This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.
Testing the association between copy number variation 57 arm-level events and 10 molecular subtypes across 501 patients, 134 significant findings detected with P value < 0.05 and Q value < 0.25.
-
1q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
-
4p gain cnv correlated to 'CN_CNMF'.
-
4q gain cnv correlated to 'CN_CNMF'.
-
5p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
-
5q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
7p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
7q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
8p gain cnv correlated to 'CN_CNMF'.
-
8q gain cnv correlated to 'CN_CNMF'.
-
11q gain cnv correlated to 'CN_CNMF'.
-
12p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
12q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
13q gain cnv correlated to 'CN_CNMF'.
-
14q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
16p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
16q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
-
17p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
17q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
18p gain cnv correlated to 'CN_CNMF'.
-
18q gain cnv correlated to 'CN_CNMF'.
-
19p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
19q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
20p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
20q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
-
21q gain cnv correlated to 'CN_CNMF'.
-
xq gain cnv correlated to 'CN_CNMF'.
-
1p loss cnv correlated to 'CN_CNMF'.
-
2p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
2q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
3q loss cnv correlated to 'CN_CNMF'.
-
6p loss cnv correlated to 'CN_CNMF'.
-
6q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
-
8p loss cnv correlated to 'CN_CNMF'.
-
8q loss cnv correlated to 'CN_CNMF'.
-
9p loss cnv correlated to 'CN_CNMF'.
-
9q loss cnv correlated to 'CN_CNMF'.
-
10p loss cnv correlated to 'CN_CNMF'.
-
10q loss cnv correlated to 'CN_CNMF'.
-
11p loss cnv correlated to 'CN_CNMF'.
-
11q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
-
13q loss cnv correlated to 'MIRSEQ_CHIERARCHICAL'.
-
15q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
22q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 57 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 134 significant findings detected.
Clinical Features |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
||
nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
22q loss | 89 (18%) | 412 |
1e-05 (0.00534) |
1e-05 (0.00534) |
0.116 (1.00) |
0.503 (1.00) |
1e-05 (0.00534) |
1e-05 (0.00534) |
0.00035 (0.144) |
5e-05 (0.023) |
0.00017 (0.0731) |
0.00023 (0.0966) |
7q gain | 20 (4%) | 481 |
1e-05 (0.00534) |
1e-05 (0.00534) |
0.572 (1.00) |
0.0141 (1.00) |
0.0001 (0.0445) |
4e-05 (0.0187) |
7e-05 (0.0316) |
1e-05 (0.00534) |
0.612 (1.00) |
0.00062 (0.249) |
17p gain | 16 (3%) | 485 |
1e-05 (0.00534) |
1e-05 (0.00534) |
0.538 (1.00) |
0.0278 (1.00) |
1e-05 (0.00534) |
1e-05 (0.00534) |
2e-05 (0.00962) |
1e-05 (0.00534) |
0.358 (1.00) |
0.00024 (0.1) |
17q gain | 18 (4%) | 483 |
1e-05 (0.00534) |
1e-05 (0.00534) |
0.635 (1.00) |
0.0153 (1.00) |
1e-05 (0.00534) |
1e-05 (0.00534) |
2e-05 (0.00962) |
1e-05 (0.00534) |
0.513 (1.00) |
0.00027 (0.112) |
2p loss | 10 (2%) | 491 |
1e-05 (0.00534) |
3e-05 (0.0141) |
0.775 (1.00) |
0.092 (1.00) |
8e-05 (0.0358) |
2e-05 (0.00962) |
1e-05 (0.00534) |
2e-05 (0.00962) |
0.235 (1.00) |
0.00036 (0.148) |
2q loss | 10 (2%) | 491 |
1e-05 (0.00534) |
2e-05 (0.00962) |
0.773 (1.00) |
0.0893 (1.00) |
0.00013 (0.0573) |
5e-05 (0.023) |
1e-05 (0.00534) |
1e-05 (0.00534) |
0.234 (1.00) |
0.00056 (0.226) |
5q gain | 17 (3%) | 484 |
1e-05 (0.00534) |
5e-05 (0.023) |
0.849 (1.00) |
0.0795 (1.00) |
0.00013 (0.0573) |
3e-05 (0.0141) |
0.0002 (0.0848) |
1e-05 (0.00534) |
0.84 (1.00) |
0.00425 (1.00) |
12p gain | 14 (3%) | 487 |
1e-05 (0.00534) |
1e-05 (0.00534) |
0.85 (1.00) |
0.0811 (1.00) |
2e-05 (0.00962) |
1e-05 (0.00534) |
6e-05 (0.0271) |
1e-05 (0.00534) |
0.552 (1.00) |
0.00242 (0.888) |
12q gain | 15 (3%) | 486 |
1e-05 (0.00534) |
1e-05 (0.00534) |
0.851 (1.00) |
0.0789 (1.00) |
1e-05 (0.00534) |
1e-05 (0.00534) |
3e-05 (0.0141) |
1e-05 (0.00534) |
0.383 (1.00) |
0.00086 (0.337) |
14q gain | 11 (2%) | 490 |
1e-05 (0.00534) |
0.00022 (0.0931) |
1 (1.00) |
0.158 (1.00) |
0.00049 (0.2) |
9e-05 (0.0401) |
0.0006 (0.242) |
5e-05 (0.023) |
0.852 (1.00) |
0.00201 (0.748) |
16p gain | 15 (3%) | 486 |
1e-05 (0.00534) |
4e-05 (0.0187) |
0.633 (1.00) |
0.0796 (1.00) |
0.00018 (0.077) |
5e-05 (0.023) |
0.00015 (0.0657) |
1e-05 (0.00534) |
0.435 (1.00) |
0.00076 (0.3) |
19q gain | 10 (2%) | 491 |
1e-05 (0.00534) |
2e-05 (0.00962) |
0.635 (1.00) |
0.0642 (1.00) |
0.0001 (0.0445) |
4e-05 (0.0187) |
2e-05 (0.00962) |
1e-05 (0.00534) |
0.637 (1.00) |
0.0016 (0.603) |
15q loss | 8 (2%) | 493 |
0.00023 (0.0966) |
0.00022 (0.0931) |
0.193 (1.00) |
0.0879 (1.00) |
0.00048 (0.196) |
0.00026 (0.108) |
7e-05 (0.0316) |
5e-05 (0.023) |
0.407 (1.00) |
0.00154 (0.585) |
7p gain | 18 (4%) | 483 |
1e-05 (0.00534) |
5e-05 (0.023) |
0.659 (1.00) |
0.0524 (1.00) |
0.00065 (0.259) |
0.00013 (0.0573) |
0.00034 (0.14) |
4e-05 (0.0187) |
0.578 (1.00) |
0.00538 (1.00) |
19p gain | 8 (2%) | 493 |
1e-05 (0.00534) |
0.00019 (0.0809) |
0.00063 (0.252) |
0.00022 (0.0931) |
7e-05 (0.0316) |
2e-05 (0.00962) |
0.449 (1.00) |
