This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and subtypes.
Testing the association between copy number variation 71 arm-level results and 10 molecular subtypes across 493 patients, 131 significant findings detected with Q value < 0.25.
-
1q gain cnv correlated to 'CN_CNMF'.
-
2p gain cnv correlated to 'CN_CNMF'.
-
2q gain cnv correlated to 'CN_CNMF'.
-
3q gain cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
-
5p gain cnv correlated to 'CN_CNMF'.
-
5q gain cnv correlated to 'CN_CNMF'.
-
7p gain cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.
-
7q gain cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.
-
8p gain cnv correlated to 'CN_CNMF'.
-
8q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
-
12p gain cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
-
12q gain cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
-
17p gain cnv correlated to 'CN_CNMF'.
-
19p gain cnv correlated to 'CN_CNMF'.
-
19q gain cnv correlated to 'CN_CNMF'.
-
20p gain cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
-
20q gain cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
-
21q gain cnv correlated to 'CN_CNMF'.
-
22q gain cnv correlated to 'CN_CNMF'.
-
1p loss cnv correlated to 'MRNA_CHIERARCHICAL', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
-
1q loss cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
-
2p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
-
2q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
3p loss cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
4q loss cnv correlated to 'CN_CNMF'.
-
6p loss cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
6q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
-
9p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
-
9q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
-
10p loss cnv correlated to 'CN_CNMF'.
-
13q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
-
14q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
-
17p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
17q loss cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
18p loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
-
18q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
-
21q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 71 arm-level results and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 131 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 | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
2q loss | 0 (0%) | 482 |
0.000249 (0.138) |
0.000374 (0.204) |
4.75e-06 (0.0029) |
1 (1.00) |
0.000129 (0.0727) |
4.42e-05 (0.0255) |
8.96e-08 (5.69e-05) |
7.91e-08 (5.04e-05) |
0.000199 (0.111) |
4.81e-12 (3.15e-09) |
17p loss | 0 (0%) | 468 |
0.000117 (0.0662) |
0.000178 (0.0998) |
4.3e-06 (0.00263) |
0.908 (1.00) |
2.92e-05 (0.017) |
5.18e-06 (0.00314) |
1.9e-06 (0.00118) |
1.5e-08 (9.62e-06) |
4.9e-07 (0.000307) |
8.54e-09 (5.48e-06) |
2p loss | 0 (0%) | 483 |
0.000249 (0.138) |
0.000374 (0.204) |
1.52e-05 (0.00898) |
0.456 (1.00) |
1.37e-05 (0.00812) |
0.000189 (0.106) |
4.72e-07 (0.000297) |
1.87e-08 (1.2e-05) |
0.000598 (0.318) |
1.25e-12 (8.26e-10) |
3p loss | 0 (0%) | 189 |
0.013 (1.00) |
0.0102 (1.00) |
6.37e-24 (4.24e-21) |
0.000521 (0.278) |
0.00012 (0.0676) |
1.78e-05 (0.0104) |
3.85e-11 (2.51e-08) |
7.09e-10 (4.57e-07) |
4.23e-05 (0.0245) |
5.08e-14 (3.37e-11) |
14q loss | 0 (0%) | 335 |
0.00179 (0.903) |
0.000956 (0.496) |
2.02e-10 (1.31e-07) |
3.06e-05 (0.0178) |
6.61e-12 (4.32e-09) |
2.08e-07 (0.000131) |
6.97e-11 (4.52e-08) |
2.8e-07 (0.000177) |
4.33e-06 (0.00264) |
0.507 (1.00) |
17q loss | 0 (0%) | 481 |
0.000668 (0.355) |
0.00077 (0.404) |
0.000224 (0.124) |
0.456 (1.00) |
1.46e-05 (0.00863) |
1.02e-05 (0.00613) |
1.91e-06 (0.00118) |
7.91e-08 (5.04e-05) |
8.98e-05 (0.0511) |
4.05e-11 (2.63e-08) |
12p gain | 0 (0%) | 415 |
0.194 (1.00) |
0.165 (1.00) |
7.99e-07 (0.000498) |
0.00104 (0.534) |
5.67e-07 (0.000355) |
0.0139 (1.00) |
1.1e-05 (0.00658) |
1.89e-05 (0.0111) |
6.95e-06 (0.00419) |
0.712 (1.00) |
12q gain | 0 (0%) | 415 |
0.194 (1.00) |
0.165 (1.00) |
7.99e-07 (0.000498) |
0.00104 (0.534) |
5.67e-07 (0.000355) |
0.0141 (1.00) |
1.1e-05 (0.00658) |
1.89e-05 (0.0111) |
6.95e-06 (0.00419) |
0.617 (1.00) |
20p gain | 0 (0%) | 427 |
0.102 (1.00) |
0.11 (1.00) |
1.05e-12 (6.9e-10) |
0.000674 (0.357) |
0.000453 (0.244) |
0.000979 (0.507) |
3.59e-06 (0.00221) |
5.29e-06 (0.00321) |
2.54e-06 (0.00157) |
0.0344 (1.00) |
20q gain | 0 (0%) | 425 |
0.0753 (1.00) |
0.092 (1.00) |
6.23e-14 (4.13e-11) |
0.000674 (0.357) |
3.54e-05 (0.0205) |
0.000855 (0.446) |
3.3e-07 (0.000207) |
1.47e-06 (0.00091) |
1.83e-07 (0.000116) |
0.035 (1.00) |
1p loss | 0 (0%) | 461 |
0.000836 (0.438) |
6.2e-05 (0.0355) |
0.00395 (1.00) |
0.198 (1.00) |
5.05e-08 (3.23e-05) |
0.000435 (0.235) |
0.0123 (1.00) |
4.64e-06 (0.00283) |
0.0187 (1.00) |
1.01e-10 (6.52e-08) |
1q loss | 0 (0%) | 472 |
0.0217 (1.00) |
0.00286 (1.00) |
2.09e-05 (0.0122) |
0.904 (1.00) |
0.000168 (0.0942) |
0.00191 (0.96) |
6.65e-05 (0.0379) |
6.27e-07 (0.000391) |
0.0493 (1.00) |
2.88e-11 (1.88e-08) |
6p loss | 0 (0%) | 435 |
0.0139 (1.00) |
0.0029 (1.00) |
4.27e-12 (2.8e-09) |
0.00899 (1.00) |
0.000122 (0.0685) |
7.03e-06 (0.00423) |
0.000722 (0.38) |
0.00105 (0.538) |
2.87e-09 (1.85e-06) |
0.000394 (0.214) |
9p loss | 0 (0%) | 406 |
0.378 (1.00) |
0.0694 (1.00) |
9.23e-25 (6.15e-22) |
3.57e-12 (2.34e-09) |
0.00463 (1.00) |
0.00726 (1.00) |
1.39e-11 (9.06e-09) |
2.71e-12 (1.78e-09) |
8.73e-09 (5.6e-06) |
0.201 (1.00) |
9q loss | 0 (0%) | 401 |
0.378 (1.00) |
0.0694 (1.00) |
4.43e-26 (2.96e-23) |
4.3e-13 (2.84e-10) |
0.000999 (0.516) |
0.0104 (1.00) |
1.31e-12 (8.65e-10) |
3.94e-14 (2.62e-11) |
3.82e-10 (2.46e-07) |
0.173 (1.00) |
3q gain | 0 (0%) | 466 |
0.0823 (1.00) |
0.0851 (1.00) |
6.58e-05 (0.0376) |
0.0804 (1.00) |
0.00718 (1.00) |
0.000107 (0.0609) |
0.000395 (0.214) |
0.00931 (1.00) |
0.000339 (0.186) |
0.00761 (1.00) |
8q gain | 0 (0%) | 459 |
0.0536 (1.00) |
0.0581 (1.00) |
2.75e-07 (0.000173) |
0.00105 (0.535) |
0.0102 (1.00) |
0.0449 (1.00) |
1.15e-07 (7.27e-05) |
4.88e-05 (0.0282) |
6.77e-06 (0.00409) |
0.0182 (1.00) |
18p loss | 0 (0%) | 447 |
0.194 (1.00) |
0.433 (1.00) |
3.02e-06 (0.00186) |
0.0194 (1.00) |
0.0183 (1.00) |
0.00473 (1.00) |
6.06e-06 (0.00366) |
0.000196 (0.109) |
0.00036 (0.197) |
0.00262 (1.00) |
13q loss | 0 (0%) | 462 |
0.0253 (1.00) |
0.0281 (1.00) |
6.36e-05 (0.0364) |
0.247 (1.00) |
0.00137 (0.698) |
0.00139 (0.704) |
0.0025 (1.00) |
0.00046 (0.247) |
0.000838 (0.438) |
0.000285 (0.157) |
21q loss | 0 (0%) | 461 |
0.0145 (1.00) |
0.0219 (1.00) |
0.000367 (0.2) |
0.479 (1.00) |
0.00501 (1.00) |
0.0399 (1.00) |
