Correlation between copy number variations of arm-level result and molecular subtypes
Pheochromocytoma and Paraganglioma (Primary solid tumor)
02 April 2015 | analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1JW8D00
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1JW8D00
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 69 arm-level events and 10 molecular subtypes across 162 patients, 139 significant findings detected with P value < 0.05 and Q value < 0.25.

- 1q gain cnv correlated to 'CN_CNMF'.

- 2p gain cnv correlated to 'METHLYATION_CNMF'.

- 5q gain cnv correlated to 'METHLYATION_CNMF'.

- 6q gain cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

- 7p gain cnv correlated to 'CN_CNMF'.

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

- 8p gain cnv correlated to 'CN_CNMF'.

- 12p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

- 13q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

- 15q gain cnv correlated to 'METHLYATION_CNMF'.

- 16q gain cnv correlated to 'CN_CNMF'.

- 18q gain cnv correlated to 'RPPA_CHIERARCHICAL'.

- 19p gain cnv correlated to 'CN_CNMF'.

- 19q gain cnv correlated to 'METHLYATION_CNMF'.

- 20q gain cnv correlated to 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

- xq gain cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_MATURE_CNMF'.

- 1p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

- 1q loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.

- 2p loss cnv correlated to 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 3p loss cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 3q loss cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

- 4q loss cnv correlated to 'MRNASEQ_CNMF'.

- 5p loss cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- 6q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 7q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_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' and 'RPPA_CHIERARCHICAL'.

- 9q loss cnv correlated to 'CN_CNMF'.

- 11p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 11q loss cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 13q loss cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.

- 14q loss cnv correlated to 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 16p loss cnv correlated to 'METHLYATION_CNMF'.

- 16q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

- 17p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 17q loss cnv correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.

- 21q loss cnv correlated to 'MRNASEQ_CNMF'.

