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 472 patients, 104 significant findings detected with Q value < 0.25.
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1p gain cnv correlated to 'CN_CNMF'.
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1q gain cnv correlated to 'METHLYATION_CNMF'.
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2p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
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2q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
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5p gain cnv correlated to 'CN_CNMF'.
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6p gain cnv correlated to 'METHLYATION_CNMF'.
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7p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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7q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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8p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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8q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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10p gain cnv correlated to 'METHLYATION_CNMF'.
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10q gain cnv correlated to 'MRNASEQ_CNMF'.
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12p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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12q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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14q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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16p gain cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
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17p gain cnv correlated to 'CN_CNMF'.
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17q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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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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20p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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20q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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21q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Xq gain cnv correlated to 'CN_CNMF'.
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1p loss cnv correlated to 'METHLYATION_CNMF'.
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3p loss cnv correlated to 'METHLYATION_CNMF'.
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4p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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4q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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5q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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6q loss cnv correlated to 'METHLYATION_CNMF'.
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8p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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9p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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9q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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13q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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15q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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16p loss cnv correlated to 'CN_CNMF'.
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16q loss cnv correlated to 'CN_CNMF'.
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17p loss cnv correlated to 'CN_CNMF'.
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18p loss cnv correlated to 'CN_CNMF'.
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18q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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19p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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19q loss cnv correlated to 'CN_CNMF'.
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20p loss cnv correlated to 'CN_CNMF'.
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21q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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22q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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, 104 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 | Fisher's exact test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
21q loss | 0 (0%) | 406 |
3.03e-12 (2.2e-09) |
1e-07 (7.09e-05) |
0.103 (1.00) |
0.0176 (1.00) |
1.42e-06 (0.000992) |
4.44e-07 (0.000312) |
3.11e-05 (0.0208) |
8.05e-07 (0.000563) |
||
7p gain | 0 (0%) | 318 |
0.754 (1.00) |
0.523 (1.00) |
3.08e-18 (2.25e-15) |
1.97e-06 (0.00137) |
8.93e-05 (0.0586) |
0.00948 (1.00) |
3.89e-06 (0.00268) |
7.47e-07 (0.000524) |
0.000553 (0.344) |
0.00525 (1.00) |
4q loss | 0 (0%) | 427 |
0.00605 (1.00) |
0.00706 (1.00) |
2.2e-10 (1.6e-07) |
4.24e-07 (0.000299) |
0.469 (1.00) |
0.578 (1.00) |
9.1e-05 (0.0597) |
9.39e-08 (6.66e-05) |
0.000386 (0.243) |
0.000579 (0.359) |
15q loss | 0 (0%) | 377 |
0.405 (1.00) |
0.219 (1.00) |
5.26e-12 (3.82e-09) |
1.41e-09 (1.02e-06) |
0.481 (1.00) |
0.0188 (1.00) |
6.09e-05 (0.0403) |
0.000418 (0.263) |
0.000269 (0.171) |
0.000239 (0.153) |
2p gain | 0 (0%) | 422 |
0.0312 (1.00) |
0.0151 (1.00) |
7e-08 (4.99e-05) |
3.89e-06 (0.00268) |
0.0781 (1.00) |
0.0301 (1.00) |
0.000256 (0.163) |
0.00124 (0.746) |
0.00021 (0.135) |
0.00512 (1.00) |
2q gain | 0 (0%) | 427 |
0.0302 (1.00) |
0.0253 (1.00) |
1.69e-06 (0.00118) |
7.92e-07 (0.000555) |
0.252 (1.00) |
0.276 (1.00) |
0.000184 (0.119) |
0.0183 (1.00) |
0.000162 (0.105) |
0.0021 (1.00) |