0.0226 (1.00) |
||
16q gain | 13 (3%) | 488 |
1e-05 (0.00534) |
0.00016 (0.0696) |
0.797 (1.00) |
0.276 (1.00) |
0.00094 (0.367) |
0.00031 (0.129) |
0.00181 (0.679) |
0.00017 (0.0731) |
0.617 (1.00) |
0.00789 (1.00) |
5p gain | 21 (4%) | 480 |
1e-05 (0.00534) |
0.00198 (0.739) |
0.529 (1.00) |
0.233 (1.00) |
0.00517 (1.00) |
0.00011 (0.0486) |
0.001 (0.389) |
0.0001 (0.0445) |
0.598 (1.00) |
0.00366 (1.00) |
20p gain | 12 (2%) | 489 |
1e-05 (0.00534) |
0.00032 (0.132) |
0.796 (1.00) |
0.0929 (1.00) |
0.00257 (0.935) |
0.0009 (0.352) |
0.00453 (1.00) |
0.00049 (0.2) |
0.913 (1.00) |
0.095 (1.00) |
1q gain | 26 (5%) | 475 |
1e-05 (0.00534) |
0.0166 (1.00) |
0.00281 (1.00) |
0.0645 (1.00) |
0.00112 (0.431) |
7e-05 (0.0316) |
0.0859 (1.00) |
0.0506 (1.00) |
0.0133 (1.00) |
0.0156 (1.00) |
20q gain | 12 (2%) | 489 |
1e-05 (0.00534) |
0.00044 (0.18) |
0.795 (1.00) |
0.0927 (1.00) |
0.00251 (0.916) |
0.00067 (0.267) |
0.00426 (1.00) |
0.00077 (0.303) |
0.915 (1.00) |
0.0931 (1.00) |
6q loss | 7 (1%) | 494 |
4e-05 (0.0187) |
0.00219 (0.808) |
0.0131 (1.00) |
0.574 (1.00) |
0.0272 (1.00) |
0.0181 (1.00) |
0.00489 (1.00) |
0.0006 (0.242) |
1 (1.00) |
0.00995 (1.00) |
11q loss | 9 (2%) | 492 |
1e-05 (0.00534) |
0.0158 (1.00) |
0.319 (1.00) |
0.812 (1.00) |
0.0152 (1.00) |
0.0184 (1.00) |
0.00051 (0.207) |
0.00248 (0.908) |
0.908 (1.00) |
0.00201 (0.748) |
4p gain | 5 (1%) | 496 |
1e-05 (0.00534) |
0.00645 (1.00) |
0.0164 (1.00) |
0.0126 (1.00) |
0.0416 (1.00) |
0.0147 (1.00) |
1 (1.00) |
0.0767 (1.00) |
||
4q gain | 5 (1%) | 496 |
5e-05 (0.023) |
0.00676 (1.00) |
0.0171 (1.00) |
0.0123 (1.00) |
0.0404 (1.00) |
0.0142 (1.00) |
1 (1.00) |
0.0772 (1.00) |
||
8p gain | 6 (1%) | 495 |
0.00015 (0.0657) |
0.416 (1.00) |
0.455 (1.00) |
0.629 (1.00) |
0.597 (1.00) |
0.536 (1.00) |
0.454 (1.00) |
0.452 (1.00) |
1 (1.00) |
1 (1.00) |
8q gain | 7 (1%) | 494 |
2e-05 (0.00962) |
0.202 (1.00) |
0.455 (1.00) |
0.633 (1.00) |
0.83 (1.00) |
0.52 (1.00) |
0.8 (1.00) |
0.63 (1.00) |
0.9 (1.00) |
0.897 (1.00) |
11q gain | 5 (1%) | 496 |
0.00016 (0.0696) |
0.0604 (1.00) |
0.779 (1.00) |
0.3 (1.00) |
0.11 (1.00) |
0.124 (1.00) |
0.0264 (1.00) |
0.0225 (1.00) |
0.311 (1.00) |
0.273 (1.00) |
13q gain | 5 (1%) | 496 |
4e-05 (0.0187) |
0.0189 (1.00) |
0.38 (1.00) |
0.213 (1.00) |
0.0492 (1.00) |
0.102 (1.00) |
0.239 (1.00) |
0.0703 (1.00) |
0.844 (1.00) |
0.197 (1.00) |
18p gain | 6 (1%) | 495 |
5e-05 (0.023) |
0.0919 (1.00) |
0.122 (1.00) |
0.267 (1.00) |
0.256 (1.00) |
0.111 (1.00) |
0.454 (1.00) |
0.399 (1.00) |
||
18q gain | 6 (1%) | 495 |
3e-05 (0.0141) |
0.092 (1.00) |
0.12 (1.00) |
0.265 (1.00) |
0.254 (1.00) |
0.114 (1.00) |
0.454 (1.00) |
0.393 (1.00) |
||
21q gain | 5 (1%) | 496 |
0.00015 (0.0657) |
0.169 (1.00) |
0.238 (1.00) |
0.488 (1.00) |
0.453 (1.00) |
0.312 (1.00) |
0.692 (1.00) |
0.681 (1.00) |
||
xq gain | 9 (2%) | 492 |
1e-05 (0.00534) |
0.011 (1.00) |
0.838 (1.00) |
0.501 (1.00) |
0.0974 (1.00) |
0.141 (1.00) |
0.277 (1.00) |
0.133 (1.00) |
0.908 (1.00) |
0.398 (1.00) |
1p loss | 4 (1%) | 497 |
0.00019 (0.0809) |
0.186 (1.00) |
0.243 (1.00) |
0.316 (1.00) |
0.115 (1.00) |
0.0663 (1.00) |
0.845 (1.00) |
0.195 (1.00) |
||
3q loss | 4 (1%) | 497 |
0.00016 (0.0696) |
0.0181 (1.00) |
0.495 (1.00) |
0.42 (1.00) |
0.0372 (1.00) |
0.0478 (1.00) |
0.00878 (1.00) |
0.00408 (1.00) |
1 (1.00) |
0.0669 (1.00) |
6p loss | 4 (1%) | 497 |
0.00016 (0.0696) |
0.0457 (1.00) |
0.46 (1.00) |
0.399 (1.00) |
0.115 (1.00) |
0.0675 (1.00) |
0.401 (1.00) |
0.195 (1.00) |
||
8p loss | 4 (1%) | 497 |
0.00018 (0.077) |
0.0181 (1.00) |
0.0358 (1.00) |
0.0471 (1.00) |
0.00784 (1.00) |
0.00398 (1.00) |
0.11 (1.00) |
0.0186 (1.00) |
||
8q loss | 4 (1%) | 497 |
0.00016 (0.0696) |
0.0182 (1.00) |
0.0355 (1.00) |
0.0464 (1.00) |
0.00841 (1.00) |
0.0039 (1.00) |
0.11 (1.00) |
0.0192 (1.00) |
||
9p loss | 19 (4%) | 482 |
1e-05 (0.00534) |
0.0377 (1.00) |
0.243 (1.00) |
0.648 (1.00) |
0.0312 (1.00) |
0.0624 (1.00) |
0.00879 (1.00) |
0.00706 (1.00) |
0.303 (1.00) |
0.00387 (1.00) |
9q loss | 25 (5%) | 476 |
1e-05 (0.00534) |
0.104 (1.00) |
0.172 (1.00) |
0.116 (1.00) |
0.171 (1.00) |
0.0628 (1.00) |
0.00979 (1.00) |
0.00637 (1.00) |
0.279 (1.00) |
0.00499 (1.00) |
10p loss | 7 (1%) | 494 |
1e-05 (0.00534) |
0.0111 (1.00) |
0.493 (1.00) |
0.42 (1.00) |
0.0195 (1.00) |
0.0153 (1.00) |
0.00466 (1.00) |
0.00069 (0.274) |
1 (1.00) |
0.0103 (1.00) |
10q loss | 6 (1%) | 495 |
1e-05 (0.00534) |
0.0291 (1.00) |
0.0516 (1.00) |
0.044 (1.00) |
0.0144 (1.00) |
0.00439 (1.00) |
1 (1.00) |
0.0287 (1.00) |
||
11p loss | 7 (1%) | 494 |
1e-05 (0.00534) |
0.0113 (1.00) |
0.494 (1.00) |
0.958 (1.00) |
0.00722 (1.00) |
0.0186 (1.00) |
0.00477 (1.00) |
0.00074 (0.293) |
0.798 (1.00) |
0.0109 (1.00) |
13q loss | 14 (3%) | 487 |
0.00164 (0.617) |
0.015 (1.00) |
0.0611 (1.00) |
0.139 (1.00) |
0.00547 (1.00) |
0.00864 (1.00) |
0.00108 (0.418) |
0.00055 (0.223) |
0.104 (1.00) |
0.013 (1.00) |
1p gain | 5 (1%) | 496 |
0.00105 (0.407) |
0.839 (1.00) |
0.922 (1.00) |
0.881 (1.00) |
0.108 (1.00) |
0.0516 (1.00) |
0.276 (1.00) |
0.142 (1.00) |
||
3p gain | 3 (1%) | 498 |
0.00159 (0.601) |
0.548 (1.00) |
0.496 (1.00) |
0.592 (1.00) |
0.305 (1.00) |
0.187 (1.00) |
1 (1.00) |
0.193 (1.00) |
||
9p gain | 3 (1%) | 498 |
0.00143 (0.545) |
0.55 (1.00) |
0.495 (1.00) |
0.588 (1.00) |
1 (1.00) |
1 (1.00) |
0.421 (1.00) |
0.632 (1.00) |
||
9q gain | 4 (1%) | 497 |
0.011 (1.00) |
0.793 (1.00) |
0.9 (1.00) |
0.361 (1.00) |
0.839 (1.00) |
1 (1.00) |
0.167 (1.00) |
0.568 (1.00) |
