This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 82 arm-level events and 5 clinical features across 246 patients, 71 significant findings detected with Q value < 0.25.
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1p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', and 'RACE'.
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3p gain cnv correlated to 'YEARS_TO_BIRTH'.
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3q gain cnv correlated to 'YEARS_TO_BIRTH'.
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5p gain cnv correlated to 'YEARS_TO_BIRTH'.
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5q gain cnv correlated to 'YEARS_TO_BIRTH'.
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6p gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
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6q gain cnv correlated to 'Time to Death'.
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7p gain cnv correlated to 'YEARS_TO_BIRTH'.
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7q gain cnv correlated to 'YEARS_TO_BIRTH'.
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8p gain cnv correlated to 'Time to Death'.
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8q gain cnv correlated to 'Time to Death'.
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9p gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
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9q gain cnv correlated to 'YEARS_TO_BIRTH'.
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11p gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
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11q gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
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12p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', and 'RACE'.
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12q gain cnv correlated to 'GENDER' and 'RACE'.
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13q gain cnv correlated to 'RACE'.
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14q gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
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16p gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
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17p gain cnv correlated to 'YEARS_TO_BIRTH'.
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18p gain cnv correlated to 'YEARS_TO_BIRTH'.
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18q gain cnv correlated to 'YEARS_TO_BIRTH'.
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19p gain cnv correlated to 'YEARS_TO_BIRTH'.
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19q gain cnv correlated to 'YEARS_TO_BIRTH'.
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20p gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
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20q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', and 'GENDER'.
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21q gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
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22q gain cnv correlated to 'YEARS_TO_BIRTH'.
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xp gain cnv correlated to 'YEARS_TO_BIRTH'.
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xq gain cnv correlated to 'ETHNICITY'.
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1p loss cnv correlated to 'GENDER'.
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2p loss cnv correlated to 'YEARS_TO_BIRTH' and 'RACE'.