8q gain | 0 (0%) | 328 |
0.0641 (1.00) |
0.191 (1.00) |
1.9e-21 (1.4e-18) |
3.32e-07 (0.000235) |
0.0357 (1.00) |
0.00424 (1.00) |
0.000925 (0.564) |
0.00117 (0.707) |
3.06e-07 (0.000216) |
3.97e-07 (0.000281) |
12p gain | 0 (0%) | 415 |
0.565 (1.00) |
0.132 (1.00) |
3.02e-14 (2.2e-11) |
8.57e-05 (0.0564) |
0.18 (1.00) |
0.115 (1.00) |
0.000964 (0.586) |
0.000375 (0.237) |
0.000257 (0.164) |
0.00357 (1.00) |
20p gain | 0 (0%) | 411 |
0.0235 (1.00) |
0.0127 (1.00) |
3.06e-06 (0.00211) |
2.78e-05 (0.0186) |
0.0249 (1.00) |
0.687 (1.00) |
5.74e-05 (0.0381) |
0.000135 (0.0881) |
0.0189 (1.00) |
0.00772 (1.00) |
20q gain | 0 (0%) | 396 |
0.00237 (1.00) |
0.00219 (1.00) |
4.8e-07 (0.000337) |
5.01e-09 (3.6e-06) |
0.00132 (0.789) |
0.0914 (1.00) |
5.59e-06 (0.00382) |
6.15e-05 (0.0407) |
0.00212 (1.00) |
0.0023 (1.00) |
4p loss | 0 (0%) | 434 |
1.26e-05 (0.00852) |
6.44e-05 (0.0425) |
0.192 (1.00) |
0.248 (1.00) |
0.000668 (0.412) |
4.13e-05 (0.0276) |
0.000102 (0.0667) |
0.0081 (1.00) |
||
7q gain | 0 (0%) | 361 |
0.388 (1.00) |
0.702 (1.00) |
5.86e-09 (4.21e-06) |
0.000472 (0.295) |
0.0789 (1.00) |
0.298 (1.00) |
1.68e-05 (0.0113) |
1.22e-05 (0.00827) |
0.142 (1.00) |
0.238 (1.00) |
12q gain | 0 (0%) | 426 |
0.565 (1.00) |
0.132 (1.00) |
2.9e-12 (2.11e-09) |
0.000184 (0.119) |
0.158 (1.00) |
0.0893 (1.00) |
0.000189 (0.122) |
0.00123 (0.744) |
0.00744 (1.00) |
0.0757 (1.00) |
14q gain | 0 (0%) | 416 |
4.9e-06 (0.00336) |
2.98e-06 (0.00206) |
0.127 (1.00) |
0.518 (1.00) |
0.000566 (0.351) |
0.0184 (1.00) |
0.0072 (1.00) |
0.000355 (0.225) |
||
5q loss | 0 (0%) | 414 |
0.0235 (1.00) |
0.0127 (1.00) |
3.4e-05 (0.0228) |
1.01e-05 (0.00685) |
0.0388 (1.00) |
0.0986 (1.00) |
0.000124 (0.0811) |
0.043 (1.00) |
0.00944 (1.00) |
0.00553 (1.00) |
18q loss | 0 (0%) | 364 |
0.42 (1.00) |
0.412 (1.00) |
1.68e-09 (1.21e-06) |
0.00016 (0.104) |
0.301 (1.00) |
0.129 (1.00) |
0.000254 (0.163) |
0.0242 (1.00) |
0.135 (1.00) |
0.95 (1.00) |
19p loss | 0 (0%) | 360 |
0.649 (1.00) |
0.688 (1.00) |
1.56e-09 (1.12e-06) |
7.15e-08 (5.09e-05) |
0.867 (1.00) |
0.69 (1.00) |
7.53e-05 (0.0496) |
0.116 (1.00) |
0.00603 (1.00) |
0.0143 (1.00) |
8p gain | 0 (0%) | 413 |
3.74e-10 (2.7e-07) |
0.00323 (1.00) |
0.598 (1.00) |
0.842 (1.00) |
4.32e-05 (0.0288) |
0.00568 (1.00) |
0.424 (1.00) |
0.176 (1.00) |
||
16p gain | 0 (0%) | 405 |
0.358 (1.00) |
0.322 (1.00) |
0.328 (1.00) |
0.000349 (0.221) |
0.0878 (1.00) |
0.448 (1.00) |
0.000179 (0.116) |
0.015 (1.00) |
0.155 (1.00) |
0.0984 (1.00) |
17q gain | 0 (0%) | 394 |
0.0447 (1.00) |
0.702 (1.00) |
4.69e-08 (3.35e-05) |
1.39e-06 (0.00097) |
0.423 (1.00) |
0.199 (1.00) |
0.00575 (1.00) |
0.0595 (1.00) |
0.0218 (1.00) |
0.0298 (1.00) |
21q gain | 0 (0%) | 431 |
0.192 (1.00) |
0.157 (1.00) |
5e-05 (0.0332) |
3.42e-05 (0.0229) |
0.0914 (1.00) |
0.0523 (1.00) |
0.23 (1.00) |
0.17 (1.00) |
0.0596 (1.00) |
0.38 (1.00) |
8p loss | 0 (0%) | 354 |
0.104 (1.00) |
0.173 (1.00) |
4.75e-14 (3.46e-11) |
2e-06 (0.00139) |
0.173 (1.00) |
0.0281 (1.00) |
0.0403 (1.00) |
0.00246 (1.00) |
0.0271 (1.00) |
0.00979 (1.00) |
9p loss | 0 (0%) | 333 |
0.155 (1.00) |
0.206 (1.00) |
2.7e-08 (1.93e-05) |
2.59e-05 (0.0174) |
0.345 (1.00) |
0.049 (1.00) |
0.00893 (1.00) |
0.0275 (1.00) |
0.797 (1.00) |
0.701 (1.00) |
9q loss | 0 (0%) | 355 |
0.462 (1.00) |
0.475 (1.00) |
8.17e-08 (5.81e-05) |
1.07e-08 (7.67e-06) |
0.323 (1.00) |
0.144 (1.00) |
0.0193 (1.00) |
0.0131 (1.00) |
0.101 (1.00) |
0.21 (1.00) |
13q loss | 0 (0%) | 363 |
0.0846 (1.00) |
0.0411 (1.00) |
3.55e-21 (2.61e-18) |
6.46e-07 (0.000454) |
0.285 (1.00) |
0.00936 (1.00) |
0.000966 (0.586) |
0.0668 (1.00) |
0.00306 (1.00) |
0.0328 (1.00) |
22q loss | 0 (0%) | 382 |
0.308 (1.00) |
0.321 (1.00) |
5.75e-10 (4.15e-07) |
4.56e-05 (0.0303) |
0.00909 (1.00) |
0.011 (1.00) |
0.0202 (1.00) |
0.00747 (1.00) |
0.000398 (0.251) |
0.00182 (1.00) |
1p gain | 0 (0%) | 414 |
1 (1.00) |
1 (1.00) |
3.6e-08 (2.57e-05) |
0.000565 (0.351) |
0.0815 (1.00) |
0.0241 (1.00) |
0.0243 (1.00) |
0.31 (1.00) |
0.635 (1.00) |
0.763 (1.00) |
1q gain | 0 (0%) | 295 |
0.465 (1.00) |
0.885 (1.00) |
0.0352 (1.00) |
1.88e-05 (0.0127) |
0.131 (1.00) |
0.146 (1.00) |
0.000659 (0.407) |
0.703 (1.00) |
0.534 (1.00) |
0.598 (1.00) |
5p gain | 0 (0%) | 294 |
0.487 (1.00) |
0.419 (1.00) |
9.1e-15 (6.65e-12) |
0.156 (1.00) |
0.233 (1.00) |
0.636 (1.00) |
0.0188 (1.00) |
0.0313 (1.00) |
0.19 (1.00) |
0.0971 (1.00) |
6p gain | 0 (0%) | 401 |
0.292 (1.00) |
0.0507 (1.00) |
0.0199 (1.00) |
3.77e-06 (0.0026) |
0.00936 (1.00) |
0.261 (1.00) |
0.00282 (1.00) |
0.261 (1.00) |
0.0703 (1.00) |
0.342 (1.00) |
10p gain | 0 (0%) | 423 |
0.0417 (1.00) |
0.00011 (0.0721) |
0.169 (1.00) |
0.16 (1.00) |
0.00385 (1.00) |
0.107 (1.00) |
0.0955 (1.00) |
0.277 (1.00) |
||
10q gain | 0 (0%) | 444 |
0.107 (1.00) |
0.0237 (1.00) |
0.555 (1.00) |
0.188 (1.00) |
1.67e-05 (0.0113) |
0.253 (1.00) |
0.609 (1.00) |
0.292 (1.00) |
||
17p gain | 0 (0%) | 444 |
8.73e-06 (0.00595) |
0.000427 (0.268) |
0.665 (1.00) |
0.533 (1.00) |
0.609 (1.00) |
0.334 (1.00) |
0.0634 (1.00) |
0.146 (1.00) |
||
18p gain | 0 (0%) | 430 |
2.13e-06 (0.00148) |
0.00112 (0.678) |
0.0711 (1.00) |
0.209 (1.00) |
0.256 (1.00) |
0.054 (1.00) |
0.0163 (1.00) |
0.0164 (1.00) |
||
18q gain | 0 (0%) | 446 |
2.2e-05 (0.0148) |
0.000608 (0.377) |
0.09 (1.00) |
0.0373 (1.00) |
0.0343 (1.00) |
0.00139 (0.834) |
0.102 (1.00) |
0.0336 (1.00) |
||
Xq gain | 0 (0%) | 453 |
0.75 (1.00) |
0.591 (1.00) |
0.000237 (0.152) |
0.0425 (1.00) |
0.433 (1.00) |
0.598 (1.00) |
0.299 (1.00) |
0.378 (1.00) |
0.625 (1.00) |
0.641 (1.00) |
1p loss | 0 (0%) | 444 |
0.00445 (1.00) |
0.000214 (0.137) |
0.111 (1.00) |
0.199 (1.00) |
0.113 (1.00) |
0.189 (1.00) |
0.789 (1.00) |
0.146 (1.00) |
||
3p loss | 0 (0%) | 379 |
0.208 (1.00) |
0.176 (1.00) |
0.000456 (0.286) |
1.53e-05 (0.0104) |
0.156 (1.00) |
0.402 (1.00) |
0.539 (1.00) |
0.036 (1.00) |
0.0313 (1.00) |
0.0211 (1.00) |
6q loss | 0 (0%) | 367 |
0.803 (1.00) |
0.722 (1.00) |
0.0704 (1.00) |
4.4e-06 (0.00302) |
0.104 (1.00) |
0.0335 (1.00) |
