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 8 molecular subtypes across 90 patients, 54 significant findings detected with P value < 0.05 and Q value < 0.25.
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2p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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4p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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4q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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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' and 'MRNASEQ_CHIERARCHICAL'.
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7p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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7q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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9p gain cnv correlated to 'CN_CNMF'.
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9q gain cnv correlated to 'CN_CNMF'.
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10p gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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10q gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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12p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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12q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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14q gain cnv correlated to 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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16p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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16q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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19p gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
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19q gain cnv correlated to 'MRNASEQ_CNMF'.
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20p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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20q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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xq gain cnv correlated to 'CN_CNMF'.
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2q loss cnv correlated to 'CN_CNMF'.
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9p loss cnv correlated to 'MRNASEQ_CNMF'.
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11q loss cnv correlated to 'CN_CNMF'.
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17p loss cnv correlated to 'METHLYATION_CNMF'.
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17q loss cnv correlated to 'CN_CNMF'.
Clinical Features |
CN CNMF |
METHLYATION CNMF |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
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nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
14q gain | 21 (23%) | 69 |
0.0141 (1.00) |
0.0557 (1.00) |
0.00038 (0.208) |
0.00082 (0.44) |
2e-05 (0.0117) |
0.00014 (0.0784) |
2e-05 (0.0117) |
2e-05 (0.0117) |
20p gain | 46 (51%) | 44 |