- 22q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- xp loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- xq loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 69 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, 139 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
1p loss | 98 (60%) | 64 | 1e-05 (0.00115) | 0.0152 (0.123) | 0.00562 (0.0636) | 0.00012 (0.0046) | 0.00291 (0.0372) | 0.00183 (0.0269) | 6e-05 (0.00244) | 0.0136 (0.114) | 0.00057 (0.0119) | 0.137 (0.439)
6q loss | 19 (12%) | 143 | 0.00097 (0.0167) | 0.00049 (0.0117) | 0.0202 (0.141) | 0.116 (0.399) | 0.00049 (0.0117) | 5e-05 (0.00244) | 0.00033 (0.00843) | 2e-05 (0.00138) | 0.0124 (0.111) | 0.00237 (0.0321)
11p loss | 54 (33%) | 108 | 1e-05 (0.00115) | 0.00056 (0.0119) | 0.00115 (0.0194) | 0.14 (0.444) | 0.00025 (0.00747) | 1e-05 (0.00115) | 3e-05 (0.00172) | 2e-05 (0.00138) | 5e-05 (0.00244) | 0.00247 (0.0328)
3p loss | 62 (38%) | 100 | 0.00061 (0.0124) | 0.0953 (0.35) | 0.0034 (0.0421) | 0.258 (0.584) | 0.00032 (0.00843) | 1e-05 (0.00115) | 0.00089 (0.0162) | 0.00121 (0.0199) | 0.00025 (0.00747) | 0.00018 (0.00654)
3q loss | 88 (54%) | 74 | 6e-05 (0.00244) | 0.521 (0.777) | 0.0565 (0.262) | 0.0261 (0.164) | 0.0429 (0.219) | 1e-05 (0.00115) | 0.00354 (0.0429) | 0.0304 (0.18) | 0.0119 (0.108) | 0.016 (0.127)
11q loss | 40 (25%) | 122 | 2e-05 (0.00138) | 0.0693 (0.297) | 0.0231 (0.152) | 0.116 (0.399) | 0.00026 (0.00747) | 0.00073 (0.0144) | 0.00019 (0.00655) | 0.00031 (0.00843) | 0.0002 (0.00657) | 0.0262 (0.164)
22q loss | 58 (36%) | 104 | 1e-05 (0.00115) | 0.0127 (0.111) | 0.365 (0.681) | 0.0842 (0.324) | 0.0322 (0.184) | 0.00207 (0.0291) | 0.0476 (0.238) | 0.0515 (0.252) | 0.0269 (0.167) | 0.0244 (0.157)
xp loss | 48 (30%) | 114 | 2e-05 (0.00138) | 0.00181 (0.0269) | 0.0584 (0.267) | 0.441 (0.741) | 0.0129 (0.112) | 0.00096 (0.0167) | 0.00254 (0.0331) | 0.0178 (0.135) | 0.24 (0.563) | 0.0182 (0.135)
xq loss | 49 (30%) | 113 | 3e-05 (0.00172) | 0.0014 (0.0225) | 0.0724 (0.298) | 0.612 (0.834) | 0.00735 (0.076) | 0.00055 (0.0119) | 0.00375 (0.0446) | 0.0104 (0.0968) | 0.212 (0.544) | 0.0133 (0.113)
13q gain | 9 (6%) | 153 | 0.0186 (0.136) | 0.0214 (0.146) | 0.243 (0.565) | 0.623 (0.836) | 0.00974 (0.0921) | 0.0094 (0.0914) | 0.024 (0.156) | 0.0535 (0.257) | 0.00964 (0.0921) | 0.36 (0.678)
17p loss | 61 (38%) | 101 | 0.00051 (0.0117) | 0.00236 (0.0321) | 0.492 (0.763) | 0.159 (0.456) | 0.0714 (0.298) | 0.0334 (0.188) | 0.0229 (0.152) | 0.0222 (0.149) | 0.214 (0.546) | 0.0139 (0.115)
xp gain | 6 (4%) | 156 | 0.152 (0.449) | 0.018 (0.135) |  |  | 0.035 (0.195) | 0.0168 (0.132) | 0.157 (0.454) | 0.0697 (0.297) | 0.0202 (0.141) | 0.299 (0.636)
7q loss | 6 (4%) | 156 | 0.0322 (0.184) | 0.48 (0.762) |  |  | 0.0404 (0.211) | 0.174 (0.486) | 0.0298 (0.18) | 0.0248 (0.159) | 0.247 (0.572) | 0.129 (0.421)
7q gain | 22 (14%) | 140 | 0.00743 (0.076) | 0.00628 (0.0688) | 0.448 (0.741) | 0.0187 (0.136) | 0.172 (0.484) | 0.284 (0.628) | 0.143 (0.444) | 0.114 (0.398) | 0.522 (0.777) | 0.46 (0.744)
12p gain | 11 (7%) | 151 | 0.011 (0.101) | 0.00737 (0.076) | 0.496 (0.763) | 0.119 (0.402) | 0.337 (0.662) | 0.324 (0.653) | 0.0192 (0.137) | 0.216 (0.547) | 0.131 (0.427) | 0.429 (0.736)
20q gain | 10 (6%) | 152 | 0.542 (0.784) | 0.167 (0.475) | 0.485 (0.763) | 1 (1.00) | 0.0302 (0.18) | 0.062 (0.277) | 0.0391 (0.206) | 0.077 (0.304) | 0.0391 (0.206) | 0.514 (0.775)
2p loss | 10 (6%) | 152 | 0.382 (0.691) | 0.0751 (0.3) | 0.747 (0.927) | 0.426 (0.736) | 0.00464 (0.0543) | 0.18 (0.493) | 0.195 (0.52) | 0.00075 (0.0144) | 0.147 (0.449) | 0.00749 (0.076)
14q loss | 20 (12%) | 142 | 0.237 (0.563) | 0.0532 (0.257) | 0.168 (0.475) | 0.204 (0.536) | 0.31 (0.638) | 0.793 (0.953) | 0.155 (0.452) | 0.00198 (0.0285) | 0.029 (0.177) | 0.00157 (0.0246)
6q gain | 8 (5%) | 154 | 0.148 (0.449) | 0.00177 (0.0269) |  |  | 0.0367 (0.198) | 0.111 (0.392) | 0.129 (0.421) | 0.183 (0.495) | 0.0809 (0.317) | 0.267 (0.599)
xq gain | 5 (3%) | 157 | 0.177 (0.493) | 0.0447 (0.225) |  |  | 0.0528 (0.256) | 0.0545 (0.258) | 0.142 (0.444) | 0.0679 (0.296) | 0.0305 (0.18) | 0.0966 (0.353)
4p loss | 11 (7%) | 151 | 0.00342 (0.0421) | 0.146 (0.449) | 0.47 (0.75) | 0.35 (0.666) | 0.0068 (0.0733) | 0.184 (0.495) | 0.293 (0.631) | 0.391 (0.699) | 0.058 (0.267) | 0.146 (0.449)
5p loss | 5 (3%) | 157 | 0.0644 (0.285) | 0.376 (0.688) |  |  | 0.0363 (0.197) | 0.0362 (0.197) | 0.141 (0.444) | 0.168 (0.475) | 0.168 (0.475) | 0.0546 (0.258)
9p loss | 11 (7%) | 151 | 0.0492 (0.244) | 0.718 (0.915) | 0.0845 (0.324) | 0.0175 (0.134) | 0.182 (0.495) | 0.181 (0.493) | 0.672 (0.877) | 0.0686 (0.296) | 0.548 (0.789) | 0.311 (0.638)
13q loss | 8 (5%) | 154 | 0.0361 (0.197) | 0.447 (0.741) | 0.0125 (0.111) | 0.671 (0.877) | 0.312 (0.638) | 0.116 (0.399) | 0.528 (0.778) | 0.226 (0.563) | 0.549 (0.789) | 0.463 (0.744)
17q loss | 19 (12%) | 143 | 6e-05 (0.00244) | 0.903 (1.00) | 0.156 (0.454) | 0.0323 (0.184) | 0.297 (0.635) | 0.23 (0.563) | 0.37 (0.681) | 0.0879 (0.331) | 0.882 (1.00) | 0.261 (0.59)
1q gain | 19 (12%) | 143 | 0.00086 (0.016) | 0.354 (0.671) | 0.913 (1.00) | 1 (1.00) | 0.49 (0.763) | 0.594 (0.822) | 0.907 (1.00) | 0.664 (0.872) | 0.487 (0.763) | 0.847 (0.977)
2p gain | 6 (4%) | 156 | 0.507 (0.774) | 0.00573 (0.0638) | 0.748 (0.927) | 1 (1.00) | 0.24 (0.563) | 0.347 (0.666) | 0.135 (0.437) | 0.335 (0.662) | 0.191 (0.512) | 0.462 (0.744)
5q gain | 7 (4%) | 155 | 0.896 (1.00) | 0.00527 (0.0606) |  |  | 0.0731 (0.298) | 0.297 (0.635) | 0.484 (0.763) | 0.38 (0.691) | 0.941 (1.00) | 0.286 (0.63)
7p gain | 27 (17%) | 135 | 0.0212 (0.146) | 0.0738 (0.298) | 0.533 (0.78) | 0.149 (0.449) | 0.139 (0.443) | 0.381 (0.691) | 0.239 (0.563) | 0.0726 (0.298) | 0.316 (0.64) | 0.0884 (0.331)
8p gain | 10 (6%) | 152 | 0.019 (0.137) | 0.369 (0.681) | 0.816 (0.965) | 1 (1.00) | 0.0869 (0.331) | 0.091 (0.336) | 0.071 (0.298) | 0.155 (0.452) | 0.454 (0.744) | 0.1 (0.361)
15q gain | 14 (9%) | 148 | 0.25 (0.576) | 0.0326 (0.184) | 0.837 (0.971) | 0.35 (0.666) | 0.314 (0.64) | 0.77 (0.944) | 0.427 (0.736) | 0.792 (0.953) | 0.557 (0.79) | 0.925 (1.00)
16q gain | 6 (4%) | 156 | 0.0145 (0.119) | 1 (1.00) |  |  | 0.27 (0.603) | 0.701 (0.902) | 1 (1.00) | 0.768 (0.944) | 0.397 (0.707) | 0.428 (0.736)
