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, 70 significant findings detected with P value < 0.05 and Q value < 0.25.
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1p gain cnv correlated to 'MRNA_CNMF'.
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1q gain cnv correlated to 'CN_CNMF'.
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2p gain cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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2q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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5p gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
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6p gain cnv correlated to 'CN_CNMF'.
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6q gain cnv correlated to 'CN_CNMF'.
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7p gain cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CHIERARCHICAL', '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' and 'RPPA_CHIERARCHICAL'.
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8q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
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11q gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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13q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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16p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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16q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
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18p gain cnv correlated to 'METHLYATION_CNMF'.
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19p gain cnv correlated to 'CN_CNMF'.
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19q 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 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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1p loss cnv correlated to 'CN_CNMF'.
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1q 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 'CN_CNMF'.
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6q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
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8p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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9q loss cnv correlated to 'MRNA_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
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10q loss cnv correlated to 'MRNA_CNMF' and 'RPPA_CHIERARCHICAL'.
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11p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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11q loss cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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14q loss cnv correlated to 'CN_CNMF'.
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15q loss cnv correlated to 'CN_CNMF'.
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16q loss cnv correlated to 'CN_CNMF'.
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17p 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'.
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19q loss cnv correlated to 'MIRSEQ_CHIERARCHICAL'.
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20p loss cnv correlated to 'CN_CNMF'.
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22q loss cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.
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 |
0.0362 (0.36) |
0.00504 (0.131) |
1e-05 (0.00107) |
0.137 (0.62) |
0.841 (1.00) |
0.0175 (0.241) |
0.00079 (0.033) |
1e-05 (0.00107) |
0.0387 (0.364) |
0.097 (0.523) |
0.597 (0.884) |
0.371 (0.768) |
7q gain | 87 (53%) | 78 |
0.0787 (0.494) |
0.0114 (0.189) |
2e-05 (0.00192) |
0.21 (0.658) |
0.954 (1.00) |
0.0234 (0.28) |
0.00503 (0.131) |
0.00101 (0.0388) |
0.248 (0.68) |
0.486 (0.846) |
1 (1.00) |
0.553 (0.877) |
16q gain | 41 (25%) | 124 |
0.188 (0.658) |
0.509 (0.855) |
1e-05 (0.00107) |
0.0065 (0.152) |
0.698 (0.932) |
0.0499 (0.39) |
0.00939 (0.173) |
0.105 (0.548) |
0.00879 (0.169) |
0.245 (0.678) |
