This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.
Testing the association between copy number variation 80 arm-level events and 12 molecular subtypes across 165 patients, 61 significant findings detected with P value < 0.05 and Q value < 0.25.
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2q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
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3p gain cnv correlated to 'CN_CNMF'.
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3q gain cnv correlated to 'CN_CNMF'.
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5p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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5q gain cnv correlated to 'CN_CNMF'.
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6p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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6q gain cnv correlated to 'METHLYATION_CNMF'.
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7p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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7q gain cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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8p gain cnv correlated to 'CN_CNMF'.
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8q gain cnv correlated to 'CN_CNMF'.
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9q gain cnv correlated to 'MRNA_CNMF'.
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11p gain cnv correlated to 'CN_CNMF'.
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11q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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13q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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16p gain cnv correlated to 'CN_CNMF'.
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16q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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17q gain cnv correlated to 'CN_CNMF'.
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20p gain cnv correlated to 'RPPA_CNMF'.
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20q gain cnv correlated to 'MRNA_CNMF', 'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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xp gain cnv correlated to 'MRNA_CNMF'.
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2p loss cnv correlated to 'CN_CNMF'.
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3q loss cnv correlated to 'MIRSEQ_CHIERARCHICAL'.
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4p loss cnv correlated to 'CN_CNMF'.
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4q loss cnv correlated to 'CN_CNMF'.
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5q loss cnv correlated to 'MRNA_CHIERARCHICAL'.
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6q loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.
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9q loss cnv correlated to 'MIRSEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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10q loss cnv correlated to 'RPPA_CHIERARCHICAL'.
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11p loss cnv correlated to 'CN_CNMF'.
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11q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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15q loss cnv correlated to 'CN_CNMF'.
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18p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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18q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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19q loss cnv correlated to 'MIRSEQ_CHIERARCHICAL'.
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20p loss cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.
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21q loss cnv correlated to 'MIRSEQ_CNMF'.
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22q loss cnv correlated to 'MIRSEQ_CNMF'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 61 significant findings detected.
Clinical Features |
MRNA CNMF |
MRNA CHIERARCHICAL |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
||
nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
7p gain | 102 (62%) | 63 |
0.00234 (0.0802) |
0.00274 (0.0877) |
1e-05 (0.0024) |
0.0032 (0.096) |
0.841 (1.00) |
0.0171 (0.261) |
0.00023 (0.0221) |
1e-05 (0.0024) |
0.0414 (0.401) |
0.0968 (0.539) |
0.593 (0.908) |
0.815 (1.00) |
7q gain | 85 (52%) | 80 |
0.0484 (0.419) |
0.00797 (0.17) |
2e-05 (0.0032) |
0.139 (0.603) |
0.865 (1.00) |
0.04 (0.392) |
0.00414 (0.114) |
0.00206 (0.0791) |
0.497 (0.877) |
0.831 (1.00) |
0.855 (1.00) |
0.856 (1.00) |
13q gain | 113 (68%) | 52 |
0.287 (0.732) |
0.384 (0.818) |
1e-05 (0.0024) |
0.072 (0.487) |
0.655 (0.935) |