18q gain | 10 (6%) | 152 | 0.347 (0.666) | 0.583 (0.816) | 1 (1.00) | 0.0386 (0.206) | 0.365 (0.681) | 0.534 (0.78) | 0.845 (0.977) | 0.439 (0.741) | 0.196 (0.52) | 0.532 (0.78)
19p gain | 20 (12%) | 142 | 0.0154 (0.123) | 0.0769 (0.304) | 0.408 (0.719) | 0.781 (0.952) | 0.749 (0.927) | 0.644 (0.859) | 0.275 (0.611) | 0.926 (1.00) | 0.21 (0.543) | 0.727 (0.922)
19q gain | 14 (9%) | 148 | 0.152 (0.449) | 0.0085 (0.0838) | 0.443 (0.741) | 0.539 (0.784) | 0.376 (0.688) | 0.228 (0.563) | 0.459 (0.744) | 0.667 (0.873) | 0.523 (0.777) | 0.489 (0.763)
1q loss | 27 (17%) | 135 | 0.895 (1.00) | 0.309 (0.638) | 0.908 (1.00) | 0.148 (0.449) | 0.124 (0.412) | 0.518 (0.775) | 0.663 (0.871) | 0.264 (0.593) | 0.0313 (0.183) | 0.239 (0.563)
4q loss | 10 (6%) | 152 | 0.0729 (0.298) | 0.241 (0.563) | 0.472 (0.75) | 0.35 (0.666) | 0.0175 (0.134) | 0.338 (0.663) | 0.417 (0.728) | 0.525 (0.777) | 0.327 (0.657) | 0.323 (0.653)
8p loss | 20 (12%) | 142 | 0.0216 (0.146) | 0.391 (0.699) | 0.445 (0.741) | 0.815 (0.965) | 0.124 (0.412) | 0.108 (0.383) | 0.715 (0.915) | 0.952 (1.00) | 0.28 (0.621) | 0.488 (0.763)
8q loss | 12 (7%) | 150 | 0.0434 (0.22) | 0.739 (0.927) | 0.151 (0.449) | 1 (1.00) | 0.33 (0.66) | 0.62 (0.836) | 0.111 (0.392) | 0.437 (0.741) | 0.928 (1.00) | 0.427 (0.736)
9q loss | 11 (7%) | 151 | 0.00786 (0.0786) | 0.61 (0.834) | 0.456 (0.744) | 0.349 (0.666) | 0.511 (0.775) | 0.627 (0.84) | 0.725 (0.921) | 0.401 (0.712) | 0.828 (0.971) | 0.441 (0.741)
16p loss | 9 (6%) | 153 | 0.335 (0.662) | 0.0426 (0.219) | 0.677 (0.877) | 0.445 (0.741) | 0.554 (0.79) | 0.361 (0.679) | 0.249 (0.575) | 0.403 (0.714) | 0.678 (0.877) | 0.771 (0.944)
16q loss | 5 (3%) | 157 | 0.739 (0.927) | 0.445 (0.741) | 0.746 (0.927) | 0.786 (0.953) | 0.446 (0.741) | 0.0276 (0.17) | 0.21 (0.543) | 0.59 (0.821) | 0.0905 (0.336) | 0.829 (0.971)
21q loss | 36 (22%) | 126 | 0.206 (0.54) | 0.0506 (0.249) | 0.31 (0.638) | 0.455 (0.744) | 0.0414 (0.215) | 0.939 (1.00) | 0.561 (0.791) | 0.603 (0.827) | 0.908 (1.00) | 0.717 (0.915)
1p gain | 7 (4%) | 155 | 0.119 (0.402) | 0.785 (0.953) |  |  | 0.673 (0.877) | 0.822 (0.968) | 0.895 (1.00) | 0.526 (0.777) | 0.835 (0.971) | 0.656 (0.866)
4p gain | 4 (2%) | 158 | 0.676 (0.877) | 0.367 (0.681) |  |  | 0.819 (0.968) | 0.552 (0.79) | 0.451 (0.743) | 0.789 (0.953) | 0.77 (0.944) | 1 (1.00)
4q gain | 3 (2%) | 159 | 0.0622 (0.277) | 0.803 (0.961) |  |  | 0.472 (0.75) | 0.739 (0.927) | 0.615 (0.835) | 0.836 (0.971) | 0.814 (0.965) | 0.463 (0.744)
5p gain | 11 (7%) | 151 | 0.62 (0.836) | 0.434 (0.741) | 0.602 (0.827) | 1 (1.00) | 0.916 (1.00) | 0.66 (0.869) | 0.854 (0.98) | 0.614 (0.835) | 0.83 (0.971) | 0.214 (0.546)
6p gain | 15 (9%) | 147 | 0.887 (1.00) | 0.257 (0.583) | 0.1 (0.361) | 0.201 (0.53) | 0.308 (0.638) | 0.37 (0.681) | 0.238 (0.563) | 0.305 (0.638) | 0.561 (0.791) | 0.51 (0.775)
8q gain | 13 (8%) | 149 | 0.241 (0.563) | 0.751 (0.929) | 0.598 (0.825) | 1 (1.00) | 0.0823 (0.319) | 0.075 (0.3) | 0.114 (0.398) | 0.201 (0.53) | 0.804 (0.961) | 0.0907 (0.336)
9p gain | 4 (2%) | 158 | 0.231 (0.563) | 0.0704 (0.298) |  |  | 0.152 (0.449) | 0.225 (0.563) | 0.29 (0.631) | 0.254 (0.579) | 0.303 (0.638) | 0.511 (0.775)
9q gain | 3 (2%) | 159 | 0.46 (0.744) | 0.139 (0.443) |  |  | 0.24 (0.563) | 0.239 (0.563) | 0.462 (0.744) | 0.346 (0.666) | 0.293 (0.631) | 0.557 (0.79)
10p gain | 12 (7%) | 150 | 0.513 (0.775) | 0.0733 (0.298) | 0.719 (0.915) | 0.118 (0.402) | 0.517 (0.775) | 0.517 (0.775) | 1 (1.00) | 0.842 (0.975) | 0.489 (0.763) | 0.179 (0.493)
10q gain | 10 (6%) | 152 | 0.103 (0.369) | 0.693 (0.894) | 0.718 (0.915) | 0.12 (0.403) | 0.492 (0.763) | 0.592 (0.821) | 0.705 (0.906) | 0.507 (0.774) | 0.426 (0.736) | 0.154 (0.452)
11p gain | 5 (3%) | 157 | 0.0875 (0.331) | 0.514 (0.775) | 0.831 (0.971) | 1 (1.00) | 0.412 (0.723) | 0.305 (0.638) | 0.539 (0.784) | 0.494 (0.763) | 0.345 (0.666) | 0.69 (0.892)
12q gain | 14 (9%) | 148 | 0.0686 (0.296) | 0.225 (0.563) | 0.851 (0.98) | 0.49 (0.763) | 0.603 (0.827) | 0.653 (0.865) | 0.0612 (0.277) | 0.291 (0.631) | 0.223 (0.561) | 0.436 (0.741)
14q gain | 4 (2%) | 158 | 0.0618 (0.277) | 0.368 (0.681) |  |  | 0.551 (0.79) | 0.554 (0.79) | 0.287 (0.63) | 0.789 (0.953) | 0.769 (0.944) | 0.872 (0.994)
16p gain | 6 (4%) | 156 | 0.239 (0.563) | 0.557 (0.79) |  |  | 0.744 (0.927) | 0.74 (0.927) | 0.384 (0.692) | 0.815 (0.965) | 0.292 (0.631) | 0.502 (0.771)
17q gain | 5 (3%) | 157 | 0.545 (0.786) | 0.312 (0.638) | 0.22 (0.555) | 0.337 (0.662) | 0.3 (0.636) | 0.304 (0.638) | 0.541 (0.784) | 0.774 (0.945) | 0.541 (0.784) | 0.212 (0.544)
18p gain | 8 (5%) | 154 | 0.149 (0.449) | 0.23 (0.563) | 1 (1.00) | 0.119 (0.402) | 0.383 (0.691) | 0.651 (0.864) | 0.465 (0.745) | 0.561 (0.791) | 0.129 (0.421) | 0.855 (0.98)
20p gain | 12 (7%) | 150 | 0.646 (0.859) | 0.367 (0.681) | 0.623 (0.836) | 0.729 (0.922) | 0.18 (0.493) | 0.343 (0.666) | 0.169 (0.475) | 0.383 (0.691) | 0.593 (0.821) | 0.59 (0.821)
21q gain | 3 (2%) | 159 | 0.251 (0.576) | 0.136 (0.439) |  |  | 0.238 (0.563) | 0.0682 (0.296) | 0.184 (0.495) | 0.409 (0.719) | 0.291 (0.631) | 0.806 (0.961)
22q gain | 3 (2%) | 159 | 0.252 (0.577) | 0.0817 (0.318) |  |  | 0.238 (0.563) | 0.15 (0.449) | 0.18 (0.493) | 0.408 (0.719) | 0.0563 (0.262) | 0.807 (0.961)
2q loss | 13 (8%) | 149 | 0.822 (0.968) | 0.45 (0.742) | 0.748 (0.927) | 0.427 (0.736) | 0.417 (0.728) | 0.143 (0.444) | 0.53 (0.78) | 0.0976 (0.355) | 0.328 (0.657) | 0.34 (0.665)
5q loss | 7 (4%) | 155 | 0.386 (0.693) | 0.785 (0.953) | 0.494 (0.763) | 1 (1.00) | 0.646 (0.859) | 0.524 (0.777) | 0.896 (1.00) | 0.358 (0.677) | 0.227 (0.563) | 0.304 (0.638)
15q loss | 3 (2%) | 159 | 0.348 (0.666) | 0.333 (0.661) |  |  | 1 (1.00) | 0.866 (0.99) | 0.617 (0.836) | 0.836 (0.971) | 0.9 (1.00) | 1 (1.00)
18p loss | 16 (10%) | 146 | 0.503 (0.771) | 0.744 (0.927) | 0.435 (0.741) | 0.208 (0.542) | 0.855 (0.98) | 0.758 (0.935) | 0.893 (1.00) | 0.312 (0.638) | 0.607 (0.831) | 0.455 (0.744)
18q loss | 6 (4%) | 156 | 0.288 (0.63) | 0.874 (0.995) | 0.833 (0.971) | 0.055 (0.258) | 0.584 (0.816) | 0.656 (0.866) | 0.573 (0.805) | 0.583 (0.816) | 0.432 (0.74) | 0.867 (0.99)
19q loss | 6 (4%) | 156 | 0.242 (0.563) | 1 (1.00) |  |  | 0.942 (1.00) | 0.943 (1.00) | 0.332 (0.661) | 0.623 (0.836) | 0.927 (1.00) | 0.932 (1.00)
20q loss | 3 (2%) | 159 | 1 (1.00) | 1 (1.00) |  |  | 1 (1.00) | 0.643 (0.859) | 0.79 (0.953) | 1 (1.00) | 0.73 (0.922) | 0.806 (0.961)

