This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 51 arm-level events and 8 clinical features across 123 patients, 62 significant findings detected with Q value < 0.25.
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1q gain cnv correlated to 'Time to Death', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
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3q gain cnv correlated to 'Time to Death' and 'HISTOLOGICAL_TYPE'.
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5p gain cnv correlated to 'HISTOLOGICAL_TYPE'.
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5q gain cnv correlated to 'HISTOLOGICAL_TYPE'.
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7p gain cnv correlated to 'HISTOLOGICAL_TYPE'.
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7q gain cnv correlated to 'HISTOLOGICAL_TYPE'.
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8p gain cnv correlated to 'HISTOLOGICAL_TYPE'.
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8q gain cnv correlated to 'HISTOLOGICAL_TYPE'.
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9p gain cnv correlated to 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'RACE'.
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9q gain cnv correlated to 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'RACE'.
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12p gain cnv correlated to 'HISTOLOGICAL_TYPE'.
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12q gain cnv correlated to 'HISTOLOGICAL_TYPE'.
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14q gain cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.
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15q gain cnv correlated to 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
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17q gain cnv correlated to 'HISTOLOGICAL_TYPE'.
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19p gain cnv correlated to 'HISTOLOGICAL_TYPE'.
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19q gain cnv correlated to 'HISTOLOGICAL_TYPE'.
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20p gain cnv correlated to 'HISTOLOGICAL_TYPE'.
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20q gain cnv correlated to 'HISTOLOGICAL_TYPE'.
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21q gain cnv correlated to 'HISTOLOGICAL_TYPE'.
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1p loss cnv correlated to 'HISTOLOGICAL_TYPE'.
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3p loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'ETHNICITY'.
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3q loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'ETHNICITY'.
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6p loss cnv correlated to 'Time to Death', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
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6q loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'ETHNICITY'.
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9p loss cnv correlated to 'HISTOLOGICAL_TYPE'.