0.0961 (0.539) |
0.00049 (0.0378) |
0.00061 (0.0378) |
0.00312 (0.096) |
0.065 (0.471) |
0.713 (0.964) |
0.473 (0.868) |
11q gain | 26 (16%) | 139 |
0.24 (0.695) |
0.428 (0.849) |
0.002 (0.0791) |
0.019 (0.266) |
0.974 (1.00) |
0.167 (0.637) |
0.00274 (0.0877) |
0.00044 (0.0378) |
0.0251 (0.304) |
0.587 (0.907) |
0.119 (0.578) |
0.156 (0.63) |
20q gain | 145 (88%) | 20 |
0.0078 (0.17) |
0.162 (0.637) |
0.00063 (0.0378) |
0.231 (0.695) |
0.0266 (0.304) |
0.144 (0.609) |
0.442 (0.854) |
0.00219 (0.0802) |
0.044 (0.405) |
0.362 (0.816) |
0.365 (0.816) |
1 (1.00) |
11q loss | 30 (18%) | 135 |
0.056 (0.448) |
0.207 (0.685) |
0.00691 (0.161) |
0.0262 (0.304) |
0.944 (1.00) |
0.435 (0.85) |
0.00871 (0.174) |
0.00761 (0.17) |
0.204 (0.685) |
0.374 (0.816) |
0.414 (0.848) |
0.666 (0.942) |
5p gain | 36 (22%) | 129 |
0.202 (0.685) |
0.0987 (0.539) |
0.00206 (0.0791) |
0.0984 (0.539) |
0.534 (0.889) |
0.713 (0.964) |
0.114 (0.567) |
4e-05 (0.0048) |
0.191 (0.679) |
0.923 (1.00) |
0.494 (0.877) |
0.627 (0.928) |
6p gain | 41 (25%) | 124 |
0.333 (0.787) |
0.562 (0.895) |
0.00862 (0.174) |
0.00364 (0.106) |
0.402 (0.834) |
0.256 (0.702) |
0.798 (0.999) |
0.468 (0.865) |
0.239 (0.695) |
0.299 (0.747) |
0.278 (0.73) |
0.806 (1.00) |
16q gain | 41 (25%) | 124 |
0.0523 (0.433) |
0.593 (0.908) |
1e-05 (0.0024) |
0.234 (0.695) |
0.702 (0.964) |
0.0505 (0.425) |
0.00961 (0.181) |
0.104 (0.549) |
0.0203 (0.266) |
0.245 (0.695) |
0.232 (0.695) |
0.916 (1.00) |
9q loss | 23 (14%) | 142 |
0.208 (0.685) |
0.45 (0.856) |
0.282 (0.73) |
0.138 (0.603) |
0.755 (0.978) |
0.947 (1.00) |
0.519 (0.877) |
0.195 (0.685) |
0.0704 (0.483) |
0.00164 (0.0787) |
0.461 (0.861) |
0.0141 (0.241) |
18p loss | 128 (78%) | 37 |
0.0579 (0.452) |
0.708 (0.964) |
0.00122 (0.0651) |
0.026 (0.304) |
0.552 (0.895) |
0.318 (0.764) |
0.117 (0.571) |
0.0151 (0.241) |
0.167 (0.637) |
0.163 (0.637) |
0.616 (0.919) |
0.59 (0.908) |
18q loss | 138 (84%) | 27 |
0.0212 (0.27) |
0.174 (0.644) |
3e-05 (0.00411) |
0.0117 (0.208) |
0.78 (0.989) |
0.14 (0.604) |
0.0727 (0.488) |
0.0194 (0.266) |
0.425 (0.848) |
0.029 (0.313) |
0.514 (0.877) |
0.538 (0.89) |
2q gain | 43 (26%) | 122 |
0.0921 (0.528) |
0.0572 (0.451) |
0.122 (0.585) |
0.0624 (0.468) |
0.793 (0.996) |
0.582 (0.904) |
0.089 (0.528) |
0.00228 (0.0802) |
0.218 (0.695) |
0.307 (0.75) |
0.16 (0.637) |
0.189 (0.676) |
3p gain | 27 (16%) | 138 |
1 (1.00) |
0.904 (1.00) |
0.00063 (0.0378) |
0.654 (0.935) |
0.239 (0.695) |
0.447 (0.854) |
0.112 (0.567) |
0.929 (1.00) |
0.379 (0.816) |
0.356 (0.816) |
0.657 (0.935) |
0.824 (1.00) |
3q gain | 34 (21%) | 131 |
0.605 (0.914) |
0.614 (0.919) |
9e-05 (0.0096) |
0.87 (1.00) |
0.432 (0.85) |
0.238 (0.695) |
0.104 (0.549) |
0.738 (0.973) |
0.216 (0.695) |
0.316 (0.761) |
0.653 (0.935) |
0.895 (1.00) |
5q gain | 24 (15%) | 141 |
0.245 (0.695) |
0.0867 (0.527) |
0.00703 (0.161) |
0.0748 (0.489) |
0.431 (0.85) |
0.603 (0.913) |
0.447 (0.854) |
0.0904 (0.528) |
0.249 (0.697) |
0.522 (0.879) |
1 (1.00) |
0.654 (0.935) |
6q gain | 36 (22%) | 129 |
0.67 (0.944) |
0.228 (0.695) |
0.0162 (0.251) |
0.00686 (0.161) |
0.632 (0.932) |
0.453 (0.856) |
0.672 (0.946) |
0.507 (0.877) |
0.341 (0.789) |
0.581 (0.904) |
0.203 (0.685) |
0.563 (0.895) |
8p gain | 42 (25%) | 123 |
0.417 (0.848) |
0.237 (0.695) |
0.00181 (0.0791) |
0.516 (0.877) |
0.18 (0.658) |
0.0388 (0.388) |
0.515 (0.877) |
0.341 (0.789) |
0.811 (1.00) |
0.285 (0.732) |
0.917 (1.00) |
0.141 (0.605) |
8q gain | 89 (54%) | 76 |
0.0374 (0.382) |
0.274 (0.727) |
2e-05 (0.0032) |
0.21 (0.685) |
0.445 (0.854) |
0.163 (0.637) |
0.603 (0.913) |
0.221 (0.695) |
0.245 (0.695) |
0.0659 (0.471) |
0.0205 (0.266) |
0.372 (0.816) |
9q gain | 33 (20%) | 132 |
0.0149 (0.241) |
0.21 (0.685) |
0.282 (0.73) |
0.47 (0.865) |
0.303 (0.75) |
0.0838 (0.516) |
0.369 (0.816) |
0.0923 (0.528) |
0.784 (0.992) |
0.621 (0.924) |
0.829 (1.00) |
0.931 (1.00) |
11p gain | 32 (19%) | 133 |
0.135 (0.603) |
0.389 (0.821) |
0.00835 (0.174) |
0.42 (0.848) |
1 (1.00) |
0.918 (1.00) |
0.134 (0.603) |
0.145 (0.609) |
0.0214 (0.27) |
0.209 (0.685) |
0.654 (0.935) |
0.538 (0.89) |
16p gain | 41 (25%) | 124 |
0.149 (0.623) |
0.853 (1.00) |
0.00143 (0.0723) |
0.273 (0.727) |
0.888 (1.00) |
0.348 (0.804) |
0.116 (0.569) |
0.37 (0.816) |
0.151 (0.626) |
0.68 (0.947) |
0.336 (0.787) |
0.982 (1.00) |
17q gain | 32 (19%) | 133 |
0.198 (0.685) |
0.943 (1.00) |
0.00696 (0.161) |
0.422 (0.848) |
0.659 (0.936) |
0.401 (0.834) |
0.367 (0.816) |
0.492 (0.877) |
0.0551 (0.445) |
0.46 (0.861) |
0.12 (0.581) |
0.638 (0.935) |
20p gain | 109 (66%) | 56 |
0.0969 (0.539) |
0.728 (0.968) |
0.138 (0.603) |
0.251 (0.697) |
0.00447 (0.119) |
0.55 (0.895) |
0.607 (0.914) |
0.564 (0.895) |
0.0977 (0.539) |
0.0453 (0.405) |
0.306 (0.75) |
0.0771 (0.493) |
xp gain | 34 (21%) | 131 |
0.0114 (0.208) |
0.143 (0.609) |
0.11 (0.565) |
0.402 (0.834) |
0.464 (0.863) |
0.795 (0.996) |
0.27 (0.725) |
0.669 (0.944) |
0.813 (1.00) |
0.849 (1.00) |