||
11p gain | 6 (1%) | 495 |
0.00112 (0.431) |
0.0284 (1.00) |
0.779 (1.00) |
0.301 (1.00) |
0.0538 (1.00) |
0.0442 (1.00) |
0.00893 (1.00) |
0.00685 (1.00) |
0.468 (1.00) |
0.0977 (1.00) |
1q loss | 3 (1%) | 498 |
0.00137 (0.523) |
0.0505 (1.00) |
0.0972 (1.00) |
0.154 (1.00) |
0.028 (1.00) |
0.0176 (1.00) |
1 (1.00) |
0.19 (1.00) |
||
3p loss | 3 (1%) | 498 |
0.00123 (0.471) |
0.0489 (1.00) |
0.0995 (1.00) |
0.152 (1.00) |
0.0266 (1.00) |
0.0162 (1.00) |
1 (1.00) |
0.192 (1.00) |
||
17p loss | 8 (2%) | 493 |
0.0145 (1.00) |
0.415 (1.00) |
1 (1.00) |
0.391 (1.00) |
0.638 (1.00) |
0.599 (1.00) |
0.0919 (1.00) |
0.162 (1.00) |
0.129 (1.00) |
0.205 (1.00) |
17q loss | 4 (1%) | 497 |
0.113 (1.00) |
0.79 (1.00) |
0.901 (1.00) |
0.666 (1.00) |
0.466 (1.00) |
0.568 (1.00) |
0.331 (1.00) |
0.684 (1.00) |
||
18p loss | 4 (1%) | 497 |
0.00191 (0.714) |
0.183 (1.00) |
1 (1.00) |
0.388 (1.00) |
0.245 (1.00) |
0.316 (1.00) |
0.0758 (1.00) |
0.0923 (1.00) |
0.531 (1.00) |
0.273 (1.00) |
18q loss | 4 (1%) | 497 |
0.0021 (0.777) |
0.185 (1.00) |
1 (1.00) |
0.387 (1.00) |
0.246 (1.00) |
0.318 (1.00) |
0.0723 (1.00) |
0.0906 (1.00) |
0.534 (1.00) |
0.277 (1.00) |
19p loss | 5 (1%) | 496 |
0.00915 (1.00) |
0.00743 (1.00) |
0.321 (1.00) |
0.237 (1.00) |
0.017 (1.00) |
0.0125 (1.00) |
0.00239 (0.88) |
0.00108 (0.418) |
0.0876 (1.00) |
0.00155 (0.587) |
21q loss | 8 (2%) | 493 |
0.0008 (0.314) |
0.163 (1.00) |
0.384 (1.00) |
0.215 (1.00) |
0.711 (1.00) |
0.42 (1.00) |
0.0932 (1.00) |
0.0291 (1.00) |
0.46 (1.00) |
0.0545 (1.00) |
xq loss | 3 (1%) | 498 |
0.0507 (1.00) |
0.049 (1.00) |
0.28 (1.00) |
0.199 (1.00) |
0.0989 (1.00) |
0.151 (1.00) |
0.0276 (1.00) |
0.0165 (1.00) |
0.111 (1.00) |
0.019 (1.00) |
P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S1. Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
1Q GAIN MUTATED | 18 | 7 | 1 |
1Q GAIN WILD-TYPE | 38 | 349 | 88 |
Figure S1. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.032
Table S2. Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 105 | 134 | 86 | 96 | 78 |
1Q GAIN MUTATED | 16 | 2 | 1 | 3 | 4 |
1Q GAIN WILD-TYPE | 89 | 132 | 85 | 93 | 74 |
Figure S2. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S3. Gene #4: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
4P GAIN MUTATED | 5 | 0 | 0 |
4P GAIN WILD-TYPE | 51 | 356 | 89 |
Figure S3. Get High-res Image Gene #4: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.023
Table S4. Gene #5: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
4Q GAIN MUTATED | 5 | 0 | 0 |
4Q GAIN WILD-TYPE | 51 | 356 | 89 |
Figure S4. Get High-res Image Gene #5: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S5. Gene #6: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
5P GAIN MUTATED | 21 | 0 | 0 |
5P GAIN WILD-TYPE | 35 | 356 | 89 |
Figure S5. Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.049
Table S6. Gene #6: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 105 | 134 | 86 | 96 | 78 |
5P GAIN MUTATED | 6 | 14 | 0 | 1 | 0 |
5P GAIN WILD-TYPE | 99 | 120 | 86 | 95 | 78 |
Figure S6. Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.044
Table S7. Gene #6: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 128 | 193 |
5P GAIN MUTATED | 7 | 13 | 1 |
5P GAIN WILD-TYPE | 172 | 115 | 192 |
Figure S7. Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S8. Gene #7: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
5Q GAIN MUTATED | 17 | 0 | 0 |
5Q GAIN WILD-TYPE | 39 | 356 | 89 |
Figure S8. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.023
Table S9. Gene #7: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 277 | 154 | 70 |
5Q GAIN MUTATED | 2 | 14 | 1 |
5Q GAIN WILD-TYPE | 275 | 140 | 69 |
Figure S9. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.057
Table S10. Gene #7: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 168 | 155 | 59 | 117 |
5Q GAIN MUTATED | 2 | 14 | 0 | 1 |
5Q GAIN WILD-TYPE | 166 | 141 | 59 | 116 |
Figure S10. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.014
Table S11. Gene #7: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 105 | 134 | 86 | 96 | 78 |
5Q GAIN MUTATED | 2 | 14 | 0 | 1 | 0 |
5Q GAIN WILD-TYPE | 103 | 120 | 86 | 95 | 78 |
Figure S11. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.085
Table S12. Gene #7: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 182 | 151 | 167 |
5Q GAIN MUTATED | 3 | 13 | 1 |
5Q GAIN WILD-TYPE | 179 | 138 | 166 |
Figure S12. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S13. Gene #7: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 128 | 193 |
5Q GAIN MUTATED | 3 | 13 | 1 |
5Q GAIN WILD-TYPE | 176 | 115 | 192 |
Figure S13. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S14. Gene #8: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
7P GAIN MUTATED | 18 | 0 | 0 |
7P GAIN WILD-TYPE | 38 | 356 | 89 |
Figure S14. Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.023
Table S15. Gene #8: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 277 | 154 | 70 |
7P GAIN MUTATED | 2 | 14 | 2 |
7P GAIN WILD-TYPE | 275 | 140 | 68 |
Figure S15. Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.057
Table S16. Gene #8: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 105 | 134 | 86 | 96 | 78 |
7P GAIN MUTATED | 2 | 14 | 1 | 1 | 0 |
7P GAIN WILD-TYPE | 103 | 120 | 85 | 95 | 78 |
Figure S16. Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.14
Table S17. Gene #8: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 182 | 151 | 167 |