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11p loss cnv correlated to 'TUMOR_TISSUE_SITE' and 'ETHNICITY'.
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11q loss cnv correlated to 'YEARS_TO_BIRTH', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
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12q loss cnv correlated to 'YEARS_TO_BIRTH'.
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16q loss cnv correlated to 'HISTOLOGICAL_TYPE'.
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17p loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'ETHNICITY'.
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17q loss cnv correlated to 'ETHNICITY'.
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18p loss cnv correlated to 'Time to Death' and 'HISTOLOGICAL_TYPE'.
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18q loss cnv correlated to 'Time to Death' and 'HISTOLOGICAL_TYPE'.
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19p loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'ETHNICITY'.
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19q loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'ETHNICITY'.
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21q loss cnv correlated to 'ETHNICITY'.
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22q loss cnv correlated to 'ETHNICITY'.
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xq loss cnv correlated to 'ETHNICITY'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
TUMOR TISSUE SITE |
GENDER |
RADIATION THERAPY |
HISTOLOGICAL TYPE |
RACE | ETHNICITY | ||
nCNV (%) | nWild-Type | logrank test | Wilcoxon-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 | |
1q gain | 23 (19%) | 100 |
2.8e-05 (0.00408) |
0.358 (0.712) |
0.585 (0.938) |
0.247 (0.622) |
0.0157 (0.139) |
3e-05 (0.00408) |
0.319 (0.681) |
0.371 (0.724) |
9p gain | 11 (9%) | 112 |
0.351 (0.711) |
0.00243 (0.0472) |
1 (1.00) |
1 (1.00) |
0.00755 (0.088) |
0.106 (0.433) |
0.0323 (0.216) |
1 (1.00) |
9q gain | 11 (9%) | 112 |
0.351 (0.711) |
0.00243 (0.0472) |
1 (1.00) |
1 (1.00) |
0.00755 (0.088) |
0.107 (0.433) |
0.0313 (0.213) |
1 (1.00) |
15q gain | 12 (10%) | 111 |
0.333 (0.697) |
0.88 (1.00) |
0.0234 (0.175) |
1 (1.00) |
0.0216 (0.166) |
0.0144 (0.134) |
1 (1.00) |
1 (1.00) |
6p loss | 21 (17%) | 102 |
0.00414 (0.0704) |
0.0898 (0.412) |
0.779 (1.00) |
0.64 (0.95) |
0.449 (0.807) |
0.00041 (0.0147) |
0.777 (1.00) |
0.00777 (0.088) |
11q loss | 7 (6%) | 116 |
0.437 (0.803) |
0.014 (0.133) |
0.178 (0.533) |
0.442 (0.803) |
0.229 (0.59) |
0.00584 (0.0781) |
0.705 (0.971) |
0.0118 (0.117) |
3q gain | 5 (4%) | 118 |
0.000347 (0.0147) |
0.093 (0.416) |
0.585 (0.938) |
0.67 (0.97) |
1 (1.00) |
0.00036 (0.0147) |
1 (1.00) |
1 (1.00) |
14q gain | 13 (11%) | 110 |
0.411 (0.765) |
0.0188 (0.149) |
1 (1.00) |
0.772 (1.00) |
0.13 (0.442) |
0.0046 (0.0751) |
0.803 (1.00) |
1 (1.00) |
3p loss | 12 (10%) | 111 |
0.141 (0.471) |
0.232 (0.591) |
0.296 (0.661) |
0.765 (1.00) |
0.336 (0.697) |
0.0114 (0.116) |
1 (1.00) |
0.00566 (0.0781) |
3q loss | 7 (6%) | 116 |
0.448 (0.807) |
0.205 (0.574) |
0.178 (0.533) |