1e-05 (0.00598) |
0.236 (1.00) |
9e-05 (0.0509) |
0.00014 (0.0784) |
0.00495 (1.00) |
0.0912 (1.00) |
0.00013 (0.0729) |
0.00372 (1.00) |
4p gain | 37 (41%) | 53 |
3e-05 (0.0174) |
0.0438 (1.00) |
5e-05 (0.0287) |
5e-05 (0.0287) |
0.295 (1.00) |
0.00193 (0.998) |
0.688 (1.00) |
0.146 (1.00) |
4q gain | 33 (37%) | 57 |
7e-05 (0.0399) |
0.0363 (1.00) |
3e-05 (0.0174) |
1e-05 (0.00598) |
0.559 (1.00) |
0.00082 (0.44) |
0.588 (1.00) |
0.0892 (1.00) |
7q gain | 48 (53%) | 42 |
2e-05 (0.0117) |
0.116 (1.00) |
1e-05 (0.00598) |
0.0001 (0.0565) |
0.915 (1.00) |
0.331 (1.00) |
1 (1.00) |
0.18 (1.00) |
12p gain | 64 (71%) | 26 |
2e-05 (0.0117) |
0.209 (1.00) |
0.00022 (0.122) |
5e-05 (0.0287) |
0.246 (1.00) |
0.209 (1.00) |
0.0698 (1.00) |
0.12 (1.00) |
16p gain | 49 (54%) | 41 |
1e-05 (0.00598) |
0.0107 (1.00) |
1e-05 (0.00598) |
1e-05 (0.00598) |
0.0466 (1.00) |
0.0262 (1.00) |
0.0122 (1.00) |
0.169 (1.00) |
16q gain | 47 (52%) | 43 |
1e-05 (0.00598) |
0.00825 (1.00) |
0.00012 (0.0676) |
1e-05 (0.00598) |
0.024 (1.00) |
0.0131 (1.00) |
0.0118 (1.00) |
0.144 (1.00) |
20q gain | 49 (54%) | 41 |
2e-05 (0.0117) |
0.0649 (1.00) |
7e-05 (0.0399) |
0.00025 (0.138) |
0.0194 (1.00) |
0.275 (1.00) |
0.00098 (0.522) |
0.0334 (1.00) |
2p gain | 13 (14%) | 77 |
0.00026 (0.143) |
0.00112 (0.594) |
0.0118 (1.00) |
0.00014 (0.0784) |
0.373 (1.00) |
0.0185 (1.00) |
0.0799 (1.00) |
0.0468 (1.00) |
5p gain | 57 (63%) | 33 |
1e-05 (0.00598) |
0.0365 (1.00) |
0.00058 (0.314) |
1e-05 (0.00598) |
0.251 (1.00) |
0.227 (1.00) |
0.0674 (1.00) |
0.342 (1.00) |
5q gain | 53 (59%) | 37 |
3e-05 (0.0174) |
0.00886 (1.00) |
0.00071 (0.383) |
3e-05 (0.0174) |
0.334 (1.00) |
0.135 (1.00) |
0.37 (1.00) |
0.388 (1.00) |
7p gain | 48 (53%) | 42 |
0.00042 (0.23) |
0.118 (1.00) |
0.00012 (0.0676) |
0.00133 (0.698) |
0.914 (1.00) |
0.55 (1.00) |
0.874 (1.00) |
0.314 (1.00) |
10p gain | 25 (28%) | 65 |
0.00079 (0.424) |
0.0588 (1.00) |
3e-05 (0.0174) |
0.00019 (0.106) |
0.0337 (1.00) |
0.511 (1.00) |
0.104 (1.00) |
0.667 (1.00) |
10q gain | 26 (29%) | 64 |
0.00057 (0.309) |
0.0712 (1.00) |
4e-05 (0.023) |
0.00045 (0.246) |
0.0203 (1.00) |
0.34 (1.00) |
0.0698 (1.00) |
0.651 (1.00) |
12q gain | 64 (71%) | 26 |
1e-05 (0.00598) |
0.311 (1.00) |
0.00068 (0.367) |
0.00014 (0.0784) |
0.236 (1.00) |
0.455 (1.00) |
0.0425 (1.00) |
0.207 (1.00) |
9p gain | 20 (22%) | 70 |
7e-05 (0.0399) |
0.0023 (1.00) |
0.00932 (1.00) |
0.0112 (1.00) |
0.385 (1.00) |
0.55 (1.00) |
0.237 (1.00) |
0.63 (1.00) |
9q gain | 29 (32%) | 61 |
0.00019 (0.106) |
0.00121 (0.639) |
0.023 (1.00) |
0.00169 (0.879) |
0.0342 (1.00) |
0.354 (1.00) |
0.0172 (1.00) |
0.36 (1.00) |
19p gain | 56 (62%) | 34 |
0.00757 (1.00) |
0.0549 (1.00) |
0.00133 (0.698) |
0.00045 (0.246) |
0.466 (1.00) |
0.471 (1.00) |
0.37 (1.00) |
0.626 (1.00) |
19q gain | 52 (58%) | 38 |
0.00051 (0.277) |
0.0498 (1.00) |
0.00036 (0.198) |
0.00114 (0.603) |
0.143 (1.00) |
0.11 (1.00) |
0.101 (1.00) |
0.192 (1.00) |
xq gain | 40 (44%) | 50 |
1e-05 (0.00598) |
0.169 (1.00) |
0.00166 (0.865) |
0.0085 (1.00) |
0.797 (1.00) |
0.151 (1.00) |
0.611 (1.00) |
0.0617 (1.00) |
2q loss | 15 (17%) | 75 |
0.0001 (0.0565) |
0.00106 (0.564) |
0.113 (1.00) |