0.0157 (1.00) |
0.154 (1.00) |
0.397 (1.00) |
0.868 (1.00) |
16p loss | 0 (0%) | 435 |
0.000307 (0.195) |
0.00182 (1.00) |
0.0447 (1.00) |
0.281 (1.00) |
0.135 (1.00) |
0.114 (1.00) |
0.0969 (1.00) |
0.0808 (1.00) |
||
16q loss | 0 (0%) | 416 |
0.0159 (1.00) |
1 (1.00) |
4.64e-06 (0.00319) |
0.00148 (0.887) |
0.00595 (1.00) |
0.00855 (1.00) |
0.00803 (1.00) |
0.228 (1.00) |
0.0149 (1.00) |
0.218 (1.00) |
17p loss | 0 (0%) | 363 |
0.13 (1.00) |
0.301 (1.00) |
5.86e-06 (0.004) |
0.00353 (1.00) |
0.0572 (1.00) |
0.21 (1.00) |
0.45 (1.00) |
0.444 (1.00) |
0.592 (1.00) |
0.6 (1.00) |
18p loss | 0 (0%) | 397 |
0.42 (1.00) |
0.412 (1.00) |
1.14e-05 (0.00777) |
0.0198 (1.00) |
0.88 (1.00) |
0.223 (1.00) |
0.0335 (1.00) |
0.289 (1.00) |
0.688 (1.00) |
0.858 (1.00) |
19q loss | 0 (0%) | 405 |
0.71 (1.00) |
0.722 (1.00) |
0.00019 (0.123) |
0.0288 (1.00) |
0.778 (1.00) |
0.433 (1.00) |
0.00814 (1.00) |
0.438 (1.00) |
0.0181 (1.00) |
0.0705 (1.00) |
20p loss | 0 (0%) | 411 |
0.192 (1.00) |
0.412 (1.00) |
0.000194 (0.125) |
0.0535 (1.00) |
0.00631 (1.00) |
0.0252 (1.00) |
0.114 (1.00) |
0.182 (1.00) |
0.725 (1.00) |
0.108 (1.00) |
3p gain | 0 (0%) | 459 |
0.0322 (1.00) |
0.0462 (1.00) |
0.137 (1.00) |
0.271 (1.00) |
0.00703 (1.00) |
0.0018 (1.00) |
0.876 (1.00) |
0.664 (1.00) |
||
3q gain | 0 (0%) | 443 |
0.0025 (1.00) |
0.00235 (1.00) |
0.0783 (1.00) |
0.0222 (1.00) |
0.00456 (1.00) |
0.107 (1.00) |
0.043 (1.00) |
0.358 (1.00) |
||
4p gain | 0 (0%) | 442 |
0.554 (1.00) |
0.418 (1.00) |
0.00352 (1.00) |
0.0102 (1.00) |
0.0727 (1.00) |
0.035 (1.00) |
0.76 (1.00) |
0.311 (1.00) |
0.491 (1.00) |
0.368 (1.00) |
4q gain | 0 (0%) | 461 |
0.0379 (1.00) |
0.838 (1.00) |
0.222 (1.00) |
0.271 (1.00) |
0.775 (1.00) |
0.232 (1.00) |
0.104 (1.00) |
0.126 (1.00) |
||
5q gain | 0 (0%) | 416 |
0.0177 (1.00) |
0.644 (1.00) |
0.0451 (1.00) |
0.000742 (0.456) |
0.541 (1.00) |
0.187 (1.00) |
0.0166 (1.00) |
0.0411 (1.00) |
0.356 (1.00) |
0.104 (1.00) |
6q gain | 0 (0%) | 452 |
0.41 (1.00) |
0.00965 (1.00) |
0.108 (1.00) |
0.0645 (1.00) |
0.0518 (1.00) |
0.463 (1.00) |
0.0606 (1.00) |
0.0232 (1.00) |
||
9p gain | 0 (0%) | 458 |
0.0173 (1.00) |
0.0112 (1.00) |
1 (1.00) |
0.843 (1.00) |
0.347 (1.00) |
0.237 (1.00) |
0.471 (1.00) |
0.227 (1.00) |
||
9q gain | 0 (0%) | 465 |
0.274 (1.00) |
0.59 (1.00) |
0.392 (1.00) |
0.269 (1.00) |
0.47 (1.00) |
1 (1.00) |
0.255 (1.00) |
0.239 (1.00) |
||
11p gain | 0 (0%) | 437 |
0.0527 (1.00) |
0.0419 (1.00) |
0.101 (1.00) |
0.476 (1.00) |
0.053 (1.00) |
0.274 (1.00) |
0.0313 (1.00) |
0.129 (1.00) |
||
11q gain | 0 (0%) | 421 |
0.12 (1.00) |
0.157 (1.00) |
0.000915 (0.559) |
0.0131 (1.00) |
0.000824 (0.505) |
0.0196 (1.00) |
0.0049 (1.00) |
0.00207 (1.00) |
0.00333 (1.00) |
0.0193 (1.00) |
13q gain | 0 (0%) | 457 |
0.226 (1.00) |
0.0272 (1.00) |
0.433 (1.00) |
0.294 (1.00) |
0.106 (1.00) |
0.163 (1.00) |
0.833 (1.00) |
0.269 (1.00) |
||
15q gain | 0 (0%) | 458 |
0.263 (1.00) |
0.542 (1.00) |
0.819 (1.00) |
0.578 (1.00) |
0.2 (1.00) |
0.212 (1.00) |
0.548 (1.00) |
0.415 (1.00) |
||
16q gain | 0 (0%) | 430 |
0.192 (1.00) |
0.0514 (1.00) |
0.428 (1.00) |
0.00977 (1.00) |
0.0253 (1.00) |
0.0252 (1.00) |
0.0103 (1.00) |
0.222 (1.00) |
0.163 (1.00) |
0.0605 (1.00) |
19p gain | 0 (0%) | 466 |
0.773 (1.00) |
0.372 (1.00) |
0.776 (1.00) |
1 (1.00) |
0.482 (1.00) |
1 (1.00) |
0.512 (1.00) |
0.862 (1.00) |
||
19q gain | 0 (0%) | 450 |
0.000461 (0.288) |
0.176 (1.00) |
0.402 (1.00) |
0.0144 (1.00) |
0.00341 (1.00) |
0.0431 (1.00) |
0.0966 (1.00) |
0.0683 (1.00) |
||
22q gain | 0 (0%) | 452 |
0.061 (1.00) |
0.13 (1.00) |
0.782 (1.00) |
0.172 (1.00) |
0.175 (1.00) |
0.398 (1.00) |
0.0929 (1.00) |
0.0564 (1.00) |
||
1q loss | 0 (0%) | 461 |
0.0619 (1.00) |
0.0811 (1.00) |
0.222 (1.00) |
0.0151 (1.00) |
0.544 (1.00) |
0.343 (1.00) |
0.418 (1.00) |
0.0968 (1.00) |
||
2p loss | 0 (0%) | 466 |
0.931 (1.00) |
0.466 (1.00) |
1 (1.00) |
0.617 (1.00) |
0.548 (1.00) |
1 (1.00) |
0.758 (1.00) |
0.862 (1.00) |
||
2q loss | 0 (0%) | 468 |
0.149 (1.00) |
0.227 (1.00) |
0.87 (1.00) |
1 (1.00) |
0.544 (1.00) |
0.797 (1.00) |
||||
3q loss | 0 (0%) | 416 |
0.554 (1.00) |
0.418 (1.00) |
0.0107 (1.00) |
0.00335 (1.00) |
0.341 (1.00) |
0.933 (1.00) |
0.14 (1.00) |
0.448 (1.00) |
0.429 (1.00) |
0.0242 (1.00) |
5p loss | 0 (0%) | 457 |
0.00645 (1.00) |
0.008 (1.00) |
0.306 (1.00) |
0.777 (1.00) |
0.64 (1.00) |
0.0348 (1.00) |
0.17 (1.00) |
0.227 (1.00) |
||
6p loss | 0 (0%) | 434 |
0.335 (1.00) |
0.308 (1.00) |
0.0252 (1.00) |
0.0374 (1.00) |
0.202 (1.00) |
0.537 (1.00) |
0.162 (1.00) |
0.973 (1.00) |
0.239 (1.00) |
0.745 (1.00) |
7p loss | 0 (0%) | 458 |
0.554 (1.00) |
0.418 (1.00) |
0.00723 (1.00) |
0.312 (1.00) |
0.522 (1.00) |
0.938 (1.00) |
0.0244 (1.00) |
0.067 (1.00) |
0.1 (1.00) |
0.801 (1.00) |
7q loss | 0 (0%) | 455 |
0.53 (1.00) |
0.186 (1.00) |
0.0305 (1.00) |
0.411 (1.00) |
0.687 (1.00) |
0.821 (1.00) |
0.315 (1.00) |
0.272 (1.00) |
1 (1.00) |
0.734 (1.00) |
8q loss | 0 (0%) | 455 |
0.000943 (0.574) |
0.09 (1.00) |
0.00124 (0.747) |
0.00526 (1.00) |
0.328 (1.00) |
0.0477 (1.00) |
0.951 (1.00) |
0.69 (1.00) |
||
10p loss | 0 (0%) | 437 |
0.901 (1.00) |
0.818 (1.00) |
0.000707 (0.435) |
0.000889 (0.544) |
0.0525 (1.00) |
0.0991 (1.00) |
0.0832 (1.00) |
0.51 (1.00) |
0.0453 (1.00) |
0.0128 (1.00) |
10q loss | 0 (0%) | 427 |
0.75 (1.00) |
0.591 (1.00) |
0.00124 (0.747) |
0.00454 (1.00) |
0.0157 (1.00) |
0.0585 (1.00) |
0.0258 (1.00) |
0.609 (1.00) |
0.311 (1.00) |
0.0264 (1.00) |
11p loss | 0 (0%) | 440 |
0.335 (1.00) |
0.102 (1.00) |
0.00053 (0.331) |
0.846 (1.00) |
0.00454 (1.00) |
0.0268 (1.00) |
0.042 (1.00) |
0.054 (1.00) |
0.159 (1.00) |
0.0977 (1.00) |
11q loss | 0 (0%) | 443 |
0.474 (1.00) |
0.157 (1.00) |
0.00271 (1.00) |
0.5 (1.00) |
0.0102 (1.00) |
0.0251 (1.00) |
0.452 (1.00) |
0.211 (1.00) |
0.384 (1.00) |
0.827 (1.00) |
12p loss | 0 (0%) | 435 |
0.728 (1.00) |
0.818 (1.00) |
0.229 (1.00) |
0.000653 (0.404) |
0.819 (1.00) |
0.534 (1.00) |
0.072 (1.00) |
0.593 (1.00) |
0.269 (1.00) |
0.711 (1.00) |
12q loss | 0 (0%) | 449 |