0.59 (0.881) |
0.76 (0.961) |
11q loss | 30 (18%) | 135 |
0.00787 (0.162) |
0.314 (0.715) |
0.00091 (0.0364) |
0.275 (0.687) |
0.944 (1.00) |
0.436 (0.821) |
0.00717 (0.156) |
0.00795 (0.162) |
0.222 (0.659) |
0.377 (0.774) |
0.277 (0.687) |
0.22 (0.659) |
2p gain | 40 (24%) | 125 |
0.758 (0.961) |
0.00736 (0.157) |
0.00021 (0.0134) |
0.0946 (0.52) |
0.547 (0.877) |
0.676 (0.928) |
0.0227 (0.276) |
0.0132 (0.204) |
0.178 (0.658) |
0.0515 (0.395) |
0.667 (0.925) |
0.612 (0.891) |
13q gain | 114 (69%) | 51 |
0.314 (0.715) |
0.299 (0.7) |
1e-05 (0.00107) |
0.0582 (0.419) |
0.562 (0.877) |
0.106 (0.551) |
0.00609 (0.15) |
0.00029 (0.0155) |
0.042 (0.373) |
0.0394 (0.367) |
1 (1.00) |
0.828 (0.997) |
2q gain | 41 (25%) | 124 |
0.365 (0.768) |
0.032 (0.344) |
0.00162 (0.0555) |
0.0287 (0.32) |
0.793 (0.977) |
0.582 (0.881) |
0.0424 (0.373) |
0.00197 (0.0591) |
0.269 (0.687) |
0.235 (0.669) |
0.134 (0.62) |
0.192 (0.658) |
8p gain | 40 (24%) | 125 |
0.448 (0.823) |
0.252 (0.683) |
0.0069 (0.155) |
0.0379 (0.364) |
0.207 (0.658) |
0.00625 (0.15) |
0.579 (0.881) |
0.299 (0.7) |
0.966 (1.00) |
0.0823 (0.497) |
0.827 (0.997) |
0.0529 (0.397) |
8q gain | 90 (55%) | 75 |
0.0884 (0.511) |
0.195 (0.658) |
1e-05 (0.00107) |
0.0213 (0.269) |
0.556 (0.877) |
0.21 (0.658) |
0.372 (0.768) |
0.205 (0.658) |
0.573 (0.88) |
0.0806 (0.496) |
0.0114 (0.189) |
0.499 (0.855) |
11q gain | 27 (16%) | 138 |
0.142 (0.63) |
0.432 (0.817) |
0.0189 (0.251) |
0.121 (0.596) |
0.991 (1.00) |
0.262 (0.687) |
0.00495 (0.131) |
0.0018 (0.0576) |
0.168 (0.658) |
0.443 (0.821) |
0.178 (0.658) |
0.274 (0.687) |
16p gain | 41 (25%) | 124 |
0.453 (0.826) |
0.777 (0.967) |
0.00023 (0.0138) |
0.0161 (0.227) |
0.887 (1.00) |
0.347 (0.757) |
0.127 (0.601) |
0.368 (0.768) |
0.351 (0.757) |
0.678 (0.928) |
0.638 (0.906) |
0.944 (1.00) |
20q gain | 146 (88%) | 19 |
0.126 (0.6) |
0.165 (0.656) |
5e-05 (0.004) |
0.0792 (0.494) |
0.0374 (0.364) |
0.244 (0.678) |
0.609 (0.889) |
0.00072 (0.0314) |
0.332 (0.739) |
0.398 (0.789) |
0.501 (0.855) |
0.695 (0.932) |
6q loss | 23 (14%) | 142 |
0.0503 (0.39) |
0.737 (0.954) |
0.0157 (0.225) |
0.137 (0.62) |
0.206 (0.658) |
0.898 (1.00) |
0.0778 (0.494) |
0.145 (0.632) |
0.142 (0.63) |
0.298 (0.7) |
0.011 (0.189) |
0.483 (0.845) |
8p loss | 75 (45%) | 90 |
0.096 (0.523) |
0.424 (0.814) |
0.00158 (0.0555) |
0.479 (0.842) |
0.17 (0.658) |
0.278 (0.687) |
0.0174 (0.241) |
0.182 (0.658) |
1 (1.00) |
0.852 (1.00) |
0.661 (0.922) |
0.0503 (0.39) |
9q loss | 23 (14%) | 142 |
0.0134 (0.204) |
0.805 (0.978) |
0.286 (0.694) |
0.223 (0.659) |
0.755 (0.961) |
0.948 (1.00) |
0.534 (0.866) |
0.197 (0.658) |
0.667 (0.925) |
0.00191 (0.0591) |
0.76 (0.961) |
0.068 (0.46) |
10q loss | 38 (23%) | 127 |
0.0133 (0.204) |
0.126 (0.6) |
0.0196 (0.251) |
0.087 (0.506) |
0.0924 (0.513) |
0.0156 (0.225) |
0.406 (0.798) |
0.0731 (0.481) |
0.93 (1.00) |
0.0868 (0.506) |
0.89 (1.00) |
0.737 (0.954) |
11p loss | 24 (15%) | 141 |
0.0275 (0.314) |
0.485 (0.846) |
0.00066 (0.0302) |
0.196 (0.658) |
0.589 (0.881) |
0.568 (0.879) |
0.0106 (0.185) |
0.204 (0.658) |
0.913 (1.00) |
0.713 (0.944) |
0.218 (0.658) |
0.229 (0.664) |
18p loss | 128 (78%) | 37 |
0.15 (0.633) |
0.672 (0.926) |
1e-05 (0.00107) |
0.0357 (0.36) |
0.551 (0.877) |
0.316 (0.717) |
0.0809 (0.496) |
0.0141 (0.212) |
0.0845 (0.5) |
0.164 (0.656) |
0.8 (0.978) |
0.833 (1) |
1p gain | 12 (7%) | 153 |
0.00837 (0.167) |
0.609 (0.889) |
0.409 (0.801) |
0.232 (0.664) |
0.251 (0.683) |
0.264 (0.687) |
0.391 (0.782) |
0.594 (0.883) |
1 (1.00) |
0.461 (0.829) |
0.576 (0.881) |
0.586 (0.881) |
1q gain | 33 (20%) | 132 |
0.178 (0.658) |
0.272 (0.687) |
0.012 (0.195) |
0.284 (0.693) |
0.23 (0.664) |
0.179 (0.658) |
0.0774 (0.494) |
0.953 (1.00) |
0.919 (1.00) |
0.841 (1.00) |
1 (1.00) |
0.35 (0.757) |
5p gain | 35 (21%) | 130 |
0.804 (0.978) |
0.119 (0.592) |
0.0195 (0.251) |
0.0841 (0.5) |
0.518 (0.855) |
0.726 (0.947) |
0.11 (0.564) |
0.00042 (0.0202) |
0.479 (0.842) |
1 (1.00) |
0.757 (0.961) |
0.602 (0.884) |
6p gain | 40 (24%) | 125 |
0.153 (0.64) |
0.594 (0.883) |
0.00011 (0.00812) |
0.351 (0.757) |
0.518 (0.855) |
0.329 (0.737) |
0.901 (1.00) |
0.501 (0.855) |
0.16 (0.648) |
0.494 (0.855) |
0.461 (0.829) |
0.962 (1.00) |
