Correlation between copy number variations of arm-level result and molecular subtypes
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
15 January 2014 | analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1FQ9V1J
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/C1FQ9V1J
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 8 molecular subtypes across 172 patients, 99 significant findings detected with P value < 0.05 and Q value < 0.25.

- 1p gain cnv correlated to 'CN_CNMF'.

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

- 2p gain cnv correlated to 'CN_CNMF'.

- 2q gain cnv correlated to 'CN_CNMF'.

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

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

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

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

- 8q gain cnv correlated to 'METHLYATION_CNMF'.

- 12p gain cnv correlated to 'CN_CNMF'.

- 12q gain cnv correlated to 'CN_CNMF'.

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

- 16q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

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

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

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

- 1p loss cnv correlated to 'CN_CNMF'.

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

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

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

- 5p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

- 5q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

- 6q loss cnv correlated to 'CN_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', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

- 11q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

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

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

- 17p loss cnv correlated to 'METHLYATION_CNMF'.

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

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

- 19q loss cnv correlated to 'CN_CNMF'.

- 21q loss cnv correlated to 'CN_CNMF'.

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

- 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 69 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, 99 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 | 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
9q loss | 24 (14%) | 148 | 3.03e-06 (0.00153) | 1.53e-07 (7.98e-05) | 1.15e-07 (6.05e-05) | 5.41e-07 (0.000278) | 0.00551 (1.00) | 6.03e-05 (0.029) | 0.0347 (1.00) | 9.58e-05 (0.0453)
7p gain | 100 (58%) | 72 | 5.47e-19 (3.02e-16) | 7.55e-08 (4e-05) | 3.55e-13 (1.93e-10) | 1.38e-07 (7.23e-05) | 0.099 (1.00) | 0.000239 (0.11) | 0.167 (1.00) | 0.0104 (1.00)
17p gain | 102 (59%) | 70 | 1.41e-17 (7.72e-15) | 1.13e-07 (5.98e-05) | 1.35e-10 (7.3e-08) | 3.84e-09 (2.06e-06) | 0.0228 (1.00) | 0.000259 (0.119) | 0.144 (1.00) | 0.00791 (1.00)
1q gain | 14 (8%) | 158 | 3.59e-06 (0.00181) | 1.14e-06 (0.000578) | 6.28e-05 (0.0301) | 0.00132 (0.575) | 0.235 (1.00) | 5.12e-05 (0.0247) | 0.383 (1.00) | 0.0262 (1.00)
7q gain | 101 (59%) | 71 | 1.87e-18 (1.03e-15) | 2.12e-07 (0.00011) | 4.88e-13 (2.65e-10) | 2.01e-07 (0.000105) | 0.141 (1.00) | 0.00126 (0.554) | 0.222 (1.00) | 0.0408 (1.00)
3p loss | 14 (8%) | 158 | 1.61e-05 (0.00798) | 4.47e-07 (0.00023) | 0.000314 (0.143) | 0.00108 (0.475) | 0.0114 (1.00) | 0.00334 (1.00) | 0.415 (1.00) | 0.000104 (0.049)
4p loss | 18 (10%) | 154 | 2.69e-07 (0.00014) | 1.02e-07 (5.42e-05) | 3.57e-07 (0.000184) | 7.8e-06 (0.0039) | 0.436 (1.00) | 0.0653 (1.00) | 0.665 (1.00) | 0.0255 (1.00)
4q loss | 19 (11%) | 153 | 7.23e-08 (3.86e-05) | 2.57e-08 (1.38e-05) | 1.27e-07 (6.64e-05) | 2.76e-05 (0.0135) | 0.599 (1.00) | 0.124 (1.00) | 0.582 (1.00) | 0.0426 (1.00)
9p loss | 22 (13%) | 150 | 1.69e-06 (0.000858) | 3.99e-07 (0.000206) | 9.89e-07 (0.000504) | 0.000187 (0.0863) | 0.0222 (1.00) | 0.00945 (1.00) | 0.0641 (1.00) | 0.0121 (1.00)
10q loss | 12 (7%) | 160 | 3.05e-06 (0.00153) | 1.91e-05 (0.00943) | 0.000746 (0.333) | 0.0275 (1.00) | 0.0607 (1.00) | 1.42e-05 (0.00707) | 0.0869 (1.00) | 0.000139 (0.0648)
13q loss | 17 (10%) | 155 | 1.21e-05 (0.00602) | 1.42e-08 (7.64e-06) | 7.84e-06 (0.00391) | 7.82e-05 (0.0372) | 0.0107 (1.00) | 0.0021 (0.896) | 0.06 (1.00) | 0.00627 (1.00)