'1q gain' versus 'CN_CNMF'

P value = 0.00086 (Fisher's exact test), Q value = 0.016

Table S1. Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
1Q GAIN MUTATED | 6 | 2 | 11
1Q GAIN WILD-TYPE | 54 | 61 | 28

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.00573 (Fisher's exact test), Q value = 0.064

Table S2. Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 78 | 44
2P GAIN MUTATED | 5 | 1 | 0
2P GAIN WILD-TYPE | 35 | 77 | 44

Figure S2. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 0.00527 (Fisher's exact test), Q value = 0.061

Table S3. Gene #7: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 78 | 44
5Q GAIN MUTATED | 2 | 0 | 5
5Q GAIN WILD-TYPE | 38 | 78 | 39

Figure S3. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.00177 (Fisher's exact test), Q value = 0.027

Table S4. Gene #9: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 78 | 44
6Q GAIN MUTATED | 2 | 0 | 6
6Q GAIN WILD-TYPE | 38 | 78 | 38

Figure S4. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 0.0367 (Fisher's exact test), Q value = 0.2

Table S5. Gene #9: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
6Q GAIN MUTATED | 1 | 1 | 6 | 0
6Q GAIN WILD-TYPE | 32 | 63 | 38 | 21

Figure S5. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.15

Table S6. Gene #10: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
7P GAIN MUTATED | 4 | 15 | 8
7P GAIN WILD-TYPE | 56 | 48 | 31

Figure S6. Get High-res Image Gene #10: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 0.00743 (Fisher's exact test), Q value = 0.076

Table S7. Gene #11: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
7Q GAIN MUTATED | 2 | 13 | 7
7Q GAIN WILD-TYPE | 58 | 50 | 32

Figure S7. Get High-res Image Gene #11: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.00628 (Fisher's exact test), Q value = 0.069

Table S8. Gene #11: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 78 | 44
7Q GAIN MUTATED | 8 | 4 | 10
7Q GAIN WILD-TYPE | 32 | 74 | 34

Figure S8. Get High-res Image Gene #11: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0187 (Fisher's exact test), Q value = 0.14

Table S9. Gene #11: '7q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 18 | 28
7Q GAIN MUTATED | 1 | 2 | 8
7Q GAIN WILD-TYPE | 30 | 16 | 20

Figure S9. Get High-res Image Gene #11: '7q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 0.019 (Fisher's exact test), Q value = 0.14

Table S10. Gene #12: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
8P GAIN MUTATED | 0 | 6 | 4
8P GAIN WILD-TYPE | 60 | 57 | 35

Figure S10. Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.1

Table S11. Gene #19: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
12P GAIN MUTATED | 1 | 3 | 7
12P GAIN WILD-TYPE | 59 | 60 | 32

Figure S11. Get High-res Image Gene #19: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 0.00737 (Fisher's exact test), Q value = 0.076

Table S12. Gene #19: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 78 | 44
12P GAIN MUTATED | 4 | 1 | 6
12P GAIN WILD-TYPE | 36 | 77 | 38

Figure S12. Get High-res Image Gene #19: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.14

Table S13. Gene #19: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 58 | 39
12P GAIN MUTATED | 9 | 1 | 1
12P GAIN WILD-TYPE | 56 | 57 | 38

Figure S13. Get High-res Image Gene #19: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.14

Table S14. Gene #21: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
13Q GAIN MUTATED | 0 | 7 | 2
13Q GAIN WILD-TYPE | 60 | 56 | 37

Figure S14. Get High-res Image Gene #21: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.0214 (Fisher's exact test), Q value = 0.15

Table S15. Gene #21: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 78 | 44
13Q GAIN MUTATED | 5 | 1 | 3
13Q GAIN WILD-TYPE | 35 | 77 | 41

Figure S15. Get High-res Image Gene #21: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 0.00974 (Fisher's exact test), Q value = 0.092

Table S16. Gene #21: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
13Q GAIN MUTATED | 2 | 0 | 6 | 1
13Q GAIN WILD-TYPE | 31 | 64 | 38 | 20

Figure S16. Get High-res Image Gene #21: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0094 (Fisher's exact test), Q value = 0.091

Table S17. Gene #21: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 64 | 43 | 21
13Q GAIN MUTATED | 2 | 0 | 6 | 1
13Q GAIN WILD-TYPE | 32 | 64 | 37 | 20

Figure S17. Get High-res Image Gene #21: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 0.024 (Fisher's exact test), Q value = 0.16

Table S18. Gene #21: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 58 | 39
13Q GAIN MUTATED | 7 | 0 | 2
13Q GAIN WILD-TYPE | 58 | 58 | 37

Figure S18. Get High-res Image Gene #21: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00964 (Fisher's exact test), Q value = 0.092

Table S19. Gene #21: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 34 | 58 | 11 | 35 | 23
13Q GAIN MUTATED | 2 | 0 | 0 | 6 | 1
13Q GAIN WILD-TYPE | 32 | 58 | 11 | 29 | 22

Figure S19. Get High-res Image Gene #21: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q gain' versus 'METHLYATION_CNMF'

P value = 0.0326 (Fisher's exact test), Q value = 0.18

Table S20. Gene #23: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 78 | 44
15Q GAIN MUTATED | 3 | 3 | 8
15Q GAIN WILD-TYPE | 37 | 75 | 36

Figure S20. Get High-res Image Gene #23: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.12

Table S21. Gene #25: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
16Q GAIN MUTATED | 2 | 0 | 4
16Q GAIN WILD-TYPE | 58 | 63 | 35

Figure S21. Get High-res Image Gene #25: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0386 (Fisher's exact test), Q value = 0.21

Table S22. Gene #28: '18q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 18 | 28
18Q GAIN MUTATED | 0 | 3 | 2
18Q GAIN WILD-TYPE | 31 | 15 | 26

Figure S22. Get High-res Image Gene #28: '18q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.12

Table S23. Gene #29: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
19P GAIN MUTATED | 2 | 10 | 8
19P GAIN WILD-TYPE | 58 | 53 | 31

Figure S23. Get High-res Image Gene #29: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 0.0085 (Fisher's exact test), Q value = 0.084

Table S24. Gene #30: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 78 | 44
19Q GAIN MUTATED | 4 | 2 | 8
19Q GAIN WILD-TYPE | 36 | 76 | 36

Figure S24. Get High-res Image Gene #30: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 0.0302 (Fisher's exact test), Q value = 0.18

Table S25. Gene #32: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
20Q GAIN MUTATED | 3 | 1 | 6 | 0
20Q GAIN WILD-TYPE | 30 | 63 | 38 | 21

Figure S25. Get High-res Image Gene #32: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 0.0391 (Fisher's exact test), Q value = 0.21

Table S26. Gene #32: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 58 | 39
20Q GAIN MUTATED | 8 | 1 | 1
20Q GAIN WILD-TYPE | 57 | 57 | 38

Figure S26. Get High-res Image Gene #32: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0391 (Fisher's exact test), Q value = 0.21

Table S27. Gene #32: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 34 | 58 | 11 | 35 | 23
20Q GAIN MUTATED | 5 | 1 | 0 | 4 | 0
20Q GAIN WILD-TYPE | 29 | 57 | 11 | 31 | 23

Figure S27. Get High-res Image Gene #32: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.13

Table S28. Gene #35: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 78 | 44
XP GAIN MUTATED | 2 | 0 | 4
XP GAIN WILD-TYPE | 38 | 78 | 40

Figure S28. Get High-res Image Gene #35: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 0.035 (Fisher's exact test), Q value = 0.19

Table S29. Gene #35: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
XP GAIN MUTATED | 3 | 0 | 3 | 0
XP GAIN WILD-TYPE | 30 | 64 | 41 | 21

Figure S29. Get High-res Image Gene #35: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.13

Table S30. Gene #35: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 64 | 43 | 21
XP GAIN MUTATED | 4 | 0 | 1 | 1
XP GAIN WILD-TYPE | 30 | 64 | 42 | 20