0.116 (0.433) |
0.229 (0.59) |
0.0281 (0.195) |
0.705 (0.971) |
0.00702 (0.0868) |
6q loss | 20 (16%) | 103 |
0.049 (0.29) |
0.124 (0.439) |
0.769 (1.00) |
1 (1.00) |
0.609 (0.938) |
0.00013 (0.00758) |
0.503 (0.874) |
0.00593 (0.0781) |
11p loss | 9 (7%) | 114 |
0.397 (0.753) |
0.155 (0.491) |
0.0239 (0.175) |
1 (1.00) |
0.489 (0.857) |
0.0508 (0.296) |
1 (1.00) |
0.00234 (0.0472) |
17p loss | 14 (11%) | 109 |
0.716 (0.976) |
0.536 (0.911) |
1 (1.00) |
0.401 (0.758) |
0.552 (0.925) |
0.00826 (0.0911) |
0.84 (1.00) |
0.0152 (0.138) |
18p loss | 7 (6%) | 116 |
0.00539 (0.0781) |
0.804 (1.00) |
0.648 (0.95) |
0.709 (0.971) |
0.689 (0.97) |
0.0241 (0.175) |
1 (1.00) |
0.0767 (0.368) |
18q loss | 7 (6%) | 116 |
0.00539 (0.0781) |
0.804 (1.00) |
0.648 (0.95) |
0.709 (0.971) |
0.689 (0.97) |
0.0247 (0.177) |
1 (1.00) |
0.0767 (0.368) |
19p loss | 3 (2%) | 120 |
0.779 (1.00) |
0.275 (0.643) |
0.121 (0.433) |
0.607 (0.938) |
0.268 (0.64) |
0.00045 (0.0147) |
1 (1.00) |
0.0175 (0.146) |
19q loss | 3 (2%) | 120 |
0.779 (1.00) |
0.275 (0.643) |
0.121 (0.433) |
0.607 (0.938) |
0.268 (0.64) |
0.00054 (0.0147) |
1 (1.00) |
0.0175 (0.146) |
5p gain | 11 (9%) | 112 |
0.176 (0.533) |
0.642 (0.95) |
0.0624 (0.327) |
0.116 (0.433) |
0.0445 (0.279) |
0.00013 (0.00758) |
0.764 (1.00) |
0.161 (0.501) |
5q gain | 9 (7%) | 114 |
0.145 (0.475) |
0.553 (0.925) |
0.41 (0.765) |
0.0859 (0.398) |
0.0612 (0.324) |
0.0003 (0.0147) |
0.733 (0.989) |
0.463 (0.821) |
7p gain | 16 (13%) | 107 |
0.113 (0.433) |
0.375 (0.724) |
0.116 (0.433) |
1 (1.00) |
0.167 (0.512) |
0.00049 (0.0147) |
1 (1.00) |
1 (1.00) |
7q gain | 16 (13%) | 107 |
0.113 (0.433) |
0.375 (0.724) |
0.116 (0.433) |
1 (1.00) |
0.167 (0.512) |
0.00067 (0.0171) |
1 (1.00) |
1 (1.00) |
8p gain | 12 (10%) | 111 |
0.128 (0.442) |
0.264 (0.64) |
0.296 (0.661) |
0.368 (0.722) |
0.336 (0.697) |
0.0187 (0.149) |
0.8 (1.00) |
1 (1.00) |
8q gain | 12 (10%) | 111 |
0.128 (0.442) |
0.264 (0.64) |
0.296 (0.661) |
0.368 (0.722) |
0.336 (0.697) |
0.019 (0.149) |
0.803 (1.00) |
1 (1.00) |
12p gain | 4 (3%) | 119 |
0.193 (0.551) |
0.388 (0.743) |
0.209 (0.574) |
0.62 (0.94) |
0.605 (0.938) |
0.0035 (0.0621) |
1 (1.00) |
0.295 (0.661) |
12q gain | 4 (3%) | 119 |
0.193 (0.551) |
0.388 (0.743) |
0.209 (0.574) |
0.62 (0.94) |
0.605 (0.938) |
0.00321 (0.0595) |
1 (1.00) |
0.295 (0.661) |
17q gain | 7 (6%) | 116 |
0.438 (0.803) |
0.574 (0.938) |
0.648 (0.95) |
1 (1.00) |
0.229 (0.59) |
0.00899 (0.0965) |
0.708 (0.971) |
1 (1.00) |
19p gain | 3 (2%) | 120 |
0.684 (0.97) |
0.354 (0.711) |
1 (1.00) |
0.607 (0.938) |
0.268 (0.64) |
0.0011 (0.0264) |
1 (1.00) |
1 (1.00) |
19q gain | 3 (2%) | 120 |
0.684 (0.97) |
0.354 (0.711) |
1 (1.00) |
0.607 (0.938) |
0.268 (0.64) |
0.00151 (0.0342) |
1 (1.00) |
1 (1.00) |
20p gain | 10 (8%) | 113 |
0.631 (0.95) |
0.867 (1.00) |
0.224 (0.59) |
1 (1.00) |
0.307 (0.667) |
6e-05 (0.00612) |
0.596 (0.938) |
0.192 (0.551) |
20q gain | 10 (8%) | 113 |
0.631 (0.95) |
0.867 (1.00) |
0.224 (0.59) |
1 (1.00) |
0.307 (0.667) |
8e-05 (0.00653) |
0.594 (0.938) |
0.192 (0.551) |
21q gain | 3 (2%) | 120 |
0.782 (1.00) |
0.221 (0.59) |
0.121 (0.433) |
