.png)
P value = 2.95e-09 (Fisher's exact test), Q value = 2e-06
Table S57. Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
6P GAIN CNV | 9 | 32 | 53 |
6P GAIN WILD-TYPE | 225 | 360 | 202 |
Figure S57. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D11V9.png)
P value = 3.86e-09 (Fisher's exact test), Q value = 2.7e-06
Table S58. Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
6P GAIN CNV | 34 | 11 | 49 |
6P GAIN WILD-TYPE | 328 | 273 | 186 |
Figure S58. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D11V10.png)
P value = 1.72e-14 (Chi-square test), Q value = 1.3e-11
Table S59. Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
6Q GAIN CNV | 5 | 5 | 10 | 39 | 2 |
6Q GAIN WILD-TYPE | 342 | 217 | 62 | 184 | 47 |
Figure S59. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D12V3.png)
P value = 0.000535 (Fisher's exact test), Q value = 0.23
Table S60. Gene #12: '6q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 147 | 133 | 117 |
6Q GAIN CNV | 20 | 7 | 2 |
6Q GAIN WILD-TYPE | 127 | 126 | 115 |
Figure S60. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D12V5.png)
P value = 4.89e-06 (Fisher's exact test), Q value = 0.0029
Table S61. Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
6Q GAIN CNV | 31 | 2 | 22 |
6Q GAIN WILD-TYPE | 203 | 146 | 424 |
Figure S61. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D12V7.png)
P value = 3.35e-06 (Fisher's exact test), Q value = 0.002
Table S62. Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
6Q GAIN CNV | 2 | 28 | 25 |
6Q GAIN WILD-TYPE | 214 | 380 | 179 |
Figure S62. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D12V8.png)
P value = 6.69e-05 (Fisher's exact test), Q value = 0.035
Table S63. Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
6Q GAIN CNV | 6 | 18 | 30 |
6Q GAIN WILD-TYPE | 228 | 374 | 225 |
Figure S63. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D12V9.png)
P value = 3.4e-06 (Fisher's exact test), Q value = 0.002
Table S64. Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
6Q GAIN CNV | 18 | 6 | 30 |
6Q GAIN WILD-TYPE | 344 | 278 | 205 |
Figure S64. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D12V10.png)
P value = 0.000482 (Fisher's exact test), Q value = 0.21
Table S65. Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
7Q GAIN CNV | 17 | 48 | 42 |
7Q GAIN WILD-TYPE | 199 | 360 | 162 |
Figure S65. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D14V8.png)
P value = 5.71e-15 (Chi-square test), Q value = 4.4e-12
Table S66. Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
8P GAIN CNV | 33 | 42 | 30 | 46 | 24 |
8P GAIN WILD-TYPE | 314 | 180 | 42 | 177 | 25 |
Figure S66. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D15V3.png)
P value = 0.00037 (Chi-square test), Q value = 0.17
Table S67. Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
8P GAIN CNV | 28 | 21 | 20 | 31 | 6 | 4 |
8P GAIN WILD-TYPE | 73 | 118 | 73 | 106 | 34 | 93 |
Figure S67. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D15V4.png)
P value = 0.00026 (Fisher's exact test), Q value = 0.12
Table S68. Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
8P GAIN CNV | 44 | 13 | 104 |
8P GAIN WILD-TYPE | 190 | 135 | 342 |
Figure S68. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D15V7.png)
P value = 1.18e-05 (Fisher's exact test), Q value = 0.0068
Table S69. Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
8P GAIN CNV | 21 | 102 | 38 |
8P GAIN WILD-TYPE | 195 | 306 | 166 |
Figure S69. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D15V8.png)
P value = 2.29e-05 (Chi-square test), Q value = 0.013
Table S70. Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
8Q GAIN CNV | 72 | 13 | 14 | 52 | 34 | 11 | 35 | 7 |
8Q GAIN WILD-TYPE | 52 | 23 | 9 | 43 | 38 | 9 | 68 | 33 |
Figure S70. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D16V1.png)
P value = 0.000315 (Fisher's exact test), Q value = 0.15
Table S71. Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 140 | 125 | 248 |
8Q GAIN CNV | 45 | 63 | 130 |
8Q GAIN WILD-TYPE | 95 | 62 | 118 |
Figure S71. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D16V2.png)
P value = 1.33e-23 (Chi-square test), Q value = 1.1e-20
Table S72. Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
8Q GAIN CNV | 72 | 118 | 35 | 118 | 38 |
8Q GAIN WILD-TYPE | 275 | 104 | 37 | 105 | 11 |
Figure S72. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D16V3.png)
P value = 8.16e-13 (Chi-square test), Q value = 6e-10
Table S73. Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
8Q GAIN CNV | 54 | 29 | 37 | 79 | 10 | 20 |
8Q GAIN WILD-TYPE | 47 | 110 | 56 | 58 | 30 | 77 |
Figure S73. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D16V4.png)
P value = 1.36e-08 (Fisher's exact test), Q value = 9.3e-06
Table S74. Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
8Q GAIN CNV | 120 | 33 | 207 |
8Q GAIN WILD-TYPE | 114 | 115 | 239 |
Figure S74. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D16V7.png)
P value = 1.11e-07 (Fisher's exact test), Q value = 7.2e-05
Table S75. Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
8Q GAIN CNV | 59 | 200 | 101 |
8Q GAIN WILD-TYPE | 157 | 208 | 103 |
Figure S75. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D16V8.png)
P value = 1.05e-09 (Fisher's exact test), Q value = 7.3e-07
Table S76. Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
8Q GAIN CNV | 61 | 172 | 138 |
8Q GAIN WILD-TYPE | 173 | 220 | 117 |
Figure S76. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D16V9.png)
P value = 5.51e-06 (Fisher's exact test), Q value = 0.0032
Table S77. Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
8Q GAIN CNV | 162 | 88 | 121 |
8Q GAIN WILD-TYPE | 200 | 196 | 114 |
Figure S77. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D16V10.png)
P value = 1.38e-08 (Chi-square test), Q value = 9.4e-06
Table S78. Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
9P GAIN CNV | 3 | 1 | 0 | 24 | 4 | 0 | 7 | 2 |
9P GAIN WILD-TYPE | 121 | 35 | 23 | 71 | 68 | 20 | 96 | 38 |
Figure S78. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D17V1.png)
P value = 1.6e-08 (Fisher's exact test), Q value = 1.1e-05
Table S79. Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 140 | 125 | 248 |
9P GAIN CNV | 4 | 27 | 10 |
9P GAIN WILD-TYPE | 136 | 98 | 238 |
Figure S79. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D17V2.png)
P value = 1.79e-08 (Chi-square test), Q value = 1.2e-05
Table S80. Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
9P GAIN CNV | 9 | 10 | 13 | 32 | 4 |
9P GAIN WILD-TYPE | 338 | 212 | 59 | 191 | 45 |
Figure S80. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D17V3.png)
P value = 0.000106 (Fisher's exact test), Q value = 0.054
Table S81. Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 110 | 126 |
9P GAIN CNV | 5 | 7 | 22 |
9P GAIN WILD-TYPE | 156 | 103 | 104 |
Figure S81. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D17V6.png)
P value = 8.46e-08 (Fisher's exact test), Q value = 5.6e-05
Table S82. Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
9P GAIN CNV | 38 | 7 | 17 |
9P GAIN WILD-TYPE | 196 | 141 | 429 |
Figure S82. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D17V7.png)
P value = 3.98e-09 (Fisher's exact test), Q value = 2.7e-06
Table S83. Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
9P GAIN CNV | 7 | 18 | 37 |
9P GAIN WILD-TYPE | 209 | 390 | 167 |
Figure S83. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D17V8.png)
P value = 1.11e-06 (Fisher's exact test), Q value = 0.00069
Table S84. Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
9P GAIN CNV | 8 | 19 | 38 |
9P GAIN WILD-TYPE | 226 | 373 | 217 |
Figure S84. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D17V9.png)
P value = 1.44e-07 (Fisher's exact test), Q value = 9.3e-05
Table S85. Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
9P GAIN CNV | 15 | 12 | 38 |
9P GAIN WILD-TYPE | 347 | 272 | 197 |
Figure S85. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D17V10.png)
P value = 0.000148 (Chi-square test), Q value = 0.073
Table S86. Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
9Q GAIN CNV | 10 | 12 | 12 | 19 | 3 |
9Q GAIN WILD-TYPE | 337 | 210 | 60 | 204 | 46 |
Figure S86. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D18V3.png)
P value = 7.38e-11 (Chi-square test), Q value = 5.3e-08
Table S87. Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
10P GAIN CNV | 10 | 3 | 0 | 33 | 18 | 2 | 3 | 3 |
10P GAIN WILD-TYPE | 114 | 33 | 23 | 62 | 54 | 18 | 100 | 37 |
Figure S87. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D19V1.png)
P value = 9.62e-08 (Fisher's exact test), Q value = 6.3e-05
Table S88. Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 140 | 125 | 248 |
10P GAIN CNV | 11 | 38 | 23 |
10P GAIN WILD-TYPE | 129 | 87 | 225 |
Figure S88. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D19V2.png)
P value = 5.04e-15 (Chi-square test), Q value = 3.8e-12
Table S89. Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
10P GAIN CNV | 11 | 23 | 10 | 60 | 6 |
10P GAIN WILD-TYPE | 336 | 199 | 62 | 163 | 43 |
Figure S89. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D19V3.png)
P value = 3.37e-15 (Chi-square test), Q value = 2.6e-12
Table S90. Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
10P GAIN CNV | 34 | 4 | 11 | 14 | 0 | 2 |
10P GAIN WILD-TYPE | 67 | 135 | 82 | 123 | 40 | 95 |
Figure S90. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D19V4.png)
P value = 2.39e-05 (Fisher's exact test), Q value = 0.013
Table S91. Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 147 | 133 | 117 |
10P GAIN CNV | 36 | 8 | 12 |
10P GAIN WILD-TYPE | 111 | 125 | 105 |
Figure S91. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D19V5.png)
P value = 1.42e-06 (Fisher's exact test), Q value = 0.00088
Table S92. Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 110 | 126 |
10P GAIN CNV | 11 | 10 | 35 |
10P GAIN WILD-TYPE | 150 | 100 | 91 |
Figure S92. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D19V6.png)
P value = 1.15e-15 (Fisher's exact test), Q value = 8.8e-13
Table S93. Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
10P GAIN CNV | 66 | 7 | 29 |
10P GAIN WILD-TYPE | 168 | 141 | 417 |
Figure S93. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D19V7.png)
P value = 2.46e-16 (Fisher's exact test), Q value = 1.9e-13
Table S94. Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
10P GAIN CNV | 8 | 33 | 61 |
10P GAIN WILD-TYPE | 208 | 375 | 143 |
Figure S94. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D19V8.png)
P value = 2.44e-12 (Fisher's exact test), Q value = 1.8e-09
Table S95. Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
10P GAIN CNV | 12 | 30 | 64 |
10P GAIN WILD-TYPE | 222 | 362 | 191 |
Figure S95. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D19V9.png)
P value = 2.15e-14 (Fisher's exact test), Q value = 1.6e-11
Table S96. Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
10P GAIN CNV | 27 | 15 | 64 |
10P GAIN WILD-TYPE | 335 | 269 | 171 |
Figure S96. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D19V10.png)
P value = 0.000533 (Chi-square test), Q value = 0.23
Table S97. Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
10Q GAIN CNV | 5 | 10 | 7 | 19 | 4 |
10Q GAIN WILD-TYPE | 342 | 212 | 65 | 204 | 45 |
Figure S97. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D20V3.png)