0.0787 (1.00) |
0.131 (1.00) |
0.886 (1.00) |
0.305 (1.00) |
0.404 (1.00) |
0.921 (1.00) |
0.386 (1.00) |
0.822 (1.00) |
||
14q loss | 0 (0%) | 426 |
0.401 (1.00) |
0.418 (1.00) |
0.0631 (1.00) |
0.0245 (1.00) |
0.0306 (1.00) |
0.00488 (1.00) |
0.0971 (1.00) |
0.665 (1.00) |
0.0755 (1.00) |
0.167 (1.00) |
17q loss | 0 (0%) | 455 |
0.155 (1.00) |
0.0222 (1.00) |
0.0661 (1.00) |
0.897 (1.00) |
0.476 (1.00) |
0.198 (1.00) |
0.854 (1.00) |
0.0271 (1.00) |
||
20q loss | 0 (0%) | 448 |
0.262 (1.00) |
0.139 (1.00) |
0.325 (1.00) |
0.306 (1.00) |
0.419 (1.00) |
0.333 (1.00) |
0.635 (1.00) |
0.555 (1.00) |
||
Xq loss | 0 (0%) | 461 |
0.253 (1.00) |
0.281 (1.00) |
0.74 (1.00) |
0.572 (1.00) |
0.0554 (1.00) |
0.363 (1.00) |
0.794 (1.00) |
0.35 (1.00) |
P value = 3.6e-08 (Fisher's exact test), Q value = 2.6e-05
Table S1. Gene #1: '1p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
1P GAIN CNV | 39 | 9 | 6 | 4 |
1P GAIN WILD-TYPE | 109 | 179 | 81 | 45 |
Figure S1. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D1V3.png)
P value = 1.88e-05 (Chi-square test), Q value = 0.013
Table S2. Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
1Q GAIN CNV | 37 | 41 | 42 | 17 | 15 |
1Q GAIN WILD-TYPE | 53 | 53 | 53 | 83 | 10 |
Figure S2. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D2V4.png)
P value = 7e-08 (Fisher's exact test), Q value = 5e-05
Table S3. Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
2P GAIN CNV | 21 | 3 | 15 | 11 |
2P GAIN WILD-TYPE | 127 | 185 | 72 | 38 |
Figure S3. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D3V3.png)
P value = 3.89e-06 (Chi-square test), Q value = 0.0027
Table S4. Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
2P GAIN CNV | 4 | 22 | 8 | 2 | 4 |
2P GAIN WILD-TYPE | 86 | 72 | 87 | 98 | 21 |
Figure S4. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D3V4.png)
P value = 0.000256 (Chi-square test), Q value = 0.16
Table S5. Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
2P GAIN CNV | 7 | 3 | 15 | 7 | 1 | 10 | 1 | 1 | 0 |
2P GAIN WILD-TYPE | 68 | 52 | 41 | 35 | 28 | 38 | 38 | 23 | 23 |
Figure S5. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D3V7.png)
P value = 0.00021 (Fisher's exact test), Q value = 0.14
Table S6. Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
2P GAIN CNV | 10 | 35 | 5 |
2P GAIN WILD-TYPE | 161 | 163 | 93 |
Figure S6. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D3V9.png)
P value = 1.69e-06 (Fisher's exact test), Q value = 0.0012
Table S7. Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
2Q GAIN CNV | 13 | 5 | 15 | 12 |
2Q GAIN WILD-TYPE | 135 | 183 | 72 | 37 |
Figure S7. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D4V3.png)
P value = 7.92e-07 (Chi-square test), Q value = 0.00055
Table S8. Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
2Q GAIN CNV | 5 | 22 | 8 | 0 | 3 |
2Q GAIN WILD-TYPE | 85 | 72 | 87 | 100 | 22 |
Figure S8. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D4V4.png)
P value = 0.000184 (Chi-square test), Q value = 0.12
Table S9. Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
2Q GAIN CNV | 5 | 4 | 14 | 9 | 1 | 6 | 0 | 1 | 0 |
2Q GAIN WILD-TYPE | 70 | 51 | 42 | 33 | 28 | 42 | 39 | 23 | 23 |
Figure S9. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D4V7.png)
P value = 0.000162 (Fisher's exact test), Q value = 0.1
Table S10. Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
2Q GAIN CNV | 10 | 32 | 3 |
2Q GAIN WILD-TYPE | 161 | 166 | 95 |
Figure S10. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D4V9.png)
P value = 9.1e-15 (Fisher's exact test), Q value = 6.7e-12
Table S11. Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
5P GAIN CNV | 93 | 39 | 24 | 22 |
5P GAIN WILD-TYPE | 55 | 149 | 63 | 27 |
Figure S11. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D9V3.png)
P value = 3.77e-06 (Chi-square test), Q value = 0.0026
Table S12. Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
6P GAIN CNV | 13 | 27 | 8 | 4 | 7 |
6P GAIN WILD-TYPE | 77 | 67 | 87 | 96 | 18 |
Figure S12. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D11V4.png)
P value = 3.08e-18 (Fisher's exact test), Q value = 2.3e-15
Table S13. Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
7P GAIN CNV | 89 | 26 | 28 | 11 |
7P GAIN WILD-TYPE | 59 | 162 | 59 | 38 |
Figure S13. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D13V3.png)
P value = 1.97e-06 (Chi-square test), Q value = 0.0014
Table S14. Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
7P GAIN CNV | 25 | 35 | 38 | 20 | 19 |
7P GAIN WILD-TYPE | 65 | 59 | 57 | 80 | 6 |
Figure S14. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D13V4.png)
P value = 8.93e-05 (Fisher's exact test), Q value = 0.059
Table S15. Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 85 | 75 | 75 |
7P GAIN CNV | 38 | 13 | 35 |
7P GAIN WILD-TYPE | 47 | 62 | 40 |
Figure S15. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D13V5.png)
P value = 3.89e-06 (Chi-square test), Q value = 0.0027
Table S16. Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
7P GAIN CNV | 40 | 27 | 19 | 6 | 4 | 12 | 13 | 10 | 2 |
7P GAIN WILD-TYPE | 35 | 28 | 37 | 36 | 25 | 36 | 26 | 14 | 21 |
Figure S16. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D13V7.png)
P value = 7.47e-07 (Fisher's exact test), Q value = 0.00052
Table S17. Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
7P GAIN CNV | 39 | 58 | 36 |
7P GAIN WILD-TYPE | 119 | 47 | 92 |
Figure S17. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D13V8.png)
P value = 5.86e-09 (Fisher's exact test), Q value = 4.2e-06
Table S18. Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
7Q GAIN CNV | 61 | 22 | 20 | 8 |
7Q GAIN WILD-TYPE | 87 | 166 | 67 | 41 |
Figure S18. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D14V3.png)
P value = 1.68e-05 (Chi-square test), Q value = 0.011
Table S19. Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
7Q GAIN CNV | 35 | 16 | 13 | 4 | 3 | 7 | 9 | 9 | 2 |
7Q GAIN WILD-TYPE | 40 | 39 | 43 | 38 | 26 | 41 | 30 | 15 | 21 |
Figure S19. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D14V7.png)