0.832 (1.00) |
0.642 (0.935) |
2p loss | 11 (7%) | 154 |
0.64 (0.935) |
0.752 (0.975) |
0.00386 (0.109) |
0.485 (0.877) |
0.589 (0.908) |
0.402 (0.834) |
0.528 (0.885) |
0.0587 (0.452) |
0.434 (0.85) |
0.606 (0.914) |
||
3q loss | 10 (6%) | 155 |
0.517 (0.877) |
0.794 (0.996) |
0.193 (0.683) |
0.41 (0.844) |
0.232 (0.695) |
0.517 (0.877) |
0.103 (0.549) |
0.219 (0.695) |
0.494 (0.877) |
0.00958 (0.181) |
0.419 (0.848) |
0.367 (0.816) |
4p loss | 59 (36%) | 106 |
0.664 (0.941) |
0.376 (0.816) |
0.00182 (0.0791) |
0.0274 (0.308) |
0.429 (0.849) |
0.23 (0.695) |
0.712 (0.964) |
0.572 (0.898) |
0.975 (1.00) |
0.1 (0.541) |
0.224 (0.695) |
0.208 (0.685) |
4q loss | 66 (40%) | 99 |
0.78 (0.989) |
0.269 (0.725) |
0.00109 (0.0616) |
0.04 (0.392) |
0.428 (0.849) |
0.0425 (0.405) |
0.767 (0.984) |
0.434 (0.85) |
0.813 (1.00) |
0.217 (0.695) |
0.567 (0.895) |
0.918 (1.00) |
5q loss | 40 (24%) | 125 |
0.0912 (0.528) |
0.0116 (0.208) |
0.218 (0.695) |
0.167 (0.637) |
0.729 (0.968) |
0.878 (1.00) |
0.927 (1.00) |
0.221 (0.695) |
0.912 (1.00) |
0.209 (0.685) |
0.113 (0.567) |
0.232 (0.695) |
6q loss | 22 (13%) | 143 |
0.166 (0.637) |
0.642 (0.935) |
0.152 (0.626) |
0.422 (0.848) |
0.206 (0.685) |
0.897 (1.00) |
0.154 (0.628) |
0.151 (0.626) |
0.262 (0.712) |
0.412 (0.847) |
0.0122 (0.212) |
0.556 (0.895) |
10q loss | 38 (23%) | 127 |
0.176 (0.649) |
0.153 (0.626) |
0.0588 (0.452) |
0.0931 (0.529) |
0.0919 (0.528) |
0.0149 (0.241) |
0.378 (0.816) |
0.074 (0.489) |
0.683 (0.95) |
0.0867 (0.527) |
0.9 (1.00) |
0.537 (0.89) |
11p loss | 23 (14%) | 142 |
0.243 (0.695) |
0.373 (0.816) |
0.00602 (0.152) |
0.203 (0.685) |
0.441 (0.854) |
0.562 (0.895) |
0.0193 (0.266) |
0.235 (0.695) |
0.977 (1.00) |
0.741 (0.973) |
0.601 (0.913) |
0.289 (0.732) |
15q loss | 73 (44%) | 92 |
0.448 (0.855) |
0.113 (0.567) |
0.00053 (0.0378) |
1 (1.00) |
0.163 (0.637) |
0.623 (0.926) |
0.441 (0.854) |
0.479 (0.873) |
0.818 (1.00) |
0.635 (0.932) |
0.906 (1.00) |
0.743 (0.973) |
19q loss | 20 (12%) | 145 |
0.832 (1.00) |
0.506 (0.877) |
0.0682 (0.471) |
0.0835 (0.516) |
0.504 (0.877) |
0.76 (0.98) |
0.553 (0.895) |
0.719 (0.967) |
0.0675 (0.471) |
0.00897 (0.176) |
1 (1.00) |
0.746 (0.975) |
20p loss | 23 (14%) | 142 |
1 (1.00) |
0.953 (1.00) |
0.0505 (0.425) |
0.282 (0.73) |
0.241 (0.695) |
0.866 (1.00) |
0.441 (0.854) |
0.674 (0.947) |
0.0323 (0.337) |
0.0223 (0.278) |
0.305 (0.75) |
0.0145 (0.241) |
21q loss | 68 (41%) | 97 |
0.287 (0.732) |
0.251 (0.697) |
0.414 (0.848) |
1 (1.00) |
0.383 (0.818) |
0.741 (0.973) |
0.822 (1.00) |
0.686 (0.95) |
0.0159 (0.25) |
0.183 (0.663) |
0.225 (0.695) |
0.068 (0.471) |
22q loss | 58 (35%) | 107 |
0.854 (1.00) |
0.312 (0.755) |
0.0654 (0.471) |
0.773 (0.987) |
0.65 (0.935) |
0.3 (0.747) |
0.34 (0.789) |
0.168 (0.637) |
0.00596 (0.152) |
0.182 (0.662) |
0.125 (0.586) |
0.0193 (0.266) |
1p gain | 12 (7%) | 153 |
0.513 (0.877) |
0.94 (1.00) |
0.826 (1.00) |
0.528 (0.885) |
0.25 (0.697) |
0.263 (0.712) |
0.334 (0.787) |
0.594 (0.908) |
0.941 (1.00) |
0.457 (0.857) |
0.87 (1.00) |
0.65 (0.935) |
1q gain | 34 (21%) | 131 |
0.587 (0.907) |
0.653 (0.935) |
0.138 (0.603) |
0.31 (0.754) |
0.235 (0.695) |
0.174 (0.644) |
0.451 (0.856) |
0.996 (1.00) |
0.541 (0.89) |
0.88 (1.00) |
0.87 (1.00) |
0.366 (0.816) |
2p gain | 41 (25%) | 124 |
0.505 (0.877) |
0.0198 (0.266) |
0.257 (0.702) |
0.0256 (0.304) |
0.546 (0.895) |
0.676 (0.947) |
0.0462 (0.407) |
0.0182 (0.266) |
0.187 (0.671) |
0.0768 (0.493) |
0.726 (0.968) |
0.504 (0.877) |
4p gain | 9 (5%) | 156 |
1 (1.00) |
0.793 (0.996) |
0.965 (1.00) |
0.766 (0.984) |
0.0716 (0.487) |
0.0319 (0.337) |
0.484 (0.877) |
0.628 (0.928) |
0.225 (0.695) |
0.374 (0.816) |
0.745 (0.975) |
0.95 (1.00) |
4q gain | 5 (3%) | 160 |
0.296 (0.743) |
0.649 (0.935) |
0.678 (0.947) |
0.0453 (0.405) |
0.162 (0.637) |
0.713 (0.964) |
1 (1.00) |
0.889 (1.00) |
1 (1.00) |
|||
9p gain | 42 (25%) | 123 |
0.0176 (0.264) |
0.197 (0.685) |
0.446 (0.854) |
0.166 (0.637) |
0.58 (0.904) |
0.153 (0.626) |
0.0501 (0.425) |
0.274 (0.727) |
0.275 (0.727) |
0.329 (0.78) |
0.863 (1.00) |
0.867 (1.00) |
10p gain | 13 (8%) | 152 |
1 (1.00) |
0.918 (1.00) |
0.337 (0.787) |
0.716 (0.965) |
0.371 (0.816) |
0.895 (1.00) |
0.524 (0.88) |
0.126 (0.587) |
0.653 (0.935) |
0.919 (1.00) |
0.614 (0.919) |
0.791 (0.996) |
10q gain | 7 (4%) | 158 |
0.516 (0.877) |
0.0815 (0.512) |
0.256 (0.702) |
1 (1.00) |
0.451 (0.856) |
0.71 (0.964) |
1 (1.00) |
0.503 (0.877) |
0.771 (0.987) |
0.862 (1.00) |
||
12p gain | 33 (20%) | 132 |
0.687 (0.95) |
0.482 (0.876) |
0.236 (0.695) |
0.725 (0.968) |
0.162 (0.637) |
0.69 (0.952) |
0.083 (0.516) |
0.202 (0.685) |
0.374 (0.816) |
0.551 (0.895) |
0.279 (0.73) |
0.867 (1.00) |
12q gain | 24 (15%) | 141 |
0.773 (0.987) |
0.52 (0.877) |
0.743 (0.973) |
0.306 (0.75) |
0.29 (0.732) |
0.504 (0.877) |
0.0431 (0.405) |
0.51 (0.877) |
0.224 (0.695) |
0.74 (0.973) |
0.0536 (0.437) |
0.949 (1.00) |
14q gain | 8 (5%) | 157 |
0.832 (1.00) |
0.916 (1.00) |
