This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.
Testing the association between copy number variation 57 arm-level events and 10 molecular subtypes across 494 patients, 163 significant findings detected with P value < 0.05 and Q value < 0.25.
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1q gain cnv correlated to 'CN_CNMF'.
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3p gain cnv correlated to 'CN_CNMF'.
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4p gain cnv correlated to 'CN_CNMF'.
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4q gain cnv correlated to 'CN_CNMF'.
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5p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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5q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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7p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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7q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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8p gain cnv correlated to 'CN_CNMF'.
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8q gain cnv correlated to 'CN_CNMF'.
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11p 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', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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12q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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13q gain cnv correlated to 'CN_CNMF'.
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14q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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16p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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16q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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17p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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17q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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18p gain cnv correlated to 'CN_CNMF'.
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18q gain cnv correlated to 'CN_CNMF'.
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19p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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19q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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20p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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20q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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21q gain cnv correlated to 'CN_CNMF'.
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xq gain cnv correlated to 'CN_CNMF'.
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1p loss cnv correlated to 'CN_CNMF'.
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1q loss cnv correlated to 'CN_CNMF'.
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2p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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2q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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3p loss cnv correlated to 'CN_CNMF'.
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3q loss cnv correlated to 'CN_CNMF'.
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6q loss cnv correlated to 'CN_CNMF'.
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8p loss cnv correlated to 'CN_CNMF'.
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8q loss cnv correlated to 'CN_CNMF'.
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9p loss cnv correlated to 'CN_CNMF'.
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9q loss cnv correlated to 'CN_CNMF'.
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10p loss cnv correlated to 'CN_CNMF'.
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10q loss cnv correlated to 'CN_CNMF'.
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11p loss cnv correlated to 'CN_CNMF'.
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11q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
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15q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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18p loss cnv correlated to 'CN_CNMF'.
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18q loss cnv correlated to 'CN_CNMF'.
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21q loss cnv correlated to 'CN_CNMF'.
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22q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 57 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 163 significant findings detected.
Clinical Features |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
||
nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
5q gain | 17 (3%) | 477 |
1.76e-22 (9.35e-20) |
3.39e-05 (0.0147) |
0.85 (1.00) |
0.00745 (1.00) |
0.000338 (0.13) |
9.22e-06 (0.00427) |
0.000344 (0.132) |
4.11e-05 (0.0178) |
9.6e-05 (0.0395) |
3.18e-05 (0.0139) |
7q gain | 20 (4%) | 474 |
6.92e-25 (3.69e-22) |
9.82e-06 (0.0045) |
0.571 (1.00) |
0.000676 (0.251) |
6.01e-05 (0.0253) |
1.13e-06 (0.000566) |
0.000144 (0.0585) |
1.15e-05 (0.00526) |
4.38e-05 (0.0188) |
9.06e-06 (0.0042) |
12p gain | 14 (3%) | 480 |
1.48e-16 (7.82e-14) |
3.71e-06 (0.00178) |
0.85 (1.00) |
0.00745 (1.00) |
1.65e-05 (0.00746) |
1.69e-06 (0.000822) |
6.05e-05 (0.0254) |
8.86e-06 (0.00412) |
9.65e-06 (0.00444) |
8.52e-06 (0.00397) |
12q gain | 15 (3%) | 479 |
2.14e-16 (1.12e-13) |
1.32e-06 (0.000646) |
0.85 (1.00) |
0.00745 (1.00) |
9.29e-06 (0.00428) |
3.61e-07 (0.000183) |
2.24e-05 (0.00988) |
2.87e-06 (0.00139) |
3.63e-06 (0.00175) |
2.66e-06 (0.00129) |
16p gain | 15 (3%) | 479 |
6.94e-18 (3.67e-15) |
1.85e-05 (0.0083) |
0.633 (1.00) |
0.0106 (1.00) |
0.000195 (0.078) |
6.61e-06 (0.00311) |
0.000192 (0.0769) |
4.25e-05 (0.0183) |
3.07e-05 (0.0134) |
3.96e-05 (0.0172) |
17p gain | 16 (3%) | 478 |
4.23e-13 (2.2e-10) |
5.64e-07 (0.000285) |
0.538 (1.00) |
0.00327 (1.00) |
4.02e-06 (0.00192) |
7.23e-08 (3.69e-05) |
8.06e-06 (0.00379) |
8.97e-07 (0.000452) |
1.33e-06 (0.000651) |
8.04e-07 (0.000406) |
17q gain | 18 (4%) | 476 |
5.03e-14 (2.62e-11) |
1.13e-06 (0.000566) |
0.633 (1.00) |
0.00271 (0.906) |
1.45e-05 (0.00656) |
2.54e-07 (0.000129) |
1.17e-05 (0.00532) |
1.46e-06 (0.000711) |
3.69e-06 (0.00177) |
1.09e-06 (0.000546) |
19q gain | 10 (2%) | 484 |
1.92e-11 (9.93e-09) |
8.44e-06 (0.00396) |
0.636 (1.00) |
0.0523 (1.00) |
5.97e-05 (0.0253) |
5.49e-06 (0.00262) |
5.49e-06 (0.00262) |
1.25e-06 (0.000615) |
2.43e-05 (0.0107) |
1.06e-06 (0.000535) |
2p loss | 10 (2%) | 484 |
1.92e-11 (9.93e-09) |
8.44e-06 (0.00396) |
0.773 (1.00) |
0.0122 (1.00) |
5.97e-05 (0.0253) |
5.49e-06 (0.00262) |
5.49e-06 (0.00262) |
1.25e-06 (0.000615) |
2.43e-05 (0.0107) |
1.06e-06 (0.000535) |
2q loss | 10 (2%) | 484 |
6.03e-13 (3.13e-10) |
8.44e-06 (0.00396) |
0.773 (1.00) |
0.0122 (1.00) |
5.97e-05 (0.0253) |
5.49e-06 (0.00262) |
5.49e-06 (0.00262) |
1.25e-06 (0.000615) |
2.43e-05 (0.0107) |
1.06e-06 (0.000535) |
7p gain | 18 (4%) | 476 |
6.29e-24 (3.35e-21) |
7.19e-05 (0.0299) |
0.66 (1.00) |
0.00219 (0.748) |
0.000338 (0.13) |
9.22e-06 (0.00427) |
0.00105 (0.38) |
0.000121 (0.0498) |
0.000259 (0.101) |
7.61e-05 (0.0315) |
