This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 36 arm-level results and 15 clinical features across 284 patients, 27 significant findings detected with Q value < 0.25.
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4p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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4q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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5p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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5q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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7p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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7q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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12p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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12q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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14q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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16p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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16q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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17p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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17q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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19p gain cnv correlated to 'HISTOLOGICAL.TYPE' and 'NUMBER.OF.LYMPH.NODES'.
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19q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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20p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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20q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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2p loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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2q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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3q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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9p loss cnv correlated to 'NEOPLASM.DISEASESTAGE'.
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9q loss cnv correlated to 'NEOPLASM.DISEASESTAGE'.
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11p loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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11q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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13q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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15q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
Clinical Features |
Time to Death |
AGE | GENDER |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
RADIATIONEXPOSURE |
DISTANT METASTASIS |
EXTRATHYROIDAL EXTENSION |
LYMPH NODE METASTASIS |
COMPLETENESS OF RESECTION |
NUMBER OF LYMPH NODES |
TUMOR STAGECODE |
NEOPLASM DISEASESTAGE |
MULTIFOCALITY |
TUMOR SIZE |
||
nCNV (%) | nWild-Type | logrank test | t-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 | Chi-square test | Fisher's exact test | t-test | t-test | Chi-square test | Fisher's exact test | t-test | |
19p gain | 3 (1%) | 281 |
1 (1.00) |
0.188 (1.00) |
0.572 (1.00) |
0.000216 (0.102) |
1 (1.00) |
1 (1.00) |
0.288 (1.00) |
1 (1.00) |
0.516 (1.00) |
0.4 (1.00) |
3.08e-14 (1.47e-11) |
0.722 (1.00) |
1 (1.00) |
0.593 (1.00) |
|
4p gain | 4 (1%) | 280 |
0.00468 (1.00) |
0.119 (1.00) |
1 (1.00) |
0.367 (1.00) |
0.184 (1.00) |
1 (1.00) |
0.18 (1.00) |
1 (1.00) |
0.36 (1.00) |
0.494 (1.00) |
3.02e-14 (1.46e-11) |
0.515 (1.00) |
0.622 (1.00) |
0.479 (1.00) |
|
4q gain | 4 (1%) | 280 |
0.00468 (1.00) |
0.119 (1.00) |
1 (1.00) |
0.367 (1.00) |
0.184 (1.00) |
1 (1.00) |
0.18 (1.00) |
1 (1.00) |
0.36 (1.00) |
0.494 (1.00) |
3.02e-14 (1.46e-11) |
0.515 (1.00) |
0.622 (1.00) |
0.479 (1.00) |
|
5p gain | 8 (3%) | 276 |
0.00468 (1.00) |
0.0796 (1.00) |
1 (1.00) |
0.0225 (1.00) |
0.336 (1.00) |
1 (1.00) |
0.0177 (1.00) |
0.729 (1.00) |
0.195 (1.00) |
0.747 (1.00) |
2.86e-14 (1.41e-11) |
0.0847 (1.00) |
0.723 (1.00) |
0.0691 (1.00) |
|
5q gain | 8 (3%) | 276 |
0.00468 (1.00) |
0.0796 (1.00) |
1 (1.00) |
0.0225 (1.00) |
0.336 (1.00) |
1 (1.00) |
0.0177 (1.00) |
0.729 (1.00) |
0.195 (1.00) |
0.747 (1.00) |
2.86e-14 (1.41e-11) |
0.0847 (1.00) |
0.723 (1.00) |
0.0691 (1.00) |
|
7p gain | 10 (4%) | 274 |
1 (1.00) |
0.0831 (1.00) |
1 (1.00) |
0.0347 (1.00) |
1 (1.00) |
1 (1.00) |
0.086 (1.00) |
0.553 (1.00) |
0.0908 (1.00) |
0.348 (1.00) |
2.75e-14 (1.37e-11) |
0.0372 (1.00) |
0.749 (1.00) |
0.187 (1.00) |
|
7q gain | 12 (4%) | 272 |
1 (1.00) |
0.0477 (1.00) |
0.737 (1.00) |
0.00469 (1.00) |
1 (1.00) |
1 (1.00) |
0.152 (1.00) |
0.79 (1.00) |
0.0499 (1.00) |
0.147 (1.00) |
2.75e-14 (1.37e-11) |
0.0723 (1.00) |
0.769 (1.00) |
0.186 (1.00) |
|
12p gain | 9 (3%) | 275 |
1 (1.00) |
0.286 (1.00) |
0.455 (1.00) |
0.019 (1.00) |
1 (1.00) |
1 (1.00) |
0.0125 (1.00) |
0.74 (1.00) |
0.152 (1.00) |
0.788 (1.00) |
2.86e-14 (1.41e-11) |
0.271 (1.00) |
1 (1.00) |
0.389 (1.00) |
|
12q gain | 9 (3%) | 275 |
1 (1.00) |
0.286 (1.00) |
0.455 (1.00) |
0.019 (1.00) |
1 (1.00) |
1 (1.00) |
0.0125 (1.00) |
0.74 (1.00) |
0.152 (1.00) |
0.788 (1.00) |
2.86e-14 (1.41e-11) |
0.271 (1.00) |
1 (1.00) |
0.389 (1.00) |
|
14q gain | 5 (2%) | 279 |
1 (1.00) |
0.536 (1.00) |
0.333 (1.00) |
0.0744 (1.00) |
1 (1.00) |
1 (1.00) |
0.132 (1.00) |
1 (1.00) |
0.464 (1.00) |
0.575 (1.00) |
3.02e-14 (1.46e-11) |
0.346 (1.00) |
0.37 (1.00) |
0.458 (1.00) |
|
16p gain | 7 (2%) | 277 |
1 (1.00) |
0.499 (1.00) |
0.196 (1.00) |
0.149 (1.00) |
1 (1.00) |
1 (1.00) |
0.519 (1.00) |
0.717 (1.00) |
0.202 (1.00) |
