This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.
Testing the association between copy number variation 51 arm-level events and 10 molecular subtypes across 80 patients, 118 significant findings detected with P value < 0.05 and Q value < 0.25.
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4p gain cnv correlated to 'CN_CNMF'.
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4q gain cnv correlated to 'CN_THRESHOLDED_CNMF'.
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6p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.
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6q gain cnv correlated to 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.
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8p gain cnv correlated to 'MRNA_CHIERARCHICAL', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.
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8q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.
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11q gain cnv correlated to 'MIR_MATURE_CHIERARCHICAL'.
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12p gain cnv correlated to 'LINCRNA_CHIERARCHICAL'.
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12q gain cnv correlated to 'LINCRNA_CHIERARCHICAL'.
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13q gain cnv correlated to 'MRNA_CHIERARCHICAL'.
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14q gain cnv correlated to 'LINCRNA_CHIERARCHICAL'.
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17p gain cnv correlated to 'LINCRNA_CHIERARCHICAL'.
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20p gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.
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20q gain cnv correlated to 'MRNA_CHIERARCHICAL', 'LINCRNA_CHIERARCHICAL', and 'CN_CNMF'.
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21q gain cnv correlated to 'MRNA_CHIERARCHICAL', 'LINCRNA_CHIERARCHICAL', and 'CN_CNMF'.
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22q gain cnv correlated to 'LINCRNA_CNMF'.
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xp gain cnv correlated to 'MIR_MATURE_CNMF' and 'METHYLATION_CNMF'.
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xq gain cnv correlated to 'MIR_MATURE_CNMF' and 'METHYLATION_CNMF'.
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1p loss cnv correlated to 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', and 'CN_THRESHOLDED_CNMF'.
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1q loss cnv correlated to 'MIR_MATURE_CHIERARCHICAL'.
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3p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.
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3q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.
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6q loss cnv correlated to 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.
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8p loss cnv correlated to 'MRNA_CHIERARCHICAL', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', and 'METHYLATION_CNMF'.
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9p loss cnv correlated to 'MRNA_CNMF' and 'CN_THRESHOLDED_CNMF'.
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9q loss cnv correlated to 'MRNA_CNMF'.
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15q loss cnv correlated to 'CN_CNMF' and 'CN_THRESHOLDED_CNMF'.
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16q loss cnv correlated to 'CN_THRESHOLDED_CNMF' and 'METHYLATION_CNMF'.
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19p loss cnv correlated to 'CN_THRESHOLDED_CNMF' and 'METHYLATION_CHIERARCHICAL'.
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19q loss cnv correlated to 'CN_THRESHOLDED_CNMF' and 'METHYLATION_CHIERARCHICAL'.
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xp loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.
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xq loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 51 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 118 significant findings detected.
Clinical Features |
MRNA CNMF |
MRNA CHIERARCHICAL |
LINCRNA CNMF |
LINCRNA CHIERARCHICAL |
MIR MATURE CNMF |
MIR MATURE CHIERARCHICAL |
CN CNMF |
CN THRESHOLDED CNMF |
METHYLATION CNMF |
METHYLATION CHIERARCHICAL |
||
nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
6p gain | 40 (50%) | 40 |
0.00864 (0.0572) |
0.00015 (0.00174) |
0.0009 (0.00883) |
5e-05 (0.000671) |
1e-05 (0.000165) |
1e-05 (0.000165) |
2e-05 (0.000309) |
3e-05 (0.000437) |
0.00094 (0.00905) |
1e-05 (0.000165) |
8q gain | 54 (68%) | 26 |
0.00541 (0.0411) |
4e-05 (0.000567) |
2e-05 (0.000309) |
1e-05 (0.000165) |
8e-05 (0.000995) |
1e-05 (0.000165) |
1e-05 (0.000165) |
1e-05 (0.000165) |
3e-05 (0.000437) |
1e-05 (0.000165) |
3p loss | 42 (52%) | 38 |
1e-05 (0.000165) |
1e-05 (0.000165) |
1e-05 (0.000165) |
1e-05 (0.000165) |
1e-05 (0.000165) |
1e-05 (0.000165) |
1e-05 (0.000165) |
1e-05 (0.000165) |
1e-05 (0.000165) |
1e-05 (0.000165) |
3q loss | 44 (55%) | 36 |
1e-05 (0.000165) |
1e-05 (0.000165) |
1e-05 (0.000165) |
1e-05 (0.000165) |
1e-05 (0.000165) |
1e-05 (0.000165) |
1e-05 (0.000165) |
1e-05 (0.000165) |
1e-05 (0.000165) |
1e-05 (0.000165) |
6q gain | 20 (25%) | 60 |
0.136 (0.372) |
0.00057 (0.00593) |
0.00701 (0.049) |
7e-05 (0.000892) |
0.00022 (0.00244) |
5e-05 (0.000671) |
0.00019 (0.00215) |
0.00026 (0.00282) |
0.0032 (0.0268) |
9e-05 (0.00109) |
6q loss | 14 (18%) | 66 |
0.0659 (0.258) |
0.00043 (0.00457) |
0.0322 (0.156) |
0.00226 (0.0199) |
0.00065 (0.00663) |
0.075 (0.275) |
6e-05 (0.000785) |
1e-05 (0.000165) |
0.00013 (0.00154) |
0.0122 (0.0767) |
xq loss | 12 (15%) | 68 |
0.0212 (0.119) |
0.00259 (0.0224) |
0.00104 (0.00982) |
0.0829 (0.292) |
0.0975 (0.325) |
0.0268 (0.135) |
0.0356 (0.166) |
0.0259 (0.134) |
0.00202 (0.0184) |
0.0183 (0.11) |
8p gain | 32 (40%) | 48 |
0.0708 (0.264) |
0.0028 (0.0238) |
0.0987 (0.325) |
0.0246 (0.134) |
0.257 (0.531) |
0.0412 (0.181) |
0.00381 (0.0308) |
0.0757 (0.276) |
0.0268 (0.135) |
0.0235 (0.13) |
8p loss | 7 (9%) | 73 |
0.161 (0.413) |
0.00594 (0.0433) |
0.0583 (0.244) |
0.0287 (0.142) |
0.0173 (0.105) |
0.112 (0.348) |
0.0153 (0.0942) |
0.00223 (0.0199) |
0.0469 (0.203) |
0.172 (0.431) |
xp loss | 11 (14%) | 69 |
0.0347 (0.164) |
0.008 (0.0537) |
0.00434 (0.0335) |
0.0922 (0.316) |
0.205 (0.48) |
0.0788 (0.283) |
0.0788 (0.283) |
0.058 (0.244) |
0.00763 (0.0519) |
0.0261 (0.134) |
20q gain | 9 (11%) | 71 |
0.366 (0.617) |
0.00401 (0.0315) |
0.124 (0.366) |
0.0201 (0.115) |
0.976 (1.00) |
0.489 (0.695) |
0.0251 (0.134) |
0.354 (0.608) |
0.678 (0.822) |
0.511 (0.715) |
21q gain | 14 (18%) | 66 |
0.106 (0.337) |
0.00548 (0.0411) |
0.105 (0.337) |
0.0039 (0.0311) |
0.0986 (0.325) |
0.656 (0.815) |
0.0389 (0.176) |
0.495 (0.699) |
0.267 (0.531) |
0.427 (0.662) |
1p loss | 18 (22%) | 62 |
0.109 (0.343) |
0.101 (0.329) |
0.417 (0.652) |
0.321 (0.583) |
0.962 (1.00) |
0.0143 (0.0892) |
0.00074 (0.0074) |
1e-05 (0.000165) |
0.068 (0.262) |
0.351 (0.608) |
20p gain | 8 (10%) | 72 |
0.703 (0.839) |
0.00579 (0.0428) |
0.0874 (0.303) |