P value = 0.000131 (Chi-square test), Q value = 0.065
Table S98. Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
11Q GAIN CNV | 9 | 7 | 2 | 22 | 6 |
11Q GAIN WILD-TYPE | 338 | 215 | 70 | 201 | 43 |
Figure S98. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D22V3.png)
P value = 9e-14 (Chi-square test), Q value = 6.7e-11
Table S99. Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
12P GAIN CNV | 4 | 44 | 15 | 44 | 8 |
12P GAIN WILD-TYPE | 343 | 178 | 57 | 179 | 41 |
Figure S99. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D23V3.png)
P value = 4.76e-05 (Chi-square test), Q value = 0.025
Table S100. Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
12P GAIN CNV | 19 | 9 | 11 | 25 | 1 | 2 |
12P GAIN WILD-TYPE | 82 | 130 | 82 | 112 | 39 | 95 |
Figure S100. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D23V4.png)
P value = 9.11e-05 (Fisher's exact test), Q value = 0.047
Table S101. Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
12P GAIN CNV | 43 | 6 | 59 |
12P GAIN WILD-TYPE | 191 | 142 | 387 |
Figure S101. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D23V7.png)
P value = 0.000256 (Fisher's exact test), Q value = 0.12
Table S102. Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
12P GAIN CNV | 14 | 54 | 40 |
12P GAIN WILD-TYPE | 202 | 354 | 164 |
Figure S102. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D23V8.png)
P value = 0.000371 (Fisher's exact test), Q value = 0.17
Table S103. Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
12P GAIN CNV | 17 | 43 | 48 |
12P GAIN WILD-TYPE | 217 | 349 | 207 |
Figure S103. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D23V9.png)
P value = 1.81e-15 (Chi-square test), Q value = 1.4e-12
Table S104. Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
12Q GAIN CNV | 5 | 46 | 16 | 14 | 6 |
12Q GAIN WILD-TYPE | 342 | 176 | 56 | 209 | 43 |
Figure S104. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D24V3.png)
P value = 8.74e-05 (Chi-square test), Q value = 0.045
Table S105. Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
12Q GAIN CNV | 4 | 13 | 11 | 24 | 1 | 1 |
12Q GAIN WILD-TYPE | 97 | 126 | 82 | 113 | 39 | 96 |
Figure S105. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D24V4.png)
P value = 5.13e-06 (Fisher's exact test), Q value = 0.003
Table S106. Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
14Q GAIN CNV | 14 | 2 | 57 |
14Q GAIN WILD-TYPE | 220 | 146 | 389 |
Figure S106. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D26V7.png)
P value = 0.000453 (Fisher's exact test), Q value = 0.2
Table S107. Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
14Q GAIN CNV | 10 | 52 | 11 |
14Q GAIN WILD-TYPE | 206 | 356 | 193 |
Figure S107. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D26V8.png)
P value = 8.16e-05 (Fisher's exact test), Q value = 0.042
Table S108. Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
14Q GAIN CNV | 7 | 49 | 19 |
14Q GAIN WILD-TYPE | 227 | 343 | 236 |
Figure S108. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D26V9.png)
P value = 1.01e-05 (Chi-square test), Q value = 0.0058
Table S109. Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
16P GAIN CNV | 41 | 6 | 8 | 18 | 15 | 5 | 53 | 10 |
16P GAIN WILD-TYPE | 83 | 30 | 15 | 77 | 57 | 15 | 50 | 30 |
Figure S109. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D28V1.png)
P value = 8.07e-05 (Fisher's exact test), Q value = 0.042
Table S110. Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 140 | 125 | 248 |
16P GAIN CNV | 38 | 22 | 96 |
16P GAIN WILD-TYPE | 102 | 103 | 152 |
Figure S110. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D28V2.png)
P value = 5.27e-07 (Chi-square test), Q value = 0.00033
Table S111. Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
16P GAIN CNV | 17 | 54 | 30 | 40 | 3 | 11 |
16P GAIN WILD-TYPE | 84 | 85 | 63 | 97 | 37 | 86 |
Figure S111. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D28V4.png)
P value = 0.000119 (Fisher's exact test), Q value = 0.059
Table S112. Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 147 | 133 | 117 |
16P GAIN CNV | 30 | 58 | 32 |
16P GAIN WILD-TYPE | 117 | 75 | 85 |
Figure S112. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D28V5.png)
P value = 6.58e-05 (Fisher's exact test), Q value = 0.035
Table S113. Gene #28: '16p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 110 | 126 |
16P GAIN CNV | 60 | 40 | 20 |
16P GAIN WILD-TYPE | 101 | 70 | 106 |
Figure S113. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D28V6.png)
P value = 1.2e-05 (Fisher's exact test), Q value = 0.0068
Table S114. Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
16P GAIN CNV | 44 | 38 | 159 |
16P GAIN WILD-TYPE | 190 | 110 | 287 |
Figure S114. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D28V7.png)
P value = 2.56e-06 (Fisher's exact test), Q value = 0.0015
Table S115. Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
16P GAIN CNV | 54 | 150 | 37 |
16P GAIN WILD-TYPE | 162 | 258 | 167 |
Figure S115. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D28V8.png)
P value = 4.01e-07 (Chi-square test), Q value = 0.00026
Table S116. Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
17Q GAIN CNV | 35 | 6 | 2 | 6 | 4 | 2 | 4 | 5 |
17Q GAIN WILD-TYPE | 89 | 30 | 21 | 89 | 68 | 18 | 99 | 35 |
Figure S116. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D31V1.png)
P value = 2.64e-18 (Chi-square test), Q value = 2.1e-15
Table S117. Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
17Q GAIN CNV | 23 | 70 | 8 | 13 | 9 |
17Q GAIN WILD-TYPE | 324 | 152 | 64 | 210 | 40 |
Figure S117. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D31V3.png)
P value = 3.27e-06 (Chi-square test), Q value = 0.002
Table S118. Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
17Q GAIN CNV | 5 | 13 | 15 | 37 | 6 | 7 |
17Q GAIN WILD-TYPE | 96 | 126 | 78 | 100 | 34 | 90 |
Figure S118. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D31V4.png)
P value = 0.000108 (Fisher's exact test), Q value = 0.054
Table S119. Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
17Q GAIN CNV | 17 | 18 | 84 |
17Q GAIN WILD-TYPE | 217 | 130 | 362 |
Figure S119. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D31V7.png)
P value = 1.19e-06 (Fisher's exact test), Q value = 0.00074
Table S120. Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
17Q GAIN CNV | 26 | 82 | 11 |
17Q GAIN WILD-TYPE | 190 | 326 | 193 |
Figure S120. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D31V8.png)
P value = 2.57e-07 (Chi-square test), Q value = 0.00017
Table S121. Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
18P GAIN CNV | 12 | 25 | 4 | 35 | 11 |
18P GAIN WILD-TYPE | 335 | 197 | 68 | 188 | 38 |
Figure S121. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D32V3.png)
P value = 1.03e-07 (Chi-square test), Q value = 6.7e-05
Table S122. Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
18P GAIN CNV | 22 | 5 | 8 | 11 | 0 | 1 |
18P GAIN WILD-TYPE | 79 | 134 | 85 | 126 | 40 | 96 |
Figure S122. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D32V4.png)
P value = 3.57e-06 (Fisher's exact test), Q value = 0.0021
Table S123. Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
18P GAIN CNV | 37 | 2 | 44 |
18P GAIN WILD-TYPE | 197 | 146 | 402 |
Figure S123. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D32V7.png)
P value = 1.42e-07 (Fisher's exact test), Q value = 9.2e-05
Table S124. Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
18P GAIN CNV | 4 | 45 | 34 |
18P GAIN WILD-TYPE | 212 | 363 | 170 |
Figure S124. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D32V8.png)
P value = 1.52e-05 (Fisher's exact test), Q value = 0.0086
Table S125. Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
18P GAIN CNV | 11 | 28 | 42 |
18P GAIN WILD-TYPE | 223 | 364 | 213 |
Figure S125. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D32V9.png)
P value = 0.000104 (Fisher's exact test), Q value = 0.053
Table S126. Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
18P GAIN CNV | 28 | 15 | 38 |
18P GAIN WILD-TYPE | 334 | 269 | 197 |
Figure S126. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D32V10.png)
P value = 6.69e-06 (Chi-square test), Q value = 0.0039
Table S127. Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
18Q GAIN CNV | 11 | 21 | 5 | 30 | 10 |
18Q GAIN WILD-TYPE | 336 | 201 | 67 | 193 | 39 |
Figure S127. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D33V3.png)
P value = 0.000346 (Fisher's exact test), Q value = 0.16
Table S128. Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
18Q GAIN CNV | 24 | 2 | 46 |
18Q GAIN WILD-TYPE | 210 | 146 | 400 |
Figure S128. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D33V7.png)
P value = 9.95e-05 (Fisher's exact test), Q value = 0.051
Table S129. Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
18Q GAIN CNV | 5 | 43 | 24 |
18Q GAIN WILD-TYPE | 211 | 365 | 180 |
Figure S129. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D33V8.png)
P value = 0.000382 (Chi-square test), Q value = 0.17
Table S130. Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
19P GAIN CNV | 15 | 11 | 11 | 27 | 5 |
19P GAIN WILD-TYPE | 332 | 211 | 61 | 196 | 44 |
Figure S130. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D34V3.png)
P value = 0.000415 (Chi-square test), Q value = 0.19
Table S131. Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
19Q GAIN CNV | 17 | 19 | 13 | 30 | 7 |
19Q GAIN WILD-TYPE | 330 | 203 | 59 | 193 | 42 |
Figure S131. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D35V3.png)
P value = 3.66e-05 (Chi-square test), Q value = 0.02
Table S132. Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
20P GAIN CNV | 42 | 6 | 6 | 26 | 32 | 13 | 21 | 6 |
20P GAIN WILD-TYPE | 82 | 30 | 17 | 69 | 40 | 7 | 82 | 34 |
Figure S132. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D36V1.png)
P value = 3.08e-23 (Chi-square test), Q value = 2.4e-20
Table S133. Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
20P GAIN CNV | 27 | 95 | 34 | 69 | 14 |
20P GAIN WILD-TYPE | 320 | 127 | 38 | 154 | 35 |
Figure S133. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D36V3.png)
P value = 3.06e-08 (Chi-square test), Q value = 2.1e-05
Table S134. Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
20P GAIN CNV | 20 | 21 | 29 | 56 | 6 | 10 |
20P GAIN WILD-TYPE | 81 | 118 | 64 | 81 | 34 | 87 |
Figure S134. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D36V4.png)
P value = 0.000293 (Fisher's exact test), Q value = 0.14
Table S135. Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
20P GAIN CNV | 39 | 116 | 77 |
20P GAIN WILD-TYPE | 195 | 276 | 178 |
Figure S135. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D36V9.png)
P value = 1.44e-05 (Chi-square test), Q value = 0.0081
Table S136. Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
20Q GAIN CNV | 56 | 7 | 5 | 26 | 33 | 12 | 21 | 10 |
20Q GAIN WILD-TYPE | 68 | 29 | 18 | 69 | 39 | 8 | 82 | 30 |
Figure S136. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D37V1.png)
P value = 3.32e-29 (Chi-square test), Q value = 2.6e-26
Table S137. Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
20Q GAIN CNV | 31 | 118 | 32 | 78 | 17 |
20Q GAIN WILD-TYPE | 316 | 104 | 40 | 145 | 32 |
Figure S137. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D37V3.png)
P value = 2.35e-14 (Chi-square test), Q value = 1.8e-11
Table S138. Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