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2q loss cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
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3p loss cnv correlated to 'YEARS_TO_BIRTH'.
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3q loss cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
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6p loss cnv correlated to 'Time to Death'.
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9p loss cnv correlated to 'YEARS_TO_BIRTH'.
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9q loss cnv correlated to 'Time to Death'.
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10p loss cnv correlated to 'YEARS_TO_BIRTH' and 'GENDER'.
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10q loss cnv correlated to 'YEARS_TO_BIRTH' and 'GENDER'.
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13q loss cnv correlated to 'YEARS_TO_BIRTH'.
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15q loss cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
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16q loss cnv correlated to 'YEARS_TO_BIRTH'.
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17q loss cnv correlated to 'Time to Death'.
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18q loss cnv correlated to 'Time to Death'.
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20p loss cnv correlated to 'YEARS_TO_BIRTH'.
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20q loss cnv correlated to 'YEARS_TO_BIRTH'.
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21q loss cnv correlated to 'YEARS_TO_BIRTH'.
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22q loss cnv correlated to 'GENDER'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
GENDER | RACE | ETHNICITY | ||
nCNV (%) | nWild-Type | logrank test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
1p gain | 54 (22%) | 192 |
0.0114 (0.122) |
0.0142 (0.129) |
0.542 (0.895) |
0.0428 (0.247) |
0.34 (0.73) |
12p gain | 42 (17%) | 204 |
0.00564 (0.105) |
8.66e-05 (0.00581) |
0.615 (0.904) |
0.04 (0.241) |
0.198 (0.56) |
20q gain | 82 (33%) | 164 |
0.0108 (0.122) |
0.000326 (0.0157) |
0.00976 (0.122) |
0.618 (0.905) |
1 (1.00) |
6p gain | 49 (20%) | 197 |
0.00123 (0.0405) |
0.0119 (0.122) |
0.338 (0.73) |
0.555 (0.895) |
1 (1.00) |
9p gain | 55 (22%) | 191 |
0.0372 (0.235) |
0.00105 (0.0392) |
0.172 (0.525) |
0.419 (0.768) |
1 (1.00) |
11p gain | 22 (9%) | 224 |
0.00449 (0.0921) |
7.73e-05 (0.00581) |
0.376 (0.74) |
0.233 (0.613) |
1 (1.00) |
11q gain | 21 (9%) | 225 |
0.000925 (0.0379) |
0.0219 (0.164) |
0.497 (0.849) |
0.355 (0.735) |
1 (1.00) |
12q gain | 33 (13%) | 213 |
0.594 (0.895) |
0.0937 (0.415) |
0.0391 (0.241) |
0.0159 (0.136) |
0.141 (0.487) |
14q gain | 55 (22%) | 191 |
0.0181 (0.152) |
0.0131 (0.127) |
0.759 (0.999) |
0.835 (1.00) |
1 (1.00) |
16p gain | 39 (16%) | 207 |
0.00596 (0.106) |
0.025 (0.18) |
0.861 (1.00) |
0.497 (0.849) |
1 (1.00) |
20p gain | 61 (25%) | 185 |
0.00177 (0.0453) |
0.00925 (0.122) |
0.0545 (0.298) |
0.357 (0.735) |
1 (1.00) |
21q gain | 55 (22%) | 191 |
0.019 (0.155) |
0.036 (0.232) |
0.288 (0.678) |
0.0504 (0.281) |
0.593 (0.895) |
2p loss | 84 (34%) | 162 |
0.343 (0.73) |
0.00815 (0.122) |
0.225 (0.603) |
0.031 (0.208) |
0.159 (0.512) |
2q loss | 67 (27%) | 179 |
0.00138 (0.0405) |
0.000344 (0.0157) |
0.473 (0.839) |
0.104 (0.439) |
0.324 (0.73) |
3q loss | 49 (20%) | 197 |
0.0149 (0.132) |
0.0136 (0.127) |
0.201 (0.562) |
0.815 (1.00) |
1 (1.00) |
10p loss | 116 (47%) | 130 |
0.876 (1.00) |
0.0197 (0.155) |