18q loss | 30 (17%) | 142 | 3.3e-05 (0.0161) | 2.97e-07 (0.000154) | 2.6e-07 (0.000135) | 0.000177 (0.0819) | 0.0654 (1.00) | 0.133 (1.00) | 0.33 (1.00) | 0.24 (1.00)
22q loss | 41 (24%) | 131 | 6.88e-07 (0.000352) | 4.73e-07 (0.000243) | 7.37e-08 (3.92e-05) | 0.00135 (0.586) | 0.136 (1.00) | 0.00011 (0.0516) | 0.0464 (1.00) | 0.0764 (1.00)
17q gain | 117 (68%) | 55 | 5.2e-12 (2.83e-09) | 0.00117 (0.515) | 9.37e-07 (0.000478) | 1.09e-05 (0.00542) | 0.293 (1.00) | 0.0743 (1.00) | 0.49 (1.00) | 0.122 (1.00)
xq gain | 54 (31%) | 118 | 1.51e-14 (8.25e-12) | 0.0064 (1.00) | 6.96e-06 (0.00349) | 7.75e-05 (0.037) | 0.00805 (1.00) | 0.00767 (1.00) | 0.0132 (1.00) | 0.136 (1.00)
10p loss | 12 (7%) | 160 | 7.31e-08 (3.9e-05) | 7.49e-05 (0.0358) | 0.000746 (0.333) | 0.164 (1.00) | 0.289 (1.00) | 0.000114 (0.0535) | 0.337 (1.00) | 0.000558 (0.252)
14q loss | 34 (20%) | 138 | 1.12e-11 (6.09e-09) | 0.00438 (1.00) | 0.000267 (0.122) | 8.21e-07 (0.000419) | 0.0755 (1.00) | 0.00436 (1.00) | 0.268 (1.00) | 0.15 (1.00)
18p loss | 28 (16%) | 144 | 0.000337 (0.153) | 3.92e-06 (0.00197) | 2.03e-06 (0.00103) | 0.000598 (0.27) | 0.0472 (1.00) | 0.113 (1.00) | 0.324 (1.00) | 0.348 (1.00)
xq loss | 20 (12%) | 152 | 2.26e-05 (0.0111) | 4.35e-05 (0.0211) | 3.08e-05 (0.015) | 0.0337 (1.00) | 0.198 (1.00) | 0.0546 (1.00) | 0.265 (1.00) | 0.0121 (1.00)
3p gain | 46 (27%) | 126 | 5.8e-19 (3.19e-16) | 0.0244 (1.00) | 6.68e-05 (0.032) | 0.082 (1.00) | 0.16 (1.00) | 0.0034 (1.00) | 0.318 (1.00) | 0.0152 (1.00)
3q gain | 55 (32%) | 117 | 1.64e-17 (8.99e-15) | 0.0342 (1.00) | 2.29e-05 (0.0113) | 0.0876 (1.00) | 0.132 (1.00) | 0.022 (1.00) | 0.435 (1.00) | 0.0208 (1.00)
16p gain | 89 (52%) | 83 | 3.34e-10 (1.8e-07) | 0.242 (1.00) | 0.000528 (0.239) | 0.0006 (0.27) | 0.0384 (1.00) | 0.0232 (1.00) | 0.00305 (1.00) | 0.017 (1.00)
16q gain | 85 (49%) | 87 | 2.88e-11 (1.56e-08) | 0.0896 (1.00) | 5.28e-05 (0.0254) | 0.00257 (1.00) | 0.00897 (1.00) | 0.0015 (0.648) | 0.00176 (0.753) | 0.00313 (1.00)
11q loss | 14 (8%) | 158 | 1.61e-05 (0.00798) | 0.000148 (0.069) | 0.0224 (1.00) | 0.0183 (1.00) | 0.0706 (1.00) | 0.071 (1.00) | 0.415 (1.00) | 0.0262 (1.00)
15q loss | 19 (11%) | 153 | 9.33e-05 (0.0442) | 0.00407 (1.00) | 0.0119 (1.00) | 1.11e-07 (5.84e-05) | 0.14 (1.00) | 0.423 (1.00) | 0.144 (1.00) | 0.16 (1.00)
1p gain | 5 (3%) | 167 | 0.000436 (0.198) | 0.00267 (1.00) | 0.0294 (1.00) | 0.0467 (1.00) | 0.236 (1.00) | 0.0412 (1.00) | 0.233 (1.00) | 0.264 (1.00)
2p gain | 32 (19%) | 140 | 7.44e-08 (3.95e-05) | 0.0123 (1.00) | 0.181 (1.00) | 0.755 (1.00) | 0.114 (1.00) | 0.706 (1.00) | 0.0451 (1.00) | 0.801 (1.00)
2q gain | 35 (20%) | 137 | 2.67e-09 (1.44e-06) | 0.0262 (1.00) | 0.529 (1.00) | 0.653 (1.00) | 0.145 (1.00) | 1 (1.00) | 0.0398 (1.00) | 0.941 (1.00)
8q gain | 15 (9%) | 157 | 0.04 (1.00) | 2.45e-05 (0.012) | 0.00472 (1.00) | 0.214 (1.00) | 0.00743 (1.00) | 0.0135 (1.00) | 0.0683 (1.00) | 0.00495 (1.00)
12p gain | 68 (40%) | 104 | 0.000236 (0.109) | 0.461 (1.00) | 0.0156 (1.00) | 0.131 (1.00) | 0.288 (1.00) | 0.069 (1.00) | 0.0597 (1.00) | 0.209 (1.00)
12q gain | 68 (40%) | 104 | 0.000236 (0.109) | 0.461 (1.00) | 0.0156 (1.00) | 0.131 (1.00) | 0.288 (1.00) | 0.069 (1.00) | 0.0597 (1.00) | 0.209 (1.00)
1p loss | 21 (12%) | 151 | 0.000121 (0.0569) | 0.0547 (1.00) | 0.00227 (0.964) | 0.00356 (1.00) | 1 (1.00) | 0.69 (1.00) | 0.953 (1.00) | 0.897 (1.00)
5p loss | 7 (4%) | 165 | 0.322 (1.00) | 0.00151 (0.654) | 0.0149 (1.00) | 3.34e-05 (0.0163) | 0.0185 (1.00) | 0.0885 (1.00) | 0.0309 (1.00) | 0.065 (1.00)
5q loss | 7 (4%) | 165 | 0.322 (1.00) | 0.00151 (0.654) | 0.0149 (1.00) | 3.34e-05 (0.0163) | 0.0185 (1.00) | 0.0885 (1.00) | 0.0309 (1.00) | 0.065 (1.00)
6q loss | 15 (9%) | 157 | 9.92e-05 (0.0468) | 0.000871 (0.386) | 0.0107 (1.00) | 0.0326 (1.00) | 0.567 (1.00) | 0.548 (1.00) | 0.703 (1.00) | 0.26 (1.00)
17p loss | 8 (5%) | 164 | 0.0153 (1.00) | 0.000166 (0.077) | 0.00178 (0.761) | 0.00336 (1.00) | 0.284 (1.00) | 0.073 (1.00) | 0.312 (1.00) | 0.0396 (1.00)
19q loss | 11 (6%) | 161 | 8.49e-05 (0.0403) | 0.0419 (1.00) | 0.092 (1.00) | 0.147 (1.00) | 0.0391 (1.00) | 0.117 (1.00) | 0.286 (1.00) | 0.051 (1.00)
21q loss | 30 (17%) | 142 | 0.000173 (0.0802) | 0.188 (1.00) | 0.668 (1.00) | 0.072 (1.00) | 0.686 (1.00) | 0.191 (1.00) | 0.284 (1.00) | 0.758 (1.00)
4p gain | 6 (3%) | 166 | 0.885 (1.00) | 0.162 (1.00) | 0.937 (1.00) | 0.87 (1.00) | 1 (1.00) | 0.196 (1.00) | 0.593 (1.00) | 0.04 (1.00)