0.041 (0.181) |
1 (1.00) |
0.351 (0.608) |
0.0615 (0.252) |
0.402 (0.632) |
0.338 (0.595) |
0.38 (0.63) |
xp gain | 10 (12%) | 70 |
0.896 (0.95) |
0.321 (0.583) |
0.652 (0.815) |
0.402 (0.632) |
0.00923 (0.0603) |
0.453 (0.677) |
0.687 (0.828) |
0.877 (0.95) |
0.00611 (0.0439) |
0.601 (0.786) |
xq gain | 9 (11%) | 71 |
0.959 (1.00) |
0.4 (0.632) |
0.397 (0.632) |
0.115 (0.352) |
0.0019 (0.0176) |
0.132 (0.368) |
0.714 (0.848) |
0.794 (0.9) |
0.0251 (0.134) |
0.458 (0.679) |
9p loss | 8 (10%) | 72 |
0.026 (0.134) |
0.34 (0.595) |
0.212 (0.481) |
0.0829 (0.292) |
0.194 (0.461) |
0.337 (0.595) |
0.0709 (0.264) |
0.0406 (0.181) |
0.149 (0.392) |
0.1 (0.328) |
15q loss | 5 (6%) | 75 |
0.457 (0.679) |
0.481 (0.687) |
0.2 (0.472) |
0.667 (0.815) |
0.215 (0.482) |
1 (1.00) |
0.0322 (0.156) |
0.00762 (0.0519) |
0.656 (0.815) |
0.482 (0.687) |
16q loss | 16 (20%) | 64 |
0.128 (0.366) |
0.0902 (0.311) |
0.563 (0.757) |
0.353 (0.608) |
0.238 (0.513) |
0.387 (0.632) |
0.212 (0.481) |
1e-05 (0.000165) |
0.0383 (0.176) |
0.3 (0.56) |
19p loss | 3 (4%) | 77 |
0.897 (0.95) |
0.13 (0.366) |
0.818 (0.913) |
0.784 (0.893) |
0.81 (0.91) |
0.129 (0.366) |
0.327 (0.584) |
0.0104 (0.0664) |
0.0652 (0.258) |
0.0335 (0.161) |
19q loss | 3 (4%) | 77 |
0.897 (0.95) |
0.128 (0.366) |
0.819 (0.913) |
0.784 (0.893) |
0.809 (0.91) |
0.127 (0.366) |
0.324 (0.584) |
0.0101 (0.0651) |
0.0668 (0.26) |
0.0342 (0.163) |
4p gain | 8 (10%) | 72 |
0.113 (0.35) |
0.125 (0.366) |
0.421 (0.656) |
0.375 (0.623) |
0.19 (0.46) |
0.308 (0.568) |
0.0386 (0.176) |
0.0866 (0.302) |
0.129 (0.366) |
0.428 (0.662) |
4q gain | 5 (6%) | 75 |
0.0683 (0.262) |
0.482 (0.687) |
0.606 (0.786) |
0.666 (0.815) |
0.469 (0.683) |
0.644 (0.814) |
0.11 (0.343) |
0.00667 (0.0472) |
0.175 (0.437) |
0.262 (0.531) |
11q gain | 9 (11%) | 71 |
0.822 (0.913) |
0.448 (0.672) |
0.32 (0.583) |
0.121 (0.365) |
0.248 (0.523) |
0.0419 (0.183) |
0.564 (0.757) |
0.691 (0.829) |
0.678 (0.822) |
0.457 (0.679) |
12p gain | 3 (4%) | 77 |
0.271 (0.531) |
0.0713 (0.264) |
0.903 (0.95) |
0.0194 (0.113) |
0.398 (0.632) |
0.54 (0.741) |
0.21 (0.481) |
0.439 (0.664) |
0.267 (0.531) |
0.292 (0.553) |
12q gain | 3 (4%) | 77 |
0.271 (0.531) |
0.0714 (0.264) |
0.902 (0.95) |
0.0204 (0.116) |
0.399 (0.632) |
0.538 (0.741) |
0.209 (0.481) |
0.435 (0.664) |
0.267 (0.531) |
0.293 (0.553) |
13q gain | 6 (8%) | 74 |
0.736 (0.863) |
0.0251 (0.134) |
0.212 (0.481) |
0.353 (0.608) |
0.383 (0.63) |
0.383 (0.63) |
0.567 (0.757) |
0.154 (0.406) |
0.645 (0.814) |
0.648 (0.814) |
14q gain | 3 (4%) | 77 |
0.272 (0.531) |
0.0698 (0.264) |
0.902 (0.95) |
0.0189 (0.112) |
0.67 (0.817) |
0.844 (0.928) |
0.0515 (0.219) |
0.0651 (0.258) |
1 (1.00) |
1 (1.00) |
17p gain | 9 (11%) | 71 |
0.147 (0.39) |
0.187 (0.458) |
0.307 (0.567) |
0.0195 (0.113) |
0.805 (0.91) |
0.446 (0.671) |
0.208 (0.481) |
0.237 (0.512) |
0.291 (0.553) |
0.716 (0.848) |
22q gain | 6 (8%) | 74 |
0.227 (0.496) |
0.365 (0.616) |
0.0366 (0.17) |
0.136 (0.372) |
0.883 (0.95) |
0.283 (0.547) |
0.564 (0.757) |
0.0617 (0.252) |
0.245 (0.518) |
0.469 (0.683) |
1q loss | 4 (5%) | 76 |
0.0958 (0.325) |
0.131 (0.366) |
0.195 (0.461) |
0.217 (0.482) |
0.263 (0.531) |
0.0282 (0.141) |
0.26 (0.531) |
0.159 (0.413) |
0.384 (0.63) |
0.181 (0.446) |
9q loss | 7 (9%) | 73 |
0.00365 (0.03) |
0.161 (0.413) |
0.481 (0.687) |
0.232 (0.505) |
0.354 (0.608) |
0.512 (0.716) |
0.243 (0.518) |
0.0633 (0.256) |
0.0657 (0.258) |
0.118 (0.357) |
1q gain | 10 (12%) | 70 |
0.895 (0.95) |
0.825 (0.914) |
0.688 (0.828) |
0.555 (0.753) |
0.294 (0.553) |
0.117 (0.357) |
0.18 (0.446) |
0.37 (0.62) |
0.322 (0.583) |
0.437 (0.664) |
2p gain | 10 (12%) | 70 |
0.747 (0.866) |
0.554 (0.753) |
0.281 (0.546) |
0.541 (0.741) |
0.932 (0.976) |
0.178 (0.442) |
0.289 (0.553) |
0.827 (0.915) |
0.168 (0.427) |
0.191 (0.461) |
2q gain | 8 (10%) | 72 |
0.595 (0.785) |
0.251 (0.527) |
0.129 (0.366) |
0.279 (0.544) |
0.609 (0.786) |
0.0804 (0.287) |
0.503 (0.707) |
0.648 (0.814) |
0.11 (0.343) |
0.134 (0.37) |
5p gain | 4 (5%) | 76 |
0.604 (0.786) |
0.757 (0.873) |
0.533 (0.74) |
0.468 (0.683) |
0.217 (0.482) |
0.812 (0.91) |
0.473 (0.686) |
0.721 (0.851) |
0.26 (0.531) |
0.396 (0.632) |
5q gain | 4 (5%) | 76 |
0.605 (0.786) |
0.759 (0.873) |
0.534 (0.74) |
0.468 (0.683) |
0.219 (0.483) |
0.811 (0.91) |
0.473 (0.686) |
0.724 (0.851) |
0.26 (0.531) |
0.399 (0.632) |
7p gain | 8 (10%) | 72 |
0.215 (0.482) |
0.193 (0.461) |
0.16 (0.413) |
0.445 (0.671) |
0.743 (0.866) |
0.912 (0.957) |
0.869 (0.95) |
0.357 (0.609) |
0.561 (0.757) |
0.543 (0.743) |
7q gain | 7 (9%) | 73 |
0.428 (0.662) |
0.0972 (0.325) |
0.295 (0.553) |
0.315 (0.578) |
0.717 (0.848) |
0.634 (0.804) |
0.665 (0.815) |
0.207 (0.481) |
0.159 (0.413) |
0.139 (0.379) |
9p gain | 4 (5%) | 76 |
0.883 (0.95) |
0.63 (0.801) |
0.476 (0.687) |
0.362 (0.613) |
0.233 (0.505) |
1 (1.00) |
0.397 (0.632) |
0.962 (1.00) |
0.205 (0.48) |
0.656 (0.815) |
9q gain | 3 (4%) | 77 |
0.6 (0.786) |
0.774 (0.887) |
0.104 (0.335) |
0.621 (0.797) |
0.188 (0.46) |
0.842 (0.928) |
0.659 (0.815) |
0.888 (0.95) |
0.375 (0.623) |
0.579 (0.768) |
11p gain | 9 (11%) | 71 |
0.745 (0.866) |
0.704 (0.839) |
0.36 (0.612) |
0.194 (0.461) |
0.141 (0.383) |
0.406 (0.637) |
0.588 (0.777) |
0.687 (0.828) |
0.492 (0.698) |
0.902 (0.95) |
16p gain | 3 (4%) | 77 |
0.215 (0.482) |
1 (1.00) |
0.615 (0.793) |
1 (1.00) |
1 (1.00) |
0.464 (0.683) |
1 (1.00) |
0.126 (0.366) |
0.271 (0.531) |
0.435 (0.664) |
17q gain | 10 (12%) | 70 |
0.327 (0.584) |
0.142 (0.383) |
0.371 (0.621) |
0.0609 (0.252) |
0.624 (0.797) |
0.244 (0.518) |
0.259 (0.531) |
0.223 (0.491) |
0.169 (0.427) |
0.439 (0.664) |
4q loss | 3 (4%) | 77 |
0.897 (0.95) |
0.388 (0.632) |
1 (1.00) |
0.702 (0.839) |
0.671 (0.817) |
0.498 (0.701) |
1 (1.00) |
0.125 (0.366) |
0.877 (0.95) |
1 (1.00) |
5q loss | 3 (4%) | 77 |
0.894 (0.95) |
1 (1.00) |
0.567 (0.757) |
0.785 (0.893) |
0.609 (0.786) |
0.467 (0.683) |
0.325 (0.584) |
0.889 (0.95) |
0.147 (0.39) |
0.762 (0.875) |
11p loss | 3 (4%) | 77 |
0.302 (0.56) |
0.33 (0.585) |
0.744 (0.866) |
0.265 (0.531) |
0.164 (0.419) |
0.724 (0.851) |
0.0507 (0.217) |
0.54 (0.741) |
0.579 (0.768) |
0.293 (0.553) |
12p loss | 3 (4%) | 77 |
1 (1.00) |
1 (1.00) |
0.82 (0.913) |
0.787 (0.894) |
0.257 (0.531) |
0.292 (0.553) |
0.663 (0.815) |
0.89 (0.95) |
0.667 (0.815) |
0.577 (0.768) |
13q loss | 3 (4%) | 77 |
0.0971 (0.325) |
1 (1.00) |
0.743 (0.866) |
0.482 (0.687) |
0.355 (0.608) |
0.623 (0.797) |
1 (1.00) |
0.126 (0.366) |
0.269 (0.531) |
0.435 (0.664) |
16p loss | 7 (9%) | 73 |
0.391 (0.632) |
0.24 (0.514) |
0.625 (0.797) |
0.33 (0.585) |
0.752 (0.87) |
0.857 (0.94) |
0.843 (0.928) |
0.26 (0.531) |
0.608 (0.786) |
0.87 (0.95) |
17p loss | 3 (4%) | 77 |
0.302 (0.56) |
0.389 (0.632) |
0.515 (0.718) |
1 (1.00) |
0.55 (0.749) |
0.146 (0.39) |
1 (1.00) |
0.661 (0.815) |
0.874 (0.95) |
0.435 (0.664) |
P value = 0.0386 (Fisher's exact test), Q value = 0.18
Table S1. Gene #4: '4p gain' versus Molecular Subtype #7: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 21 | 37 | 2 | 2 |
4P GAIN MUTATED | 0 | 6 | 2 | 0 | 0 |
4P GAIN WILD-TYPE | 18 | 15 | 35 | 2 | 2 |
Figure S1. Get High-res Image Gene #4: '4p gain' versus Molecular Subtype #7: 'CN_CNMF'