14q gain | 11 (2%) | 483 |
3.23e-10 (1.66e-07) |
0.000161 (0.0652) |
1 (1.00) |
0.079 (1.00) |
0.000574 (0.213) |
7.22e-05 (0.03) |
0.000461 (0.173) |
0.000151 (0.0611) |
0.00123 (0.435) |
0.000114 (0.0468) |
19p gain | 8 (2%) | 486 |
2.19e-10 (1.13e-07) |
0.000139 (0.0568) |
0.000723 (0.267) |
4.14e-05 (0.0179) |
6.43e-05 (0.0269) |
1.99e-05 (0.0088) |
0.000242 (0.0953) |
1.75e-05 (0.00787) |
||
15q loss | 8 (2%) | 486 |
5.63e-05 (0.024) |
0.000139 (0.0568) |
0.193 (1.00) |
0.126 (1.00) |
0.000723 (0.267) |
4.14e-05 (0.0179) |
6.43e-05 (0.0269) |
1.99e-05 (0.0088) |
0.000242 (0.0953) |
1.75e-05 (0.00787) |
22q loss | 86 (17%) | 408 |
7.48e-90 (4e-87) |
1.1e-05 (0.00501) |
0.123 (1.00) |
0.15 (1.00) |
1.12e-08 (5.75e-06) |
6.74e-05 (0.0281) |
0.000956 (0.351) |
0.000342 (0.131) |
3.12e-06 (0.00151) |
0.000206 (0.0819) |
16q gain | 13 (3%) | 481 |
6.49e-17 (3.43e-14) |
0.000121 (0.0498) |
0.795 (1.00) |
0.0363 (1.00) |
0.00103 (0.376) |
9.26e-05 (0.0383) |
0.00171 (0.604) |
0.000387 (0.146) |
0.000182 (0.0732) |
0.000336 (0.13) |
5p gain | 21 (4%) | 473 |
4.18e-23 (2.22e-20) |
0.00093 (0.342) |
0.53 (1.00) |
0.0969 (1.00) |
0.00656 (1.00) |
0.000409 (0.154) |
0.00411 (1.00) |
0.000523 (0.195) |
0.0011 (0.398) |
0.00031 (0.12) |
20p gain | 12 (2%) | 482 |
1.42e-15 (7.47e-13) |
0.000376 (0.143) |
0.795 (1.00) |
0.0193 (1.00) |
0.00319 (1.00) |
0.000202 (0.0807) |
0.00466 (1.00) |
0.00111 (0.4) |
0.000508 (0.19) |
0.000981 (0.359) |
20q gain | 12 (2%) | 482 |
1.42e-15 (7.47e-13) |
0.000376 (0.143) |
0.795 (1.00) |
0.0193 (1.00) |
0.00319 (1.00) |
0.000202 (0.0807) |
0.00466 (1.00) |
0.00111 (0.4) |
0.000508 (0.19) |
0.000981 (0.359) |
11q loss | 9 (2%) | 485 |
3.28e-06 (0.00158) |
0.0106 (1.00) |
0.321 (1.00) |
0.794 (1.00) |
0.0173 (1.00) |
0.00797 (1.00) |
0.000352 (0.134) |
0.00336 (1.00) |
0.00122 (0.433) |
0.00275 (0.914) |
1q gain | 24 (5%) | 470 |
9.81e-06 (0.0045) |
0.0289 (1.00) |
0.00112 (0.401) |
0.0319 (1.00) |
0.00111 (0.4) |
0.00259 (0.869) |
0.146 (1.00) |
0.0524 (1.00) |
0.0941 (1.00) |
0.0219 (1.00) |
3p gain | 3 (1%) | 491 |
0.0003 (0.117) |
0.582 (1.00) |
0.56 (1.00) |
0.362 (1.00) |
0.207 (1.00) |
0.355 (1.00) |
0.323 (1.00) |
0.27 (1.00) |
||
4p gain | 5 (1%) | 489 |
1.16e-06 (0.000576) |
0.00581 (1.00) |
0.0176 (1.00) |
0.00275 (0.914) |
0.0268 (1.00) |
0.0215 (1.00) |
0.0687 (1.00) |
0.0216 (1.00) |
||
4q gain | 5 (1%) | 489 |
1.16e-06 (0.000576) |
0.00581 (1.00) |
0.0176 (1.00) |
0.00275 (0.914) |
0.0268 (1.00) |
0.0215 (1.00) |
0.0687 (1.00) |
0.0216 (1.00) |
||
8p gain | 6 (1%) | 488 |
0.000364 (0.139) |
0.551 (1.00) |
0.457 (1.00) |
0.655 (1.00) |
0.623 (1.00) |
0.476 (1.00) |
0.526 (1.00) |
0.294 (1.00) |
0.334 (1.00) |
0.341 (1.00) |
8q gain | 7 (1%) | 487 |
4.62e-05 (0.0198) |
0.378 (1.00) |
0.457 (1.00) |
0.655 (1.00) |
0.908 (1.00) |
0.639 (1.00) |
0.799 (1.00) |
0.561 (1.00) |
0.318 (1.00) |
0.629 (1.00) |
11p gain | 6 (1%) | 488 |
0.000191 (0.0768) |
0.0263 (1.00) |
0.78 (1.00) |
0.284 (1.00) |
0.0524 (1.00) |
0.0128 (1.00) |
0.0146 (1.00) |
0.00351 (1.00) |
0.00237 (0.804) |
0.00392 (1.00) |
11q gain | 5 (1%) | 489 |
1.6e-05 (0.00726) |
0.0757 (1.00) |
0.78 (1.00) |
0.284 (1.00) |
0.116 (1.00) |
0.0435 (1.00) |
0.0415 (1.00) |
0.0115 (1.00) |
0.00735 (1.00) |
0.0127 (1.00) |
13q gain | 5 (1%) | 489 |
1.16e-06 (0.000576) |
0.0173 (1.00) |
0.384 (1.00) |
0.0523 (1.00) |
0.0423 (1.00) |
0.0135 (1.00) |
0.169 (1.00) |
0.139 (1.00) |
0.21 (1.00) |
0.148 (1.00) |
18p gain | 6 (1%) | 488 |
1.16e-06 (0.000576) |
0.0973 (1.00) |
0.116 (1.00) |
0.0435 (1.00) |
0.255 (1.00) |
0.0841 (1.00) |
0.0259 (1.00) |
0.107 (1.00) |
||
18q gain | 6 (1%) | 488 |
1.16e-06 (0.000576) |
0.0973 (1.00) |
0.116 (1.00) |
0.0435 (1.00) |
0.255 (1.00) |
0.0841 (1.00) |
0.0259 (1.00) |
0.107 (1.00) |
||
21q gain | 5 (1%) | 489 |
1.6e-05 (0.00726) |
0.249 (1.00) |
0.238 (1.00) |
0.152 (1.00) |
0.451 (1.00) |
0.229 (1.00) |
0.0687 (1.00) |
0.318 (1.00) |
||
xq gain | 9 (2%) | 485 |
2.7e-07 (0.000137) |
0.0217 (1.00) |
0.839 (1.00) |
0.25 (1.00) |
0.091 (1.00) |
0.0503 (1.00) |
0.337 (1.00) |
0.207 (1.00) |
0.483 (1.00) |
0.196 (1.00) |
1p loss | 4 (1%) | 490 |
1.89e-05 (0.00846) |
0.22 (1.00) |
0.238 (1.00) |
0.152 (1.00) |
0.0755 (1.00) |
0.0676 (1.00) |
0.129 (1.00) |
0.0942 (1.00) |
||
1q loss | 3 (1%) | 491 |
0.0003 (0.117) |
0.0585 (1.00) |
0.0961 (1.00) |
0.037 (1.00) |
0.0278 (1.00) |
0.018 (1.00) |
0.0701 (1.00) |
0.0172 (1.00) |
||
3p loss | 3 (1%) | 491 |
0.0003 (0.117) |
0.0585 (1.00) |
0.0961 (1.00) |
0.037 (1.00) |
0.0278 (1.00) |
0.018 (1.00) |
0.0701 (1.00) |
0.0172 (1.00) |
||
3q loss | 4 (1%) | 490 |
1.89e-05 (0.00846) |
0.0149 (1.00) |
0.495 (1.00) |
0.364 (1.00) |
0.0423 (1.00) |
0.0135 (1.00) |
0.00833 (1.00) |
0.00467 (1.00) |
0.0227 (1.00) |
0.00439 (1.00) |
6q loss | 7 (1%) | 487 |
4.62e-05 (0.0198) |
0.0038 (1.00) |
0.0129 (1.00) |
0.364 (1.00) |
0.0339 (1.00) |
0.00531 (1.00) |
0.00316 (1.00) |
0.00196 (0.685) |
0.00954 (1.00) |
0.00199 (0.685) |
8p loss | 4 (1%) | 490 |
1.89e-05 (0.00846) |
0.0149 (1.00) |
0.0423 (1.00) |
0.0135 (1.00) |
0.00833 (1.00) |
0.00467 (1.00) |
0.0227 (1.00) |
0.00439 (1.00) |
||
8q loss | 4 (1%) | 490 |
1.89e-05 (0.00846) |
0.0149 (1.00) |
0.0423 (1.00) |
0.0135 (1.00) |
0.00833 (1.00) |
0.00467 (1.00) |
0.0227 (1.00) |
0.00439 (1.00) |
||
9p loss | 19 (4%) | 475 |
2.94e-12 (1.53e-09) |
0.0258 (1.00) |
0.243 (1.00) |
0.368 (1.00) |
0.0304 (1.00) |
0.00862 (1.00) |
0.00659 (1.00) |
0.00303 (0.996) |
0.00966 (1.00) |
0.00181 (0.637) |
9q loss | 24 (5%) | 470 |
9.23e-15 (4.83e-12) |
0.0481 (1.00) |
0.173 (1.00) |
0.0332 (1.00) |
0.0974 (1.00) |
0.0138 (1.00) |
0.00917 (1.00) |
0.00675 (1.00) |
0.0117 (1.00) |
0.00437 (1.00) |
10p loss | 7 (1%) | 487 |
3.94e-09 (2.03e-06) |
0.00956 (1.00) |
0.495 (1.00) |
0.364 (1.00) |
0.0195 (1.00) |
0.00531 (1.00) |
0.00316 (1.00) |
0.00196 (0.685) |
0.00954 (1.00) |
0.00199 (0.685) |
10q loss | 6 (1%) | 488 |
6.87e-08 (3.52e-05) |
0.0263 (1.00) |
0.0524 (1.00) |
0.0128 (1.00) |
0.00929 (1.00) |
0.00658 (1.00) |
0.0259 (1.00) |
0.00664 (1.00) |
||
11p loss | 7 (1%) | 487 |
7.98e-08 (4.07e-05) |
0.00956 (1.00) |
0.495 (1.00) |
1 (1.00) |
0.00648 (1.00) |
0.00531 (1.00) |
0.00316 (1.00) |
0.00196 (0.685) |
0.00954 (1.00) |
0.00199 (0.685) |
18p loss | 4 (1%) | 490 |
0.000207 (0.0819) |
0.22 (1.00) |
1 (1.00) |
0.284 (1.00) |
0.238 (1.00) |
0.152 (1.00) |
0.115 (1.00) |
0.037 (1.00) |
0.0227 (1.00) |
0.0402 (1.00) |
18q loss | 4 (1%) | 490 |
0.000207 (0.0819) |
0.22 (1.00) |
1 (1.00) |
0.284 (1.00) |
0.238 (1.00) |
0.152 (1.00) |
0.115 (1.00) |
0.037 (1.00) |
0.0227 (1.00) |
0.0402 (1.00) |
21q loss | 8 (2%) | 486 |
5.63e-05 (0.024) |
0.221 (1.00) |
0.384 (1.00) |
0.0523 (1.00) |
0.219 (1.00) |
0.279 (1.00) |
0.0744 (1.00) |
0.307 (1.00) |
0.0974 (1.00) |
0.0642 (1.00) |
1p gain | 3 (1%) | 491 |
0.253 (1.00) |
0.745 (1.00) |
0.489 (1.00) |
1 (1.00) |
0.413 (1.00) |
0.621 (1.00) |
0.216 (1.00) |
0.485 (1.00) |
||
9p gain | 3 (1%) | 491 |
0.00246 (0.832) |
0.582 (1.00) |
0.56 (1.00) |
0.362 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||
9q gain | 4 (1%) | 490 |
0.0101 (1.00) |
0.649 (1.00) |
0.304 (1.00) |
0.77 (1.00) |
1 (1.00) |
0.822 (1.00) |
1 (1.00) |
0.828 (1.00) |
||
6p loss | 4 (1%) | 490 |
0.00236 (0.804) |
0.0594 (1.00) |
0.456 (1.00) |
0.152 (1.00) |
0.0755 (1.00) |
0.0676 (1.00) |
0.129 (1.00) |
0.0942 (1.00) |
||
13q loss | 14 (3%) | 480 |
0.00844 (1.00) |
0.02 (1.00) |
0.0614 (1.00) |
0.893 (1.00) |
0.00606 (1.00) |
0.00515 (1.00) |
0.00199 (0.685) |
0.00197 (0.685) |