0.0535 (1.00) |
0.0313 (1.00) |
0.729 (1.00) |
0.115 (1.00) |
0.835 (1.00) |
9p loss | 20 (22%) | 70 |
0.00127 (0.668) |
0.0479 (1.00) |
6e-05 (0.0343) |
0.00125 (0.659) |
0.0092 (1.00) |
0.137 (1.00) |
0.0587 (1.00) |
0.204 (1.00) |
11q loss | 23 (26%) | 67 |
8e-05 (0.0454) |
0.00271 (1.00) |
0.133 (1.00) |
0.128 (1.00) |
0.104 (1.00) |
0.824 (1.00) |
0.217 (1.00) |
0.899 (1.00) |
17p loss | 32 (36%) | 58 |
0.00109 (0.579) |
0.00019 (0.106) |
0.0117 (1.00) |
0.0135 (1.00) |
0.0812 (1.00) |
0.00286 (1.00) |
0.0508 (1.00) |
0.0141 (1.00) |
17q loss | 24 (27%) | 66 |
0.00028 (0.154) |
0.00541 (1.00) |
0.12 (1.00) |
0.0334 (1.00) |
0.0666 (1.00) |
0.0199 (1.00) |
0.0759 (1.00) |
0.182 (1.00) |
1p gain | 4 (4%) | 86 |
0.119 (1.00) |
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1q gain | 8 (9%) | 82 |
0.12 (1.00) |
0.654 (1.00) |
0.0467 (1.00) |
0.0776 (1.00) |
0.0647 (1.00) |
0.242 (1.00) |
0.298 (1.00) |
0.23 (1.00) |
2q gain | 12 (13%) | 78 |
0.0037 (1.00) |
0.00225 (1.00) |
0.018 (1.00) |
0.00263 (1.00) |
0.0556 (1.00) |
0.00431 (1.00) |
0.0196 (1.00) |
0.00352 (1.00) |
3p gain | 13 (14%) | 77 |
0.0925 (1.00) |
0.0687 (1.00) |
0.329 (1.00) |
0.362 (1.00) |
0.409 (1.00) |
0.107 (1.00) |
0.31 (1.00) |
0.601 (1.00) |
3q gain | 15 (17%) | 75 |
0.0599 (1.00) |
0.0518 (1.00) |
0.0521 (1.00) |
0.793 (1.00) |
0.652 (1.00) |
0.246 (1.00) |
0.56 (1.00) |
0.856 (1.00) |
6p gain | 18 (20%) | 72 |
0.0617 (1.00) |
0.683 (1.00) |
0.0671 (1.00) |
0.472 (1.00) |
0.162 (1.00) |
0.0549 (1.00) |
0.209 (1.00) |
0.0253 (1.00) |
6q gain | 16 (18%) | 74 |
0.00232 (1.00) |
0.458 (1.00) |
0.199 (1.00) |
0.294 (1.00) |
0.298 (1.00) |
0.196 (1.00) |
0.26 (1.00) |
0.161 (1.00) |
8p gain | 32 (36%) | 58 |
0.00177 (0.917) |
0.139 (1.00) |
0.167 (1.00) |
0.145 (1.00) |
0.113 (1.00) |
0.174 (1.00) |
0.0261 (1.00) |
0.0605 (1.00) |
8q gain | 38 (42%) | 52 |
0.0187 (1.00) |
0.291 (1.00) |
0.416 (1.00) |
0.231 (1.00) |
0.496 (1.00) |
0.261 (1.00) |
0.0963 (1.00) |
0.121 (1.00) |
11p gain | 5 (6%) | 85 |
0.111 (1.00) |
|||||||
11q gain | 6 (7%) | 84 |
0.174 (1.00) |
0.176 (1.00) |
0.0443 (1.00) |
0.0787 (1.00) |
0.187 (1.00) |
0.371 (1.00) |
0.445 (1.00) |
0.16 (1.00) |
13q gain | 6 (7%) | 84 |
1 (1.00) |
0.464 (1.00) |
0.0385 (1.00) |
0.639 (1.00) |
0.14 (1.00) |
0.913 (1.00) |
0.3 (1.00) |
0.394 (1.00) |
15q gain | 11 (12%) | 79 |
0.215 (1.00) |
0.0454 (1.00) |
0.0105 (1.00) |
0.00482 (1.00) |
0.361 (1.00) |
0.00073 (0.393) |
0.248 (1.00) |
0.00583 (1.00) |
17p gain | 5 (6%) | 85 |
0.0883 (1.00) |
0.337 (1.00) |
0.685 (1.00) |
0.144 (1.00) |
0.205 (1.00) |
0.794 (1.00) |
0.141 (1.00) |
0.929 (1.00) |
17q gain | 7 (8%) | 83 |
0.0145 (1.00) |
0.338 (1.00) |
0.689 (1.00) |
0.144 (1.00) |
0.211 (1.00) |
0.793 (1.00) |
0.14 (1.00) |
0.928 (1.00) |
18p gain | 6 (7%) | 84 |
0.493 (1.00) |
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18q gain | 5 (6%) | 85 |
0.66 (1.00) |
|||||||
21q gain | 31 (34%) | 59 |
0.0371 (1.00) |
0.00888 (1.00) |
0.0195 (1.00) |
0.00091 (0.486) |
0.0131 (1.00) |
0.0205 (1.00) |
0.0259 (1.00) |
0.154 (1.00) |
22q gain | 3 (3%) | 87 |
0.375 (1.00) |
|||||||
1p loss | 29 (32%) | 61 |
0.202 (1.00) |
0.141 (1.00) |
0.438 (1.00) |
0.065 (1.00) |