6q gain | 35 (21%) | 130 |
0.447 (0.823) |
0.193 (0.658) |
3e-05 (0.00262) |
0.26 (0.687) |
0.631 (0.9) |
0.453 (0.826) |
0.501 (0.855) |
0.53 (0.86) |
0.0529 (0.397) |
0.422 (0.813) |
0.206 (0.658) |
0.558 (0.877) |
18p gain | 8 (5%) | 157 |
0.503 (0.855) |
0.731 (0.949) |
0.261 (0.687) |
0.0127 (0.203) |
0.936 (1.00) |
0.907 (1.00) |
0.878 (1.00) |
0.384 (0.78) |
0.632 (0.9) |
0.558 (0.877) |
1 (1.00) |
1 (1.00) |
19p gain | 33 (20%) | 132 |
0.26 (0.687) |
0.455 (0.827) |
0.00212 (0.0617) |
0.828 (0.997) |
0.984 (1.00) |
0.196 (0.658) |
0.856 (1.00) |
0.0622 (0.433) |
0.882 (1.00) |
0.918 (1.00) |
0.516 (0.855) |
0.277 (0.687) |
19q gain | 33 (20%) | 132 |
0.572 (0.88) |
0.653 (0.915) |
0.0145 (0.214) |
0.289 (0.699) |
0.882 (1.00) |
0.664 (0.924) |
0.803 (0.978) |
0.149 (0.633) |
0.523 (0.855) |
0.496 (0.855) |
0.518 (0.855) |
0.279 (0.687) |
20p gain | 105 (64%) | 60 |
0.355 (0.762) |
0.285 (0.693) |
0.0548 (0.408) |
0.588 (0.881) |
0.00242 (0.0683) |
0.441 (0.821) |
0.216 (0.658) |
0.823 (0.997) |
0.175 (0.658) |
0.148 (0.633) |
0.187 (0.658) |
0.524 (0.856) |
1p loss | 46 (28%) | 119 |
0.384 (0.78) |
0.0694 (0.46) |
0.00134 (0.0495) |
0.213 (0.658) |
0.395 (0.785) |
0.173 (0.658) |
0.252 (0.683) |
0.17 (0.658) |
0.329 (0.737) |
0.61 (0.889) |
0.926 (1.00) |
0.443 (0.821) |
1q loss | 28 (17%) | 137 |
0.651 (0.915) |
0.194 (0.658) |
0.00041 (0.0202) |
0.222 (0.659) |
0.762 (0.961) |
0.151 (0.634) |
0.0336 (0.351) |
0.382 (0.779) |
0.389 (0.781) |
0.372 (0.768) |
0.914 (1.00) |
0.122 (0.597) |
3q loss | 10 (6%) | 155 |
0.504 (0.855) |
0.856 (1.00) |
0.105 (0.548) |
0.154 (0.641) |
0.231 (0.664) |
0.515 (0.855) |
0.21 (0.658) |
0.22 (0.659) |
0.465 (0.829) |
0.0101 (0.184) |
0.293 (0.7) |
0.615 (0.893) |
4p loss | 60 (36%) | 105 |
0.218 (0.658) |
0.5 (0.855) |
0.00027 (0.0152) |
0.559 (0.877) |
0.429 (0.816) |
0.231 (0.664) |
0.685 (0.931) |
0.56 (0.877) |
0.678 (0.928) |
0.1 (0.532) |
0.259 (0.687) |
0.372 (0.768) |
4q loss | 67 (41%) | 98 |
0.463 (0.829) |
0.368 (0.768) |
1e-05 (0.00107) |
0.18 (0.658) |
0.425 (0.814) |
0.0412 (0.373) |
0.764 (0.961) |
0.438 (0.821) |
0.655 (0.915) |
0.217 (0.658) |
0.609 (0.889) |
0.852 (1.00) |
5q loss | 40 (24%) | 125 |
0.0427 (0.373) |
0.0265 (0.311) |
0.0017 (0.0563) |
0.704 (0.938) |
0.731 (0.949) |
0.878 (1.00) |
0.918 (1.00) |
0.221 (0.659) |
0.846 (1.00) |
0.21 (0.658) |
0.272 (0.687) |
0.112 (0.567) |
14q loss | 67 (41%) | 98 |
0.487 (0.846) |
0.187 (0.658) |
1e-05 (0.00107) |
0.123 (0.597) |
0.957 (1.00) |
0.897 (1.00) |
0.364 (0.768) |
0.077 (0.494) |
0.314 (0.715) |
0.199 (0.658) |
0.601 (0.884) |
0.952 (1.00) |
15q loss | 72 (44%) | 93 |
0.0466 (0.389) |
0.15 (0.633) |
0.00014 (0.0096) |
0.864 (1.00) |
0.0989 (0.528) |
0.629 (0.9) |
0.448 (0.823) |
0.404 (0.797) |
0.792 (0.977) |
0.563 (0.877) |
0.845 (1.00) |
0.755 (0.961) |
16q loss | 14 (8%) | 151 |
0.0913 (0.512) |
0.852 (1.00) |
0.00546 (0.138) |
0.937 (1.00) |
0.389 (0.781) |
0.668 (0.925) |
0.251 (0.683) |
0.955 (1.00) |
0.246 (0.678) |
0.858 (1.00) |
0.726 (0.947) |
0.569 (0.88) |
17p loss | 105 (64%) | 60 |
0.562 (0.877) |
0.137 (0.62) |
0.00856 (0.168) |
0.44 (0.821) |
0.573 (0.88) |
0.59 (0.881) |
0.435 (0.821) |
0.566 (0.879) |
0.972 (1.00) |
0.268 (0.687) |
0.519 (0.855) |
0.866 (1.00) |
18q loss | 138 (84%) | 27 |
0.0363 (0.36) |
0.2 (0.658) |
1e-05 (0.00107) |
0.0814 (0.496) |
0.78 (0.97) |
0.138 (0.621) |
0.0321 (0.344) |
0.0194 (0.251) |
0.225 (0.664) |
0.0274 (0.314) |
0.558 (0.877) |
0.824 (0.997) |
19q loss | 22 (13%) | 143 |
0.214 (0.658) |
0.577 (0.881) |
0.309 (0.711) |
0.893 (1.00) |
0.64 (0.906) |
0.68 (0.928) |
0.352 (0.757) |
0.514 (0.855) |
0.0617 (0.433) |
0.00923 (0.173) |
0.763 (0.961) |
0.766 (0.961) |
20p loss | 24 (15%) | 141 |
0.616 (0.893) |
0.702 (0.936) |
0.00696 (0.155) |
0.495 (0.855) |
0.161 (0.648) |
0.889 (1.00) |
0.191 (0.658) |
0.685 (0.931) |
0.774 (0.967) |
0.183 (0.658) |
0.723 (0.947) |
0.179 (0.658) |
22q loss | 58 (35%) | 107 |
0.439 (0.821) |
0.238 (0.671) |
0.11 (0.564) |
0.872 (1.00) |
0.65 (0.914) |
0.297 (0.7) |
0.463 (0.829) |
0.168 (0.658) |
0.322 (0.727) |
0.181 (0.658) |
0.124 (0.6) |
0.0104 (0.185) |
3p gain | 27 (16%) | 138 |
0.457 (0.829) |
0.89 (1.00) |
0.245 (0.678) |
0.233 (0.666) |