P value = 1.22e-05 (Fisher's exact test), Q value = 0.0083
Table S20. Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
7Q GAIN CNV | 29 | 45 | 24 |
7Q GAIN WILD-TYPE | 129 | 60 | 104 |
Figure S20. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D14V8.png)
P value = 3.74e-10 (Fisher's exact test), Q value = 2.7e-07
Table S21. Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
8P GAIN CNV | 14 | 11 | 11 | 23 |
8P GAIN WILD-TYPE | 134 | 177 | 76 | 26 |
Figure S21. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D15V3.png)
P value = 4.32e-05 (Chi-square test), Q value = 0.029
Table S22. Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
8P GAIN CNV | 3 | 6 | 5 | 5 | 2 | 17 | 2 | 3 | 2 |
8P GAIN WILD-TYPE | 72 | 49 | 51 | 37 | 27 | 31 | 37 | 21 | 21 |
Figure S22. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D15V7.png)
P value = 1.9e-21 (Fisher's exact test), Q value = 1.4e-18
Table S23. Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
8Q GAIN CNV | 56 | 17 | 34 | 37 |
8Q GAIN WILD-TYPE | 92 | 171 | 53 | 12 |
Figure S23. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D16V3.png)
P value = 3.32e-07 (Chi-square test), Q value = 0.00023
Table S24. Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
8Q GAIN CNV | 17 | 48 | 34 | 16 | 8 |
8Q GAIN WILD-TYPE | 73 | 46 | 61 | 84 | 17 |
Figure S24. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D16V4.png)
P value = 3.06e-07 (Fisher's exact test), Q value = 0.00022
Table S25. Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
8Q GAIN CNV | 27 | 81 | 34 |
8Q GAIN WILD-TYPE | 144 | 117 | 64 |
Figure S25. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D16V9.png)
P value = 3.97e-07 (Fisher's exact test), Q value = 0.00028
Table S26. Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
8Q GAIN CNV | 27 | 100 | 15 |
8Q GAIN WILD-TYPE | 137 | 144 | 44 |
Figure S26. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D16V10.png)
P value = 0.00011 (Chi-square test), Q value = 0.072
Table S27. Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
10P GAIN CNV | 4 | 17 | 18 | 3 | 1 |
10P GAIN WILD-TYPE | 86 | 77 | 77 | 97 | 24 |
Figure S27. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D19V4.png)
P value = 1.67e-05 (Chi-square test), Q value = 0.011
Table S28. Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
10Q GAIN CNV | 3 | 0 | 3 | 11 | 2 | 3 | 1 | 1 | 0 |
10Q GAIN WILD-TYPE | 72 | 55 | 53 | 31 | 27 | 45 | 38 | 23 | 23 |
Figure S28. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D20V7.png)
P value = 3.02e-14 (Fisher's exact test), Q value = 2.2e-11
Table S29. Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
12P GAIN CNV | 16 | 3 | 32 | 6 |
12P GAIN WILD-TYPE | 132 | 185 | 55 | 43 |
Figure S29. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D23V3.png)
P value = 8.57e-05 (Chi-square test), Q value = 0.056
Table S30. Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
12P GAIN CNV | 1 | 22 | 9 | 10 | 3 |
12P GAIN WILD-TYPE | 89 | 72 | 86 | 90 | 22 |
Figure S30. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D23V4.png)
P value = 0.000375 (Fisher's exact test), Q value = 0.24
Table S31. Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
12P GAIN CNV | 9 | 12 | 27 |
12P GAIN WILD-TYPE | 149 | 93 | 101 |
Figure S31. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D23V8.png)
P value = 0.000257 (Fisher's exact test), Q value = 0.16
Table S32. Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
12P GAIN CNV | 9 | 37 | 10 |
12P GAIN WILD-TYPE | 162 | 161 | 88 |
Figure S32. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D23V9.png)
P value = 2.9e-12 (Fisher's exact test), Q value = 2.1e-09
Table S33. Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
12Q GAIN CNV | 9 | 3 | 27 | 7 |
12Q GAIN WILD-TYPE | 139 | 185 | 60 | 42 |
Figure S33. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D24V3.png)
P value = 0.000184 (Chi-square test), Q value = 0.12
Table S34. Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
12Q GAIN CNV | 1 | 18 | 5 | 7 | 3 |
12Q GAIN WILD-TYPE | 89 | 76 | 90 | 93 | 22 |
Figure S34. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D24V4.png)
P value = 0.000189 (Chi-square test), Q value = 0.12
Table S35. Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
12Q GAIN CNV | 7 | 1 | 5 | 3 | 4 | 14 | 5 | 0 | 0 |
12Q GAIN WILD-TYPE | 68 | 54 | 51 | 39 | 25 | 34 | 34 | 24 | 23 |
Figure S35. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D24V7.png)
P value = 4.9e-06 (Fisher's exact test), Q value = 0.0034
Table S36. Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
14Q GAIN CNV | 19 | 9 | 12 | 16 |
14Q GAIN WILD-TYPE | 129 | 179 | 75 | 33 |
Figure S36. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D26V3.png)
P value = 2.98e-06 (Chi-square test), Q value = 0.0021
Table S37. Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
14Q GAIN CNV | 8 | 26 | 8 | 4 | 6 |
14Q GAIN WILD-TYPE | 82 | 68 | 87 | 96 | 19 |
Figure S37. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D26V4.png)
P value = 0.000355 (Fisher's exact test), Q value = 0.22
Table S38. Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
14Q GAIN CNV | 7 | 38 | 10 |
14Q GAIN WILD-TYPE | 157 | 206 | 49 |
Figure S38. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D26V10.png)
P value = 0.000349 (Chi-square test), Q value = 0.22
Table S39. Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
16P GAIN CNV | 23 | 10 | 9 | 7 | 7 |
16P GAIN WILD-TYPE | 67 | 84 | 86 | 93 | 18 |
Figure S39. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D28V4.png)
P value = 0.000179 (Chi-square test), Q value = 0.12
Table S40. Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
16P GAIN CNV | 8 | 20 | 2 | 5 | 3 | 5 | 7 | 5 | 2 |
16P GAIN WILD-TYPE | 67 | 35 | 54 | 37 | 26 | 43 | 32 | 19 | 21 |
Figure S40. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D28V7.png)
P value = 8.73e-06 (Fisher's exact test), Q value = 0.006
Table S41. Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