Figure S30. Get High-res Image Gene #35: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0202 (Fisher's exact test), Q value = 0.14

Table S31. Gene #35: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 34 | 58 | 11 | 35 | 23
XP GAIN MUTATED | 4 | 0 | 1 | 1 | 0
XP GAIN WILD-TYPE | 30 | 58 | 10 | 34 | 23

Figure S31. Get High-res Image Gene #35: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 0.0447 (Fisher's exact test), Q value = 0.22

Table S32. Gene #36: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 78 | 44
XQ GAIN MUTATED | 2 | 0 | 3
XQ GAIN WILD-TYPE | 38 | 78 | 41

Figure S32. Get High-res Image Gene #36: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0305 (Fisher's exact test), Q value = 0.18

Table S33. Gene #36: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 34 | 58 | 11 | 35 | 23
XQ GAIN MUTATED | 4 | 0 | 0 | 1 | 0
XQ GAIN WILD-TYPE | 30 | 58 | 11 | 34 | 23

Figure S33. Get High-res Image Gene #36: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0011

Table S34. Gene #37: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
1P LOSS MUTATED | 51 | 24 | 23
1P LOSS WILD-TYPE | 9 | 39 | 16

Figure S34. Get High-res Image Gene #37: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.12

Table S35. Gene #37: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 78 | 44
1P LOSS MUTATED | 19 | 56 | 23
1P LOSS WILD-TYPE | 21 | 22 | 21

Figure S35. Get High-res Image Gene #37: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'RPPA_CNMF'

P value = 0.00562 (Fisher's exact test), Q value = 0.064

Table S36. Gene #37: '1p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 13 | 9 | 20 | 5 | 17 | 13
1P LOSS MUTATED | 9 | 6 | 17 | 1 | 7 | 4
1P LOSS WILD-TYPE | 4 | 3 | 3 | 4 | 10 | 9

Figure S36. Get High-res Image Gene #37: '1p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'1p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.0046

Table S37. Gene #37: '1p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 18 | 28
1P LOSS MUTATED | 11 | 17 | 16
1P LOSS WILD-TYPE | 20 | 1 | 12

Figure S37. Get High-res Image Gene #37: '1p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.00291 (Fisher's exact test), Q value = 0.037

Table S38. Gene #37: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
1P LOSS MUTATED | 20 | 49 | 19 | 10
1P LOSS WILD-TYPE | 13 | 15 | 25 | 11

Figure S38. Get High-res Image Gene #37: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00183 (Fisher's exact test), Q value = 0.027

Table S39. Gene #37: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 64 | 43 | 21
1P LOSS MUTATED | 15 | 50 | 23 | 10
1P LOSS WILD-TYPE | 19 | 14 | 20 | 11

Figure S39. Get High-res Image Gene #37: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0024

Table S40. Gene #37: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 58 | 39
1P LOSS MUTATED | 29 | 47 | 22
1P LOSS WILD-TYPE | 36 | 11 | 17

Figure S40. Get High-res Image Gene #37: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.11

Table S41. Gene #37: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 66 | 54 | 18 | 24
1P LOSS MUTATED | 31 | 41 | 11 | 15
1P LOSS WILD-TYPE | 35 | 13 | 7 | 9

Figure S41. Get High-res Image Gene #37: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.012

Table S42. Gene #37: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 34 | 58 | 11 | 35 | 23
1P LOSS MUTATED | 16 | 48 | 6 | 17 | 11
1P LOSS WILD-TYPE | 18 | 10 | 5 | 18 | 12

Figure S42. Get High-res Image Gene #37: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.18

Table S43. Gene #38: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 34 | 58 | 11 | 35 | 23
1Q LOSS MUTATED | 3 | 9 | 0 | 12 | 3
1Q LOSS WILD-TYPE | 31 | 49 | 11 | 23 | 20

Figure S43. Get High-res Image Gene #38: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 0.00464 (Fisher's exact test), Q value = 0.054

Table S44. Gene #39: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
2P LOSS MUTATED | 0 | 1 | 7 | 2
2P LOSS WILD-TYPE | 33 | 63 | 37 | 19

Figure S44. Get High-res Image Gene #39: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00075 (Fisher's exact test), Q value = 0.014

Table S45. Gene #39: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 66 | 54 | 18 | 24
2P LOSS MUTATED | 3 | 0 | 5 | 2
2P LOSS WILD-TYPE | 63 | 54 | 13 | 22

Figure S45. Get High-res Image Gene #39: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00749 (Fisher's exact test), Q value = 0.076

Table S46. Gene #39: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 71 | 53 | 18 | 19
2P LOSS MUTATED | 3 | 2 | 5 | 0
2P LOSS WILD-TYPE | 68 | 51 | 13 | 19

Figure S46. Get High-res Image Gene #39: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.012

Table S47. Gene #41: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
3P LOSS MUTATED | 17 | 20 | 25
3P LOSS WILD-TYPE | 43 | 43 | 14

Figure S47. Get High-res Image Gene #41: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'RPPA_CNMF'

P value = 0.0034 (Fisher's exact test), Q value = 0.042

Table S48. Gene #41: '3p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 13 | 9 | 20 | 5 | 17 | 13
3P LOSS MUTATED | 1 | 2 | 9 | 4 | 4 | 9
3P LOSS WILD-TYPE | 12 | 7 | 11 | 1 | 13 | 4

Figure S48. Get High-res Image Gene #41: '3p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0084

Table S49. Gene #41: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
3P LOSS MUTATED | 16 | 19 | 25 | 2
3P LOSS WILD-TYPE | 17 | 45 | 19 | 19

Figure S49. Get High-res Image Gene #41: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0011

Table S50. Gene #41: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 64 | 43 | 21
3P LOSS MUTATED | 9 | 21 | 30 | 2
3P LOSS WILD-TYPE | 25 | 43 | 13 | 19

Figure S50. Get High-res Image Gene #41: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.016

Table S51. Gene #41: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 58 | 39
3P LOSS MUTATED | 35 | 20 | 7
3P LOSS WILD-TYPE | 30 | 38 | 32

Figure S51. Get High-res Image Gene #41: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00121 (Fisher's exact test), Q value = 0.02

Table S52. Gene #41: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 66 | 54 | 18 | 24
3P LOSS MUTATED | 36 | 17 | 6 | 3
3P LOSS WILD-TYPE | 30 | 37 | 12 | 21

Figure S52. Get High-res Image Gene #41: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0075

Table S53. Gene #41: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 34 | 58 | 11 | 35 | 23
3P LOSS MUTATED | 13 | 16 | 2 | 25 | 6
3P LOSS WILD-TYPE | 21 | 42 | 9 | 10 | 17

Figure S53. Get High-res Image Gene #41: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.0065

Table S54. Gene #41: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 71 | 53 | 18 | 19
3P LOSS MUTATED | 20 | 33 | 6 | 3
3P LOSS WILD-TYPE | 51 | 20 | 12 | 16

Figure S54. Get High-res Image Gene #41: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0024

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
3Q LOSS MUTATED | 36 | 22 | 30
3Q LOSS WILD-TYPE | 24 | 41 | 9

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

'3q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0261 (Fisher's exact test), Q value = 0.16

Table S56. Gene #42: '3q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 18 | 28
3Q LOSS MUTATED | 11 | 13 | 17
3Q LOSS WILD-TYPE | 20 | 5 | 11

Figure S56. Get High-res Image Gene #42: '3q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 0.0429 (Fisher's exact test), Q value = 0.22

Table S57. Gene #42: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
3Q LOSS MUTATED | 20 | 40 | 22 | 6
3Q LOSS WILD-TYPE | 13 | 24 | 22 | 15

Figure S57. Get High-res Image Gene #42: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0011

Table S58. Gene #42: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 64 | 43 | 21
3Q LOSS MUTATED | 6 | 42 | 33 | 7
3Q LOSS WILD-TYPE | 28 | 22 | 10 | 14