0.469 (1.00) |
0.41 (1.00) |
0.784 (1.00) |
0.406 (1.00) |
1q loss | 20 (22%) | 70 |
0.584 (1.00) |
0.0891 (1.00) |
0.962 (1.00) |
0.601 (1.00) |
0.367 (1.00) |
0.841 (1.00) |
0.594 (1.00) |
0.609 (1.00) |
2p loss | 17 (19%) | 73 |
0.00056 (0.304) |
0.0272 (1.00) |
0.612 (1.00) |
0.267 (1.00) |
0.0377 (1.00) |
0.769 (1.00) |
0.127 (1.00) |
0.76 (1.00) |
3p loss | 20 (22%) | 70 |
0.0597 (1.00) |
0.143 (1.00) |
0.112 (1.00) |
0.135 (1.00) |
0.523 (1.00) |
0.391 (1.00) |
0.195 (1.00) |
0.306 (1.00) |
3q loss | 20 (22%) | 70 |
0.0164 (1.00) |
0.166 (1.00) |
0.0222 (1.00) |
0.0292 (1.00) |
0.193 (1.00) |
0.338 (1.00) |
0.0403 (1.00) |
0.185 (1.00) |
4p loss | 10 (11%) | 80 |
0.0168 (1.00) |
0.234 (1.00) |
0.0234 (1.00) |
0.081 (1.00) |
0.308 (1.00) |
0.931 (1.00) |
0.424 (1.00) |
0.903 (1.00) |
4q loss | 11 (12%) | 79 |
0.0469 (1.00) |
0.0975 (1.00) |
0.0075 (1.00) |
0.0277 (1.00) |
0.252 (1.00) |
0.81 (1.00) |
0.383 (1.00) |
0.761 (1.00) |
5p loss | 8 (9%) | 82 |
0.275 (1.00) |
0.05 (1.00) |
0.23 (1.00) |
0.0104 (1.00) |
0.774 (1.00) |
0.298 (1.00) |
0.455 (1.00) |
0.962 (1.00) |
5q loss | 7 (8%) | 83 |
0.863 (1.00) |
0.656 (1.00) |
0.278 (1.00) |
0.136 (1.00) |
0.659 (1.00) |
0.128 (1.00) |
0.863 (1.00) |
0.333 (1.00) |
6p loss | 19 (21%) | 71 |
0.0303 (1.00) |
0.85 (1.00) |
0.622 (1.00) |
0.692 (1.00) |
0.624 (1.00) |
0.0993 (1.00) |
0.815 (1.00) |
0.162 (1.00) |
6q loss | 22 (24%) | 68 |
0.00738 (1.00) |
0.862 (1.00) |
0.634 (1.00) |
0.692 (1.00) |
0.729 (1.00) |
0.177 (1.00) |
0.74 (1.00) |
0.0687 (1.00) |
7p loss | 5 (6%) | 85 |
0.275 (1.00) |
0.585 (1.00) |
0.91 (1.00) |
0.891 (1.00) |
0.816 (1.00) |
0.416 (1.00) |
0.684 (1.00) |
0.13 (1.00) |
7q loss | 6 (7%) | 84 |
0.192 (1.00) |
0.304 (1.00) |
0.62 (1.00) |
0.658 (1.00) |
1 (1.00) |
0.233 (1.00) |
0.596 (1.00) |
0.0712 (1.00) |
8p loss | 16 (18%) | 74 |
0.00308 (1.00) |
0.224 (1.00) |
0.181 (1.00) |
0.141 (1.00) |
0.181 (1.00) |
0.0226 (1.00) |
0.0171 (1.00) |
0.00696 (1.00) |
8q loss | 12 (13%) | 78 |
0.00147 (0.769) |
0.0869 (1.00) |
0.0319 (1.00) |
0.124 (1.00) |
0.0782 (1.00) |
0.0352 (1.00) |
0.0332 (1.00) |
0.116 (1.00) |
9q loss | 11 (12%) | 79 |
0.142 (1.00) |
0.934 (1.00) |
0.0821 (1.00) |
0.322 (1.00) |
0.557 (1.00) |
0.495 (1.00) |
0.83 (1.00) |
0.282 (1.00) |
10p loss | 12 (13%) | 78 |
0.736 (1.00) |
0.428 (1.00) |
0.264 (1.00) |
1 (1.00) |
0.683 (1.00) |
0.71 (1.00) |
0.618 (1.00) |
0.749 (1.00) |
10q loss | 10 (11%) | 80 |
0.39 (1.00) |
0.624 (1.00) |
0.534 (1.00) |
1 (1.00) |
1 (1.00) |
0.709 (1.00) |
0.892 (1.00) |
0.824 (1.00) |
11p loss | 24 (27%) | 66 |
0.00173 (0.898) |
0.0174 (1.00) |
0.221 (1.00) |
0.187 (1.00) |
0.28 (1.00) |
0.891 (1.00) |
0.447 (1.00) |
0.925 (1.00) |
12p loss | 5 (6%) | 85 |
0.229 (1.00) |
0.255 (1.00) |
0.62 (1.00) |
0.0386 (1.00) |
0.104 (1.00) |
0.517 (1.00) |
0.0108 (1.00) |
0.0171 (1.00) |
12q loss | 4 (4%) | 86 |
0.248 (1.00) |
0.0495 (1.00) |
0.441 (1.00) |
0.0097 (1.00) |
0.33 (1.00) |
0.237 (1.00) |
0.0422 (1.00) |
0.00337 (1.00) |
13q loss | 39 (43%) | 51 |
0.01 (1.00) |
0.0795 (1.00) |
0.625 (1.00) |
0.884 (1.00) |
0.753 (1.00) |
0.302 (1.00) |
0.91 (1.00) |
0.285 (1.00) |
14q loss | 18 (20%) | 72 |
0.0275 (1.00) |
