Correlation between copy number variations of arm-level result and molecular subtypes
Adrenocortical Carcinoma (Primary solid tumor)
15 July 2014 | analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1ZS2V51
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/C1ZS2V51
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 80 arm-level events and 8 molecular subtypes across 90 patients, 54 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

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

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

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

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

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

- 9p gain cnv correlated to 'CN_CNMF'.

- 9q gain cnv correlated to 'CN_CNMF'.

- 10p gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- 10q gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- 12p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 12q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- 14q gain cnv correlated to 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

- 19p gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

- 19q gain cnv correlated to 'MRNASEQ_CNMF'.

- 20p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

- 20q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- xq gain cnv correlated to 'CN_CNMF'.

- 2q loss cnv correlated to 'CN_CNMF'.

- 9p loss cnv correlated to 'MRNASEQ_CNMF'.

- 11q loss cnv correlated to 'CN_CNMF'.

- 17p loss cnv correlated to 'METHLYATION_CNMF'.

- 17q loss cnv correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 80 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, 54 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
14q gain | 21 (23%) | 69 | 0.0141 (1.00) | 0.0557 (1.00) | 0.00038 (0.208) | 0.00082 (0.44) | 2e-05 (0.0117) | 0.00014 (0.0784) | 2e-05 (0.0117) | 2e-05 (0.0117)
20p gain | 46 (51%) | 44 | 1e-05 (0.00598) | 0.236 (1.00) | 9e-05 (0.0509) | 0.00014 (0.0784) | 0.00495 (1.00) | 0.0912 (1.00) | 0.00013 (0.0729) | 0.00372 (1.00)
4p gain | 37 (41%) | 53 | 3e-05 (0.0174) | 0.0438 (1.00) | 5e-05 (0.0287) | 5e-05 (0.0287) | 0.295 (1.00) | 0.00193 (0.998) | 0.688 (1.00) | 0.146 (1.00)
4q gain | 33 (37%) | 57 | 7e-05 (0.0399) | 0.0363 (1.00) | 3e-05 (0.0174) | 1e-05 (0.00598) | 0.559 (1.00) | 0.00082 (0.44) | 0.588 (1.00) | 0.0892 (1.00)
7q gain | 48 (53%) | 42 | 2e-05 (0.0117) | 0.116 (1.00) | 1e-05 (0.00598) | 0.0001 (0.0565) | 0.915 (1.00) | 0.331 (1.00) | 1 (1.00) | 0.18 (1.00)
12p gain | 64 (71%) | 26 | 2e-05 (0.0117) | 0.209 (1.00) | 0.00022 (0.122) | 5e-05 (0.0287) | 0.246 (1.00) | 0.209 (1.00) | 0.0698 (1.00) | 0.12 (1.00)
