Correlation between copy number variations of arm-level result and molecular subtypes
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
16 April 2014 | analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C13N2221
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C13N2221
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.

Summary

Testing the association between copy number variation 70 arm-level events and 8 molecular subtypes across 197 patients, 105 significant findings detected with P value < 0.05 and Q value < 0.25.

- 1p gain cnv correlated to 'METHLYATION_CNMF'.

- 1q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

- 2p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 2q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 3p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 3q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 5p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- 5q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- 6q gain cnv correlated to 'METHLYATION_CNMF'.

- 7p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 7q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 11q gain cnv correlated to 'CN_CNMF'.

- 16p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 16q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 17p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 17q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- xq gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

- 1p loss cnv correlated to 'CN_CNMF'.

- 1q loss cnv correlated to 'CN_CNMF'.

- 3p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 4p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

- 4q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

- 5p loss cnv correlated to 'METHLYATION_CNMF'.

- 5q loss cnv correlated to 'METHLYATION_CNMF'.

- 9p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 9q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 10p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

- 10q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 11q loss cnv correlated to 'CN_CNMF'.

- 13q loss cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

- 14q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

- 15q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 16q loss cnv correlated to 'METHLYATION_CNMF'.

- 17p loss cnv correlated to 'METHLYATION_CNMF'.

- 18p loss cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

- 18q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

- 21q loss cnv correlated to 'CN_CNMF'.

- 22q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

- xq loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 70 arm-level events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 105 significant findings detected.