P value = 0.00667 (Fisher's exact test), Q value = 0.047
Table S2. Gene #5: '4q gain' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2 |
4Q GAIN MUTATED | 0 | 3 | 0 | 1 | 0 | 0 | 1 | 0 |
4Q GAIN WILD-TYPE | 16 | 4 | 22 | 11 | 2 | 14 | 4 | 2 |
Figure S2. Get High-res Image Gene #5: '4q gain' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

P value = 0.00864 (Fisher's exact test), Q value = 0.057
Table S3. Gene #8: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 11 | 29 | 21 | 8 |
6P GAIN MUTATED | 4 | 3 | 22 | 9 | 2 |
6P GAIN WILD-TYPE | 7 | 8 | 7 | 12 | 6 |
Figure S3. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0017
Table S4. Gene #8: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 15 | 27 | 23 |
6P GAIN MUTATED | 5 | 8 | 22 | 5 |
6P GAIN WILD-TYPE | 10 | 7 | 5 | 18 |
Figure S4. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 9e-04 (Fisher's exact test), Q value = 0.0088
Table S5. Gene #8: '6p gain' versus Molecular Subtype #3: 'LINCRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 7 | 28 | 11 | 16 |
6P GAIN MUTATED | 5 | 3 | 13 | 4 | 15 |
6P GAIN WILD-TYPE | 13 | 4 | 15 | 7 | 1 |
Figure S5. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #3: 'LINCRNA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00067
Table S6. Gene #8: '6p gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 21 | 24 | 20 | 15 |
6P GAIN MUTATED | 4 | 17 | 6 | 13 |
6P GAIN WILD-TYPE | 17 | 7 | 14 | 2 |
Figure S6. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S7. Gene #8: '6p gain' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 13 | 21 | 18 | 24 | 4 |
6P GAIN MUTATED | 1 | 8 | 7 | 22 | 2 |
6P GAIN WILD-TYPE | 12 | 13 | 11 | 2 | 2 |
Figure S7. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S8. Gene #8: '6p gain' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 21 | 20 | 8 | 17 | 14 |
6P GAIN MUTATED | 2 | 7 | 4 | 16 | 11 |
6P GAIN WILD-TYPE | 19 | 13 | 4 | 1 | 3 |
Figure S8. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031
Table S9. Gene #8: '6p gain' versus Molecular Subtype #7: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 21 | 37 | 2 | 2 |
6P GAIN MUTATED | 4 | 7 | 29 | 0 | 0 |
6P GAIN WILD-TYPE | 14 | 14 | 8 | 2 | 2 |
Figure S9. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #7: 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00044
Table S10. Gene #8: '6p gain' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2 |
6P GAIN MUTATED | 3 | 2 | 16 | 10 | 2 | 2 | 3 | 2 |
6P GAIN WILD-TYPE | 13 | 5 | 6 | 2 | 0 | 12 | 2 | 0 |
Figure S10. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