16p gain | 49 (54%) | 41 | 1e-05 (0.00598) | 0.0107 (1.00) | 1e-05 (0.00598) | 1e-05 (0.00598) | 0.0466 (1.00) | 0.0262 (1.00) | 0.0122 (1.00) | 0.169 (1.00)
16q gain | 47 (52%) | 43 | 1e-05 (0.00598) | 0.00825 (1.00) | 0.00012 (0.0676) | 1e-05 (0.00598) | 0.024 (1.00) | 0.0131 (1.00) | 0.0118 (1.00) | 0.144 (1.00)
20q gain | 49 (54%) | 41 | 2e-05 (0.0117) | 0.0649 (1.00) | 7e-05 (0.0399) | 0.00025 (0.138) | 0.0194 (1.00) | 0.275 (1.00) | 0.00098 (0.522) | 0.0334 (1.00)
2p gain | 13 (14%) | 77 | 0.00026 (0.143) | 0.00112 (0.594) | 0.0118 (1.00) | 0.00014 (0.0784) | 0.373 (1.00) | 0.0185 (1.00) | 0.0799 (1.00) | 0.0468 (1.00)
5p gain | 57 (63%) | 33 | 1e-05 (0.00598) | 0.0365 (1.00) | 0.00058 (0.314) | 1e-05 (0.00598) | 0.251 (1.00) | 0.227 (1.00) | 0.0674 (1.00) | 0.342 (1.00)
5q gain | 53 (59%) | 37 | 3e-05 (0.0174) | 0.00886 (1.00) | 0.00071 (0.383) | 3e-05 (0.0174) | 0.334 (1.00) | 0.135 (1.00) | 0.37 (1.00) | 0.388 (1.00)
7p gain | 48 (53%) | 42 | 0.00042 (0.23) | 0.118 (1.00) | 0.00012 (0.0676) | 0.00133 (0.698) | 0.914 (1.00) | 0.55 (1.00) | 0.874 (1.00) | 0.314 (1.00)
10p gain | 25 (28%) | 65 | 0.00079 (0.424) | 0.0588 (1.00) | 3e-05 (0.0174) | 0.00019 (0.106) | 0.0337 (1.00) | 0.511 (1.00) | 0.104 (1.00) | 0.667 (1.00)
10q gain | 26 (29%) | 64 | 0.00057 (0.309) | 0.0712 (1.00) | 4e-05 (0.023) | 0.00045 (0.246) | 0.0203 (1.00) | 0.34 (1.00) | 0.0698 (1.00) | 0.651 (1.00)
12q gain | 64 (71%) | 26 | 1e-05 (0.00598) | 0.311 (1.00) | 0.00068 (0.367) | 0.00014 (0.0784) | 0.236 (1.00) | 0.455 (1.00) | 0.0425 (1.00) | 0.207 (1.00)
9p gain | 20 (22%) | 70 | 7e-05 (0.0399) | 0.0023 (1.00) | 0.00932 (1.00) | 0.0112 (1.00) | 0.385 (1.00) | 0.55 (1.00) | 0.237 (1.00) | 0.63 (1.00)
9q gain | 29 (32%) | 61 | 0.00019 (0.106) | 0.00121 (0.639) | 0.023 (1.00) | 0.00169 (0.879) | 0.0342 (1.00) | 0.354 (1.00) | 0.0172 (1.00) | 0.36 (1.00)
19p gain | 56 (62%) | 34 | 0.00757 (1.00) | 0.0549 (1.00) | 0.00133 (0.698) | 0.00045 (0.246) | 0.466 (1.00) | 0.471 (1.00) | 0.37 (1.00) | 0.626 (1.00)
19q gain | 52 (58%) | 38 | 0.00051 (0.277) | 0.0498 (1.00) | 0.00036 (0.198) | 0.00114 (0.603) | 0.143 (1.00) | 0.11 (1.00) | 0.101 (1.00) | 0.192 (1.00)
xq gain | 40 (44%) | 50 | 1e-05 (0.00598) | 0.169 (1.00) | 0.00166 (0.865) | 0.0085 (1.00) | 0.797 (1.00) | 0.151 (1.00) | 0.611 (1.00) | 0.0617 (1.00)
2q loss | 15 (17%) | 75 | 0.0001 (0.0565) | 0.00106 (0.564) | 0.113 (1.00) | 0.0535 (1.00) | 0.0313 (1.00) | 0.729 (1.00) | 0.115 (1.00) | 0.835 (1.00)
9p loss | 20 (22%) | 70 | 0.00127 (0.668) | 0.0479 (1.00) | 6e-05 (0.0343) | 0.00125 (0.659) | 0.0092 (1.00) | 0.137 (1.00) | 0.0587 (1.00) | 0.204 (1.00)