17P GAIN CNV | 5 | 3 | 13 | 7 |
17P GAIN WILD-TYPE | 143 | 185 | 74 | 42 |
Figure S41. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D30V3.png)
P value = 4.69e-08 (Fisher's exact test), Q value = 3.3e-05
Table S42. Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
17Q GAIN CNV | 37 | 9 | 22 | 10 |
17Q GAIN WILD-TYPE | 111 | 179 | 65 | 39 |
Figure S42. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D31V3.png)
P value = 1.39e-06 (Chi-square test), Q value = 0.00097
Table S43. Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
17Q GAIN CNV | 9 | 26 | 20 | 3 | 9 |
17Q GAIN WILD-TYPE | 81 | 68 | 75 | 97 | 16 |
Figure S43. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D31V4.png)
P value = 2.13e-06 (Fisher's exact test), Q value = 0.0015
Table S44. Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
18P GAIN CNV | 22 | 5 | 4 | 11 |
18P GAIN WILD-TYPE | 126 | 183 | 83 | 38 |
Figure S44. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D32V3.png)
P value = 2.2e-05 (Fisher's exact test), Q value = 0.015
Table S45. Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
18Q GAIN CNV | 12 | 2 | 3 | 9 |
18Q GAIN WILD-TYPE | 136 | 186 | 84 | 40 |
Figure S45. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D33V3.png)
P value = 3.06e-06 (Fisher's exact test), Q value = 0.0021
Table S46. Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
20P GAIN CNV | 15 | 11 | 22 | 13 |
20P GAIN WILD-TYPE | 133 | 177 | 65 | 36 |
Figure S46. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D36V3.png)
P value = 2.78e-05 (Chi-square test), Q value = 0.019
Table S47. Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
20P GAIN CNV | 7 | 26 | 9 | 6 | 5 |
20P GAIN WILD-TYPE | 83 | 68 | 86 | 94 | 20 |
Figure S47. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D36V4.png)
P value = 5.74e-05 (Chi-square test), Q value = 0.038
Table S48. Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
20P GAIN CNV | 7 | 4 | 19 | 6 | 3 | 12 | 2 | 1 | 1 |
20P GAIN WILD-TYPE | 68 | 51 | 37 | 36 | 26 | 36 | 37 | 23 | 22 |
Figure S48. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D36V7.png)
P value = 0.000135 (Fisher's exact test), Q value = 0.088
Table S49. Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
20P GAIN CNV | 15 | 8 | 32 |
20P GAIN WILD-TYPE | 143 | 97 | 96 |
Figure S49. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D36V8.png)
P value = 4.8e-07 (Fisher's exact test), Q value = 0.00034
Table S50. Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
20Q GAIN CNV | 27 | 11 | 26 | 12 |
20Q GAIN WILD-TYPE | 121 | 177 | 61 | 37 |
Figure S50. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D37V3.png)
P value = 5.01e-09 (Chi-square test), Q value = 3.6e-06
Table S51. Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
20Q GAIN CNV | 8 | 30 | 9 | 7 | 11 |
20Q GAIN WILD-TYPE | 82 | 64 | 86 | 93 | 14 |
Figure S51. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D37V4.png)
P value = 5.59e-06 (Chi-square test), Q value = 0.0038
Table S52. Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
20Q GAIN CNV | 8 | 7 | 24 | 5 | 5 | 14 | 3 | 3 | 1 |
20Q GAIN WILD-TYPE | 67 | 48 | 32 | 37 | 24 | 34 | 36 | 21 | 22 |
Figure S52. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D37V7.png)
P value = 6.15e-05 (Fisher's exact test), Q value = 0.041
Table S53. Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
20Q GAIN CNV | 20 | 11 | 39 |
20Q GAIN WILD-TYPE | 138 | 94 | 89 |
Figure S53. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D37V8.png)
P value = 5e-05 (Fisher's exact test), Q value = 0.033
Table S54. Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
21Q GAIN CNV | 27 | 8 | 4 | 2 |
21Q GAIN WILD-TYPE | 121 | 180 | 83 | 47 |
Figure S54. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D38V3.png)
P value = 3.42e-05 (Chi-square test), Q value = 0.023
Table S55. Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
21Q GAIN CNV | 8 | 7 | 11 | 1 | 8 |
21Q GAIN WILD-TYPE | 82 | 87 | 84 | 99 | 17 |
Figure S55. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D38V4.png)
P value = 0.000237 (Fisher's exact test), Q value = 0.15
Table S56. Gene #40: 'Xq gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
XQ GAIN CNV | 10 | 0 | 6 | 3 |
XQ GAIN WILD-TYPE | 138 | 188 | 81 | 46 |
Figure S56. Get High-res Image Gene #40: 'Xq gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D40V3.png)
P value = 0.000214 (Chi-square test), Q value = 0.14
Table S57. Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
1P LOSS CNV | 5 | 15 | 3 | 1 | 1 |
1P LOSS WILD-TYPE | 85 | 79 | 92 | 99 | 24 |
Figure S57. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D41V4.png)
P value = 1.53e-05 (Chi-square test), Q value = 0.01
Table S58. Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
3P LOSS CNV | 14 | 33 | 22 | 6 | 6 |
3P LOSS WILD-TYPE | 76 | 61 | 73 | 94 | 19 |
Figure S58. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D45V4.png)
P value = 1.26e-05 (Fisher's exact test), Q value = 0.0085
Table S59. Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
4P LOSS CNV | 12 | 4 | 11 | 11 |
4P LOSS WILD-TYPE | 136 | 184 | 76 | 38 |
Figure S59. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D47V3.png)
P value = 6.44e-05 (Chi-square test), Q value = 0.042
Table S60. Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
4P LOSS CNV | 2 | 17 | 5 | 3 | 4 |
4P LOSS WILD-TYPE | 88 | 77 | 90 | 97 | 21 |
Figure S60. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D47V4.png)
P value = 4.13e-05 (Fisher's exact test), Q value = 0.028
Table S61. Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
4P LOSS CNV | 4 | 7 | 22 |
4P LOSS WILD-TYPE | 154 | 98 | 106 |
Figure S61. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D47V8.png)
P value = 0.000102 (Fisher's exact test), Q value = 0.067
Table S62. Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
4P LOSS CNV | 7 | 28 | 2 |
4P LOSS WILD-TYPE | 164 | 170 | 96 |
Figure S62. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D47V9.png)
P value = 2.2e-10 (Fisher's exact test), Q value = 1.6e-07