0.114 (0.567) |
0.227 (0.695) |
0.723 (0.968) |
0.864 (1.00) |
0.495 (0.877) |
0.911 (1.00) |
0.13 (0.599) |
0.862 (1.00) |
||
15q gain | 3 (2%) | 162 |
0.419 (0.848) |
0.486 (0.877) |
0.356 (0.816) |
0.644 (0.935) |
||||||||
17p gain | 8 (5%) | 157 |
0.11 (0.565) |
0.379 (0.816) |
0.231 (0.695) |
0.468 (0.865) |
0.76 (0.98) |
0.328 (0.78) |
0.421 (0.848) |
0.685 (0.95) |
0.488 (0.877) |
0.444 (0.854) |
||
18p gain | 8 (5%) | 157 |
0.515 (0.877) |
0.389 (0.821) |
0.218 (0.695) |
0.731 (0.969) |
0.938 (1.00) |
0.907 (1.00) |
0.679 (0.947) |
0.385 (0.818) |
0.503 (0.877) |
0.558 (0.895) |
1 (1.00) |
0.895 (1.00) |
18q gain | 6 (4%) | 159 |
0.793 (0.996) |
0.381 (0.818) |
0.863 (1.00) |
0.586 (0.907) |
0.532 (0.887) |
0.226 (0.695) |
0.654 (0.935) |
0.628 (0.928) |
1 (1.00) |
0.892 (1.00) |
||
19p gain | 33 (20%) | 132 |
0.0656 (0.471) |
0.419 (0.848) |
0.106 (0.55) |
0.766 (0.984) |
0.99 (1.00) |
0.539 (0.89) |
0.562 (0.895) |
0.0279 (0.308) |
0.135 (0.603) |
0.958 (1.00) |
1 (1.00) |
0.972 (1.00) |
19q gain | 32 (19%) | 133 |
0.0815 (0.512) |
0.532 (0.887) |
0.0745 (0.489) |
0.53 (0.887) |
0.883 (1.00) |
0.872 (1.00) |
0.226 (0.695) |
0.125 (0.586) |
0.36 (0.816) |
0.581 (0.904) |
1 (1.00) |
0.973 (1.00) |
21q gain | 10 (6%) | 155 |
0.54 (0.89) |
0.658 (0.935) |
0.633 (0.932) |
1 (1.00) |
0.0776 (0.493) |
0.305 (0.75) |
0.946 (1.00) |
0.921 (1.00) |
0.292 (0.736) |
0.724 (0.968) |
||
22q gain | 9 (5%) | 156 |
0.726 (0.968) |
0.0611 (0.465) |
0.074 (0.489) |
1 (1.00) |
0.0913 (0.528) |
0.935 (1.00) |
0.351 (0.809) |
0.2 (0.685) |
1 (1.00) |
1 (1.00) |
||
xq gain | 34 (21%) | 131 |
0.157 (0.63) |
0.382 (0.818) |
0.045 (0.405) |
0.289 (0.732) |
0.129 (0.599) |
0.511 (0.877) |
0.104 (0.549) |
0.644 (0.935) |
0.981 (1.00) |
1 (1.00) |
0.455 (0.856) |
0.212 (0.69) |
1p loss | 46 (28%) | 119 |
0.69 (0.952) |
0.0266 (0.304) |
0.0517 (0.431) |
0.188 (0.673) |
0.394 (0.831) |
0.171 (0.641) |
0.366 (0.816) |
0.168 (0.637) |
0.441 (0.854) |
0.611 (0.918) |
0.558 (0.895) |
0.567 (0.895) |
1q loss | 26 (16%) | 139 |
0.912 (1.00) |
0.0573 (0.451) |
0.257 (0.702) |
0.0286 (0.312) |
0.972 (1.00) |
0.271 (0.725) |
0.0669 (0.471) |
0.463 (0.862) |
0.561 (0.895) |
0.229 (0.695) |
0.497 (0.877) |
0.274 (0.727) |
2q loss | 6 (4%) | 159 |
1 (1.00) |
0.568 (0.895) |
0.0538 (0.437) |
0.28 (0.73) |
0.518 (0.877) |
0.813 (1.00) |
0.0645 (0.471) |
0.204 (0.685) |
0.47 (0.865) |
|||
3p loss | 15 (9%) | 150 |
1 (1.00) |
0.367 (0.816) |
0.206 (0.685) |
0.776 (0.989) |
0.245 (0.695) |
0.22 (0.695) |
0.157 (0.63) |
0.556 (0.895) |
0.453 (0.856) |
0.137 (0.603) |
0.098 (0.539) |
0.0442 (0.405) |
5p loss | 26 (16%) | 139 |
0.241 (0.695) |
0.817 (1.00) |
0.137 (0.603) |
0.179 (0.655) |
0.506 (0.877) |
0.677 (0.947) |
0.879 (1.00) |
0.125 (0.586) |
0.724 (0.968) |
0.578 (0.903) |
0.17 (0.639) |
0.243 (0.695) |
6p loss | 13 (8%) | 152 |
0.543 (0.893) |
0.93 (1.00) |
0.699 (0.961) |
0.123 (0.586) |
0.425 (0.848) |
0.857 (1.00) |
0.751 (0.975) |
0.277 (0.73) |
0.564 (0.895) |
0.253 (0.699) |
||
7q loss | 3 (2%) | 162 |
0.358 (0.816) |
0.719 (0.967) |
0.44 (0.854) |
0.0366 (0.378) |
0.761 (0.981) |
0.859 (1.00) |
1 (1.00) |
|||||
8p loss | 73 (44%) | 92 |
0.124 (0.586) |
0.248 (0.697) |
0.133 (0.603) |
0.965 (1.00) |
0.146 (0.61) |
0.572 (0.898) |
0.0232 (0.286) |
0.119 (0.578) |
0.892 (1.00) |
0.973 (1.00) |
0.733 (0.971) |
0.231 (0.695) |
8q loss | 11 (7%) | 154 |
0.686 (0.95) |
0.715 (0.965) |
0.406 (0.839) |
0.466 (0.865) |
0.599 (0.913) |
0.312 (0.755) |
0.546 (0.895) |
0.324 (0.771) |
0.865 (1.00) |
0.3 (0.747) |
0.167 (0.637) |
0.406 (0.839) |
9p loss | 23 (14%) | 142 |
0.634 (0.932) |
0.616 (0.919) |
0.321 (0.766) |
0.14 (0.603) |
0.707 (0.964) |
0.81 (1.00) |
0.813 (1.00) |
0.515 (0.877) |
0.31 (0.754) |
0.0455 (0.405) |
0.713 (0.964) |
0.038 (0.384) |
10p loss | 33 (20%) | 132 |
0.144 (0.609) |
0.172 (0.642) |
0.138 (0.603) |
0.068 (0.471) |
0.0919 (0.528) |
0.0444 (0.405) |
0.198 (0.685) |
0.456 (0.856) |
0.838 (1.00) |
0.114 (0.567) |
0.819 (1.00) |
0.751 (0.975) |
12p loss | 22 (13%) | 143 |
0.424 (0.848) |
0.285 (0.732) |
0.656 (0.935) |
0.399 (0.834) |
0.951 (1.00) |
0.554 (0.895) |
0.751 (0.975) |
0.431 (0.85) |
0.454 (0.856) |
0.777 (0.989) |
0.0673 (0.471) |
0.506 (0.877) |
12q loss | 19 (12%) | 146 |
0.501 (0.877) |
0.77 (0.987) |
0.24 (0.695) |
0.931 (1.00) |
0.213 (0.69) |
0.603 (0.913) |
0.832 (1.00) |
0.255 (0.702) |
0.379 (0.816) |
0.321 (0.766) |
0.27 (0.725) |
0.868 (1.00) |
13q loss | 8 (5%) | 157 |
0.518 (0.877) |
1 (1.00) |
0.655 (0.935) |
0.106 (0.55) |
0.706 (0.964) |
0.627 (0.928) |
1 (1.00) |
0.495 (0.877) |
0.177 (0.649) |
1 (1.00) |
||
14q loss | 67 (41%) | 98 |
0.502 (0.877) |
0.246 (0.696) |
0.02 (0.266) |
0.571 (0.898) |
0.955 (1.00) |
0.899 (1.00) |
0.384 (0.818) |
0.0753 (0.489) |
0.336 (0.787) |
0.199 (0.685) |
0.751 (0.975) |
0.781 (0.989) |
16p loss | 9 (5%) | 156 |
0.376 (0.816) |
0.758 (0.98) |
0.1 (0.541) |
0.0616 (0.466) |
0.359 (0.816) |