0.201 (1.00) |
2.97e-14 (1.44e-11) |
0.559 (1.00) |
0.723 (1.00) |
0.494 (1.00) |
|
16q gain | 5 (2%) | 279 |
1 (1.00) |
0.339 (1.00) |
0.333 (1.00) |
0.494 (1.00) |
1 (1.00) |
1 (1.00) |
0.429 (1.00) |
1 (1.00) |
0.464 (1.00) |
0.575 (1.00) |
3.02e-14 (1.46e-11) |
0.346 (1.00) |
1 (1.00) |
0.412 (1.00) |
|
17p gain | 7 (2%) | 277 |
1 (1.00) |
0.533 (1.00) |
0.196 (1.00) |
0.0189 (1.00) |
1 (1.00) |
1 (1.00) |
0.219 (1.00) |
0.3 (1.00) |
0.273 (1.00) |
0.699 (1.00) |
2.91e-14 (1.42e-11) |
0.113 (1.00) |
1 (1.00) |
0.504 (1.00) |
|
17q gain | 8 (3%) | 276 |
1 (1.00) |
0.746 (1.00) |
0.118 (1.00) |
0.0261 (1.00) |
1 (1.00) |
1 (1.00) |
0.18 (1.00) |
0.317 (1.00) |
0.195 (1.00) |
0.747 (1.00) |
2.86e-14 (1.41e-11) |
0.184 (1.00) |
1 (1.00) |
0.796 (1.00) |
|
19q gain | 4 (1%) | 280 |
0.00468 (1.00) |
0.0704 (1.00) |
1 (1.00) |
0.00146 (0.683) |
0.184 (1.00) |
1 (1.00) |
0.18 (1.00) |
0.606 (1.00) |
0.36 (1.00) |
0.494 (1.00) |
3.02e-14 (1.46e-11) |
0.515 (1.00) |
1 (1.00) |
0.344 (1.00) |
|
20p gain | 4 (1%) | 280 |
1 (1.00) |
0.562 (1.00) |
0.575 (1.00) |
0.0455 (1.00) |
1 (1.00) |
1 (1.00) |
0.18 (1.00) |
0.606 (1.00) |
0.545 (1.00) |
1 (1.00) |
3.08e-14 (1.47e-11) |
0.164 (1.00) |
1 (1.00) |
0.124 (1.00) |
|
20q gain | 4 (1%) | 280 |
1 (1.00) |
0.562 (1.00) |
0.575 (1.00) |
0.0455 (1.00) |
1 (1.00) |
1 (1.00) |
0.18 (1.00) |
0.606 (1.00) |
0.545 (1.00) |
1 (1.00) |
3.08e-14 (1.47e-11) |
0.164 (1.00) |
1 (1.00) |
0.124 (1.00) |
|
2p loss | 7 (2%) | 277 |
1 (1.00) |
0.195 (1.00) |
0.682 (1.00) |
0.0414 (1.00) |
1 (1.00) |
1 (1.00) |
0.219 (1.00) |
0.3 (1.00) |
0.103 (1.00) |
0.699 (1.00) |
2.86e-14 (1.41e-11) |
0.00421 (1.00) |
1 (1.00) |
0.948 (1.00) |
|
2q loss | 6 (2%) | 278 |
1 (1.00) |
0.0385 (1.00) |
1 (1.00) |
0.0165 (1.00) |
1 (1.00) |
1 (1.00) |
0.295 (1.00) |
0.411 (1.00) |
0.16 (1.00) |
0.642 (1.00) |
2.91e-14 (1.42e-11) |
0.000772 (0.363) |
0.684 (1.00) |
0.439 (1.00) |
|
3q loss | 3 (1%) | 281 |
1 (1.00) |
0.204 (1.00) |
1 (1.00) |
0.057 (1.00) |
1 (1.00) |
1 (1.00) |
0.288 (1.00) |
1 (1.00) |
0.516 (1.00) |
1 (1.00) |
3.08e-14 (1.47e-11) |
0.0339 (1.00) |
1 (1.00) |
0.17 (1.00) |
|
9p loss | 5 (2%) | 279 |
1 (1.00) |
0.909 (1.00) |
0.333 (1.00) |
0.494 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.4 (1.00) |
0.54 (1.00) |
1 (1.00) |
0.439 (1.00) |
7.71e-05 (0.0364) |
0.684 (1.00) |
0.863 (1.00) |
|
9q loss | 7 (2%) | 277 |
1 (1.00) |
0.347 (1.00) |
0.682 (1.00) |
0.149 (1.00) |
0.301 (1.00) |
0.275 (1.00) |
0.519 (1.00) |
0.3 (1.00) |
0.521 (1.00) |
1 (1.00) |
0.76 (1.00) |
1.88e-05 (0.00888) |
0.723 (1.00) |
0.985 (1.00) |
|
11p loss | 4 (1%) | 280 |
0.00468 (1.00) |
0.031 (1.00) |
0.273 (1.00) |
0.145 (1.00) |
0.184 (1.00) |
1 (1.00) |
0.18 (1.00) |
0.606 (1.00) |
0.36 (1.00) |
0.494 (1.00) |
3.02e-14 (1.46e-11) |
0.515 (1.00) |
0.622 (1.00) |
0.238 (1.00) |
|
11q loss | 5 (2%) | 279 |
0.00468 (1.00) |
0.0187 (1.00) |
0.109 (1.00) |
0.085 (1.00) |
0.225 (1.00) |
1 (1.00) |
0.132 (1.00) |
0.4 (1.00) |
0.243 (1.00) |
0.575 (1.00) |
2.97e-14 (1.44e-11) |