0.00192 (0.966) |
1.72e-05 (0.0101) |
0.24 (1.00) |
9.51e-06 (0.00571) |
7p gain | 0 (0%) | 366 |
0.877 (1.00) |
0.939 (1.00) |
5.05e-06 (0.00307) |
0.0543 (1.00) |
0.000268 (0.148) |
0.00565 (1.00) |
0.068 (1.00) |
0.0824 (1.00) |
0.0251 (1.00) |
0.703 (1.00) |
7q gain | 0 (0%) | 364 |
0.877 (1.00) |
0.939 (1.00) |
1.36e-05 (0.00809) |
0.0417 (1.00) |
0.000118 (0.0665) |
0.000718 (0.378) |
0.0581 (1.00) |
0.131 (1.00) |
0.0129 (1.00) |
0.481 (1.00) |
6q loss | 0 (0%) | 411 |
0.0393 (1.00) |
0.0125 (1.00) |
6.34e-17 (4.21e-14) |
0.121 (1.00) |
0.0014 (0.71) |
0.00103 (0.532) |
0.204 (1.00) |
0.478 (1.00) |
1.42e-05 (0.00843) |
0.00226 (1.00) |
18q loss | 0 (0%) | 445 |
0.259 (1.00) |
0.238 (1.00) |
3.61e-06 (0.00221) |
0.0324 (1.00) |
0.0551 (1.00) |
0.0128 (1.00) |
2.87e-05 (0.0167) |
0.000574 (0.306) |
0.000948 (0.493) |
0.00546 (1.00) |
1q gain | 0 (0%) | 461 |
0.611 (1.00) |
1 (1.00) |
1.05e-05 (0.00625) |
0.452 (1.00) |
0.434 (1.00) |
0.19 (1.00) |
0.00972 (1.00) |
0.15 (1.00) |
0.0134 (1.00) |
0.189 (1.00) |
2p gain | 0 (0%) | 445 |
0.561 (1.00) |
0.472 (1.00) |
1.08e-06 (0.000674) |
0.653 (1.00) |
0.0462 (1.00) |
0.783 (1.00) |
0.144 (1.00) |
0.0785 (1.00) |
0.228 (1.00) |
0.16 (1.00) |
2q gain | 0 (0%) | 444 |
0.561 (1.00) |
0.472 (1.00) |
4.9e-05 (0.0282) |
0.824 (1.00) |
0.0528 (1.00) |
0.862 (1.00) |
0.0519 (1.00) |
0.0498 (1.00) |
0.146 (1.00) |
0.16 (1.00) |
5p gain | 0 (0%) | 352 |
0.593 (1.00) |
0.592 (1.00) |
1.25e-05 (0.00745) |
0.441 (1.00) |
0.0817 (1.00) |
0.0546 (1.00) |
0.0458 (1.00) |
0.00844 (1.00) |
0.0362 (1.00) |
0.00595 (1.00) |
5q gain | 0 (0%) | 337 |
0.105 (1.00) |
0.121 (1.00) |
5.87e-05 (0.0337) |
0.375 (1.00) |
0.158 (1.00) |
0.175 (1.00) |
0.0381 (1.00) |
0.00512 (1.00) |
0.116 (1.00) |
0.00141 (0.714) |
8p gain | 0 (0%) | 479 |
5.42e-05 (0.0312) |
0.0796 (1.00) |
0.0868 (1.00) |
0.146 (1.00) |
0.000978 (0.507) |
0.000683 (0.361) |
0.00302 (1.00) |
0.117 (1.00) |
||
17p gain | 0 (0%) | 477 |
0.00522 (1.00) |
0.00665 (1.00) |
0.000357 (0.196) |
0.42 (1.00) |
0.321 (1.00) |
0.0336 (1.00) |
0.191 (1.00) |
0.0327 (1.00) |
0.726 (1.00) |
0.0488 (1.00) |
19p gain | 0 (0%) | 468 |
0.189 (1.00) |
0.197 (1.00) |
3.37e-05 (0.0196) |
0.34 (1.00) |
0.0448 (1.00) |
0.397 (1.00) |
0.0428 (1.00) |
0.0115 (1.00) |
0.0423 (1.00) |
0.066 (1.00) |
19q gain | 0 (0%) | 465 |
0.0536 (1.00) |
0.0581 (1.00) |
3e-06 (0.00185) |
0.201 (1.00) |
0.056 (1.00) |
0.154 (1.00) |
0.0185 (1.00) |
0.00414 (1.00) |
0.014 (1.00) |
0.066 (1.00) |
21q gain | 0 (0%) | 460 |
0.82 (1.00) |
0.815 (1.00) |
0.000117 (0.0663) |
0.0986 (1.00) |
0.0368 (1.00) |
0.836 (1.00) |
0.0709 (1.00) |
0.08 (1.00) |
0.295 (1.00) |
0.811 (1.00) |
22q gain | 0 (0%) | 468 |
0.58 (1.00) |
0.039 (1.00) |
0.000399 (0.216) |
0.0756 (1.00) |
0.452 (1.00) |
0.217 (1.00) |
0.826 (1.00) |
0.846 (1.00) |
0.965 (1.00) |
0.844 (1.00) |
4q loss | 0 (0%) | 465 |
1 (1.00) |
1 (1.00) |
0.000221 (0.123) |
0.255 (1.00) |
0.251 (1.00) |
0.313 (1.00) |
0.0631 (1.00) |
0.0573 (1.00) |
0.969 (1.00) |
0.371 (1.00) |
10p loss | 0 (0%) | 461 |
0.026 (1.00) |
0.0287 (1.00) |
0.000201 (0.112) |
0.382 (1.00) |
0.195 (1.00) |
0.037 (1.00) |
0.0123 (1.00) |
0.0197 (1.00) |
0.155 (1.00) |
0.00047 (0.252) |
1p gain | 0 (0%) | 488 |
0.627 (1.00) |
0.439 (1.00) |
0.0359 (1.00) |
0.846 (1.00) |
0.85 (1.00) |
0.457 (1.00) |
1 (1.00) |
|||
3p gain | 0 (0%) | 486 |
0.386 (1.00) |
1 (1.00) |
0.102 (1.00) |
0.00329 (1.00) |
0.294 (1.00) |
0.161 (1.00) |
0.0114 (1.00) |
0.0528 (1.00) |
||
4p gain | 0 (0%) | 485 |
0.206 (1.00) |
0.608 (1.00) |
0.428 (1.00) |
0.0803 (1.00) |
0.0257 (1.00) |
0.378 (1.00) |
0.0005 (0.268) |
0.0407 (1.00) |
||
4q gain | 0 (0%) | 485 |
0.67 (1.00) |
0.795 (1.00) |
0.878 (1.00) |
0.338 (1.00) |
0.0112 (1.00) |
0.509 (1.00) |
0.00394 (1.00) |
0.147 (1.00) |
||
6p gain | 0 (0%) | 487 |
0.77 (1.00) |
0.555 (1.00) |
0.819 (1.00) |
0.877 (1.00) |
0.215 (1.00) |
0.449 (1.00) |
0.342 (1.00) |
0.389 (1.00) |
||
6q gain | 0 (0%) | 488 |
0.532 (1.00) |
0.795 (1.00) |
0.571 (1.00) |
0.626 (1.00) |
0.442 (1.00) |
0.571 (1.00) |
0.737 (1.00) |
0.431 (1.00) |
||
9p gain | 0 (0%) | 485 |
0.741 (1.00) |
0.249 (1.00) |
0.17 (1.00) |
0.17 (1.00) |
0.103 (1.00) |
0.0571 (1.00) |
0.902 (1.00) |
0.0306 (1.00) |
||
9q gain | 0 (0%) | 485 |
0.283 (1.00) |
1 (1.00) |
0.104 (1.00) |
0.338 (1.00) |
0.523 (1.00) |
0.636 (1.00) |
0.602 (1.00) |
0.178 (1.00) |
||
10p gain | 0 (0%) | 487 |
0.39 (1.00) |
1 (1.00) |
0.981 (1.00) |
1 (1.00) |
0.267 (1.00) |
0.311 (1.00) |
0.77 (1.00) |
0.389 (1.00) |
||
10q gain | 0 (0%) | 489 |
0.184 (1.00) |
1 (1.00) |
0.716 (1.00) |
0.615 (1.00) |
0.688 (1.00) |
0.508 (1.00) |
0.832 (1.00) |
0.367 (1.00) |
||
11p gain | 0 (0%) | 476 |
0.769 (1.00) |
0.778 (1.00) |
0.000529 (0.283) |
0.771 (1.00) |
0.437 (1.00) |
0.395 (1.00) |
0.491 (1.00) |
0.265 (1.00) |
0.95 (1.00) |
0.41 (1.00) |
11q gain | 0 (0%) | 478 |
0.769 (1.00) |
0.778 (1.00) |
0.00118 (0.601) |
0.698 (1.00) |
0.541 (1.00) |
0.48 (1.00) |
0.586 (1.00) |
0.505 (1.00) |
0.946 (1.00) |
0.355 (1.00) |
13q gain | 0 (0%) | 479 |
0.742 (1.00) |
0.077 (1.00) |
0.467 (1.00) |
0.771 (1.00) |
0.0685 (1.00) |
0.636 (1.00) |
0.614 (1.00) |
0.914 (1.00) |
||
14q gain | 0 (0%) | 488 |
0.0496 (1.00) |
0.608 (1.00) |
0.869 (1.00) |
0.0596 (1.00) |
0.00354 (1.00) |
0.0477 (1.00) |
0.0659 (1.00) |
0.00534 (1.00) |
||
15q gain | 0 (0%) | 479 |
0.0947 (1.00) |
0.578 (1.00) |
0.644 (1.00) |
0.237 (1.00) |
0.116 (1.00) |
0.379 (1.00) |
0.835 (1.00) |
0.503 (1.00) |
||
16p gain | 0 (0%) | 428 |
0.1 (1.00) |
0.212 (1.00) |
0.153 (1.00) |
0.689 (1.00) |
0.0115 (1.00) |
0.0663 (1.00) |
0.635 (1.00) |
0.113 (1.00) |
0.156 (1.00) |
0.598 (1.00) |
16q gain | 0 (0%) | 435 |
0.0706 (1.00) |
0.171 (1.00) |
0.175 (1.00) |
0.909 (1.00) |
0.0443 (1.00) |
0.122 (1.00) |
0.696 (1.00) |
0.336 (1.00) |
0.23 (1.00) |
0.903 (1.00) |
17q gain | 0 (0%) | 471 |
0.00827 (1.00) |
0.0102 (1.00) |
0.00481 (1.00) |
0.119 (1.00) |
0.553 (1.00) |
0.0547 (1.00) |
0.253 (1.00) |
0.00949 (1.00) |
0.417 (1.00) |
0.0225 (1.00) |
18p gain | 0 (0%) | 475 |
0.0764 (1.00) |
0.039 (1.00) |
0.238 (1.00) |
0.153 (1.00) |
0.319 (1.00) |
0.143 (1.00) |
0.0977 (1.00) |
0.41 (1.00) |
0.909 (1.00) |
0.744 (1.00) |
18q gain | 0 (0%) | 475 |
0.0764 (1.00) |
0.039 (1.00) |
0.238 (1.00) |
0.153 (1.00) |
0.319 (1.00) |
0.143 (1.00) |
0.0977 (1.00) |
0.41 (1.00) |
0.909 (1.00) |
0.744 (1.00) |
Xq gain | 0 (0%) | 482 |
0.414 (1.00) |
0.432 (1.00) |
0.639 (1.00) |
0.578 (1.00) |
0.392 (1.00) |
0.483 (1.00) |
0.198 (1.00) |
0.277 (1.00) |
0.363 (1.00) |
0.306 (1.00) |
3q loss | 0 (0%) | 420 |
0.701 (1.00) |
0.7 (1.00) |
0.00144 (0.725) |
0.192 (1.00) |
0.182 (1.00) |
0.00661 (1.00) |