0.00187 (0.653) |
0.00261 (0.874) |
17p loss | 8 (2%) | 486 |
0.00182 (0.638) |
0.335 (1.00) |
1 (1.00) |
0.284 (1.00) |
0.649 (1.00) |
0.328 (1.00) |
0.33 (1.00) |
0.307 (1.00) |
0.672 (1.00) |
0.282 (1.00) |
17q loss | 4 (1%) | 490 |
0.0538 (1.00) |
0.649 (1.00) |
0.897 (1.00) |
0.77 (1.00) |
0.399 (1.00) |
0.689 (1.00) |
0.847 (1.00) |
0.573 (1.00) |
||
19p loss | 5 (1%) | 489 |
0.0251 (1.00) |
0.00581 (1.00) |
0.321 (1.00) |
0.118 (1.00) |
0.0176 (1.00) |
0.00275 (0.914) |
0.00249 (0.838) |
0.0012 (0.429) |
0.00735 (1.00) |
0.00111 (0.4) |
xq loss | 3 (1%) | 491 |
0.0219 (1.00) |
0.0585 (1.00) |
0.278 (1.00) |
0.364 (1.00) |
0.0961 (1.00) |
0.037 (1.00) |
0.0278 (1.00) |
0.018 (1.00) |
0.0701 (1.00) |
0.0172 (1.00) |
P value = 9.81e-06 (Fisher's exact test), Q value = 0.0045
Table S1. Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
1Q GAIN MUTATED | 9 | 14 | 1 |
1Q GAIN WILD-TYPE | 25 | 369 | 76 |
Figure S1. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.12
Table S2. Gene #3: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
3P GAIN MUTATED | 3 | 0 | 0 |
3P GAIN WILD-TYPE | 31 | 383 | 77 |
Figure S2. Get High-res Image Gene #3: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.00058
Table S3. Gene #4: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
4P GAIN MUTATED | 5 | 0 | 0 |
4P GAIN WILD-TYPE | 29 | 383 | 77 |
Figure S3. Get High-res Image Gene #4: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.00058
Table S4. Gene #5: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
4Q GAIN MUTATED | 5 | 0 | 0 |
4Q GAIN WILD-TYPE | 29 | 383 | 77 |
Figure S4. Get High-res Image Gene #5: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 4.18e-23 (Fisher's exact test), Q value = 2.2e-20
Table S5. Gene #6: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
5P GAIN MUTATED | 19 | 2 | 0 |
5P GAIN WILD-TYPE | 15 | 381 | 77 |
Figure S5. Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.000409 (Fisher's exact test), Q value = 0.15
Table S6. Gene #6: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 134 | 288 | 64 |
5P GAIN MUTATED | 14 | 7 | 0 |
5P GAIN WILD-TYPE | 120 | 281 | 64 |
Figure S6. Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.000523 (Fisher's exact test), Q value = 0.2
Table S7. Gene #6: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 130 | 208 |
5P GAIN MUTATED | 1 | 13 | 7 |
5P GAIN WILD-TYPE | 154 | 117 | 201 |
Figure S7. Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.12
Table S8. Gene #6: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 199 | 128 | 166 |
5P GAIN MUTATED | 7 | 13 | 1 |
5P GAIN WILD-TYPE | 192 | 115 | 165 |
Figure S8. Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.76e-22 (Fisher's exact test), Q value = 9.4e-20
Table S9. Gene #7: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
5Q GAIN MUTATED | 17 | 0 | 0 |
5Q GAIN WILD-TYPE | 17 | 383 | 77 |
Figure S9. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 3.39e-05 (Fisher's exact test), Q value = 0.015
Table S10. Gene #7: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 151 | 83 | 260 |
5Q GAIN MUTATED | 14 | 1 | 2 |
5Q GAIN WILD-TYPE | 137 | 82 | 258 |
Figure S10. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.000338 (Fisher's exact test), Q value = 0.13
Table S11. Gene #7: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 152 | 53 | 118 | 163 |
5Q GAIN MUTATED | 14 | 0 | 1 | 2 |
5Q GAIN WILD-TYPE | 138 | 53 | 117 | 161 |
Figure S11. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 9.22e-06 (Fisher's exact test), Q value = 0.0043
Table S12. Gene #7: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 134 | 288 | 64 |
5Q GAIN MUTATED | 14 | 3 | 0 |
5Q GAIN WILD-TYPE | 120 | 285 | 64 |
Figure S12. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.000344 (Fisher's exact test), Q value = 0.13
Table S13. Gene #7: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 150 | 173 | 170 |
5Q GAIN MUTATED | 13 | 2 | 2 |
5Q GAIN WILD-TYPE | 137 | 171 | 168 |
Figure S13. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 4.11e-05 (Fisher's exact test), Q value = 0.018
Table S14. Gene #7: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 130 | 208 |
5Q GAIN MUTATED | 1 | 13 | 3 |
5Q GAIN WILD-TYPE | 154 | 117 | 205 |
Figure S14. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 9.6e-05 (Fisher's exact test), Q value = 0.04
Table S15. Gene #7: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 169 | 161 |
5Q GAIN MUTATED | 14 | 1 | 2 |
5Q GAIN WILD-TYPE | 149 | 168 | 159 |
Figure S15. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 3.18e-05 (Fisher's exact test), Q value = 0.014
Table S16. Gene #7: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 199 | 128 | 166 |
5Q GAIN MUTATED | 3 | 13 | 1 |
5Q GAIN WILD-TYPE | 196 | 115 | 165 |
Figure S16. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.29e-24 (Fisher's exact test), Q value = 3.3e-21
Table S17. Gene #8: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
7P GAIN MUTATED | 18 | 0 | 0 |
7P GAIN WILD-TYPE | 16 | 383 | 77 |
Figure S17. Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 7.19e-05 (Fisher's exact test), Q value = 0.03
Table S18. Gene #8: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 151 | 83 | 260 |
7P GAIN MUTATED | 14 | 2 | 2 |
7P GAIN WILD-TYPE | 137 | 81 | 258 |
Figure S18. Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.000338 (Fisher's exact test), Q value = 0.13
Table S19. Gene #8: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 152 | 53 | 118 | 163 |
7P GAIN MUTATED | 14 | 0 | 1 | 2 |
7P GAIN WILD-TYPE | 138 | 53 | 117 | 161 |
Figure S19. Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 9.22e-06 (Fisher's exact test), Q value = 0.0043
Table S20. Gene #8: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 134 | 288 | 64 |
7P GAIN MUTATED | 14 | 3 | 0 |
7P GAIN WILD-TYPE | 120 | 285 | 64 |
Figure S20. Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.000121 (Fisher's exact test), Q value = 0.05
Table S21. Gene #8: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 130 | 208 |
7P GAIN MUTATED | 1 | 13 | 4 |
7P GAIN WILD-TYPE | 154 | 117 | 204 |
Figure S21. Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.000259 (Fisher's exact test), Q value = 0.1
Table S22. Gene #8: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 169 | 161 |
7P GAIN MUTATED | 14 | 1 | 3 |
7P GAIN WILD-TYPE | 149 | 168 | 158 |
Figure S22. Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 7.61e-05 (Fisher's exact test), Q value = 0.032
Table S23. Gene #8: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 199 | 128 | 166 |
7P GAIN MUTATED | 4 | 13 | 1 |
7P GAIN WILD-TYPE | 195 | 115 | 165 |
Figure S23. Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.92e-25 (Fisher's exact test), Q value = 3.7e-22
Table S24. Gene #9: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
7Q GAIN MUTATED | 19 | 0 | 1 |
7Q GAIN WILD-TYPE | 15 | 383 | 76 |
Figure S24. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 9.82e-06 (Fisher's exact test), Q value = 0.0045
Table S25. Gene #9: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 151 | 83 | 260 |
7Q GAIN MUTATED | 16 | 2 | 2 |
7Q GAIN WILD-TYPE | 135 | 81 | 258 |
Figure S25. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 6.01e-05 (Fisher's exact test), Q value = 0.025
Table S26. Gene #9: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 152 | 53 | 118 | 163 |
7Q GAIN MUTATED | 16 | 0 | 1 | 2 |
7Q GAIN WILD-TYPE | 136 | 53 | 117 | 161 |
Figure S26. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 1.13e-06 (Fisher's exact test), Q value = 0.00057