0.238 (0.671) |
0.448 (0.823) |
0.177 (0.658) |
0.929 (1.00) |
0.299 (0.7) |
0.359 (0.768) |
0.655 (0.915) |
0.71 (0.943) |
3q gain | 33 (20%) | 132 |
0.73 (0.949) |
0.55 (0.877) |
0.0216 (0.269) |
0.276 (0.687) |
0.392 (0.782) |
0.179 (0.658) |
0.124 (0.6) |
0.732 (0.949) |
0.307 (0.709) |
0.253 (0.683) |
0.627 (0.9) |
0.96 (1.00) |
4p gain | 9 (5%) | 156 |
0.423 (0.814) |
0.941 (1.00) |
0.697 (0.932) |
0.918 (1.00) |
0.0694 (0.46) |
0.0323 (0.344) |
0.513 (0.855) |
0.63 (0.9) |
0.184 (0.658) |
0.374 (0.77) |
0.726 (0.947) |
0.913 (1.00) |
4q gain | 5 (3%) | 160 |
0.277 (0.687) |
0.783 (0.971) |
0.686 (0.931) |
0.0453 (0.384) |
0.161 (0.648) |
0.621 (0.897) |
1 (1.00) |
0.845 (1.00) |
1 (1.00) |
|||
5q gain | 24 (15%) | 141 |
0.269 (0.687) |
0.036 (0.36) |
0.211 (0.658) |
0.348 (0.757) |
0.429 (0.816) |
0.604 (0.886) |
0.48 (0.842) |
0.0903 (0.512) |
1 (1.00) |
0.523 (0.855) |
1 (1.00) |
0.481 (0.842) |
9p gain | 43 (26%) | 122 |
0.189 (0.658) |
0.387 (0.78) |
0.0478 (0.39) |
0.0326 (0.344) |
0.441 (0.821) |
0.191 (0.658) |
0.0565 (0.414) |
0.297 (0.7) |
0.191 (0.658) |
0.217 (0.658) |
0.959 (1.00) |
0.745 (0.96) |
9q gain | 35 (21%) | 130 |
0.469 (0.832) |
0.526 (0.858) |
0.21 (0.658) |
0.0918 (0.512) |
0.19 (0.658) |
0.0988 (0.528) |
0.335 (0.744) |
0.302 (0.703) |
0.599 (0.884) |
0.589 (0.881) |
0.864 (1.00) |
0.841 (1.00) |
10p gain | 12 (7%) | 153 |
0.716 (0.946) |
0.159 (0.648) |
0.428 (0.816) |
0.27 (0.687) |
0.368 (0.768) |
0.894 (1.00) |
0.142 (0.63) |
0.203 (0.658) |
0.83 (0.999) |
1 (1.00) |
0.842 (1.00) |
0.694 (0.932) |
10q gain | 7 (4%) | 158 |
0.276 (0.687) |
0.166 (0.658) |
0.255 (0.686) |
0.794 (0.977) |
0.452 (0.826) |
0.712 (0.944) |
0.832 (1) |
0.501 (0.855) |
0.639 (0.906) |
0.861 (1.00) |
||
11p gain | 32 (19%) | 133 |
0.0948 (0.52) |
0.43 (0.816) |
0.112 (0.567) |
0.416 (0.812) |
0.989 (1.00) |
0.751 (0.961) |
0.187 (0.658) |
0.146 (0.632) |
0.085 (0.5) |
0.208 (0.658) |
0.263 (0.687) |
0.718 (0.946) |
12p gain | 33 (20%) | 132 |
0.21 (0.658) |
0.136 (0.62) |
0.188 (0.658) |
0.246 (0.678) |
0.161 (0.648) |
0.692 (0.932) |
0.0437 (0.378) |
0.201 (0.658) |
0.765 (0.961) |
0.549 (0.877) |
0.312 (0.715) |
0.67 (0.926) |
12q gain | 21 (13%) | 144 |
0.205 (0.658) |
0.265 (0.687) |
0.96 (1.00) |
0.66 (0.921) |
0.274 (0.687) |
0.548 (0.877) |
0.028 (0.316) |
0.387 (0.78) |
0.347 (0.757) |
0.802 (0.978) |
0.156 (0.644) |
1 (1.00) |
14q gain | 8 (5%) | 157 |
0.601 (0.884) |
0.687 (0.931) |
0.0969 (0.523) |
0.253 (0.683) |
0.722 (0.947) |
0.861 (1.00) |
0.473 (0.837) |
0.912 (1.00) |
0.64 (0.906) |
0.861 (1.00) |
||
15q gain | 4 (2%) | 161 |
0.293 (0.7) |
0.102 (0.54) |
0.506 (0.855) |
1 (1.00) |
0.539 (0.871) |
0.599 (0.884) |
0.392 (0.782) |
0.761 (0.961) |
||||
17p gain | 10 (6%) | 155 |
0.0252 (0.298) |
0.0816 (0.496) |
0.586 (0.881) |
0.182 (0.658) |
0.925 (1.00) |
0.468 (0.832) |
0.427 (0.816) |
0.422 (0.813) |
0.275 (0.687) |
0.332 (0.739) |
||
17q gain | 31 (19%) | 134 |
0.754 (0.961) |
0.697 (0.932) |
0.0194 (0.251) |
0.256 (0.686) |
0.798 (0.978) |
0.28 (0.687) |
0.783 (0.971) |
0.221 (0.659) |
0.8 (0.978) |
0.277 (0.687) |
0.389 (0.781) |
0.37 (0.768) |
18q gain | 6 (4%) | 159 |
0.464 (0.829) |
0.0325 (0.344) |
0.863 (1.00) |
0.587 (0.881) |
0.648 (0.914) |
0.229 (0.664) |
0.555 (0.877) |
0.627 (0.9) |
1 (1.00) |
1 (1.00) |
||
21q gain | 10 (6%) | 155 |
0.048 (0.39) |
0.992 (1.00) |
0.116 (0.581) |
0.565 (0.879) |
0.0785 (0.494) |
0.304 (0.704) |
0.451 (0.826) |
0.921 (1.00) |
1 (1.00) |
0.726 (0.947) |
||
22q gain | 9 (5%) | 156 |
0.228 (0.664) |
0.0491 (0.39) |
0.0674 (0.459) |
0.546 (0.877) |
0.0905 (0.512) |
0.936 (1.00) |
0.366 (0.768) |
0.197 (0.658) |
0.873 (1.00) |
1 (1.00) |
||
xp gain | 31 (19%) | 134 |
0.041 (0.373) |
0.137 (0.62) |
0.133 (0.62) |
0.52 (0.855) |
0.514 (0.855) |
0.942 (1.00) |
0.3 (0.7) |
0.573 (0.88) |
0.643 (0.908) |
0.763 (0.961) |
0.344 (0.757) |
0.405 (0.798) |
xq gain | 32 (19%) | 133 |
0.293 (0.7) |
0.509 (0.855) |
0.198 (0.658) |
0.52 (0.855) |
0.134 (0.62) |
0.68 (0.928) |
0.0572 (0.416) |
0.642 (0.908) |
0.596 (0.884) |
0.805 (0.978) |
0.237 (0.671) |
0.3 (0.7) |
2p loss | 11 (7%) | 154 |
0.18 (0.658) |
0.516 (0.855) |
0.12 (0.596) |
0.757 (0.961) |
0.592 (0.882) |
0.402 (0.795) |