|  | Clinical Features | CN CNMF | METHLYATION CNMF | MRNASEQ CNMF | MRNASEQ CHIERARCHICAL | MIRSEQ CNMF | MIRSEQ CHIERARCHICAL | MIRSEQ MATURE CNMF | MIRSEQ MATURE CHIERARCHICAL
| nCNV (%) | nWild-Type | Chi-square test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test
16q gain | 101 (51%) | 96 | 2.13e-09 (1.14e-06) | 1.13e-08 (6.01e-06) | 8.32e-08 (4.36e-05) | 1.26e-09 (6.75e-07) | 0.0016 (0.699) | 0.0132 (1.00) | 9.58e-05 (0.0453) | 0.000225 (0.105)
xq gain | 63 (32%) | 134 | 7.77e-18 (4.33e-15) | 2.44e-07 (0.000127) | 1.5e-07 (7.84e-05) | 6.08e-10 (3.26e-07) | 0.00765 (1.00) | 0.0649 (1.00) | 0.000427 (0.196) | 0.00249 (1.00)
3p loss | 14 (7%) | 183 | 8.71e-05 (0.0415) | 1.2e-06 (0.00061) | 3.88e-05 (0.0187) | 0.000446 (0.203) | 0.267 (1.00) | 0.0053 (1.00) | 0.0404 (1.00) | 5.06e-06 (0.00253)
9q loss | 24 (12%) | 173 | 9.84e-05 (0.0464) | 2.2e-09 (1.17e-06) | 1.09e-08 (5.82e-06) | 3.49e-05 (0.0169) | 0.1 (1.00) | 0.000868 (0.39) | 0.0635 (1.00) | 8.37e-06 (0.00414)
3p gain | 55 (28%) | 142 | 9.27e-18 (5.15e-15) | 1.06e-05 (0.00523) | 9.1e-07 (0.000463) | 4.78e-06 (0.00239) | 0.0795 (1.00) | 0.284 (1.00) | 0.0915 (1.00) | 0.013 (1.00)
3q gain | 65 (33%) | 132 | 1.46e-16 (8.07e-14) | 7.11e-06 (0.00354) | 2.56e-07 (0.000133) | 0.000151 (0.0712) | 0.0489 (1.00) | 0.0937 (1.00) | 0.162 (1.00) | 0.00285 (1.00)
7p gain | 117 (59%) | 80 | 2.22e-16 (1.23e-13) | 2.1e-06 (0.00106) | 3.62e-14 (1.99e-11) | 2.76e-13 (1.5e-10) | 0.161 (1.00) | 0.492 (1.00) | 0.0993 (1.00) | 0.00128 (0.567)
7q gain | 118 (60%) | 79 | 6.05e-16 (3.34e-13) | 5.14e-06 (0.00256) | 1.45e-13 (7.96e-11) | 6.29e-13 (3.42e-10) | 0.221 (1.00) | 0.653 (1.00) | 0.143 (1.00) | 0.0047 (1.00)
16p gain | 105 (53%) | 92 | 3.45e-08 (1.82e-05) | 7.34e-09 (3.91e-06) | 1.28e-06 (0.000646) | 3.4e-10 (1.83e-07) | 0.0122 (1.00) | 0.0185 (1.00) | 0.000677 (0.307) | 0.000964 (0.431)
17p gain | 118 (60%) | 79 | 6.51e-16 (3.58e-13) | 2.04e-07 (0.000106) | 2.55e-13 (1.39e-10) | 9.34e-12 (5.06e-09) | 0.0937 (1.00) | 0.178 (1.00) | 0.0254 (1.00) | 0.00327 (1.00)
9p loss | 22 (11%) | 175 | 3.49e-06 (0.00175) | 3.39e-07 (0.000175) | 1.05e-07 (5.48e-05) | 8.61e-05 (0.0412) | 0.151 (1.00) | 0.0514 (1.00) | 0.169 (1.00) | 0.00167 (0.727)
10q loss | 12 (6%) | 185 | 0.000379 (0.175) | 7.12e-06 (0.00354) | 0.000342 (0.159) | 0.0187 (1.00) | 0.187 (1.00) | 0.00151 (0.663) | 0.0514 (1.00) | 0.000217 (0.102)
1q gain | 14 (7%) | 183 | 8.71e-05 (0.0415) | 2.57e-10 (1.39e-07) | 3.88e-05 (0.0187) | 0.00386 (1.00) | 0.413 (1.00) | 0.125 (1.00) | 0.61 (1.00) | 0.0105 (1.00)
17q gain | 133 (68%) | 64 | 5.4e-12 (2.93e-09) | 0.00147 (0.646) | 6.31e-08 (3.32e-05) | 5.79e-08 (3.05e-05) | 0.448 (1.00) | 0.316 (1.00) | 0.364 (1.00) | 0.0722 (1.00)
4p loss | 18 (9%) | 179 | 2.93e-05 (0.0143) | 1.61e-13 (8.83e-11) | 9.95e-07 (0.000505) | 0.00383 (1.00) | 0.332 (1.00) | 0.173 (1.00) | 0.706 (1.00) | 0.00586 (1.00)
4q loss | 19 (10%) | 178 | 2.25e-07 (0.000117) | 8.74e-11 (4.73e-08) | 3.41e-07 (0.000175) | 0.0062 (1.00) | 0.409 (1.00) | 0.374 (1.00) | 0.842 (1.00) | 0.0527 (1.00)
10p loss | 12 (6%) | 185 | 1.61e-05 (0.00792) | 8.85e-05 (0.0421) | 0.000342 (0.159) | 0.0509 (1.00) | 0.566 (1.00) | 0.00444 (1.00) | 0.235 (1.00) | 0.00328 (1.00)
14q loss | 35 (18%) | 162 | 8.06e-17 (4.48e-14) | 7.82e-05 (0.0375) | 0.000506 (0.23) | 0.0021 (0.911) | 0.382 (1.00) | 0.489 (1.00) | 0.255 (1.00) | 0.216 (1.00)
18q loss | 32 (16%) | 165 | 0.000385 (0.177) | 6e-10 (3.23e-07) | 4.51e-08 (2.38e-05) | 0.0014 (0.619) | 0.0519 (1.00) | 0.327 (1.00) | 0.0778 (1.00) | 0.0166 (1.00)
22q loss | 44 (22%) | 153 | 1.52e-05 (0.00748) | 1.26e-08 (6.69e-06) | 1.5e-07 (7.84e-05) | 0.00572 (1.00) | 0.515 (1.00) | 0.0394 (1.00) | 0.106 (1.00) | 0.0107 (1.00)
xq loss | 20 (10%) | 177 | 2.45e-06 (0.00123) | 4.64e-07 (0.000238) | 0.000195 (0.0916) | 0.105 (1.00) | 0.0974 (1.00) | 0.102 (1.00) | 0.167 (1.00) | 0.0348 (1.00)
2p gain | 36 (18%) | 161 | 9.4e-29 (5.25e-26) | 9.46e-05 (0.0449) | 0.0283 (1.00) | 0.0488 (1.00) | 0.0838 (1.00) | 0.659 (1.00) | 0.0135 (1.00) | 0.566 (1.00)
2q gain | 39 (20%) | 158 | 1.19e-28 (6.64e-26) | 3.13e-05 (0.0152) | 0.0483 (1.00) | 0.043 (1.00) | 0.108 (1.00) | 0.896 (1.00) | 0.0242 (1.00) | 0.882 (1.00)
5p gain | 26 (13%) | 171 | 1.34e-06 (0.000678) | 0.101 (1.00) | 0.0389 (1.00) | 2.12e-05 (0.0104) | 0.111 (1.00) | 0.191 (1.00) | 0.0374 (1.00) | 0.355 (1.00)
5q gain | 26 (13%) | 171 | 1.76e-05 (0.00863) | 0.169 (1.00) | 0.0729 (1.00) | 2.12e-05 (0.0104) | 0.111 (1.00) | 0.429 (1.00) | 0.12 (1.00) | 0.707 (1.00)
13q loss | 18 (9%) | 179 | 0.0113 (1.00) | 1.31e-13 (7.21e-11) | 1.52e-05 (0.00748) | 0.0163 (1.00) | 0.0264 (1.00) | 0.00872 (1.00) | 0.0659 (1.00) | 0.000851 (0.383)
15q loss | 19 (10%) | 178 | 3.74e-05 (0.0181) | 4.07e-05 (0.0196) | 0.004 (1.00) | 0.00792 (1.00) | 0.187 (1.00) | 0.214 (1.00) | 0.124 (1.00) | 0.16 (1.00)
18p loss | 30 (15%) | 167 | 0.00349 (1.00) | 7.62e-08 (4e-05) | 4.04e-07 (0.000208) | 0.00308 (1.00) | 0.0432 (1.00) | 0.465 (1.00) | 0.0515 (1.00) | 0.0446 (1.00)
1p gain | 5 (3%) | 192 | 0.0331 (1.00) | 8.84e-07 (0.000451) | 0.0217 (1.00) | 0.194 (1.00) | 0.13 (1.00) | 0.289 (1.00) | 0.106 (1.00) | 0.0266 (1.00)
6q gain | 6 (3%) | 191 | 0.0326 (1.00) | 0.00037 (0.171) | 0.131 (1.00) | 0.673 (1.00) | 0.127 (1.00) | 0.745 (1.00) | 0.244 (1.00) | 0.166 (1.00)
11q gain | 8 (4%) | 189 | 0.000435 (0.199) | 0.00124 (0.553) | 0.146 (1.00) | 0.0317 (1.00) | 0.363 (1.00) | 1 (1.00) | 0.288 (1.00) | 0.593 (1.00)
1p loss | 21 (11%) | 176 | 1.3e-06 (0.000656) | 0.0114 (1.00) | 0.00746 (1.00) | 0.412 (1.00) | 1 (1.00) | 0.343 (1.00) | 1 (1.00) | 0.879 (1.00)