11q loss | 23 (26%) | 67 | 8e-05 (0.0454) | 0.00271 (1.00) | 0.133 (1.00) | 0.128 (1.00) | 0.104 (1.00) | 0.824 (1.00) | 0.217 (1.00) | 0.899 (1.00)
17p loss | 32 (36%) | 58 | 0.00109 (0.579) | 0.00019 (0.106) | 0.0117 (1.00) | 0.0135 (1.00) | 0.0812 (1.00) | 0.00286 (1.00) | 0.0508 (1.00) | 0.0141 (1.00)
17q loss | 24 (27%) | 66 | 0.00028 (0.154) | 0.00541 (1.00) | 0.12 (1.00) | 0.0334 (1.00) | 0.0666 (1.00) | 0.0199 (1.00) | 0.0759 (1.00) | 0.182 (1.00)
1p gain | 4 (4%) | 86 | 0.119 (1.00) |  |  |  |  |  |  |
1q gain | 8 (9%) | 82 | 0.12 (1.00) | 0.654 (1.00) | 0.0467 (1.00) | 0.0776 (1.00) | 0.0647 (1.00) | 0.242 (1.00) | 0.298 (1.00) | 0.23 (1.00)
2q gain | 12 (13%) | 78 | 0.0037 (1.00) | 0.00225 (1.00) | 0.018 (1.00) | 0.00263 (1.00) | 0.0556 (1.00) | 0.00431 (1.00) | 0.0196 (1.00) | 0.00352 (1.00)
3p gain | 13 (14%) | 77 | 0.0925 (1.00) | 0.0687 (1.00) | 0.329 (1.00) | 0.362 (1.00) | 0.409 (1.00) | 0.107 (1.00) | 0.31 (1.00) | 0.601 (1.00)
3q gain | 15 (17%) | 75 | 0.0599 (1.00) | 0.0518 (1.00) | 0.0521 (1.00) | 0.793 (1.00) | 0.652 (1.00) | 0.246 (1.00) | 0.56 (1.00) | 0.856 (1.00)
6p gain | 18 (20%) | 72 | 0.0617 (1.00) | 0.683 (1.00) | 0.0671 (1.00) | 0.472 (1.00) | 0.162 (1.00) | 0.0549 (1.00) | 0.209 (1.00) | 0.0253 (1.00)
6q gain | 16 (18%) | 74 | 0.00232 (1.00) | 0.458 (1.00) | 0.199 (1.00) | 0.294 (1.00) | 0.298 (1.00) | 0.196 (1.00) | 0.26 (1.00) | 0.161 (1.00)
8p gain | 32 (36%) | 58 | 0.00177 (0.917) | 0.139 (1.00) | 0.167 (1.00) | 0.145 (1.00) | 0.113 (1.00) | 0.174 (1.00) | 0.0261 (1.00) | 0.0605 (1.00)
8q gain | 38 (42%) | 52 | 0.0187 (1.00) | 0.291 (1.00) | 0.416 (1.00) | 0.231 (1.00) | 0.496 (1.00) | 0.261 (1.00) | 0.0963 (1.00) | 0.121 (1.00)
11p gain | 5 (6%) | 85 | 0.111 (1.00) |  |  |  |  |  |  |
11q gain | 6 (7%) | 84 | 0.174 (1.00) | 0.176 (1.00) | 0.0443 (1.00) | 0.0787 (1.00) | 0.187 (1.00) | 0.371 (1.00) | 0.445 (1.00) | 0.16 (1.00)
13q gain | 6 (7%) | 84 | 1 (1.00) | 0.464 (1.00) | 0.0385 (1.00) | 0.639 (1.00) | 0.14 (1.00) | 0.913 (1.00) | 0.3 (1.00) | 0.394 (1.00)
15q gain | 11 (12%) | 79 | 0.215 (1.00) | 0.0454 (1.00) | 0.0105 (1.00) | 0.00482 (1.00) | 0.361 (1.00) | 0.00073 (0.393) | 0.248 (1.00) | 0.00583 (1.00)
17p gain | 5 (6%) | 85 | 0.0883 (1.00) | 0.337 (1.00) | 0.685 (1.00) | 0.144 (1.00) | 0.205 (1.00) | 0.794 (1.00) | 0.141 (1.00) | 0.929 (1.00)
17q gain | 7 (8%) | 83 | 0.0145 (1.00) | 0.338 (1.00) | 0.689 (1.00) | 0.144 (1.00) | 0.211 (1.00) | 0.793 (1.00) | 0.14 (1.00) | 0.928 (1.00)
18p gain | 6 (7%) | 84 | 0.493 (1.00) |  |  |  |  |  |  |