4q gain | 5 (3%) | 167 | 1 (1.00) | 0.162 (1.00) | 1 (1.00) | 0.52 (1.00) | 0.739 (1.00) | 0.639 (1.00) | 0.45 (1.00) | 0.192 (1.00)
5p gain | 26 (15%) | 146 | 0.00089 (0.392) | 0.00144 (0.624) | 0.106 (1.00) | 0.000617 (0.277) | 0.0685 (1.00) | 0.0972 (1.00) | 0.235 (1.00) | 0.305 (1.00)
5q gain | 26 (15%) | 146 | 0.00226 (0.963) | 0.00811 (1.00) | 0.107 (1.00) | 0.000617 (0.277) | 0.0685 (1.00) | 0.297 (1.00) | 0.235 (1.00) | 0.368 (1.00)
6p gain | 8 (5%) | 164 | 0.167 (1.00) | 0.0459 (1.00) | 0.0364 (1.00) | 0.244 (1.00) | 0.0298 (1.00) | 0.104 (1.00) | 0.00941 (1.00) | 0.291 (1.00)
6q gain | 6 (3%) | 166 | 0.0442 (1.00) | 0.0413 (1.00) | 0.172 (1.00) | 0.373 (1.00) | 0.165 (1.00) | 0.247 (1.00) | 0.065 (1.00) | 0.426 (1.00)
8p gain | 12 (7%) | 160 | 0.141 (1.00) | 0.00289 (1.00) | 0.134 (1.00) | 0.859 (1.00) | 0.108 (1.00) | 0.0544 (1.00) | 0.312 (1.00) | 0.0321 (1.00)
9p gain | 3 (2%) | 169 | 0.697 (1.00) |  | 0.261 (1.00) | 0.0951 (1.00) | 0.775 (1.00) | 0.0876 (1.00) | 0.777 (1.00) | 0.0594 (1.00)
10p gain | 5 (3%) | 167 | 0.0494 (1.00) | 0.0398 (1.00) | 0.651 (1.00) | 1 (1.00) | 0.163 (1.00) | 0.41 (1.00) | 0.13 (1.00) | 0.353 (1.00)
10q gain | 5 (3%) | 167 | 0.0494 (1.00) | 0.0398 (1.00) | 0.651 (1.00) | 1 (1.00) | 0.163 (1.00) | 0.41 (1.00) | 0.13 (1.00) | 0.353 (1.00)
11p gain | 8 (5%) | 164 | 0.0153 (1.00) | 0.00151 (0.654) | 0.657 (1.00) | 0.0124 (1.00) | 0.0775 (1.00) | 0.358 (1.00) | 1 (1.00) | 0.249 (1.00)
11q gain | 7 (4%) | 165 | 0.00996 (1.00) | 0.000671 (0.3) | 0.513 (1.00) | 0.0347 (1.00) | 0.177 (1.00) | 0.869 (1.00) | 1 (1.00) | 0.588 (1.00)
13q gain | 19 (11%) | 153 | 0.0467 (1.00) | 1 (1.00) | 0.318 (1.00) | 0.722 (1.00) | 1 (1.00) | 1 (1.00) | 0.923 (1.00) | 1 (1.00)
14q gain | 3 (2%) | 169 | 0.258 (1.00) | 0.0398 (1.00) | 0.557 (1.00) | 0.0951 (1.00) | 1 (1.00) | 0.0876 (1.00) | 1 (1.00) | 0.0594 (1.00)
15q gain | 5 (3%) | 167 | 0.0173 (1.00) | 0.0413 (1.00) | 0.299 (1.00) | 0.0731 (1.00) | 0.527 (1.00) | 0.639 (1.00) | 0.736 (1.00) | 0.353 (1.00)
18p gain | 9 (5%) | 163 | 0.17 (1.00) | 0.423 (1.00) | 0.714 (1.00) | 0.911 (1.00) | 0.138 (1.00) | 0.0432 (1.00) | 0.358 (1.00) | 0.21 (1.00)
18q gain | 5 (3%) | 167 | 0.151 (1.00) | 0.253 (1.00) | 0.527 (1.00) | 1 (1.00) | 0.623 (1.00) | 0.239 (1.00) | 0.627 (1.00) | 1 (1.00)
19p gain | 3 (2%) | 169 | 0.258 (1.00) | 0.457 (1.00) | 0.557 (1.00) | 0.412 (1.00) | 0.525 (1.00) | 0.0146 (1.00) | 0.51 (1.00) | 0.295 (1.00)
19q gain | 3 (2%) | 169 | 0.258 (1.00) | 0.457 (1.00) | 0.557 (1.00) | 0.412 (1.00) | 0.525 (1.00) | 0.0146 (1.00) | 0.51 (1.00) | 0.295 (1.00)
20p gain | 58 (34%) | 114 | 0.00127 (0.555) | 0.108 (1.00) | 0.0777 (1.00) | 0.323 (1.00) | 0.301 (1.00) | 0.646 (1.00) | 0.879 (1.00) | 0.758 (1.00)
20q gain | 60 (35%) | 112 | 0.00551 (1.00) | 0.109 (1.00) | 0.142 (1.00) | 0.452 (1.00) | 0.276 (1.00) | 0.729 (1.00) | 0.8 (1.00) | 0.747 (1.00)
21q gain | 12 (7%) | 160 | 1 (1.00) | 0.413 (1.00) | 0.0523 (1.00) | 0.102 (1.00) | 0.393 (1.00) | 0.516 (1.00) | 0.227 (1.00) | 0.337 (1.00)
1q loss | 13 (8%) | 159 | 0.0467 (1.00) | 0.471 (1.00) | 0.632 (1.00) | 0.00455 (1.00) | 0.877 (1.00) | 0.21 (1.00) | 0.516 (1.00) | 0.366 (1.00)
3q loss | 4 (2%) | 168 | 0.00248 (1.00) | 0.0104 (1.00) | 0.117 (1.00) | 0.0228 (1.00) | 0.328 (1.00) | 0.585 (1.00) | 0.388 (1.00) | 0.0564 (1.00)
6p loss | 12 (7%) | 160 | 0.0066 (1.00) | 0.0419 (1.00) | 0.0453 (1.00) | 0.0142 (1.00) | 0.49 (1.00) | 0.399 (1.00) | 0.869 (1.00) | 0.337 (1.00)
8p loss | 6 (3%) | 166 | 0.0442 (1.00) | 1 (1.00) | 0.608 (1.00) | 0.419 (1.00) | 0.374 (1.00) | 0.196 (1.00) | 0.38 (1.00) | 0.118 (1.00)
8q loss | 4 (2%) | 168 | 0.0931 (1.00) | 1 (1.00) | 0.421 (1.00) | 0.0951 (1.00) | 1 (1.00) | 0.438 (1.00) | 1 (1.00) | 0.381 (1.00)
11p loss | 10 (6%) | 162 | 0.000836 (0.371) | 0.00389 (1.00) | 0.0146 (1.00) | 0.0278 (1.00) | 0.0846 (1.00) | 0.172 (1.00) | 0.428 (1.00) | 0.0135 (1.00)
16p loss | 4 (2%) | 168 | 0.0931 (1.00) | 0.0104 (1.00) | 0.117 (1.00) | 0.0228 (1.00) | 1 (1.00) | 0.585 (1.00) | 1 (1.00) | 0.0564 (1.00)
16q loss | 5 (3%) | 167 | 0.0173 (1.00) | 0.00267 (1.00) | 0.0294 (1.00) | 0.0467 (1.00) | 0.623 (1.00) | 0.318 (1.00) | 0.627 (1.00) | 0.00835 (1.00)
19p loss | 12 (7%) | 160 | 0.000874 (0.386) | 0.0107 (1.00) | 0.111 (1.00) | 0.0329 (1.00) | 0.0284 (1.00) | 0.0521 (1.00) | 0.566 (1.00) | 0.0182 (1.00)