Table S27. Gene #9: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 134 | 288 | 64 |
7Q GAIN MUTATED | 16 | 3 | 0 |
7Q GAIN WILD-TYPE | 118 | 285 | 64 |
Figure S27. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.000144 (Fisher's exact test), Q value = 0.058
Table S28. Gene #9: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 150 | 173 | 170 |
7Q GAIN MUTATED | 15 | 2 | 3 |
7Q GAIN WILD-TYPE | 135 | 171 | 167 |
Figure S28. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 1.15e-05 (Fisher's exact test), Q value = 0.0053
Table S29. Gene #9: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 130 | 208 |
7Q GAIN MUTATED | 1 | 15 | 4 |
7Q GAIN WILD-TYPE | 154 | 115 | 204 |
Figure S29. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 4.38e-05 (Fisher's exact test), Q value = 0.019
Table S30. Gene #9: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 169 | 161 |
7Q GAIN MUTATED | 16 | 1 | 3 |
7Q GAIN WILD-TYPE | 147 | 168 | 158 |
Figure S30. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 9.06e-06 (Fisher's exact test), Q value = 0.0042
Table S31. Gene #9: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 199 | 128 | 166 |
7Q GAIN MUTATED | 4 | 15 | 1 |
7Q GAIN WILD-TYPE | 195 | 113 | 165 |
Figure S31. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000364 (Fisher's exact test), Q value = 0.14
Table S32. Gene #10: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
8P GAIN MUTATED | 4 | 2 | 0 |
8P GAIN WILD-TYPE | 30 | 381 | 77 |
Figure S32. Get High-res Image Gene #10: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 4.62e-05 (Fisher's exact test), Q value = 0.02
Table S33. Gene #11: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
8Q GAIN MUTATED | 5 | 2 | 0 |
8Q GAIN WILD-TYPE | 29 | 381 | 77 |
Figure S33. Get High-res Image Gene #11: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.000191 (Fisher's exact test), Q value = 0.077
Table S34. Gene #14: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
11P GAIN MUTATED | 4 | 1 | 1 |
11P GAIN WILD-TYPE | 30 | 382 | 76 |
Figure S34. Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1.6e-05 (Fisher's exact test), Q value = 0.0073
Table S35. Gene #15: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
11Q GAIN MUTATED | 4 | 0 | 1 |
11Q GAIN WILD-TYPE | 30 | 383 | 76 |
Figure S35. Get High-res Image Gene #15: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1.48e-16 (Fisher's exact test), Q value = 7.8e-14
Table S36. Gene #16: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
12P GAIN MUTATED | 13 | 0 | 1 |
12P GAIN WILD-TYPE | 21 | 383 | 76 |
Figure S36. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 3.71e-06 (Fisher's exact test), Q value = 0.0018
Table S37. Gene #16: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 151 | 83 | 260 |
12P GAIN MUTATED | 13 | 0 | 1 |
12P GAIN WILD-TYPE | 138 | 83 | 259 |
Figure S37. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 1.65e-05 (Fisher's exact test), Q value = 0.0075
Table S38. Gene #16: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 152 | 53 | 118 | 163 |
12P GAIN MUTATED | 13 | 0 | 1 | 0 |
12P GAIN WILD-TYPE | 139 | 53 | 117 | 163 |
Figure S38. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 1.69e-06 (Fisher's exact test), Q value = 0.00082
Table S39. Gene #16: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 134 | 288 | 64 |
12P GAIN MUTATED | 13 | 1 | 0 |
12P GAIN WILD-TYPE | 121 | 287 | 64 |
Figure S39. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 6.05e-05 (Fisher's exact test), Q value = 0.025
Table S40. Gene #16: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 150 | 173 | 170 |
12P GAIN MUTATED | 12 | 1 | 1 |
12P GAIN WILD-TYPE | 138 | 172 | 169 |
Figure S40. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 8.86e-06 (Fisher's exact test), Q value = 0.0041
Table S41. Gene #16: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 130 | 208 |
12P GAIN MUTATED | 1 | 12 | 1 |
12P GAIN WILD-TYPE | 154 | 118 | 207 |
Figure S41. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 9.65e-06 (Fisher's exact test), Q value = 0.0044
Table S42. Gene #16: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 169 | 161 |
12P GAIN MUTATED | 13 | 0 | 1 |
12P GAIN WILD-TYPE | 150 | 169 | 160 |
Figure S42. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 8.52e-06 (Fisher's exact test), Q value = 0.004
Table S43. Gene #16: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 199 | 128 | 166 |
12P GAIN MUTATED | 1 | 12 | 1 |
12P GAIN WILD-TYPE | 198 | 116 | 165 |
Figure S43. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.14e-16 (Fisher's exact test), Q value = 1.1e-13
Table S44. Gene #17: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
12Q GAIN MUTATED | 13 | 0 | 2 |
12Q GAIN WILD-TYPE | 21 | 383 | 75 |
Figure S44. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1.32e-06 (Fisher's exact test), Q value = 0.00065
Table S45. Gene #17: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 151 | 83 | 260 |
12Q GAIN MUTATED | 14 | 0 | 1 |
12Q GAIN WILD-TYPE | 137 | 83 | 259 |
Figure S45. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 9.29e-06 (Fisher's exact test), Q value = 0.0043
Table S46. Gene #17: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 152 | 53 | 118 | 163 |
12Q GAIN MUTATED | 14 | 0 | 1 | 0 |
12Q GAIN WILD-TYPE | 138 | 53 | 117 | 163 |
Figure S46. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 3.61e-07 (Fisher's exact test), Q value = 0.00018
Table S47. Gene #17: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 134 | 288 | 64 |
12Q GAIN MUTATED | 14 | 1 | 0 |
12Q GAIN WILD-TYPE | 120 | 287 | 64 |
Figure S47. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 2.24e-05 (Fisher's exact test), Q value = 0.0099
Table S48. Gene #17: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 150 | 173 | 170 |
12Q GAIN MUTATED | 13 | 1 | 1 |
12Q GAIN WILD-TYPE | 137 | 172 | 169 |
Figure S48. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 2.87e-06 (Fisher's exact test), Q value = 0.0014
Table S49. Gene #17: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 130 | 208 |
12Q GAIN MUTATED | 1 | 13 | 1 |
12Q GAIN WILD-TYPE | 154 | 117 | 207 |
Figure S49. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 3.63e-06 (Fisher's exact test), Q value = 0.0017
Table S50. Gene #17: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 169 | 161 |
12Q GAIN MUTATED | 14 | 0 | 1 |
12Q GAIN WILD-TYPE | 149 | 169 | 160 |
Figure S50. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 2.66e-06 (Fisher's exact test), Q value = 0.0013
Table S51. Gene #17: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 199 | 128 | 166 |
12Q GAIN MUTATED | 1 | 13 | 1 |
12Q GAIN WILD-TYPE | 198 | 115 | 165 |
Figure S51. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.00058
Table S52. Gene #18: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
13Q GAIN MUTATED | 5 | 0 | 0 |
13Q GAIN WILD-TYPE | 29 | 383 | 77 |
Figure S52. Get High-res Image Gene #18: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 3.23e-10 (Fisher's exact test), Q value = 1.7e-07
Table S53. Gene #19: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
14Q GAIN MUTATED | 9 | 1 | 1 |
14Q GAIN WILD-TYPE | 25 | 382 | 76 |
Figure S53. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.000161 (Fisher's exact test), Q value = 0.065
Table S54. Gene #19: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 151 | 83 | 260 |
14Q GAIN MUTATED | 10 | 0 | 1 |