0.518 (1.00) |
0.804 (1.00) |
0.822 (1.00) |
0.00986 (1.00) |
4p loss | 0 (0%) | 458 |
0.289 (1.00) |
0.296 (1.00) |
0.0658 (1.00) |
0.274 (1.00) |
0.816 (1.00) |
0.948 (1.00) |
0.0888 (1.00) |
0.366 (1.00) |
0.513 (1.00) |
0.749 (1.00) |
8p loss | 0 (0%) | 399 |
0.777 (1.00) |
0.781 (1.00) |
0.047 (1.00) |
0.706 (1.00) |
0.724 (1.00) |
0.5 (1.00) |
0.185 (1.00) |
0.633 (1.00) |
0.173 (1.00) |
0.45 (1.00) |
8q loss | 0 (0%) | 456 |
0.49 (1.00) |
0.586 (1.00) |
0.747 (1.00) |
0.255 (1.00) |
0.54 (1.00) |
0.785 (1.00) |
0.112 (1.00) |
0.0266 (1.00) |
0.709 (1.00) |
0.41 (1.00) |
10q loss | 0 (0%) | 445 |
0.0972 (1.00) |
0.119 (1.00) |
0.00263 (1.00) |
0.0409 (1.00) |
0.22 (1.00) |
0.0125 (1.00) |
0.095 (1.00) |
0.126 (1.00) |
0.312 (1.00) |
0.0146 (1.00) |
11p loss | 0 (0%) | 488 |
0.121 (1.00) |
0.608 (1.00) |
0.156 (1.00) |
0.0359 (1.00) |
0.359 (1.00) |
0.462 (1.00) |
0.545 (1.00) |
0.0879 (1.00) |
||
11q loss | 0 (0%) | 486 |
0.0527 (1.00) |
0.826 (1.00) |
0.0533 (1.00) |
0.215 (1.00) |
0.377 (1.00) |
0.311 (1.00) |
0.349 (1.00) |
0.0298 (1.00) |
||
15q loss | 0 (0%) | 481 |
0.58 (1.00) |
0.584 (1.00) |
0.0213 (1.00) |
0.373 (1.00) |
0.451 (1.00) |
0.704 (1.00) |
0.0733 (1.00) |
0.136 (1.00) |
0.232 (1.00) |
1 (1.00) |
16q loss | 0 (0%) | 488 |
0.0135 (1.00) |
0.167 (1.00) |
0.456 (1.00) |
1 (1.00) |
0.292 (1.00) |
0.832 (1.00) |
0.262 (1.00) |
|||
19p loss | 0 (0%) | 489 |
0.184 (1.00) |
0.332 (1.00) |
0.279 (1.00) |
0.0359 (1.00) |
0.341 (1.00) |
0.379 (1.00) |
0.832 (1.00) |
0.262 (1.00) |
||
20p loss | 0 (0%) | 487 |
0.0475 (1.00) |
1 (1.00) |
0.0172 (1.00) |
0.877 (1.00) |
0.267 (1.00) |
0.747 (1.00) |
0.0721 (1.00) |
0.232 (1.00) |
||
22q loss | 0 (0%) | 482 |
0.00501 (1.00) |
0.161 (1.00) |
0.0462 (1.00) |
0.393 (1.00) |
0.000888 (0.463) |
0.0191 (1.00) |
0.363 (1.00) |
0.531 (1.00) |
||
Xq loss | 0 (0%) | 486 |
0.0394 (1.00) |
0.0772 (1.00) |
0.308 (1.00) |
0.826 (1.00) |
0.381 (1.00) |
0.564 (1.00) |
0.0676 (1.00) |
0.00763 (1.00) |
0.0269 (1.00) |
0.00846 (1.00) |
P value = 1.05e-05 (Fisher's exact test), Q value = 0.0063
Table S1. Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
1Q GAIN CNV | 21 | 6 | 5 |
1Q GAIN WILD-TYPE | 111 | 191 | 159 |
Figure S1. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D2V3.png)
P value = 1.08e-06 (Fisher's exact test), Q value = 0.00067
Table S2. Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
2P GAIN CNV | 29 | 9 | 10 |
2P GAIN WILD-TYPE | 103 | 188 | 154 |
Figure S2. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D3V3.png)
P value = 4.9e-05 (Fisher's exact test), Q value = 0.028
Table S3. Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
2Q GAIN CNV | 27 | 12 | 10 |
2Q GAIN WILD-TYPE | 105 | 185 | 154 |
Figure S3. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D4V3.png)
P value = 6.58e-05 (Fisher's exact test), Q value = 0.038
Table S4. Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
3Q GAIN CNV | 16 | 2 | 9 |
3Q GAIN WILD-TYPE | 116 | 195 | 155 |
Figure S4. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D6V3.png)
P value = 0.000107 (Fisher's exact test), Q value = 0.061
Table S5. Gene #6: '3q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 152 | 109 |
3Q GAIN CNV | 3 | 8 | 15 |
3Q GAIN WILD-TYPE | 183 | 144 | 94 |
Figure S5. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D6V6.png)
P value = 0.000395 (Fisher's exact test), Q value = 0.21
Table S6. Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
3Q GAIN CNV | 4 | 20 | 3 |
3Q GAIN WILD-TYPE | 193 | 159 | 94 |
Figure S6. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D6V7.png)
P value = 0.000339 (Fisher's exact test), Q value = 0.19
Table S7. Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 191 | 169 |
3Q GAIN CNV | 5 | 3 | 19 |
3Q GAIN WILD-TYPE | 110 | 188 | 150 |
Figure S7. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D6V9.png)
P value = 1.25e-05 (Fisher's exact test), Q value = 0.0075
Table S8. Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
5P GAIN CNV | 58 | 52 | 31 |
5P GAIN WILD-TYPE | 74 | 145 | 133 |
Figure S8. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D9V3.png)
P value = 5.87e-05 (Fisher's exact test), Q value = 0.034
Table S9. Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
5Q GAIN CNV | 59 | 63 | 34 |
5Q GAIN WILD-TYPE | 73 | 134 | 130 |
Figure S9. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D10V3.png)
P value = 5.05e-06 (Fisher's exact test), Q value = 0.0031
Table S10. Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
7P GAIN CNV | 55 | 34 | 38 |
7P GAIN WILD-TYPE | 77 | 163 | 126 |
Figure S10. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D13V3.png)
P value = 0.000268 (Chi-square test), Q value = 0.15
Table S11. Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 100 | 88 | 84 | 75 | 43 | 57 |
7P GAIN CNV | 18 | 11 | 26 | 31 | 11 | 19 |
7P GAIN WILD-TYPE | 82 | 77 | 58 | 44 | 32 | 38 |
Figure S11. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D13V5.png)
P value = 1.36e-05 (Fisher's exact test), Q value = 0.0081
Table S12. Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
7Q GAIN CNV | 54 | 34 | 41 |
7Q GAIN WILD-TYPE | 78 | 163 | 123 |
Figure S12. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D14V3.png)
P value = 0.000118 (Chi-square test), Q value = 0.067
Table S13. Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 100 | 88 | 84 | 75 | 43 | 57 |
7Q GAIN CNV | 17 | 12 | 27 | 31 | 10 | 21 |
7Q GAIN WILD-TYPE | 83 | 76 | 57 | 44 | 33 | 36 |
Figure S13. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D14V5.png)
P value = 5.42e-05 (Fisher's exact test), Q value = 0.031
Table S14. Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
8P GAIN CNV | 10 | 0 | 4 |
8P GAIN WILD-TYPE | 122 | 197 | 160 |
Figure S14. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D15V3.png)
P value = 2.75e-07 (Fisher's exact test), Q value = 0.00017
Table S15. Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
8Q GAIN CNV | 19 | 1 | 14 |
8Q GAIN WILD-TYPE | 113 | 196 | 150 |
Figure S15. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D16V3.png)
P value = 1.15e-07 (Fisher's exact test), Q value = 7.3e-05
Table S16. Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
8Q GAIN CNV | 1 | 25 | 5 |
8Q GAIN WILD-TYPE | 196 | 154 | 92 |
Figure S16. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D16V7.png)
P value = 4.88e-05 (Fisher's exact test), Q value = 0.028
Table S17. Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
8Q GAIN CNV | 3 | 4 | 24 |
8Q GAIN WILD-TYPE | 66 | 210 | 166 |
Figure S17. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D16V8.png)
P value = 6.77e-06 (Fisher's exact test), Q value = 0.0041