P value = 0.00094 (Fisher's exact test), Q value = 0.009
Table S11. Gene #8: '6p gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 28 | 13 | 16 | 23 |
6P GAIN MUTATED | 8 | 7 | 6 | 19 |
6P GAIN WILD-TYPE | 20 | 6 | 10 | 4 |
Figure S11. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S12. Gene #8: '6p gain' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 40 | 15 | 25 |
6P GAIN MUTATED | 9 | 10 | 21 |
6P GAIN WILD-TYPE | 31 | 5 | 4 |
Figure S12. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

P value = 0.00057 (Fisher's exact test), Q value = 0.0059
Table S13. Gene #9: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 15 | 27 | 23 |
6Q GAIN MUTATED | 1 | 5 | 13 | 1 |
6Q GAIN WILD-TYPE | 14 | 10 | 14 | 22 |
Figure S13. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 0.00701 (Fisher's exact test), Q value = 0.049
Table S14. Gene #9: '6q gain' versus Molecular Subtype #3: 'LINCRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 7 | 28 | 11 | 16 |
6Q GAIN MUTATED | 2 | 2 | 7 | 0 | 9 |
6Q GAIN WILD-TYPE | 16 | 5 | 21 | 11 | 7 |
Figure S14. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #3: 'LINCRNA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00089
Table S15. Gene #9: '6q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 21 | 24 | 20 | 15 |
6Q GAIN MUTATED | 0 | 13 | 2 | 5 |
6Q GAIN WILD-TYPE | 21 | 11 | 18 | 10 |
Figure S15. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.0024
Table S16. Gene #9: '6q gain' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 13 | 21 | 18 | 24 | 4 |
6Q GAIN MUTATED | 0 | 1 | 5 | 13 | 1 |
6Q GAIN WILD-TYPE | 13 | 20 | 13 | 11 | 3 |
Figure S16. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00067
Table S17. Gene #9: '6q gain' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 21 | 20 | 8 | 17 | 14 |
6Q GAIN MUTATED | 0 | 2 | 2 | 8 | 8 |
6Q GAIN WILD-TYPE | 21 | 18 | 6 | 9 | 6 |
Figure S17. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.0022
Table S18. Gene #9: '6q gain' versus Molecular Subtype #7: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 21 | 37 | 2 | 2 |
6Q GAIN MUTATED | 1 | 1 | 18 | 0 | 0 |
6Q GAIN WILD-TYPE | 17 | 20 | 19 | 2 | 2 |
Figure S18. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #7: 'CN_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0028
Table S19. Gene #9: '6q gain' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2 |
6Q GAIN MUTATED | 1 | 0 | 8 | 7 | 1 | 0 | 1 | 2 |
6Q GAIN WILD-TYPE | 15 | 7 | 14 | 5 | 1 | 14 | 4 | 0 |
Figure S19. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

P value = 0.0032 (Fisher's exact test), Q value = 0.027
Table S20. Gene #9: '6q gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 28 | 13 | 16 | 23 |
6Q GAIN MUTATED | 1 | 4 | 5 | 10 |
6Q GAIN WILD-TYPE | 27 | 9 | 11 | 13 |
Figure S20. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.0011
Table S21. Gene #9: '6q gain' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 40 | 15 | 25 |
6Q GAIN MUTATED | 2 | 6 | 12 |
6Q GAIN WILD-TYPE | 38 | 9 | 13 |
Figure S21. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

P value = 0.0028 (Fisher's exact test), Q value = 0.024
Table S22. Gene #12: '8p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 15 | 27 | 23 |
8P GAIN MUTATED | 6 | 7 | 4 | 15 |
8P GAIN WILD-TYPE | 9 | 8 | 23 | 8 |
Figure S22. Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 0.0246 (Fisher's exact test), Q value = 0.13
Table S23. Gene #12: '8p gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 21 | 24 | 20 | 15 |
8P GAIN MUTATED | 11 | 5 | 12 | 4 |
8P GAIN WILD-TYPE | 10 | 19 | 8 | 11 |
Figure S23. Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

P value = 0.0412 (Fisher's exact test), Q value = 0.18
Table S24. Gene #12: '8p gain' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 21 | 20 | 8 | 17 | 14 |
8P GAIN MUTATED | 13 | 10 | 1 | 4 | 4 |
8P GAIN WILD-TYPE | 8 | 10 | 7 | 13 | 10 |
Figure S24. Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

P value = 0.00381 (Fisher's exact test), Q value = 0.031
Table S25. Gene #12: '8p gain' versus Molecular Subtype #7: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 21 | 37 | 2 | 2 |
8P GAIN MUTATED | 12 | 11 | 8 | 0 | 1 |
8P GAIN WILD-TYPE | 6 | 10 | 29 | 2 | 1 |
Figure S25. Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #7: 'CN_CNMF'

P value = 0.0268 (Fisher's exact test), Q value = 0.14
Table S26. Gene #12: '8p gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 28 | 13 | 16 | 23 |
8P GAIN MUTATED | 16 | 2 | 8 | 6 |
8P GAIN WILD-TYPE | 12 | 11 | 8 | 17 |
Figure S26. Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 0.13
Table S27. Gene #12: '8p gain' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 40 | 15 | 25 |
8P GAIN MUTATED | 22 | 4 | 6 |
8P GAIN WILD-TYPE | 18 | 11 | 19 |
Figure S27. Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

P value = 0.00541 (Fisher's exact test), Q value = 0.041
Table S28. Gene #13: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 11 | 29 | 21 | 8 |
8Q GAIN MUTATED | 10 | 9 | 13 | 14 | 8 |
8Q GAIN WILD-TYPE | 1 | 2 | 16 | 7 | 0 |
Figure S28. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00057
Table S29. Gene #13: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 15 | 27 | 23 |
8Q GAIN MUTATED | 15 | 9 | 10 | 20 |
8Q GAIN WILD-TYPE | 0 | 6 | 17 | 3 |
Figure S29. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031
Table S30. Gene #13: '8q gain' versus Molecular Subtype #3: 'LINCRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 7 | 28 | 11 | 16 |
8Q GAIN MUTATED | 18 | 0 | 20 | 6 | 10 |
8Q GAIN WILD-TYPE | 0 | 7 | 8 | 5 | 6 |
Figure S30. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #3: 'LINCRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S31. Gene #13: '8q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 21 | 24 | 20 | 15 |
8Q GAIN MUTATED | 20 | 9 | 18 | 7 |
8Q GAIN WILD-TYPE | 1 | 15 | 2 | 8 |
Figure S31. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.001
Table S32. Gene #13: '8q gain' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 13 | 21 | 18 | 24 | 4 |
8Q GAIN MUTATED | 11 | 20 | 5 | 16 | 2 |
8Q GAIN WILD-TYPE | 2 | 1 | 13 | 8 | 2 |
Figure S32. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S33. Gene #13: '8q gain' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 21 | 20 | 8 | 17 | 14 |
8Q GAIN MUTATED | 20 | 18 | 1 | 8 | 7 |
8Q GAIN WILD-TYPE | 1 | 2 | 7 | 9 | 7 |
Figure S33. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S34. Gene #13: '8q gain' versus Molecular Subtype #7: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 21 | 37 | 2 | 2 |
8Q GAIN MUTATED | 16 | 20 | 14 | 2 | 2 |
8Q GAIN WILD-TYPE | 2 | 1 | 23 | 0 | 0 |
Figure S34. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #7: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S35. Gene #13: '8q gain' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2 |
8Q GAIN MUTATED | 15 | 7 | 4 | 8 | 2 | 12 | 5 | 1 |
8Q GAIN WILD-TYPE | 1 | 0 | 18 | 4 | 0 | 2 | 0 | 1 |
Figure S35. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00044
Table S36. Gene #13: '8q gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 28 | 13 | 16 | 23 |
8Q GAIN MUTATED | 27 | 3 | 12 | 12 |
8Q GAIN WILD-TYPE | 1 | 10 | 4 | 11 |
Figure S36. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S37. Gene #13: '8q gain' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 40 | 15 | 25 |
8Q GAIN MUTATED | 37 | 5 | 12 |
8Q GAIN WILD-TYPE | 3 | 10 | 13 |
Figure S37. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