0.00714 (0.113) |
0.195 (0.56) |
0.369 (0.735) |
10q loss | 126 (51%) | 120 |
0.483 (0.846) |
0.00954 (0.122) |
0.0104 (0.122) |
0.24 (0.62) |
0.168 (0.523) |
15q loss | 42 (17%) | 204 |
9.15e-05 (0.00581) |
0.00936 (0.122) |
0.401 (0.751) |
0.337 (0.73) |
0.587 (0.895) |
3p gain | 37 (15%) | 209 |
0.704 (0.943) |
0.0405 (0.241) |
0.479 (0.846) |
0.0997 (0.426) |
1 (1.00) |
3q gain | 34 (14%) | 212 |
0.97 (1.00) |
0.0134 (0.127) |
0.581 (0.895) |
0.12 (0.45) |
1 (1.00) |
5p gain | 95 (39%) | 151 |
0.909 (1.00) |
0.00129 (0.0405) |
0.694 (0.941) |
0.724 (0.964) |
1 (1.00) |
5q gain | 70 (28%) | 176 |
0.527 (0.882) |
0.0264 (0.183) |
0.395 (0.751) |
0.395 (0.751) |
1 (1.00) |
6q gain | 48 (20%) | 198 |
0.0119 (0.122) |
0.0507 (0.281) |
0.147 (0.494) |
0.684 (0.932) |
1 (1.00) |
7p gain | 79 (32%) | 167 |
0.373 (0.738) |
9e-06 (0.00123) |
0.892 (1.00) |
0.492 (0.849) |
0.662 (0.917) |
7q gain | 66 (27%) | 180 |
0.115 (0.444) |
4.22e-07 (0.000173) |
0.149 (0.494) |
0.795 (1.00) |
0.136 (0.477) |
8p gain | 52 (21%) | 194 |
0.022 (0.164) |
0.11 (0.439) |
1 (1.00) |
0.0462 (0.263) |
0.335 (0.73) |
8q gain | 63 (26%) | 183 |
0.00688 (0.113) |
0.311 (0.716) |
0.56 (0.895) |
0.0952 (0.415) |
0.136 (0.477) |
9q gain | 71 (29%) | 175 |
0.948 (1.00) |
6.69e-06 (0.00123) |
0.4 (0.751) |
0.684 (0.932) |
1 (1.00) |
13q gain | 13 (5%) | 233 |
0.703 (0.943) |
0.213 (0.589) |
0.095 (0.415) |
0.0201 (0.155) |
1 (1.00) |
17p gain | 58 (24%) | 188 |
0.149 (0.494) |
0.0247 (0.18) |
0.549 (0.895) |
0.242 (0.62) |
1 (1.00) |
18p gain | 49 (20%) | 197 |
0.367 (0.735) |
0.0102 (0.122) |
0.426 (0.776) |
0.333 (0.73) |
0.585 (0.895) |
18q gain | 33 (13%) | 213 |
0.634 (0.913) |
0.00954 (0.122) |
0.262 (0.648) |
0.367 (0.735) |
1 (1.00) |
19p gain | 82 (33%) | 164 |
0.11 (0.439) |
9.92e-05 (0.00581) |
0.0776 (0.374) |
0.932 (1.00) |
0.332 (0.73) |
19q gain | 62 (25%) | 184 |
0.387 (0.747) |
0.00244 (0.0555) |
0.141 (0.487) |
0.845 (1.00) |
1 (1.00) |
22q gain | 58 (24%) | 188 |
0.604 (0.895) |
0.00202 (0.0486) |
0.452 (0.813) |
0.922 (1.00) |
0.112 (0.441) |
xp gain | 72 (29%) | 174 |
0.639 (0.916) |
0.0418 (0.245) |
0.0916 (0.415) |
0.931 (1.00) |
0.332 (0.73) |
xq gain | 32 (13%) | 214 |
0.316 (0.718) |
0.302 (0.7) |
0.57 (0.895) |
1 (1.00) |
0.0156 (0.136) |
1p loss | 30 (12%) | 216 |
0.0645 (0.328) |
0.117 (0.445) |
0.0101 (0.122) |
0.278 (0.662) |
1 (1.00) |
3p loss | 56 (23%) | 190 |
0.0933 (0.415) |
0.0193 (0.155) |
0.763 (0.999) |
0.913 (1.00) |
1 (1.00) |
6p loss | 57 (23%) | 189 |
0.00655 (0.112) |
0.99 (1.00) |
0.545 (0.895) |
0.655 (0.917) |
1 (1.00) |
9p loss | 81 (33%) | 165 |
0.25 (0.635) |
0.00372 (0.0802) |
0.224 (0.603) |
0.495 (0.849) |
1 (1.00) |
9q loss | 49 (20%) | 197 |
0.028 (0.191) |
0.107 (0.439) |
0.633 (0.913) |
0.19 (0.553) |
1 (1.00) |
13q loss | 130 (53%) | 116 |
0.602 (0.895) |
0.00172 (0.0453) |
0.0734 (0.363) |
0.941 (1.00) |
0.657 (0.917) |
16q loss | 120 (49%) | 126 |
0.176 (0.526) |
0.00529 (0.103) |
0.056 (0.302) |
0.116 (0.444) |
0.672 (0.925) |
17q loss | 46 (19%) | 200 |
0.0344 (0.227) |
0.0662 (0.331) |
0.625 (0.912) |
0.342 (0.73) |
0.585 (0.895) |
18q loss | 69 (28%) | 177 |
0.0132 (0.127) |
0.108 (0.439) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
20p loss | 52 (21%) | 194 |
0.596 (0.895) |
0.0115 (0.122) |
0.214 (0.589) |
0.544 (0.895) |
1 (1.00) |
20q loss | 24 (10%) | 222 |
0.899 (1.00) |
0.0362 (0.232) |
0.202 (0.562) |
1 (1.00) |
1 (1.00) |
21q loss | 48 (20%) | 198 |
0.186 (0.544) |
0.0257 (0.181) |
0.872 (1.00) |
0.902 (1.00) |
1 (1.00) |
22q loss | 63 (26%) | 183 |
0.859 (1.00) |