20Q GAIN CNV | 22 | 23 | 34 | 72 | 7 | 10 |
20Q GAIN WILD-TYPE | 79 | 116 | 59 | 65 | 33 | 87 |
Figure S138. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D37V4.png)
P value = 3.01e-05 (Fisher's exact test), Q value = 0.016
Table S139. Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
20Q GAIN CNV | 70 | 27 | 168 |
20Q GAIN WILD-TYPE | 164 | 121 | 278 |
Figure S139. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D37V7.png)
P value = 2.95e-06 (Fisher's exact test), Q value = 0.0018
Table S140. Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
20Q GAIN CNV | 46 | 163 | 56 |
20Q GAIN WILD-TYPE | 170 | 245 | 148 |
Figure S140. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D37V8.png)
P value = 5.37e-06 (Fisher's exact test), Q value = 0.0031
Table S141. Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
20Q GAIN CNV | 43 | 141 | 86 |
20Q GAIN WILD-TYPE | 191 | 251 | 169 |
Figure S141. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D37V9.png)
P value = 5.97e-05 (Chi-square test), Q value = 0.031
Table S142. Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
21Q GAIN CNV | 12 | 0 | 1 | 17 | 19 | 5 | 7 | 2 |
21Q GAIN WILD-TYPE | 112 | 36 | 22 | 78 | 53 | 15 | 96 | 38 |
Figure S142. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D38V1.png)
P value = 0.00019 (Fisher's exact test), Q value = 0.092
Table S143. Gene #38: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 140 | 125 | 248 |
21Q GAIN CNV | 7 | 27 | 29 |
21Q GAIN WILD-TYPE | 133 | 98 | 219 |
Figure S143. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D38V2.png)
P value = 7.1e-10 (Chi-square test), Q value = 5e-07
Table S144. Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
21Q GAIN CNV | 13 | 21 | 16 | 44 | 10 |
21Q GAIN WILD-TYPE | 334 | 201 | 56 | 179 | 39 |
Figure S144. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D38V3.png)
P value = 4.67e-09 (Chi-square test), Q value = 3.2e-06
Table S145. Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
21Q GAIN CNV | 26 | 7 | 17 | 10 | 1 | 2 |
21Q GAIN WILD-TYPE | 75 | 132 | 76 | 127 | 39 | 95 |
Figure S145. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D38V4.png)
P value = 2.05e-11 (Fisher's exact test), Q value = 1.5e-08
Table S146. Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
21Q GAIN CNV | 55 | 3 | 38 |
21Q GAIN WILD-TYPE | 179 | 145 | 408 |
Figure S146. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D38V7.png)
P value = 1.13e-10 (Fisher's exact test), Q value = 8e-08
Table S147. Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
21Q GAIN CNV | 6 | 42 | 48 |
21Q GAIN WILD-TYPE | 210 | 366 | 156 |
Figure S147. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D38V8.png)
P value = 3.95e-05 (Fisher's exact test), Q value = 0.021
Table S148. Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
21Q GAIN CNV | 14 | 37 | 47 |
21Q GAIN WILD-TYPE | 220 | 355 | 208 |
Figure S148. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D38V9.png)
P value = 3.66e-07 (Fisher's exact test), Q value = 0.00023
Table S149. Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
21Q GAIN CNV | 35 | 15 | 48 |
21Q GAIN WILD-TYPE | 327 | 269 | 187 |
Figure S149. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D38V10.png)
P value = 3.75e-08 (Chi-square test), Q value = 2.5e-05
Table S150. Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
22Q GAIN CNV | 2 | 10 | 1 | 26 | 4 |
22Q GAIN WILD-TYPE | 345 | 212 | 71 | 197 | 45 |
Figure S150. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D39V3.png)
P value = 4.84e-06 (Fisher's exact test), Q value = 0.0028
Table S151. Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
22Q GAIN CNV | 23 | 0 | 15 |
22Q GAIN WILD-TYPE | 211 | 148 | 431 |
Figure S151. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D39V7.png)
P value = 1.57e-06 (Fisher's exact test), Q value = 0.00097
Table S152. Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
22Q GAIN CNV | 2 | 13 | 23 |
22Q GAIN WILD-TYPE | 214 | 395 | 181 |
Figure S152. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D39V8.png)
P value = 1.03e-06 (Fisher's exact test), Q value = 0.00065
Table S153. Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
22Q GAIN CNV | 16 | 2 | 24 |
22Q GAIN WILD-TYPE | 346 | 282 | 211 |
Figure S153. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D39V10.png)
P value = 0.000165 (Fisher's exact test), Q value = 0.081
Table S154. Gene #40: 'Xq gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 140 | 125 | 248 |
XQ GAIN CNV | 1 | 11 | 3 |
XQ GAIN WILD-TYPE | 139 | 114 | 245 |
Figure S154. Get High-res Image Gene #40: 'Xq gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D40V2.png)
P value = 0.000166 (Chi-square test), Q value = 0.082
Table S155. Gene #40: 'Xq gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
XQ GAIN CNV | 2 | 3 | 2 | 14 | 0 |
XQ GAIN WILD-TYPE | 345 | 219 | 70 | 209 | 49 |
Figure S155. Get High-res Image Gene #40: 'Xq gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D40V3.png)
P value = 0.000388 (Fisher's exact test), Q value = 0.18
Table S156. Gene #40: 'Xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
XQ GAIN CNV | 13 | 0 | 6 |
XQ GAIN WILD-TYPE | 221 | 148 | 440 |
Figure S156. Get High-res Image Gene #40: 'Xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D40V7.png)
P value = 1.47e-05 (Fisher's exact test), Q value = 0.0083
Table S157. Gene #40: 'Xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
XQ GAIN CNV | 1 | 4 | 14 |
XQ GAIN WILD-TYPE | 215 | 404 | 190 |
Figure S157. Get High-res Image Gene #40: 'Xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D40V8.png)
P value = 4.83e-05 (Fisher's exact test), Q value = 0.026
Table S158. Gene #40: 'Xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
XQ GAIN CNV | 0 | 5 | 14 |
XQ GAIN WILD-TYPE | 234 | 387 | 241 |
Figure S158. Get High-res Image Gene #40: 'Xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D40V9.png)
P value = 0.000182 (Fisher's exact test), Q value = 0.089
Table S159. Gene #40: 'Xq gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
XQ GAIN CNV | 5 | 1 | 13 |
XQ GAIN WILD-TYPE | 357 | 283 | 222 |
Figure S159. Get High-res Image Gene #40: 'Xq gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D40V10.png)
P value = 0.000228 (Chi-square test), Q value = 0.11
Table S160. Gene #41: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
1P LOSS CNV | 24 | 3 | 1 | 4 | 19 | 0 | 15 | 3 |
1P LOSS WILD-TYPE | 100 | 33 | 22 | 91 | 53 | 20 | 88 | 37 |
Figure S160. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D41V1.png)
P value = 3.98e-10 (Fisher's exact test), Q value = 2.8e-07
Table S161. Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 140 | 125 | 248 |
1P LOSS CNV | 7 | 4 | 58 |
1P LOSS WILD-TYPE | 133 | 121 | 190 |
Figure S161. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D41V2.png)
P value = 2.44e-23 (Chi-square test), Q value = 1.9e-20
Table S162. Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
1P LOSS CNV | 13 | 57 | 30 | 17 | 6 |
1P LOSS WILD-TYPE | 334 | 165 | 42 | 206 | 43 |
Figure S162. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D41V3.png)
P value = 1.84e-06 (Chi-square test), Q value = 0.0011
Table S163. Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
1P LOSS CNV | 7 | 13 | 23 | 29 | 5 | 2 |
1P LOSS WILD-TYPE | 94 | 126 | 70 | 108 | 35 | 95 |
Figure S163. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D41V4.png)
P value = 3.92e-11 (Fisher's exact test), Q value = 2.8e-08
Table S164. Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
1P LOSS CNV | 14 | 5 | 92 |
1P LOSS WILD-TYPE | 220 | 143 | 354 |
Figure S164. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D41V7.png)
P value = 2.18e-13 (Fisher's exact test), Q value = 1.6e-10
Table S165. Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
1P LOSS CNV | 12 | 91 | 8 |
1P LOSS WILD-TYPE | 204 | 317 | 196 |
Figure S165. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D41V8.png)
P value = 0.000177 (Fisher's exact test), Q value = 0.086
Table S166. Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
1P LOSS CNV | 69 | 33 | 18 |
1P LOSS WILD-TYPE | 293 | 251 | 217 |
Figure S166. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D41V10.png)
P value = 3.09e-05 (Fisher's exact test), Q value = 0.017
Table S167. Gene #43: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 140 | 125 | 248 |
2P LOSS CNV | 6 | 3 | 36 |
2P LOSS WILD-TYPE | 134 | 122 | 212 |
Figure S167. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D43V2.png)
P value = 2.58e-12 (Chi-square test), Q value = 1.9e-09
Table S168. Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
2P LOSS CNV | 5 | 34 | 15 | 12 | 9 |
2P LOSS WILD-TYPE | 342 | 188 | 57 | 211 | 40 |
Figure S168. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D43V3.png)
P value = 1.72e-07 (Chi-square test), Q value = 0.00011
Table S169. Gene #43: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
2P LOSS CNV | 1 | 7 | 9 | 24 | 1 | 0 |
2P LOSS WILD-TYPE | 100 | 132 | 84 | 113 | 39 | 97 |
Figure S169. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D43V4.png)
P value = 2.09e-07 (Fisher's exact test), Q value = 0.00013
Table S170. Gene #43: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
2P LOSS CNV | 6 | 5 | 59 |
2P LOSS WILD-TYPE | 228 | 143 | 387 |
Figure S170. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D43V7.png)
P value = 7.81e-07 (Fisher's exact test), Q value = 0.00049
Table S171. Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
2P LOSS CNV | 10 | 55 | 5 |
2P LOSS WILD-TYPE | 206 | 353 | 199 |
Figure S171. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D43V8.png)
P value = 0.000265 (Fisher's exact test), Q value = 0.12
Table S172. Gene #43: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
2P LOSS CNV | 10 | 48 | 13 |
2P LOSS WILD-TYPE | 224 | 344 | 242 |
Figure S172. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D43V9.png)
P value = 0.00057 (Fisher's exact test), Q value = 0.24
Table S173. Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
2P LOSS CNV | 44 | 18 | 9 |
2P LOSS WILD-TYPE | 318 | 266 | 226 |
Figure S173. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D43V10.png)
P value = 0.000444 (Fisher's exact test), Q value = 0.2
Table S174. Gene #44: '2q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 140 | 125 | 248 |
2Q LOSS CNV | 6 | 9 | 40 |
2Q LOSS WILD-TYPE | 134 | 116 | 208 |
Figure S174. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D44V2.png)
P value = 2.48e-12 (Chi-square test), Q value = 1.8e-09
Table S175. Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
2Q LOSS CNV | 5 | 41 | 16 | 21 | 8 |
2Q LOSS WILD-TYPE | 342 | 181 | 56 | 202 | 41 |
Figure S175. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D44V3.png)
P value = 4.01e-06 (Chi-square test), Q value = 0.0024
Table S176. Gene #44: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
2Q LOSS CNV | 8 | 7 | 11 | 26 | 1 | 0 |
2Q LOSS WILD-TYPE | 93 | 132 | 82 | 111 | 39 | 97 |
Figure S176. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D44V4.png)
P value = 0.000387 (Fisher's exact test), Q value = 0.18
Table S177. Gene #44: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
2Q LOSS CNV | 19 | 5 | 61 |
2Q LOSS WILD-TYPE | 215 | 143 | 385 |
Figure S177. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D44V7.png)
P value = 0.000322 (Fisher's exact test), Q value = 0.15