P value = 0.0419 (Fisher's exact test), Q value = 0.18
Table S38. Gene #17: '11q gain' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 21 | 20 | 8 | 17 | 14 |
11Q GAIN MUTATED | 0 | 2 | 0 | 5 | 2 |
11Q GAIN WILD-TYPE | 21 | 18 | 8 | 12 | 12 |
Figure S38. Get High-res Image Gene #17: '11q gain' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

P value = 0.0194 (Fisher's exact test), Q value = 0.11
Table S39. Gene #18: '12p gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 21 | 24 | 20 | 15 |
12P GAIN MUTATED | 0 | 0 | 3 | 0 |
12P GAIN WILD-TYPE | 21 | 24 | 17 | 15 |
Figure S39. Get High-res Image Gene #18: '12p gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

P value = 0.0204 (Fisher's exact test), Q value = 0.12
Table S40. Gene #19: '12q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 21 | 24 | 20 | 15 |
12Q GAIN MUTATED | 0 | 0 | 3 | 0 |
12Q GAIN WILD-TYPE | 21 | 24 | 17 | 15 |
Figure S40. Get High-res Image Gene #19: '12q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

P value = 0.0251 (Fisher's exact test), Q value = 0.13
Table S41. Gene #20: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 15 | 27 | 23 |
13Q GAIN MUTATED | 0 | 3 | 0 | 3 |
13Q GAIN WILD-TYPE | 15 | 12 | 27 | 20 |
Figure S41. Get High-res Image Gene #20: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.11
Table S42. Gene #21: '14q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 21 | 24 | 20 | 15 |
14Q GAIN MUTATED | 0 | 0 | 3 | 0 |
14Q GAIN WILD-TYPE | 21 | 24 | 17 | 15 |
Figure S42. Get High-res Image Gene #21: '14q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

P value = 0.0195 (Fisher's exact test), Q value = 0.11
Table S43. Gene #23: '17p gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 21 | 24 | 20 | 15 |
17P GAIN MUTATED | 0 | 4 | 5 | 0 |
17P GAIN WILD-TYPE | 21 | 20 | 15 | 15 |
Figure S43. Get High-res Image Gene #23: '17p gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

P value = 0.00579 (Fisher's exact test), Q value = 0.043
Table S44. Gene #25: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 15 | 27 | 23 |
20P GAIN MUTATED | 0 | 4 | 0 | 4 |
20P GAIN WILD-TYPE | 15 | 11 | 27 | 19 |
Figure S44. Get High-res Image Gene #25: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 0.041 (Fisher's exact test), Q value = 0.18
Table S45. Gene #25: '20p gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 21 | 24 | 20 | 15 |
20P GAIN MUTATED | 0 | 4 | 4 | 0 |
20P GAIN WILD-TYPE | 21 | 20 | 16 | 15 |
Figure S45. Get High-res Image Gene #25: '20p gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

P value = 0.00401 (Fisher's exact test), Q value = 0.031
Table S46. Gene #26: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 15 | 27 | 23 |
20Q GAIN MUTATED | 0 | 4 | 0 | 5 |
20Q GAIN WILD-TYPE | 15 | 11 | 27 | 18 |
Figure S46. Get High-res Image Gene #26: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 0.0201 (Fisher's exact test), Q value = 0.12
Table S47. Gene #26: '20q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 21 | 24 | 20 | 15 |
20Q GAIN MUTATED | 0 | 4 | 5 | 0 |
20Q GAIN WILD-TYPE | 21 | 20 | 15 | 15 |
Figure S47. Get High-res Image Gene #26: '20q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

P value = 0.0251 (Fisher's exact test), Q value = 0.13
Table S48. Gene #26: '20q gain' versus Molecular Subtype #7: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 21 | 37 | 2 | 2 |
20Q GAIN MUTATED | 6 | 0 | 3 | 0 | 0 |
20Q GAIN WILD-TYPE | 12 | 21 | 34 | 2 | 2 |
Figure S48. Get High-res Image Gene #26: '20q gain' versus Molecular Subtype #7: 'CN_CNMF'

P value = 0.00548 (Fisher's exact test), Q value = 0.041
Table S49. Gene #27: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 15 | 27 | 23 |
21Q GAIN MUTATED | 1 | 3 | 1 | 9 |
21Q GAIN WILD-TYPE | 14 | 12 | 26 | 14 |
Figure S49. Get High-res Image Gene #27: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 0.0039 (Fisher's exact test), Q value = 0.031
Table S50. Gene #27: '21q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 21 | 24 | 20 | 15 |
21Q GAIN MUTATED | 1 | 3 | 9 | 1 |
21Q GAIN WILD-TYPE | 20 | 21 | 11 | 14 |
Figure S50. Get High-res Image Gene #27: '21q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

P value = 0.0389 (Fisher's exact test), Q value = 0.18
Table S51. Gene #27: '21q gain' versus Molecular Subtype #7: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 21 | 37 | 2 | 2 |
21Q GAIN MUTATED | 7 | 3 | 3 | 1 | 0 |
21Q GAIN WILD-TYPE | 11 | 18 | 34 | 1 | 2 |
Figure S51. Get High-res Image Gene #27: '21q gain' versus Molecular Subtype #7: 'CN_CNMF'

P value = 0.0366 (Fisher's exact test), Q value = 0.17
Table S52. Gene #28: '22q gain' versus Molecular Subtype #3: 'LINCRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 7 | 28 | 11 | 16 |
22Q GAIN MUTATED | 0 | 0 | 6 | 0 | 0 |
22Q GAIN WILD-TYPE | 18 | 7 | 22 | 11 | 16 |
Figure S52. Get High-res Image Gene #28: '22q gain' versus Molecular Subtype #3: 'LINCRNA_CNMF'

P value = 0.00923 (Fisher's exact test), Q value = 0.06
Table S53. Gene #29: 'xp gain' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 13 | 21 | 18 | 24 | 4 |
XP GAIN MUTATED | 1 | 0 | 1 | 8 | 0 |
XP GAIN WILD-TYPE | 12 | 21 | 17 | 16 | 4 |
Figure S53. Get High-res Image Gene #29: 'xp gain' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

P value = 0.00611 (Fisher's exact test), Q value = 0.044
Table S54. Gene #29: 'xp gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 28 | 13 | 16 | 23 |
XP GAIN MUTATED | 1 | 0 | 6 | 3 |
XP GAIN WILD-TYPE | 27 | 13 | 10 | 20 |
Figure S54. Get High-res Image Gene #29: 'xp gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'