7P GAIN MUTATED | 4 | 13 | 1 |
7P GAIN WILD-TYPE | 178 | 138 | 166 |
Figure S17. Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.019
Table S18. Gene #8: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 128 | 193 |
7P GAIN MUTATED | 4 | 13 | 1 |
7P GAIN WILD-TYPE | 175 | 115 | 192 |
Figure S18. Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S19. Gene #9: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
7Q GAIN MUTATED | 19 | 0 | 1 |
7Q GAIN WILD-TYPE | 37 | 356 | 88 |
Figure S19. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S20. Gene #9: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 277 | 154 | 70 |
7Q GAIN MUTATED | 2 | 16 | 2 |
7Q GAIN WILD-TYPE | 275 | 138 | 68 |
Figure S20. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.044
Table S21. Gene #9: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 168 | 155 | 59 | 117 |
7Q GAIN MUTATED | 2 | 16 | 1 | 1 |
7Q GAIN WILD-TYPE | 166 | 139 | 58 | 116 |
Figure S21. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.019
Table S22. Gene #9: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 105 | 134 | 86 | 96 | 78 |
7Q GAIN MUTATED | 2 | 16 | 1 | 1 | 0 |
7Q GAIN WILD-TYPE | 103 | 118 | 85 | 95 | 78 |
Figure S22. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.032
Table S23. Gene #9: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 182 | 151 | 167 |
7Q GAIN MUTATED | 4 | 15 | 1 |
7Q GAIN WILD-TYPE | 178 | 136 | 166 |
Figure S23. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S24. Gene #9: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 128 | 193 |
7Q GAIN MUTATED | 4 | 15 | 1 |
7Q GAIN WILD-TYPE | 175 | 113 | 192 |
Figure S24. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.25
Table S25. Gene #9: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 165 | 126 | 179 |
7Q GAIN MUTATED | 5 | 11 | 1 |
7Q GAIN WILD-TYPE | 160 | 115 | 178 |
Figure S25. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.066
Table S26. Gene #10: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
8P GAIN MUTATED | 5 | 1 | 0 |
8P GAIN WILD-TYPE | 51 | 355 | 89 |
Figure S26. Get High-res Image Gene #10: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096
Table S27. Gene #11: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
8Q GAIN MUTATED | 6 | 1 | 0 |
8Q GAIN WILD-TYPE | 50 | 355 | 89 |
Figure S27. Get High-res Image Gene #11: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.07
Table S28. Gene #15: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
11Q GAIN MUTATED | 4 | 0 | 1 |
11Q GAIN WILD-TYPE | 52 | 356 | 88 |
Figure S28. Get High-res Image Gene #15: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S29. Gene #16: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
12P GAIN MUTATED | 13 | 0 | 1 |
12P GAIN WILD-TYPE | 43 | 356 | 88 |
Figure S29. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S30. Gene #16: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 277 | 154 | 70 |
12P GAIN MUTATED | 1 | 13 | 0 |
12P GAIN WILD-TYPE | 276 | 141 | 70 |
Figure S30. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096
Table S31. Gene #16: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 168 | 155 | 59 | 117 |
12P GAIN MUTATED | 0 | 13 | 0 | 1 |
12P GAIN WILD-TYPE | 168 | 142 | 59 | 116 |
Figure S31. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S32. Gene #16: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 105 | 134 | 86 | 96 | 78 |
12P GAIN MUTATED | 0 | 13 | 0 | 1 | 0 |
12P GAIN WILD-TYPE | 105 | 121 | 86 | 95 | 78 |
Figure S32. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.027
Table S33. Gene #16: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 182 | 151 | 167 |
12P GAIN MUTATED | 1 | 12 | 1 |
12P GAIN WILD-TYPE | 181 | 139 | 166 |
Figure S33. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S34. Gene #16: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 128 | 193 |
12P GAIN MUTATED | 1 | 12 | 1 |
12P GAIN WILD-TYPE | 178 | 116 | 192 |
Figure S34. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S35. Gene #17: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
12Q GAIN MUTATED | 14 | 0 | 1 |
12Q GAIN WILD-TYPE | 42 | 356 | 88 |
Figure S35. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S36. Gene #17: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 277 | 154 | 70 |
12Q GAIN MUTATED | 1 | 14 | 0 |
12Q GAIN WILD-TYPE | 276 | 140 | 70 |
Figure S36. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S37. Gene #17: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 168 | 155 | 59 | 117 |
12Q GAIN MUTATED | 0 | 14 | 0 | 1 |
12Q GAIN WILD-TYPE | 168 | 141 | 59 | 116 |
Figure S37. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S38. Gene #17: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 105 | 134 | 86 | 96 | 78 |
12Q GAIN MUTATED | 0 | 14 | 0 | 1 | 0 |
12Q GAIN WILD-TYPE | 105 | 120 | 86 | 95 | 78 |
Figure S38. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.014
Table S39. Gene #17: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 182 | 151 | 167 |
12Q GAIN MUTATED | 1 | 13 | 1 |
12Q GAIN WILD-TYPE | 181 | 138 | 166 |
Figure S39. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S40. Gene #17: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 128 | 193 |
12Q GAIN MUTATED | 1 | 13 | 1 |
12Q GAIN WILD-TYPE | 178 | 115 | 192 |
Figure S40. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.019
Table S41. Gene #18: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
13Q GAIN MUTATED | 5 | 0 | 0 |
13Q GAIN WILD-TYPE | 51 | 356 | 89 |