0.444 (1.00) |
0.0181 (1.00) |
0.047 (1.00) |
0.413 (1.00) |
0.53 (1.00) |
0.272 (1.00) |
0.9 (1.00) |
15q loss | 21 (23%) | 69 |
0.0182 (1.00) |
0.414 (1.00) |
0.11 (1.00) |
0.231 (1.00) |
0.607 (1.00) |
0.0404 (1.00) |
0.373 (1.00) |
0.162 (1.00) |
16p loss | 6 (7%) | 84 |
0.173 (1.00) |
0.0506 (1.00) |
0.00209 (1.00) |
0.00412 (1.00) |
0.0133 (1.00) |
0.443 (1.00) |
0.0311 (1.00) |
0.537 (1.00) |
16q loss | 5 (6%) | 85 |
0.318 (1.00) |
0.0771 (1.00) |
0.0582 (1.00) |
0.0856 (1.00) |
0.167 (1.00) |
0.303 (1.00) |
0.361 (1.00) |
0.894 (1.00) |
18p loss | 37 (41%) | 53 |
0.0261 (1.00) |
0.259 (1.00) |
0.776 (1.00) |
0.646 (1.00) |
0.692 (1.00) |
0.693 (1.00) |
0.875 (1.00) |
0.284 (1.00) |
18q loss | 35 (39%) | 55 |
0.0456 (1.00) |
0.426 (1.00) |
0.824 (1.00) |
0.935 (1.00) |
0.496 (1.00) |
0.914 (1.00) |
0.76 (1.00) |
0.0993 (1.00) |
19p loss | 5 (6%) | 85 |
0.112 (1.00) |
0.443 (1.00) |
0.157 (1.00) |
0.0132 (1.00) |
0.139 (1.00) |
0.715 (1.00) |
0.214 (1.00) |
0.0321 (1.00) |
19q loss | 4 (4%) | 86 |
0.247 (1.00) |
0.705 (1.00) |
0.773 (1.00) |
0.119 (1.00) |
0.783 (1.00) |
0.205 (1.00) |
0.216 (1.00) |
0.0321 (1.00) |
20p loss | 9 (10%) | 81 |
0.0103 (1.00) |
0.303 (1.00) |
0.215 (1.00) |
0.127 (1.00) |
0.0681 (1.00) |
0.443 (1.00) |
0.17 (1.00) |
0.764 (1.00) |
20q loss | 3 (3%) | 87 |
0.456 (1.00) |
|||||||
21q loss | 15 (17%) | 75 |
0.00871 (1.00) |
0.337 (1.00) |
0.256 (1.00) |
0.252 (1.00) |
0.223 (1.00) |
0.51 (1.00) |
0.233 (1.00) |
0.815 (1.00) |
22q loss | 48 (53%) | 42 |
0.0777 (1.00) |
0.081 (1.00) |
0.62 (1.00) |
0.282 (1.00) |
0.874 (1.00) |
0.828 (1.00) |
0.8 (1.00) |
0.729 (1.00) |
xq loss | 17 (19%) | 73 |
0.00153 (0.799) |
0.246 (1.00) |
0.0337 (1.00) |
0.0448 (1.00) |
0.652 (1.00) |
0.172 (1.00) |
0.139 (1.00) |
0.45 (1.00) |
P value = 0.00026 (Fisher's exact test), Q value = 0.14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 24 | 15 | 10 | 9 |
2P GAIN MUTATED | 12 | 0 | 1 | 0 | 0 |
2P GAIN WILD-TYPE | 20 | 24 | 14 | 10 | 9 |
P value = 0.00014 (Fisher's exact test), Q value = 0.078
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 23 | 7 | 24 |
2P GAIN MUTATED | 8 | 0 | 1 | 0 |
2P GAIN WILD-TYPE | 15 | 23 | 6 | 24 |
P value = 3e-05 (Fisher's exact test), Q value = 0.017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 24 | 15 | 10 | 9 |
4P GAIN MUTATED | 3 | 13 | 10 | 4 | 7 |
4P GAIN WILD-TYPE | 29 | 11 | 5 | 6 | 2 |
P value = 5e-05 (Fisher's exact test), Q value = 0.029
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 13 | 17 | 23 |
4P GAIN MUTATED | 1 | 8 | 11 | 10 |
4P GAIN WILD-TYPE | 23 | 5 | 6 | 13 |
P value = 5e-05 (Fisher's exact test), Q value = 0.029
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 23 | 7 | 24 |
4P GAIN MUTATED | 2 | 15 | 0 | 13 |
4P GAIN WILD-TYPE | 21 | 8 | 7 | 11 |
P value = 7e-05 (Fisher's exact test), Q value = 0.04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 24 | 15 | 10 | 9 |
4Q GAIN MUTATED | 2 | 12 | 9 | 4 | 6 |
4Q GAIN WILD-TYPE | 30 | 12 | 6 | 6 | 3 |
P value = 3e-05 (Fisher's exact test), Q value = 0.017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 13 | 17 | 23 |
4Q GAIN MUTATED | 0 | 8 | 9 | 10 |
4Q GAIN WILD-TYPE | 24 | 5 | 8 | 13 |