0.518 (0.877) |
0.187 (0.671) |
0.912 (1.00) |
0.563 (0.895) |
1 (1.00) |
0.251 (0.697) |
0.488 (0.877) |
16q loss | 15 (9%) | 150 |
0.281 (0.73) |
0.678 (0.947) |
0.0475 (0.415) |
0.338 (0.789) |
0.499 (0.877) |
0.878 (1.00) |
0.399 (0.834) |
0.996 (1.00) |
0.867 (1.00) |
1 (1.00) |
0.939 (1.00) |
0.963 (1.00) |
17p loss | 107 (65%) | 58 |
0.206 (0.685) |
0.375 (0.816) |
0.092 (0.528) |
0.197 (0.685) |
0.709 (0.964) |
0.602 (0.913) |
0.621 (0.924) |
0.591 (0.908) |
0.981 (1.00) |
0.399 (0.834) |
0.29 (0.732) |
0.665 (0.941) |
17q loss | 26 (16%) | 139 |
0.904 (1.00) |
0.738 (0.973) |
0.0278 (0.308) |
0.0891 (0.528) |
0.794 (0.996) |
0.138 (0.603) |
0.115 (0.567) |
0.337 (0.787) |
0.867 (1.00) |
0.946 (1.00) |
0.421 (0.848) |
0.476 (0.868) |
19p loss | 21 (13%) | 144 |
0.727 (0.968) |
0.835 (1.00) |
0.135 (0.603) |
0.0304 (0.324) |
0.699 (0.961) |
0.866 (1.00) |
0.592 (0.908) |
0.566 (0.895) |
0.376 (0.816) |
0.0191 (0.266) |
0.965 (1.00) |
0.741 (0.973) |
xp loss | 25 (15%) | 140 |
0.289 (0.732) |
0.898 (1.00) |
0.302 (0.748) |
0.476 (0.868) |
0.386 (0.818) |
0.105 (0.549) |
0.426 (0.848) |
0.859 (1.00) |
0.977 (1.00) |
0.576 (0.901) |
0.568 (0.895) |
0.779 (0.989) |
xq loss | 24 (15%) | 141 |
0.608 (0.915) |
0.475 (0.868) |
0.71 (0.964) |
0.316 (0.761) |
0.869 (1.00) |
0.295 (0.741) |
0.565 (0.895) |
0.955 (1.00) |
0.84 (1.00) |
0.371 (0.816) |
0.474 (0.868) |
0.806 (1.00) |
P value = 0.00228 (Fisher's exact test), Q value = 0.08
Table S1. Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 27 | 36 | 12 | 19 | 32 | 18 | 20 |
2Q GAIN MUTATED | 14 | 6 | 2 | 6 | 10 | 0 | 4 |
2Q GAIN WILD-TYPE | 13 | 30 | 10 | 13 | 22 | 18 | 16 |
Figure S1. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D4V8.png)
P value = 0.00063 (Fisher's exact test), Q value = 0.038
Table S2. Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
3P GAIN MUTATED | 3 | 10 | 9 | 5 |
3P GAIN WILD-TYPE | 63 | 22 | 22 | 31 |
Figure S2. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D5V3.png)
P value = 9e-05 (Fisher's exact test), Q value = 0.0096
Table S3. Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
3Q GAIN MUTATED | 4 | 12 | 11 | 7 |
3Q GAIN WILD-TYPE | 62 | 20 | 20 | 29 |
Figure S3. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D6V3.png)
P value = 0.00206 (Fisher's exact test), Q value = 0.079
Table S4. Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
5P GAIN MUTATED | 5 | 10 | 9 | 12 |
5P GAIN WILD-TYPE | 61 | 22 | 22 | 24 |
Figure S4. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D9V3.png)
P value = 4e-05 (Fisher's exact test), Q value = 0.0048
Table S5. Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 27 | 36 | 12 | 19 | 32 | 18 | 20 |
5P GAIN MUTATED | 8 | 2 | 9 | 2 | 10 | 2 | 3 |
5P GAIN WILD-TYPE | 19 | 34 | 3 | 17 | 22 | 16 | 17 |
Figure S5. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D9V8.png)
P value = 0.00703 (Fisher's exact test), Q value = 0.16
Table S6. Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
5Q GAIN MUTATED | 3 | 6 | 5 | 10 |
5Q GAIN WILD-TYPE | 63 | 26 | 26 | 26 |
Figure S6. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D10V3.png)
P value = 0.00862 (Fisher's exact test), Q value = 0.17
Table S7. Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
6P GAIN MUTATED | 11 | 15 | 9 | 6 |
6P GAIN WILD-TYPE | 55 | 17 | 22 | 30 |
Figure S7. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D11V3.png)
P value = 0.00364 (Fisher's exact test), Q value = 0.11
Table S8. Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 28 | 39 | 29 |
6P GAIN MUTATED | 14 | 5 | 7 |
6P GAIN WILD-TYPE | 14 | 34 | 22 |
Figure S8. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D11V4.png)
P value = 0.00686 (Fisher's exact test), Q value = 0.16
Table S9. Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 28 | 39 | 29 |
6Q GAIN MUTATED | 13 | 5 | 6 |
6Q GAIN WILD-TYPE | 15 | 34 | 23 |
Figure S9. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D12V4.png)
P value = 0.00234 (Fisher's exact test), Q value = 0.08
Table S10. Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 25 | 22 | 22 |
7P GAIN MUTATED | 8 | 11 | 18 |
7P GAIN WILD-TYPE | 17 | 11 | 4 |
Figure S10. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D13V1.png)
P value = 0.00274 (Fisher's exact test), Q value = 0.088
Table S11. Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 6 | 13 | 13 | 9 | 8 | 9 | 8 | 3 |
7P GAIN MUTATED | 1 | 3 | 7 | 7 | 7 | 5 | 7 | 0 |
7P GAIN WILD-TYPE | 5 | 10 | 6 | 2 | 1 | 4 | 1 | 3 |
Figure S11. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D13V2.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0024
Table S12. Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
7P GAIN MUTATED | 24 | 26 | 28 | 24 |
7P GAIN WILD-TYPE | 42 | 6 | 3 | 12 |
Figure S12. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D13V3.png)
P value = 0.0032 (Fisher's exact test), Q value = 0.096
Table S13. Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 28 | 39 | 29 |