14Q GAIN WILD-TYPE | 141 | 83 | 259 |
Figure S54. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.000574 (Fisher's exact test), Q value = 0.21
Table S55. Gene #19: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 152 | 53 | 118 | 163 |
14Q GAIN MUTATED | 10 | 0 | 0 | 1 |
14Q GAIN WILD-TYPE | 142 | 53 | 118 | 162 |
Figure S55. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 7.22e-05 (Fisher's exact test), Q value = 0.03
Table S56. Gene #19: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 134 | 288 | 64 |
14Q GAIN MUTATED | 10 | 1 | 0 |
14Q GAIN WILD-TYPE | 124 | 287 | 64 |
Figure S56. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.000461 (Fisher's exact test), Q value = 0.17
Table S57. Gene #19: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 150 | 173 | 170 |
14Q GAIN MUTATED | 9 | 0 | 2 |
14Q GAIN WILD-TYPE | 141 | 173 | 168 |
Figure S57. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 0.000151 (Fisher's exact test), Q value = 0.061
Table S58. Gene #19: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 130 | 208 |
14Q GAIN MUTATED | 0 | 9 | 2 |
14Q GAIN WILD-TYPE | 155 | 121 | 206 |
Figure S58. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.000114 (Fisher's exact test), Q value = 0.047
Table S59. Gene #19: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 199 | 128 | 166 |
14Q GAIN MUTATED | 2 | 9 | 0 |
14Q GAIN WILD-TYPE | 197 | 119 | 166 |
Figure S59. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.94e-18 (Fisher's exact test), Q value = 3.7e-15
Table S60. Gene #20: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
16P GAIN MUTATED | 14 | 0 | 1 |
16P GAIN WILD-TYPE | 20 | 383 | 76 |
Figure S60. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.0083
Table S61. Gene #20: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 151 | 83 | 260 |
16P GAIN MUTATED | 13 | 1 | 1 |
16P GAIN WILD-TYPE | 138 | 82 | 259 |
Figure S61. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.000195 (Fisher's exact test), Q value = 0.078
Table S62. Gene #20: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 152 | 53 | 118 | 163 |
16P GAIN MUTATED | 13 | 0 | 1 | 1 |
16P GAIN WILD-TYPE | 139 | 53 | 117 | 162 |
Figure S62. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 6.61e-06 (Fisher's exact test), Q value = 0.0031
Table S63. Gene #20: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 134 | 288 | 64 |
16P GAIN MUTATED | 13 | 2 | 0 |
16P GAIN WILD-TYPE | 121 | 286 | 64 |
Figure S63. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.000192 (Fisher's exact test), Q value = 0.077
Table S64. Gene #20: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 150 | 173 | 170 |
16P GAIN MUTATED | 12 | 1 | 2 |
16P GAIN WILD-TYPE | 138 | 172 | 168 |
Figure S64. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 4.25e-05 (Fisher's exact test), Q value = 0.018
Table S65. Gene #20: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 130 | 208 |
16P GAIN MUTATED | 1 | 12 | 2 |
16P GAIN WILD-TYPE | 154 | 118 | 206 |
Figure S65. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 3.07e-05 (Fisher's exact test), Q value = 0.013
Table S66. Gene #20: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 169 | 161 |
16P GAIN MUTATED | 13 | 0 | 2 |
16P GAIN WILD-TYPE | 150 | 169 | 159 |
Figure S66. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 3.96e-05 (Fisher's exact test), Q value = 0.017
Table S67. Gene #20: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 199 | 128 | 166 |
16P GAIN MUTATED | 2 | 12 | 1 |
16P GAIN WILD-TYPE | 197 | 116 | 165 |
Figure S67. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.49e-17 (Fisher's exact test), Q value = 3.4e-14
Table S68. Gene #21: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
16Q GAIN MUTATED | 13 | 0 | 0 |
16Q GAIN WILD-TYPE | 21 | 383 | 77 |
Figure S68. Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.000121 (Fisher's exact test), Q value = 0.05
Table S69. Gene #21: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 151 | 83 | 260 |
16Q GAIN MUTATED | 11 | 1 | 1 |
16Q GAIN WILD-TYPE | 140 | 82 | 259 |
Figure S69. Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 9.26e-05 (Fisher's exact test), Q value = 0.038
Table S70. Gene #21: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 134 | 288 | 64 |
16Q GAIN MUTATED | 11 | 2 | 0 |
16Q GAIN WILD-TYPE | 123 | 286 | 64 |
Figure S70. Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.000387 (Fisher's exact test), Q value = 0.15
Table S71. Gene #21: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 130 | 208 |
16Q GAIN MUTATED | 1 | 10 | 2 |
16Q GAIN WILD-TYPE | 154 | 120 | 206 |
Figure S71. Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.000182 (Fisher's exact test), Q value = 0.073
Table S72. Gene #21: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 169 | 161 |
16Q GAIN MUTATED | 11 | 0 | 2 |
16Q GAIN WILD-TYPE | 152 | 169 | 159 |
Figure S72. Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.000336 (Fisher's exact test), Q value = 0.13
Table S73. Gene #21: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 199 | 128 | 166 |
16Q GAIN MUTATED | 2 | 10 | 1 |
16Q GAIN WILD-TYPE | 197 | 118 | 165 |
Figure S73. Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.23e-13 (Fisher's exact test), Q value = 2.2e-10
Table S74. Gene #22: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
17P GAIN MUTATED | 12 | 2 | 2 |
17P GAIN WILD-TYPE | 22 | 381 | 75 |
Figure S74. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 5.64e-07 (Fisher's exact test), Q value = 0.00029
Table S75. Gene #22: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 151 | 83 | 260 |
17P GAIN MUTATED | 15 | 0 | 1 |
17P GAIN WILD-TYPE | 136 | 83 | 259 |
Figure S75. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 4.02e-06 (Fisher's exact test), Q value = 0.0019
Table S76. Gene #22: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 152 | 53 | 118 | 163 |
17P GAIN MUTATED | 15 | 0 | 1 | 0 |
17P GAIN WILD-TYPE | 137 | 53 | 117 | 163 |
Figure S76. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 7.23e-08 (Fisher's exact test), Q value = 3.7e-05
Table S77. Gene #22: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 134 | 288 | 64 |
17P GAIN MUTATED | 15 | 1 | 0 |
17P GAIN WILD-TYPE | 119 | 287 | 64 |
Figure S77. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 8.06e-06 (Fisher's exact test), Q value = 0.0038
Table S78. Gene #22: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 150 | 173 | 170 |
17P GAIN MUTATED | 14 | 1 | 1 |
17P GAIN WILD-TYPE | 136 | 172 | 169 |
Figure S78. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 8.97e-07 (Fisher's exact test), Q value = 0.00045
Table S79. Gene #22: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 130 | 208 |
17P GAIN MUTATED | 1 | 14 | 1 |
17P GAIN WILD-TYPE | 154 | 116 | 207 |
Figure S79. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 1.33e-06 (Fisher's exact test), Q value = 0.00065
Table S80. Gene #22: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 169 | 161 |
17P GAIN MUTATED | 15 | 0 | 1 |
17P GAIN WILD-TYPE | 148 | 169 | 160 |
Figure S80. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 8.04e-07 (Fisher's exact test), Q value = 0.00041
Table S81. Gene #22: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 199 | 128 | 166 |
17P GAIN MUTATED | 1 | 14 | 1 |
17P GAIN WILD-TYPE | 198 | 114 | 165 |
Figure S81. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.03e-14 (Fisher's exact test), Q value = 2.6e-11
Table S82. Gene #23: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