P value = 0.0019 (Fisher's exact test), Q value = 0.018
Table S55. Gene #30: 'xq gain' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 13 | 21 | 18 | 24 | 4 |
XQ GAIN MUTATED | 1 | 0 | 0 | 8 | 0 |
XQ GAIN WILD-TYPE | 12 | 21 | 18 | 16 | 4 |
Figure S55. Get High-res Image Gene #30: 'xq gain' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

P value = 0.0251 (Fisher's exact test), Q value = 0.13
Table S56. Gene #30: 'xq gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 28 | 13 | 16 | 23 |
XQ GAIN MUTATED | 1 | 0 | 5 | 3 |
XQ GAIN WILD-TYPE | 27 | 13 | 11 | 20 |
Figure S56. Get High-res Image Gene #30: 'xq gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'

P value = 0.0143 (Fisher's exact test), Q value = 0.089
Table S57. Gene #31: '1p loss' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 21 | 20 | 8 | 17 | 14 |
1P LOSS MUTATED | 9 | 2 | 0 | 6 | 1 |
1P LOSS WILD-TYPE | 12 | 18 | 8 | 11 | 13 |
Figure S57. Get High-res Image Gene #31: '1p loss' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

P value = 0.00074 (Fisher's exact test), Q value = 0.0074
Table S58. Gene #31: '1p loss' versus Molecular Subtype #7: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 21 | 37 | 2 | 2 |
1P LOSS MUTATED | 11 | 2 | 5 | 0 | 0 |
1P LOSS WILD-TYPE | 7 | 19 | 32 | 2 | 2 |
Figure S58. Get High-res Image Gene #31: '1p loss' versus Molecular Subtype #7: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S59. Gene #31: '1p loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2 |
1P LOSS MUTATED | 11 | 1 | 2 | 1 | 0 | 0 | 1 | 2 |
1P LOSS WILD-TYPE | 5 | 6 | 20 | 11 | 2 | 14 | 4 | 0 |
Figure S59. Get High-res Image Gene #31: '1p loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

P value = 0.0282 (Fisher's exact test), Q value = 0.14
Table S60. Gene #32: '1q loss' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 21 | 20 | 8 | 17 | 14 |
1Q LOSS MUTATED | 4 | 0 | 0 | 0 | 0 |
1Q LOSS WILD-TYPE | 17 | 20 | 8 | 17 | 14 |
Figure S60. Get High-res Image Gene #32: '1q loss' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S61. Gene #33: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 11 | 29 | 21 | 8 |
3P LOSS MUTATED | 11 | 7 | 1 | 15 | 8 |
3P LOSS WILD-TYPE | 0 | 4 | 28 | 6 | 0 |
Figure S61. Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S62. Gene #33: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 15 | 27 | 23 |
3P LOSS MUTATED | 15 | 3 | 1 | 23 |
3P LOSS WILD-TYPE | 0 | 12 | 26 | 0 |
Figure S62. Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S63. Gene #33: '3p loss' versus Molecular Subtype #3: 'LINCRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 7 | 28 | 11 | 16 |
3P LOSS MUTATED | 18 | 0 | 17 | 6 | 1 |
3P LOSS WILD-TYPE | 0 | 7 | 11 | 5 | 15 |
Figure S63. Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #3: 'LINCRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S64. Gene #33: '3p loss' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 21 | 24 | 20 | 15 |
3P LOSS MUTATED | 20 | 1 | 20 | 1 |
3P LOSS WILD-TYPE | 1 | 23 | 0 | 14 |
Figure S64. Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S65. Gene #33: '3p loss' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 13 | 21 | 18 | 24 | 4 |
3P LOSS MUTATED | 11 | 20 | 6 | 3 | 2 |
3P LOSS WILD-TYPE | 2 | 1 | 12 | 21 | 2 |
Figure S65. Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S66. Gene #33: '3p loss' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 21 | 20 | 8 | 17 | 14 |
3P LOSS MUTATED | 21 | 17 | 0 | 2 | 2 |
3P LOSS WILD-TYPE | 0 | 3 | 8 | 15 | 12 |
Figure S66. Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S67. Gene #33: '3p loss' versus Molecular Subtype #7: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 21 | 37 | 2 | 2 |
3P LOSS MUTATED | 17 | 21 | 1 | 2 | 1 |
3P LOSS WILD-TYPE | 1 | 0 | 36 | 0 | 1 |
Figure S67. Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #7: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S68. Gene #33: '3p loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2 |
3P LOSS MUTATED | 15 | 7 | 0 | 0 | 1 | 14 | 5 | 0 |
3P LOSS WILD-TYPE | 1 | 0 | 22 | 12 | 1 | 0 | 0 | 2 |
Figure S68. Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S69. Gene #33: '3p loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 28 | 13 | 16 | 23 |
3P LOSS MUTATED | 28 | 1 | 11 | 2 |
3P LOSS WILD-TYPE | 0 | 12 | 5 | 21 |
Figure S69. Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S70. Gene #33: '3p loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 40 | 15 | 25 |
3P LOSS MUTATED | 40 | 0 | 2 |
3P LOSS WILD-TYPE | 0 | 15 | 23 |
Figure S70. Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S71. Gene #34: '3q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 11 | 29 | 21 | 8 |
3Q LOSS MUTATED | 11 | 7 | 3 | 15 | 8 |
3Q LOSS WILD-TYPE | 0 | 4 | 26 | 6 | 0 |
Figure S71. Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S72. Gene #34: '3q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 15 | 27 | 23 |
3Q LOSS MUTATED | 15 | 4 | 2 | 23 |
3Q LOSS WILD-TYPE | 0 | 11 | 25 | 0 |
Figure S72. Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S73. Gene #34: '3q loss' versus Molecular Subtype #3: 'LINCRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 7 | 28 | 11 | 16 |
3Q LOSS MUTATED | 18 | 0 | 17 | 7 | 2 |
3Q LOSS WILD-TYPE | 0 | 7 | 11 | 4 | 14 |
Figure S73. Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #3: 'LINCRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S74. Gene #34: '3q loss' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 21 | 24 | 20 | 15 |
3Q LOSS MUTATED | 21 | 1 | 20 | 2 |
3Q LOSS WILD-TYPE | 0 | 23 | 0 | 13 |
Figure S74. Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S75. Gene #34: '3q loss' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 13 | 21 | 18 | 24 | 4 |
3Q LOSS MUTATED | 11 | 21 | 7 | 3 | 2 |
3Q LOSS WILD-TYPE | 2 | 0 | 11 | 21 | 2 |
Figure S75. Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S76. Gene #34: '3q loss' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 21 | 20 | 8 | 17 | 14 |
3Q LOSS MUTATED | 21 | 18 | 1 | 2 | 2 |
3Q LOSS WILD-TYPE | 0 | 2 | 7 | 15 | 12 |
Figure S76. Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S77. Gene #34: '3q loss' versus Molecular Subtype #7: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 21 | 37 | 2 | 2 |
3Q LOSS MUTATED | 17 | 21 | 2 | 2 | 2 |
3Q LOSS WILD-TYPE | 1 | 0 | 35 | 0 | 0 |
Figure S77. Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #7: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S78. Gene #34: '3q loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2 |
3Q LOSS MUTATED | 16 | 7 | 0 | 0 | 2 | 14 | 5 | 0 |
3Q LOSS WILD-TYPE | 0 | 0 | 22 | 12 | 0 | 0 | 0 | 2 |
Figure S78. Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S79. Gene #34: '3q loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 28 | 13 | 16 | 23 |
3Q LOSS MUTATED | 28 | 3 | 11 | 2 |
3Q LOSS WILD-TYPE | 0 | 10 | 5 | 21 |
Figure S79. Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S80. Gene #34: '3q loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 40 | 15 | 25 |
3Q LOSS MUTATED | 40 | 2 | 2 |
3Q LOSS WILD-TYPE | 0 | 13 | 23 |
Figure S80. Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.0046
Table S81. Gene #37: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 15 | 27 | 23 |
6Q LOSS MUTATED | 6 | 1 | 0 | 7 |
6Q LOSS WILD-TYPE | 9 | 14 | 27 | 16 |
Figure S81. Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 0.0322 (Fisher's exact test), Q value = 0.16
Table S82. Gene #37: '6q loss' versus Molecular Subtype #3: 'LINCRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 7 | 28 | 11 | 16 |
6Q LOSS MUTATED | 7 | 0 | 6 | 0 | 1 |
6Q LOSS WILD-TYPE | 11 | 7 | 22 | 11 | 15 |
Figure S82. Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #3: 'LINCRNA_CNMF'