0.107 (0.433) |
1 (1.00) |
0.005 (0.0781) |
1 (1.00) |
1 (1.00) |
1p loss | 5 (4%) | 118 |
0.593 (0.938) |
0.148 (0.475) |
1 (1.00) |
0.67 (0.97) |
0.0459 (0.279) |
0.0135 (0.132) |
1 (1.00) |
0.0535 (0.303) |
9p loss | 4 (3%) | 119 |
0.693 (0.971) |
0.131 (0.442) |
0.209 (0.574) |
0.349 (0.711) |
0.605 (0.938) |
0.00051 (0.0147) |
1 (1.00) |
0.295 (0.661) |
12q loss | 7 (6%) | 116 |
0.327 (0.696) |
0.0168 (0.146) |
0.648 (0.95) |
0.116 (0.433) |
0.689 (0.97) |
0.314 (0.673) |
0.709 (0.971) |
0.103 (0.433) |
16q loss | 13 (11%) | 110 |
0.0664 (0.343) |
0.845 (1.00) |
0.479 (0.847) |
0.772 (1.00) |
0.13 (0.442) |
1e-05 (0.00408) |
0.821 (1.00) |
0.0735 (0.361) |
17q loss | 6 (5%) | 117 |
0.601 (0.938) |
0.209 (0.574) |
0.612 (0.938) |
0.681 (0.97) |
0.41 (0.765) |
0.0478 (0.287) |
0.65 (0.951) |
0.00702 (0.0868) |
21q loss | 9 (7%) | 114 |
0.454 (0.812) |
0.0542 (0.303) |
0.105 (0.433) |
1 (1.00) |
0.489 (0.857) |
0.146 (0.475) |
1 (1.00) |
0.0258 (0.182) |
22q loss | 13 (11%) | 110 |
0.83 (1.00) |
0.0919 (0.416) |
0.157 (0.492) |
0.772 (1.00) |
0.059 (0.318) |
0.0698 (0.347) |
1 (1.00) |
0.0113 (0.116) |
xq loss | 5 (4%) | 118 |
0.153 (0.488) |
0.583 (0.938) |
1 (1.00) |
0.193 (0.551) |
0.337 (0.697) |
0.209 (0.574) |
1 (1.00) |
0.0336 (0.221) |
1p gain | 6 (5%) | 117 |
0.304 (0.667) |
0.696 (0.971) |
0.119 (0.433) |
0.425 (0.789) |
1 (1.00) |
0.274 (0.643) |
0.647 (0.95) |
0.356 (0.711) |
18p gain | 3 (2%) | 120 |
0.721 (0.978) |
0.679 (0.97) |
0.528 (0.901) |
1 (1.00) |
0.268 (0.64) |
0.079 (0.373) |
1 (1.00) |
0.23 (0.59) |
18q gain | 3 (2%) | 120 |
0.721 (0.978) |
0.679 (0.97) |
0.528 (0.901) |
1 (1.00) |
0.268 (0.64) |
0.0794 (0.373) |
1 (1.00) |
0.23 (0.59) |
22q gain | 4 (3%) | 119 |
0.685 (0.97) |
0.0938 (0.416) |
0.575 (0.938) |
0.349 (0.711) |
1 (1.00) |
0.0688 (0.347) |
0.499 (0.869) |
1 (1.00) |
xq gain | 4 (3%) | 119 |
0.106 (0.433) |
0.142 (0.472) |
1 (1.00) |
1 (1.00) |
0.605 (0.938) |
0.0957 (0.42) |
1 (1.00) |
1 (1.00) |
4p loss | 5 (4%) | 118 |
0.44 (0.803) |
0.522 (0.901) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.041 (0.261) |
1 (1.00) |
1 (1.00) |
4q loss | 4 (3%) | 119 |
0.462 (0.821) |
0.948 (1.00) |
1 (1.00) |
0.62 (0.94) |
0.605 (0.938) |
0.0694 (0.347) |
1 (1.00) |
1 (1.00) |
10p loss | 3 (2%) | 120 |
0.779 (1.00) |
0.286 (0.661) |
0.528 (0.901) |
0.607 (0.938) |
0.55 (0.925) |
0.296 (0.661) |
1 (1.00) |
0.23 (0.59) |
12p loss | 8 (7%) | 115 |
0.396 (0.753) |
0.039 (0.252) |
1 (1.00) |
0.276 (0.643) |
0.443 (0.803) |
0.11 (0.433) |
1 (1.00) |
0.131 (0.442) |
13q loss | 14 (11%) | 109 |
0.311 (0.671) |
0.254 (0.635) |
0.187 (0.551) |
0.78 (1.00) |
0.233 (0.591) |
0.107 (0.433) |
0.837 (1.00) |
0.0592 (0.318) |
16p loss | 5 (4%) | 118 |
0.602 (0.938) |
0.544 (0.92) |
0.302 (0.667) |
0.367 (0.722) |
0.0459 (0.279) |
0.181 (0.539) |
0.305 (0.667) |
0.0535 (0.303) |
xp loss | 8 (7%) | 115 |
0.0552 (0.304) |
0.216 (0.588) |
1 (1.00) |
1 (1.00) |
0.12 (0.433) |
0.148 (0.475) |
0.735 (0.989) |
0.103 (0.433) |
P value = 2.8e-05 (logrank test), Q value = 0.0041
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 122 | 9 | 0.5 - 150.4 (40.6) |