17Q GAIN MUTATED | 13 | 2 | 3 |
17Q GAIN WILD-TYPE | 21 | 381 | 74 |
Figure S82. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1.13e-06 (Fisher's exact test), Q value = 0.00057
Table S83. Gene #23: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 151 | 83 | 260 |
17Q GAIN MUTATED | 16 | 0 | 2 |
17Q GAIN WILD-TYPE | 135 | 83 | 258 |
Figure S83. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 1.45e-05 (Fisher's exact test), Q value = 0.0066
Table S84. Gene #23: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 152 | 53 | 118 | 163 |
17Q GAIN MUTATED | 16 | 0 | 1 | 1 |
17Q GAIN WILD-TYPE | 136 | 53 | 117 | 162 |
Figure S84. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 2.54e-07 (Fisher's exact test), Q value = 0.00013
Table S85. Gene #23: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 134 | 288 | 64 |
17Q GAIN MUTATED | 16 | 2 | 0 |
17Q GAIN WILD-TYPE | 118 | 286 | 64 |
Figure S85. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 1.17e-05 (Fisher's exact test), Q value = 0.0053
Table S86. Gene #23: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 150 | 173 | 170 |
17Q GAIN MUTATED | 15 | 2 | 1 |
17Q GAIN WILD-TYPE | 135 | 171 | 169 |
Figure S86. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 1.46e-06 (Fisher's exact test), Q value = 0.00071
Table S87. Gene #23: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 130 | 208 |
17Q GAIN MUTATED | 1 | 15 | 2 |
17Q GAIN WILD-TYPE | 154 | 115 | 206 |
Figure S87. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 3.69e-06 (Fisher's exact test), Q value = 0.0018
Table S88. Gene #23: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 169 | 161 |
17Q GAIN MUTATED | 16 | 1 | 1 |
17Q GAIN WILD-TYPE | 147 | 168 | 160 |
Figure S88. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 1.09e-06 (Fisher's exact test), Q value = 0.00055
Table S89. Gene #23: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 199 | 128 | 166 |
17Q GAIN MUTATED | 2 | 15 | 1 |
17Q GAIN WILD-TYPE | 197 | 113 | 165 |
Figure S89. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.00058
Table S90. Gene #24: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
18P GAIN MUTATED | 5 | 0 | 1 |
18P GAIN WILD-TYPE | 29 | 383 | 76 |
Figure S90. Get High-res Image Gene #24: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.00058
Table S91. Gene #25: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
18Q GAIN MUTATED | 5 | 0 | 1 |
18Q GAIN WILD-TYPE | 29 | 383 | 76 |
Figure S91. Get High-res Image Gene #25: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 2.19e-10 (Fisher's exact test), Q value = 1.1e-07
Table S92. Gene #26: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
19P GAIN MUTATED | 8 | 0 | 0 |
19P GAIN WILD-TYPE | 26 | 383 | 77 |
Figure S92. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.000139 (Fisher's exact test), Q value = 0.057
Table S93. Gene #26: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 151 | 83 | 260 |
19P GAIN MUTATED | 8 | 0 | 0 |
19P GAIN WILD-TYPE | 143 | 83 | 260 |
Figure S93. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 4.14e-05 (Fisher's exact test), Q value = 0.018
Table S94. Gene #26: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 134 | 288 | 64 |
19P GAIN MUTATED | 8 | 0 | 0 |
19P GAIN WILD-TYPE | 126 | 288 | 64 |
Figure S94. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 6.43e-05 (Fisher's exact test), Q value = 0.027
Table S95. Gene #26: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 150 | 173 | 170 |
19P GAIN MUTATED | 8 | 0 | 0 |
19P GAIN WILD-TYPE | 142 | 173 | 170 |
Figure S95. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 1.99e-05 (Fisher's exact test), Q value = 0.0088
Table S96. Gene #26: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 130 | 208 |
19P GAIN MUTATED | 0 | 8 | 0 |
19P GAIN WILD-TYPE | 155 | 122 | 208 |
Figure S96. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.000242 (Fisher's exact test), Q value = 0.095
Table S97. Gene #26: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 169 | 161 |
19P GAIN MUTATED | 8 | 0 | 0 |
19P GAIN WILD-TYPE | 155 | 169 | 161 |
Figure S97. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 1.75e-05 (Fisher's exact test), Q value = 0.0079
Table S98. Gene #26: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 199 | 128 | 166 |
19P GAIN MUTATED | 0 | 8 | 0 |
19P GAIN WILD-TYPE | 199 | 120 | 166 |
Figure S98. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.92e-11 (Fisher's exact test), Q value = 9.9e-09
Table S99. Gene #27: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
19Q GAIN MUTATED | 9 | 0 | 1 |
19Q GAIN WILD-TYPE | 25 | 383 | 76 |
Figure S99. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 8.44e-06 (Fisher's exact test), Q value = 0.004
Table S100. Gene #27: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 151 | 83 | 260 |
19Q GAIN MUTATED | 10 | 0 | 0 |
19Q GAIN WILD-TYPE | 141 | 83 | 260 |
Figure S100. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 5.97e-05 (Fisher's exact test), Q value = 0.025
Table S101. Gene #27: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 152 | 53 | 118 | 163 |
19Q GAIN MUTATED | 10 | 0 | 0 | 0 |
19Q GAIN WILD-TYPE | 142 | 53 | 118 | 163 |
Figure S101. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 5.49e-06 (Fisher's exact test), Q value = 0.0026
Table S102. Gene #27: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 134 | 288 | 64 |
19Q GAIN MUTATED | 10 | 0 | 0 |
19Q GAIN WILD-TYPE | 124 | 288 | 64 |
Figure S102. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 5.49e-06 (Fisher's exact test), Q value = 0.0026
Table S103. Gene #27: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 150 | 173 | 170 |
19Q GAIN MUTATED | 10 | 0 | 0 |
19Q GAIN WILD-TYPE | 140 | 173 | 170 |
Figure S103. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 1.25e-06 (Fisher's exact test), Q value = 0.00061
Table S104. Gene #27: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 130 | 208 |
19Q GAIN MUTATED | 0 | 10 | 0 |
19Q GAIN WILD-TYPE | 155 | 120 | 208 |
Figure S104. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 2.43e-05 (Fisher's exact test), Q value = 0.011
Table S105. Gene #27: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 169 | 161 |
19Q GAIN MUTATED | 10 | 0 | 0 |
19Q GAIN WILD-TYPE | 153 | 169 | 161 |
Figure S105. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 1.06e-06 (Fisher's exact test), Q value = 0.00054
Table S106. Gene #27: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 199 | 128 | 166 |
19Q GAIN MUTATED | 0 | 10 | 0 |
19Q GAIN WILD-TYPE | 199 | 118 | 166 |
Figure S106. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.42e-15 (Fisher's exact test), Q value = 7.5e-13
Table S107. Gene #28: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
20P GAIN MUTATED | 12 | 0 | 0 |
20P GAIN WILD-TYPE | 22 | 383 | 77 |
Figure S107. Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.000376 (Fisher's exact test), Q value = 0.14
Table S108. Gene #28: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 151 | 83 | 260 |
20P GAIN MUTATED | 10 | 1 | 1 |
20P GAIN WILD-TYPE | 141 | 82 | 259 |
Figure S108. Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.000202 (Fisher's exact test), Q value = 0.081
Table S109. Gene #28: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 134 | 288 | 64 |
20P GAIN MUTATED | 10 | 2 | 0 |
20P GAIN WILD-TYPE | 124 | 286 | 64 |
Figure S109. Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.000508 (Fisher's exact test), Q value = 0.19