Table S63. Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
4Q LOSS CNV | 15 | 1 | 17 | 12 |
4Q LOSS WILD-TYPE | 133 | 187 | 70 | 37 |
Figure S63. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D48V3.png)
P value = 4.24e-07 (Chi-square test), Q value = 3e-04
Table S64. Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
4Q LOSS CNV | 2 | 21 | 4 | 4 | 5 |
4Q LOSS WILD-TYPE | 88 | 73 | 91 | 96 | 20 |
Figure S64. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D48V4.png)
P value = 9.1e-05 (Chi-square test), Q value = 0.06
Table S65. Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
4Q LOSS CNV | 5 | 1 | 11 | 2 | 1 | 13 | 3 | 3 | 0 |
4Q LOSS WILD-TYPE | 70 | 54 | 45 | 40 | 28 | 35 | 36 | 21 | 23 |
Figure S65. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D48V7.png)
P value = 9.39e-08 (Fisher's exact test), Q value = 6.7e-05
Table S66. Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
4Q LOSS CNV | 5 | 5 | 29 |
4Q LOSS WILD-TYPE | 153 | 100 | 99 |
Figure S66. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D48V8.png)
P value = 0.000386 (Fisher's exact test), Q value = 0.24
Table S67. Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
4Q LOSS CNV | 7 | 31 | 6 |
4Q LOSS WILD-TYPE | 164 | 167 | 92 |
Figure S67. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D48V9.png)
P value = 3.4e-05 (Fisher's exact test), Q value = 0.023
Table S68. Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
5Q LOSS CNV | 23 | 8 | 19 | 8 |
5Q LOSS WILD-TYPE | 125 | 180 | 68 | 41 |
Figure S68. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D50V3.png)
P value = 1.01e-05 (Chi-square test), Q value = 0.0069
Table S69. Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
5Q LOSS CNV | 5 | 24 | 13 | 3 | 5 |
5Q LOSS WILD-TYPE | 85 | 70 | 82 | 97 | 20 |
Figure S69. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D50V4.png)
P value = 0.000124 (Chi-square test), Q value = 0.081
Table S70. Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
5Q LOSS CNV | 16 | 2 | 16 | 5 | 5 | 5 | 0 | 2 | 0 |
5Q LOSS WILD-TYPE | 59 | 53 | 40 | 37 | 24 | 43 | 39 | 22 | 23 |
Figure S70. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D50V7.png)
P value = 4.4e-06 (Chi-square test), Q value = 0.003
Table S71. Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
6Q LOSS CNV | 29 | 29 | 27 | 4 | 4 |
6Q LOSS WILD-TYPE | 61 | 65 | 68 | 96 | 21 |
Figure S71. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D52V4.png)
P value = 4.75e-14 (Fisher's exact test), Q value = 3.5e-11
Table S72. Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
8P LOSS CNV | 69 | 18 | 24 | 7 |
8P LOSS WILD-TYPE | 79 | 170 | 63 | 42 |
Figure S72. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D55V3.png)
P value = 2e-06 (Chi-square test), Q value = 0.0014
Table S73. Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
8P LOSS CNV | 17 | 25 | 33 | 10 | 14 |
8P LOSS WILD-TYPE | 73 | 69 | 62 | 90 | 11 |
Figure S73. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D55V4.png)
P value = 2.7e-08 (Fisher's exact test), Q value = 1.9e-05
Table S74. Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
9P LOSS CNV | 50 | 35 | 46 | 8 |
9P LOSS WILD-TYPE | 98 | 153 | 41 | 41 |
Figure S74. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D57V3.png)
P value = 2.59e-05 (Chi-square test), Q value = 0.017
Table S75. Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
9P LOSS CNV | 26 | 43 | 27 | 13 | 10 |
9P LOSS WILD-TYPE | 64 | 51 | 68 | 87 | 15 |
Figure S75. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D57V4.png)
P value = 8.17e-08 (Fisher's exact test), Q value = 5.8e-05
Table S76. Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
9Q LOSS CNV | 44 | 22 | 37 | 14 |
9Q LOSS WILD-TYPE | 104 | 166 | 50 | 35 |
Figure S76. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D58V3.png)
P value = 1.07e-08 (Chi-square test), Q value = 7.7e-06
Table S77. Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
9Q LOSS CNV | 18 | 43 | 17 | 9 | 10 |
9Q LOSS WILD-TYPE | 72 | 51 | 78 | 91 | 15 |
Figure S77. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D58V4.png)
P value = 3.55e-21 (Fisher's exact test), Q value = 2.6e-18
Table S78. Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
13Q LOSS CNV | 58 | 4 | 31 | 16 |
13Q LOSS WILD-TYPE | 90 | 184 | 56 | 33 |
Figure S78. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D65V3.png)
P value = 6.46e-07 (Chi-square test), Q value = 0.00045
Table S79. Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
13Q LOSS CNV | 18 | 25 | 21 | 8 | 15 |
13Q LOSS WILD-TYPE | 72 | 69 | 74 | 92 | 10 |
Figure S79. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D65V4.png)
P value = 5.26e-12 (Fisher's exact test), Q value = 3.8e-09
Table S80. Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
15Q LOSS CNV | 48 | 9 | 22 | 16 |
15Q LOSS WILD-TYPE | 100 | 179 | 65 | 33 |
Figure S80. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D67V3.png)
P value = 1.41e-09 (Chi-square test), Q value = 1e-06
Table S81. Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
15Q LOSS CNV | 11 | 32 | 21 | 4 | 13 |
15Q LOSS WILD-TYPE | 79 | 62 | 74 | 96 | 12 |
Figure S81. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D67V4.png)
P value = 6.09e-05 (Chi-square test), Q value = 0.04
Table S82. Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
15Q LOSS CNV | 23 | 17 | 16 | 1 | 3 | 14 | 3 | 1 | 2 |
15Q LOSS WILD-TYPE | 52 | 38 | 40 | 41 | 26 | 34 | 36 | 23 | 21 |
Figure S82. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D67V7.png)
P value = 0.000269 (Fisher's exact test), Q value = 0.17
Table S83. Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
15Q LOSS CNV | 19 | 55 | 20 |
15Q LOSS WILD-TYPE | 152 | 143 | 78 |
Figure S83. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D67V9.png)
P value = 0.000239 (Fisher's exact test), Q value = 0.15
Table S84. Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
15Q LOSS CNV | 17 | 64 | 13 |
15Q LOSS WILD-TYPE | 147 | 180 | 46 |