1Q GAIN MUTATED | 23 | 6 | 1.6 - 114.7 (30.6) |
1Q GAIN WILD-TYPE | 99 | 3 | 0.5 - 150.4 (42.1) |
P value = 0.0157 (Fisher's exact test), Q value = 0.14
nPatients | NO | YES |
---|---|---|
ALL | 81 | 42 |
1Q GAIN MUTATED | 10 | 13 |
1Q GAIN WILD-TYPE | 71 | 29 |
P value = 3e-05 (Fisher's exact test), Q value = 0.0041
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
1Q GAIN MUTATED | 1 | 2 | 1 | 6 | 6 | 7 |
1Q GAIN WILD-TYPE | 16 | 36 | 14 | 24 | 6 | 4 |
P value = 0.000347 (logrank test), Q value = 0.015
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 122 | 9 | 0.5 - 150.4 (40.6) |
3Q GAIN MUTATED | 5 | 2 | 1.6 - 93.7 (28.0) |
3Q GAIN WILD-TYPE | 117 | 7 | 0.5 - 150.4 (41.2) |
P value = 0.00036 (Fisher's exact test), Q value = 0.015
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
3Q GAIN MUTATED | 0 | 0 | 0 | 0 | 3 | 2 |
3Q GAIN WILD-TYPE | 17 | 38 | 15 | 30 | 9 | 9 |
P value = 0.00013 (Fisher's exact test), Q value = 0.0076
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
5P GAIN MUTATED | 0 | 0 | 0 | 4 | 5 | 2 |
5P GAIN WILD-TYPE | 17 | 38 | 15 | 26 | 7 | 9 |
P value = 3e-04 (Fisher's exact test), Q value = 0.015
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
5Q GAIN MUTATED | 0 | 0 | 0 | 3 | 5 | 1 |
5Q GAIN WILD-TYPE | 17 | 38 | 15 | 27 | 7 | 10 |
P value = 0.00049 (Fisher's exact test), Q value = 0.015
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
7P GAIN MUTATED | 0 | 2 | 1 | 7 | 6 | 0 |
7P GAIN WILD-TYPE | 17 | 36 | 14 | 23 | 6 | 11 |
P value = 0.00067 (Fisher's exact test), Q value = 0.017
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
7Q GAIN MUTATED | 0 | 2 | 1 | 7 | 6 | 0 |
7Q GAIN WILD-TYPE | 17 | 36 | 14 | 23 | 6 | 11 |
P value = 0.0187 (Fisher's exact test), Q value = 0.15
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
8P GAIN MUTATED | 0 | 1 | 2 | 4 | 1 | 4 |
8P GAIN WILD-TYPE | 17 | 37 | 13 | 26 | 11 | 7 |
P value = 0.019 (Fisher's exact test), Q value = 0.15
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
8Q GAIN MUTATED | 0 | 1 | 2 | 4 | 1 | 4 |
8Q GAIN WILD-TYPE | 17 | 37 | 13 | 26 | 11 | 7 |
P value = 0.00243 (Wilcoxon-test), Q value = 0.047
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 122 | 58.3 (13.0) |
9P GAIN MUTATED | 11 | 45.7 (15.0) |
9P GAIN WILD-TYPE | 111 | 59.5 (12.2) |
P value = 0.00755 (Fisher's exact test), Q value = 0.088
nPatients | NO | YES |
---|---|---|
ALL | 81 | 42 |
9P GAIN MUTATED | 3 | 8 |
9P GAIN WILD-TYPE | 78 | 34 |
P value = 0.0323 (Fisher's exact test), Q value = 0.22
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 13 | 6 | 102 |
9P GAIN MUTATED | 4 | 0 | 7 |
9P GAIN WILD-TYPE | 9 | 6 | 95 |
P value = 0.00243 (Wilcoxon-test), Q value = 0.047
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 122 | 58.3 (13.0) |
9Q GAIN MUTATED | 11 | 45.7 (15.0) |
9Q GAIN WILD-TYPE | 111 | 59.5 (12.2) |
P value = 0.00755 (Fisher's exact test), Q value = 0.088
nPatients | NO | YES |
---|---|---|
ALL | 81 | 42 |
9Q GAIN MUTATED | 3 | 8 |
9Q GAIN WILD-TYPE | 78 | 34 |
P value = 0.0313 (Fisher's exact test), Q value = 0.21