Table S110. Gene #28: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 169 | 161 |
20P GAIN MUTATED | 10 | 0 | 2 |
20P GAIN WILD-TYPE | 153 | 169 | 159 |
Figure S110. Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 1.42e-15 (Fisher's exact test), Q value = 7.5e-13
Table S111. Gene #29: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
20Q GAIN MUTATED | 12 | 0 | 0 |
20Q GAIN WILD-TYPE | 22 | 383 | 77 |
Figure S111. Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.000376 (Fisher's exact test), Q value = 0.14
Table S112. Gene #29: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 151 | 83 | 260 |
20Q GAIN MUTATED | 10 | 1 | 1 |
20Q GAIN WILD-TYPE | 141 | 82 | 259 |
Figure S112. Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.000202 (Fisher's exact test), Q value = 0.081
Table S113. Gene #29: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 134 | 288 | 64 |
20Q GAIN MUTATED | 10 | 2 | 0 |
20Q GAIN WILD-TYPE | 124 | 286 | 64 |
Figure S113. Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.000508 (Fisher's exact test), Q value = 0.19
Table S114. Gene #29: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 169 | 161 |
20Q GAIN MUTATED | 10 | 0 | 2 |
20Q GAIN WILD-TYPE | 153 | 169 | 159 |
Figure S114. Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 1.6e-05 (Fisher's exact test), Q value = 0.0073
Table S115. Gene #30: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
21Q GAIN MUTATED | 4 | 0 | 1 |
21Q GAIN WILD-TYPE | 30 | 383 | 76 |
Figure S115. Get High-res Image Gene #30: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 2.7e-07 (Fisher's exact test), Q value = 0.00014
Table S116. Gene #31: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
XQ GAIN MUTATED | 7 | 2 | 0 |
XQ GAIN WILD-TYPE | 27 | 381 | 77 |
Figure S116. Get High-res Image Gene #31: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0085
Table S117. Gene #32: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
1P LOSS MUTATED | 4 | 0 | 0 |
1P LOSS WILD-TYPE | 30 | 383 | 77 |
Figure S117. Get High-res Image Gene #32: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.12
Table S118. Gene #33: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
1Q LOSS MUTATED | 3 | 0 | 0 |
1Q LOSS WILD-TYPE | 31 | 383 | 77 |
Figure S118. Get High-res Image Gene #33: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1.92e-11 (Fisher's exact test), Q value = 9.9e-09
Table S119. Gene #34: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
2P LOSS MUTATED | 9 | 0 | 1 |
2P LOSS WILD-TYPE | 25 | 383 | 76 |
Figure S119. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 8.44e-06 (Fisher's exact test), Q value = 0.004
Table S120. Gene #34: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 151 | 83 | 260 |
2P LOSS MUTATED | 10 | 0 | 0 |
2P LOSS WILD-TYPE | 141 | 83 | 260 |
Figure S120. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 5.97e-05 (Fisher's exact test), Q value = 0.025
Table S121. Gene #34: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 152 | 53 | 118 | 163 |
2P LOSS MUTATED | 10 | 0 | 0 | 0 |
2P LOSS WILD-TYPE | 142 | 53 | 118 | 163 |
Figure S121. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 5.49e-06 (Fisher's exact test), Q value = 0.0026
Table S122. Gene #34: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 134 | 288 | 64 |
2P LOSS MUTATED | 10 | 0 | 0 |
2P LOSS WILD-TYPE | 124 | 288 | 64 |
Figure S122. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 5.49e-06 (Fisher's exact test), Q value = 0.0026
Table S123. Gene #34: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 150 | 173 | 170 |
2P LOSS MUTATED | 10 | 0 | 0 |
2P LOSS WILD-TYPE | 140 | 173 | 170 |
Figure S123. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 1.25e-06 (Fisher's exact test), Q value = 0.00061
Table S124. Gene #34: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 130 | 208 |
2P LOSS MUTATED | 0 | 10 | 0 |
2P LOSS WILD-TYPE | 155 | 120 | 208 |
Figure S124. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 2.43e-05 (Fisher's exact test), Q value = 0.011
Table S125. Gene #34: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 169 | 161 |
2P LOSS MUTATED | 10 | 0 | 0 |
2P LOSS WILD-TYPE | 153 | 169 | 161 |
Figure S125. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 1.06e-06 (Fisher's exact test), Q value = 0.00054
Table S126. Gene #34: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 199 | 128 | 166 |
2P LOSS MUTATED | 0 | 10 | 0 |
2P LOSS WILD-TYPE | 199 | 118 | 166 |
Figure S126. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.03e-13 (Fisher's exact test), Q value = 3.1e-10
Table S127. Gene #35: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
2Q LOSS MUTATED | 10 | 0 | 0 |
2Q LOSS WILD-TYPE | 24 | 383 | 77 |
Figure S127. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 8.44e-06 (Fisher's exact test), Q value = 0.004
Table S128. Gene #35: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 151 | 83 | 260 |
2Q LOSS MUTATED | 10 | 0 | 0 |
2Q LOSS WILD-TYPE | 141 | 83 | 260 |
Figure S128. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 5.97e-05 (Fisher's exact test), Q value = 0.025
Table S129. Gene #35: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 152 | 53 | 118 | 163 |
2Q LOSS MUTATED | 10 | 0 | 0 | 0 |
2Q LOSS WILD-TYPE | 142 | 53 | 118 | 163 |
Figure S129. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 5.49e-06 (Fisher's exact test), Q value = 0.0026
Table S130. Gene #35: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 134 | 288 | 64 |
2Q LOSS MUTATED | 10 | 0 | 0 |
2Q LOSS WILD-TYPE | 124 | 288 | 64 |
Figure S130. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 5.49e-06 (Fisher's exact test), Q value = 0.0026
Table S131. Gene #35: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 150 | 173 | 170 |
2Q LOSS MUTATED | 10 | 0 | 0 |
2Q LOSS WILD-TYPE | 140 | 173 | 170 |
Figure S131. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 1.25e-06 (Fisher's exact test), Q value = 0.00061
Table S132. Gene #35: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 130 | 208 |
2Q LOSS MUTATED | 0 | 10 | 0 |
2Q LOSS WILD-TYPE | 155 | 120 | 208 |
Figure S132. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 2.43e-05 (Fisher's exact test), Q value = 0.011
Table S133. Gene #35: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 169 | 161 |
2Q LOSS MUTATED | 10 | 0 | 0 |
2Q LOSS WILD-TYPE | 153 | 169 | 161 |
Figure S133. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 1.06e-06 (Fisher's exact test), Q value = 0.00054
Table S134. Gene #35: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 199 | 128 | 166 |
2Q LOSS MUTATED | 0 | 10 | 0 |
2Q LOSS WILD-TYPE | 199 | 118 | 166 |
Figure S134. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.12
Table S135. Gene #36: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
3P LOSS MUTATED | 3 | 0 | 0 |
3P LOSS WILD-TYPE | 31 | 383 | 77 |
Figure S135. Get High-res Image Gene #36: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0085
Table S136. Gene #37: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
3Q LOSS MUTATED | 4 | 0 | 0 |
3Q LOSS WILD-TYPE | 30 | 383 | 77 |
Figure S136. Get High-res Image Gene #37: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 4.62e-05 (Fisher's exact test), Q value = 0.02
Table S137. Gene #39: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
6Q LOSS MUTATED | 5 | 2 | 0 |
6Q LOSS WILD-TYPE | 29 | 381 | 77 |
Figure S137. Get High-res Image Gene #39: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0085
Table S138. Gene #40: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