Figure S41. Get High-res Image Gene #18: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S42. Gene #19: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
14Q GAIN MUTATED | 10 | 0 | 1 |
14Q GAIN WILD-TYPE | 46 | 356 | 88 |
Figure S42. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.093
Table S43. Gene #19: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 277 | 154 | 70 |
14Q GAIN MUTATED | 1 | 10 | 0 |
14Q GAIN WILD-TYPE | 276 | 144 | 70 |
Figure S43. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.2
Table S44. Gene #19: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 168 | 155 | 59 | 117 |
14Q GAIN MUTATED | 1 | 10 | 0 | 0 |
14Q GAIN WILD-TYPE | 167 | 145 | 59 | 117 |
Figure S44. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.04
Table S45. Gene #19: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 105 | 134 | 86 | 96 | 78 |
14Q GAIN MUTATED | 0 | 10 | 0 | 0 | 1 |
14Q GAIN WILD-TYPE | 105 | 124 | 86 | 96 | 77 |
Figure S45. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.24
Table S46. Gene #19: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 182 | 151 | 167 |
14Q GAIN MUTATED | 2 | 9 | 0 |
14Q GAIN WILD-TYPE | 180 | 142 | 167 |
Figure S46. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.023
Table S47. Gene #19: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 128 | 193 |
14Q GAIN MUTATED | 2 | 9 | 0 |
14Q GAIN WILD-TYPE | 177 | 119 | 193 |
Figure S47. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S48. Gene #20: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
16P GAIN MUTATED | 14 | 0 | 1 |
16P GAIN WILD-TYPE | 42 | 356 | 88 |
Figure S48. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.019
Table S49. Gene #20: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 277 | 154 | 70 |
16P GAIN MUTATED | 1 | 13 | 1 |
16P GAIN WILD-TYPE | 276 | 141 | 69 |
Figure S49. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.077
Table S50. Gene #20: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 168 | 155 | 59 | 117 |
16P GAIN MUTATED | 1 | 13 | 0 | 1 |
16P GAIN WILD-TYPE | 167 | 142 | 59 | 116 |
Figure S50. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.023
Table S51. Gene #20: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 105 | 134 | 86 | 96 | 78 |
16P GAIN MUTATED | 1 | 13 | 0 | 1 | 0 |
16P GAIN WILD-TYPE | 104 | 121 | 86 | 95 | 78 |
Figure S51. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.066
Table S52. Gene #20: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 182 | 151 | 167 |
16P GAIN MUTATED | 2 | 12 | 1 |
16P GAIN WILD-TYPE | 180 | 139 | 166 |
Figure S52. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S53. Gene #20: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 128 | 193 |
16P GAIN MUTATED | 2 | 12 | 1 |
16P GAIN WILD-TYPE | 177 | 116 | 192 |
Figure S53. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S54. Gene #21: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
16Q GAIN MUTATED | 13 | 0 | 0 |
16Q GAIN WILD-TYPE | 43 | 356 | 89 |
Figure S54. Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.07
Table S55. Gene #21: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 277 | 154 | 70 |
16Q GAIN MUTATED | 1 | 11 | 1 |
16Q GAIN WILD-TYPE | 276 | 143 | 69 |
Figure S55. Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.13
Table S56. Gene #21: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 105 | 134 | 86 | 96 | 78 |
16Q GAIN MUTATED | 1 | 11 | 0 | 1 | 0 |
16Q GAIN WILD-TYPE | 104 | 123 | 86 | 95 | 78 |
Figure S56. Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.073
Table S57. Gene #21: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 128 | 193 |
16Q GAIN MUTATED | 2 | 10 | 1 |
16Q GAIN WILD-TYPE | 177 | 118 | 192 |
Figure S57. Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S58. Gene #22: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
17P GAIN MUTATED | 12 | 2 | 2 |
17P GAIN WILD-TYPE | 44 | 354 | 87 |
Figure S58. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S59. Gene #22: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 277 | 154 | 70 |
17P GAIN MUTATED | 1 | 15 | 0 |
17P GAIN WILD-TYPE | 276 | 139 | 70 |
Figure S59. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S60. Gene #22: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 168 | 155 | 59 | 117 |
17P GAIN MUTATED | 0 | 15 | 0 | 1 |
17P GAIN WILD-TYPE | 168 | 140 | 59 | 116 |
Figure S60. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S61. Gene #22: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 105 | 134 | 86 | 96 | 78 |
17P GAIN MUTATED | 0 | 15 | 0 | 1 | 0 |
17P GAIN WILD-TYPE | 105 | 119 | 86 | 95 | 78 |
Figure S61. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096
Table S62. Gene #22: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 182 | 151 | 167 |
17P GAIN MUTATED | 1 | 14 | 1 |
17P GAIN WILD-TYPE | 181 | 137 | 166 |
Figure S62. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S63. Gene #22: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 128 | 193 |
17P GAIN MUTATED | 1 | 14 | 1 |
17P GAIN WILD-TYPE | 178 | 114 | 192 |
Figure S63. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.1
Table S64. Gene #22: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 165 | 126 | 179 |
17P GAIN MUTATED | 2 | 10 | 1 |
17P GAIN WILD-TYPE | 163 | 116 | 178 |
Figure S64. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S65. Gene #23: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
17Q GAIN MUTATED | 13 | 2 | 3 |