7P GAIN MUTATED | 24 | 19 | 22 |
7P GAIN WILD-TYPE | 4 | 20 | 7 |
Figure S13. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D13V4.png)
P value = 0.00023 (Fisher's exact test), Q value = 0.022
Table S14. Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 29 | 14 | 33 | 28 | 60 |
7P GAIN MUTATED | 24 | 7 | 13 | 24 | 33 |
7P GAIN WILD-TYPE | 5 | 7 | 20 | 4 | 27 |
Figure S14. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D13V7.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0024
Table S15. Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 27 | 36 | 12 | 19 | 32 | 18 | 20 |
7P GAIN MUTATED | 25 | 17 | 9 | 13 | 20 | 3 | 14 |
7P GAIN WILD-TYPE | 2 | 19 | 3 | 6 | 12 | 15 | 6 |
Figure S15. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D13V8.png)
P value = 0.00797 (Fisher's exact test), Q value = 0.17
Table S16. Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 6 | 13 | 13 | 9 | 8 | 9 | 8 | 3 |
7Q GAIN MUTATED | 1 | 3 | 7 | 4 | 7 | 4 | 7 | 0 |
7Q GAIN WILD-TYPE | 5 | 10 | 6 | 5 | 1 | 5 | 1 | 3 |
Figure S16. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D14V2.png)
P value = 2e-05 (Fisher's exact test), Q value = 0.0032
Table S17. Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
7Q GAIN MUTATED | 18 | 23 | 22 | 22 |
7Q GAIN WILD-TYPE | 48 | 9 | 9 | 14 |
Figure S17. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D14V3.png)
P value = 0.00414 (Fisher's exact test), Q value = 0.11
Table S18. Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 29 | 14 | 33 | 28 | 60 |
7Q GAIN MUTATED | 17 | 5 | 11 | 22 | 29 |
7Q GAIN WILD-TYPE | 12 | 9 | 22 | 6 | 31 |
Figure S18. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D14V7.png)
P value = 0.00206 (Fisher's exact test), Q value = 0.079
Table S19. Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 27 | 36 | 12 | 19 | 32 | 18 | 20 |
7Q GAIN MUTATED | 19 | 12 | 8 | 12 | 18 | 3 | 12 |
7Q GAIN WILD-TYPE | 8 | 24 | 4 | 7 | 14 | 15 | 8 |
Figure S19. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D14V8.png)
P value = 0.00181 (Fisher's exact test), Q value = 0.079
Table S20. Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
8P GAIN MUTATED | 10 | 8 | 6 | 18 |
8P GAIN WILD-TYPE | 56 | 24 | 25 | 18 |
Figure S20. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D15V3.png)
P value = 2e-05 (Fisher's exact test), Q value = 0.0032
Table S21. Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
8Q GAIN MUTATED | 29 | 13 | 15 | 32 |
8Q GAIN WILD-TYPE | 37 | 19 | 16 | 4 |
Figure S21. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D16V3.png)
P value = 0.0149 (Fisher's exact test), Q value = 0.24
Table S22. Gene #18: '9q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 25 | 22 | 22 |
9Q GAIN MUTATED | 1 | 8 | 5 |
9Q GAIN WILD-TYPE | 24 | 14 | 17 |
Figure S22. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D18V1.png)
P value = 0.00835 (Fisher's exact test), Q value = 0.17
Table S23. Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
11P GAIN MUTATED | 8 | 6 | 13 | 5 |
11P GAIN WILD-TYPE | 58 | 26 | 18 | 31 |
Figure S23. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D21V3.png)
P value = 0.002 (Fisher's exact test), Q value = 0.079
Table S24. Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
11Q GAIN MUTATED | 7 | 5 | 12 | 2 |
11Q GAIN WILD-TYPE | 59 | 27 | 19 | 34 |
Figure S24. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D22V3.png)
P value = 0.00274 (Fisher's exact test), Q value = 0.088
Table S25. Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 29 | 14 | 33 | 28 | 60 |
11Q GAIN MUTATED | 7 | 1 | 0 | 9 | 9 |
11Q GAIN WILD-TYPE | 22 | 13 | 33 | 19 | 51 |
Figure S25. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D22V7.png)
P value = 0.00044 (Fisher's exact test), Q value = 0.038
Table S26. Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 27 | 36 | 12 | 19 | 32 | 18 | 20 |
11Q GAIN MUTATED | 9 | 1 | 0 | 7 | 7 | 1 | 1 |
11Q GAIN WILD-TYPE | 18 | 35 | 12 | 12 | 25 | 17 | 19 |
Figure S26. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D22V8.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0024
Table S27. Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
13Q GAIN MUTATED | 32 | 30 | 26 | 25 |
13Q GAIN WILD-TYPE | 34 | 2 | 5 | 11 |
Figure S27. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D25V3.png)
P value = 0.00049 (Fisher's exact test), Q value = 0.038
Table S28. Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 29 | 14 | 33 | 28 | 60 |
13Q GAIN MUTATED | 19 | 11 | 16 | 27 | 39 |
13Q GAIN WILD-TYPE | 10 | 3 | 17 | 1 | 21 |
Figure S28. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D25V7.png)
P value = 0.00061 (Fisher's exact test), Q value = 0.038
Table S29. Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 27 | 36 | 12 | 19 | 32 | 18 | 20 |
13Q GAIN MUTATED | 21 | 25 | 7 | 17 | 25 | 4 | 13 |
13Q GAIN WILD-TYPE | 6 | 11 | 5 | 2 | 7 | 14 | 7 |
Figure S29. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D25V8.png)