1q loss | 13 (7%) | 184 | 0.000441 (0.201) | 0.236 (1.00) | 0.328 (1.00) | 0.51 (1.00) | 0.678 (1.00) | 0.142 (1.00) | 0.72 (1.00) | 0.298 (1.00)
5p loss | 7 (4%) | 190 | 0.333 (1.00) | 8.3e-07 (0.000425) | 0.0309 (1.00) | 0.00358 (1.00) | 0.00634 (1.00) | 0.0584 (1.00) | 0.0111 (1.00) | 0.0452 (1.00)
5q loss | 7 (4%) | 190 | 0.439 (1.00) | 8.3e-07 (0.000425) | 0.0309 (1.00) | 0.00358 (1.00) | 0.00634 (1.00) | 0.0584 (1.00) | 0.0111 (1.00) | 0.0452 (1.00)
11q loss | 14 (7%) | 183 | 0.000373 (0.172) | 0.00124 (0.551) | 0.00348 (1.00) | 0.234 (1.00) | 0.551 (1.00) | 0.378 (1.00) | 0.242 (1.00) | 0.165 (1.00)
16q loss | 5 (3%) | 192 | 0.0117 (1.00) | 0.000346 (0.161) | 0.0217 (1.00) | 0.194 (1.00) | 0.536 (1.00) | 0.374 (1.00) | 0.629 (1.00) | 0.0193 (1.00)
17p loss | 8 (4%) | 189 | 0.14 (1.00) | 8e-05 (0.0383) | 0.000925 (0.414) | 0.0272 (1.00) | 0.179 (1.00) | 0.109 (1.00) | 0.226 (1.00) | 0.0465 (1.00)
21q loss | 32 (16%) | 165 | 0.000151 (0.0712) | 0.153 (1.00) | 0.546 (1.00) | 1 (1.00) | 0.577 (1.00) | 0.704 (1.00) | 0.321 (1.00) | 0.848 (1.00)
4p gain | 6 (3%) | 191 | 0.333 (1.00) | 0.542 (1.00) | 0.393 (1.00) | 0.877 (1.00) | 1 (1.00) | 0.373 (1.00) | 1 (1.00) | 0.251 (1.00)
4q gain | 5 (3%) | 192 | 0.687 (1.00) | 0.542 (1.00) | 0.628 (1.00) | 1 (1.00) | 1 (1.00) | 0.85 (1.00) | 0.742 (1.00) | 0.675 (1.00)
6p gain | 8 (4%) | 189 | 0.217 (1.00) | 0.00556 (1.00) | 0.021 (1.00) | 0.226 (1.00) | 0.0753 (1.00) | 0.373 (1.00) | 0.356 (1.00) | 0.0465 (1.00)
8p gain | 14 (7%) | 183 | 0.406 (1.00) | 0.139 (1.00) | 0.0248 (1.00) | 0.266 (1.00) | 0.227 (1.00) | 0.172 (1.00) | 0.61 (1.00) | 0.112 (1.00)
8q gain | 17 (9%) | 180 | 0.173 (1.00) | 0.00142 (0.626) | 0.00266 (1.00) | 0.115 (1.00) | 0.0464 (1.00) | 0.082 (1.00) | 0.144 (1.00) | 0.0377 (1.00)
9p gain | 3 (2%) | 194 | 0.543 (1.00) |  | 0.194 (1.00) | 0.284 (1.00) | 1 (1.00) | 0.187 (1.00) | 0.508 (1.00) | 0.0874 (1.00)
10p gain | 5 (3%) | 192 | 0.106 (1.00) | 0.619 (1.00) | 0.517 (1.00) | 1 (1.00) | 0.374 (1.00) | 0.459 (1.00) | 0.231 (1.00) | 0.423 (1.00)
10q gain | 5 (3%) | 192 | 0.106 (1.00) | 0.619 (1.00) | 0.517 (1.00) | 1 (1.00) | 0.374 (1.00) | 0.459 (1.00) | 0.231 (1.00) | 0.423 (1.00)
11p gain | 10 (5%) | 187 | 0.0269 (1.00) | 0.00384 (1.00) | 0.144 (1.00) | 0.0326 (1.00) | 0.435 (1.00) | 0.824 (1.00) | 0.361 (1.00) | 0.529 (1.00)
12p gain | 80 (41%) | 117 | 0.000805 (0.364) | 0.156 (1.00) | 0.0452 (1.00) | 0.0014 (0.618) | 0.194 (1.00) | 0.0249 (1.00) | 0.109 (1.00) | 0.06 (1.00)
12q gain | 80 (41%) | 117 | 0.000805 (0.364) | 0.156 (1.00) | 0.0452 (1.00) | 0.0014 (0.618) | 0.194 (1.00) | 0.0249 (1.00) | 0.109 (1.00) | 0.06 (1.00)
13q gain | 22 (11%) | 175 | 0.219 (1.00) | 0.526 (1.00) | 0.242 (1.00) | 0.832 (1.00) | 0.745 (1.00) | 1 (1.00) | 0.722 (1.00) | 0.753 (1.00)
14q gain | 3 (2%) | 194 | 0.722 (1.00) | 0.0666 (1.00) | 0.194 (1.00) | 0.284 (1.00) | 1 (1.00) | 0.187 (1.00) | 1 (1.00) | 0.0874 (1.00)
15q gain | 5 (3%) | 192 | 0.0331 (1.00) | 0.174 (1.00) | 0.202 (1.00) | 0.165 (1.00) | 0.536 (1.00) | 0.572 (1.00) | 0.443 (1.00) | 0.675 (1.00)
18p gain | 9 (5%) | 188 | 0.412 (1.00) | 0.226 (1.00) | 0.661 (1.00) | 0.693 (1.00) | 0.25 (1.00) | 0.00458 (1.00) | 0.195 (1.00) | 0.0675 (1.00)
18q gain | 5 (3%) | 192 | 0.232 (1.00) | 0.452 (1.00) | 0.589 (1.00) | 0.23 (1.00) | 1 (1.00) | 0.0633 (1.00) | 0.629 (1.00) | 0.675 (1.00)
19p gain | 3 (2%) | 194 | 0.162 (1.00) | 0.561 (1.00) | 0.194 (1.00) | 0.503 (1.00) | 0.323 (1.00) | 0.536 (1.00) | 0.289 (1.00) | 0.491 (1.00)
19q gain | 3 (2%) | 194 | 0.162 (1.00) | 0.561 (1.00) | 0.194 (1.00) | 0.503 (1.00) | 0.323 (1.00) | 0.536 (1.00) | 0.289 (1.00) | 0.491 (1.00)
20p gain | 66 (34%) | 131 | 0.000554 (0.252) | 0.0105 (1.00) | 0.0255 (1.00) | 0.0627 (1.00) | 0.0453 (1.00) | 0.69 (1.00) | 0.161 (1.00) | 0.344 (1.00)
20q gain | 68 (35%) | 129 | 0.00197 (0.857) | 0.00717 (1.00) | 0.0624 (1.00) | 0.0848 (1.00) | 0.0313 (1.00) | 0.823 (1.00) | 0.183 (1.00) | 0.52 (1.00)
21q gain | 12 (6%) | 185 | 0.248 (1.00) | 0.53 (1.00) | 0.0353 (1.00) | 0.231 (1.00) | 0.931 (1.00) | 0.438 (1.00) | 0.531 (1.00) | 0.762 (1.00)
22q gain | 3 (2%) | 194 | 0.365 (1.00) | 0.791 (1.00) | 0.512 (1.00) | 0.778 (1.00) | 0.0696 (1.00) | 0.28 (1.00) | 0.198 (1.00) | 0.23 (1.00)
3q loss | 4 (2%) | 193 | 0.0739 (1.00) | 0.00545 (1.00) | 0.0652 (1.00) | 0.101 (1.00) | 0.128 (1.00) | 0.503 (1.00) | 0.207 (1.00) | 0.0824 (1.00)
6p loss | 13 (7%) | 184 | 0.0926 (1.00) | 0.0194 (1.00) | 0.0997 (1.00) | 0.333 (1.00) | 0.445 (1.00) | 0.283 (1.00) | 0.469 (1.00) | 0.563 (1.00)
6q loss | 16 (8%) | 181 | 0.0152 (1.00) | 0.0247 (1.00) | 0.0231 (1.00) | 0.327 (1.00) | 1 (1.00) | 0.567 (1.00) | 0.692 (1.00) | 0.109 (1.00)
8p loss | 7 (4%) | 190 | 0.516 (1.00) | 0.992 (1.00) | 0.278 (1.00) | 0.501 (1.00) | 0.312 (1.00) | 0.108 (1.00) | 0.396 (1.00) | 0.067 (1.00)
8q loss | 4 (2%) | 193 | 0.426 (1.00) | 0.663 (1.00) | 0.328 (1.00) | 0.682 (1.00) | 0.847 (1.00) | 0.652 (1.00) | 1 (1.00) | 0.586 (1.00)
11p loss | 10 (5%) | 187 | 0.0231 (1.00) | 0.00202 (0.876) | 0.029 (1.00) | 0.331 (1.00) | 0.777 (1.00) | 0.182 (1.00) | 0.303 (1.00) | 0.0708 (1.00)
16p loss | 4 (2%) | 193 | 0.0649 (1.00) | 0.00545 (1.00) | 0.0652 (1.00) | 0.101 (1.00) | 0.847 (1.00) | 0.374 (1.00) | 1 (1.00) | 0.0824 (1.00)
19p loss | 12 (6%) | 185 | 0.00407 (1.00) | 0.0562 (1.00) | 0.0464 (1.00) | 0.0856 (1.00) | 0.295 (1.00) | 0.185 (1.00) | 0.0739 (1.00) | 0.31 (1.00)
19q loss | 11 (6%) | 186 | 0.0126 (1.00) | 0.0146 (1.00) | 0.0708 (1.00) | 0.575 (1.00) | 0.468 (1.00) | 0.28 (1.00) | 0.135 (1.00) | 0.106 (1.00)