'1p gain' versus 'CN_CNMF'

P value = 0.000436 (Fisher's exact test), Q value = 0.2

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
1P GAIN MUTATED | 0 | 0 | 0 | 5
1P GAIN WILD-TYPE | 33 | 68 | 37 | 29

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

'1q gain' versus 'CN_CNMF'

P value = 3.59e-06 (Fisher's exact test), Q value = 0.0018

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
1Q GAIN MUTATED | 0 | 2 | 1 | 11
1Q GAIN WILD-TYPE | 33 | 66 | 36 | 23

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 1.14e-06 (Fisher's exact test), Q value = 0.00058

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
1Q GAIN MUTATED | 0 | 12 | 1
1Q GAIN WILD-TYPE | 43 | 31 | 69

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 6.28e-05 (Fisher's exact test), Q value = 0.03

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
1Q GAIN MUTATED | 13 | 0 | 1 | 0
1Q GAIN WILD-TYPE | 45 | 49 | 30 | 23

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

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.12e-05 (Fisher's exact test), Q value = 0.025

Table S5. Gene #2: '1q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 80 | 74
1Q GAIN MUTATED | 5 | 0 | 9
1Q GAIN WILD-TYPE | 13 | 80 | 65

Figure S5. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 7.44e-08 (Fisher's exact test), Q value = 3.9e-05

Table S6. Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
2P GAIN MUTATED | 12 | 2 | 3 | 15
2P GAIN WILD-TYPE | 21 | 66 | 34 | 19

Figure S6. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'CN_CNMF'

P value = 2.67e-09 (Fisher's exact test), Q value = 1.4e-06

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
2Q GAIN MUTATED | 13 | 2 | 3 | 17
2Q GAIN WILD-TYPE | 20 | 66 | 34 | 17

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

'3p gain' versus 'CN_CNMF'

P value = 5.8e-19 (Fisher's exact test), Q value = 3.2e-16

Table S8. Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
3P GAIN MUTATED | 31 | 6 | 5 | 4
3P GAIN WILD-TYPE | 2 | 62 | 32 | 30

Figure S8. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 6.68e-05 (Fisher's exact test), Q value = 0.032

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
3P GAIN MUTATED | 4 | 19 | 12 | 9
3P GAIN WILD-TYPE | 54 | 30 | 19 | 14

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

'3q gain' versus 'CN_CNMF'

P value = 1.64e-17 (Fisher's exact test), Q value = 9e-15

Table S10. Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
3Q GAIN MUTATED | 32 | 9 | 6 | 8
3Q GAIN WILD-TYPE | 1 | 59 | 31 | 26

Figure S10. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 2.29e-05 (Fisher's exact test), Q value = 0.011

Table S11. Gene #6: '3q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
3Q GAIN MUTATED | 6 | 19 | 14 | 13
3Q GAIN WILD-TYPE | 52 | 30 | 17 | 10

Figure S11. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 5.47e-19 (Fisher's exact test), Q value = 3e-16

Table S12. Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
7P GAIN MUTATED | 31 | 19 | 37 | 13
7P GAIN WILD-TYPE | 2 | 49 | 0 | 21

Figure S12. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 7.55e-08 (Fisher's exact test), Q value = 4e-05

Table S13. Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
7P GAIN MUTATED | 20 | 13 | 57
7P GAIN WILD-TYPE | 23 | 30 | 13

Figure S13. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 3.55e-13 (Fisher's exact test), Q value = 1.9e-10

Table S14. Gene #13: '7p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
7P GAIN MUTATED | 14 | 44 | 15 | 20
7P GAIN WILD-TYPE | 44 | 5 | 16 | 3

Figure S14. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.38e-07 (Fisher's exact test), Q value = 7.2e-05