Table S18. Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 191 | 169 |
8Q GAIN CNV | 6 | 3 | 24 |
8Q GAIN WILD-TYPE | 109 | 188 | 145 |
Figure S18. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D16V9.png)
P value = 7.99e-07 (Fisher's exact test), Q value = 5e-04
Table S19. Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
12P GAIN CNV | 37 | 13 | 28 |
12P GAIN WILD-TYPE | 95 | 184 | 136 |
Figure S19. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D23V3.png)
P value = 5.67e-07 (Chi-square test), Q value = 0.00035
Table S20. Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 100 | 88 | 84 | 75 | 43 | 57 |
12P GAIN CNV | 4 | 9 | 20 | 9 | 6 | 21 |
12P GAIN WILD-TYPE | 96 | 79 | 64 | 66 | 37 | 36 |
Figure S20. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D23V5.png)
P value = 1.1e-05 (Fisher's exact test), Q value = 0.0066
Table S21. Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
12P GAIN CNV | 15 | 45 | 12 |
12P GAIN WILD-TYPE | 182 | 134 | 85 |
Figure S21. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D23V7.png)
P value = 1.89e-05 (Fisher's exact test), Q value = 0.011
Table S22. Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
12P GAIN CNV | 7 | 18 | 47 |
12P GAIN WILD-TYPE | 62 | 196 | 143 |
Figure S22. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D23V8.png)
P value = 6.95e-06 (Fisher's exact test), Q value = 0.0042
Table S23. Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 191 | 169 |
12P GAIN CNV | 13 | 18 | 47 |
12P GAIN WILD-TYPE | 102 | 173 | 122 |
Figure S23. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D23V9.png)
P value = 7.99e-07 (Fisher's exact test), Q value = 5e-04
Table S24. Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
12Q GAIN CNV | 37 | 13 | 28 |
12Q GAIN WILD-TYPE | 95 | 184 | 136 |
Figure S24. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D24V3.png)
P value = 5.67e-07 (Chi-square test), Q value = 0.00035
Table S25. Gene #24: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 100 | 88 | 84 | 75 | 43 | 57 |
12Q GAIN CNV | 4 | 9 | 20 | 9 | 6 | 21 |
12Q GAIN WILD-TYPE | 96 | 79 | 64 | 66 | 37 | 36 |
Figure S25. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D24V5.png)
P value = 1.1e-05 (Fisher's exact test), Q value = 0.0066
Table S26. Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
12Q GAIN CNV | 15 | 45 | 12 |
12Q GAIN WILD-TYPE | 182 | 134 | 85 |
Figure S26. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D24V7.png)
P value = 1.89e-05 (Fisher's exact test), Q value = 0.011
Table S27. Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
12Q GAIN CNV | 7 | 18 | 47 |
12Q GAIN WILD-TYPE | 62 | 196 | 143 |
Figure S27. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D24V8.png)
P value = 6.95e-06 (Fisher's exact test), Q value = 0.0042
Table S28. Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 191 | 169 |
12Q GAIN CNV | 13 | 18 | 47 |
12Q GAIN WILD-TYPE | 102 | 173 | 122 |
Figure S28. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D24V9.png)
P value = 0.000357 (Fisher's exact test), Q value = 0.2
Table S29. Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
17P GAIN CNV | 6 | 0 | 10 |
17P GAIN WILD-TYPE | 126 | 197 | 154 |
Figure S29. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D30V3.png)
P value = 3.37e-05 (Fisher's exact test), Q value = 0.02
Table S30. Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
19P GAIN CNV | 14 | 1 | 10 |
19P GAIN WILD-TYPE | 118 | 196 | 154 |
Figure S30. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D34V3.png)
P value = 3e-06 (Fisher's exact test), Q value = 0.0019
Table S31. Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
19Q GAIN CNV | 17 | 1 | 10 |
19Q GAIN WILD-TYPE | 115 | 196 | 154 |
Figure S31. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D35V3.png)
P value = 1.05e-12 (Fisher's exact test), Q value = 6.9e-10
Table S32. Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
20P GAIN CNV | 36 | 3 | 27 |
20P GAIN WILD-TYPE | 96 | 194 | 137 |
Figure S32. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D36V3.png)
P value = 0.000453 (Chi-square test), Q value = 0.24
Table S33. Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 100 | 88 | 84 | 75 | 43 | 57 |
20P GAIN CNV | 4 | 9 | 13 | 15 | 4 | 16 |
20P GAIN WILD-TYPE | 96 | 79 | 71 | 60 | 39 | 41 |
Figure S33. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D36V5.png)
P value = 3.59e-06 (Fisher's exact test), Q value = 0.0022
Table S34. Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
20P GAIN CNV | 12 | 42 | 10 |
20P GAIN WILD-TYPE | 185 | 137 | 87 |
Figure S34. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D36V7.png)
P value = 5.29e-06 (Fisher's exact test), Q value = 0.0032
Table S35. Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
20P GAIN CNV | 8 | 13 | 43 |
20P GAIN WILD-TYPE | 61 | 201 | 147 |
Figure S35. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D36V8.png)
P value = 2.54e-06 (Fisher's exact test), Q value = 0.0016
Table S36. Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 191 | 169 |
20P GAIN CNV | 11 | 13 | 42 |
20P GAIN WILD-TYPE | 104 | 178 | 127 |
Figure S36. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D36V9.png)
P value = 6.23e-14 (Fisher's exact test), Q value = 4.1e-11
Table S37. Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
20Q GAIN CNV | 39 | 3 | 26 |
20Q GAIN WILD-TYPE | 93 | 194 | 138 |
Figure S37. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D37V3.png)
P value = 3.54e-05 (Chi-square test), Q value = 0.021
Table S38. Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 100 | 88 | 84 | 75 | 43 | 57 |
20Q GAIN CNV | 4 | 8 | 14 | 15 | 4 | 18 |
20Q GAIN WILD-TYPE | 96 | 80 | 70 | 60 | 39 | 39 |
Figure S38. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D37V5.png)
P value = 3.3e-07 (Fisher's exact test), Q value = 0.00021
Table S39. Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
20Q GAIN CNV | 12 | 45 | 9 |
20Q GAIN WILD-TYPE | 185 | 134 | 88 |
Figure S39. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D37V7.png)
P value = 1.47e-06 (Fisher's exact test), Q value = 0.00091
Table S40. Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
20Q GAIN CNV | 8 | 13 | 45 |
20Q GAIN WILD-TYPE | 61 | 201 | 145 |
Figure S40. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D37V8.png)
P value = 1.83e-07 (Fisher's exact test), Q value = 0.00012
Table S41. Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 191 | 169 |
20Q GAIN CNV | 10 | 13 | 45 |
20Q GAIN WILD-TYPE | 105 | 178 | 124 |
Figure S41. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D37V9.png)
P value = 0.000117 (Fisher's exact test), Q value = 0.066