'1p gain' versus 'METHLYATION_CNMF'

P value = 8.84e-07 (Chi-square test), Q value = 0.00045

Table S1. Gene #1: '1p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
1P GAIN MUTATED | 0 | 5 | 0 | 0 | 0
1P GAIN WILD-TYPE | 38 | 19 | 33 | 48 | 38

Figure S1. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q gain' versus 'CN_CNMF'

P value = 8.71e-05 (Chi-square test), Q value = 0.042

Table S2. Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
1Q GAIN MUTATED | 2 | 0 | 9 | 0 | 3
1Q GAIN WILD-TYPE | 69 | 40 | 28 | 21 | 25

Figure S2. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 2.57e-10 (Chi-square test), Q value = 1.4e-07

Table S3. Gene #2: '1q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
1Q GAIN MUTATED | 1 | 10 | 2 | 0 | 0
1Q GAIN WILD-TYPE | 37 | 14 | 31 | 48 | 38

Figure S3. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 3.88e-05 (Fisher's exact test), Q value = 0.019

Table S4. Gene #2: '1q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
1Q GAIN MUTATED | 1 | 13 | 0 | 0
1Q GAIN WILD-TYPE | 38 | 54 | 59 | 32

Figure S4. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 9.4e-29 (Chi-square test), Q value = 5.3e-26

Table S5. Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
2P GAIN MUTATED | 1 | 2 | 6 | 0 | 27
2P GAIN WILD-TYPE | 70 | 38 | 31 | 21 | 1

Figure S5. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 9.46e-05 (Chi-square test), Q value = 0.045

Table S6. Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
2P GAIN MUTATED | 3 | 7 | 4 | 18 | 1
2P GAIN WILD-TYPE | 35 | 17 | 29 | 30 | 37

Figure S6. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q gain' versus 'CN_CNMF'

P value = 1.19e-28 (Chi-square test), Q value = 6.6e-26

Table S7. Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
2Q GAIN MUTATED | 1 | 2 | 7 | 1 | 28
2Q GAIN WILD-TYPE | 70 | 38 | 30 | 20 | 0

Figure S7. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 3.13e-05 (Chi-square test), Q value = 0.015

Table S8. Gene #4: '2q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
2Q GAIN MUTATED | 4 | 7 | 4 | 20 | 1
2Q GAIN WILD-TYPE | 34 | 17 | 29 | 28 | 37

Figure S8. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p gain' versus 'CN_CNMF'

P value = 9.27e-18 (Chi-square test), Q value = 5.2e-15

Table S9. Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
3P GAIN MUTATED | 8 | 6 | 3 | 20 | 18
3P GAIN WILD-TYPE | 63 | 34 | 34 | 1 | 10

Figure S9. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'METHLYATION_CNMF'

P value = 1.06e-05 (Chi-square test), Q value = 0.0052

Table S10. Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
3P GAIN MUTATED | 11 | 3 | 3 | 26 | 6
3P GAIN WILD-TYPE | 27 | 21 | 30 | 22 | 32

Figure S10. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 9.1e-07 (Fisher's exact test), Q value = 0.00046

Table S11. Gene #5: '3p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
3P GAIN MUTATED | 19 | 4 | 22 | 10
3P GAIN WILD-TYPE | 20 | 63 | 37 | 22

Figure S11. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.78e-06 (Fisher's exact test), Q value = 0.0024

Table S12. Gene #5: '3p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 71 | 56
3P GAIN MUTATED | 34 | 15 | 6
3P GAIN WILD-TYPE | 36 | 56 | 50

Figure S12. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 1.46e-16 (Chi-square test), Q value = 8.1e-14

Table S13. Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
3Q GAIN MUTATED | 12 | 7 | 5 | 21 | 20
3Q GAIN WILD-TYPE | 59 | 33 | 32 | 0 | 8

Figure S13. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 7.11e-06 (Chi-square test), Q value = 0.0035

Table S14. Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
3Q GAIN MUTATED | 12 | 4 | 5 | 30 | 8
3Q GAIN WILD-TYPE | 26 | 20 | 28 | 18 | 30

Figure S14. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 2.56e-07 (Fisher's exact test), Q value = 0.00013

Table S15. Gene #6: '3q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
3Q GAIN MUTATED | 22 | 6 | 22 | 15
3Q GAIN WILD-TYPE | 17 | 61 | 37 | 17

Figure S15. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000151 (Fisher's exact test), Q value = 0.071

Table S16. Gene #6: '3q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 71 | 56
3Q GAIN MUTATED | 36 | 19 | 10
3Q GAIN WILD-TYPE | 34 | 52 | 46

Figure S16. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1.34e-06 (Chi-square test), Q value = 0.00068

Table S17. Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
5P GAIN MUTATED | 5 | 0 | 15 | 3 | 3
5P GAIN WILD-TYPE | 66 | 40 | 22 | 18 | 25