Table S15. Gene #13: '7p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
7P GAIN MUTATED | 9 | 31 | 53
7P GAIN WILD-TYPE | 22 | 35 | 11

Figure S15. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000239 (Fisher's exact test), Q value = 0.11

Table S16. Gene #13: '7p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 80 | 74
7P GAIN MUTATED | 3 | 55 | 42
7P GAIN WILD-TYPE | 15 | 25 | 32

Figure S16. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1.87e-18 (Fisher's exact test), Q value = 1e-15

Table S17. Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
7Q GAIN MUTATED | 31 | 20 | 37 | 13
7Q GAIN WILD-TYPE | 2 | 48 | 0 | 21

Figure S17. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 2.12e-07 (Fisher's exact test), Q value = 0.00011

Table S18. Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
7Q GAIN MUTATED | 20 | 14 | 57
7Q GAIN WILD-TYPE | 23 | 29 | 13

Figure S18. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 4.88e-13 (Fisher's exact test), Q value = 2.7e-10

Table S19. Gene #14: '7q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
7Q GAIN MUTATED | 14 | 44 | 16 | 20
7Q GAIN WILD-TYPE | 44 | 5 | 15 | 3

Figure S19. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.01e-07 (Fisher's exact test), Q value = 0.00011

Table S20. Gene #14: '7q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
7Q GAIN MUTATED | 9 | 32 | 53
7Q GAIN WILD-TYPE | 22 | 34 | 11

Figure S20. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'METHLYATION_CNMF'

P value = 2.45e-05 (Fisher's exact test), Q value = 0.012

Table S21. Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
8Q GAIN MUTATED | 1 | 11 | 1
8Q GAIN WILD-TYPE | 42 | 32 | 69

Figure S21. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 0.000236 (Fisher's exact test), Q value = 0.11

Table S22. Gene #22: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
12P GAIN MUTATED | 21 | 16 | 20 | 11
12P GAIN WILD-TYPE | 12 | 52 | 17 | 23

Figure S22. Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 0.000236 (Fisher's exact test), Q value = 0.11

Table S23. Gene #23: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
12Q GAIN MUTATED | 21 | 16 | 20 | 11
12Q GAIN WILD-TYPE | 12 | 52 | 17 | 23

Figure S23. Get High-res Image Gene #23: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 3.34e-10 (Fisher's exact test), Q value = 1.8e-07

Table S24. Gene #27: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
16P GAIN MUTATED | 33 | 28 | 15 | 13
16P GAIN WILD-TYPE | 0 | 40 | 22 | 21

Figure S24. Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.000528 (Fisher's exact test), Q value = 0.24

Table S25. Gene #27: '16p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
16P GAIN MUTATED | 19 | 28 | 24 | 13
16P GAIN WILD-TYPE | 39 | 21 | 7 | 10

Figure S25. Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 2.88e-11 (Fisher's exact test), Q value = 1.6e-08

Table S26. Gene #28: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
16Q GAIN MUTATED | 33 | 28 | 14 | 10
16Q GAIN WILD-TYPE | 0 | 40 | 23 | 24

Figure S26. Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 5.28e-05 (Fisher's exact test), Q value = 0.025

Table S27. Gene #28: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
16Q GAIN MUTATED | 16 | 27 | 24 | 13
16Q GAIN WILD-TYPE | 42 | 22 | 7 | 10

Figure S27. Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 1.41e-17 (Fisher's exact test), Q value = 7.7e-15

Table S28. Gene #29: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
17P GAIN MUTATED | 32 | 21 | 36 | 13
17P GAIN WILD-TYPE | 1 | 47 | 1 | 21

Figure S28. Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 1.13e-07 (Fisher's exact test), Q value = 6e-05

Table S29. Gene #29: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
17P GAIN MUTATED | 19 | 15 | 58
17P GAIN WILD-TYPE | 24 | 28 | 12

Figure S29. Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 1.35e-10 (Fisher's exact test), Q value = 7.3e-08

Table S30. Gene #29: '17p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
17P GAIN MUTATED | 15 | 44 | 19 | 15
17P GAIN WILD-TYPE | 43 | 5 | 12 | 8

Figure S30. Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.84e-09 (Fisher's exact test), Q value = 2.1e-06

Table S31. Gene #29: '17p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
17P GAIN MUTATED | 7 | 32 | 54
17P GAIN WILD-TYPE | 24 | 34 | 10

Figure S31. Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000259 (Fisher's exact test), Q value = 0.12

Table S32. Gene #29: '17p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 80 | 74
17P GAIN MUTATED | 3 | 55 | 44
17P GAIN WILD-TYPE | 15 | 25 | 30

Figure S32. Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 5.2e-12 (Fisher's exact test), Q value = 2.8e-09

Table S33. Gene #30: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
17Q GAIN MUTATED | 32 | 29 | 36 | 20
17Q GAIN WILD-TYPE | 1 | 39 | 1 | 14

Figure S33. Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 9.37e-07 (Fisher's exact test), Q value = 0.00048

Table S34. Gene #30: '17q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
17Q GAIN MUTATED | 25 | 45 | 22 | 16
17Q GAIN WILD-TYPE | 33 | 4 | 9 | 7

Figure S34. Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.09e-05 (Fisher's exact test), Q value = 0.0054

Table S35. Gene #30: '17q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
17Q GAIN MUTATED | 12 | 41 | 55
17Q GAIN WILD-TYPE | 19 | 25 | 9

Figure S35. Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 1.51e-14 (Fisher's exact test), Q value = 8.2e-12

Table S36. Gene #38: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
XQ GAIN MUTATED | 28 | 5 | 15 | 6
XQ GAIN WILD-TYPE | 5 | 63 | 22 | 28

Figure S36. Get High-res Image Gene #38: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 6.96e-06 (Fisher's exact test), Q value = 0.0035

Table S37. Gene #38: 'xq gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
XQ GAIN MUTATED | 6 | 27 | 12 | 7
XQ GAIN WILD-TYPE | 52 | 22 | 19 | 16