17Q GAIN WILD-TYPE | 43 | 354 | 86 |
Figure S65. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S66. Gene #23: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 277 | 154 | 70 |
17Q GAIN MUTATED | 2 | 16 | 0 |
17Q GAIN WILD-TYPE | 275 | 138 | 70 |
Figure S66. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S67. Gene #23: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 168 | 155 | 59 | 117 |
17Q GAIN MUTATED | 1 | 16 | 0 | 1 |
17Q GAIN WILD-TYPE | 167 | 139 | 59 | 116 |
Figure S67. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S68. Gene #23: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 105 | 134 | 86 | 96 | 78 |
17Q GAIN MUTATED | 1 | 16 | 0 | 1 | 0 |
17Q GAIN WILD-TYPE | 104 | 118 | 86 | 95 | 78 |
Figure S68. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096
Table S69. Gene #23: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 182 | 151 | 167 |
17Q GAIN MUTATED | 2 | 15 | 1 |
17Q GAIN WILD-TYPE | 180 | 136 | 166 |
Figure S69. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S70. Gene #23: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 128 | 193 |
17Q GAIN MUTATED | 2 | 15 | 1 |
17Q GAIN WILD-TYPE | 177 | 113 | 192 |
Figure S70. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.11
Table S71. Gene #23: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 165 | 126 | 179 |
17Q GAIN MUTATED | 3 | 11 | 1 |
17Q GAIN WILD-TYPE | 162 | 115 | 178 |
Figure S71. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.023
Table S72. Gene #24: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
18P GAIN MUTATED | 5 | 0 | 1 |
18P GAIN WILD-TYPE | 51 | 356 | 88 |
Figure S72. Get High-res Image Gene #24: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.014
Table S73. Gene #25: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
18Q GAIN MUTATED | 5 | 0 | 1 |
18Q GAIN WILD-TYPE | 51 | 356 | 88 |
Figure S73. Get High-res Image Gene #25: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S74. Gene #26: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
19P GAIN MUTATED | 8 | 0 | 0 |
19P GAIN WILD-TYPE | 48 | 356 | 89 |
Figure S74. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.081
Table S75. Gene #26: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 277 | 154 | 70 |
19P GAIN MUTATED | 0 | 8 | 0 |
19P GAIN WILD-TYPE | 277 | 146 | 70 |
Figure S75. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.093
Table S76. Gene #26: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 105 | 134 | 86 | 96 | 78 |
19P GAIN MUTATED | 0 | 8 | 0 | 0 | 0 |
19P GAIN WILD-TYPE | 105 | 126 | 86 | 96 | 78 |
Figure S76. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.032
Table S77. Gene #26: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 182 | 151 | 167 |
19P GAIN MUTATED | 0 | 8 | 0 |
19P GAIN WILD-TYPE | 182 | 143 | 167 |
Figure S77. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096
Table S78. Gene #26: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 128 | 193 |
19P GAIN MUTATED | 0 | 8 | 0 |
19P GAIN WILD-TYPE | 179 | 120 | 193 |
Figure S78. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S79. Gene #27: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
19Q GAIN MUTATED | 10 | 0 | 0 |
19Q GAIN WILD-TYPE | 46 | 356 | 89 |
Figure S79. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096
Table S80. Gene #27: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 277 | 154 | 70 |
19Q GAIN MUTATED | 0 | 10 | 0 |
19Q GAIN WILD-TYPE | 277 | 144 | 70 |
Figure S80. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.044
Table S81. Gene #27: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 168 | 155 | 59 | 117 |
19Q GAIN MUTATED | 0 | 10 | 0 | 0 |
19Q GAIN WILD-TYPE | 168 | 145 | 59 | 117 |
Figure S81. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.019
Table S82. Gene #27: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 105 | 134 | 86 | 96 | 78 |
19Q GAIN MUTATED | 0 | 10 | 0 | 0 | 0 |
19Q GAIN WILD-TYPE | 105 | 124 | 86 | 96 | 78 |
Figure S82. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096
Table S83. Gene #27: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 182 | 151 | 167 |
19Q GAIN MUTATED | 0 | 10 | 0 |
19Q GAIN WILD-TYPE | 182 | 141 | 167 |
Figure S83. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S84. Gene #27: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 128 | 193 |
19Q GAIN MUTATED | 0 | 10 | 0 |
19Q GAIN WILD-TYPE | 179 | 118 | 193 |
Figure S84. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S85. Gene #28: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
20P GAIN MUTATED | 12 | 0 | 0 |
20P GAIN WILD-TYPE | 44 | 356 | 89 |
Figure S85. Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.13
Table S86. Gene #28: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 277 | 154 | 70 |
20P GAIN MUTATED | 1 | 10 | 1 |
20P GAIN WILD-TYPE | 276 | 144 | 69 |
Figure S86. Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.2
Table S87. Gene #28: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 128 | 193 |
20P GAIN MUTATED | 2 | 9 | 1 |
20P GAIN WILD-TYPE | 177 | 119 | 192 |
Figure S87. Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S88. Gene #29: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
20Q GAIN MUTATED | 12 | 0 | 0 |
20Q GAIN WILD-TYPE | 44 | 356 | 89 |
Figure S88. Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.18
Table S89. Gene #29: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 277 | 154 | 70 |
20Q GAIN MUTATED | 1 | 10 | 1 |
20Q GAIN WILD-TYPE | 276 | 144 | 69 |