P value = 0.00226 (Fisher's exact test), Q value = 0.02
Table S83. Gene #37: '6q loss' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 21 | 24 | 20 | 15 |
6Q LOSS MUTATED | 6 | 0 | 7 | 1 |
6Q LOSS WILD-TYPE | 15 | 24 | 13 | 14 |
Figure S83. Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

P value = 0.00065 (Fisher's exact test), Q value = 0.0066
Table S84. Gene #37: '6q loss' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 13 | 21 | 18 | 24 | 4 |
6Q LOSS MUTATED | 4 | 9 | 0 | 1 | 0 |
6Q LOSS WILD-TYPE | 9 | 12 | 18 | 23 | 4 |
Figure S84. Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00078
Table S85. Gene #37: '6q loss' versus Molecular Subtype #7: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 21 | 37 | 2 | 2 |
6Q LOSS MUTATED | 2 | 11 | 1 | 0 | 0 |
6Q LOSS WILD-TYPE | 16 | 10 | 36 | 2 | 2 |
Figure S85. Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #7: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S86. Gene #37: '6q loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2 |
6Q LOSS MUTATED | 1 | 7 | 0 | 1 | 1 | 0 | 4 | 0 |
6Q LOSS WILD-TYPE | 15 | 0 | 22 | 11 | 1 | 14 | 1 | 2 |
Figure S86. Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0015
Table S87. Gene #37: '6q loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 28 | 13 | 16 | 23 |
6Q LOSS MUTATED | 12 | 0 | 0 | 2 |
6Q LOSS WILD-TYPE | 16 | 13 | 16 | 21 |
Figure S87. Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.077
Table S88. Gene #37: '6q loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 40 | 15 | 25 |
6Q LOSS MUTATED | 12 | 0 | 2 |
6Q LOSS WILD-TYPE | 28 | 15 | 23 |
Figure S88. Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

P value = 0.00594 (Fisher's exact test), Q value = 0.043
Table S89. Gene #38: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 15 | 27 | 23 |
8P LOSS MUTATED | 5 | 0 | 1 | 1 |
8P LOSS WILD-TYPE | 10 | 15 | 26 | 22 |
Figure S89. Get High-res Image Gene #38: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 0.0287 (Fisher's exact test), Q value = 0.14
Table S90. Gene #38: '8p loss' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 21 | 24 | 20 | 15 |
8P LOSS MUTATED | 5 | 0 | 1 | 1 |
8P LOSS WILD-TYPE | 16 | 24 | 19 | 14 |
Figure S90. Get High-res Image Gene #38: '8p loss' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

P value = 0.0173 (Fisher's exact test), Q value = 0.1
Table S91. Gene #38: '8p loss' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 13 | 21 | 18 | 24 | 4 |
8P LOSS MUTATED | 2 | 5 | 0 | 0 | 0 |
8P LOSS WILD-TYPE | 11 | 16 | 18 | 24 | 4 |
Figure S91. Get High-res Image Gene #38: '8p loss' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.094
Table S92. Gene #38: '8p loss' versus Molecular Subtype #7: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 21 | 37 | 2 | 2 |
8P LOSS MUTATED | 0 | 6 | 1 | 0 | 0 |
8P LOSS WILD-TYPE | 18 | 15 | 36 | 2 | 2 |
Figure S92. Get High-res Image Gene #38: '8p loss' versus Molecular Subtype #7: 'CN_CNMF'

P value = 0.00223 (Fisher's exact test), Q value = 0.02
Table S93. Gene #38: '8p loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2 |
8P LOSS MUTATED | 0 | 4 | 0 | 1 | 0 | 1 | 1 | 0 |
8P LOSS WILD-TYPE | 16 | 3 | 22 | 11 | 2 | 13 | 4 | 2 |
Figure S93. Get High-res Image Gene #38: '8p loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

P value = 0.0469 (Fisher's exact test), Q value = 0.2
Table S94. Gene #38: '8p loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 28 | 13 | 16 | 23 |
8P LOSS MUTATED | 6 | 0 | 0 | 1 |
8P LOSS WILD-TYPE | 22 | 13 | 16 | 22 |
Figure S94. Get High-res Image Gene #38: '8p loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

P value = 0.026 (Fisher's exact test), Q value = 0.13
Table S95. Gene #39: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 11 | 29 | 21 | 8 |
9P LOSS MUTATED | 4 | 0 | 1 | 3 | 0 |
9P LOSS WILD-TYPE | 7 | 11 | 28 | 18 | 8 |
Figure S95. Get High-res Image Gene #39: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 0.0406 (Fisher's exact test), Q value = 0.18
Table S96. Gene #39: '9p loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2 |
9P LOSS MUTATED | 4 | 1 | 0 | 0 | 0 | 1 | 1 | 1 |
9P LOSS WILD-TYPE | 12 | 6 | 22 | 12 | 2 | 13 | 4 | 1 |
Figure S96. Get High-res Image Gene #39: '9p loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

P value = 0.00365 (Fisher's exact test), Q value = 0.03
Table S97. Gene #40: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 11 | 29 | 21 | 8 |
9Q LOSS MUTATED | 4 | 0 | 0 | 3 | 0 |
9Q LOSS WILD-TYPE | 7 | 11 | 29 | 18 | 8 |
Figure S97. Get High-res Image Gene #40: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 0.0322 (Fisher's exact test), Q value = 0.16
Table S98. Gene #44: '15q loss' versus Molecular Subtype #7: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 21 | 37 | 2 | 2 |
15Q LOSS MUTATED | 3 | 0 | 1 | 0 | 1 |
15Q LOSS WILD-TYPE | 15 | 21 | 36 | 2 | 1 |
Figure S98. Get High-res Image Gene #44: '15q loss' versus Molecular Subtype #7: 'CN_CNMF'

P value = 0.00762 (Fisher's exact test), Q value = 0.052
Table S99. Gene #44: '15q loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2 |
15Q LOSS MUTATED | 3 | 0 | 0 | 0 | 1 | 0 | 0 | 1 |
15Q LOSS WILD-TYPE | 13 | 7 | 22 | 12 | 1 | 14 | 5 | 1 |
Figure S99. Get High-res Image Gene #44: '15q loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016
Table S100. Gene #46: '16q loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2 |
16Q LOSS MUTATED | 3 | 7 | 1 | 2 | 0 | 1 | 0 | 2 |
16Q LOSS WILD-TYPE | 13 | 0 | 21 | 10 | 2 | 13 | 5 | 0 |
Figure S100. Get High-res Image Gene #46: '16q loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