Table S178. Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
2Q LOSS CNV | 11 | 59 | 15 |
2Q LOSS WILD-TYPE | 205 | 349 | 189 |
Figure S178. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D44V8.png)
P value = 0.000495 (Fisher's exact test), Q value = 0.22
Table S179. Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
2Q LOSS CNV | 10 | 53 | 24 |
2Q LOSS WILD-TYPE | 224 | 339 | 231 |
Figure S179. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D44V9.png)
P value = 0.000423 (Fisher's exact test), Q value = 0.19
Table S180. Gene #44: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
2Q LOSS CNV | 52 | 15 | 20 |
2Q LOSS WILD-TYPE | 310 | 269 | 215 |
Figure S180. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D44V10.png)
P value = 2.58e-09 (Chi-square test), Q value = 1.8e-06
Table S181. Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
3P LOSS CNV | 9 | 32 | 5 | 42 | 4 |
3P LOSS WILD-TYPE | 338 | 190 | 67 | 181 | 45 |
Figure S181. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D45V3.png)
P value = 3.42e-05 (Chi-square test), Q value = 0.019
Table S182. Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
3P LOSS CNV | 16 | 2 | 14 | 18 | 3 | 2 |
3P LOSS WILD-TYPE | 85 | 137 | 79 | 119 | 37 | 95 |
Figure S182. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D45V4.png)
P value = 5.31e-05 (Fisher's exact test), Q value = 0.028
Table S183. Gene #45: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 110 | 126 |
3P LOSS CNV | 14 | 4 | 27 |
3P LOSS WILD-TYPE | 147 | 106 | 99 |
Figure S183. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D45V6.png)
P value = 3.32e-05 (Fisher's exact test), Q value = 0.018
Table S184. Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
3P LOSS CNV | 42 | 8 | 34 |
3P LOSS WILD-TYPE | 192 | 140 | 412 |
Figure S184. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D45V7.png)
P value = 0.000279 (Fisher's exact test), Q value = 0.13
Table S185. Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
3P LOSS CNV | 13 | 35 | 36 |
3P LOSS WILD-TYPE | 203 | 373 | 168 |
Figure S185. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D45V8.png)
P value = 2.18e-06 (Fisher's exact test), Q value = 0.0013
Table S186. Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
3P LOSS CNV | 14 | 27 | 47 |
3P LOSS WILD-TYPE | 220 | 365 | 208 |
Figure S186. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D45V9.png)
P value = 0.000443 (Fisher's exact test), Q value = 0.2
Table S187. Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
3P LOSS CNV | 39 | 14 | 35 |
3P LOSS WILD-TYPE | 323 | 270 | 200 |
Figure S187. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D45V10.png)
P value = 4.5e-12 (Chi-square test), Q value = 3.3e-09
Table S188. Gene #47: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
4P LOSS CNV | 18 | 4 | 1 | 41 | 33 | 4 | 13 | 3 |
4P LOSS WILD-TYPE | 106 | 32 | 22 | 54 | 39 | 16 | 90 | 37 |
Figure S188. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D47V1.png)
P value = 1.24e-12 (Fisher's exact test), Q value = 9.1e-10
Table S189. Gene #47: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 140 | 125 | 248 |
4P LOSS CNV | 9 | 55 | 53 |
4P LOSS WILD-TYPE | 131 | 70 | 195 |
Figure S189. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D47V2.png)
P value = 9.98e-28 (Chi-square test), Q value = 7.9e-25
Table S190. Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
4P LOSS CNV | 18 | 38 | 24 | 97 | 8 |
4P LOSS WILD-TYPE | 329 | 184 | 48 | 126 | 41 |
Figure S190. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D47V3.png)
P value = 3.87e-14 (Chi-square test), Q value = 2.9e-11
Table S191. Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
4P LOSS CNV | 44 | 19 | 22 | 14 | 4 | 3 |
4P LOSS WILD-TYPE | 57 | 120 | 71 | 123 | 36 | 94 |
Figure S191. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D47V4.png)
P value = 0.00014 (Fisher's exact test), Q value = 0.069
Table S192. Gene #47: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 147 | 133 | 117 |
4P LOSS CNV | 52 | 25 | 17 |
4P LOSS WILD-TYPE | 95 | 108 | 100 |
Figure S192. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D47V5.png)
P value = 7.57e-06 (Fisher's exact test), Q value = 0.0044
Table S193. Gene #47: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 110 | 126 |
4P LOSS CNV | 30 | 15 | 49 |
4P LOSS WILD-TYPE | 131 | 95 | 77 |
Figure S193. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D47V6.png)
P value = 2.85e-17 (Fisher's exact test), Q value = 2.2e-14
Table S194. Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
4P LOSS CNV | 92 | 7 | 76 |
4P LOSS WILD-TYPE | 142 | 141 | 370 |
Figure S194. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D47V7.png)
P value = 9.21e-18 (Fisher's exact test), Q value = 7.2e-15
Table S195. Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
4P LOSS CNV | 15 | 75 | 85 |
4P LOSS WILD-TYPE | 201 | 333 | 119 |
Figure S195. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D47V8.png)
P value = 6.76e-14 (Fisher's exact test), Q value = 5.1e-11
Table S196. Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
4P LOSS CNV | 21 | 66 | 93 |
4P LOSS WILD-TYPE | 213 | 326 | 162 |
Figure S196. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D47V9.png)
P value = 5.98e-15 (Fisher's exact test), Q value = 4.6e-12
Table S197. Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
4P LOSS CNV | 65 | 26 | 89 |
4P LOSS WILD-TYPE | 297 | 258 | 146 |
Figure S197. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D47V10.png)
P value = 1.79e-06 (Chi-square test), Q value = 0.0011
Table S198. Gene #48: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
4Q LOSS CNV | 17 | 5 | 1 | 32 | 25 | 2 | 12 | 3 |
4Q LOSS WILD-TYPE | 107 | 31 | 22 | 63 | 47 | 18 | 91 | 37 |
Figure S198. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D48V1.png)
P value = 2.1e-08 (Fisher's exact test), Q value = 1.4e-05
Table S199. Gene #48: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 140 | 125 | 248 |
4Q LOSS CNV | 8 | 42 | 47 |
4Q LOSS WILD-TYPE | 132 | 83 | 201 |
Figure S199. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D48V2.png)
P value = 7.17e-21 (Chi-square test), Q value = 5.6e-18
Table S200. Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
4Q LOSS CNV | 17 | 30 | 26 | 75 | 7 |
4Q LOSS WILD-TYPE | 330 | 192 | 46 | 148 | 42 |
Figure S200. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D48V3.png)
P value = 1.19e-10 (Chi-square test), Q value = 8.5e-08
Table S201. Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
4Q LOSS CNV | 37 | 20 | 16 | 12 | 4 | 2 |
4Q LOSS WILD-TYPE | 64 | 119 | 77 | 125 | 36 | 95 |
Figure S201. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D48V4.png)
P value = 4.88e-12 (Fisher's exact test), Q value = 3.6e-09
Table S202. Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
4Q LOSS CNV | 73 | 6 | 68 |
4Q LOSS WILD-TYPE | 161 | 142 | 378 |
Figure S202. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D48V7.png)
P value = 1.13e-12 (Fisher's exact test), Q value = 8.3e-10
Table S203. Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
4Q LOSS CNV | 13 | 66 | 68 |
4Q LOSS WILD-TYPE | 203 | 342 | 136 |
Figure S203. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D48V8.png)
P value = 4.17e-07 (Fisher's exact test), Q value = 0.00027
Table S204. Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
4Q LOSS CNV | 20 | 61 | 68 |
4Q LOSS WILD-TYPE | 214 | 331 | 187 |
Figure S204. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D48V9.png)
P value = 4.61e-10 (Fisher's exact test), Q value = 3.2e-07
Table S205. Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
4Q LOSS CNV | 51 | 26 | 72 |
4Q LOSS WILD-TYPE | 311 | 258 | 163 |
Figure S205. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D48V10.png)
P value = 1.49e-08 (Chi-square test), Q value = 1e-05
Table S206. Gene #49: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
5P LOSS CNV | 4 | 2 | 2 | 24 | 9 | 0 | 3 | 0 |
5P LOSS WILD-TYPE | 120 | 34 | 21 | 71 | 63 | 20 | 100 | 40 |
Figure S206. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D49V1.png)
P value = 4.14e-06 (Fisher's exact test), Q value = 0.0024
Table S207. Gene #49: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 140 | 125 | 248 |
5P LOSS CNV | 3 | 24 | 17 |
5P LOSS WILD-TYPE | 137 | 101 | 231 |
Figure S207. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D49V2.png)
P value = 8.97e-21 (Chi-square test), Q value = 7e-18
Table S208. Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
5P LOSS CNV | 2 | 13 | 3 | 52 | 3 |
5P LOSS WILD-TYPE | 345 | 209 | 69 | 171 | 46 |
Figure S208. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D49V3.png)
P value = 4.03e-12 (Chi-square test), Q value = 3e-09
Table S209. Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
5P LOSS CNV | 25 | 2 | 5 | 11 | 0 | 1 |
5P LOSS WILD-TYPE | 76 | 137 | 88 | 126 | 40 | 96 |
Figure S209. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D49V4.png)
P value = 4.28e-05 (Fisher's exact test), Q value = 0.023
Table S210. Gene #49: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 147 | 133 | 117 |
5P LOSS CNV | 27 | 5 | 6 |
5P LOSS WILD-TYPE | 120 | 128 | 111 |
Figure S210. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D49V5.png)
P value = 6.72e-06 (Fisher's exact test), Q value = 0.0039
Table S211. Gene #49: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 110 | 126 |
5P LOSS CNV | 7 | 5 | 26 |
5P LOSS WILD-TYPE | 154 | 105 | 100 |
Figure S211. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D49V6.png)
P value = 1.79e-08 (Fisher's exact test), Q value = 1.2e-05
Table S212. Gene #49: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
5P LOSS CNV | 38 | 1 | 27 |
5P LOSS WILD-TYPE | 196 | 147 | 419 |
Figure S212. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D49V7.png)
P value = 3.4e-08 (Fisher's exact test), Q value = 2.3e-05
Table S213. Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
5P LOSS CNV | 4 | 27 | 35 |
5P LOSS WILD-TYPE | 212 | 381 | 169 |
Figure S213. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D49V8.png)
P value = 1.86e-14 (Fisher's exact test), Q value = 1.4e-11
Table S214. Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
5P LOSS CNV | 4 | 17 | 51 |
5P LOSS WILD-TYPE | 230 | 375 | 204 |
Figure S214. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D49V9.png)
P value = 1.1e-16 (Fisher's exact test), Q value = 8.5e-14
Table S215. Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
5P LOSS CNV | 19 | 3 | 50 |
5P LOSS WILD-TYPE | 343 | 281 | 185 |
Figure S215. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D49V10.png)
P value = 4.14e-19 (Chi-square test), Q value = 3.2e-16
Table S216. Gene #50: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
5Q LOSS CNV | 9 | 3 | 3 | 44 | 13 | 0 | 3 | 1 |
5Q LOSS WILD-TYPE | 115 | 33 | 20 | 51 | 59 | 20 | 100 | 39 |
Figure S216. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D50V1.png)
P value = 9.95e-15 (Fisher's exact test), Q value = 7.6e-12
Table S217. Gene #50: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 140 | 125 | 248 |
5Q LOSS CNV | 5 | 47 | 24 |
5Q LOSS WILD-TYPE | 135 | 78 | 224 |
Figure S217. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D50V2.png)
P value = 4.59e-45 (Chi-square test), Q value = 3.7e-42
Table S218. Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