Figure S58. Get High-res Image Gene #42: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 0.00354 (Fisher's exact test), Q value = 0.043

Table S59. Gene #42: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 58 | 39
3Q LOSS MUTATED | 39 | 37 | 12
3Q LOSS WILD-TYPE | 26 | 21 | 27

Figure S59. Get High-res Image Gene #42: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0304 (Fisher's exact test), Q value = 0.18

Table S60. Gene #42: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 66 | 54 | 18 | 24
3Q LOSS MUTATED | 39 | 34 | 5 | 10
3Q LOSS WILD-TYPE | 27 | 20 | 13 | 14

Figure S60. Get High-res Image Gene #42: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.11

Table S61. Gene #42: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 34 | 58 | 11 | 35 | 23
3Q LOSS MUTATED | 11 | 38 | 4 | 23 | 12
3Q LOSS WILD-TYPE | 23 | 20 | 7 | 12 | 11

Figure S61. Get High-res Image Gene #42: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.016 (Fisher's exact test), Q value = 0.13

Table S62. Gene #42: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 71 | 53 | 18 | 19
3Q LOSS MUTATED | 39 | 36 | 5 | 8
3Q LOSS WILD-TYPE | 32 | 17 | 13 | 11

Figure S62. Get High-res Image Gene #42: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 0.00342 (Fisher's exact test), Q value = 0.042

Table S63. Gene #43: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
4P LOSS MUTATED | 0 | 5 | 6
4P LOSS WILD-TYPE | 60 | 58 | 33

Figure S63. Get High-res Image Gene #43: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.0068 (Fisher's exact test), Q value = 0.073

Table S64. Gene #43: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
4P LOSS MUTATED | 0 | 3 | 8 | 0
4P LOSS WILD-TYPE | 33 | 61 | 36 | 21

Figure S64. Get High-res Image Gene #43: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 0.13

Table S65. Gene #44: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
4Q LOSS MUTATED | 0 | 3 | 7 | 0
4Q LOSS WILD-TYPE | 33 | 61 | 37 | 21

Figure S65. Get High-res Image Gene #44: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.2

Table S66. Gene #45: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
5P LOSS MUTATED | 1 | 0 | 4 | 0
5P LOSS WILD-TYPE | 32 | 64 | 40 | 21

Figure S66. Get High-res Image Gene #45: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0362 (Fisher's exact test), Q value = 0.2

Table S67. Gene #45: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 64 | 43 | 21
5P LOSS MUTATED | 1 | 0 | 4 | 0
5P LOSS WILD-TYPE | 33 | 64 | 39 | 21

Figure S67. Get High-res Image Gene #45: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 0.00097 (Fisher's exact test), Q value = 0.017

Table S68. Gene #47: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
6Q LOSS MUTATED | 13 | 1 | 5
6Q LOSS WILD-TYPE | 47 | 62 | 34

Figure S68. Get High-res Image Gene #47: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.012

Table S69. Gene #47: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 78 | 44
6Q LOSS MUTATED | 1 | 17 | 1
6Q LOSS WILD-TYPE | 39 | 61 | 43

Figure S69. Get High-res Image Gene #47: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'RPPA_CNMF'

P value = 0.0202 (Fisher's exact test), Q value = 0.14

Table S70. Gene #47: '6q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 13 | 9 | 20 | 5 | 17 | 13
6Q LOSS MUTATED | 2 | 1 | 8 | 0 | 0 | 1
6Q LOSS WILD-TYPE | 11 | 8 | 12 | 5 | 17 | 12

Figure S70. Get High-res Image Gene #47: '6q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.012

Table S71. Gene #47: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
6Q LOSS MUTATED | 1 | 16 | 1 | 1
6Q LOSS WILD-TYPE | 32 | 48 | 43 | 20

Figure S71. Get High-res Image Gene #47: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.0024

Table S72. Gene #47: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 64 | 43 | 21
6Q LOSS MUTATED | 0 | 17 | 1 | 1
6Q LOSS WILD-TYPE | 34 | 47 | 42 | 20

Figure S72. Get High-res Image Gene #47: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0084

Table S73. Gene #47: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 58 | 39
6Q LOSS MUTATED | 1 | 14 | 4
6Q LOSS WILD-TYPE | 64 | 44 | 35

Figure S73. Get High-res Image Gene #47: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0014

Table S74. Gene #47: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 66 | 54 | 18 | 24
6Q LOSS MUTATED | 1 | 16 | 1 | 1
6Q LOSS WILD-TYPE | 65 | 38 | 17 | 23

Figure S74. Get High-res Image Gene #47: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.11

Table S75. Gene #47: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 34 | 58 | 11 | 35 | 23
6Q LOSS MUTATED | 2 | 14 | 1 | 1 | 1
6Q LOSS WILD-TYPE | 32 | 44 | 10 | 34 | 22

Figure S75. Get High-res Image Gene #47: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00237 (Fisher's exact test), Q value = 0.032

Table S76. Gene #47: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 71 | 53 | 18 | 19
6Q LOSS MUTATED | 16 | 1 | 1 | 1
6Q LOSS WILD-TYPE | 55 | 52 | 17 | 18

Figure S76. Get High-res Image Gene #47: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 0.0322 (Fisher's exact test), Q value = 0.18

Table S77. Gene #48: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
7Q LOSS MUTATED | 5 | 0 | 1
7Q LOSS WILD-TYPE | 55 | 63 | 38

Figure S77. Get High-res Image Gene #48: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 0.0404 (Fisher's exact test), Q value = 0.21

Table S78. Gene #48: '7q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
7Q LOSS MUTATED | 0 | 6 | 0 | 0
7Q LOSS WILD-TYPE | 33 | 58 | 44 | 21

Figure S78. Get High-res Image Gene #48: '7q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.18

Table S79. Gene #48: '7q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 58 | 39
7Q LOSS MUTATED | 0 | 5 | 1
7Q LOSS WILD-TYPE | 65 | 53 | 38

Figure S79. Get High-res Image Gene #48: '7q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0248 (Fisher's exact test), Q value = 0.16

Table S80. Gene #48: '7q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 66 | 54 | 18 | 24
7Q LOSS MUTATED | 0 | 5 | 1 | 0
7Q LOSS WILD-TYPE | 66 | 49 | 17 | 24

Figure S80. Get High-res Image Gene #48: '7q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 0.0216 (Fisher's exact test), Q value = 0.15

Table S81. Gene #49: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
8P LOSS MUTATED | 8 | 3 | 9
8P LOSS WILD-TYPE | 52 | 60 | 30

Figure S81. Get High-res Image Gene #49: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'CN_CNMF'

P value = 0.0434 (Fisher's exact test), Q value = 0.22

Table S82. Gene #50: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
8Q LOSS MUTATED | 6 | 1 | 5
8Q LOSS WILD-TYPE | 54 | 62 | 34

Figure S82. Get High-res Image Gene #50: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 0.0492 (Fisher's exact test), Q value = 0.24

Table S83. Gene #51: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
9P LOSS MUTATED | 5 | 1 | 5
9P LOSS WILD-TYPE | 55 | 62 | 34

Figure S83. Get High-res Image Gene #51: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0175 (Fisher's exact test), Q value = 0.13

Table S84. Gene #51: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 18 | 28
9P LOSS MUTATED | 0 | 0 | 4
9P LOSS WILD-TYPE | 31 | 18 | 24

Figure S84. Get High-res Image Gene #51: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 0.00786 (Fisher's exact test), Q value = 0.079

Table S85. Gene #52: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
9Q LOSS MUTATED | 3 | 1 | 7
9Q LOSS WILD-TYPE | 57 | 62 | 32

Figure S85. Get High-res Image Gene #52: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0011