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 13 | 6 | 102 |
9Q GAIN MUTATED | 4 | 0 | 7 |
9Q GAIN WILD-TYPE | 9 | 6 | 95 |
P value = 0.0035 (Fisher's exact test), Q value = 0.062
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
12P GAIN MUTATED | 0 | 0 | 0 | 1 | 0 | 3 |
12P GAIN WILD-TYPE | 17 | 38 | 15 | 29 | 12 | 8 |
P value = 0.00321 (Fisher's exact test), Q value = 0.06
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
12Q GAIN MUTATED | 0 | 0 | 0 | 1 | 0 | 3 |
12Q GAIN WILD-TYPE | 17 | 38 | 15 | 29 | 12 | 8 |
P value = 0.0188 (Wilcoxon-test), Q value = 0.15
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 122 | 58.3 (13.0) |
14Q GAIN MUTATED | 13 | 49.4 (15.4) |
14Q GAIN WILD-TYPE | 109 | 59.3 (12.4) |
P value = 0.0046 (Fisher's exact test), Q value = 0.075
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
14Q GAIN MUTATED | 0 | 1 | 1 | 8 | 3 | 0 |
14Q GAIN WILD-TYPE | 17 | 37 | 14 | 22 | 9 | 11 |
P value = 0.0234 (Fisher's exact test), Q value = 0.18
nPatients | ANTERIOR MEDIASTINUM | THYMUS |
---|---|---|
ALL | 27 | 96 |
15Q GAIN MUTATED | 6 | 6 |
15Q GAIN WILD-TYPE | 21 | 90 |
P value = 0.0216 (Fisher's exact test), Q value = 0.17
nPatients | NO | YES |
---|---|---|
ALL | 81 | 42 |
15Q GAIN MUTATED | 4 | 8 |
15Q GAIN WILD-TYPE | 77 | 34 |
P value = 0.0144 (Fisher's exact test), Q value = 0.13
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
15Q GAIN MUTATED | 1 | 1 | 1 | 3 | 5 | 1 |
15Q GAIN WILD-TYPE | 16 | 37 | 14 | 27 | 7 | 10 |
P value = 0.00899 (Fisher's exact test), Q value = 0.097
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
17Q GAIN MUTATED | 2 | 0 | 0 | 1 | 1 | 3 |
17Q GAIN WILD-TYPE | 15 | 38 | 15 | 29 | 11 | 8 |
P value = 0.0011 (Fisher's exact test), Q value = 0.026
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
19P GAIN MUTATED | 0 | 0 | 0 | 0 | 3 | 0 |
19P GAIN WILD-TYPE | 17 | 38 | 15 | 30 | 9 | 11 |
P value = 0.00151 (Fisher's exact test), Q value = 0.034
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
19Q GAIN MUTATED | 0 | 0 | 0 | 0 | 3 | 0 |
19Q GAIN WILD-TYPE | 17 | 38 | 15 | 30 | 9 | 11 |
P value = 6e-05 (Fisher's exact test), Q value = 0.0061
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
20P GAIN MUTATED | 0 | 0 | 0 | 2 | 4 | 4 |
20P GAIN WILD-TYPE | 17 | 38 | 15 | 28 | 8 | 7 |
P value = 8e-05 (Fisher's exact test), Q value = 0.0065
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
20Q GAIN MUTATED | 0 | 0 | 0 | 2 | 4 | 4 |
20Q GAIN WILD-TYPE | 17 | 38 | 15 | 28 | 8 | 7 |
P value = 0.005 (Fisher's exact test), Q value = 0.078
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
21Q GAIN MUTATED | 0 | 0 | 0 | 0 | 1 | 2 |
21Q GAIN WILD-TYPE | 17 | 38 | 15 | 30 | 11 | 9 |
P value = 0.0135 (Fisher's exact test), Q value = 0.13
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
1P LOSS MUTATED | 0 | 0 | 0 | 1 | 2 | 2 |
1P LOSS WILD-TYPE | 17 | 38 | 15 | 29 | 10 | 9 |
P value = 0.0114 (Fisher's exact test), Q value = 0.12
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
3P LOSS MUTATED | 0 | 1 | 0 | 6 | 3 | 2 |
3P LOSS WILD-TYPE | 17 | 37 | 15 | 24 | 9 | 9 |
P value = 0.00566 (Fisher's exact test), Q value = 0.078