5Q LOSS CNV | 4 | 15 | 4 | 94 | 7 |
5Q LOSS WILD-TYPE | 343 | 207 | 68 | 129 | 42 |
Figure S218. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D50V3.png)
P value = 1.21e-32 (Chi-square test), Q value = 9.6e-30
Table S219. Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
5Q LOSS CNV | 50 | 3 | 5 | 16 | 0 | 2 |
5Q LOSS WILD-TYPE | 51 | 136 | 88 | 121 | 40 | 95 |
Figure S219. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D50V4.png)
P value = 1.86e-09 (Fisher's exact test), Q value = 1.3e-06
Table S220. Gene #50: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 147 | 133 | 117 |
5Q LOSS CNV | 46 | 6 | 13 |
5Q LOSS WILD-TYPE | 101 | 127 | 104 |
Figure S220. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D50V5.png)
P value = 6.93e-11 (Fisher's exact test), Q value = 5e-08
Table S221. Gene #50: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 110 | 126 |
5Q LOSS CNV | 12 | 8 | 45 |
5Q LOSS WILD-TYPE | 149 | 102 | 81 |
Figure S221. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D50V6.png)
P value = 4.87e-22 (Fisher's exact test), Q value = 3.8e-19
Table S222. Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
5Q LOSS CNV | 79 | 4 | 34 |
5Q LOSS WILD-TYPE | 155 | 144 | 412 |
Figure S222. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D50V7.png)
P value = 9.55e-24 (Fisher's exact test), Q value = 7.6e-21
Table S223. Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
5Q LOSS CNV | 7 | 35 | 75 |
5Q LOSS WILD-TYPE | 209 | 373 | 129 |
Figure S223. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D50V8.png)
P value = 1.06e-27 (Fisher's exact test), Q value = 8.4e-25
Table S224. Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
5Q LOSS CNV | 9 | 23 | 89 |
5Q LOSS WILD-TYPE | 225 | 369 | 166 |
Figure S224. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D50V9.png)
P value = 1.15e-33 (Fisher's exact test), Q value = 9.2e-31
Table S225. Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
5Q LOSS CNV | 27 | 5 | 89 |
5Q LOSS WILD-TYPE | 335 | 279 | 146 |
Figure S225. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D50V10.png)
P value = 9.32e-05 (Fisher's exact test), Q value = 0.048
Table S226. Gene #51: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 140 | 125 | 248 |
6P LOSS CNV | 21 | 4 | 44 |
6P LOSS WILD-TYPE | 119 | 121 | 204 |
Figure S226. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D51V2.png)
P value = 1.09e-09 (Chi-square test), Q value = 7.6e-07
Table S227. Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
6P LOSS CNV | 21 | 52 | 10 | 16 | 10 |
6P LOSS WILD-TYPE | 326 | 170 | 62 | 207 | 39 |
Figure S227. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D51V3.png)
P value = 4.96e-05 (Chi-square test), Q value = 0.026
Table S228. Gene #51: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
6P LOSS CNV | 4 | 13 | 11 | 29 | 2 | 4 |
6P LOSS WILD-TYPE | 97 | 126 | 82 | 108 | 38 | 93 |
Figure S228. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D51V4.png)
P value = 1.23e-05 (Fisher's exact test), Q value = 0.007
Table S229. Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
6P LOSS CNV | 14 | 12 | 78 |
6P LOSS WILD-TYPE | 220 | 136 | 368 |
Figure S229. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D51V7.png)
P value = 1.85e-05 (Fisher's exact test), Q value = 0.01
Table S230. Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
6P LOSS CNV | 23 | 71 | 10 |
6P LOSS WILD-TYPE | 193 | 337 | 194 |
Figure S230. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D51V8.png)
P value = 0.000394 (Fisher's exact test), Q value = 0.18
Table S231. Gene #51: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
6P LOSS CNV | 62 | 29 | 16 |
6P LOSS WILD-TYPE | 300 | 255 | 219 |
Figure S231. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D51V10.png)
P value = 4.71e-05 (Chi-square test), Q value = 0.025
Table S232. Gene #52: '6q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
6Q LOSS CNV | 40 | 10 | 4 | 6 | 9 | 1 | 19 | 11 |
6Q LOSS WILD-TYPE | 84 | 26 | 19 | 89 | 63 | 19 | 84 | 29 |
Figure S232. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D52V1.png)
P value = 9.19e-07 (Fisher's exact test), Q value = 0.00058
Table S233. Gene #52: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 140 | 125 | 248 |
6Q LOSS CNV | 32 | 6 | 62 |
6Q LOSS WILD-TYPE | 108 | 119 | 186 |
Figure S233. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D52V2.png)
P value = 1.2e-14 (Chi-square test), Q value = 9.1e-12
Table S234. Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
6Q LOSS CNV | 44 | 79 | 13 | 19 | 16 |
6Q LOSS WILD-TYPE | 303 | 143 | 59 | 204 | 33 |
Figure S234. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D52V3.png)
P value = 6.48e-08 (Chi-square test), Q value = 4.3e-05
Table S235. Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
6Q LOSS CNV | 6 | 30 | 18 | 44 | 5 | 5 |
6Q LOSS WILD-TYPE | 95 | 109 | 75 | 93 | 35 | 92 |
Figure S235. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D52V4.png)
P value = 0.00055 (Fisher's exact test), Q value = 0.24
Table S236. Gene #52: '6q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 147 | 133 | 117 |
6Q LOSS CNV | 14 | 33 | 29 |
6Q LOSS WILD-TYPE | 133 | 100 | 88 |
Figure S236. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D52V5.png)
P value = 2.4e-08 (Fisher's exact test), Q value = 1.6e-05
Table S237. Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
6Q LOSS CNV | 18 | 27 | 114 |
6Q LOSS WILD-TYPE | 216 | 121 | 332 |
Figure S237. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D52V7.png)
P value = 5.38e-07 (Fisher's exact test), Q value = 0.00034
Table S238. Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
6Q LOSS CNV | 46 | 98 | 15 |
6Q LOSS WILD-TYPE | 170 | 310 | 189 |
Figure S238. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D52V8.png)
P value = 2.54e-06 (Fisher's exact test), Q value = 0.0015
Table S239. Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
6Q LOSS CNV | 90 | 56 | 21 |
6Q LOSS WILD-TYPE | 272 | 228 | 214 |
Figure S239. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D52V10.png)
P value = 9.93e-06 (Chi-square test), Q value = 0.0057
Table S240. Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
7P LOSS CNV | 3 | 17 | 4 | 23 | 1 |
7P LOSS WILD-TYPE | 344 | 205 | 68 | 200 | 48 |
Figure S240. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D53V3.png)
P value = 0.000451 (Fisher's exact test), Q value = 0.2
Table S241. Gene #53: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
7P LOSS CNV | 3 | 24 | 20 |
7P LOSS WILD-TYPE | 213 | 384 | 184 |
Figure S241. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D53V8.png)
P value = 0.000466 (Fisher's exact test), Q value = 0.2
Table S242. Gene #53: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
7P LOSS CNV | 25 | 4 | 18 |
7P LOSS WILD-TYPE | 337 | 280 | 217 |
Figure S242. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D53V10.png)
P value = 0.000443 (Chi-square test), Q value = 0.2
Table S243. Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
7Q LOSS CNV | 11 | 21 | 8 | 24 | 0 |
7Q LOSS WILD-TYPE | 336 | 201 | 64 | 199 | 49 |
Figure S243. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D54V3.png)
P value = 1.37e-05 (Fisher's exact test), Q value = 0.0078
Table S244. Gene #54: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
7Q LOSS CNV | 38 | 5 | 18 |
7Q LOSS WILD-TYPE | 324 | 279 | 217 |
Figure S244. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D54V10.png)
P value = 0.000103 (Chi-square test), Q value = 0.052
Table S245. Gene #55: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
8P LOSS CNV | 54 | 9 | 4 | 24 | 29 | 4 | 16 | 15 |
8P LOSS WILD-TYPE | 70 | 27 | 19 | 71 | 43 | 16 | 87 | 25 |
Figure S245. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D55V1.png)
P value = 2.58e-15 (Chi-square test), Q value = 2e-12
Table S246. Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
8P LOSS CNV | 56 | 97 | 10 | 92 | 15 |
8P LOSS WILD-TYPE | 291 | 125 | 62 | 131 | 34 |
Figure S246. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D55V3.png)
P value = 9.84e-08 (Chi-square test), Q value = 6.4e-05
Table S247. Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
8P LOSS CNV | 34 | 23 | 32 | 61 | 8 | 14 |
8P LOSS WILD-TYPE | 67 | 116 | 61 | 76 | 32 | 83 |
Figure S247. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D55V4.png)
P value = 2.39e-05 (Chi-square test), Q value = 0.013
Table S248. Gene #57: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
9P LOSS CNV | 42 | 8 | 5 | 17 | 26 | 5 | 11 | 2 |
9P LOSS WILD-TYPE | 82 | 28 | 18 | 78 | 46 | 15 | 92 | 38 |
Figure S248. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D57V1.png)
P value = 5.07e-19 (Chi-square test), Q value = 4e-16
Table S249. Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
9P LOSS CNV | 22 | 82 | 9 | 65 | 12 |
9P LOSS WILD-TYPE | 325 | 140 | 63 | 158 | 37 |
Figure S249. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D57V3.png)
P value = 1.08e-13 (Chi-square test), Q value = 8.1e-11
Table S250. Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
9P LOSS CNV | 23 | 5 | 29 | 48 | 8 | 3 |
9P LOSS WILD-TYPE | 78 | 134 | 64 | 89 | 32 | 94 |
Figure S250. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D57V4.png)
P value = 3.34e-06 (Fisher's exact test), Q value = 0.002
Table S251. Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
9P LOSS CNV | 56 | 11 | 112 |
9P LOSS WILD-TYPE | 178 | 137 | 334 |
Figure S251. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D57V7.png)
P value = 7.71e-06 (Fisher's exact test), Q value = 0.0045
Table S252. Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
9P LOSS CNV | 23 | 108 | 48 |
9P LOSS WILD-TYPE | 193 | 300 | 156 |
Figure S252. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D57V8.png)
P value = 5.65e-05 (Fisher's exact test), Q value = 0.03
Table S253. Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
9P LOSS CNV | 26 | 92 | 64 |
9P LOSS WILD-TYPE | 208 | 300 | 191 |
Figure S253. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D57V9.png)
P value = 2.37e-07 (Fisher's exact test), Q value = 0.00015
Table S254. Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
9P LOSS CNV | 92 | 29 | 61 |
9P LOSS WILD-TYPE | 270 | 255 | 174 |
Figure S254. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D57V10.png)
P value = 9.61e-16 (Chi-square test), Q value = 7.4e-13
Table S255. Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
9Q LOSS CNV | 12 | 57 | 8 | 56 | 14 |
9Q LOSS WILD-TYPE | 335 | 165 | 64 | 167 | 35 |
Figure S255. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D58V3.png)
P value = 1.74e-12 (Chi-square test), Q value = 1.3e-09
Table S256. Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
9Q LOSS CNV | 30 | 3 | 17 | 36 | 3 | 2 |
9Q LOSS WILD-TYPE | 71 | 136 | 76 | 101 | 37 | 95 |
Figure S256. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D58V4.png)
P value = 9.07e-08 (Fisher's exact test), Q value = 6e-05
Table S257. Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
9Q LOSS CNV | 49 | 4 | 81 |
9Q LOSS WILD-TYPE | 185 | 144 | 365 |
Figure S257. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D58V7.png)
P value = 8.3e-06 (Fisher's exact test), Q value = 0.0048
Table S258. Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
9Q LOSS CNV | 14 | 79 | 41 |
9Q LOSS WILD-TYPE | 202 | 329 | 163 |