0.274 (0.661) |
0.0406 (0.241) |
1 (1.00) |
0.593 (0.895) |
1q gain | 47 (19%) | 199 |
0.776 (1.00) |
0.0649 (0.328) |
0.144 (0.492) |
0.905 (1.00) |
0.587 (0.895) |
2p gain | 21 (9%) | 225 |
0.183 (0.544) |
0.163 (0.514) |
0.821 (1.00) |
0.645 (0.917) |
0.368 (0.735) |
2q gain | 21 (9%) | 225 |
0.634 (0.913) |
0.235 (0.614) |
0.256 (0.648) |
0.428 (0.777) |
0.368 (0.735) |
4p gain | 65 (26%) | 181 |
0.197 (0.56) |
0.633 (0.913) |
0.565 (0.895) |
0.857 (1.00) |
1 (1.00) |
4q gain | 44 (18%) | 202 |
0.16 (0.512) |
0.366 (0.735) |
0.408 (0.76) |
1 (1.00) |
1 (1.00) |
10p gain | 22 (9%) | 224 |
0.295 (0.686) |
0.511 (0.865) |
0.658 (0.917) |
0.822 (1.00) |
1 (1.00) |
10q gain | 11 (4%) | 235 |
0.36 (0.735) |
0.941 (1.00) |
0.759 (0.999) |
1 (1.00) |
1 (1.00) |
15q gain | 61 (25%) | 185 |
0.517 (0.872) |
0.0576 (0.303) |
0.0758 (0.37) |
0.654 (0.917) |
0.106 (0.439) |
16q gain | 20 (8%) | 226 |
0.605 (0.895) |
0.82 (1.00) |
0.643 (0.917) |
1 (1.00) |
1 (1.00) |
17q gain | 53 (22%) | 193 |
0.947 (1.00) |
0.174 (0.525) |
0.165 (0.517) |
0.133 (0.477) |
0.6 (0.895) |
1q loss | 37 (15%) | 209 |
0.774 (1.00) |
0.483 (0.846) |
0.287 (0.678) |
0.789 (1.00) |
0.527 (0.882) |
4p loss | 41 (17%) | 205 |
0.385 (0.747) |
0.134 (0.477) |
0.391 (0.75) |
0.383 (0.747) |
1 (1.00) |
4q loss | 50 (20%) | 196 |
0.761 (0.999) |
0.192 (0.553) |
0.0572 (0.303) |
0.509 (0.865) |
0.585 (0.895) |
5p loss | 20 (8%) | 226 |
0.461 (0.825) |
0.369 (0.735) |
0.353 (0.735) |
0.317 (0.718) |
1 (1.00) |
5q loss | 34 (14%) | 212 |
0.276 (0.661) |
0.0788 (0.375) |
0.581 (0.895) |
0.58 (0.895) |
1 (1.00) |
6q loss | 50 (20%) | 196 |
0.123 (0.46) |
0.766 (1.00) |
0.343 (0.73) |
0.911 (1.00) |
1 (1.00) |
7p loss | 31 (13%) | 215 |
0.914 (1.00) |
0.357 (0.735) |
0.0848 (0.398) |
0.185 (0.544) |
1 (1.00) |
7q loss | 33 (13%) | 213 |
0.0854 (0.398) |
0.42 (0.768) |
0.576 (0.895) |
0.698 (0.941) |
1 (1.00) |
8p loss | 58 (24%) | 188 |
0.274 (0.661) |
0.492 (0.849) |
0.652 (0.917) |
0.0998 (0.426) |
0.587 (0.895) |
8q loss | 43 (17%) | 203 |
0.782 (1.00) |
0.0942 (0.415) |
0.4 (0.751) |
0.132 (0.477) |
0.588 (0.895) |
11p loss | 91 (37%) | 155 |
0.468 (0.835) |
0.259 (0.648) |
0.792 (1.00) |
0.933 (1.00) |
0.16 (0.512) |
11q loss | 87 (35%) | 159 |
0.269 (0.66) |
0.697 (0.941) |
1 (1.00) |
0.667 (0.921) |
0.172 (0.525) |
12p loss | 63 (26%) | 183 |
0.718 (0.959) |
0.136 (0.477) |
0.661 (0.917) |
0.173 (0.525) |
0.328 (0.73) |
12q loss | 52 (21%) | 194 |
0.849 (1.00) |
0.263 (0.648) |
0.352 (0.735) |
0.238 (0.619) |
0.586 (0.895) |
14q loss | 59 (24%) | 187 |
0.109 (0.439) |
0.42 (0.768) |
0.882 (1.00) |
0.388 (0.747) |
0.589 (0.895) |
16p loss | 72 (29%) | 174 |
0.661 (0.917) |
0.161 (0.512) |
0.261 (0.648) |
0.148 (0.494) |
1 (1.00) |
17p loss | 55 (22%) | 191 |
0.272 (0.661) |
0.217 (0.592) |
0.759 (0.999) |
0.451 (0.813) |
1 (1.00) |
18p loss | 60 (24%) | 186 |
0.0645 (0.328) |
0.419 (0.768) |
0.882 (1.00) |
0.919 (1.00) |
1 (1.00) |
19p loss | 21 (9%) | 225 |
0.682 (0.932) |
0.597 (0.895) |
0.821 (1.00) |
0.233 (0.613) |
1 (1.00) |
19q loss | 38 (15%) | 208 |
0.98 (1.00) |
0.934 (1.00) |
0.861 (1.00) |
0.496 (0.849) |
0.218 (0.592) |
xp loss | 58 (24%) | 188 |
0.615 (0.904) |
0.132 (0.477) |
0.292 (0.684) |
0.313 (0.716) |
0.588 (0.895) |
xq loss | 96 (39%) | 150 |
0.233 (0.613) |
0.535 (0.891) |
0.116 (0.444) |
0.38 (0.745) |
0.159 (0.512) |
P value = 0.0114 (logrank test), Q value = 0.12
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 244 | 82 | 0.1 - 188.2 (23.3) |
1P GAIN MUTATED | 54 | 22 | 0.5 - 106.5 (18.3) |
1P GAIN WILD-TYPE | 190 | 60 | 0.1 - 188.2 (26.1) |