P value = 0.00312 (Fisher's exact test), Q value = 0.096
Table S30. Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 42 | 17 | 8 | 56 |
13Q GAIN MUTATED | 15 | 37 | 9 | 6 | 32 |
13Q GAIN WILD-TYPE | 3 | 5 | 8 | 2 | 24 |
Figure S30. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D25V9.png)
P value = 0.00143 (Fisher's exact test), Q value = 0.072
Table S31. Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
16P GAIN MUTATED | 7 | 14 | 11 | 9 |
16P GAIN WILD-TYPE | 59 | 18 | 20 | 27 |
Figure S31. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D28V3.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0024
Table S32. Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
16Q GAIN MUTATED | 5 | 15 | 13 | 8 |
16Q GAIN WILD-TYPE | 61 | 17 | 18 | 28 |
Figure S32. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D29V3.png)
P value = 0.00961 (Fisher's exact test), Q value = 0.18
Table S33. Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 29 | 14 | 33 | 28 | 60 |
16Q GAIN MUTATED | 11 | 1 | 4 | 12 | 12 |
16Q GAIN WILD-TYPE | 18 | 13 | 29 | 16 | 48 |
Figure S33. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D29V7.png)
P value = 0.00696 (Fisher's exact test), Q value = 0.16
Table S34. Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
17Q GAIN MUTATED | 9 | 3 | 13 | 7 |
17Q GAIN WILD-TYPE | 57 | 29 | 18 | 29 |
Figure S34. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D31V3.png)
P value = 0.00447 (Fisher's exact test), Q value = 0.12
Table S35. Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 42 | 27 | 25 | 30 | 3 |
20P GAIN MUTATED | 34 | 22 | 13 | 15 | 1 |
20P GAIN WILD-TYPE | 8 | 5 | 12 | 15 | 2 |
Figure S35. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D36V5.png)
P value = 0.0078 (Fisher's exact test), Q value = 0.17
Table S36. Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 25 | 22 | 22 |
20Q GAIN MUTATED | 22 | 15 | 22 |
20Q GAIN WILD-TYPE | 3 | 7 | 0 |
Figure S36. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D37V1.png)
P value = 0.00063 (Fisher's exact test), Q value = 0.038
Table S37. Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
20Q GAIN MUTATED | 53 | 32 | 31 | 29 |
20Q GAIN WILD-TYPE | 13 | 0 | 0 | 7 |
Figure S37. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D37V3.png)
P value = 0.00219 (Fisher's exact test), Q value = 0.08
Table S38. Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 27 | 36 | 12 | 19 | 32 | 18 | 20 |
20Q GAIN MUTATED | 26 | 33 | 9 | 18 | 30 | 10 | 18 |
20Q GAIN WILD-TYPE | 1 | 3 | 3 | 1 | 2 | 8 | 2 |
Figure S38. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D37V8.png)
P value = 0.0114 (Fisher's exact test), Q value = 0.21
Table S39. Gene #40: 'xp gain' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 25 | 22 | 22 |
XP GAIN MUTATED | 4 | 1 | 9 |
XP GAIN WILD-TYPE | 21 | 21 | 13 |
Figure S39. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D40V1.png)
P value = 0.00386 (Fisher's exact test), Q value = 0.11
Table S40. Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
2P LOSS MUTATED | 0 | 5 | 2 | 4 |
2P LOSS WILD-TYPE | 66 | 27 | 29 | 32 |
Figure S40. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D44V3.png)
P value = 0.00958 (Fisher's exact test), Q value = 0.18
Table S41. Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 22 | 63 | 56 |
3Q LOSS MUTATED | 5 | 4 | 1 |
3Q LOSS WILD-TYPE | 17 | 59 | 55 |
Figure S41. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D47V10.png)
P value = 0.00182 (Fisher's exact test), Q value = 0.079
Table S42. Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
4P LOSS MUTATED | 15 | 20 | 12 | 12 |
4P LOSS WILD-TYPE | 51 | 12 | 19 | 24 |
Figure S42. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D48V3.png)
P value = 0.00109 (Fisher's exact test), Q value = 0.062
Table S43. Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
4Q LOSS MUTATED | 16 | 21 | 14 | 15 |
4Q LOSS WILD-TYPE | 50 | 11 | 17 | 21 |
Figure S43. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D49V3.png)
P value = 0.0116 (Fisher's exact test), Q value = 0.21
Table S44. Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 6 | 13 | 13 | 9 | 8 | 9 | 8 | 3 |
5Q LOSS MUTATED | 0 | 3 | 1 | 6 | 3 | 0 | 2 | 0 |
5Q LOSS WILD-TYPE | 6 | 10 | 12 | 3 | 5 | 9 | 6 | 3 |
Figure S44. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D51V2.png)
P value = 0.0122 (Fisher's exact test), Q value = 0.21
Table S45. Gene #53: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 9 | 14 | 14 | 13 |
6Q LOSS MUTATED | 0 | 0 | 4 | 0 |
6Q LOSS WILD-TYPE | 9 | 14 | 10 | 13 |
Figure S45. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
![](D53V11.png)
P value = 0.00164 (Fisher's exact test), Q value = 0.079
Table S46. Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 22 | 63 | 56 |
9Q LOSS MUTATED | 9 | 5 | 7 |
9Q LOSS WILD-TYPE | 13 | 58 | 49 |
Figure S46. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D58V10.png)