P value = 1e-05 (Fisher's exact test), Q value = 0.006
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 23 | 7 | 24 |
4Q GAIN MUTATED | 1 | 15 | 0 | 11 |
4Q GAIN WILD-TYPE | 22 | 8 | 7 | 13 |
P value = 1e-05 (Fisher's exact test), Q value = 0.006
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 24 | 15 | 10 | 9 |
5P GAIN MUTATED | 10 | 22 | 13 | 4 | 8 |
5P GAIN WILD-TYPE | 22 | 2 | 2 | 6 | 1 |
P value = 1e-05 (Fisher's exact test), Q value = 0.006
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 23 | 7 | 24 |
5P GAIN MUTATED | 6 | 18 | 3 | 22 |
5P GAIN WILD-TYPE | 17 | 5 | 4 | 2 |
P value = 3e-05 (Fisher's exact test), Q value = 0.017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 24 | 15 | 10 | 9 |
5Q GAIN MUTATED | 9 | 19 | 13 | 4 | 8 |
5Q GAIN WILD-TYPE | 23 | 5 | 2 | 6 | 1 |
P value = 3e-05 (Fisher's exact test), Q value = 0.017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 23 | 7 | 24 |
5Q GAIN MUTATED | 5 | 19 | 3 | 20 |
5Q GAIN WILD-TYPE | 18 | 4 | 4 | 4 |
P value = 0.00042 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 24 | 15 | 10 | 9 |
7P GAIN MUTATED | 9 | 18 | 12 | 3 | 6 |
7P GAIN WILD-TYPE | 23 | 6 | 3 | 7 | 3 |
P value = 0.00012 (Fisher's exact test), Q value = 0.068
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 13 | 17 | 23 |
7P GAIN MUTATED | 6 | 12 | 13 | 11 |
7P GAIN WILD-TYPE | 18 | 1 | 4 | 12 |
P value = 2e-05 (Fisher's exact test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 24 | 15 | 10 | 9 |
7Q GAIN MUTATED | 8 | 18 | 13 | 3 | 6 |
7Q GAIN WILD-TYPE | 24 | 6 | 2 | 7 | 3 |
P value = 1e-05 (Fisher's exact test), Q value = 0.006
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 13 | 17 | 23 |
7Q GAIN MUTATED | 5 | 13 | 13 | 11 |
7Q GAIN WILD-TYPE | 19 | 0 | 4 | 12 |
P value = 1e-04 (Fisher's exact test), Q value = 0.056
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 23 | 7 | 24 |
7Q GAIN MUTATED | 6 | 20 | 2 | 14 |
7Q GAIN WILD-TYPE | 17 | 3 | 5 | 10 |
P value = 7e-05 (Fisher's exact test), Q value = 0.04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 24 | 15 | 10 | 9 |
9P GAIN MUTATED | 2 | 3 | 10 | 1 | 4 |
9P GAIN WILD-TYPE | 30 | 21 | 5 | 9 | 5 |
P value = 0.00019 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 24 | 15 | 10 | 9 |
9Q GAIN MUTATED | 7 | 3 | 12 | 3 | 4 |
9Q GAIN WILD-TYPE | 25 | 21 | 3 | 7 | 5 |
P value = 3e-05 (Fisher's exact test), Q value = 0.017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 13 | 17 | 23 |
10P GAIN MUTATED | 6 | 11 | 4 | 2 |
10P GAIN WILD-TYPE | 18 | 2 | 13 | 21 |
P value = 0.00019 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 23 | 7 | 24 |
10P GAIN MUTATED | 7 | 14 | 1 | 1 |
10P GAIN WILD-TYPE | 16 | 9 | 6 | 23 |
P value = 4e-05 (Fisher's exact test), Q value = 0.023
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 13 | 17 | 23 |
10Q GAIN MUTATED | 7 | 11 | 3 | 2 |
10Q GAIN WILD-TYPE | 17 | 2 | 14 | 21 |
P value = 0.00045 (Fisher's exact test), Q value = 0.25
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 23 | 7 | 24 |
10Q GAIN MUTATED | 8 | 13 | 1 | 1 |
10Q GAIN WILD-TYPE | 15 | 10 | 6 | 23 |
P value = 2e-05 (Fisher's exact test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 24 | 15 | 10 | 9 |