P value = 0.0142 (Wilcoxon-test), Q value = 0.13
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
1P GAIN MUTATED | 54 | 65.2 (13.5) |
1P GAIN WILD-TYPE | 191 | 60.2 (14.6) |
P value = 0.0428 (Fisher's exact test), Q value = 0.25
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 6 | 18 | 194 |
1P GAIN MUTATED | 0 | 8 | 42 |
1P GAIN WILD-TYPE | 6 | 10 | 152 |
P value = 0.0405 (Wilcoxon-test), Q value = 0.24
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
3P GAIN MUTATED | 37 | 65.8 (13.0) |
3P GAIN WILD-TYPE | 208 | 60.5 (14.6) |
P value = 0.0134 (Wilcoxon-test), Q value = 0.13
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
3Q GAIN MUTATED | 34 | 66.9 (12.9) |
3Q GAIN WILD-TYPE | 211 | 60.4 (14.6) |
P value = 0.00129 (Wilcoxon-test), Q value = 0.041
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
5P GAIN MUTATED | 94 | 65.1 (12.9) |
5P GAIN WILD-TYPE | 151 | 58.9 (14.9) |
P value = 0.0264 (Wilcoxon-test), Q value = 0.18
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
5Q GAIN MUTATED | 70 | 64.7 (13.5) |
5Q GAIN WILD-TYPE | 175 | 59.9 (14.7) |
P value = 0.00123 (logrank test), Q value = 0.041
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 244 | 82 | 0.1 - 188.2 (23.3) |
6P GAIN MUTATED | 49 | 24 | 0.1 - 143.4 (19.9) |
6P GAIN WILD-TYPE | 195 | 58 | 0.1 - 188.2 (25.1) |
P value = 0.0119 (Wilcoxon-test), Q value = 0.12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
6P GAIN MUTATED | 48 | 66.2 (12.9) |
6P GAIN WILD-TYPE | 197 | 60.1 (14.6) |
P value = 0.0119 (logrank test), Q value = 0.12
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 244 | 82 | 0.1 - 188.2 (23.3) |
6Q GAIN MUTATED | 47 | 21 | 0.6 - 143.4 (22.0) |
6Q GAIN WILD-TYPE | 197 | 61 | 0.1 - 188.2 (24.0) |
P value = 9e-06 (Wilcoxon-test), Q value = 0.0012
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
7P GAIN MUTATED | 78 | 66.9 (12.6) |
7P GAIN WILD-TYPE | 167 | 58.7 (14.6) |
P value = 4.22e-07 (Wilcoxon-test), Q value = 0.00017
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
7Q GAIN MUTATED | 66 | 68.8 (10.3) |
7Q GAIN WILD-TYPE | 179 | 58.5 (14.8) |
P value = 0.022 (logrank test), Q value = 0.16
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 244 | 82 | 0.1 - 188.2 (23.3) |
8P GAIN MUTATED | 52 | 22 | 0.1 - 106.5 (17.0) |
8P GAIN WILD-TYPE | 192 | 60 | 0.1 - 188.2 (25.2) |
P value = 0.00688 (logrank test), Q value = 0.11
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 244 | 82 | 0.1 - 188.2 (23.3) |
8Q GAIN MUTATED | 63 | 27 | 0.1 - 106.5 (15.9) |
8Q GAIN WILD-TYPE | 181 | 55 | 0.1 - 188.2 (26.5) |
P value = 0.0372 (logrank test), Q value = 0.23
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 244 | 82 | 0.1 - 188.2 (23.3) |
9P GAIN MUTATED | 54 | 25 | 1.1 - 96.9 (21.5) |
9P GAIN WILD-TYPE | 190 | 57 | 0.1 - 188.2 (24.5) |
P value = 0.00105 (Wilcoxon-test), Q value = 0.039
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
9P GAIN MUTATED | 54 | 66.7 (14.1) |
9P GAIN WILD-TYPE | 191 | 59.8 (14.3) |
P value = 6.69e-06 (Wilcoxon-test), Q value = 0.0012
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
9Q GAIN MUTATED | 71 | 67.6 (13.7) |
9Q GAIN WILD-TYPE | 174 | 58.8 (14.0) |
P value = 0.00449 (logrank test), Q value = 0.092
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 244 | 82 | 0.1 - 188.2 (23.3) |
11P GAIN MUTATED | 22 | 13 | 1.1 - 123.8 (16.1) |
11P GAIN WILD-TYPE | 222 | 69 | 0.1 - 188.2 (25.1) |
P value = 7.73e-05 (Wilcoxon-test), Q value = 0.0058
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
11P GAIN MUTATED | 22 | 72.2 (12.9) |