Figure S17. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.12e-05 (Fisher's exact test), Q value = 0.01

Table S18. Gene #9: '5p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 71 | 56
5P GAIN MUTATED | 2 | 20 | 4
5P GAIN WILD-TYPE | 68 | 51 | 52

Figure S18. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 1.76e-05 (Chi-square test), Q value = 0.0086

Table S19. Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
5Q GAIN MUTATED | 6 | 0 | 14 | 3 | 3
5Q GAIN WILD-TYPE | 65 | 40 | 23 | 18 | 25

Figure S19. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.12e-05 (Fisher's exact test), Q value = 0.01

Table S20. Gene #10: '5q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 71 | 56
5Q GAIN MUTATED | 2 | 20 | 4
5Q GAIN WILD-TYPE | 68 | 51 | 52

Figure S20. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.00037 (Chi-square test), Q value = 0.17

Table S21. Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
6Q GAIN MUTATED | 0 | 4 | 0 | 0 | 1
6Q GAIN WILD-TYPE | 38 | 20 | 33 | 48 | 37

Figure S21. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 2.22e-16 (Chi-square test), Q value = 1.2e-13

Table S22. Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
7P GAIN MUTATED | 23 | 40 | 11 | 20 | 23
7P GAIN WILD-TYPE | 48 | 0 | 26 | 1 | 5

Figure S22. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 2.1e-06 (Chi-square test), Q value = 0.0011

Table S23. Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
7P GAIN MUTATED | 18 | 9 | 11 | 39 | 30
7P GAIN WILD-TYPE | 20 | 15 | 22 | 9 | 8

Figure S23. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 3.62e-14 (Fisher's exact test), Q value = 2e-11

Table S24. Gene #13: '7p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
7P GAIN MUTATED | 21 | 17 | 53 | 26
7P GAIN WILD-TYPE | 18 | 50 | 6 | 6

Figure S24. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.76e-13 (Fisher's exact test), Q value = 1.5e-10

Table S25. Gene #13: '7p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 71 | 56
7P GAIN MUTATED | 65 | 27 | 25
7P GAIN WILD-TYPE | 5 | 44 | 31

Figure S25. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 6.05e-16 (Chi-square test), Q value = 3.3e-13

Table S26. Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
7Q GAIN MUTATED | 23 | 40 | 12 | 20 | 23
7Q GAIN WILD-TYPE | 48 | 0 | 25 | 1 | 5

Figure S26. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 5.14e-06 (Chi-square test), Q value = 0.0026

Table S27. Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
7Q GAIN MUTATED | 18 | 9 | 12 | 39 | 30
7Q GAIN WILD-TYPE | 20 | 15 | 21 | 9 | 8

Figure S27. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1.45e-13 (Fisher's exact test), Q value = 8e-11

Table S28. Gene #14: '7q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
7Q GAIN MUTATED | 21 | 18 | 53 | 26
7Q GAIN WILD-TYPE | 18 | 49 | 6 | 6

Figure S28. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.29e-13 (Fisher's exact test), Q value = 3.4e-10

Table S29. Gene #14: '7q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 71 | 56
7Q GAIN MUTATED | 65 | 28 | 25
7Q GAIN WILD-TYPE | 5 | 43 | 31

Figure S29. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 0.000435 (Chi-square test), Q value = 0.2

Table S30. Gene #21: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
11Q GAIN MUTATED | 0 | 0 | 6 | 0 | 2
11Q GAIN WILD-TYPE | 71 | 40 | 31 | 21 | 26

Figure S30. Get High-res Image Gene #21: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 3.45e-08 (Chi-square test), Q value = 1.8e-05

Table S31. Gene #27: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
16P GAIN MUTATED | 30 | 17 | 13 | 21 | 24
16P GAIN WILD-TYPE | 41 | 23 | 24 | 0 | 4

Figure S31. Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 7.34e-09 (Chi-square test), Q value = 3.9e-06

Table S32. Gene #27: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
16P GAIN MUTATED | 20 | 8 | 16 | 44 | 10
16P GAIN WILD-TYPE | 18 | 16 | 17 | 4 | 28

Figure S32. Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 1.28e-06 (Fisher's exact test), Q value = 0.00065

Table S33. Gene #27: '16p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
16P GAIN MUTATED | 32 | 20 | 36 | 17
16P GAIN WILD-TYPE | 7 | 47 | 23 | 15

Figure S33. Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.4e-10 (Fisher's exact test), Q value = 1.8e-07

Table S34. Gene #27: '16p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 71 | 56
16P GAIN MUTATED | 54 | 40 | 11
16P GAIN WILD-TYPE | 16 | 31 | 45

Figure S34. Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 2.13e-09 (Chi-square test), Q value = 1.1e-06

Table S35. Gene #28: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
16Q GAIN MUTATED | 30 | 16 | 10 | 21 | 24
16Q GAIN WILD-TYPE | 41 | 24 | 27 | 0 | 4

Figure S35. Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 1.13e-08 (Chi-square test), Q value = 6e-06

Table S36. Gene #28: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
16Q GAIN MUTATED | 20 | 7 | 15 | 43 | 10
16Q GAIN WILD-TYPE | 18 | 17 | 18 | 5 | 28

Figure S36. Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 8.32e-08 (Fisher's exact test), Q value = 4.4e-05

Table S37. Gene #28: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
16Q GAIN MUTATED | 32 | 17 | 35 | 17
16Q GAIN WILD-TYPE | 7 | 50 | 24 | 15

Figure S37. Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.26e-09 (Fisher's exact test), Q value = 6.8e-07

Table S38. Gene #28: '16q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 71 | 56
16Q GAIN MUTATED | 53 | 37 | 11
16Q GAIN WILD-TYPE | 17 | 34 | 45

Figure S38. Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.58e-05 (Fisher's exact test), Q value = 0.045

Table S39. Gene #28: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 57 | 71 | 69
16Q GAIN MUTATED | 35 | 22 | 44
16Q GAIN WILD-TYPE | 22 | 49 | 25

Figure S39. Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000225 (Fisher's exact test), Q value = 0.11

Table S40. Gene #28: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 75 | 99 | 23
16Q GAIN MUTATED | 27 | 65 | 9
16Q GAIN WILD-TYPE | 48 | 34 | 14

Figure S40. Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 6.51e-16 (Chi-square test), Q value = 3.6e-13

Table S41. Gene #29: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
17P GAIN MUTATED | 26 | 39 | 9 | 19 | 25
17P GAIN WILD-TYPE | 45 | 1 | 28 | 2 | 3