0.186 (1.00) |
1 (1.00) |
0.238 (1.00) |
|
13q loss | 9 (3%) | 275 |
0.00468 (1.00) |
0.0339 (1.00) |
0.242 (1.00) |
0.0631 (1.00) |
0.37 (1.00) |
0.00325 (1.00) |
0.391 (1.00) |
0.74 (1.00) |
0.135 (1.00) |
0.431 (1.00) |
2.81e-14 (1.39e-11) |
0.173 (1.00) |
0.501 (1.00) |
0.478 (1.00) |
|
15q loss | 3 (1%) | 281 |
1 (1.00) |
0.412 (1.00) |
0.572 (1.00) |
0.0431 (1.00) |
1 (1.00) |
1 (1.00) |
0.288 (1.00) |
1 (1.00) |
0.516 (1.00) |
1 (1.00) |
3.08e-14 (1.47e-11) |
0.0339 (1.00) |
1 (1.00) |
0.407 (1.00) |
|
1q gain | 8 (3%) | 276 |
1 (1.00) |
0.166 (1.00) |
0.428 (1.00) |
0.311 (1.00) |
0.336 (1.00) |
1 (1.00) |
0.765 (1.00) |
0.00282 (1.00) |
0.319 (1.00) |
0.309 (1.00) |
0.452 (1.00) |
0.0796 (1.00) |
0.172 (1.00) |
0.681 (1.00) |
|
11p gain | 3 (1%) | 281 |
1 (1.00) |
0.725 (1.00) |
1 (1.00) |
0.0141 (1.00) |
1 (1.00) |
1 (1.00) |
0.288 (1.00) |
1 (1.00) |
0.566 (1.00) |
1 (1.00) |
0.446 (1.00) |
0.622 (1.00) |
0.0135 (1.00) |
||
1p loss | 3 (1%) | 281 |
1 (1.00) |
0.184 (1.00) |
0.572 (1.00) |
0.435 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.516 (1.00) |
1 (1.00) |
0.0339 (1.00) |
0.622 (1.00) |
|||
10p loss | 3 (1%) | 281 |
1 (1.00) |
0.0334 (1.00) |
1 (1.00) |
0.435 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.516 (1.00) |
1 (1.00) |
0.0339 (1.00) |
1 (1.00) |
|||
10q loss | 3 (1%) | 281 |
1 (1.00) |
0.0334 (1.00) |
1 (1.00) |
0.435 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.516 (1.00) |
1 (1.00) |
0.0339 (1.00) |
1 (1.00) |
|||
17p loss | 4 (1%) | 280 |
1 (1.00) |
0.537 (1.00) |
0.575 (1.00) |
0.802 (1.00) |
0.0128 (1.00) |
1 (1.00) |
0.652 (1.00) |
0.0446 (1.00) |
0.213 (1.00) |
1 (1.00) |
0.556 (1.00) |
0.0835 (1.00) |
0.37 (1.00) |
0.242 (1.00) |
|
18p loss | 3 (1%) | 281 |
1 (1.00) |
0.958 (1.00) |
0.572 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.865 (1.00) |
1 (1.00) |
0.0561 (1.00) |
0.0502 (1.00) |
0.622 (1.00) |
0.976 (1.00) |
|
18q loss | 3 (1%) | 281 |
1 (1.00) |
0.958 (1.00) |
0.572 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.865 (1.00) |
1 (1.00) |
0.0561 (1.00) |
0.0502 (1.00) |
0.622 (1.00) |
0.976 (1.00) |
|
21q loss | 5 (2%) | 279 |
1 (1.00) |
0.0273 (1.00) |
0.606 (1.00) |
0.318 (1.00) |
1 (1.00) |
1 (1.00) |
0.429 (1.00) |
0.4 (1.00) |
0.54 (1.00) |
0.575 (1.00) |
0.993 (1.00) |
0.00626 (1.00) |
0.37 (1.00) |
0.797 (1.00) |
|
22q loss | 36 (13%) | 248 |
1 (1.00) |
0.408 (1.00) |
1 (1.00) |
0.00112 (0.526) |
0.229 (1.00) |
1 (1.00) |
0.402 (1.00) |
0.135 (1.00) |
0.17 (1.00) |
0.551 (1.00) |
0.462 (1.00) |
0.545 (1.00) |
0.21 (1.00) |
0.627 (1.00) |
P value = 3.02e-14 (t-test), Q value = 1.5e-11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 225 | 2.8 (5.2) |
4P GAIN MUTATED | 4 | 0.0 (0.0) |
4P GAIN WILD-TYPE | 221 | 2.9 (5.3) |
P value = 3.02e-14 (t-test), Q value = 1.5e-11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 225 | 2.8 (5.2) |
4Q GAIN MUTATED | 4 | 0.0 (0.0) |
4Q GAIN WILD-TYPE | 221 | 2.9 (5.3) |