11P GAIN WILD-TYPE | 223 | 60.2 (14.2) |
P value = 0.000925 (logrank test), Q value = 0.038
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 244 | 82 | 0.1 - 188.2 (23.3) |
11Q GAIN MUTATED | 21 | 14 | 1.1 - 123.8 (18.1) |
11Q GAIN WILD-TYPE | 223 | 68 | 0.1 - 188.2 (25.1) |
P value = 0.0219 (Wilcoxon-test), Q value = 0.16
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
11Q GAIN MUTATED | 21 | 67.6 (15.5) |
11Q GAIN WILD-TYPE | 224 | 60.7 (14.3) |
P value = 0.00564 (logrank test), Q value = 0.11
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 244 | 82 | 0.1 - 188.2 (23.3) |
12P GAIN MUTATED | 42 | 21 | 0.1 - 106.5 (16.9) |
12P GAIN WILD-TYPE | 202 | 61 | 0.1 - 188.2 (24.7) |
P value = 8.66e-05 (Wilcoxon-test), Q value = 0.0058
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
12P GAIN MUTATED | 42 | 69.0 (12.1) |
12P GAIN WILD-TYPE | 203 | 59.7 (14.5) |
P value = 0.04 (Fisher's exact test), Q value = 0.24
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 6 | 18 | 194 |
12P GAIN MUTATED | 2 | 0 | 36 |
12P GAIN WILD-TYPE | 4 | 18 | 158 |
P value = 0.0391 (Fisher's exact test), Q value = 0.24
nPatients | FEMALE | MALE |
---|---|---|
ALL | 132 | 114 |
12Q GAIN MUTATED | 12 | 21 |
12Q GAIN WILD-TYPE | 120 | 93 |
P value = 0.0159 (Fisher's exact test), Q value = 0.14
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 6 | 18 | 194 |
12Q GAIN MUTATED | 3 | 0 | 27 |
12Q GAIN WILD-TYPE | 3 | 18 | 167 |
P value = 0.0201 (Fisher's exact test), Q value = 0.16
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 6 | 18 | 194 |
13Q GAIN MUTATED | 0 | 4 | 8 |
13Q GAIN WILD-TYPE | 6 | 14 | 186 |
P value = 0.0181 (logrank test), Q value = 0.15
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 244 | 82 | 0.1 - 188.2 (23.3) |
14Q GAIN MUTATED | 55 | 27 | 0.6 - 108.1 (19.7) |
14Q GAIN WILD-TYPE | 189 | 55 | 0.1 - 188.2 (25.1) |
P value = 0.0131 (Wilcoxon-test), Q value = 0.13
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
14Q GAIN MUTATED | 55 | 65.6 (15.4) |
14Q GAIN WILD-TYPE | 190 | 60.1 (14.0) |
P value = 0.00596 (logrank test), Q value = 0.11
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 244 | 82 | 0.1 - 188.2 (23.3) |
16P GAIN MUTATED | 39 | 21 | 0.5 - 86.1 (23.5) |
16P GAIN WILD-TYPE | 205 | 61 | 0.1 - 188.2 (23.1) |
P value = 0.025 (Wilcoxon-test), Q value = 0.18
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
16P GAIN MUTATED | 39 | 66.2 (13.8) |
16P GAIN WILD-TYPE | 206 | 60.4 (14.5) |
P value = 0.0247 (Wilcoxon-test), Q value = 0.18
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
17P GAIN MUTATED | 57 | 65.3 (12.9) |
17P GAIN WILD-TYPE | 188 | 60.1 (14.8) |
P value = 0.0102 (Wilcoxon-test), Q value = 0.12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
18P GAIN MUTATED | 49 | 65.9 (12.5) |
18P GAIN WILD-TYPE | 196 | 60.2 (14.7) |
P value = 0.00954 (Wilcoxon-test), Q value = 0.12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
18Q GAIN MUTATED | 32 | 67.1 (13.7) |
18Q GAIN WILD-TYPE | 213 | 60.4 (14.4) |
P value = 9.92e-05 (Wilcoxon-test), Q value = 0.0058
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
19P GAIN MUTATED | 81 | 66.1 (12.7) |
19P GAIN WILD-TYPE | 164 | 58.9 (14.8) |
P value = 0.00244 (Wilcoxon-test), Q value = 0.055
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
19Q GAIN MUTATED | 61 | 66.2 (12.3) |
19Q GAIN WILD-TYPE | 184 | 59.7 (14.8) |
P value = 0.00177 (logrank test), Q value = 0.045
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 244 | 82 | 0.1 - 188.2 (23.3) |
20P GAIN MUTATED | 61 | 27 | 0.1 - 106.5 (19.7) |