Figure S84. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D67V10.png)
P value = 0.000307 (Fisher's exact test), Q value = 0.19
Table S85. Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
16P LOSS CNV | 15 | 4 | 13 | 5 |
16P LOSS WILD-TYPE | 133 | 184 | 74 | 44 |
Figure S85. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D68V3.png)
P value = 4.64e-06 (Fisher's exact test), Q value = 0.0032
Table S86. Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
16Q LOSS CNV | 28 | 6 | 15 | 7 |
16Q LOSS WILD-TYPE | 120 | 182 | 72 | 42 |
Figure S86. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D69V3.png)
P value = 5.86e-06 (Fisher's exact test), Q value = 0.004
Table S87. Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
17P LOSS CNV | 53 | 23 | 20 | 13 |
17P LOSS WILD-TYPE | 95 | 165 | 67 | 36 |
Figure S87. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D70V3.png)
P value = 1.14e-05 (Fisher's exact test), Q value = 0.0078
Table S88. Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
18P LOSS CNV | 35 | 14 | 22 | 4 |
18P LOSS WILD-TYPE | 113 | 174 | 65 | 45 |
Figure S88. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D72V3.png)
P value = 1.68e-09 (Fisher's exact test), Q value = 1.2e-06
Table S89. Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
18Q LOSS CNV | 52 | 22 | 31 | 3 |
18Q LOSS WILD-TYPE | 96 | 166 | 56 | 46 |
Figure S89. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D73V3.png)
P value = 0.00016 (Chi-square test), Q value = 0.1
Table S90. Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
18Q LOSS CNV | 23 | 21 | 29 | 11 | 13 |
18Q LOSS WILD-TYPE | 67 | 73 | 66 | 89 | 12 |
Figure S90. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D73V4.png)
P value = 0.000254 (Chi-square test), Q value = 0.16
Table S91. Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
18Q LOSS CNV | 24 | 21 | 14 | 2 | 10 | 5 | 8 | 3 | 2 |
18Q LOSS WILD-TYPE | 51 | 34 | 42 | 40 | 19 | 43 | 31 | 21 | 21 |
Figure S91. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D73V7.png)
P value = 1.56e-09 (Fisher's exact test), Q value = 1.1e-06
Table S92. Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
19P LOSS CNV | 32 | 22 | 41 | 17 |
19P LOSS WILD-TYPE | 116 | 166 | 46 | 32 |
Figure S92. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D74V3.png)
P value = 7.15e-08 (Chi-square test), Q value = 5.1e-05
Table S93. Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
19P LOSS CNV | 20 | 39 | 15 | 6 | 5 |
19P LOSS WILD-TYPE | 70 | 55 | 80 | 94 | 20 |
Figure S93. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D74V4.png)
P value = 7.53e-05 (Chi-square test), Q value = 0.05
Table S94. Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
19P LOSS CNV | 16 | 14 | 16 | 23 | 7 | 14 | 6 | 3 | 0 |
19P LOSS WILD-TYPE | 59 | 41 | 40 | 19 | 22 | 34 | 33 | 21 | 23 |
Figure S94. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D74V7.png)
P value = 0.00019 (Fisher's exact test), Q value = 0.12
Table S95. Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
19Q LOSS CNV | 27 | 12 | 21 | 7 |
19Q LOSS WILD-TYPE | 121 | 176 | 66 | 42 |
Figure S95. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D75V3.png)
P value = 0.000194 (Fisher's exact test), Q value = 0.13
Table S96. Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
20P LOSS CNV | 30 | 11 | 16 | 4 |
20P LOSS WILD-TYPE | 118 | 177 | 71 | 45 |
Figure S96. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D76V3.png)
P value = 3.03e-12 (Fisher's exact test), Q value = 2.2e-09
Table S97. Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
21Q LOSS CNV | 13 | 8 | 30 | 15 |
21Q LOSS WILD-TYPE | 135 | 180 | 57 | 34 |
Figure S97. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D78V3.png)
P value = 1e-07 (Chi-square test), Q value = 7.1e-05
Table S98. Gene #78: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
21Q LOSS CNV | 8 | 31 | 8 | 6 | 3 |
21Q LOSS WILD-TYPE | 82 | 63 | 87 | 94 | 22 |
Figure S98. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D78V4.png)
P value = 1.42e-06 (Chi-square test), Q value = 0.00099
Table S99. Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
21Q LOSS CNV | 4 | 4 | 11 | 6 | 5 | 20 | 5 | 2 | 0 |
21Q LOSS WILD-TYPE | 71 | 51 | 45 | 36 | 24 | 28 | 34 | 22 | 23 |
Figure S99. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D78V7.png)
P value = 4.44e-07 (Fisher's exact test), Q value = 0.00031
Table S100. Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
21Q LOSS CNV | 13 | 7 | 37 |
21Q LOSS WILD-TYPE | 145 | 98 | 91 |
Figure S100. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D78V8.png)
P value = 3.11e-05 (Fisher's exact test), Q value = 0.021
Table S101. Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
21Q LOSS CNV | 12 | 44 | 8 |
21Q LOSS WILD-TYPE | 159 | 154 | 90 |
Figure S101. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D78V9.png)
P value = 8.05e-07 (Fisher's exact test), Q value = 0.00056
Table S102. Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
21Q LOSS CNV | 11 | 52 | 1 |
21Q LOSS WILD-TYPE | 153 | 192 | 58 |
Figure S102. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D78V10.png)
P value = 5.75e-10 (Fisher's exact test), Q value = 4.2e-07
Table S103. Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
22Q LOSS CNV | 39 | 10 | 24 | 17 |
22Q LOSS WILD-TYPE | 109 | 178 | 63 | 32 |
Figure S103. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D79V3.png)
P value = 4.56e-05 (Chi-square test), Q value = 0.03
Table S104. Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
22Q LOSS CNV | 12 | 32 | 14 | 9 | 7 |
22Q LOSS WILD-TYPE | 78 | 62 | 81 | 91 | 18 |
Figure S104. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D79V4.png)
-
Mutation data file = broad_values_by_arm.mutsig.cluster.txt
-
Molecular subtypes file = LUAD-TP.transferedmergedcluster.txt
-
Number of patients = 472
-
Number of significantly arm-level cnvs = 80
-
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 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 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.