Figure S258. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D58V8.png)
P value = 4.12e-05 (Fisher's exact test), Q value = 0.022
Table S259. Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
9Q LOSS CNV | 18 | 64 | 56 |
9Q LOSS WILD-TYPE | 216 | 328 | 199 |
Figure S259. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D58V9.png)
P value = 2.12e-10 (Fisher's exact test), Q value = 1.5e-07
Table S260. Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
9Q LOSS CNV | 64 | 15 | 59 |
9Q LOSS WILD-TYPE | 298 | 269 | 176 |
Figure S260. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D58V10.png)
P value = 2.55e-06 (Chi-square test), Q value = 0.0015
Table S261. Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
10P LOSS CNV | 6 | 28 | 8 | 27 | 6 |
10P LOSS WILD-TYPE | 341 | 194 | 64 | 196 | 43 |
Figure S261. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D59V3.png)
P value = 0.000512 (Chi-square test), Q value = 0.22
Table S262. Gene #60: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
10Q LOSS CNV | 25 | 2 | 7 | 17 | 9 | 2 | 6 | 0 |
10Q LOSS WILD-TYPE | 99 | 34 | 16 | 78 | 63 | 18 | 97 | 40 |
Figure S262. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D60V1.png)
P value = 4.34e-14 (Chi-square test), Q value = 3.3e-11
Table S263. Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
10Q LOSS CNV | 6 | 38 | 8 | 53 | 6 |
10Q LOSS WILD-TYPE | 341 | 184 | 64 | 170 | 43 |
Figure S263. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D60V3.png)
P value = 9.95e-07 (Chi-square test), Q value = 0.00062
Table S264. Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
10Q LOSS CNV | 23 | 6 | 15 | 23 | 3 | 1 |
10Q LOSS WILD-TYPE | 78 | 133 | 78 | 114 | 37 | 96 |
Figure S264. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D60V4.png)
P value = 5.36e-05 (Fisher's exact test), Q value = 0.028
Table S265. Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
10Q LOSS CNV | 41 | 5 | 60 |
10Q LOSS WILD-TYPE | 193 | 143 | 386 |
Figure S265. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D60V7.png)
P value = 0.000363 (Fisher's exact test), Q value = 0.17
Table S266. Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
10Q LOSS CNV | 12 | 61 | 33 |
10Q LOSS WILD-TYPE | 204 | 347 | 171 |
Figure S266. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D60V8.png)
P value = 8.5e-15 (Chi-square test), Q value = 6.5e-12
Table S267. Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
11P LOSS CNV | 12 | 58 | 15 | 54 | 5 |
11P LOSS WILD-TYPE | 335 | 164 | 57 | 169 | 44 |
Figure S267. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D61V3.png)
P value = 8.61e-08 (Chi-square test), Q value = 5.7e-05
Table S268. Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
11P LOSS CNV | 21 | 9 | 22 | 32 | 3 | 1 |
11P LOSS WILD-TYPE | 80 | 130 | 71 | 105 | 37 | 96 |
Figure S268. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D61V4.png)
P value = 5.61e-05 (Fisher's exact test), Q value = 0.03
Table S269. Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
11P LOSS CNV | 73 | 24 | 44 |
11P LOSS WILD-TYPE | 289 | 260 | 191 |
Figure S269. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D61V10.png)
P value = 2.01e-07 (Chi-square test), Q value = 0.00013
Table S270. Gene #62: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
11Q LOSS CNV | 60 | 13 | 4 | 14 | 18 | 3 | 19 | 9 |
11Q LOSS WILD-TYPE | 64 | 23 | 19 | 81 | 54 | 17 | 84 | 31 |
Figure S270. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D62V1.png)
P value = 0.000327 (Fisher's exact test), Q value = 0.15
Table S271. Gene #62: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 140 | 125 | 248 |
11Q LOSS CNV | 36 | 19 | 85 |
11Q LOSS WILD-TYPE | 104 | 106 | 163 |
Figure S271. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D62V2.png)
P value = 2.04e-31 (Chi-square test), Q value = 1.6e-28
Table S272. Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
11Q LOSS CNV | 34 | 120 | 23 | 45 | 7 |
11Q LOSS WILD-TYPE | 313 | 102 | 49 | 178 | 42 |
Figure S272. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D62V3.png)
P value = 1.5e-11 (Chi-square test), Q value = 1.1e-08
Table S273. Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
11Q LOSS CNV | 16 | 27 | 34 | 58 | 8 | 4 |
11Q LOSS WILD-TYPE | 85 | 112 | 59 | 79 | 32 | 93 |
Figure S273. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D62V4.png)
P value = 4.03e-06 (Fisher's exact test), Q value = 0.0024
Table S274. Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
11Q LOSS CNV | 37 | 33 | 146 |
11Q LOSS WILD-TYPE | 197 | 115 | 300 |
Figure S274. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D62V7.png)
P value = 1.26e-05 (Fisher's exact test), Q value = 0.0072
Table S275. Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
11Q LOSS CNV | 55 | 131 | 30 |
11Q LOSS WILD-TYPE | 161 | 277 | 174 |
Figure S275. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D62V8.png)
P value = 3.01e-05 (Fisher's exact test), Q value = 0.016
Table S276. Gene #62: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
11Q LOSS CNV | 121 | 59 | 44 |
11Q LOSS WILD-TYPE | 241 | 225 | 191 |
Figure S276. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D62V10.png)
P value = 1.57e-06 (Chi-square test), Q value = 0.00097
Table S277. Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
12P LOSS CNV | 18 | 7 | 1 | 10 | 7 | 1 |
12P LOSS WILD-TYPE | 83 | 132 | 92 | 127 | 33 | 96 |
Figure S277. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D63V4.png)
P value = 7.88e-05 (Fisher's exact test), Q value = 0.041
Table S278. Gene #63: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
12P LOSS CNV | 33 | 6 | 23 |
12P LOSS WILD-TYPE | 201 | 142 | 423 |
Figure S278. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D63V7.png)
P value = 0.000244 (Fisher's exact test), Q value = 0.12
Table S279. Gene #64: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 140 | 125 | 248 |
12Q LOSS CNV | 3 | 18 | 12 |
12Q LOSS WILD-TYPE | 137 | 107 | 236 |
Figure S279. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D64V2.png)
P value = 9.88e-05 (Chi-square test), Q value = 0.05
Table S280. Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
12Q LOSS CNV | 10 | 9 | 4 | 27 | 2 |
12Q LOSS WILD-TYPE | 337 | 213 | 68 | 196 | 47 |
Figure S280. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D64V3.png)
P value = 4.1e-09 (Chi-square test), Q value = 2.8e-06
Table S281. Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
12Q LOSS CNV | 20 | 2 | 2 | 8 | 2 | 1 |
12Q LOSS WILD-TYPE | 81 | 137 | 91 | 129 | 38 | 96 |
Figure S281. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D64V4.png)
P value = 4.09e-08 (Fisher's exact test), Q value = 2.7e-05
Table S282. Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
12Q LOSS CNV | 31 | 2 | 13 |
12Q LOSS WILD-TYPE | 203 | 146 | 433 |
Figure S282. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D64V7.png)
P value = 1.98e-07 (Fisher's exact test), Q value = 0.00013
Table S283. Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
12Q LOSS CNV | 4 | 14 | 28 |
12Q LOSS WILD-TYPE | 212 | 394 | 176 |
Figure S283. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D64V8.png)
P value = 3.21e-06 (Fisher's exact test), Q value = 0.0019
Table S284. Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
12Q LOSS CNV | 6 | 13 | 31 |
12Q LOSS WILD-TYPE | 228 | 379 | 224 |
Figure S284. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D64V9.png)
P value = 1.34e-06 (Fisher's exact test), Q value = 0.00083
Table S285. Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
12Q LOSS CNV | 13 | 7 | 30 |
12Q LOSS WILD-TYPE | 349 | 277 | 205 |
Figure S285. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D64V10.png)
P value = 0.000134 (Chi-square test), Q value = 0.066
Table S286. Gene #65: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
13Q LOSS CNV | 58 | 10 | 4 | 31 | 25 | 4 | 22 | 5 |
13Q LOSS WILD-TYPE | 66 | 26 | 19 | 64 | 47 | 16 | 81 | 35 |
Figure S286. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D65V1.png)
P value = 1.62e-27 (Chi-square test), Q value = 1.3e-24
Table S287. Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
13Q LOSS CNV | 28 | 100 | 31 | 80 | 28 |
13Q LOSS WILD-TYPE | 319 | 122 | 41 | 143 | 21 |
Figure S287. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D65V3.png)
P value = 2.84e-10 (Chi-square test), Q value = 2e-07
Table S288. Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
13Q LOSS CNV | 36 | 26 | 44 | 51 | 3 | 11 |
13Q LOSS WILD-TYPE | 65 | 113 | 49 | 86 | 37 | 86 |
Figure S288. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D65V4.png)
P value = 0.000411 (Fisher's exact test), Q value = 0.18
Table S289. Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
13Q LOSS CNV | 81 | 26 | 146 |
13Q LOSS WILD-TYPE | 153 | 122 | 300 |
Figure S289. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D65V7.png)
P value = 0.000523 (Fisher's exact test), Q value = 0.23
Table S290. Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
13Q LOSS CNV | 44 | 142 | 67 |
13Q LOSS WILD-TYPE | 172 | 266 | 137 |
Figure S290. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D65V8.png)
P value = 2.49e-08 (Fisher's exact test), Q value = 1.7e-05
Table S291. Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
13Q LOSS CNV | 36 | 131 | 95 |
13Q LOSS WILD-TYPE | 198 | 261 | 160 |
Figure S291. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D65V9.png)
P value = 1.09e-10 (Chi-square test), Q value = 7.8e-08
Table S292. Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
14Q LOSS CNV | 25 | 1 | 2 | 36 | 8 | 3 | 5 | 0 |
14Q LOSS WILD-TYPE | 99 | 35 | 21 | 59 | 64 | 17 | 98 | 40 |
Figure S292. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D66V1.png)
P value = 8.5e-08 (Fisher's exact test), Q value = 5.6e-05
Table S293. Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 140 | 125 | 248 |
14Q LOSS CNV | 7 | 38 | 35 |
14Q LOSS WILD-TYPE | 133 | 87 | 213 |
Figure S293. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D66V2.png)
P value = 2.6e-22 (Chi-square test), Q value = 2e-19
Table S294. Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
14Q LOSS CNV | 10 | 29 | 9 | 75 | 13 |
14Q LOSS WILD-TYPE | 337 | 193 | 63 | 148 | 36 |
Figure S294. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D66V3.png)
P value = 6.83e-16 (Chi-square test), Q value = 5.3e-13
Table S295. Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
14Q LOSS CNV | 39 | 5 | 16 | 18 | 1 | 3 |
14Q LOSS WILD-TYPE | 62 | 134 | 77 | 119 | 39 | 94 |
Figure S295. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D66V4.png)
P value = 0.000185 (Fisher's exact test), Q value = 0.09
Table S296. Gene #66: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 147 | 133 | 117 |
14Q LOSS CNV | 39 | 12 | 14 |
14Q LOSS WILD-TYPE | 108 | 121 | 103 |
Figure S296. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D66V5.png)
P value = 8.52e-05 (Fisher's exact test), Q value = 0.044
Table S297. Gene #66: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 110 | 126 |
14Q LOSS CNV | 18 | 11 | 36 |
14Q LOSS WILD-TYPE | 143 | 99 | 90 |
Figure S297. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D66V6.png)
P value = 2.46e-11 (Fisher's exact test), Q value = 1.8e-08
Table S298. Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
14Q LOSS CNV | 66 | 6 | 52 |
14Q LOSS WILD-TYPE | 168 | 142 | 394 |