20P GAIN WILD-TYPE | 183 | 55 | 0.1 - 188.2 (25.1) |
P value = 0.00925 (Wilcoxon-test), Q value = 0.12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
20P GAIN MUTATED | 61 | 65.8 (13.6) |
20P GAIN WILD-TYPE | 184 | 59.8 (14.5) |
P value = 0.0108 (logrank test), Q value = 0.12
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 244 | 82 | 0.1 - 188.2 (23.3) |
20Q GAIN MUTATED | 82 | 35 | 0.1 - 143.4 (20.1) |
20Q GAIN WILD-TYPE | 162 | 47 | 0.1 - 188.2 (25.2) |
P value = 0.000326 (Wilcoxon-test), Q value = 0.016
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
20Q GAIN MUTATED | 82 | 66.0 (13.1) |
20Q GAIN WILD-TYPE | 163 | 58.9 (14.6) |
P value = 0.00976 (Fisher's exact test), Q value = 0.12
nPatients | FEMALE | MALE |
---|---|---|
ALL | 132 | 114 |
20Q GAIN MUTATED | 34 | 48 |
20Q GAIN WILD-TYPE | 98 | 66 |
P value = 0.019 (logrank test), Q value = 0.16
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 244 | 82 | 0.1 - 188.2 (23.3) |
21Q GAIN MUTATED | 55 | 25 | 0.1 - 108.1 (19.9) |
21Q GAIN WILD-TYPE | 189 | 57 | 0.1 - 188.2 (24.3) |
P value = 0.036 (Wilcoxon-test), Q value = 0.23
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
21Q GAIN MUTATED | 54 | 65.0 (12.3) |
21Q GAIN WILD-TYPE | 191 | 60.3 (14.9) |
P value = 0.00202 (Wilcoxon-test), Q value = 0.049
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
22Q GAIN MUTATED | 58 | 66.3 (12.6) |
22Q GAIN WILD-TYPE | 187 | 59.8 (14.7) |
P value = 0.0418 (Wilcoxon-test), Q value = 0.24
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
XP GAIN MUTATED | 71 | 64.3 (13.4) |
XP GAIN WILD-TYPE | 174 | 60.1 (14.8) |
P value = 0.0156 (Fisher's exact test), Q value = 0.14
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 5 | 191 |
XQ GAIN MUTATED | 3 | 22 |
XQ GAIN WILD-TYPE | 2 | 169 |
P value = 0.0101 (Fisher's exact test), Q value = 0.12
nPatients | FEMALE | MALE |
---|---|---|
ALL | 132 | 114 |
1P LOSS MUTATED | 23 | 7 |
1P LOSS WILD-TYPE | 109 | 107 |
P value = 0.00815 (Wilcoxon-test), Q value = 0.12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
2P LOSS MUTATED | 83 | 64.8 (13.7) |
2P LOSS WILD-TYPE | 162 | 59.5 (14.6) |
P value = 0.031 (Fisher's exact test), Q value = 0.21
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 6 | 18 | 194 |
2P LOSS MUTATED | 0 | 10 | 66 |
2P LOSS WILD-TYPE | 6 | 8 | 128 |
P value = 0.00138 (logrank test), Q value = 0.041
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 244 | 82 | 0.1 - 188.2 (23.3) |
2Q LOSS MUTATED | 66 | 28 | 0.1 - 96.9 (18.8) |
2Q LOSS WILD-TYPE | 178 | 54 | 0.1 - 188.2 (25.2) |
P value = 0.000344 (Wilcoxon-test), Q value = 0.016
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
2Q LOSS MUTATED | 66 | 66.6 (13.5) |
2Q LOSS WILD-TYPE | 179 | 59.4 (14.4) |
P value = 0.0193 (Wilcoxon-test), Q value = 0.16
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
3P LOSS MUTATED | 56 | 64.7 (15.7) |
3P LOSS WILD-TYPE | 189 | 60.3 (14.0) |
P value = 0.0149 (logrank test), Q value = 0.13
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 244 | 82 | 0.1 - 188.2 (23.3) |
3Q LOSS MUTATED | 48 | 22 | 1.1 - 188.2 (17.8) |
3Q LOSS WILD-TYPE | 196 | 60 | 0.1 - 143.4 (25.2) |
P value = 0.0136 (Wilcoxon-test), Q value = 0.13
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
3Q LOSS MUTATED | 49 | 65.3 (14.7) |
3Q LOSS WILD-TYPE | 196 | 60.3 (14.3) |
P value = 0.00655 (logrank test), Q value = 0.11
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 244 | 82 | 0.1 - 188.2 (23.3) |
6P LOSS MUTATED | 57 | 11 | 0.1 - 188.2 (26.6) |
6P LOSS WILD-TYPE | 187 | 71 | 0.1 - 143.4 (21.4) |