Figure S41. Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 2.04e-07 (Chi-square test), Q value = 0.00011

Table S42. Gene #29: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
17P GAIN MUTATED | 17 | 9 | 11 | 39 | 32
17P GAIN WILD-TYPE | 21 | 15 | 22 | 9 | 6

Figure S42. Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 2.55e-13 (Fisher's exact test), Q value = 1.4e-10

Table S43. Gene #29: '17p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
17P GAIN MUTATED | 27 | 16 | 52 | 23
17P GAIN WILD-TYPE | 12 | 51 | 7 | 9

Figure S43. Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.34e-12 (Fisher's exact test), Q value = 5.1e-09

Table S44. Gene #29: '17p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 71 | 56
17P GAIN MUTATED | 64 | 32 | 22
17P GAIN WILD-TYPE | 6 | 39 | 34

Figure S44. Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 5.4e-12 (Chi-square test), Q value = 2.9e-09

Table S45. Gene #30: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
17Q GAIN MUTATED | 33 | 39 | 15 | 19 | 27
17Q GAIN WILD-TYPE | 38 | 1 | 22 | 2 | 1

Figure S45. Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 6.31e-08 (Fisher's exact test), Q value = 3.3e-05

Table S46. Gene #30: '17q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
17Q GAIN MUTATED | 30 | 27 | 52 | 24
17Q GAIN WILD-TYPE | 9 | 40 | 7 | 8

Figure S46. Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.79e-08 (Fisher's exact test), Q value = 3.1e-05

Table S47. Gene #30: '17q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 71 | 56
17Q GAIN MUTATED | 64 | 42 | 27
17Q GAIN WILD-TYPE | 6 | 29 | 29

Figure S47. Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 7.77e-18 (Chi-square test), Q value = 4.3e-15

Table S48. Gene #39: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
XQ GAIN MUTATED | 5 | 15 | 3 | 18 | 22
XQ GAIN WILD-TYPE | 66 | 25 | 34 | 3 | 6

Figure S48. Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 2.44e-07 (Chi-square test), Q value = 0.00013

Table S49. Gene #39: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
XQ GAIN MUTATED | 8 | 2 | 6 | 31 | 9
XQ GAIN WILD-TYPE | 30 | 22 | 27 | 17 | 29

Figure S49. Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 1.5e-07 (Fisher's exact test), Q value = 7.8e-05

Table S50. Gene #39: 'xq gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
XQ GAIN MUTATED | 18 | 6 | 31 | 8
XQ GAIN WILD-TYPE | 21 | 61 | 28 | 24

Figure S50. Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.08e-10 (Fisher's exact test), Q value = 3.3e-07

Table S51. Gene #39: 'xq gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 71 | 56
XQ GAIN MUTATED | 42 | 16 | 5
XQ GAIN WILD-TYPE | 28 | 55 | 51

Figure S51. Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000427 (Fisher's exact test), Q value = 0.2

Table S52. Gene #39: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 57 | 71 | 69
XQ GAIN MUTATED | 18 | 12 | 33
XQ GAIN WILD-TYPE | 39 | 59 | 36

Figure S52. Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1.3e-06 (Chi-square test), Q value = 0.00066

Table S53. Gene #40: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
1P LOSS MUTATED | 4 | 0 | 13 | 0 | 4
1P LOSS WILD-TYPE | 67 | 40 | 24 | 21 | 24

Figure S53. Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'CN_CNMF'

P value = 0.000441 (Chi-square test), Q value = 0.2

Table S54. Gene #41: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
1Q LOSS MUTATED | 2 | 0 | 8 | 0 | 3
1Q LOSS WILD-TYPE | 69 | 40 | 29 | 21 | 25

Figure S54. Get High-res Image Gene #41: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 8.71e-05 (Chi-square test), Q value = 0.042

Table S55. Gene #42: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
3P LOSS MUTATED | 2 | 0 | 9 | 0 | 3
3P LOSS WILD-TYPE | 69 | 40 | 28 | 21 | 25

Figure S55. Get High-res Image Gene #42: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1.2e-06 (Chi-square test), Q value = 0.00061

Table S56. Gene #42: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
3P LOSS MUTATED | 0 | 7 | 6 | 0 | 0
3P LOSS WILD-TYPE | 38 | 17 | 27 | 48 | 38

Figure S56. Get High-res Image Gene #42: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 3.88e-05 (Fisher's exact test), Q value = 0.019

Table S57. Gene #42: '3p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
3P LOSS MUTATED | 1 | 13 | 0 | 0
3P LOSS WILD-TYPE | 38 | 54 | 59 | 32

Figure S57. Get High-res Image Gene #42: '3p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000446 (Fisher's exact test), Q value = 0.2

Table S58. Gene #42: '3p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 71 | 56
3P LOSS MUTATED | 0 | 11 | 3
3P LOSS WILD-TYPE | 70 | 60 | 53

Figure S58. Get High-res Image Gene #42: '3p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.06e-06 (Fisher's exact test), Q value = 0.0025

Table S59. Gene #42: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 75 | 99 | 23
3P LOSS MUTATED | 5 | 1 | 8
3P LOSS WILD-TYPE | 70 | 98 | 15

Figure S59. Get High-res Image Gene #42: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 2.93e-05 (Chi-square test), Q value = 0.014

Table S60. Gene #44: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
4P LOSS MUTATED | 4 | 0 | 11 | 0 | 3
4P LOSS WILD-TYPE | 67 | 40 | 26 | 21 | 25

Figure S60. Get High-res Image Gene #44: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1.61e-13 (Chi-square test), Q value = 8.8e-11

Table S61. Gene #44: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
4P LOSS MUTATED | 1 | 13 | 2 | 1 | 0
4P LOSS WILD-TYPE | 37 | 11 | 31 | 47 | 38

Figure S61. Get High-res Image Gene #44: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 9.95e-07 (Fisher's exact test), Q value = 0.00051

Table S62. Gene #44: '4p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
4P LOSS MUTATED | 1 | 17 | 0 | 0
4P LOSS WILD-TYPE | 38 | 50 | 59 | 32

Figure S62. Get High-res Image Gene #44: '4p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 2.25e-07 (Chi-square test), Q value = 0.00012

Table S63. Gene #45: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
4Q LOSS MUTATED | 3 | 0 | 13 | 0 | 3
4Q LOSS WILD-TYPE | 68 | 40 | 24 | 21 | 25

Figure S63. Get High-res Image Gene #45: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 8.74e-11 (Chi-square test), Q value = 4.7e-08

Table S64. Gene #45: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
4Q LOSS MUTATED | 1 | 12 | 4 | 1 | 0
4Q LOSS WILD-TYPE | 37 | 12 | 29 | 47 | 38