18q gain | 5 (6%) | 85 | 0.66 (1.00) |  |  |  |  |  |  |
21q gain | 31 (34%) | 59 | 0.0371 (1.00) | 0.00888 (1.00) | 0.0195 (1.00) | 0.00091 (0.486) | 0.0131 (1.00) | 0.0205 (1.00) | 0.0259 (1.00) | 0.154 (1.00)
22q gain | 3 (3%) | 87 | 0.375 (1.00) |  |  |  |  |  |  |
1p loss | 29 (32%) | 61 | 0.202 (1.00) | 0.141 (1.00) | 0.438 (1.00) | 0.065 (1.00) | 0.469 (1.00) | 0.41 (1.00) | 0.784 (1.00) | 0.406 (1.00)
1q loss | 20 (22%) | 70 | 0.584 (1.00) | 0.0891 (1.00) | 0.962 (1.00) | 0.601 (1.00) | 0.367 (1.00) | 0.841 (1.00) | 0.594 (1.00) | 0.609 (1.00)
2p loss | 17 (19%) | 73 | 0.00056 (0.304) | 0.0272 (1.00) | 0.612 (1.00) | 0.267 (1.00) | 0.0377 (1.00) | 0.769 (1.00) | 0.127 (1.00) | 0.76 (1.00)
3p loss | 20 (22%) | 70 | 0.0597 (1.00) | 0.143 (1.00) | 0.112 (1.00) | 0.135 (1.00) | 0.523 (1.00) | 0.391 (1.00) | 0.195 (1.00) | 0.306 (1.00)
3q loss | 20 (22%) | 70 | 0.0164 (1.00) | 0.166 (1.00) | 0.0222 (1.00) | 0.0292 (1.00) | 0.193 (1.00) | 0.338 (1.00) | 0.0403 (1.00) | 0.185 (1.00)
4p loss | 10 (11%) | 80 | 0.0168 (1.00) | 0.234 (1.00) | 0.0234 (1.00) | 0.081 (1.00) | 0.308 (1.00) | 0.931 (1.00) | 0.424 (1.00) | 0.903 (1.00)
4q loss | 11 (12%) | 79 | 0.0469 (1.00) | 0.0975 (1.00) | 0.0075 (1.00) | 0.0277 (1.00) | 0.252 (1.00) | 0.81 (1.00) | 0.383 (1.00) | 0.761 (1.00)
5p loss | 8 (9%) | 82 | 0.275 (1.00) | 0.05 (1.00) | 0.23 (1.00) | 0.0104 (1.00) | 0.774 (1.00) | 0.298 (1.00) | 0.455 (1.00) | 0.962 (1.00)
5q loss | 7 (8%) | 83 | 0.863 (1.00) | 0.656 (1.00) | 0.278 (1.00) | 0.136 (1.00) | 0.659 (1.00) | 0.128 (1.00) | 0.863 (1.00) | 0.333 (1.00)
6p loss | 19 (21%) | 71 | 0.0303 (1.00) | 0.85 (1.00) | 0.622 (1.00) | 0.692 (1.00) | 0.624 (1.00) | 0.0993 (1.00) | 0.815 (1.00) | 0.162 (1.00)
6q loss | 22 (24%) | 68 | 0.00738 (1.00) | 0.862 (1.00) | 0.634 (1.00) | 0.692 (1.00) | 0.729 (1.00) | 0.177 (1.00) | 0.74 (1.00) | 0.0687 (1.00)
7p loss | 5 (6%) | 85 | 0.275 (1.00) | 0.585 (1.00) | 0.91 (1.00) | 0.891 (1.00) | 0.816 (1.00) | 0.416 (1.00) | 0.684 (1.00) | 0.13 (1.00)
7q loss | 6 (7%) | 84 | 0.192 (1.00) | 0.304 (1.00) | 0.62 (1.00) | 0.658 (1.00) | 1 (1.00) | 0.233 (1.00) | 0.596 (1.00) | 0.0712 (1.00)
8p loss | 16 (18%) | 74 | 0.00308 (1.00) | 0.224 (1.00) | 0.181 (1.00) | 0.141 (1.00) | 0.181 (1.00) | 0.0226 (1.00) | 0.0171 (1.00) | 0.00696 (1.00)
8q loss | 12 (13%) | 78 | 0.00147 (0.769) | 0.0869 (1.00) | 0.0319 (1.00) | 0.124 (1.00) | 0.0782 (1.00) | 0.0352 (1.00) | 0.0332 (1.00) | 0.116 (1.00)
9q loss | 11 (12%) | 79 | 0.142 (1.00) | 0.934 (1.00) | 0.0821 (1.00) | 0.322 (1.00) | 0.557 (1.00) | 0.495 (1.00) | 0.83 (1.00) | 0.282 (1.00)