12P GAIN MUTATED | 14 | 24 | 14 | 5 | 7 |
12P GAIN WILD-TYPE | 18 | 0 | 1 | 5 | 2 |
P value = 0.00022 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 13 | 17 | 23 |
12P GAIN MUTATED | 9 | 13 | 14 | 18 |
12P GAIN WILD-TYPE | 15 | 0 | 3 | 5 |
P value = 5e-05 (Fisher's exact test), Q value = 0.029
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 23 | 7 | 24 |
12P GAIN MUTATED | 10 | 20 | 2 | 22 |
12P GAIN WILD-TYPE | 13 | 3 | 5 | 2 |
P value = 1e-05 (Fisher's exact test), Q value = 0.006
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 24 | 15 | 10 | 9 |
12Q GAIN MUTATED | 14 | 24 | 15 | 4 | 7 |
12Q GAIN WILD-TYPE | 18 | 0 | 0 | 6 | 2 |
P value = 0.00014 (Fisher's exact test), Q value = 0.078
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 23 | 7 | 24 |
12Q GAIN MUTATED | 11 | 20 | 2 | 22 |
12Q GAIN WILD-TYPE | 12 | 3 | 5 | 2 |
P value = 0.00038 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 13 | 17 | 23 |
14Q GAIN MUTATED | 2 | 6 | 8 | 1 |
14Q GAIN WILD-TYPE | 22 | 7 | 9 | 22 |
P value = 2e-05 (Fisher's exact test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 36 | 16 | 26 |
14Q GAIN MUTATED | 17 | 0 | 1 |
14Q GAIN WILD-TYPE | 19 | 16 | 25 |
P value = 0.00014 (Fisher's exact test), Q value = 0.078
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 16 | 27 | 11 | 20 | 4 |
14Q GAIN MUTATED | 7 | 0 | 3 | 5 | 3 |
14Q GAIN WILD-TYPE | 9 | 27 | 8 | 15 | 1 |
P value = 2e-05 (Fisher's exact test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 37 | 18 | 23 |
14Q GAIN MUTATED | 17 | 1 | 0 |
14Q GAIN WILD-TYPE | 20 | 17 | 23 |
P value = 2e-05 (Fisher's exact test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 8 | 25 | 8 | 18 | 9 | 10 |
14Q GAIN MUTATED | 5 | 0 | 4 | 5 | 4 | 0 |
14Q GAIN WILD-TYPE | 3 | 25 | 4 | 13 | 5 | 10 |
P value = 1e-05 (Fisher's exact test), Q value = 0.006
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 24 | 15 | 10 | 9 |
16P GAIN MUTATED | 6 | 24 | 10 | 4 | 5 |
16P GAIN WILD-TYPE | 26 | 0 | 5 | 6 | 4 |
P value = 1e-05 (Fisher's exact test), Q value = 0.006
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 13 | 17 | 23 |
16P GAIN MUTATED | 3 | 10 | 13 | 16 |
16P GAIN WILD-TYPE | 21 | 3 | 4 | 7 |
P value = 1e-05 (Fisher's exact test), Q value = 0.006
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 23 | 7 | 24 |
16P GAIN MUTATED | 4 | 20 | 0 | 18 |
16P GAIN WILD-TYPE | 19 | 3 | 7 | 6 |
P value = 1e-05 (Fisher's exact test), Q value = 0.006
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 24 | 15 | 10 | 9 |
16Q GAIN MUTATED | 6 | 23 | 10 | 3 | 5 |
16Q GAIN WILD-TYPE | 26 | 1 | 5 | 7 | 4 |
P value = 0.00012 (Fisher's exact test), Q value = 0.068
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 13 | 17 | 23 |
16Q GAIN MUTATED | 4 | 9 | 13 | 16 |
16Q GAIN WILD-TYPE | 20 | 4 | 4 | 7 |
P value = 1e-05 (Fisher's exact test), Q value = 0.006
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 23 | 7 | 24 |
16Q GAIN MUTATED | 4 | 19 | 1 | 18 |
16Q GAIN WILD-TYPE | 19 | 4 | 6 | 6 |
P value = 0.00045 (Fisher's exact test), Q value = 0.25
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 23 | 7 | 24 |
19P GAIN MUTATED | 14 | 21 | 1 | 12 |