Table S42. Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
21Q GAIN CNV | 20 | 6 | 7 |
21Q GAIN WILD-TYPE | 112 | 191 | 157 |
Figure S42. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D38V3.png)
P value = 0.000399 (Fisher's exact test), Q value = 0.22
Table S43. Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
22Q GAIN CNV | 15 | 3 | 7 |
22Q GAIN WILD-TYPE | 117 | 194 | 157 |
Figure S43. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D39V3.png)
P value = 6.2e-05 (Fisher's exact test), Q value = 0.036
Table S44. Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 14 | 23 | 33 |
1P LOSS CNV | 8 | 1 | 2 |
1P LOSS WILD-TYPE | 6 | 22 | 31 |
Figure S44. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D41V2.png)
P value = 5.05e-08 (Chi-square test), Q value = 3.2e-05
Table S45. Gene #41: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 100 | 88 | 84 | 75 | 43 | 57 |
1P LOSS CNV | 3 | 1 | 3 | 16 | 3 | 0 |
1P LOSS WILD-TYPE | 97 | 87 | 81 | 59 | 40 | 57 |
Figure S45. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D41V5.png)
P value = 0.000435 (Fisher's exact test), Q value = 0.24
Table S46. Gene #41: '1p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 152 | 109 |
1P LOSS CNV | 10 | 2 | 14 |
1P LOSS WILD-TYPE | 176 | 150 | 95 |
Figure S46. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D41V6.png)
P value = 4.64e-06 (Fisher's exact test), Q value = 0.0028
Table S47. Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
1P LOSS CNV | 15 | 9 | 6 |
1P LOSS WILD-TYPE | 54 | 205 | 184 |
Figure S47. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D41V8.png)
P value = 1.01e-10 (Fisher's exact test), Q value = 6.5e-08
Table S48. Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 35 | 160 | 280 |
1P LOSS CNV | 15 | 4 | 13 |
1P LOSS WILD-TYPE | 20 | 156 | 267 |
Figure S48. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D41V10.png)
P value = 2.09e-05 (Fisher's exact test), Q value = 0.012
Table S49. Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
1Q LOSS CNV | 2 | 2 | 17 |
1Q LOSS WILD-TYPE | 130 | 195 | 147 |
Figure S49. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D42V3.png)
P value = 0.000168 (Chi-square test), Q value = 0.094
Table S50. Gene #42: '1q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 100 | 88 | 84 | 75 | 43 | 57 |
1Q LOSS CNV | 3 | 0 | 1 | 10 | 2 | 1 |
1Q LOSS WILD-TYPE | 97 | 88 | 83 | 65 | 41 | 56 |
Figure S50. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D42V5.png)
P value = 6.65e-05 (Fisher's exact test), Q value = 0.038
Table S51. Gene #42: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
1Q LOSS CNV | 5 | 3 | 13 |
1Q LOSS WILD-TYPE | 192 | 176 | 84 |
Figure S51. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D42V7.png)
P value = 6.27e-07 (Fisher's exact test), Q value = 0.00039
Table S52. Gene #42: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
1Q LOSS CNV | 13 | 5 | 3 |
1Q LOSS WILD-TYPE | 56 | 209 | 187 |
Figure S52. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D42V8.png)
P value = 2.88e-11 (Fisher's exact test), Q value = 1.9e-08
Table S53. Gene #42: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 35 | 160 | 280 |
1Q LOSS CNV | 13 | 3 | 5 |
1Q LOSS WILD-TYPE | 22 | 157 | 275 |
Figure S53. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D42V10.png)
P value = 0.000249 (Fisher's exact test), Q value = 0.14
Table S54. Gene #43: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 33 | 24 | 13 |
2P LOSS CNV | 0 | 1 | 5 |
2P LOSS WILD-TYPE | 33 | 23 | 8 |
Figure S54. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D43V1.png)
P value = 0.000374 (Fisher's exact test), Q value = 0.2
Table S55. Gene #43: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 14 | 23 | 33 |
2P LOSS CNV | 5 | 1 | 0 |
2P LOSS WILD-TYPE | 9 | 22 | 33 |
Figure S55. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D43V2.png)
P value = 1.52e-05 (Fisher's exact test), Q value = 0.009
Table S56. Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
2P LOSS CNV | 0 | 0 | 10 |
2P LOSS WILD-TYPE | 132 | 197 | 154 |
Figure S56. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D43V3.png)
P value = 1.37e-05 (Chi-square test), Q value = 0.0081
Table S57. Gene #43: '2p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 100 | 88 | 84 | 75 | 43 | 57 |
2P LOSS CNV | 0 | 0 | 0 | 6 | 0 | 0 |
2P LOSS WILD-TYPE | 100 | 88 | 84 | 69 | 43 | 57 |
Figure S57. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D43V5.png)
P value = 0.000189 (Fisher's exact test), Q value = 0.11
Table S58. Gene #43: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 152 | 109 |
2P LOSS CNV | 0 | 0 | 6 |
2P LOSS WILD-TYPE | 186 | 152 | 103 |
Figure S58. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D43V6.png)
P value = 4.72e-07 (Fisher's exact test), Q value = 3e-04
Table S59. Gene #43: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
2P LOSS CNV | 0 | 0 | 9 |
2P LOSS WILD-TYPE | 197 | 179 | 88 |
Figure S59. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D43V7.png)
P value = 1.87e-08 (Fisher's exact test), Q value = 1.2e-05
Table S60. Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
2P LOSS CNV | 9 | 0 | 0 |
2P LOSS WILD-TYPE | 60 | 214 | 190 |
Figure S60. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D43V8.png)
P value = 1.25e-12 (Fisher's exact test), Q value = 8.3e-10
Table S61. Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 35 | 160 | 280 |
2P LOSS CNV | 10 | 0 | 0 |
2P LOSS WILD-TYPE | 25 | 160 | 280 |
Figure S61. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D43V10.png)
P value = 0.000249 (Fisher's exact test), Q value = 0.14
Table S62. Gene #44: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 33 | 24 | 13 |
2Q LOSS CNV | 0 | 1 | 5 |
2Q LOSS WILD-TYPE | 33 | 23 | 8 |
Figure S62. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D44V1.png)
P value = 0.000374 (Fisher's exact test), Q value = 0.2
Table S63. Gene #44: '2q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 14 | 23 | 33 |
2Q LOSS CNV | 5 | 1 | 0 |
2Q LOSS WILD-TYPE | 9 | 22 | 33 |
Figure S63. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D44V2.png)
P value = 4.75e-06 (Fisher's exact test), Q value = 0.0029
Table S64. Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
2Q LOSS CNV | 0 | 0 | 11 |
2Q LOSS WILD-TYPE | 132 | 197 | 153 |
Figure S64. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D44V3.png)
P value = 0.000129 (Chi-square test), Q value = 0.073
Table S65. Gene #44: '2q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 100 | 88 | 84 | 75 | 43 | 57 |
2Q LOSS CNV | 0 | 0 | 0 | 6 | 0 | 1 |
2Q LOSS WILD-TYPE | 100 | 88 | 84 | 69 | 43 | 56 |