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 9 | 100 |
3P LOSS MUTATED | 4 | 7 |
3P LOSS WILD-TYPE | 5 | 93 |
P value = 0.0281 (Fisher's exact test), Q value = 0.19
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
3Q LOSS MUTATED | 0 | 0 | 0 | 4 | 2 | 1 |
3Q LOSS WILD-TYPE | 17 | 38 | 15 | 26 | 10 | 10 |
P value = 0.00702 (Fisher's exact test), Q value = 0.087
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 9 | 100 |
3Q LOSS MUTATED | 3 | 3 |
3Q LOSS WILD-TYPE | 6 | 97 |
P value = 0.00414 (logrank test), Q value = 0.07
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 122 | 9 | 0.5 - 150.4 (40.6) |
6P LOSS MUTATED | 21 | 4 | 5.9 - 97.4 (28.0) |
6P LOSS WILD-TYPE | 101 | 5 | 0.5 - 150.4 (42.1) |
P value = 0.00041 (Fisher's exact test), Q value = 0.015
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
6P LOSS MUTATED | 1 | 2 | 0 | 8 | 5 | 5 |
6P LOSS WILD-TYPE | 16 | 36 | 15 | 22 | 7 | 6 |
P value = 0.00777 (Fisher's exact test), Q value = 0.088
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 9 | 100 |
6P LOSS MUTATED | 5 | 14 |
6P LOSS WILD-TYPE | 4 | 86 |
P value = 0.00013 (Fisher's exact test), Q value = 0.0076
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
6Q LOSS MUTATED | 0 | 2 | 0 | 8 | 5 | 5 |
6Q LOSS WILD-TYPE | 17 | 36 | 15 | 22 | 7 | 6 |
P value = 0.00593 (Fisher's exact test), Q value = 0.078
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 9 | 100 |
6Q LOSS MUTATED | 5 | 13 |
6Q LOSS WILD-TYPE | 4 | 87 |
P value = 0.00051 (Fisher's exact test), Q value = 0.015
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
9P LOSS MUTATED | 0 | 0 | 0 | 0 | 1 | 3 |
9P LOSS WILD-TYPE | 17 | 38 | 15 | 30 | 11 | 8 |
P value = 0.0239 (Fisher's exact test), Q value = 0.18
nPatients | ANTERIOR MEDIASTINUM | THYMUS |
---|---|---|
ALL | 27 | 96 |
11P LOSS MUTATED | 5 | 4 |
11P LOSS WILD-TYPE | 22 | 92 |
P value = 0.00234 (Fisher's exact test), Q value = 0.047
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 9 | 100 |
11P LOSS MUTATED | 4 | 5 |
11P LOSS WILD-TYPE | 5 | 95 |
P value = 0.014 (Wilcoxon-test), Q value = 0.13
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 122 | 58.3 (13.0) |
11Q LOSS MUTATED | 7 | 44.4 (16.5) |
11Q LOSS WILD-TYPE | 115 | 59.1 (12.4) |
P value = 0.00584 (Fisher's exact test), Q value = 0.078
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
11Q LOSS MUTATED | 0 | 0 | 0 | 4 | 3 | 0 |
11Q LOSS WILD-TYPE | 17 | 38 | 15 | 26 | 9 | 11 |
P value = 0.0118 (Fisher's exact test), Q value = 0.12
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 9 | 100 |
11Q LOSS MUTATED | 3 | 4 |
11Q LOSS WILD-TYPE | 6 | 96 |
P value = 0.0168 (Wilcoxon-test), Q value = 0.15
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 122 | 58.3 (13.0) |
12Q LOSS MUTATED | 7 | 44.6 (17.0) |
12Q LOSS WILD-TYPE | 115 | 59.1 (12.3) |
P value = 1e-05 (Fisher's exact test), Q value = 0.0041
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
16Q LOSS MUTATED | 0 | 1 | 0 | 2 | 1 | 9 |
16Q LOSS WILD-TYPE | 17 | 37 | 15 | 28 | 11 | 2 |
P value = 0.00826 (Fisher's exact test), Q value = 0.091