P value = 0.0383 (Fisher's exact test), Q value = 0.18
Table S101. Gene #46: '16q loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 28 | 13 | 16 | 23 |
16Q LOSS MUTATED | 10 | 0 | 3 | 3 |
16Q LOSS WILD-TYPE | 18 | 13 | 13 | 20 |
Figure S101. Get High-res Image Gene #46: '16q loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.066
Table S102. Gene #48: '19p loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2 |
19P LOSS MUTATED | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 1 |
19P LOSS WILD-TYPE | 16 | 7 | 21 | 12 | 1 | 14 | 5 | 1 |
Figure S102. Get High-res Image Gene #48: '19p loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

P value = 0.0335 (Fisher's exact test), Q value = 0.16
Table S103. Gene #48: '19p loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 40 | 15 | 25 |
19P LOSS MUTATED | 0 | 0 | 3 |
19P LOSS WILD-TYPE | 40 | 15 | 22 |
Figure S103. Get High-res Image Gene #48: '19p loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.065
Table S104. Gene #49: '19q loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2 |
19Q LOSS MUTATED | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 1 |
19Q LOSS WILD-TYPE | 16 | 7 | 21 | 12 | 1 | 14 | 5 | 1 |
Figure S104. Get High-res Image Gene #49: '19q loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

P value = 0.0342 (Fisher's exact test), Q value = 0.16
Table S105. Gene #49: '19q loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 40 | 15 | 25 |
19Q LOSS MUTATED | 0 | 0 | 3 |
19Q LOSS WILD-TYPE | 40 | 15 | 22 |
Figure S105. Get High-res Image Gene #49: '19q loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

P value = 0.0347 (Fisher's exact test), Q value = 0.16
Table S106. Gene #50: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 11 | 29 | 21 | 8 |
XP LOSS MUTATED | 2 | 0 | 2 | 7 | 0 |
XP LOSS WILD-TYPE | 9 | 11 | 27 | 14 | 8 |
Figure S106. Get High-res Image Gene #50: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 0.008 (Fisher's exact test), Q value = 0.054
Table S107. Gene #50: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 15 | 27 | 23 |
XP LOSS MUTATED | 0 | 1 | 2 | 8 |
XP LOSS WILD-TYPE | 15 | 14 | 25 | 15 |
Figure S107. Get High-res Image Gene #50: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 0.00434 (Fisher's exact test), Q value = 0.034
Table S108. Gene #50: 'xp loss' versus Molecular Subtype #3: 'LINCRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 7 | 28 | 11 | 16 |
XP LOSS MUTATED | 0 | 0 | 7 | 4 | 0 |
XP LOSS WILD-TYPE | 18 | 7 | 21 | 7 | 16 |
Figure S108. Get High-res Image Gene #50: 'xp loss' versus Molecular Subtype #3: 'LINCRNA_CNMF'

P value = 0.00763 (Fisher's exact test), Q value = 0.052
Table S109. Gene #50: 'xp loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 28 | 13 | 16 | 23 |
XP LOSS MUTATED | 4 | 1 | 6 | 0 |
XP LOSS WILD-TYPE | 24 | 12 | 10 | 23 |
Figure S109. Get High-res Image Gene #50: 'xp loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

P value = 0.0261 (Fisher's exact test), Q value = 0.13
Table S110. Gene #50: 'xp loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 40 | 15 | 25 |
XP LOSS MUTATED | 8 | 3 | 0 |
XP LOSS WILD-TYPE | 32 | 12 | 25 |
Figure S110. Get High-res Image Gene #50: 'xp loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

P value = 0.0212 (Fisher's exact test), Q value = 0.12
Table S111. Gene #51: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 11 | 29 | 21 | 8 |
XQ LOSS MUTATED | 3 | 0 | 2 | 7 | 0 |
XQ LOSS WILD-TYPE | 8 | 11 | 27 | 14 | 8 |
Figure S111. Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 0.00259 (Fisher's exact test), Q value = 0.022
Table S112. Gene #51: 'xq loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 15 | 27 | 23 |
XQ LOSS MUTATED | 0 | 1 | 2 | 9 |
XQ LOSS WILD-TYPE | 15 | 14 | 25 | 14 |
Figure S112. Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 0.00104 (Fisher's exact test), Q value = 0.0098
Table S113. Gene #51: 'xq loss' versus Molecular Subtype #3: 'LINCRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 7 | 28 | 11 | 16 |
XQ LOSS MUTATED | 0 | 0 | 7 | 5 | 0 |
XQ LOSS WILD-TYPE | 18 | 7 | 21 | 6 | 16 |
Figure S113. Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #3: 'LINCRNA_CNMF'

P value = 0.0268 (Fisher's exact test), Q value = 0.14
Table S114. Gene #51: 'xq loss' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 21 | 20 | 8 | 17 | 14 |
XQ LOSS MUTATED | 8 | 1 | 0 | 2 | 1 |
XQ LOSS WILD-TYPE | 13 | 19 | 8 | 15 | 13 |
Figure S114. Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

P value = 0.0356 (Fisher's exact test), Q value = 0.17
Table S115. Gene #51: 'xq loss' versus Molecular Subtype #7: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 21 | 37 | 2 | 2 |
XQ LOSS MUTATED | 6 | 3 | 2 | 0 | 1 |
XQ LOSS WILD-TYPE | 12 | 18 | 35 | 2 | 1 |
Figure S115. Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #7: 'CN_CNMF'

P value = 0.0259 (Fisher's exact test), Q value = 0.13
Table S116. Gene #51: 'xq loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2 |
XQ LOSS MUTATED | 6 | 2 | 1 | 0 | 0 | 1 | 1 | 1 |
XQ LOSS WILD-TYPE | 10 | 5 | 21 | 12 | 2 | 13 | 4 | 1 |
Figure S116. Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

P value = 0.00202 (Fisher's exact test), Q value = 0.018
Table S117. Gene #51: 'xq loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 28 | 13 | 16 | 23 |
XQ LOSS MUTATED | 4 | 1 | 7 | 0 |
XQ LOSS WILD-TYPE | 24 | 12 | 9 | 23 |
Figure S117. Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

P value = 0.0183 (Fisher's exact test), Q value = 0.11
Table S118. Gene #51: 'xq loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 40 | 15 | 25 |
XQ LOSS MUTATED | 9 | 3 | 0 |
XQ LOSS WILD-TYPE | 31 | 12 | 25 |
Figure S118. Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

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Copy number data file = broad_values_by_arm.txt from GISTIC pipeline
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Processed Copy number data file = /cromwell_root/fc-f5144117-2d5a-42c2-8998-5b38e52db5d9/18c76f9c-e604-4517-bc19-4bda4cb583f6/correlate_genomic_events_all/597ba7df-da6d-44b2-a96c-e44efd0c26c0/call-preprocess_genomic_event/transformed.cor.cli.txt
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Molecular subtypes file = /cromwell_root/fc-f5144117-2d5a-42c2-8998-5b38e52db5d9/9d897bdb-7a9a-423a-ad17-06f28ae98803/aggregate_clusters_workflow/1d8bac82-5a1d-4cd2-aeb1-8ddd0e1e7a20/call-aggregate_clusters/TCGA-UVM-TP.transposedmergedcluster.txt
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Number of patients = 80
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Number of significantly arm-level cnvs = 51
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Number of molecular subtypes = 10
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Exclude genes that fewer than K tumors have mutations, K = 3
For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.