0.478 (0.842) |
0.0593 (0.422) |
0.421 (0.813) |
0.605 (0.887) |
||
2q loss | 7 (4%) | 158 |
0.362 (0.768) |
0.157 (0.646) |
0.204 (0.658) |
0.278 (0.687) |
0.521 (0.855) |
0.468 (0.832) |
0.0501 (0.39) |
0.0645 (0.442) |
0.266 (0.687) |
|||
3p loss | 15 (9%) | 150 |
0.889 (1.00) |
0.797 (0.978) |
0.0627 (0.433) |
0.126 (0.6) |
0.243 (0.678) |
0.218 (0.658) |
0.245 (0.678) |
0.556 (0.877) |
0.478 (0.842) |
0.135 (0.62) |
0.0627 (0.433) |
0.113 (0.567) |
5p loss | 27 (16%) | 138 |
0.0738 (0.482) |
0.924 (1.00) |
0.052 (0.396) |
0.581 (0.881) |
0.406 (0.798) |
0.823 (0.997) |
0.87 (1.00) |
0.247 (0.68) |
0.301 (0.7) |
0.679 (0.928) |
0.347 (0.757) |
0.0384 (0.364) |
6p loss | 14 (8%) | 151 |
0.381 (0.779) |
0.418 (0.813) |
0.37 (0.768) |
0.149 (0.633) |
0.385 (0.78) |
0.694 (0.932) |
0.624 (0.9) |
0.167 (0.658) |
0.859 (1.00) |
0.578 (0.881) |
||
7q loss | 3 (2%) | 162 |
0.11 (0.564) |
0.718 (0.946) |
0.439 (0.821) |
0.0455 (0.384) |
0.76 (0.961) |
0.773 (0.967) |
1 (1.00) |
|||||
8q loss | 10 (6%) | 155 |
1 (1.00) |
0.446 (0.823) |
0.415 (0.812) |
0.161 (0.648) |
0.761 (0.961) |
0.145 (0.632) |
0.585 (0.881) |
0.339 (0.751) |
0.903 (1.00) |
0.421 (0.813) |
0.0913 (0.512) |
0.367 (0.768) |
9p loss | 23 (14%) | 142 |
0.0343 (0.354) |
0.933 (1.00) |
0.495 (0.855) |
0.316 (0.717) |
0.707 (0.94) |
0.81 (0.984) |
0.458 (0.829) |
0.513 (0.855) |
0.905 (1.00) |
0.0474 (0.39) |
0.91 (1.00) |
0.149 (0.633) |
10p loss | 34 (21%) | 131 |
0.149 (0.633) |
0.0687 (0.46) |
0.0382 (0.364) |
0.0499 (0.39) |
0.0906 (0.512) |
0.0442 (0.379) |
0.306 (0.708) |
0.574 (0.88) |
0.789 (0.976) |
0.137 (0.62) |
0.845 (1.00) |
0.883 (1.00) |
12p loss | 23 (14%) | 142 |
0.554 (0.877) |
0.626 (0.9) |
0.18 (0.658) |
0.28 (0.687) |
0.918 (1.00) |
0.567 (0.879) |
0.695 (0.932) |
0.34 (0.751) |
0.486 (0.846) |
0.776 (0.967) |
0.145 (0.632) |
0.617 (0.893) |
12q loss | 24 (15%) | 141 |
0.585 (0.881) |
0.631 (0.9) |
0.0403 (0.372) |
0.38 (0.779) |
0.34 (0.751) |
0.837 (1.00) |
0.786 (0.974) |
0.28 (0.687) |
0.269 (0.687) |
0.269 (0.687) |
0.774 (0.967) |
1 (1.00) |
13q loss | 6 (4%) | 159 |
0.0419 (0.373) |
0.228 (0.664) |
0.285 (0.693) |
0.754 (0.961) |
1 (1.00) |
0.348 (0.757) |
0.74 (0.956) |
0.861 (1.00) |
||||
16p loss | 9 (5%) | 156 |
0.215 (0.658) |
0.893 (1.00) |
0.229 (0.664) |
0.284 (0.693) |
0.356 (0.764) |
0.517 (0.855) |
0.175 (0.658) |
0.912 (1.00) |
0.561 (0.877) |
1 (1.00) |
0.653 (0.915) |
0.535 (0.867) |
17q loss | 28 (17%) | 137 |
0.674 (0.927) |
0.665 (0.924) |
0.0559 (0.413) |
0.462 (0.829) |
0.672 (0.926) |
0.238 (0.671) |
0.352 (0.757) |
0.362 (0.768) |
0.529 (0.86) |
0.547 (0.877) |
0.33 (0.738) |
1 (1.00) |
19p loss | 24 (15%) | 141 |
0.51 (0.855) |
0.835 (1.00) |
0.0585 (0.419) |
0.957 (1.00) |
0.718 (0.946) |
0.854 (1.00) |
0.325 (0.733) |
0.296 (0.7) |
0.293 (0.7) |
0.0223 (0.275) |
0.562 (0.877) |
0.689 (0.932) |
21q loss | 68 (41%) | 97 |
0.174 (0.658) |
0.367 (0.768) |
0.42 (0.813) |
0.964 (1.00) |
0.382 (0.779) |
0.744 (0.96) |
0.931 (1.00) |
0.691 (0.932) |
0.589 (0.881) |
0.182 (0.658) |
0.208 (0.658) |
0.0793 (0.494) |
xp loss | 28 (17%) | 137 |
0.916 (1.00) |
0.75 (0.961) |
0.0845 (0.5) |
0.216 (0.658) |
0.436 (0.821) |
0.297 (0.7) |
0.791 (0.977) |
0.693 (0.932) |
0.804 (0.978) |
0.459 (0.829) |
0.942 (1.00) |
0.774 (0.967) |
xq loss | 26 (16%) | 139 |
0.983 (1.00) |
0.523 (0.855) |
0.191 (0.658) |
0.214 (0.658) |
0.884 (1.00) |
0.63 (0.9) |
0.723 (0.947) |
0.884 (1.00) |
0.87 (1.00) |
0.31 (0.712) |
0.863 (1.00) |
0.859 (1.00) |
P value = 0.00837 (Fisher's exact test), Q value = 0.17
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 13 | 8 | 20 | 13 | 15 |
1P GAIN MUTATED | 0 | 3 | 2 | 0 | 0 |
1P GAIN WILD-TYPE | 13 | 5 | 18 | 13 | 15 |
P value = 0.012 (Fisher's exact test), Q value = 0.19
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
1Q GAIN MUTATED | 5 | 4 | 7 | 15 | 2 |
1Q GAIN WILD-TYPE | 21 | 36 | 20 | 27 | 28 |
P value = 0.00736 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 6 | 10 | 7 | 9 | 9 | 8 | 9 | 8 | 3 |
2P GAIN MUTATED | 3 | 0 | 0 | 1 | 0 | 3 | 0 | 3 | 0 |
2P GAIN WILD-TYPE | 3 | 10 | 7 | 8 | 9 | 5 | 9 | 5 | 3 |
P value = 0.00021 (Fisher's exact test), Q value = 0.013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