Figure S298. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D66V7.png)
P value = 1.53e-11 (Fisher's exact test), Q value = 1.1e-08
Table S299. Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
14Q LOSS CNV | 11 | 53 | 60 |
14Q LOSS WILD-TYPE | 205 | 355 | 144 |
Figure S299. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D66V8.png)
P value = 5.57e-13 (Fisher's exact test), Q value = 4.1e-10
Table S300. Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
14Q LOSS CNV | 19 | 34 | 74 |
14Q LOSS WILD-TYPE | 215 | 358 | 181 |
Figure S300. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D66V9.png)
P value = 1.18e-13 (Fisher's exact test), Q value = 8.8e-11
Table S301. Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
14Q LOSS CNV | 36 | 20 | 71 |
14Q LOSS WILD-TYPE | 326 | 264 | 164 |
Figure S301. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D66V10.png)
P value = 0.000121 (Fisher's exact test), Q value = 0.06
Table S302. Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 140 | 125 | 248 |
15Q LOSS CNV | 13 | 37 | 49 |
15Q LOSS WILD-TYPE | 127 | 88 | 199 |
Figure S302. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D67V2.png)
P value = 3.85e-17 (Chi-square test), Q value = 3e-14
Table S303. Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
15Q LOSS CNV | 19 | 37 | 28 | 68 | 10 |
15Q LOSS WILD-TYPE | 328 | 185 | 44 | 155 | 39 |
Figure S303. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D67V3.png)
P value = 4.94e-07 (Chi-square test), Q value = 0.00031
Table S304. Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
15Q LOSS CNV | 36 | 15 | 19 | 22 | 3 | 8 |
15Q LOSS WILD-TYPE | 65 | 124 | 74 | 115 | 37 | 89 |
Figure S304. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D67V4.png)
P value = 0.000106 (Fisher's exact test), Q value = 0.054
Table S305. Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
15Q LOSS CNV | 61 | 14 | 74 |
15Q LOSS WILD-TYPE | 173 | 134 | 372 |
Figure S305. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D67V7.png)
P value = 0.000116 (Fisher's exact test), Q value = 0.058
Table S306. Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
15Q LOSS CNV | 22 | 74 | 53 |
15Q LOSS WILD-TYPE | 194 | 334 | 151 |
Figure S306. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D67V8.png)
P value = 7.41e-05 (Fisher's exact test), Q value = 0.039
Table S307. Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
15Q LOSS CNV | 27 | 63 | 67 |
15Q LOSS WILD-TYPE | 207 | 329 | 188 |
Figure S307. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D67V9.png)
P value = 3.04e-06 (Fisher's exact test), Q value = 0.0018
Table S308. Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
15Q LOSS CNV | 64 | 29 | 64 |
15Q LOSS WILD-TYPE | 298 | 255 | 171 |
Figure S308. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D67V10.png)
P value = 1.42e-05 (Chi-square test), Q value = 0.008
Table S309. Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
16P LOSS CNV | 5 | 19 | 2 | 25 | 4 |
16P LOSS WILD-TYPE | 342 | 203 | 70 | 198 | 45 |
Figure S309. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D68V3.png)
P value = 2.47e-05 (Chi-square test), Q value = 0.014
Table S310. Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
16P LOSS CNV | 14 | 1 | 7 | 5 | 0 | 2 |
16P LOSS WILD-TYPE | 87 | 138 | 86 | 132 | 40 | 95 |
Figure S310. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D68V4.png)
P value = 0.000225 (Fisher's exact test), Q value = 0.11
Table S311. Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
16P LOSS CNV | 4 | 23 | 26 |
16P LOSS WILD-TYPE | 230 | 369 | 229 |
Figure S311. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D68V9.png)
P value = 0.000233 (Fisher's exact test), Q value = 0.11
Table S312. Gene #68: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
16P LOSS CNV | 20 | 7 | 26 |
16P LOSS WILD-TYPE | 342 | 277 | 209 |
Figure S312. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D68V10.png)
P value = 7.08e-08 (Chi-square test), Q value = 4.7e-05
Table S313. Gene #69: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
16Q LOSS CNV | 59 | 20 | 13 | 16 | 33 | 7 | 62 | 23 |
16Q LOSS WILD-TYPE | 65 | 16 | 10 | 79 | 39 | 13 | 41 | 17 |
Figure S313. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D69V1.png)
P value = 1.75e-13 (Fisher's exact test), Q value = 1.3e-10
Table S314. Gene #69: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 140 | 125 | 248 |
16Q LOSS CNV | 76 | 21 | 136 |
16Q LOSS WILD-TYPE | 64 | 104 | 112 |
Figure S314. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D69V2.png)
P value = 9.63e-12 (Chi-square test), Q value = 7e-09
Table S315. Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
16Q LOSS CNV | 161 | 107 | 46 | 50 | 26 |
16Q LOSS WILD-TYPE | 186 | 115 | 26 | 173 | 23 |
Figure S315. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D69V3.png)
P value = 6.1e-17 (Chi-square test), Q value = 4.7e-14
Table S316. Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
16Q LOSS CNV | 18 | 95 | 45 | 58 | 13 | 20 |
16Q LOSS WILD-TYPE | 83 | 44 | 48 | 79 | 27 | 77 |
Figure S316. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D69V4.png)
P value = 8.18e-06 (Fisher's exact test), Q value = 0.0047
Table S317. Gene #69: '16q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 147 | 133 | 117 |
16Q LOSS CNV | 40 | 73 | 54 |
16Q LOSS WILD-TYPE | 107 | 60 | 63 |
Figure S317. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D69V5.png)
P value = 1.02e-09 (Fisher's exact test), Q value = 7.1e-07
Table S318. Gene #69: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 110 | 126 |
16Q LOSS CNV | 90 | 52 | 25 |
16Q LOSS WILD-TYPE | 71 | 58 | 101 |
Figure S318. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D69V6.png)
P value = 1.01e-16 (Fisher's exact test), Q value = 7.8e-14
Table S319. Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
16Q LOSS CNV | 48 | 72 | 238 |
16Q LOSS WILD-TYPE | 186 | 76 | 208 |
Figure S319. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D69V7.png)
P value = 8.02e-20 (Fisher's exact test), Q value = 6.3e-17
Table S320. Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
16Q LOSS CNV | 116 | 209 | 33 |
16Q LOSS WILD-TYPE | 100 | 199 | 171 |
Figure S320. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D69V8.png)
P value = 9.39e-15 (Fisher's exact test), Q value = 7.1e-12
Table S321. Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
16Q LOSS CNV | 106 | 213 | 59 |
16Q LOSS WILD-TYPE | 128 | 179 | 196 |
Figure S321. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D69V9.png)
P value = 4.4e-18 (Fisher's exact test), Q value = 3.4e-15
Table S322. Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
16Q LOSS CNV | 162 | 167 | 49 |
16Q LOSS WILD-TYPE | 200 | 117 | 186 |
Figure S322. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D69V10.png)
P value = 8.23e-06 (Chi-square test), Q value = 0.0048
Table S323. Gene #70: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
17P LOSS CNV | 58 | 19 | 11 | 40 | 47 | 3 | 27 | 15 |
17P LOSS WILD-TYPE | 66 | 17 | 12 | 55 | 25 | 17 | 76 | 25 |
Figure S323. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D70V1.png)
P value = 6.2e-14 (Chi-square test), Q value = 4.6e-11
Table S324. Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
17P LOSS CNV | 87 | 122 | 25 | 117 | 22 |
17P LOSS WILD-TYPE | 260 | 100 | 47 | 106 | 27 |
Figure S324. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D70V3.png)
P value = 5.8e-08 (Chi-square test), Q value = 3.9e-05
Table S325. Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
17P LOSS CNV | 38 | 47 | 47 | 75 | 14 | 16 |
17P LOSS WILD-TYPE | 63 | 92 | 46 | 62 | 26 | 81 |
Figure S325. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D70V4.png)
P value = 1.08e-10 (Chi-square test), Q value = 7.7e-08
Table S326. Gene #71: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
17Q LOSS CNV | 17 | 2 | 2 | 29 | 30 | 0 | 5 | 7 |
17Q LOSS WILD-TYPE | 107 | 34 | 21 | 66 | 42 | 20 | 98 | 33 |
Figure S326. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D71V1.png)
P value = 1.72e-06 (Fisher's exact test), Q value = 0.0011
Table S327. Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 140 | 125 | 248 |
17Q LOSS CNV | 12 | 41 | 39 |
17Q LOSS WILD-TYPE | 128 | 84 | 209 |
Figure S327. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D71V2.png)
P value = 8.88e-11 (Chi-square test), Q value = 6.4e-08
Table S328. Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
17Q LOSS CNV | 24 | 34 | 11 | 66 | 8 |
17Q LOSS WILD-TYPE | 323 | 188 | 61 | 157 | 41 |
Figure S328. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D71V3.png)
P value = 7.48e-05 (Chi-square test), Q value = 0.039
Table S329. Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
17Q LOSS CNV | 25 | 7 | 13 | 23 | 2 | 8 |
17Q LOSS WILD-TYPE | 76 | 132 | 80 | 114 | 38 | 89 |
Figure S329. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D71V4.png)
P value = 9.69e-10 (Fisher's exact test), Q value = 6.8e-07
Table S330. Gene #71: '17q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 147 | 133 | 117 |
17Q LOSS CNV | 51 | 7 | 19 |
17Q LOSS WILD-TYPE | 96 | 126 | 98 |
Figure S330. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D71V5.png)
P value = 6.4e-07 (Fisher's exact test), Q value = 4e-04
Table S331. Gene #71: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 110 | 126 |
17Q LOSS CNV | 16 | 17 | 44 |
17Q LOSS WILD-TYPE | 145 | 93 | 82 |
Figure S331. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D71V6.png)
P value = 1.9e-10 (Fisher's exact test), Q value = 1.3e-07
Table S332. Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
17Q LOSS CNV | 71 | 13 | 50 |
17Q LOSS WILD-TYPE | 163 | 135 | 396 |
Figure S332. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D71V7.png)
P value = 4.84e-08 (Fisher's exact test), Q value = 3.2e-05
Table S333. Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
17Q LOSS CNV | 20 | 54 | 60 |
17Q LOSS WILD-TYPE | 196 | 354 | 144 |
Figure S333. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D71V8.png)
P value = 9.64e-07 (Fisher's exact test), Q value = 6e-04
Table S334. Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
17Q LOSS CNV | 26 | 46 | 67 |
17Q LOSS WILD-TYPE | 208 | 346 | 188 |
Figure S334. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D71V9.png)
P value = 2.69e-05 (Fisher's exact test), Q value = 0.015
Table S335. Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
17Q LOSS CNV | 50 | 30 | 59 |
17Q LOSS WILD-TYPE | 312 | 254 | 176 |
Figure S335. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D71V10.png)
P value = 0.000377 (Chi-square test), Q value = 0.17
Table S336. Gene #72: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
18P LOSS CNV | 27 | 5 | 4 | 13 | 30 | 5 | 14 | 9 |
18P LOSS WILD-TYPE | 97 | 31 | 19 | 82 | 42 | 15 | 89 | 31 |
Figure S336. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D72V1.png)
P value = 6.18e-10 (Chi-square test), Q value = 4.3e-07
Table S337. Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
18P LOSS CNV | 28 | 57 | 24 | 57 | 9 |
18P LOSS WILD-TYPE | 319 | 165 | 48 | 166 | 40 |
Figure S337. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D72V3.png)
P value = 3.32e-06 (Chi-square test), Q value = 0.002
Table S338. Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
18P LOSS CNV | 13 | 14 | 30 | 36 | 3 | 11 |