Figure S37. Get High-res Image Gene #38: 'xq gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.75e-05 (Fisher's exact test), Q value = 0.037

Table S38. Gene #38: 'xq gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
XQ GAIN MUTATED | 2 | 19 | 31
XQ GAIN WILD-TYPE | 29 | 47 | 33

Figure S38. Get High-res Image Gene #38: 'xq gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 0.000121 (Fisher's exact test), Q value = 0.057

Table S39. Gene #39: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
1P LOSS MUTATED | 1 | 9 | 0 | 11
1P LOSS WILD-TYPE | 32 | 59 | 37 | 23

Figure S39. Get High-res Image Gene #39: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 1.61e-05 (Fisher's exact test), Q value = 0.008

Table S40. Gene #41: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
3P LOSS MUTATED | 0 | 4 | 0 | 10
3P LOSS WILD-TYPE | 33 | 64 | 37 | 24

Figure S40. Get High-res Image Gene #41: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 4.47e-07 (Fisher's exact test), Q value = 0.00023

Table S41. Gene #41: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
3P LOSS MUTATED | 1 | 12 | 0
3P LOSS WILD-TYPE | 42 | 31 | 70

Figure S41. Get High-res Image Gene #41: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 0.000314 (Fisher's exact test), Q value = 0.14

Table S42. Gene #41: '3p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
3P LOSS MUTATED | 12 | 0 | 2 | 0
3P LOSS WILD-TYPE | 46 | 49 | 29 | 23

Figure S42. Get High-res Image Gene #41: '3p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000104 (Fisher's exact test), Q value = 0.049

Table S43. Gene #41: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 14 | 87 | 71
3P LOSS MUTATED | 5 | 1 | 8
3P LOSS WILD-TYPE | 9 | 86 | 63

Figure S43. Get High-res Image Gene #41: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 2.69e-07 (Fisher's exact test), Q value = 0.00014

Table S44. Gene #43: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
4P LOSS MUTATED | 0 | 5 | 0 | 13
4P LOSS WILD-TYPE | 33 | 63 | 37 | 21

Figure S44. Get High-res Image Gene #43: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1.02e-07 (Fisher's exact test), Q value = 5.4e-05

Table S45. Gene #43: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
4P LOSS MUTATED | 1 | 15 | 1
4P LOSS WILD-TYPE | 42 | 28 | 69

Figure S45. Get High-res Image Gene #43: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 3.57e-07 (Fisher's exact test), Q value = 0.00018

Table S46. Gene #43: '4p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
4P LOSS MUTATED | 17 | 0 | 0 | 0
4P LOSS WILD-TYPE | 41 | 49 | 31 | 23

Figure S46. Get High-res Image Gene #43: '4p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.8e-06 (Fisher's exact test), Q value = 0.0039

Table S47. Gene #43: '4p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
4P LOSS MUTATED | 10 | 7 | 0
4P LOSS WILD-TYPE | 21 | 59 | 64

Figure S47. Get High-res Image Gene #43: '4p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 7.23e-08 (Fisher's exact test), Q value = 3.9e-05

Table S48. Gene #44: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
4Q LOSS MUTATED | 0 | 5 | 0 | 14
4Q LOSS WILD-TYPE | 33 | 63 | 37 | 20

Figure S48. Get High-res Image Gene #44: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 2.57e-08 (Fisher's exact test), Q value = 1.4e-05

Table S49. Gene #44: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
4Q LOSS MUTATED | 1 | 16 | 1
4Q LOSS WILD-TYPE | 42 | 27 | 69

Figure S49. Get High-res Image Gene #44: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1.27e-07 (Fisher's exact test), Q value = 6.6e-05

Table S50. Gene #44: '4q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
4Q LOSS MUTATED | 18 | 0 | 0 | 0
4Q LOSS WILD-TYPE | 40 | 49 | 31 | 23

Figure S50. Get High-res Image Gene #44: '4q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.76e-05 (Fisher's exact test), Q value = 0.014

Table S51. Gene #44: '4q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
4Q LOSS MUTATED | 9 | 9 | 0
4Q LOSS WILD-TYPE | 22 | 57 | 64

Figure S51. Get High-res Image Gene #44: '4q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.34e-05 (Fisher's exact test), Q value = 0.016

Table S52. Gene #45: '5p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
5P LOSS MUTATED | 6 | 0 | 0
5P LOSS WILD-TYPE | 25 | 66 | 64

Figure S52. Get High-res Image Gene #45: '5p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.34e-05 (Fisher's exact test), Q value = 0.016

Table S53. Gene #46: '5q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
5Q LOSS MUTATED | 6 | 0 | 0
5Q LOSS WILD-TYPE | 25 | 66 | 64

Figure S53. Get High-res Image Gene #46: '5q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 9.92e-05 (Fisher's exact test), Q value = 0.047

Table S54. Gene #48: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
6Q LOSS MUTATED | 1 | 4 | 0 | 10
6Q LOSS WILD-TYPE | 32 | 64 | 37 | 24

Figure S54. Get High-res Image Gene #48: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1.69e-06 (Fisher's exact test), Q value = 0.00086

Table S55. Gene #51: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
9P LOSS MUTATED | 1 | 7 | 0 | 14
9P LOSS WILD-TYPE | 32 | 61 | 37 | 20

Figure S55. Get High-res Image Gene #51: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 3.99e-07 (Fisher's exact test), Q value = 0.00021

Table S56. Gene #51: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
9P LOSS MUTATED | 5 | 14 | 0
9P LOSS WILD-TYPE | 38 | 29 | 70

Figure S56. Get High-res Image Gene #51: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 9.89e-07 (Fisher's exact test), Q value = 5e-04

Table S57. Gene #51: '9p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
9P LOSS MUTATED | 19 | 0 | 1 | 1
9P LOSS WILD-TYPE | 39 | 49 | 30 | 22

Figure S57. Get High-res Image Gene #51: '9p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000187 (Fisher's exact test), Q value = 0.086

Table S58. Gene #51: '9p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
9P LOSS MUTATED | 9 | 11 | 1
9P LOSS WILD-TYPE | 22 | 55 | 63