P value = 0.0141 (Fisher's exact test), Q value = 0.24
Table S47. Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 9 | 13 | 18 | 5 | 5 |
9Q LOSS MUTATED | 5 | 1 | 1 | 1 | 0 |
9Q LOSS WILD-TYPE | 4 | 12 | 17 | 4 | 5 |
Figure S47. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D58V12.png)
P value = 0.0149 (Fisher's exact test), Q value = 0.24
Table S48. Gene #60: '10q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 20 | 20 | 24 | 18 | 29 | 16 |
10Q LOSS MUTATED | 2 | 3 | 10 | 1 | 6 | 7 |
10Q LOSS WILD-TYPE | 18 | 17 | 14 | 17 | 23 | 9 |
Figure S48. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D60V6.png)
P value = 0.00602 (Fisher's exact test), Q value = 0.15
Table S49. Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
11P LOSS MUTATED | 5 | 8 | 1 | 9 |
11P LOSS WILD-TYPE | 61 | 24 | 30 | 27 |
Figure S49. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D61V3.png)
P value = 0.00691 (Fisher's exact test), Q value = 0.16
Table S50. Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
11Q LOSS MUTATED | 9 | 9 | 1 | 11 |
11Q LOSS WILD-TYPE | 57 | 23 | 30 | 25 |
Figure S50. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D62V3.png)
P value = 0.00871 (Fisher's exact test), Q value = 0.17
Table S51. Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 29 | 14 | 33 | 28 | 60 |
11Q LOSS MUTATED | 3 | 5 | 11 | 1 | 10 |
11Q LOSS WILD-TYPE | 26 | 9 | 22 | 27 | 50 |
Figure S51. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D62V7.png)
P value = 0.00761 (Fisher's exact test), Q value = 0.17
Table S52. Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 27 | 36 | 12 | 19 | 32 | 18 | 20 |
11Q LOSS MUTATED | 1 | 11 | 4 | 2 | 2 | 6 | 4 |
11Q LOSS WILD-TYPE | 26 | 25 | 8 | 17 | 30 | 12 | 16 |
Figure S52. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D62V8.png)
P value = 0.00053 (Fisher's exact test), Q value = 0.038
Table S53. Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
15Q LOSS MUTATED | 17 | 21 | 15 | 20 |
15Q LOSS WILD-TYPE | 49 | 11 | 16 | 16 |
Figure S53. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D67V3.png)
P value = 0.00122 (Fisher's exact test), Q value = 0.065
Table S54. Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
18P LOSS MUTATED | 42 | 26 | 30 | 30 |
18P LOSS WILD-TYPE | 24 | 6 | 1 | 6 |
Figure S54. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D72V3.png)
P value = 0.0151 (Fisher's exact test), Q value = 0.24
Table S55. Gene #72: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 27 | 36 | 12 | 19 | 32 | 18 | 20 |
18P LOSS MUTATED | 26 | 27 | 7 | 17 | 25 | 10 | 15 |
18P LOSS WILD-TYPE | 1 | 9 | 5 | 2 | 7 | 8 | 5 |
Figure S55. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D72V8.png)
P value = 3e-05 (Fisher's exact test), Q value = 0.0041
Table S56. Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
18Q LOSS MUTATED | 45 | 28 | 31 | 34 |
18Q LOSS WILD-TYPE | 21 | 4 | 0 | 2 |
Figure S56. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D73V3.png)
P value = 0.0117 (Fisher's exact test), Q value = 0.21
Table S57. Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 28 | 39 | 29 |
18Q LOSS MUTATED | 28 | 30 | 25 |
18Q LOSS WILD-TYPE | 0 | 9 | 4 |
Figure S57. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D73V4.png)
P value = 0.00897 (Fisher's exact test), Q value = 0.18
Table S58. Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 22 | 63 | 56 |
19Q LOSS MUTATED | 7 | 8 | 3 |
19Q LOSS WILD-TYPE | 15 | 55 | 53 |
Figure S58. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D75V10.png)
P value = 0.0145 (Fisher's exact test), Q value = 0.24
Table S59. Gene #76: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 9 | 13 | 18 | 5 | 5 |
20P LOSS MUTATED | 2 | 5 | 0 | 0 | 0 |
20P LOSS WILD-TYPE | 7 | 8 | 18 | 5 | 5 |
Figure S59. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D76V12.png)
P value = 0.0159 (Fisher's exact test), Q value = 0.25
Table S60. Gene #77: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 42 | 17 | 8 | 56 |
21Q LOSS MUTATED | 7 | 22 | 2 | 6 | 24 |
21Q LOSS WILD-TYPE | 11 | 20 | 15 | 2 | 32 |
Figure S60. Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D77V9.png)
P value = 0.00596 (Fisher's exact test), Q value = 0.15
Table S61. Gene #78: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 42 | 17 | 8 | 56 |
22Q LOSS MUTATED | 4 | 24 | 2 | 4 | 20 |
22Q LOSS WILD-TYPE | 14 | 18 | 15 | 4 | 36 |
Figure S61. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D78V9.png)
-
Copy number data file = broad_values_by_arm.txt from GISTIC pipeline
-
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/READ-TP/19781849/transformed.cor.cli.txt
-
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/READ-TP/20140629/READ-TP.transferedmergedcluster.txt
-
Number of patients = 165
-
Number of significantly arm-level cnvs = 80
-
Number of molecular subtypes = 12
-
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.
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.