Figure S65. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D44V5.png)
P value = 4.42e-05 (Fisher's exact test), Q value = 0.026
Table S66. Gene #44: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 152 | 109 |
2Q LOSS CNV | 0 | 0 | 7 |
2Q LOSS WILD-TYPE | 186 | 152 | 102 |
Figure S66. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D44V6.png)
P value = 8.96e-08 (Fisher's exact test), Q value = 5.7e-05
Table S67. Gene #44: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
2Q LOSS CNV | 0 | 0 | 10 |
2Q LOSS WILD-TYPE | 197 | 179 | 87 |
Figure S67. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D44V7.png)
P value = 7.91e-08 (Fisher's exact test), Q value = 5e-05
Table S68. Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
2Q LOSS CNV | 9 | 0 | 1 |
2Q LOSS WILD-TYPE | 60 | 214 | 189 |
Figure S68. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D44V8.png)
P value = 0.000199 (Fisher's exact test), Q value = 0.11
Table S69. Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 191 | 169 |
2Q LOSS CNV | 1 | 0 | 10 |
2Q LOSS WILD-TYPE | 114 | 191 | 159 |
Figure S69. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D44V9.png)
P value = 4.81e-12 (Fisher's exact test), Q value = 3.1e-09
Table S70. Gene #44: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 35 | 160 | 280 |
2Q LOSS CNV | 10 | 1 | 0 |
2Q LOSS WILD-TYPE | 25 | 159 | 280 |
Figure S70. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D44V10.png)
P value = 6.37e-24 (Fisher's exact test), Q value = 4.2e-21
Table S71. Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
3P LOSS CNV | 107 | 148 | 49 |
3P LOSS WILD-TYPE | 25 | 49 | 115 |
Figure S71. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D45V3.png)
P value = 0.00012 (Chi-square test), Q value = 0.068
Table S72. Gene #45: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 100 | 88 | 84 | 75 | 43 | 57 |
3P LOSS CNV | 77 | 47 | 54 | 40 | 33 | 26 |
3P LOSS WILD-TYPE | 23 | 41 | 30 | 35 | 10 | 31 |
Figure S72. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D45V5.png)
P value = 1.78e-05 (Fisher's exact test), Q value = 0.01
Table S73. Gene #45: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 152 | 109 |
3P LOSS CNV | 130 | 100 | 47 |
3P LOSS WILD-TYPE | 56 | 52 | 62 |
Figure S73. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D45V6.png)
P value = 3.85e-11 (Fisher's exact test), Q value = 2.5e-08
Table S74. Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
3P LOSS CNV | 154 | 95 | 39 |
3P LOSS WILD-TYPE | 43 | 84 | 58 |
Figure S74. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D45V7.png)
P value = 7.09e-10 (Fisher's exact test), Q value = 4.6e-07
Table S75. Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
3P LOSS CNV | 23 | 160 | 105 |
3P LOSS WILD-TYPE | 46 | 54 | 85 |
Figure S75. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D45V8.png)
P value = 4.23e-05 (Fisher's exact test), Q value = 0.024
Table S76. Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 191 | 169 |
3P LOSS CNV | 63 | 140 | 88 |
3P LOSS WILD-TYPE | 52 | 51 | 81 |
Figure S76. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D45V9.png)
P value = 5.08e-14 (Fisher's exact test), Q value = 3.4e-11
Table S77. Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 35 | 160 | 280 |
3P LOSS CNV | 7 | 75 | 209 |
3P LOSS WILD-TYPE | 28 | 85 | 71 |
Figure S77. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D45V10.png)
P value = 0.000221 (Fisher's exact test), Q value = 0.12
Table S78. Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
4Q LOSS CNV | 16 | 3 | 9 |
4Q LOSS WILD-TYPE | 116 | 194 | 155 |
Figure S78. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D48V3.png)
P value = 4.27e-12 (Fisher's exact test), Q value = 2.8e-09
Table S79. Gene #49: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
6P LOSS CNV | 37 | 4 | 17 |
6P LOSS WILD-TYPE | 95 | 193 | 147 |
Figure S79. Get High-res Image Gene #49: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D49V3.png)
P value = 0.000122 (Chi-square test), Q value = 0.068
Table S80. Gene #49: '6p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 100 | 88 | 84 | 75 | 43 | 57 |
6P LOSS CNV | 10 | 3 | 9 | 14 | 1 | 15 |
6P LOSS WILD-TYPE | 90 | 85 | 75 | 61 | 42 | 42 |
Figure S80. Get High-res Image Gene #49: '6p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D49V5.png)
P value = 7.03e-06 (Fisher's exact test), Q value = 0.0042
Table S81. Gene #49: '6p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 152 | 109 |
6P LOSS CNV | 8 | 19 | 25 |
6P LOSS WILD-TYPE | 178 | 133 | 84 |
Figure S81. Get High-res Image Gene #49: '6p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D49V6.png)
P value = 2.87e-09 (Fisher's exact test), Q value = 1.8e-06
Table S82. Gene #49: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 191 | 169 |
6P LOSS CNV | 3 | 12 | 41 |
6P LOSS WILD-TYPE | 112 | 179 | 128 |
Figure S82. Get High-res Image Gene #49: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D49V9.png)
P value = 0.000394 (Fisher's exact test), Q value = 0.21
Table S83. Gene #49: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 35 | 160 | 280 |
6P LOSS CNV | 12 | 19 | 25 |
6P LOSS WILD-TYPE | 23 | 141 | 255 |
Figure S83. Get High-res Image Gene #49: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D49V10.png)
P value = 6.34e-17 (Fisher's exact test), Q value = 4.2e-14
Table S84. Gene #50: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
6Q LOSS CNV | 54 | 9 | 19 |
6Q LOSS WILD-TYPE | 78 | 188 | 145 |
Figure S84. Get High-res Image Gene #50: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D50V3.png)
P value = 1.42e-05 (Fisher's exact test), Q value = 0.0084
Table S85. Gene #50: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 191 | 169 |
6Q LOSS CNV | 8 | 26 | 46 |
6Q LOSS WILD-TYPE | 107 | 165 | 123 |
Figure S85. Get High-res Image Gene #50: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D50V9.png)
P value = 9.23e-25 (Fisher's exact test), Q value = 6.2e-22
Table S86. Gene #53: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
9P LOSS CNV | 60 | 3 | 24 |
9P LOSS WILD-TYPE | 72 | 194 | 140 |
Figure S86. Get High-res Image Gene #53: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D53V3.png)
P value = 3.57e-12 (Fisher's exact test), Q value = 2.3e-09
Table S87. Gene #53: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 96 | 118 | 64 |
9P LOSS CNV | 38 | 3 | 10 |
9P LOSS WILD-TYPE | 58 | 115 | 54 |
Figure S87. Get High-res Image Gene #53: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D53V4.png)
P value = 1.39e-11 (Fisher's exact test), Q value = 9.1e-09
Table S88. Gene #53: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