Figure S64. Get High-res Image Gene #45: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 3.41e-07 (Fisher's exact test), Q value = 0.00018

Table S65. Gene #45: '4q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
4Q LOSS MUTATED | 1 | 18 | 0 | 0
4Q LOSS WILD-TYPE | 38 | 49 | 59 | 32

Figure S65. Get High-res Image Gene #45: '4q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 8.3e-07 (Chi-square test), Q value = 0.00042

Table S66. Gene #46: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
5P LOSS MUTATED | 1 | 6 | 0 | 0 | 0
5P LOSS WILD-TYPE | 37 | 18 | 33 | 48 | 38

Figure S66. Get High-res Image Gene #46: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 8.3e-07 (Chi-square test), Q value = 0.00042

Table S67. Gene #47: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
5Q LOSS MUTATED | 1 | 6 | 0 | 0 | 0
5Q LOSS WILD-TYPE | 37 | 18 | 33 | 48 | 38

Figure S67. Get High-res Image Gene #47: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 3.49e-06 (Chi-square test), Q value = 0.0017

Table S68. Gene #52: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
9P LOSS MUTATED | 8 | 0 | 13 | 0 | 1
9P LOSS WILD-TYPE | 63 | 40 | 24 | 21 | 27

Figure S68. Get High-res Image Gene #52: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 3.39e-07 (Chi-square test), Q value = 0.00018

Table S69. Gene #52: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
9P LOSS MUTATED | 4 | 10 | 5 | 0 | 0
9P LOSS WILD-TYPE | 34 | 14 | 28 | 48 | 38

Figure S69. Get High-res Image Gene #52: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1.05e-07 (Fisher's exact test), Q value = 5.5e-05

Table S70. Gene #52: '9p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
9P LOSS MUTATED | 2 | 20 | 0 | 0
9P LOSS WILD-TYPE | 37 | 47 | 59 | 32

Figure S70. Get High-res Image Gene #52: '9p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.61e-05 (Fisher's exact test), Q value = 0.041

Table S71. Gene #52: '9p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 71 | 56
9P LOSS MUTATED | 0 | 13 | 9
9P LOSS WILD-TYPE | 70 | 58 | 47

Figure S71. Get High-res Image Gene #52: '9p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 9.84e-05 (Chi-square test), Q value = 0.046

Table S72. Gene #53: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
9Q LOSS MUTATED | 10 | 0 | 12 | 0 | 2
9Q LOSS WILD-TYPE | 61 | 40 | 25 | 21 | 26

Figure S72. Get High-res Image Gene #53: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 2.2e-09 (Chi-square test), Q value = 1.2e-06

Table S73. Gene #53: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
9Q LOSS MUTATED | 4 | 12 | 5 | 0 | 0
9Q LOSS WILD-TYPE | 34 | 12 | 28 | 48 | 38

Figure S73. Get High-res Image Gene #53: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1.09e-08 (Fisher's exact test), Q value = 5.8e-06

Table S74. Gene #53: '9q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
9Q LOSS MUTATED | 2 | 22 | 0 | 0
9Q LOSS WILD-TYPE | 37 | 45 | 59 | 32

Figure S74. Get High-res Image Gene #53: '9q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.49e-05 (Fisher's exact test), Q value = 0.017

Table S75. Gene #53: '9q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 71 | 56
9Q LOSS MUTATED | 0 | 13 | 11
9Q LOSS WILD-TYPE | 70 | 58 | 45

Figure S75. Get High-res Image Gene #53: '9q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.37e-06 (Fisher's exact test), Q value = 0.0041

Table S76. Gene #53: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 75 | 99 | 23
9Q LOSS MUTATED | 15 | 2 | 7
9Q LOSS WILD-TYPE | 60 | 97 | 16

Figure S76. Get High-res Image Gene #53: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1.61e-05 (Chi-square test), Q value = 0.0079

Table S77. Gene #54: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
10P LOSS MUTATED | 0 | 0 | 8 | 0 | 4
10P LOSS WILD-TYPE | 71 | 40 | 29 | 21 | 24

Figure S77. Get High-res Image Gene #54: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 8.85e-05 (Chi-square test), Q value = 0.042

Table S78. Gene #54: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
10P LOSS MUTATED | 0 | 6 | 3 | 1 | 0
10P LOSS WILD-TYPE | 38 | 18 | 30 | 47 | 38

Figure S78. Get High-res Image Gene #54: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.000342 (Fisher's exact test), Q value = 0.16

Table S79. Gene #54: '10p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
10P LOSS MUTATED | 0 | 11 | 1 | 0
10P LOSS WILD-TYPE | 39 | 56 | 58 | 32

Figure S79. Get High-res Image Gene #54: '10p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 0.000379 (Chi-square test), Q value = 0.17

Table S80. Gene #55: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
10Q LOSS MUTATED | 1 | 0 | 7 | 0 | 4
10Q LOSS WILD-TYPE | 70 | 40 | 30 | 21 | 24

Figure S80. Get High-res Image Gene #55: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 7.12e-06 (Chi-square test), Q value = 0.0035

Table S81. Gene #55: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
10Q LOSS MUTATED | 0 | 7 | 3 | 1 | 0
10Q LOSS WILD-TYPE | 38 | 17 | 30 | 47 | 38

Figure S81. Get High-res Image Gene #55: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.000342 (Fisher's exact test), Q value = 0.16

Table S82. Gene #55: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
10Q LOSS MUTATED | 0 | 11 | 1 | 0
10Q LOSS WILD-TYPE | 39 | 56 | 58 | 32

Figure S82. Get High-res Image Gene #55: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000217 (Fisher's exact test), Q value = 0.1

Table S83. Gene #55: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 75 | 99 | 23
10Q LOSS MUTATED | 5 | 1 | 6
10Q LOSS WILD-TYPE | 70 | 98 | 17

Figure S83. Get High-res Image Gene #55: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 0.000373 (Chi-square test), Q value = 0.17

Table S84. Gene #57: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
11Q LOSS MUTATED | 2 | 0 | 8 | 0 | 4
11Q LOSS WILD-TYPE | 69 | 40 | 29 | 21 | 24

Figure S84. Get High-res Image Gene #57: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 1.31e-13 (Chi-square test), Q value = 7.2e-11

Table S85. Gene #58: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
13Q LOSS MUTATED | 0 | 13 | 2 | 2 | 0
13Q LOSS WILD-TYPE | 38 | 11 | 31 | 46 | 38

Figure S85. Get High-res Image Gene #58: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1.52e-05 (Fisher's exact test), Q value = 0.0075