Figure S89. Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.066
Table S90. Gene #30: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
21Q GAIN MUTATED | 4 | 0 | 1 |
21Q GAIN WILD-TYPE | 52 | 356 | 88 |
Figure S90. Get High-res Image Gene #30: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S91. Gene #31: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
XQ GAIN MUTATED | 8 | 1 | 0 |
XQ GAIN WILD-TYPE | 48 | 355 | 89 |
Figure S91. Get High-res Image Gene #31: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.081
Table S92. Gene #32: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
1P LOSS MUTATED | 4 | 0 | 0 |
1P LOSS WILD-TYPE | 52 | 356 | 89 |
Figure S92. Get High-res Image Gene #32: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S93. Gene #34: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
2P LOSS MUTATED | 9 | 0 | 1 |
2P LOSS WILD-TYPE | 47 | 356 | 88 |
Figure S93. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.014
Table S94. Gene #34: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 277 | 154 | 70 |
2P LOSS MUTATED | 0 | 10 | 0 |
2P LOSS WILD-TYPE | 277 | 144 | 70 |
Figure S94. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.036
Table S95. Gene #34: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 168 | 155 | 59 | 117 |
2P LOSS MUTATED | 0 | 10 | 0 | 0 |
2P LOSS WILD-TYPE | 168 | 145 | 59 | 117 |
Figure S95. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096
Table S96. Gene #34: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 105 | 134 | 86 | 96 | 78 |
2P LOSS MUTATED | 0 | 10 | 0 | 0 | 0 |
2P LOSS WILD-TYPE | 105 | 124 | 86 | 96 | 78 |
Figure S96. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S97. Gene #34: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 182 | 151 | 167 |
2P LOSS MUTATED | 0 | 10 | 0 |
2P LOSS WILD-TYPE | 182 | 141 | 167 |
Figure S97. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096
Table S98. Gene #34: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 128 | 193 |
2P LOSS MUTATED | 0 | 10 | 0 |
2P LOSS WILD-TYPE | 179 | 118 | 193 |
Figure S98. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.15
Table S99. Gene #34: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 165 | 126 | 179 |
2P LOSS MUTATED | 1 | 7 | 0 |
2P LOSS WILD-TYPE | 164 | 119 | 179 |
Figure S99. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S100. Gene #35: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
2Q LOSS MUTATED | 10 | 0 | 0 |
2Q LOSS WILD-TYPE | 46 | 356 | 89 |
Figure S100. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096
Table S101. Gene #35: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 277 | 154 | 70 |
2Q LOSS MUTATED | 0 | 10 | 0 |
2Q LOSS WILD-TYPE | 277 | 144 | 70 |
Figure S101. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.057
Table S102. Gene #35: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 168 | 155 | 59 | 117 |
2Q LOSS MUTATED | 0 | 10 | 0 | 0 |
2Q LOSS WILD-TYPE | 168 | 145 | 59 | 117 |
Figure S102. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.023
Table S103. Gene #35: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 105 | 134 | 86 | 96 | 78 |
2Q LOSS MUTATED | 0 | 10 | 0 | 0 | 0 |
2Q LOSS WILD-TYPE | 105 | 124 | 86 | 96 | 78 |
Figure S103. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S104. Gene #35: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 182 | 151 | 167 |
2Q LOSS MUTATED | 0 | 10 | 0 |
2Q LOSS WILD-TYPE | 182 | 141 | 167 |
Figure S104. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S105. Gene #35: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 128 | 193 |
2Q LOSS MUTATED | 0 | 10 | 0 |
2Q LOSS WILD-TYPE | 179 | 118 | 193 |
Figure S105. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.23
Table S106. Gene #35: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 165 | 126 | 179 |
2Q LOSS MUTATED | 1 | 7 | 0 |
2Q LOSS WILD-TYPE | 164 | 119 | 179 |
Figure S106. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.07
Table S107. Gene #37: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
3Q LOSS MUTATED | 4 | 0 | 0 |
3Q LOSS WILD-TYPE | 52 | 356 | 89 |
Figure S107. Get High-res Image Gene #37: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.07
Table S108. Gene #38: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
6P LOSS MUTATED | 4 | 0 | 0 |
6P LOSS WILD-TYPE | 52 | 356 | 89 |
Figure S108. Get High-res Image Gene #38: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.019
Table S109. Gene #39: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
6Q LOSS MUTATED | 6 | 1 | 0 |
6Q LOSS WILD-TYPE | 50 | 355 | 89 |
Figure S109. Get High-res Image Gene #39: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.24
Table S110. Gene #39: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 128 | 193 |
6Q LOSS MUTATED | 1 | 6 | 0 |
6Q LOSS WILD-TYPE | 178 | 122 | 193 |
Figure S110. Get High-res Image Gene #39: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.077
Table S111. Gene #40: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
8P LOSS MUTATED | 4 | 0 | 0 |
8P LOSS WILD-TYPE | 52 | 356 | 89 |
Figure S111. Get High-res Image Gene #40: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.07
Table S112. Gene #41: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
8Q LOSS MUTATED | 4 | 0 | 0 |
8Q LOSS WILD-TYPE | 52 | 356 | 89 |
Figure S112. Get High-res Image Gene #41: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S113. Gene #42: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