2P GAIN MUTATED | 9 | 19 | 2 | 8 | 2 |
2P GAIN WILD-TYPE | 17 | 21 | 25 | 34 | 28 |
P value = 0.0132 (Fisher's exact test), Q value = 0.2
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 27 | 36 | 12 | 19 | 32 | 18 | 20 |
2P GAIN MUTATED | 12 | 8 | 2 | 7 | 7 | 0 | 3 |
2P GAIN WILD-TYPE | 15 | 28 | 10 | 12 | 25 | 18 | 17 |
P value = 0.00162 (Fisher's exact test), Q value = 0.056
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
2Q GAIN MUTATED | 7 | 19 | 5 | 8 | 2 |
2Q GAIN WILD-TYPE | 19 | 21 | 22 | 34 | 28 |
P value = 0.00197 (Fisher's exact test), Q value = 0.059
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 | 9 | 0 | 3 |
2Q GAIN WILD-TYPE | 13 | 30 | 10 | 13 | 23 | 18 | 17 |
P value = 0.00042 (Fisher's exact test), Q value = 0.02
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 | 8 | 2 | 10 | 2 | 3 |
5P GAIN WILD-TYPE | 19 | 34 | 4 | 17 | 22 | 16 | 17 |
P value = 0.00011 (Fisher's exact test), Q value = 0.0081
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
6P GAIN MUTATED | 9 | 12 | 13 | 5 | 1 |
6P GAIN WILD-TYPE | 17 | 28 | 14 | 37 | 29 |
P value = 3e-05 (Fisher's exact test), Q value = 0.0026
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
6Q GAIN MUTATED | 6 | 13 | 13 | 3 | 0 |
6Q GAIN WILD-TYPE | 20 | 27 | 14 | 39 | 30 |
P value = 0.00504 (Fisher's exact test), Q value = 0.13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 6 | 10 | 7 | 9 | 9 | 8 | 9 | 8 | 3 |
7P GAIN MUTATED | 1 | 6 | 2 | 2 | 7 | 7 | 5 | 7 | 0 |
7P GAIN WILD-TYPE | 5 | 4 | 5 | 7 | 2 | 1 | 4 | 1 | 3 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
7P GAIN MUTATED | 12 | 35 | 21 | 25 | 9 |
7P GAIN WILD-TYPE | 14 | 5 | 6 | 17 | 21 |
P value = 0.0175 (Fisher's exact test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 20 | 20 | 24 | 18 | 29 | 16 |
7P GAIN MUTATED | 14 | 13 | 17 | 9 | 13 | 15 |
7P GAIN WILD-TYPE | 6 | 7 | 7 | 9 | 16 | 1 |
P value = 0.00079 (Fisher's exact test), Q value = 0.033
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 14 | 33 | 28 | 57 |
7P GAIN MUTATED | 26 | 7 | 13 | 23 | 32 |
7P GAIN WILD-TYPE | 6 | 7 | 20 | 5 | 25 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0011
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 |
P value = 0.0114 (Fisher's exact test), Q value = 0.19
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 6 | 10 | 7 | 9 | 9 | 8 | 9 | 8 | 3 |
7Q GAIN MUTATED | 1 | 6 | 2 | 2 | 5 | 7 | 4 | 7 | 0 |
7Q GAIN WILD-TYPE | 5 | 4 | 5 | 7 | 4 | 1 | 5 | 1 | 3 |
P value = 2e-05 (Fisher's exact test), Q value = 0.0019
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
7Q GAIN MUTATED | 8 | 30 | 20 | 21 | 8 |
7Q GAIN WILD-TYPE | 18 | 10 | 7 | 21 | 22 |
P value = 0.00503 (Fisher's exact test), Q value = 0.13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 14 | 33 | 28 | 57 |
7Q GAIN MUTATED | 19 | 5 | 11 | 22 | 29 |
7Q GAIN WILD-TYPE | 13 | 9 | 22 | 6 | 28 |
P value = 0.00101 (Fisher's exact test), Q value = 0.039
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 | 13 | 19 | 3 | 12 |
7Q GAIN WILD-TYPE | 8 | 24 | 4 | 6 | 13 | 15 | 8 |
P value = 0.0069 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
8P GAIN MUTATED | 5 | 10 | 8 | 16 | 1 |
8P GAIN WILD-TYPE | 21 | 30 | 19 | 26 | 29 |
P value = 0.00625 (Fisher's exact test), Q value = 0.15
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 20 | 20 | 24 | 18 | 29 | 16 |
8P GAIN MUTATED | 3 | 2 | 11 | 9 | 4 | 5 |
8P GAIN WILD-TYPE | 17 | 18 | 13 | 9 | 25 | 11 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
8Q GAIN MUTATED | 16 | 22 | 12 | 37 | 3 |
8Q GAIN WILD-TYPE | 10 | 18 | 15 | 5 | 27 |
P value = 0.0114 (Fisher's exact test), Q value = 0.19
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 17 | 14 | 13 | 6 |
8Q GAIN MUTATED | 12 | 14 | 7 | 3 |
8Q GAIN WILD-TYPE | 5 | 0 | 6 | 3 |
P value = 0.00495 (Fisher's exact test), Q value = 0.13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 14 | 33 | 28 | 57 |
11Q GAIN MUTATED | 7 | 2 | 0 | 9 | 9 |
11Q GAIN WILD-TYPE | 25 | 12 | 33 | 19 | 48 |
P value = 0.0018 (Fisher's exact test), Q value = 0.058
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 | 2 | 0 | 7 | 7 | 1 | 1 |
11Q GAIN WILD-TYPE | 18 | 34 | 12 | 12 | 25 | 17 | 19 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