18P LOSS WILD-TYPE | 88 | 125 | 63 | 101 | 37 | 86 |
Figure S338. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D72V4.png)
P value = 6.11e-13 (Chi-square test), Q value = 4.5e-10
Table S339. Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
18Q LOSS CNV | 24 | 58 | 26 | 61 | 8 |
18Q LOSS WILD-TYPE | 323 | 164 | 46 | 162 | 41 |
Figure S339. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D73V3.png)
P value = 7.01e-08 (Chi-square test), Q value = 4.6e-05
Table S340. Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
18Q LOSS CNV | 21 | 15 | 33 | 36 | 2 | 7 |
18Q LOSS WILD-TYPE | 80 | 124 | 60 | 101 | 38 | 90 |
Figure S340. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D73V4.png)
P value = 1.65e-05 (Chi-square test), Q value = 0.0093
Table S341. Gene #74: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
19P LOSS CNV | 17 | 4 | 0 | 5 | 15 | 1 | 1 | 0 |
19P LOSS WILD-TYPE | 107 | 32 | 23 | 90 | 57 | 19 | 102 | 40 |
Figure S341. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D74V1.png)
P value = 0.000461 (Fisher's exact test), Q value = 0.2
Table S342. Gene #74: '19p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 140 | 125 | 248 |
19P LOSS CNV | 3 | 8 | 32 |
19P LOSS WILD-TYPE | 137 | 117 | 216 |
Figure S342. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D74V2.png)
P value = 7.77e-13 (Chi-square test), Q value = 5.7e-10
Table S343. Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
19P LOSS CNV | 1 | 38 | 2 | 19 | 7 |
19P LOSS WILD-TYPE | 346 | 184 | 70 | 204 | 42 |
Figure S343. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D74V3.png)
P value = 1.43e-08 (Chi-square test), Q value = 9.7e-06
Table S344. Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
19P LOSS CNV | 8 | 0 | 7 | 23 | 0 | 0 |
19P LOSS WILD-TYPE | 93 | 139 | 86 | 114 | 40 | 97 |
Figure S344. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D74V4.png)
P value = 0.000554 (Fisher's exact test), Q value = 0.24
Table S345. Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
19P LOSS CNV | 26 | 2 | 37 |
19P LOSS WILD-TYPE | 208 | 146 | 409 |
Figure S345. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D74V7.png)
P value = 0.000512 (Fisher's exact test), Q value = 0.22
Table S346. Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
19P LOSS CNV | 5 | 42 | 18 |
19P LOSS WILD-TYPE | 211 | 366 | 186 |
Figure S346. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D74V8.png)
P value = 0.000287 (Fisher's exact test), Q value = 0.13
Table S347. Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
19P LOSS CNV | 5 | 33 | 27 |
19P LOSS WILD-TYPE | 229 | 359 | 228 |
Figure S347. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D74V9.png)
P value = 7.41e-05 (Chi-square test), Q value = 0.039
Table S348. Gene #75: '19q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
19Q LOSS CNV | 14 | 3 | 0 | 3 | 13 | 1 | 1 | 0 |
19Q LOSS WILD-TYPE | 110 | 33 | 23 | 92 | 59 | 19 | 102 | 40 |
Figure S348. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D75V1.png)
P value = 3.66e-10 (Chi-square test), Q value = 2.6e-07
Table S349. Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
19Q LOSS CNV | 2 | 30 | 0 | 15 | 6 |
19Q LOSS WILD-TYPE | 345 | 192 | 72 | 208 | 43 |
Figure S349. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D75V3.png)
P value = 1.62e-05 (Chi-square test), Q value = 0.0091
Table S350. Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
19Q LOSS CNV | 7 | 0 | 6 | 16 | 0 | 0 |
19Q LOSS WILD-TYPE | 94 | 139 | 87 | 121 | 40 | 97 |
Figure S350. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D75V4.png)
P value = 8.9e-06 (Fisher's exact test), Q value = 0.0051
Table S351. Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
19Q LOSS CNV | 1 | 36 | 14 |
19Q LOSS WILD-TYPE | 215 | 372 | 190 |
Figure S351. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D75V8.png)
P value = 0.00046 (Fisher's exact test), Q value = 0.2
Table S352. Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
19Q LOSS CNV | 34 | 7 | 10 |
19Q LOSS WILD-TYPE | 328 | 277 | 225 |
Figure S352. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D75V10.png)
P value = 1.42e-06 (Chi-square test), Q value = 0.00088
Table S353. Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
20P LOSS CNV | 3 | 20 | 2 | 21 | 7 |
20P LOSS WILD-TYPE | 344 | 202 | 70 | 202 | 42 |
Figure S353. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D76V3.png)
P value = 2.42e-05 (Chi-square test), Q value = 0.013
Table S354. Gene #76: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
20P LOSS CNV | 15 | 1 | 5 | 9 | 1 | 1 |
20P LOSS WILD-TYPE | 86 | 138 | 88 | 128 | 39 | 96 |
Figure S354. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D76V4.png)
P value = 0.000252 (Fisher's exact test), Q value = 0.12
Table S355. Gene #76: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
20P LOSS CNV | 3 | 23 | 21 |
20P LOSS WILD-TYPE | 213 | 385 | 183 |
Figure S355. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D76V8.png)
P value = 0.000176 (Fisher's exact test), Q value = 0.086
Table S356. Gene #76: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
20P LOSS CNV | 7 | 15 | 28 |
20P LOSS WILD-TYPE | 227 | 377 | 227 |
Figure S356. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D76V9.png)
P value = 0.000223 (Fisher's exact test), Q value = 0.11
Table S357. Gene #76: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
20P LOSS CNV | 22 | 5 | 23 |
20P LOSS WILD-TYPE | 340 | 279 | 212 |
Figure S357. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D76V10.png)
P value = 6.97e-05 (Chi-square test), Q value = 0.036
Table S358. Gene #77: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
20Q LOSS CNV | 1 | 7 | 2 | 14 | 5 |
20Q LOSS WILD-TYPE | 346 | 215 | 70 | 209 | 44 |
Figure S358. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D77V3.png)
P value = 2.82e-06 (Chi-square test), Q value = 0.0017
Table S359. Gene #77: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
20Q LOSS CNV | 11 | 0 | 1 | 3 | 0 | 1 |
20Q LOSS WILD-TYPE | 90 | 139 | 92 | 134 | 40 | 96 |
Figure S359. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D77V4.png)
P value = 0.00032 (Fisher's exact test), Q value = 0.15
Table S360. Gene #77: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
20Q LOSS CNV | 1 | 9 | 14 |
20Q LOSS WILD-TYPE | 215 | 399 | 190 |
Figure S360. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D77V8.png)
P value = 0.000443 (Fisher's exact test), Q value = 0.2
Table S361. Gene #77: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
20Q LOSS CNV | 3 | 7 | 18 |
20Q LOSS WILD-TYPE | 231 | 385 | 237 |
Figure S361. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D77V9.png)
P value = 3.3e-05 (Fisher's exact test), Q value = 0.018
Table S362. Gene #77: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
20Q LOSS CNV | 8 | 2 | 18 |
20Q LOSS WILD-TYPE | 354 | 282 | 217 |
Figure S362. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D77V10.png)
P value = 1.67e-06 (Chi-square test), Q value = 0.001
Table S363. Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
21Q LOSS CNV | 9 | 31 | 9 | 28 | 9 |
21Q LOSS WILD-TYPE | 338 | 191 | 63 | 195 | 40 |
Figure S363. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D78V3.png)
P value = 4.25e-05 (Chi-square test), Q value = 0.023
Table S364. Gene #79: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 124 | 36 | 23 | 95 | 72 | 20 | 103 | 40 |
22Q LOSS CNV | 63 | 17 | 7 | 17 | 19 | 5 | 37 | 13 |
22Q LOSS WILD-TYPE | 61 | 19 | 16 | 78 | 53 | 15 | 66 | 27 |
Figure S364. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D79V1.png)
P value = 1.42e-07 (Fisher's exact test), Q value = 9.2e-05
Table S365. Gene #79: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 140 | 125 | 248 |
22Q LOSS CNV | 52 | 19 | 107 |
22Q LOSS WILD-TYPE | 88 | 106 | 141 |
Figure S365. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D79V2.png)
P value = 2.97e-06 (Chi-square test), Q value = 0.0018
Table S366. Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 347 | 222 | 72 | 223 | 49 |
22Q LOSS CNV | 90 | 93 | 34 | 64 | 25 |
22Q LOSS WILD-TYPE | 257 | 129 | 38 | 159 | 24 |
Figure S366. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D79V3.png)
P value = 5.32e-07 (Chi-square test), Q value = 0.00034
Table S367. Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 101 | 139 | 93 | 137 | 40 | 97 |
22Q LOSS CNV | 26 | 46 | 38 | 67 | 8 | 15 |
22Q LOSS WILD-TYPE | 75 | 93 | 55 | 70 | 32 | 82 |
Figure S367. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D79V4.png)
P value = 0.000476 (Fisher's exact test), Q value = 0.21
Table S368. Gene #79: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 147 | 133 | 117 |
22Q LOSS CNV | 37 | 63 | 39 |
22Q LOSS WILD-TYPE | 110 | 70 | 78 |
Figure S368. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D79V5.png)
P value = 1.64e-05 (Fisher's exact test), Q value = 0.0092
Table S369. Gene #79: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 110 | 126 |
22Q LOSS CNV | 74 | 40 | 25 |
22Q LOSS WILD-TYPE | 87 | 70 | 101 |
Figure S369. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D79V6.png)
P value = 2.18e-10 (Fisher's exact test), Q value = 1.5e-07
Table S370. Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 148 | 446 |
22Q LOSS CNV | 45 | 40 | 193 |
22Q LOSS WILD-TYPE | 189 | 108 | 253 |
Figure S370. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D79V7.png)
P value = 2.62e-11 (Fisher's exact test), Q value = 1.9e-08
Table S371. Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 216 | 408 | 204 |
22Q LOSS CNV | 74 | 173 | 31 |
22Q LOSS WILD-TYPE | 142 | 235 | 173 |
Figure S371. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D79V8.png)
P value = 1.57e-08 (Fisher's exact test), Q value = 1.1e-05
Table S372. Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 234 | 392 | 255 |
22Q LOSS CNV | 68 | 170 | 55 |
22Q LOSS WILD-TYPE | 166 | 222 | 200 |
Figure S372. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D79V9.png)
P value = 0.000171 (Fisher's exact test), Q value = 0.084
Table S373. Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
22Q LOSS CNV | 137 | 103 | 53 |
22Q LOSS WILD-TYPE | 225 | 181 | 182 |
Figure S373. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D79V10.png)
P value = 0.000357 (Fisher's exact test), Q value = 0.16
Table S374. Gene #80: 'Xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 362 | 284 | 235 |
XQ LOSS CNV | 16 | 1 | 13 |
XQ LOSS WILD-TYPE | 346 | 283 | 222 |
Figure S374. Get High-res Image Gene #80: 'Xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D80V10.png)
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Mutation data file = broad_values_by_arm.mutsig.cluster.txt
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Molecular subtypes file = BRCA-TP.transferedmergedcluster.txt
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Number of patients = 913
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Number of significantly arm-level cnvs = 80
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Number of molecular subtypes = 10
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Exclude genes that fewer than K tumors have mutations, K = 3
For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R
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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.