19P GAIN WILD-TYPE | 9 | 2 | 6 | 12 |
P value = 0.00036 (Fisher's exact test), Q value = 0.2
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 13 | 17 | 23 |
19Q GAIN MUTATED | 10 | 13 | 12 | 9 |
19Q GAIN WILD-TYPE | 14 | 0 | 5 | 14 |
P value = 1e-05 (Fisher's exact test), Q value = 0.006
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 24 | 15 | 10 | 9 |
20P GAIN MUTATED | 7 | 22 | 9 | 2 | 6 |
20P GAIN WILD-TYPE | 25 | 2 | 6 | 8 | 3 |
P value = 9e-05 (Fisher's exact test), Q value = 0.051
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 13 | 17 | 23 |
20P GAIN MUTATED | 4 | 9 | 8 | 18 |
20P GAIN WILD-TYPE | 20 | 4 | 9 | 5 |
P value = 0.00014 (Fisher's exact test), Q value = 0.078
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 23 | 7 | 24 |
20P GAIN MUTATED | 6 | 12 | 1 | 20 |
20P GAIN WILD-TYPE | 17 | 11 | 6 | 4 |
P value = 0.00013 (Fisher's exact test), Q value = 0.073
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 37 | 18 | 23 |
20P GAIN MUTATED | 13 | 7 | 20 |
20P GAIN WILD-TYPE | 24 | 11 | 3 |
P value = 2e-05 (Fisher's exact test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 24 | 15 | 10 | 9 |
20Q GAIN MUTATED | 9 | 21 | 11 | 2 | 6 |
20Q GAIN WILD-TYPE | 23 | 3 | 4 | 8 | 3 |
P value = 7e-05 (Fisher's exact test), Q value = 0.04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 13 | 17 | 23 |
20Q GAIN MUTATED | 5 | 11 | 8 | 18 |
20Q GAIN WILD-TYPE | 19 | 2 | 9 | 5 |
P value = 0.00025 (Fisher's exact test), Q value = 0.14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 23 | 7 | 24 |
20Q GAIN MUTATED | 6 | 14 | 2 | 20 |
20Q GAIN WILD-TYPE | 17 | 9 | 5 | 4 |
P value = 1e-05 (Fisher's exact test), Q value = 0.006
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 24 | 15 | 10 | 9 |
XQ GAIN MUTATED | 6 | 20 | 9 | 2 | 3 |
XQ GAIN WILD-TYPE | 26 | 4 | 6 | 8 | 6 |
P value = 1e-04 (Fisher's exact test), Q value = 0.056
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 24 | 15 | 10 | 9 |
2Q LOSS MUTATED | 1 | 2 | 2 | 6 | 4 |
2Q LOSS WILD-TYPE | 31 | 22 | 13 | 4 | 5 |
P value = 6e-05 (Fisher's exact test), Q value = 0.034
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 13 | 17 | 23 |
9P LOSS MUTATED | 14 | 1 | 3 | 1 |
9P LOSS WILD-TYPE | 10 | 12 | 14 | 22 |
P value = 8e-05 (Fisher's exact test), Q value = 0.045
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 24 | 15 | 10 | 9 |
11Q LOSS MUTATED | 4 | 3 | 3 | 8 | 5 |
11Q LOSS WILD-TYPE | 28 | 21 | 12 | 2 | 4 |
P value = 0.00019 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 11 | 20 | 18 | 11 |
17P LOSS MUTATED | 11 | 0 | 12 | 4 | 1 |
17P LOSS WILD-TYPE | 7 | 11 | 8 | 14 | 10 |
P value = 0.00028 (Fisher's exact test), Q value = 0.15
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 24 | 15 | 10 | 9 |
17Q LOSS MUTATED | 7 | 3 | 6 | 8 | 0 |
17Q LOSS WILD-TYPE | 25 | 21 | 9 | 2 | 9 |
-
Copy number data file = transformed.cor.cli.txt
-
Molecular subtypes file = ACC-TP.transferedmergedcluster.txt
-
Number of patients = 90
-
Number of significantly arm-level cnvs = 80
-
Number of molecular subtypes = 8
-
Exclude genes that fewer than K tumors have mutations, K = 3
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.