13Q GAIN MUTATED | 17 | 33 | 26 | 27 | 11 |
13Q GAIN WILD-TYPE | 9 | 7 | 1 | 15 | 19 |
P value = 0.00609 (Fisher's exact test), Q value = 0.15
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 14 | 33 | 28 | 57 |
13Q GAIN MUTATED | 22 | 11 | 17 | 26 | 37 |
13Q GAIN WILD-TYPE | 10 | 3 | 16 | 2 | 20 |
P value = 0.00029 (Fisher's exact test), Q value = 0.015
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 | 22 | 25 | 7 | 17 | 25 | 4 | 13 |
13Q GAIN WILD-TYPE | 5 | 11 | 5 | 2 | 7 | 14 | 7 |
P value = 0.00023 (Fisher's exact test), Q value = 0.014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
16P GAIN MUTATED | 3 | 16 | 12 | 9 | 1 |
16P GAIN WILD-TYPE | 23 | 24 | 15 | 33 | 29 |
P value = 0.0161 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 14 | 23 | 17 | 25 | 17 |
16P GAIN MUTATED | 0 | 5 | 9 | 7 | 4 |
16P GAIN WILD-TYPE | 14 | 18 | 8 | 18 | 13 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
16Q GAIN MUTATED | 4 | 16 | 14 | 7 | 0 |
16Q GAIN WILD-TYPE | 22 | 24 | 13 | 35 | 30 |
P value = 0.0065 (Fisher's exact test), Q value = 0.15
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 14 | 23 | 17 | 25 | 17 |
16Q GAIN MUTATED | 0 | 6 | 10 | 7 | 4 |
16Q GAIN WILD-TYPE | 14 | 17 | 7 | 18 | 13 |
P value = 0.00939 (Fisher's exact test), Q value = 0.17
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 14 | 33 | 28 | 57 |
16Q GAIN MUTATED | 13 | 1 | 4 | 11 | 11 |
16Q GAIN WILD-TYPE | 19 | 13 | 29 | 17 | 46 |
P value = 0.00879 (Fisher's exact test), Q value = 0.17
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 24 | 55 | 62 |
16Q GAIN MUTATED | 11 | 15 | 9 |
16Q GAIN WILD-TYPE | 13 | 40 | 53 |
P value = 0.0127 (Fisher's exact test), Q value = 0.2
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 14 | 23 | 17 | 25 | 17 |
18P GAIN MUTATED | 2 | 0 | 0 | 0 | 3 |
18P GAIN WILD-TYPE | 12 | 23 | 17 | 25 | 14 |
P value = 0.00212 (Fisher's exact test), Q value = 0.062
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
19P GAIN MUTATED | 5 | 17 | 3 | 6 | 2 |
19P GAIN WILD-TYPE | 21 | 23 | 24 | 36 | 28 |
P value = 0.0145 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
19Q GAIN MUTATED | 5 | 15 | 6 | 5 | 2 |
19Q GAIN WILD-TYPE | 21 | 25 | 21 | 37 | 28 |
P value = 0.00242 (Fisher's exact test), Q value = 0.068
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 42 | 27 | 25 | 30 | 3 |
20P GAIN MUTATED | 33 | 21 | 12 | 13 | 1 |
20P GAIN WILD-TYPE | 9 | 6 | 13 | 17 | 2 |
P value = 5e-05 (Fisher's exact test), Q value = 0.004
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
20Q GAIN MUTATED | 24 | 40 | 27 | 35 | 20 |
20Q GAIN WILD-TYPE | 2 | 0 | 0 | 7 | 10 |
P value = 0.00072 (Fisher's exact test), Q value = 0.031
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 | 31 | 10 | 18 |
20Q GAIN WILD-TYPE | 1 | 3 | 3 | 1 | 1 | 8 | 2 |
P value = 0.00134 (Fisher's exact test), Q value = 0.049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
1P LOSS MUTATED | 10 | 16 | 10 | 9 | 1 |
1P LOSS WILD-TYPE | 16 | 24 | 17 | 33 | 29 |
P value = 0.00041 (Fisher's exact test), Q value = 0.02
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
1Q LOSS MUTATED | 8 | 12 | 5 | 3 | 0 |
1Q LOSS WILD-TYPE | 18 | 28 | 22 | 39 | 30 |
P value = 0.0101 (Fisher's exact test), Q value = 0.18
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 22 | 63 | 56 |
3Q LOSS MUTATED | 5 | 4 | 1 |
3Q LOSS WILD-TYPE | 17 | 59 | 55 |
P value = 0.00027 (Fisher's exact test), Q value = 0.015
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
4P LOSS MUTATED | 13 | 15 | 16 | 14 | 2 |
4P LOSS WILD-TYPE | 13 | 25 | 11 | 28 | 28 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
4Q LOSS MUTATED | 15 | 17 | 18 | 15 | 2 |
4Q LOSS WILD-TYPE | 11 | 23 | 9 | 27 | 28 |
P value = 0.0017 (Fisher's exact test), Q value = 0.056
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
5Q LOSS MUTATED | 7 | 10 | 9 | 14 | 0 |
5Q LOSS WILD-TYPE | 19 | 30 | 18 | 28 | 30 |
P value = 0.0157 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
6Q LOSS MUTATED | 4 | 2 | 1 | 12 | 4 |
6Q LOSS WILD-TYPE | 22 | 38 | 26 | 30 | 26 |
P value = 0.011 (Fisher's exact test), Q value = 0.19
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 17 | 14 | 13 | 6 |