8P LOSS MUTATED | 4 | 0 | 0 |
8P LOSS WILD-TYPE | 30 | 383 | 77 |
Figure S138. Get High-res Image Gene #40: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0085
Table S139. Gene #41: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
8Q LOSS MUTATED | 4 | 0 | 0 |
8Q LOSS WILD-TYPE | 30 | 383 | 77 |
Figure S139. Get High-res Image Gene #41: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 2.94e-12 (Fisher's exact test), Q value = 1.5e-09
Table S140. Gene #42: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
9P LOSS MUTATED | 13 | 5 | 1 |
9P LOSS WILD-TYPE | 21 | 378 | 76 |
Figure S140. Get High-res Image Gene #42: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 9.23e-15 (Fisher's exact test), Q value = 4.8e-12
Table S141. Gene #43: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
9Q LOSS MUTATED | 16 | 7 | 1 |
9Q LOSS WILD-TYPE | 18 | 376 | 76 |
Figure S141. Get High-res Image Gene #43: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 3.94e-09 (Fisher's exact test), Q value = 2e-06
Table S142. Gene #44: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
10P LOSS MUTATED | 7 | 0 | 0 |
10P LOSS WILD-TYPE | 27 | 383 | 77 |
Figure S142. Get High-res Image Gene #44: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 6.87e-08 (Fisher's exact test), Q value = 3.5e-05
Table S143. Gene #45: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
10Q LOSS MUTATED | 6 | 0 | 0 |
10Q LOSS WILD-TYPE | 28 | 383 | 77 |
Figure S143. Get High-res Image Gene #45: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 7.98e-08 (Fisher's exact test), Q value = 4.1e-05
Table S144. Gene #46: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
11P LOSS MUTATED | 6 | 0 | 1 |
11P LOSS WILD-TYPE | 28 | 383 | 76 |
Figure S144. Get High-res Image Gene #46: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 3.28e-06 (Fisher's exact test), Q value = 0.0016
Table S145. Gene #47: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
11Q LOSS MUTATED | 6 | 2 | 1 |
11Q LOSS WILD-TYPE | 28 | 381 | 76 |
Figure S145. Get High-res Image Gene #47: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.000352 (Fisher's exact test), Q value = 0.13
Table S146. Gene #47: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 150 | 173 | 170 |
11Q LOSS MUTATED | 8 | 0 | 1 |
11Q LOSS WILD-TYPE | 142 | 173 | 169 |
Figure S146. Get High-res Image Gene #47: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 5.63e-05 (Fisher's exact test), Q value = 0.024
Table S147. Gene #49: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
15Q LOSS MUTATED | 5 | 2 | 1 |
15Q LOSS WILD-TYPE | 29 | 381 | 76 |
Figure S147. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.000139 (Fisher's exact test), Q value = 0.057
Table S148. Gene #49: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 151 | 83 | 260 |
15Q LOSS MUTATED | 8 | 0 | 0 |
15Q LOSS WILD-TYPE | 143 | 83 | 260 |
Figure S148. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 4.14e-05 (Fisher's exact test), Q value = 0.018
Table S149. Gene #49: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 134 | 288 | 64 |
15Q LOSS MUTATED | 8 | 0 | 0 |
15Q LOSS WILD-TYPE | 126 | 288 | 64 |
Figure S149. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 6.43e-05 (Fisher's exact test), Q value = 0.027
Table S150. Gene #49: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 150 | 173 | 170 |
15Q LOSS MUTATED | 8 | 0 | 0 |
15Q LOSS WILD-TYPE | 142 | 173 | 170 |
Figure S150. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 1.99e-05 (Fisher's exact test), Q value = 0.0088
Table S151. Gene #49: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 130 | 208 |
15Q LOSS MUTATED | 0 | 8 | 0 |
15Q LOSS WILD-TYPE | 155 | 122 | 208 |
Figure S151. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.000242 (Fisher's exact test), Q value = 0.095
Table S152. Gene #49: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 169 | 161 |
15Q LOSS MUTATED | 8 | 0 | 0 |
15Q LOSS WILD-TYPE | 155 | 169 | 161 |
Figure S152. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 1.75e-05 (Fisher's exact test), Q value = 0.0079
Table S153. Gene #49: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 199 | 128 | 166 |
15Q LOSS MUTATED | 0 | 8 | 0 |
15Q LOSS WILD-TYPE | 199 | 120 | 166 |
Figure S153. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000207 (Fisher's exact test), Q value = 0.082
Table S154. Gene #52: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
18P LOSS MUTATED | 3 | 0 | 1 |
18P LOSS WILD-TYPE | 31 | 383 | 76 |
Figure S154. Get High-res Image Gene #52: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.000207 (Fisher's exact test), Q value = 0.082
Table S155. Gene #53: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
18Q LOSS MUTATED | 3 | 0 | 1 |
18Q LOSS WILD-TYPE | 31 | 383 | 76 |
Figure S155. Get High-res Image Gene #53: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 5.63e-05 (Fisher's exact test), Q value = 0.024
Table S156. Gene #55: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
21Q LOSS MUTATED | 5 | 2 | 1 |
21Q LOSS WILD-TYPE | 29 | 381 | 76 |
Figure S156. Get High-res Image Gene #55: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 7.48e-90 (Fisher's exact test), Q value = 4e-87
Table S157. Gene #56: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
22Q LOSS MUTATED | 9 | 0 | 77 |
22Q LOSS WILD-TYPE | 25 | 383 | 0 |
Figure S157. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1.1e-05 (Fisher's exact test), Q value = 0.005
Table S158. Gene #56: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 151 | 83 | 260 |
22Q LOSS MUTATED | 45 | 7 | 34 |
22Q LOSS WILD-TYPE | 106 | 76 | 226 |
Figure S158. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 1.12e-08 (Fisher's exact test), Q value = 5.7e-06
Table S159. Gene #56: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 152 | 53 | 118 | 163 |
22Q LOSS MUTATED | 43 | 7 | 27 | 7 |
22Q LOSS WILD-TYPE | 109 | 46 | 91 | 156 |
Figure S159. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 6.74e-05 (Fisher's exact test), Q value = 0.028
Table S160. Gene #56: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 134 | 288 | 64 |
22Q LOSS MUTATED | 40 | 35 | 9 |
22Q LOSS WILD-TYPE | 94 | 253 | 55 |
Figure S160. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.000342 (Fisher's exact test), Q value = 0.13
Table S161. Gene #56: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 130 | 208 |
22Q LOSS MUTATED | 22 | 38 | 26 |
22Q LOSS WILD-TYPE | 133 | 92 | 182 |
Figure S161. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 3.12e-06 (Fisher's exact test), Q value = 0.0015
Table S162. Gene #56: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 169 | 161 |
22Q LOSS MUTATED | 49 | 18 | 19 |
22Q LOSS WILD-TYPE | 114 | 151 | 142 |
Figure S162. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.000206 (Fisher's exact test), Q value = 0.082
Table S163. Gene #56: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 199 | 128 | 166 |
22Q LOSS MUTATED | 24 | 38 | 24 |
22Q LOSS WILD-TYPE | 175 | 90 | 142 |
Figure S163. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

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Copy number data file = transformed.cor.cli.txt
-
Molecular subtypes file = THCA-TP.transferedmergedcluster.txt
-
Number of patients = 494
-
Number of significantly arm-level cnvs = 57
-
Number of molecular subtypes = 10
-
Exclude genes that fewer than K tumors have mutations, K = 3
For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.