9P LOSS MUTATED | 15 | 2 | 2 |
9P LOSS WILD-TYPE | 41 | 354 | 87 |
Figure S113. Get High-res Image Gene #42: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S114. Gene #43: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
9Q LOSS MUTATED | 20 | 2 | 3 |
9Q LOSS WILD-TYPE | 36 | 354 | 86 |
Figure S114. Get High-res Image Gene #43: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S115. Gene #44: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
10P LOSS MUTATED | 7 | 0 | 0 |
10P LOSS WILD-TYPE | 49 | 356 | 89 |
Figure S115. Get High-res Image Gene #44: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S116. Gene #45: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
10Q LOSS MUTATED | 6 | 0 | 0 |
10Q LOSS WILD-TYPE | 50 | 356 | 89 |
Figure S116. Get High-res Image Gene #45: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S117. Gene #46: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
11P LOSS MUTATED | 6 | 0 | 1 |
11P LOSS WILD-TYPE | 50 | 356 | 88 |
Figure S117. Get High-res Image Gene #46: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S118. Gene #47: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
11Q LOSS MUTATED | 7 | 1 | 1 |
11Q LOSS WILD-TYPE | 49 | 355 | 88 |
Figure S118. Get High-res Image Gene #47: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.21
Table S119. Gene #47: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 182 | 151 | 167 |
11Q LOSS MUTATED | 1 | 8 | 0 |
11Q LOSS WILD-TYPE | 181 | 143 | 167 |
Figure S119. Get High-res Image Gene #47: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.22
Table S120. Gene #48: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 128 | 193 |
13Q LOSS MUTATED | 0 | 9 | 5 |
13Q LOSS WILD-TYPE | 179 | 119 | 188 |
Figure S120. Get High-res Image Gene #48: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.097
Table S121. Gene #49: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
15Q LOSS MUTATED | 5 | 1 | 2 |
15Q LOSS WILD-TYPE | 51 | 355 | 87 |
Figure S121. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.093
Table S122. Gene #49: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 277 | 154 | 70 |
15Q LOSS MUTATED | 0 | 8 | 0 |
15Q LOSS WILD-TYPE | 277 | 146 | 70 |
Figure S122. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.2
Table S123. Gene #49: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 168 | 155 | 59 | 117 |
15Q LOSS MUTATED | 0 | 8 | 0 | 0 |
15Q LOSS WILD-TYPE | 168 | 147 | 59 | 117 |
Figure S123. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.11
Table S124. Gene #49: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 105 | 134 | 86 | 96 | 78 |
15Q LOSS MUTATED | 0 | 8 | 0 | 0 | 0 |
15Q LOSS WILD-TYPE | 105 | 126 | 86 | 96 | 78 |
Figure S124. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.032
Table S125. Gene #49: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 182 | 151 | 167 |
15Q LOSS MUTATED | 0 | 8 | 0 |
15Q LOSS WILD-TYPE | 182 | 143 | 167 |
Figure S125. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.023
Table S126. Gene #49: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 128 | 193 |
15Q LOSS MUTATED | 0 | 8 | 0 |
15Q LOSS WILD-TYPE | 179 | 120 | 193 |
Figure S126. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S127. Gene #56: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 356 | 89 |
22Q LOSS MUTATED | 13 | 0 | 76 |
22Q LOSS WILD-TYPE | 43 | 356 | 13 |
Figure S127. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S128. Gene #56: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 277 | 154 | 70 |
22Q LOSS MUTATED | 36 | 47 | 6 |
22Q LOSS WILD-TYPE | 241 | 107 | 64 |
Figure S128. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S129. Gene #56: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 168 | 155 | 59 | 117 |
22Q LOSS MUTATED | 8 | 47 | 8 | 26 |
22Q LOSS WILD-TYPE | 160 | 108 | 51 | 91 |
Figure S129. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053
Table S130. Gene #56: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 105 | 134 | 86 | 96 | 78 |
22Q LOSS MUTATED | 9 | 42 | 13 | 23 | 2 |
22Q LOSS WILD-TYPE | 96 | 92 | 73 | 73 | 76 |
Figure S130. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.14
Table S131. Gene #56: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 182 | 151 | 167 |
22Q LOSS MUTATED | 23 | 43 | 23 |
22Q LOSS WILD-TYPE | 159 | 108 | 144 |
Figure S131. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.023
Table S132. Gene #56: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 128 | 193 |
22Q LOSS MUTATED | 21 | 40 | 28 |
22Q LOSS WILD-TYPE | 158 | 88 | 165 |
Figure S132. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.073
Table S133. Gene #56: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 160 | 164 | 146 |
22Q LOSS MUTATED | 17 | 23 | 41 |
22Q LOSS WILD-TYPE | 143 | 141 | 105 |
Figure S133. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.097
Table S134. Gene #56: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 165 | 126 | 179 |
22Q LOSS MUTATED | 22 | 37 | 22 |
22Q LOSS WILD-TYPE | 143 | 89 | 157 |
Figure S134. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

-
Copy number data file = transformed.cor.cli.txt
-
Molecular subtypes file = THCA-TP.transferedmergedcluster.txt
-
Number of patients = 501
-
Number of significantly arm-level cnvs = 57
-
Number of molecular subtypes = 10
-
Exclude genes that fewer than K tumors have mutations, K = 3
For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.