Figure S58. Get High-res Image Gene #51: '9p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 3.03e-06 (Fisher's exact test), Q value = 0.0015

Table S59. Gene #52: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
9Q LOSS MUTATED | 1 | 9 | 0 | 14
9Q LOSS WILD-TYPE | 32 | 59 | 37 | 20

Figure S59. Get High-res Image Gene #52: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1.53e-07 (Fisher's exact test), Q value = 8e-05

Table S60. Gene #52: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
9Q LOSS MUTATED | 6 | 15 | 0
9Q LOSS WILD-TYPE | 37 | 28 | 70

Figure S60. Get High-res Image Gene #52: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1.15e-07 (Fisher's exact test), Q value = 6.1e-05

Table S61. Gene #52: '9q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
9Q LOSS MUTATED | 21 | 0 | 1 | 1
9Q LOSS WILD-TYPE | 37 | 49 | 30 | 22

Figure S61. Get High-res Image Gene #52: '9q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.41e-07 (Fisher's exact test), Q value = 0.00028

Table S62. Gene #52: '9q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
9Q LOSS MUTATED | 12 | 11 | 0
9Q LOSS WILD-TYPE | 19 | 55 | 64

Figure S62. Get High-res Image Gene #52: '9q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.03e-05 (Fisher's exact test), Q value = 0.029

Table S63. Gene #52: '9q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 80 | 74
9Q LOSS MUTATED | 5 | 2 | 17
9Q LOSS WILD-TYPE | 13 | 78 | 57

Figure S63. Get High-res Image Gene #52: '9q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S64. Gene #52: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 14 | 87 | 71
9Q LOSS MUTATED | 4 | 3 | 17
9Q LOSS WILD-TYPE | 10 | 84 | 54

Figure S64. Get High-res Image Gene #52: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 7.31e-08 (Fisher's exact test), Q value = 3.9e-05

Table S65. Gene #53: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
10P LOSS MUTATED | 0 | 1 | 0 | 11
10P LOSS WILD-TYPE | 33 | 67 | 37 | 23

Figure S65. Get High-res Image Gene #53: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 7.49e-05 (Fisher's exact test), Q value = 0.036

Table S66. Gene #53: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
10P LOSS MUTATED | 0 | 9 | 1
10P LOSS WILD-TYPE | 43 | 34 | 69

Figure S66. Get High-res Image Gene #53: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000114 (Fisher's exact test), Q value = 0.053

Table S67. Gene #53: '10p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 80 | 74
10P LOSS MUTATED | 6 | 1 | 5
10P LOSS WILD-TYPE | 12 | 79 | 69

Figure S67. Get High-res Image Gene #53: '10p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 3.05e-06 (Fisher's exact test), Q value = 0.0015

Table S68. Gene #54: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
10Q LOSS MUTATED | 0 | 2 | 0 | 10
10Q LOSS WILD-TYPE | 33 | 66 | 37 | 24

Figure S68. Get High-res Image Gene #54: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 1.91e-05 (Fisher's exact test), Q value = 0.0094

Table S69. Gene #54: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
10Q LOSS MUTATED | 0 | 10 | 1
10Q LOSS WILD-TYPE | 43 | 33 | 69

Figure S69. Get High-res Image Gene #54: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.42e-05 (Fisher's exact test), Q value = 0.0071

Table S70. Gene #54: '10q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 80 | 74
10Q LOSS MUTATED | 6 | 0 | 6
10Q LOSS WILD-TYPE | 12 | 80 | 68

Figure S70. Get High-res Image Gene #54: '10q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000139 (Fisher's exact test), Q value = 0.065

Table S71. Gene #54: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 14 | 87 | 71
10Q LOSS MUTATED | 5 | 1 | 6
10Q LOSS WILD-TYPE | 9 | 86 | 65

Figure S71. Get High-res Image Gene #54: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1.61e-05 (Fisher's exact test), Q value = 0.008

Table S72. Gene #56: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
11Q LOSS MUTATED | 0 | 4 | 0 | 10
11Q LOSS WILD-TYPE | 33 | 64 | 37 | 24

Figure S72. Get High-res Image Gene #56: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 0.000148 (Fisher's exact test), Q value = 0.069

Table S73. Gene #56: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
11Q LOSS MUTATED | 1 | 11 | 2
11Q LOSS WILD-TYPE | 42 | 32 | 68

Figure S73. Get High-res Image Gene #56: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 1.21e-05 (Fisher's exact test), Q value = 0.006

Table S74. Gene #57: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
13Q LOSS MUTATED | 0 | 6 | 0 | 11
13Q LOSS WILD-TYPE | 33 | 62 | 37 | 23

Figure S74. Get High-res Image Gene #57: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 1.42e-08 (Fisher's exact test), Q value = 7.6e-06

Table S75. Gene #57: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
13Q LOSS MUTATED | 0 | 15 | 1
13Q LOSS WILD-TYPE | 43 | 28 | 69

Figure S75. Get High-res Image Gene #57: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 7.84e-06 (Fisher's exact test), Q value = 0.0039

Table S76. Gene #57: '13q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
13Q LOSS MUTATED | 16 | 1 | 0 | 0
13Q LOSS WILD-TYPE | 42 | 48 | 31 | 23

Figure S76. Get High-res Image Gene #57: '13q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.82e-05 (Fisher's exact test), Q value = 0.037

Table S77. Gene #57: '13q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
13Q LOSS MUTATED | 10 | 6 | 1
13Q LOSS WILD-TYPE | 21 | 60 | 63

Figure S77. Get High-res Image Gene #57: '13q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1.12e-11 (Fisher's exact test), Q value = 6.1e-09

Table S78. Gene #58: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
14Q LOSS MUTATED | 1 | 11 | 0 | 22
14Q LOSS WILD-TYPE | 32 | 57 | 37 | 12

Figure S78. Get High-res Image Gene #58: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 0.000267 (Fisher's exact test), Q value = 0.12

Table S79. Gene #58: '14q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
14Q LOSS MUTATED | 21 | 2 | 5 | 3
14Q LOSS WILD-TYPE | 37 | 47 | 26 | 20