6Q LOSS MUTATED | 0 | 4 | 0 | 0 |
6Q LOSS WILD-TYPE | 17 | 10 | 13 | 6 |
P value = 0.00158 (Fisher's exact test), Q value = 0.056
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
8P LOSS MUTATED | 12 | 22 | 13 | 24 | 4 |
8P LOSS WILD-TYPE | 14 | 18 | 14 | 18 | 26 |
P value = 0.0174 (Fisher's exact test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 14 | 33 | 28 | 57 |
8P LOSS MUTATED | 14 | 6 | 7 | 14 | 33 |
8P LOSS WILD-TYPE | 18 | 8 | 26 | 14 | 24 |
P value = 0.0134 (Fisher's exact test), Q value = 0.2
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 13 | 8 | 20 | 13 | 15 |
9Q LOSS MUTATED | 0 | 0 | 8 | 1 | 2 |
9Q LOSS WILD-TYPE | 13 | 8 | 12 | 12 | 13 |
P value = 0.00191 (Fisher's exact test), Q value = 0.059
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 22 | 63 | 56 |
9Q LOSS MUTATED | 9 | 5 | 7 |
9Q LOSS WILD-TYPE | 13 | 58 | 49 |
P value = 0.0133 (Fisher's exact test), Q value = 0.2
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 13 | 8 | 20 | 13 | 15 |
10Q LOSS MUTATED | 3 | 5 | 4 | 3 | 0 |
10Q LOSS WILD-TYPE | 10 | 3 | 16 | 10 | 15 |
P value = 0.0156 (Fisher's exact test), Q value = 0.23
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 |
P value = 0.00066 (Fisher's exact test), Q value = 0.03
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
11P LOSS MUTATED | 2 | 1 | 10 | 9 | 2 |
11P LOSS WILD-TYPE | 24 | 39 | 17 | 33 | 28 |
P value = 0.0106 (Fisher's exact test), Q value = 0.18
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 14 | 33 | 28 | 57 |
11P LOSS MUTATED | 4 | 4 | 9 | 0 | 7 |
11P LOSS WILD-TYPE | 28 | 10 | 24 | 28 | 50 |
P value = 0.00787 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 13 | 8 | 20 | 13 | 15 |
11Q LOSS MUTATED | 2 | 5 | 3 | 2 | 0 |
11Q LOSS WILD-TYPE | 11 | 3 | 17 | 11 | 15 |
P value = 0.00091 (Fisher's exact test), Q value = 0.036
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
11Q LOSS MUTATED | 4 | 1 | 10 | 12 | 3 |
11Q LOSS WILD-TYPE | 22 | 39 | 17 | 30 | 27 |
P value = 0.00717 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 14 | 33 | 28 | 57 |
11Q LOSS MUTATED | 3 | 5 | 11 | 1 | 10 |
11Q LOSS WILD-TYPE | 29 | 9 | 22 | 27 | 47 |
P value = 0.00795 (Fisher's exact test), Q value = 0.16
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 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
14Q LOSS MUTATED | 15 | 24 | 15 | 11 | 2 |
14Q LOSS WILD-TYPE | 11 | 16 | 12 | 31 | 28 |
P value = 0.00014 (Fisher's exact test), Q value = 0.0096
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
15Q LOSS MUTATED | 13 | 20 | 14 | 23 | 2 |
15Q LOSS WILD-TYPE | 13 | 20 | 13 | 19 | 28 |
P value = 0.00546 (Fisher's exact test), Q value = 0.14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
16Q LOSS MUTATED | 3 | 1 | 0 | 9 | 1 |
16Q LOSS WILD-TYPE | 23 | 39 | 27 | 33 | 29 |
P value = 0.00856 (Fisher's exact test), Q value = 0.17
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
17P LOSS MUTATED | 18 | 24 | 20 | 32 | 11 |
17P LOSS WILD-TYPE | 8 | 16 | 7 | 10 | 19 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
18P LOSS MUTATED | 20 | 39 | 23 | 34 | 12 |
18P LOSS WILD-TYPE | 6 | 1 | 4 | 8 | 18 |
P value = 0.0141 (Fisher's exact test), Q value = 0.21
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 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
18Q LOSS MUTATED | 21 | 40 | 24 | 39 | 14 |
18Q LOSS WILD-TYPE | 5 | 0 | 3 | 3 | 16 |
P value = 0.00923 (Fisher's exact test), Q value = 0.17
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 22 | 63 | 56 |
19Q LOSS MUTATED | 7 | 10 | 3 |
19Q LOSS WILD-TYPE | 15 | 53 | 53 |
P value = 0.00696 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 26 | 40 | 27 | 42 | 30 |
20P LOSS MUTATED | 0 | 9 | 4 | 10 | 1 |
20P LOSS WILD-TYPE | 26 | 31 | 23 | 32 | 29 |
P value = 0.0104 (Fisher's exact test), Q value = 0.18
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 12 | 16 | 6 | 5 |
22Q LOSS MUTATED | 9 | 3 | 8 | 2 | 0 |
22Q LOSS WILD-TYPE | 2 | 9 | 8 | 4 | 5 |
-
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/22532765/transformed.cor.cli.txt
-
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/READ-TP/22541962/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.