Table S86. Gene #53: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
11P LOSS MUTATED | 1 | 36 | 17
11P LOSS WILD-TYPE | 59 | 27 | 22

Figure S86. Get High-res Image Gene #53: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.012

Table S87. Gene #53: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 78 | 44
11P LOSS MUTATED | 21 | 15 | 18
11P LOSS WILD-TYPE | 19 | 63 | 26

Figure S87. Get High-res Image Gene #53: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'RPPA_CNMF'

P value = 0.00115 (Fisher's exact test), Q value = 0.019

Table S88. Gene #53: '11p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 13 | 9 | 20 | 5 | 17 | 13
11P LOSS MUTATED | 3 | 1 | 2 | 3 | 9 | 9
11P LOSS WILD-TYPE | 10 | 8 | 18 | 2 | 8 | 4

Figure S88. Get High-res Image Gene #53: '11p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0075

Table S89. Gene #53: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
11P LOSS MUTATED | 12 | 11 | 25 | 6
11P LOSS WILD-TYPE | 21 | 53 | 19 | 15

Figure S89. Get High-res Image Gene #53: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0011

Table S90. Gene #53: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 64 | 43 | 21
11P LOSS MUTATED | 11 | 9 | 28 | 6
11P LOSS WILD-TYPE | 23 | 55 | 15 | 15

Figure S90. Get High-res Image Gene #53: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0017

Table S91. Gene #53: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 58 | 39
11P LOSS MUTATED | 34 | 9 | 11
11P LOSS WILD-TYPE | 31 | 49 | 28

Figure S91. Get High-res Image Gene #53: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0014

Table S92. Gene #53: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 66 | 54 | 18 | 24
11P LOSS MUTATED | 37 | 6 | 5 | 6
11P LOSS WILD-TYPE | 29 | 48 | 13 | 18

Figure S92. Get High-res Image Gene #53: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0024

Table S93. Gene #53: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 34 | 58 | 11 | 35 | 23
11P LOSS MUTATED | 12 | 7 | 3 | 20 | 11
11P LOSS WILD-TYPE | 22 | 51 | 8 | 15 | 12

Figure S93. Get High-res Image Gene #53: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00247 (Fisher's exact test), Q value = 0.033

Table S94. Gene #53: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 71 | 53 | 18 | 19
11P LOSS MUTATED | 15 | 28 | 5 | 5
11P LOSS WILD-TYPE | 56 | 25 | 13 | 14

Figure S94. Get High-res Image Gene #53: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0014

Table S95. Gene #54: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
11Q LOSS MUTATED | 3 | 24 | 13
11Q LOSS WILD-TYPE | 57 | 39 | 26

Figure S95. Get High-res Image Gene #54: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'RPPA_CNMF'

P value = 0.0231 (Fisher's exact test), Q value = 0.15

Table S96. Gene #54: '11q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 13 | 9 | 20 | 5 | 17 | 13
11Q LOSS MUTATED | 4 | 1 | 4 | 2 | 9 | 9
11Q LOSS WILD-TYPE | 9 | 8 | 16 | 3 | 8 | 4

Figure S96. Get High-res Image Gene #54: '11q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0075

Table S97. Gene #54: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
11Q LOSS MUTATED | 8 | 7 | 21 | 4
11Q LOSS WILD-TYPE | 25 | 57 | 23 | 17

Figure S97. Get High-res Image Gene #54: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00073 (Fisher's exact test), Q value = 0.014

Table S98. Gene #54: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 64 | 43 | 21
11Q LOSS MUTATED | 9 | 8 | 20 | 3
11Q LOSS WILD-TYPE | 25 | 56 | 23 | 18

Figure S98. Get High-res Image Gene #54: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0066

Table S99. Gene #54: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 58 | 39
11Q LOSS MUTATED | 26 | 5 | 9
11Q LOSS WILD-TYPE | 39 | 53 | 30

Figure S99. Get High-res Image Gene #54: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.0084

Table S100. Gene #54: '11q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 66 | 54 | 18 | 24
11Q LOSS MUTATED | 27 | 5 | 2 | 6
11Q LOSS WILD-TYPE | 39 | 49 | 16 | 18

Figure S100. Get High-res Image Gene #54: '11q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0066

Table S101. Gene #54: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 34 | 58 | 11 | 35 | 23
11Q LOSS MUTATED | 9 | 5 | 2 | 18 | 6
11Q LOSS WILD-TYPE | 25 | 53 | 9 | 17 | 17

Figure S101. Get High-res Image Gene #54: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0262 (Fisher's exact test), Q value = 0.16

Table S102. Gene #54: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 71 | 53 | 18 | 19
11Q LOSS MUTATED | 13 | 21 | 2 | 4
11Q LOSS WILD-TYPE | 58 | 32 | 16 | 15

Figure S102. Get High-res Image Gene #54: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 0.0361 (Fisher's exact test), Q value = 0.2

Table S103. Gene #55: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
13Q LOSS MUTATED | 5 | 0 | 3
13Q LOSS WILD-TYPE | 55 | 63 | 36

Figure S103. Get High-res Image Gene #55: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'RPPA_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.11

Table S104. Gene #55: '13q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 13 | 9 | 20 | 5 | 17 | 13
13Q LOSS MUTATED | 0 | 1 | 0 | 2 | 1 | 0
13Q LOSS WILD-TYPE | 13 | 8 | 20 | 3 | 16 | 13

Figure S104. Get High-res Image Gene #55: '13q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00198 (Fisher's exact test), Q value = 0.028

Table S105. Gene #56: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 66 | 54 | 18 | 24
14Q LOSS MUTATED | 5 | 5 | 8 | 2
14Q LOSS WILD-TYPE | 61 | 49 | 10 | 22

Figure S105. Get High-res Image Gene #56: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.029 (Fisher's exact test), Q value = 0.18

Table S106. Gene #56: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 34 | 58 | 11 | 35 | 23
14Q LOSS MUTATED | 10 | 4 | 0 | 4 | 2
14Q LOSS WILD-TYPE | 24 | 54 | 11 | 31 | 21

Figure S106. Get High-res Image Gene #56: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00157 (Fisher's exact test), Q value = 0.025

Table S107. Gene #56: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 71 | 53 | 18 | 19
14Q LOSS MUTATED | 5 | 5 | 8 | 2
14Q LOSS WILD-TYPE | 66 | 48 | 10 | 17

Figure S107. Get High-res Image Gene #56: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.0426 (Fisher's exact test), Q value = 0.22

Table S108. Gene #58: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 78 | 44
16P LOSS MUTATED | 5 | 4 | 0
16P LOSS WILD-TYPE | 35 | 74 | 44

Figure S108. Get High-res Image Gene #58: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0276 (Fisher's exact test), Q value = 0.17

Table S109. Gene #59: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 64 | 43 | 21
16Q LOSS MUTATED | 4 | 1 | 0 | 0
16Q LOSS WILD-TYPE | 30 | 63 | 43 | 21

Figure S109. Get High-res Image Gene #59: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.012

Table S110. Gene #60: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
17P LOSS MUTATED | 20 | 16 | 25
17P LOSS WILD-TYPE | 40 | 47 | 14

Figure S110. Get High-res Image Gene #60: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00236 (Fisher's exact test), Q value = 0.032

Table S111. Gene #60: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 78 | 44
17P LOSS MUTATED | 9 | 40 | 12
17P LOSS WILD-TYPE | 31 | 38 | 32

Figure S111. Get High-res Image Gene #60: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0334 (Fisher's exact test), Q value = 0.19

Table S112. Gene #60: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 64 | 43 | 21
17P LOSS MUTATED | 10 | 33 | 13 | 5
17P LOSS WILD-TYPE | 24 | 31 | 30 | 16

Figure S112. Get High-res Image Gene #60: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 0.0229 (Fisher's exact test), Q value = 0.15