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
17P LOSS MUTATED | 3 | 1 | 0 | 3 | 3 | 4 |
17P LOSS WILD-TYPE | 14 | 37 | 15 | 27 | 9 | 7 |
P value = 0.0152 (Fisher's exact test), Q value = 0.14
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 9 | 100 |
17P LOSS MUTATED | 4 | 10 |
17P LOSS WILD-TYPE | 5 | 90 |
P value = 0.00702 (Fisher's exact test), Q value = 0.087
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 9 | 100 |
17Q LOSS MUTATED | 3 | 3 |
17Q LOSS WILD-TYPE | 6 | 97 |
P value = 0.00539 (logrank test), Q value = 0.078
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 122 | 9 | 0.5 - 150.4 (40.6) |
18P LOSS MUTATED | 7 | 2 | 5.9 - 82.7 (49.4) |
18P LOSS WILD-TYPE | 115 | 7 | 0.5 - 150.4 (40.1) |
P value = 0.0241 (Fisher's exact test), Q value = 0.18
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
18P LOSS MUTATED | 1 | 0 | 0 | 2 | 3 | 1 |
18P LOSS WILD-TYPE | 16 | 38 | 15 | 28 | 9 | 10 |
P value = 0.00539 (logrank test), Q value = 0.078
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 122 | 9 | 0.5 - 150.4 (40.6) |
18Q LOSS MUTATED | 7 | 2 | 5.9 - 82.7 (49.4) |
18Q LOSS WILD-TYPE | 115 | 7 | 0.5 - 150.4 (40.1) |
P value = 0.0247 (Fisher's exact test), Q value = 0.18
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
18Q LOSS MUTATED | 1 | 0 | 0 | 2 | 3 | 1 |
18Q LOSS WILD-TYPE | 16 | 38 | 15 | 28 | 9 | 10 |
P value = 0.00045 (Fisher's exact test), Q value = 0.015
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
19P LOSS MUTATED | 0 | 0 | 0 | 0 | 0 | 3 |
19P LOSS WILD-TYPE | 17 | 38 | 15 | 30 | 12 | 8 |
P value = 0.0175 (Fisher's exact test), Q value = 0.15
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 9 | 100 |
19P LOSS MUTATED | 2 | 1 |
19P LOSS WILD-TYPE | 7 | 99 |
P value = 0.00054 (Fisher's exact test), Q value = 0.015
nPatients | THYMOMA; TYPE A | THYMOMA; TYPE AB | THYMOMA; TYPE B1 | THYMOMA; TYPE B2 | THYMOMA; TYPE B3 | THYMOMA; TYPE C |
---|---|---|---|---|---|---|
ALL | 17 | 38 | 15 | 30 | 12 | 11 |
19Q LOSS MUTATED | 0 | 0 | 0 | 0 | 0 | 3 |
19Q LOSS WILD-TYPE | 17 | 38 | 15 | 30 | 12 | 8 |
P value = 0.0175 (Fisher's exact test), Q value = 0.15
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 9 | 100 |
19Q LOSS MUTATED | 2 | 1 |
19Q LOSS WILD-TYPE | 7 | 99 |
P value = 0.0258 (Fisher's exact test), Q value = 0.18
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 9 | 100 |
21Q LOSS MUTATED | 3 | 6 |
21Q LOSS WILD-TYPE | 6 | 94 |
P value = 0.0113 (Fisher's exact test), Q value = 0.12
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 9 | 100 |
22Q LOSS MUTATED | 4 | 9 |
22Q LOSS WILD-TYPE | 5 | 91 |
P value = 0.0336 (Fisher's exact test), Q value = 0.22
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 9 | 100 |
XQ LOSS MUTATED | 2 | 2 |
XQ LOSS WILD-TYPE | 7 | 98 |
-
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/THYM-TP/22516316/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/THYM-TP/22507339/THYM-TP.merged_data.txt
-
Number of patients = 123
-
Number of significantly arm-level cnvs = 51
-
Number of selected clinical features = 8
-
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.