P value = 0.00372 (Wilcoxon-test), Q value = 0.08
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
9P LOSS MUTATED | 81 | 65.1 (13.6) |
9P LOSS WILD-TYPE | 164 | 59.5 (14.6) |
P value = 0.028 (logrank test), Q value = 0.19
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 244 | 82 | 0.1 - 188.2 (23.3) |
9Q LOSS MUTATED | 49 | 23 | 0.1 - 188.2 (16.9) |
9Q LOSS WILD-TYPE | 195 | 59 | 0.1 - 135.5 (24.3) |
P value = 0.0197 (Wilcoxon-test), Q value = 0.16
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
10P LOSS MUTATED | 116 | 63.5 (14.5) |
10P LOSS WILD-TYPE | 129 | 59.4 (14.2) |
P value = 0.00714 (Fisher's exact test), Q value = 0.11
nPatients | FEMALE | MALE |
---|---|---|
ALL | 132 | 114 |
10P LOSS MUTATED | 73 | 43 |
10P LOSS WILD-TYPE | 59 | 71 |
P value = 0.00954 (Wilcoxon-test), Q value = 0.12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
10Q LOSS MUTATED | 126 | 63.8 (13.3) |
10Q LOSS WILD-TYPE | 119 | 58.7 (15.2) |
P value = 0.0104 (Fisher's exact test), Q value = 0.12
nPatients | FEMALE | MALE |
---|---|---|
ALL | 132 | 114 |
10Q LOSS MUTATED | 78 | 48 |
10Q LOSS WILD-TYPE | 54 | 66 |
P value = 0.00172 (Wilcoxon-test), Q value = 0.045
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
13Q LOSS MUTATED | 130 | 64.0 (14.0) |
13Q LOSS WILD-TYPE | 115 | 58.3 (14.5) |
P value = 9.15e-05 (logrank test), Q value = 0.0058
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 244 | 82 | 0.1 - 188.2 (23.3) |
15Q LOSS MUTATED | 40 | 23 | 0.1 - 143.4 (20.0) |
15Q LOSS WILD-TYPE | 204 | 59 | 0.1 - 188.2 (24.7) |
P value = 0.00936 (Wilcoxon-test), Q value = 0.12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
15Q LOSS MUTATED | 42 | 66.5 (13.0) |
15Q LOSS WILD-TYPE | 203 | 60.2 (14.6) |
P value = 0.00529 (Wilcoxon-test), Q value = 0.1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
16Q LOSS MUTATED | 119 | 63.7 (13.7) |
16Q LOSS WILD-TYPE | 126 | 59.0 (14.9) |
P value = 0.0344 (logrank test), Q value = 0.23
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 244 | 82 | 0.1 - 188.2 (23.3) |
17Q LOSS MUTATED | 46 | 20 | 0.1 - 88.6 (21.1) |
17Q LOSS WILD-TYPE | 198 | 62 | 0.1 - 188.2 (23.8) |
P value = 0.0132 (logrank test), Q value = 0.13
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 244 | 82 | 0.1 - 188.2 (23.3) |
18Q LOSS MUTATED | 69 | 30 | 0.1 - 188.2 (18.9) |
18Q LOSS WILD-TYPE | 175 | 52 | 0.1 - 135.5 (25.7) |
P value = 0.0115 (Wilcoxon-test), Q value = 0.12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
20P LOSS MUTATED | 52 | 65.5 (11.9) |
20P LOSS WILD-TYPE | 193 | 60.2 (14.9) |
P value = 0.0362 (Wilcoxon-test), Q value = 0.23
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
20Q LOSS MUTATED | 24 | 67.4 (10.8) |
20Q LOSS WILD-TYPE | 221 | 60.7 (14.7) |
P value = 0.0257 (Wilcoxon-test), Q value = 0.18
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 61.3 (14.5) |
21Q LOSS MUTATED | 48 | 65.6 (11.6) |
21Q LOSS WILD-TYPE | 197 | 60.3 (14.9) |
P value = 0.0406 (Fisher's exact test), Q value = 0.24
nPatients | FEMALE | MALE |
---|---|---|
ALL | 132 | 114 |
22Q LOSS MUTATED | 41 | 22 |
22Q LOSS WILD-TYPE | 91 | 92 |
-
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/SARC-TP/15098587/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/SARC-TP/15087563/SARC-TP.merged_data.txt
-
Number of patients = 246
-
Number of significantly arm-level cnvs = 82
-
Number of selected clinical features = 5
-
Exclude regions that fewer than K tumors have mutations, K = 3
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R
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.