10p loss | 12 (13%) | 78 | 0.736 (1.00) | 0.428 (1.00) | 0.264 (1.00) | 1 (1.00) | 0.683 (1.00) | 0.71 (1.00) | 0.618 (1.00) | 0.749 (1.00)
10q loss | 10 (11%) | 80 | 0.39 (1.00) | 0.624 (1.00) | 0.534 (1.00) | 1 (1.00) | 1 (1.00) | 0.709 (1.00) | 0.892 (1.00) | 0.824 (1.00)
11p loss | 24 (27%) | 66 | 0.00173 (0.898) | 0.0174 (1.00) | 0.221 (1.00) | 0.187 (1.00) | 0.28 (1.00) | 0.891 (1.00) | 0.447 (1.00) | 0.925 (1.00)
12p loss | 5 (6%) | 85 | 0.229 (1.00) | 0.255 (1.00) | 0.62 (1.00) | 0.0386 (1.00) | 0.104 (1.00) | 0.517 (1.00) | 0.0108 (1.00) | 0.0171 (1.00)
12q loss | 4 (4%) | 86 | 0.248 (1.00) | 0.0495 (1.00) | 0.441 (1.00) | 0.0097 (1.00) | 0.33 (1.00) | 0.237 (1.00) | 0.0422 (1.00) | 0.00337 (1.00)
13q loss | 39 (43%) | 51 | 0.01 (1.00) | 0.0795 (1.00) | 0.625 (1.00) | 0.884 (1.00) | 0.753 (1.00) | 0.302 (1.00) | 0.91 (1.00) | 0.285 (1.00)
14q loss | 18 (20%) | 72 | 0.0275 (1.00) | 0.444 (1.00) | 0.0181 (1.00) | 0.047 (1.00) | 0.413 (1.00) | 0.53 (1.00) | 0.272 (1.00) | 0.9 (1.00)
15q loss | 21 (23%) | 69 | 0.0182 (1.00) | 0.414 (1.00) | 0.11 (1.00) | 0.231 (1.00) | 0.607 (1.00) | 0.0404 (1.00) | 0.373 (1.00) | 0.162 (1.00)
16p loss | 6 (7%) | 84 | 0.173 (1.00) | 0.0506 (1.00) | 0.00209 (1.00) | 0.00412 (1.00) | 0.0133 (1.00) | 0.443 (1.00) | 0.0311 (1.00) | 0.537 (1.00)
16q loss | 5 (6%) | 85 | 0.318 (1.00) | 0.0771 (1.00) | 0.0582 (1.00) | 0.0856 (1.00) | 0.167 (1.00) | 0.303 (1.00) | 0.361 (1.00) | 0.894 (1.00)
18p loss | 37 (41%) | 53 | 0.0261 (1.00) | 0.259 (1.00) | 0.776 (1.00) | 0.646 (1.00) | 0.692 (1.00) | 0.693 (1.00) | 0.875 (1.00) | 0.284 (1.00)
18q loss | 35 (39%) | 55 | 0.0456 (1.00) | 0.426 (1.00) | 0.824 (1.00) | 0.935 (1.00) | 0.496 (1.00) | 0.914 (1.00) | 0.76 (1.00) | 0.0993 (1.00)
19p loss | 5 (6%) | 85 | 0.112 (1.00) | 0.443 (1.00) | 0.157 (1.00) | 0.0132 (1.00) | 0.139 (1.00) | 0.715 (1.00) | 0.214 (1.00) | 0.0321 (1.00)
19q loss | 4 (4%) | 86 | 0.247 (1.00) | 0.705 (1.00) | 0.773 (1.00) | 0.119 (1.00) | 0.783 (1.00) | 0.205 (1.00) | 0.216 (1.00) | 0.0321 (1.00)
20p loss | 9 (10%) | 81 | 0.0103 (1.00) | 0.303 (1.00) | 0.215 (1.00) | 0.127 (1.00) | 0.0681 (1.00) | 0.443 (1.00) | 0.17 (1.00) | 0.764 (1.00)
20q loss | 3 (3%) | 87 | 0.456 (1.00) |  |  |  |  |  |  |
21q loss | 15 (17%) | 75 | 0.00871 (1.00) | 0.337 (1.00) | 0.256 (1.00) | 0.252 (1.00) | 0.223 (1.00) | 0.51 (1.00) | 0.233 (1.00) | 0.815 (1.00)
22q loss | 48 (53%) | 42 | 0.0777 (1.00) | 0.081 (1.00) | 0.62 (1.00) | 0.282 (1.00) | 0.874 (1.00) | 0.828 (1.00) | 0.8 (1.00) | 0.729 (1.00)
xq loss | 17 (19%) | 73 | 0.00153 (0.799) | 0.246 (1.00) | 0.0337 (1.00) | 0.0448 (1.00) | 0.652 (1.00) | 0.172 (1.00) | 0.139 (1.00) | 0.45 (1.00)