Figure S79. Get High-res Image Gene #58: '14q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.21e-07 (Fisher's exact test), Q value = 0.00042

Table S80. Gene #58: '14q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
14Q LOSS MUTATED | 16 | 12 | 3
14Q LOSS WILD-TYPE | 15 | 54 | 61

Figure S80. Get High-res Image Gene #58: '14q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 9.33e-05 (Fisher's exact test), Q value = 0.044

Table S81. Gene #59: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
15Q LOSS MUTATED | 1 | 7 | 0 | 11
15Q LOSS WILD-TYPE | 32 | 61 | 37 | 23

Figure S81. Get High-res Image Gene #59: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.11e-07 (Fisher's exact test), Q value = 5.8e-05

Table S82. Gene #59: '15q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
15Q LOSS MUTATED | 13 | 3 | 1
15Q LOSS WILD-TYPE | 18 | 63 | 63

Figure S82. Get High-res Image Gene #59: '15q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.000166 (Fisher's exact test), Q value = 0.077

Table S83. Gene #62: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
17P LOSS MUTATED | 0 | 7 | 0
17P LOSS WILD-TYPE | 43 | 36 | 70

Figure S83. Get High-res Image Gene #62: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 0.000337 (Fisher's exact test), Q value = 0.15

Table S84. Gene #63: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
18P LOSS MUTATED | 1 | 12 | 2 | 13
18P LOSS WILD-TYPE | 32 | 56 | 35 | 21

Figure S84. Get High-res Image Gene #63: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 3.92e-06 (Fisher's exact test), Q value = 0.002

Table S85. Gene #63: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
18P LOSS MUTATED | 4 | 18 | 4
18P LOSS WILD-TYPE | 39 | 25 | 66

Figure S85. Get High-res Image Gene #63: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 2.03e-06 (Fisher's exact test), Q value = 0.001

Table S86. Gene #63: '18p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
18P LOSS MUTATED | 20 | 0 | 2 | 2
18P LOSS WILD-TYPE | 38 | 49 | 29 | 21

Figure S86. Get High-res Image Gene #63: '18p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 3.3e-05 (Fisher's exact test), Q value = 0.016

Table S87. Gene #64: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
18Q LOSS MUTATED | 1 | 12 | 2 | 15
18Q LOSS WILD-TYPE | 32 | 56 | 35 | 19

Figure S87. Get High-res Image Gene #64: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 2.97e-07 (Fisher's exact test), Q value = 0.00015

Table S88. Gene #64: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
18Q LOSS MUTATED | 4 | 20 | 4
18Q LOSS WILD-TYPE | 39 | 23 | 66

Figure S88. Get High-res Image Gene #64: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 2.6e-07 (Fisher's exact test), Q value = 0.00014

Table S89. Gene #64: '18q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
18Q LOSS MUTATED | 22 | 0 | 2 | 2
18Q LOSS WILD-TYPE | 36 | 49 | 29 | 21

Figure S89. Get High-res Image Gene #64: '18q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000177 (Fisher's exact test), Q value = 0.082

Table S90. Gene #64: '18q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
18Q LOSS MUTATED | 10 | 14 | 2
18Q LOSS WILD-TYPE | 21 | 52 | 62

Figure S90. Get High-res Image Gene #64: '18q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 8.49e-05 (Fisher's exact test), Q value = 0.04

Table S91. Gene #66: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
19Q LOSS MUTATED | 1 | 0 | 2 | 8
19Q LOSS WILD-TYPE | 32 | 68 | 35 | 26

Figure S91. Get High-res Image Gene #66: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 0.000173 (Fisher's exact test), Q value = 0.08

Table S92. Gene #67: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
21Q LOSS MUTATED | 8 | 5 | 3 | 14
21Q LOSS WILD-TYPE | 25 | 63 | 34 | 20

Figure S92. Get High-res Image Gene #67: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 6.88e-07 (Fisher's exact test), Q value = 0.00035

Table S93. Gene #68: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
22Q LOSS MUTATED | 1 | 15 | 5 | 20
22Q LOSS WILD-TYPE | 32 | 53 | 32 | 14

Figure S93. Get High-res Image Gene #68: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 4.73e-07 (Fisher's exact test), Q value = 0.00024

Table S94. Gene #68: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
22Q LOSS MUTATED | 5 | 24 | 9
22Q LOSS WILD-TYPE | 38 | 19 | 61

Figure S94. Get High-res Image Gene #68: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 7.37e-08 (Fisher's exact test), Q value = 3.9e-05

Table S95. Gene #68: '22q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
22Q LOSS MUTATED | 29 | 5 | 4 | 0
22Q LOSS WILD-TYPE | 29 | 44 | 27 | 23

Figure S95. Get High-res Image Gene #68: '22q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.052

Table S96. Gene #68: '22q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 80 | 74
22Q LOSS MUTATED | 12 | 13 | 16
22Q LOSS WILD-TYPE | 6 | 67 | 58

Figure S96. Get High-res Image Gene #68: '22q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 2.26e-05 (Fisher's exact test), Q value = 0.011

Table S97. Gene #69: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
XQ LOSS MUTATED | 2 | 4 | 1 | 13
XQ LOSS WILD-TYPE | 31 | 64 | 36 | 21

Figure S97. Get High-res Image Gene #69: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 4.35e-05 (Fisher's exact test), Q value = 0.021

Table S98. Gene #69: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
XQ LOSS MUTATED | 1 | 13 | 3
XQ LOSS WILD-TYPE | 42 | 30 | 67

Figure S98. Get High-res Image Gene #69: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 3.08e-05 (Fisher's exact test), Q value = 0.015

Table S99. Gene #69: 'xq loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
XQ LOSS MUTATED | 16 | 2 | 0 | 0
XQ LOSS WILD-TYPE | 42 | 47 | 31 | 23

Figure S99. Get High-res Image Gene #69: '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 = 172

- Number of significantly arm-level cnvs = 69

- Number of molecular subtypes = 8

- 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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