9P LOSS CNV | 14 | 60 | 9 |
9P LOSS WILD-TYPE | 183 | 119 | 88 |
Figure S88. Get High-res Image Gene #53: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D53V7.png)
P value = 2.71e-12 (Fisher's exact test), Q value = 1.8e-09
Table S89. Gene #53: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
9P LOSS CNV | 5 | 15 | 63 |
9P LOSS WILD-TYPE | 64 | 199 | 127 |
Figure S89. Get High-res Image Gene #53: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D53V8.png)
P value = 8.73e-09 (Fisher's exact test), Q value = 5.6e-06
Table S90. Gene #53: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 191 | 169 |
9P LOSS CNV | 13 | 17 | 55 |
9P LOSS WILD-TYPE | 102 | 174 | 114 |
Figure S90. Get High-res Image Gene #53: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D53V9.png)
P value = 4.43e-26 (Fisher's exact test), Q value = 3e-23
Table S91. Gene #54: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
9Q LOSS CNV | 64 | 4 | 24 |
9Q LOSS WILD-TYPE | 68 | 193 | 140 |
Figure S91. Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D54V3.png)
P value = 4.3e-13 (Fisher's exact test), Q value = 2.8e-10
Table S92. Gene #54: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 96 | 118 | 64 |
9Q LOSS CNV | 40 | 3 | 10 |
9Q LOSS WILD-TYPE | 56 | 115 | 54 |
Figure S92. Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D54V4.png)
P value = 1.31e-12 (Fisher's exact test), Q value = 8.7e-10
Table S93. Gene #54: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
9Q LOSS CNV | 15 | 64 | 9 |
9Q LOSS WILD-TYPE | 182 | 115 | 88 |
Figure S93. Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D54V7.png)
P value = 3.94e-14 (Fisher's exact test), Q value = 2.6e-11
Table S94. Gene #54: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
9Q LOSS CNV | 5 | 15 | 68 |
9Q LOSS WILD-TYPE | 64 | 199 | 122 |
Figure S94. Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D54V8.png)
P value = 3.82e-10 (Fisher's exact test), Q value = 2.5e-07
Table S95. Gene #54: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 191 | 169 |
9Q LOSS CNV | 13 | 17 | 59 |
9Q LOSS WILD-TYPE | 102 | 174 | 110 |
Figure S95. Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D54V9.png)
P value = 0.000201 (Fisher's exact test), Q value = 0.11
Table S96. Gene #55: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
10P LOSS CNV | 10 | 3 | 19 |
10P LOSS WILD-TYPE | 122 | 194 | 145 |
Figure S96. Get High-res Image Gene #55: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D55V3.png)
P value = 6.36e-05 (Fisher's exact test), Q value = 0.036
Table S97. Gene #59: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
13Q LOSS CNV | 14 | 2 | 15 |
13Q LOSS WILD-TYPE | 118 | 195 | 149 |
Figure S97. Get High-res Image Gene #59: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D59V3.png)
P value = 0.00046 (Fisher's exact test), Q value = 0.25
Table S98. Gene #59: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
13Q LOSS CNV | 7 | 4 | 19 |
13Q LOSS WILD-TYPE | 62 | 210 | 171 |
Figure S98. Get High-res Image Gene #59: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D59V8.png)
P value = 0.000285 (Fisher's exact test), Q value = 0.16
Table S99. Gene #59: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 35 | 160 | 280 |
13Q LOSS CNV | 7 | 15 | 9 |
13Q LOSS WILD-TYPE | 28 | 145 | 271 |
Figure S99. Get High-res Image Gene #59: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D59V10.png)
P value = 2.02e-10 (Fisher's exact test), Q value = 1.3e-07
Table S100. Gene #60: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
14Q LOSS CNV | 73 | 41 | 44 |
14Q LOSS WILD-TYPE | 59 | 156 | 120 |
Figure S100. Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D60V3.png)
P value = 3.06e-05 (Fisher's exact test), Q value = 0.018
Table S101. Gene #60: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 96 | 118 | 64 |
14Q LOSS CNV | 43 | 20 | 23 |
14Q LOSS WILD-TYPE | 53 | 98 | 41 |
Figure S101. Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D60V4.png)
P value = 6.61e-12 (Chi-square test), Q value = 4.3e-09
Table S102. Gene #60: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 100 | 88 | 84 | 75 | 43 | 57 |
14Q LOSS CNV | 20 | 18 | 54 | 18 | 11 | 28 |
14Q LOSS WILD-TYPE | 80 | 70 | 30 | 57 | 32 | 29 |
Figure S102. Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D60V5.png)
P value = 2.08e-07 (Fisher's exact test), Q value = 0.00013
Table S103. Gene #60: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 152 | 109 |
14Q LOSS CNV | 37 | 73 | 39 |
14Q LOSS WILD-TYPE | 149 | 79 | 70 |
Figure S103. Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D60V6.png)
P value = 6.97e-11 (Fisher's exact test), Q value = 4.5e-08
Table S104. Gene #60: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
14Q LOSS CNV | 54 | 88 | 11 |
14Q LOSS WILD-TYPE | 143 | 91 | 86 |
Figure S104. Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D60V7.png)
P value = 2.8e-07 (Fisher's exact test), Q value = 0.00018
Table S105. Gene #60: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
14Q LOSS CNV | 8 | 60 | 85 |
14Q LOSS WILD-TYPE | 61 | 154 | 105 |
Figure S105. Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D60V8.png)
P value = 4.33e-06 (Fisher's exact test), Q value = 0.0026
Table S106. Gene #60: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 191 | 169 |
14Q LOSS CNV | 25 | 50 | 79 |
14Q LOSS WILD-TYPE | 90 | 141 | 90 |
Figure S106. Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D60V9.png)
P value = 0.000117 (Fisher's exact test), Q value = 0.066
Table S107. Gene #63: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 33 | 24 | 13 |
17P LOSS CNV | 0 | 3 | 6 |
17P LOSS WILD-TYPE | 33 | 21 | 7 |
Figure S107. Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D63V1.png)
P value = 0.000178 (Fisher's exact test), Q value = 0.1
Table S108. Gene #63: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 14 | 23 | 33 |
17P LOSS CNV | 6 | 3 | 0 |
17P LOSS WILD-TYPE | 8 | 20 | 33 |
Figure S108. Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D63V2.png)
P value = 4.3e-06 (Fisher's exact test), Q value = 0.0026
Table S109. Gene #63: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
17P LOSS CNV | 12 | 0 | 13 |
17P LOSS WILD-TYPE | 120 | 197 | 151 |
Figure S109. Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D63V3.png)
P value = 2.92e-05 (Chi-square test), Q value = 0.017
Table S110. Gene #63: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 100 | 88 | 84 | 75 | 43 | 57 |
17P LOSS CNV | 1 | 1 | 2 | 10 | 0 | 7 |
17P LOSS WILD-TYPE | 99 | 87 | 82 | 65 | 43 | 50 |
Figure S110. Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D63V5.png)
P value = 5.18e-06 (Fisher's exact test), Q value = 0.0031