'2p gain' versus 'CN_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.14

Table S1. Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 32 | 24 | 15 | 10 | 9
2P GAIN MUTATED | 12 | 0 | 1 | 0 | 0
2P GAIN WILD-TYPE | 20 | 24 | 14 | 10 | 9

Figure S1. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.078

Table S2. Gene #3: '2p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
2P GAIN MUTATED | 8 | 0 | 1 | 0
2P GAIN WILD-TYPE | 15 | 23 | 6 | 24

Figure S2. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S3. Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 32 | 24 | 15 | 10 | 9
4P GAIN MUTATED | 3 | 13 | 10 | 4 | 7
4P GAIN WILD-TYPE | 29 | 11 | 5 | 6 | 2

Figure S3. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.029

Table S4. Gene #7: '4p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
4P GAIN MUTATED | 1 | 8 | 11 | 10
4P GAIN WILD-TYPE | 23 | 5 | 6 | 13

Figure S4. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.029

Table S5. Gene #7: '4p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
4P GAIN MUTATED | 2 | 15 | 0 | 13
4P GAIN WILD-TYPE | 21 | 8 | 7 | 11

Figure S5. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.04

Table S6. Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 32 | 24 | 15 | 10 | 9
4Q GAIN MUTATED | 2 | 12 | 9 | 4 | 6
4Q GAIN WILD-TYPE | 30 | 12 | 6 | 6 | 3

Figure S6. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S7. Gene #8: '4q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
4Q GAIN MUTATED | 0 | 8 | 9 | 10
4Q GAIN WILD-TYPE | 24 | 5 | 8 | 13

Figure S7. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S8. Gene #8: '4q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
4Q GAIN MUTATED | 1 | 15 | 0 | 11
4Q GAIN WILD-TYPE | 22 | 8 | 7 | 13

Figure S8. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S9. Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 32 | 24 | 15 | 10 | 9
5P GAIN MUTATED | 10 | 22 | 13 | 4 | 8
5P GAIN WILD-TYPE | 22 | 2 | 2 | 6 | 1

Figure S9. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S10. Gene #9: '5p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
5P GAIN MUTATED | 6 | 18 | 3 | 22
5P GAIN WILD-TYPE | 17 | 5 | 4 | 2

Figure S10. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S11. Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 32 | 24 | 15 | 10 | 9
5Q GAIN MUTATED | 9 | 19 | 13 | 4 | 8
5Q GAIN WILD-TYPE | 23 | 5 | 2 | 6 | 1

Figure S11. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S12. Gene #10: '5q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
5Q GAIN MUTATED | 5 | 19 | 3 | 20
5Q GAIN WILD-TYPE | 18 | 4 | 4 | 4

Figure S12. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.23

Table S13. Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 32 | 24 | 15 | 10 | 9
7P GAIN MUTATED | 9 | 18 | 12 | 3 | 6
7P GAIN WILD-TYPE | 23 | 6 | 3 | 7 | 3

Figure S13. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.068

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
7P GAIN MUTATED | 6 | 12 | 13 | 11
7P GAIN WILD-TYPE | 18 | 1 | 4 | 12

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

'7q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S15. Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 32 | 24 | 15 | 10 | 9
7Q GAIN MUTATED | 8 | 18 | 13 | 3 | 6
7Q GAIN WILD-TYPE | 24 | 6 | 2 | 7 | 3

Figure S15. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S16. Gene #14: '7q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
7Q GAIN MUTATED | 5 | 13 | 13 | 11
7Q GAIN WILD-TYPE | 19 | 0 | 4 | 12

Figure S16. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.056

Table S17. Gene #14: '7q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
7Q GAIN MUTATED | 6 | 20 | 2 | 14
7Q GAIN WILD-TYPE | 17 | 3 | 5 | 10