Table S113. Gene #60: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 58 | 39
17P LOSS MUTATED | 20 | 30 | 11
17P LOSS WILD-TYPE | 45 | 28 | 28

Figure S113. Get High-res Image Gene #60: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0222 (Fisher's exact test), Q value = 0.15

Table S114. Gene #60: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 66 | 54 | 18 | 24
17P LOSS MUTATED | 18 | 29 | 7 | 7
17P LOSS WILD-TYPE | 48 | 25 | 11 | 17

Figure S114. Get High-res Image Gene #60: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0139 (Fisher's exact test), Q value = 0.12

Table S115. Gene #60: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 71 | 53 | 18 | 19
17P LOSS MUTATED | 36 | 12 | 7 | 6
17P LOSS WILD-TYPE | 35 | 41 | 11 | 13

Figure S115. Get High-res Image Gene #60: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0024

Table S116. Gene #61: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
17Q LOSS MUTATED | 4 | 2 | 13
17Q LOSS WILD-TYPE | 56 | 61 | 26

Figure S116. Get High-res Image Gene #61: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0323 (Fisher's exact test), Q value = 0.18

Table S117. Gene #61: '17q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 18 | 28
17Q LOSS MUTATED | 1 | 1 | 7
17Q LOSS WILD-TYPE | 30 | 17 | 21

Figure S117. Get High-res Image Gene #61: '17q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.0414 (Fisher's exact test), Q value = 0.21

Table S118. Gene #66: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
21Q LOSS MUTATED | 2 | 15 | 14 | 5
21Q LOSS WILD-TYPE | 31 | 49 | 30 | 16

Figure S118. Get High-res Image Gene #66: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0011

Table S119. Gene #67: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
22Q LOSS MUTATED | 35 | 8 | 15
22Q LOSS WILD-TYPE | 25 | 55 | 24

Figure S119. Get High-res Image Gene #67: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.11

Table S120. Gene #67: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 78 | 44
22Q LOSS MUTATED | 10 | 37 | 11
22Q LOSS WILD-TYPE | 30 | 41 | 33

Figure S120. Get High-res Image Gene #67: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 0.0322 (Fisher's exact test), Q value = 0.18

Table S121. Gene #67: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
22Q LOSS MUTATED | 9 | 31 | 10 | 8
22Q LOSS WILD-TYPE | 24 | 33 | 34 | 13

Figure S121. Get High-res Image Gene #67: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00207 (Fisher's exact test), Q value = 0.029

Table S122. Gene #67: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 64 | 43 | 21
22Q LOSS MUTATED | 11 | 33 | 7 | 7
22Q LOSS WILD-TYPE | 23 | 31 | 36 | 14

Figure S122. Get High-res Image Gene #67: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 0.0476 (Fisher's exact test), Q value = 0.24

Table S123. Gene #67: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 58 | 39
22Q LOSS MUTATED | 16 | 25 | 17
22Q LOSS WILD-TYPE | 49 | 33 | 22

Figure S123. Get High-res Image Gene #67: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0269 (Fisher's exact test), Q value = 0.17

Table S124. Gene #67: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 34 | 58 | 11 | 35 | 23
22Q LOSS MUTATED | 12 | 29 | 4 | 6 | 7
22Q LOSS WILD-TYPE | 22 | 29 | 7 | 29 | 16

Figure S124. Get High-res Image Gene #67: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0244 (Fisher's exact test), Q value = 0.16

Table S125. Gene #67: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 71 | 53 | 18 | 19
22Q LOSS MUTATED | 33 | 11 | 6 | 8
22Q LOSS WILD-TYPE | 38 | 42 | 12 | 11

Figure S125. Get High-res Image Gene #67: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0014

Table S126. Gene #68: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
XP LOSS MUTATED | 22 | 7 | 19
XP LOSS WILD-TYPE | 38 | 56 | 20

Figure S126. Get High-res Image Gene #68: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 0.00181 (Fisher's exact test), Q value = 0.027

Table S127. Gene #68: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 78 | 44
XP LOSS MUTATED | 9 | 33 | 6
XP LOSS WILD-TYPE | 31 | 45 | 38

Figure S127. Get High-res Image Gene #68: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.11

Table S128. Gene #68: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
XP LOSS MUTATED | 10 | 27 | 9 | 2
XP LOSS WILD-TYPE | 23 | 37 | 35 | 19

Figure S128. Get High-res Image Gene #68: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00096 (Fisher's exact test), Q value = 0.017

Table S129. Gene #68: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 64 | 43 | 21
XP LOSS MUTATED | 7 | 29 | 11 | 1
XP LOSS WILD-TYPE | 27 | 35 | 32 | 20

Figure S129. Get High-res Image Gene #68: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 0.00254 (Fisher's exact test), Q value = 0.033

Table S130. Gene #68: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 58 | 39
XP LOSS MUTATED | 13 | 27 | 8
XP LOSS WILD-TYPE | 52 | 31 | 31

Figure S130. Get High-res Image Gene #68: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0178 (Fisher's exact test), Q value = 0.13

Table S131. Gene #68: 'xp loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 66 | 54 | 18 | 24
XP LOSS MUTATED | 15 | 23 | 7 | 3
XP LOSS WILD-TYPE | 51 | 31 | 11 | 21

Figure S131. Get High-res Image Gene #68: 'xp loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0182 (Fisher's exact test), Q value = 0.13

Table S132. Gene #68: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 71 | 53 | 18 | 19
XP LOSS MUTATED | 27 | 13 | 7 | 1
XP LOSS WILD-TYPE | 44 | 40 | 11 | 18

Figure S132. Get High-res Image Gene #68: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0017

Table S133. Gene #69: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
XQ LOSS MUTATED | 22 | 7 | 20
XQ LOSS WILD-TYPE | 38 | 56 | 19

Figure S133. Get High-res Image Gene #69: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.0014 (Fisher's exact test), Q value = 0.022

Table S134. Gene #69: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 78 | 44
XQ LOSS MUTATED | 9 | 34 | 6
XQ LOSS WILD-TYPE | 31 | 44 | 38

Figure S134. Get High-res Image Gene #69: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 0.00735 (Fisher's exact test), Q value = 0.076

Table S135. Gene #69: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
XQ LOSS MUTATED | 10 | 28 | 9 | 2
XQ LOSS WILD-TYPE | 23 | 36 | 35 | 19

Figure S135. Get High-res Image Gene #69: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.012

Table S136. Gene #69: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 64 | 43 | 21
XQ LOSS MUTATED | 7 | 30 | 11 | 1
XQ LOSS WILD-TYPE | 27 | 34 | 32 | 20

Figure S136. Get High-res Image Gene #69: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.00375 (Fisher's exact test), Q value = 0.045

Table S137. Gene #69: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 58 | 39
XQ LOSS MUTATED | 13 | 27 | 9
XQ LOSS WILD-TYPE | 52 | 31 | 30

Figure S137. Get High-res Image Gene #69: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.097

Table S138. Gene #69: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 66 | 54 | 18 | 24
XQ LOSS MUTATED | 15 | 24 | 7 | 3
XQ LOSS WILD-TYPE | 51 | 30 | 11 | 21

Figure S138. Get High-res Image Gene #69: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0133 (Fisher's exact test), Q value = 0.11

Table S139. Gene #69: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 71 | 53 | 18 | 19
XQ LOSS MUTATED | 28 | 13 | 7 | 1
XQ LOSS WILD-TYPE | 43 | 40 | 11 | 18

Figure S139. Get High-res Image Gene #69: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

- Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

- Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PCPG-TP/15096455/transformed.cor.cli.txt

- Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PCPG-TP/15107813/PCPG-TP.transferedmergedcluster.txt

- Number of patients = 162

- Number of significantly arm-level cnvs = 69

- Number of molecular subtypes = 10

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

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] 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)
[2] 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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