Table S86. Gene #58: '13q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
13Q LOSS MUTATED | 0 | 16 | 2 | 0
13Q LOSS WILD-TYPE | 39 | 51 | 57 | 32

Figure S86. Get High-res Image Gene #58: '13q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 8.06e-17 (Chi-square test), Q value = 4.5e-14

Table S87. Gene #59: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
14Q LOSS MUTATED | 5 | 0 | 25 | 0 | 5
14Q LOSS WILD-TYPE | 66 | 40 | 12 | 21 | 23

Figure S87. Get High-res Image Gene #59: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 7.82e-05 (Chi-square test), Q value = 0.038

Table S88. Gene #59: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
14Q LOSS MUTATED | 10 | 11 | 3 | 6 | 1
14Q LOSS WILD-TYPE | 28 | 13 | 30 | 42 | 37

Figure S88. Get High-res Image Gene #59: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 0.000506 (Fisher's exact test), Q value = 0.23

Table S89. Gene #59: '14q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
14Q LOSS MUTATED | 7 | 22 | 4 | 2
14Q LOSS WILD-TYPE | 32 | 45 | 55 | 30

Figure S89. Get High-res Image Gene #59: '14q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 3.74e-05 (Chi-square test), Q value = 0.018

Table S90. Gene #60: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
15Q LOSS MUTATED | 4 | 0 | 11 | 0 | 4
15Q LOSS WILD-TYPE | 67 | 40 | 26 | 21 | 24

Figure S90. Get High-res Image Gene #60: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 4.07e-05 (Chi-square test), Q value = 0.02

Table S91. Gene #60: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
15Q LOSS MUTATED | 7 | 8 | 1 | 2 | 0
15Q LOSS WILD-TYPE | 31 | 16 | 32 | 46 | 38

Figure S91. Get High-res Image Gene #60: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 0.000346 (Chi-square test), Q value = 0.16

Table S92. Gene #62: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
16Q LOSS MUTATED | 0 | 4 | 1 | 0 | 0
16Q LOSS WILD-TYPE | 38 | 20 | 32 | 48 | 38

Figure S92. Get High-res Image Gene #62: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 8e-05 (Chi-square test), Q value = 0.038

Table S93. Gene #63: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
17P LOSS MUTATED | 0 | 5 | 2 | 0 | 0
17P LOSS WILD-TYPE | 38 | 19 | 31 | 48 | 38

Figure S93. Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 7.62e-08 (Chi-square test), Q value = 4e-05

Table S94. Gene #64: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
18P LOSS MUTATED | 2 | 13 | 8 | 2 | 3
18P LOSS WILD-TYPE | 36 | 11 | 25 | 46 | 35

Figure S94. Get High-res Image Gene #64: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 4.04e-07 (Fisher's exact test), Q value = 0.00021

Table S95. Gene #64: '18p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
18P LOSS MUTATED | 3 | 24 | 1 | 2
18P LOSS WILD-TYPE | 36 | 43 | 58 | 30

Figure S95. Get High-res Image Gene #64: '18p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 0.000385 (Chi-square test), Q value = 0.18

Table S96. Gene #65: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
18Q LOSS MUTATED | 12 | 2 | 14 | 0 | 4
18Q LOSS WILD-TYPE | 59 | 38 | 23 | 21 | 24

Figure S96. Get High-res Image Gene #65: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 6e-10 (Chi-square test), Q value = 3.2e-07

Table S97. Gene #65: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
18Q LOSS MUTATED | 2 | 15 | 8 | 2 | 3
18Q LOSS WILD-TYPE | 36 | 9 | 25 | 46 | 35

Figure S97. Get High-res Image Gene #65: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 4.51e-08 (Fisher's exact test), Q value = 2.4e-05

Table S98. Gene #65: '18q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
18Q LOSS MUTATED | 3 | 26 | 1 | 2
18Q LOSS WILD-TYPE | 36 | 41 | 58 | 30

Figure S98. Get High-res Image Gene #65: '18q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 0.000151 (Chi-square test), Q value = 0.071

Table S99. Gene #68: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
21Q LOSS MUTATED | 5 | 4 | 9 | 2 | 12
21Q LOSS WILD-TYPE | 66 | 36 | 28 | 19 | 16

Figure S99. Get High-res Image Gene #68: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1.52e-05 (Chi-square test), Q value = 0.0075

Table S100. Gene #69: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
22Q LOSS MUTATED | 15 | 4 | 19 | 0 | 6
22Q LOSS WILD-TYPE | 56 | 36 | 18 | 21 | 22

Figure S100. Get High-res Image Gene #69: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1.26e-08 (Chi-square test), Q value = 6.7e-06

Table S101. Gene #69: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
22Q LOSS MUTATED | 5 | 15 | 14 | 6 | 1
22Q LOSS WILD-TYPE | 33 | 9 | 19 | 42 | 37

Figure S101. Get High-res Image Gene #69: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1.5e-07 (Fisher's exact test), Q value = 7.8e-05

Table S102. Gene #69: '22q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
22Q LOSS MUTATED | 7 | 31 | 4 | 2
22Q LOSS WILD-TYPE | 32 | 36 | 55 | 30

Figure S102. Get High-res Image Gene #69: '22q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 2.45e-06 (Chi-square test), Q value = 0.0012

Table S103. Gene #70: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
XQ LOSS MUTATED | 4 | 1 | 13 | 1 | 1
XQ LOSS WILD-TYPE | 67 | 39 | 24 | 20 | 27

Figure S103. Get High-res Image Gene #70: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 4.64e-07 (Chi-square test), Q value = 0.00024

Table S104. Gene #70: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
XQ LOSS MUTATED | 1 | 10 | 3 | 2 | 1
XQ LOSS WILD-TYPE | 37 | 14 | 30 | 46 | 37

Figure S104. Get High-res Image Gene #70: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 0.000195 (Fisher's exact test), Q value = 0.092

Table S105. Gene #70: 'xq loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
XQ LOSS MUTATED | 2 | 16 | 2 | 0
XQ LOSS WILD-TYPE | 37 | 51 | 57 | 32

Figure S105. Get High-res Image Gene #70: 'xq loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

Methods & Data
Input

- Copy number data file = transformed.cor.cli.txt

- Molecular subtypes file = KIRP-TP.transferedmergedcluster.txt

- Number of patients = 197

- Number of significantly arm-level cnvs = 70

- Number of molecular subtypes = 8

- Exclude genes that fewer than K tumors have mutations, K = 3

Chi-square test

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

Fisher's exact test

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

Q value calculation

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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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