Table S111. Gene #63: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 152 | 109 |
17P LOSS CNV | 2 | 4 | 15 |
17P LOSS WILD-TYPE | 184 | 148 | 94 |
Figure S111. Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D63V6.png)
P value = 1.9e-06 (Fisher's exact test), Q value = 0.0012
Table S112. Gene #63: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
17P LOSS CNV | 0 | 12 | 11 |
17P LOSS WILD-TYPE | 197 | 167 | 86 |
Figure S112. Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D63V7.png)
P value = 1.5e-08 (Fisher's exact test), Q value = 9.6e-06
Table S113. Gene #63: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
17P LOSS CNV | 12 | 0 | 11 |
17P LOSS WILD-TYPE | 57 | 214 | 179 |
Figure S113. Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D63V8.png)
P value = 4.9e-07 (Fisher's exact test), Q value = 0.00031
Table S114. Gene #63: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 191 | 169 |
17P LOSS CNV | 3 | 1 | 21 |
17P LOSS WILD-TYPE | 112 | 190 | 148 |
Figure S114. Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D63V9.png)
P value = 8.54e-09 (Fisher's exact test), Q value = 5.5e-06
Table S115. Gene #63: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 35 | 160 | 280 |
17P LOSS CNV | 12 | 7 | 6 |
17P LOSS WILD-TYPE | 23 | 153 | 274 |
Figure S115. Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D63V10.png)
P value = 0.000224 (Fisher's exact test), Q value = 0.12
Table S116. Gene #64: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
17Q LOSS CNV | 2 | 0 | 10 |
17Q LOSS WILD-TYPE | 130 | 197 | 154 |
Figure S116. Get High-res Image Gene #64: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D64V3.png)
P value = 1.46e-05 (Chi-square test), Q value = 0.0086
Table S117. Gene #64: '17q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 100 | 88 | 84 | 75 | 43 | 57 |
17Q LOSS CNV | 0 | 0 | 0 | 7 | 0 | 1 |
17Q LOSS WILD-TYPE | 100 | 88 | 84 | 68 | 43 | 56 |
Figure S117. Get High-res Image Gene #64: '17q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D64V5.png)
P value = 1.02e-05 (Fisher's exact test), Q value = 0.0061
Table S118. Gene #64: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 152 | 109 |
17Q LOSS CNV | 0 | 0 | 8 |
17Q LOSS WILD-TYPE | 186 | 152 | 101 |
Figure S118. Get High-res Image Gene #64: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D64V6.png)
P value = 1.91e-06 (Fisher's exact test), Q value = 0.0012
Table S119. Gene #64: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
17Q LOSS CNV | 0 | 1 | 9 |
17Q LOSS WILD-TYPE | 197 | 178 | 88 |
Figure S119. Get High-res Image Gene #64: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D64V7.png)
P value = 7.91e-08 (Fisher's exact test), Q value = 5e-05
Table S120. Gene #64: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
17Q LOSS CNV | 9 | 0 | 1 |
17Q LOSS WILD-TYPE | 60 | 214 | 189 |
Figure S120. Get High-res Image Gene #64: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D64V8.png)
P value = 8.98e-05 (Fisher's exact test), Q value = 0.051
Table S121. Gene #64: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 191 | 169 |
17Q LOSS CNV | 1 | 0 | 11 |
17Q LOSS WILD-TYPE | 114 | 191 | 158 |
Figure S121. Get High-res Image Gene #64: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D64V9.png)
P value = 4.05e-11 (Fisher's exact test), Q value = 2.6e-08
Table S122. Gene #64: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 35 | 160 | 280 |
17Q LOSS CNV | 10 | 0 | 2 |
17Q LOSS WILD-TYPE | 25 | 160 | 278 |
Figure S122. Get High-res Image Gene #64: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D64V10.png)
P value = 3.02e-06 (Fisher's exact test), Q value = 0.0019
Table S123. Gene #65: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
18P LOSS CNV | 26 | 6 | 14 |
18P LOSS WILD-TYPE | 106 | 191 | 150 |
Figure S123. Get High-res Image Gene #65: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D65V3.png)
P value = 6.06e-06 (Fisher's exact test), Q value = 0.0037
Table S124. Gene #65: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
18P LOSS CNV | 8 | 32 | 4 |
18P LOSS WILD-TYPE | 189 | 147 | 93 |
Figure S124. Get High-res Image Gene #65: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D65V7.png)
P value = 0.000196 (Fisher's exact test), Q value = 0.11
Table S125. Gene #65: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
18P LOSS CNV | 7 | 8 | 29 |
18P LOSS WILD-TYPE | 62 | 206 | 161 |
Figure S125. Get High-res Image Gene #65: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D65V8.png)
P value = 0.00036 (Fisher's exact test), Q value = 0.2
Table S126. Gene #65: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 191 | 169 |
18P LOSS CNV | 10 | 8 | 28 |
18P LOSS WILD-TYPE | 105 | 183 | 141 |
Figure S126. Get High-res Image Gene #65: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D65V9.png)
P value = 3.61e-06 (Fisher's exact test), Q value = 0.0022
Table S127. Gene #66: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
18Q LOSS CNV | 27 | 7 | 14 |
18Q LOSS WILD-TYPE | 105 | 190 | 150 |
Figure S127. Get High-res Image Gene #66: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D66V3.png)
P value = 2.87e-05 (Fisher's exact test), Q value = 0.017
Table S128. Gene #66: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
18Q LOSS CNV | 9 | 32 | 5 |
18Q LOSS WILD-TYPE | 188 | 147 | 92 |
Figure S128. Get High-res Image Gene #66: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D66V7.png)
P value = 0.000367 (Fisher's exact test), Q value = 0.2
Table S129. Gene #69: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 132 | 197 | 164 |
21Q LOSS CNV | 6 | 5 | 21 |
21Q LOSS WILD-TYPE | 126 | 192 | 143 |
Figure S129. Get High-res Image Gene #69: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D69V3.png)
P value = 1.72e-05 (Fisher's exact test), Q value = 0.01
Table S130. Gene #69: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
21Q LOSS CNV | 14 | 6 | 9 |
21Q LOSS WILD-TYPE | 55 | 208 | 181 |
Figure S130. Get High-res Image Gene #69: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D69V8.png)
P value = 9.51e-06 (Fisher's exact test), Q value = 0.0057
Table S131. Gene #69: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 35 | 160 | 280 |
21Q LOSS CNV | 11 | 8 | 13 |
21Q LOSS WILD-TYPE | 24 | 152 | 267 |
Figure S131. Get High-res Image Gene #69: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D69V10.png)
-
Mutation data file = broad_values_by_arm.mutsig.cluster.txt
-
Molecular subtypes file = KIRC-TP.transferedmergedcluster.txt
-
Number of patients = 493
-
Number of significantly arm-level cnvs = 71
-
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.