Figure S17. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.04

Table S18. Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 32 | 24 | 15 | 10 | 9
9P GAIN MUTATED | 2 | 3 | 10 | 1 | 4
9P GAIN WILD-TYPE | 30 | 21 | 5 | 9 | 5

Figure S18. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.11

Table S19. Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 32 | 24 | 15 | 10 | 9
9Q GAIN MUTATED | 7 | 3 | 12 | 3 | 4
9Q GAIN WILD-TYPE | 25 | 21 | 3 | 7 | 5

Figure S19. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S20. Gene #19: '10p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
10P GAIN MUTATED | 6 | 11 | 4 | 2
10P GAIN WILD-TYPE | 18 | 2 | 13 | 21

Figure S20. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.11

Table S21. Gene #19: '10p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
10P GAIN MUTATED | 7 | 14 | 1 | 1
10P GAIN WILD-TYPE | 16 | 9 | 6 | 23

Figure S21. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.023

Table S22. Gene #20: '10q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
10Q GAIN MUTATED | 7 | 11 | 3 | 2
10Q GAIN WILD-TYPE | 17 | 2 | 14 | 21

Figure S22. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.25

Table S23. Gene #20: '10q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
10Q GAIN MUTATED | 8 | 13 | 1 | 1
10Q GAIN WILD-TYPE | 15 | 10 | 6 | 23

Figure S23. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S24. Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 32 | 24 | 15 | 10 | 9
12P GAIN MUTATED | 14 | 24 | 14 | 5 | 7
12P GAIN WILD-TYPE | 18 | 0 | 1 | 5 | 2

Figure S24. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.12

Table S25. Gene #23: '12p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
12P GAIN MUTATED | 9 | 13 | 14 | 18
12P GAIN WILD-TYPE | 15 | 0 | 3 | 5

Figure S25. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.029

Table S26. Gene #23: '12p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
12P GAIN MUTATED | 10 | 20 | 2 | 22
12P GAIN WILD-TYPE | 13 | 3 | 5 | 2

Figure S26. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S27. Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 32 | 24 | 15 | 10 | 9
12Q GAIN MUTATED | 14 | 24 | 15 | 4 | 7
12Q GAIN WILD-TYPE | 18 | 0 | 0 | 6 | 2

Figure S27. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.078

Table S28. Gene #24: '12q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
12Q GAIN MUTATED | 11 | 20 | 2 | 22
12Q GAIN WILD-TYPE | 12 | 3 | 5 | 2

Figure S28. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.21

Table S29. Gene #26: '14q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
14Q GAIN MUTATED | 2 | 6 | 8 | 1
14Q GAIN WILD-TYPE | 22 | 7 | 9 | 22

Figure S29. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S30. Gene #26: '14q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 16 | 26
14Q GAIN MUTATED | 17 | 0 | 1
14Q GAIN WILD-TYPE | 19 | 16 | 25

Figure S30. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.078

Table S31. Gene #26: '14q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 27 | 11 | 20 | 4
14Q GAIN MUTATED | 7 | 0 | 3 | 5 | 3
14Q GAIN WILD-TYPE | 9 | 27 | 8 | 15 | 1

Figure S31. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S32. Gene #26: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 37 | 18 | 23
14Q GAIN MUTATED | 17 | 1 | 0
14Q GAIN WILD-TYPE | 20 | 17 | 23

Figure S32. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S33. Gene #26: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 25 | 8 | 18 | 9 | 10
14Q GAIN MUTATED | 5 | 0 | 4 | 5 | 4 | 0
14Q GAIN WILD-TYPE | 3 | 25 | 4 | 13 | 5 | 10

Figure S33. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S34. Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 32 | 24 | 15 | 10 | 9
16P GAIN MUTATED | 6 | 24 | 10 | 4 | 5
16P GAIN WILD-TYPE | 26 | 0 | 5 | 6 | 4

Figure S34. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S35. Gene #28: '16p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
16P GAIN MUTATED | 3 | 10 | 13 | 16
16P GAIN WILD-TYPE | 21 | 3 | 4 | 7

Figure S35. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S36. Gene #28: '16p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
16P GAIN MUTATED | 4 | 20 | 0 | 18
16P GAIN WILD-TYPE | 19 | 3 | 7 | 6

Figure S36. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S37. Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 32 | 24 | 15 | 10 | 9
16Q GAIN MUTATED | 6 | 23 | 10 | 3 | 5
16Q GAIN WILD-TYPE | 26 | 1 | 5 | 7 | 4

Figure S37. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.068

Table S38. Gene #29: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
16Q GAIN MUTATED | 4 | 9 | 13 | 16
16Q GAIN WILD-TYPE | 20 | 4 | 4 | 7

Figure S38. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S39. Gene #29: '16q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
16Q GAIN MUTATED | 4 | 19 | 1 | 18
16Q GAIN WILD-TYPE | 19 | 4 | 6 | 6

Figure S39. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.25

Table S40. Gene #34: '19p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
19P GAIN MUTATED | 14 | 21 | 1 | 12
19P GAIN WILD-TYPE | 9 | 2 | 6 | 12

Figure S40. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.2

Table S41. Gene #35: '19q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
19Q GAIN MUTATED | 10 | 13 | 12 | 9
19Q GAIN WILD-TYPE | 14 | 0 | 5 | 14

Figure S41. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S42. Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 32 | 24 | 15 | 10 | 9
20P GAIN MUTATED | 7 | 22 | 9 | 2 | 6
20P GAIN WILD-TYPE | 25 | 2 | 6 | 8 | 3

Figure S42. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.051

Table S43. Gene #36: '20p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
20P GAIN MUTATED | 4 | 9 | 8 | 18
20P GAIN WILD-TYPE | 20 | 4 | 9 | 5

Figure S43. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.078

Table S44. Gene #36: '20p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
20P GAIN MUTATED | 6 | 12 | 1 | 20
20P GAIN WILD-TYPE | 17 | 11 | 6 | 4

Figure S44. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.073

Table S45. Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 37 | 18 | 23
20P GAIN MUTATED | 13 | 7 | 20
20P GAIN WILD-TYPE | 24 | 11 | 3

Figure S45. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S46. Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 32 | 24 | 15 | 10 | 9
20Q GAIN MUTATED | 9 | 21 | 11 | 2 | 6
20Q GAIN WILD-TYPE | 23 | 3 | 4 | 8 | 3

Figure S46. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.04

Table S47. Gene #37: '20q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
20Q GAIN MUTATED | 5 | 11 | 8 | 18
20Q GAIN WILD-TYPE | 19 | 2 | 9 | 5

Figure S47. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.14

Table S48. Gene #37: '20q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
20Q GAIN MUTATED | 6 | 14 | 2 | 20
20Q GAIN WILD-TYPE | 17 | 9 | 5 | 4

Figure S48. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S49. Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 32 | 24 | 15 | 10 | 9
XQ GAIN MUTATED | 6 | 20 | 9 | 2 | 3
XQ GAIN WILD-TYPE | 26 | 4 | 6 | 8 | 6

Figure S49. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.056

Table S50. Gene #44: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 32 | 24 | 15 | 10 | 9
2Q LOSS MUTATED | 1 | 2 | 2 | 6 | 4
2Q LOSS WILD-TYPE | 31 | 22 | 13 | 4 | 5

Figure S50. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.034

Table S51. Gene #57: '9p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
9P LOSS MUTATED | 14 | 1 | 3 | 1
9P LOSS WILD-TYPE | 10 | 12 | 14 | 22

Figure S51. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.045

Table S52. Gene #62: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 32 | 24 | 15 | 10 | 9
11Q LOSS MUTATED | 4 | 3 | 3 | 8 | 5
11Q LOSS WILD-TYPE | 28 | 21 | 12 | 2 | 4

Figure S52. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.11

Table S53. Gene #70: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
17P LOSS MUTATED | 11 | 0 | 12 | 4 | 1
17P LOSS WILD-TYPE | 7 | 11 | 8 | 14 | 10

Figure S53. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.15

Table S54. Gene #71: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 32 | 24 | 15 | 10 | 9
17Q LOSS MUTATED | 7 | 3 | 6 | 8 | 0
17Q LOSS WILD-TYPE | 25 | 21 | 9 | 2 | 9

Figure S54. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data
Input

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

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

- Number of patients = 90

- Number of significantly arm-level cnvs = 80

- 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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