P value = 2.86e-14 (t-test), Q value = 1.4e-11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 225 | 2.8 (5.2) |
5P GAIN MUTATED | 7 | 0.0 (0.0) |
5P GAIN WILD-TYPE | 218 | 2.9 (5.3) |
P value = 2.86e-14 (t-test), Q value = 1.4e-11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 225 | 2.8 (5.2) |
5Q GAIN MUTATED | 7 | 0.0 (0.0) |
5Q GAIN WILD-TYPE | 218 | 2.9 (5.3) |
P value = 2.75e-14 (t-test), Q value = 1.4e-11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 225 | 2.8 (5.2) |
7P GAIN MUTATED | 9 | 0.0 (0.0) |
7P GAIN WILD-TYPE | 216 | 2.9 (5.3) |
P value = 2.75e-14 (t-test), Q value = 1.4e-11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 225 | 2.8 (5.2) |
7Q GAIN MUTATED | 9 | 0.0 (0.0) |
7Q GAIN WILD-TYPE | 216 | 2.9 (5.3) |
P value = 2.86e-14 (t-test), Q value = 1.4e-11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 225 | 2.8 (5.2) |
12P GAIN MUTATED | 7 | 0.0 (0.0) |
12P GAIN WILD-TYPE | 218 | 2.9 (5.3) |
P value = 2.86e-14 (t-test), Q value = 1.4e-11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 225 | 2.8 (5.2) |
12Q GAIN MUTATED | 7 | 0.0 (0.0) |
12Q GAIN WILD-TYPE | 218 | 2.9 (5.3) |
P value = 3.02e-14 (t-test), Q value = 1.5e-11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 225 | 2.8 (5.2) |
14Q GAIN MUTATED | 4 | 0.0 (0.0) |
14Q GAIN WILD-TYPE | 221 | 2.9 (5.3) |
P value = 2.97e-14 (t-test), Q value = 1.4e-11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 225 | 2.8 (5.2) |
16P GAIN MUTATED | 5 | 0.0 (0.0) |
16P GAIN WILD-TYPE | 220 | 2.9 (5.3) |
P value = 3.02e-14 (t-test), Q value = 1.5e-11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 225 | 2.8 (5.2) |
16Q GAIN MUTATED | 4 | 0.0 (0.0) |
16Q GAIN WILD-TYPE | 221 | 2.9 (5.3) |
P value = 2.91e-14 (t-test), Q value = 1.4e-11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 225 | 2.8 (5.2) |
17P GAIN MUTATED | 6 | 0.0 (0.0) |
17P GAIN WILD-TYPE | 219 | 2.9 (5.3) |
P value = 2.86e-14 (t-test), Q value = 1.4e-11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 225 | 2.8 (5.2) |
17Q GAIN MUTATED | 7 | 0.0 (0.0) |
17Q GAIN WILD-TYPE | 218 | 2.9 (5.3) |
P value = 0.000216 (Fisher's exact test), Q value = 0.1
nPatients | OTHER | THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL | THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) | THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES) |
---|---|---|---|---|
ALL | 18 | 167 | 69 | 30 |
19P GAIN MUTATED | 3 | 0 | 0 | 0 |
19P GAIN WILD-TYPE | 15 | 167 | 69 | 30 |
P value = 3.08e-14 (t-test), Q value = 1.5e-11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 225 | 2.8 (5.2) |
19P GAIN MUTATED | 3 | 0.0 (0.0) |
19P GAIN WILD-TYPE | 222 | 2.9 (5.3) |
P value = 3.02e-14 (t-test), Q value = 1.5e-11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 225 | 2.8 (5.2) |
19Q GAIN MUTATED | 4 | 0.0 (0.0) |
19Q GAIN WILD-TYPE | 221 | 2.9 (5.3) |
P value = 3.08e-14 (t-test), Q value = 1.5e-11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 225 | 2.8 (5.2) |
20P GAIN MUTATED | 3 | 0.0 (0.0) |
20P GAIN WILD-TYPE | 222 | 2.9 (5.3) |
P value = 3.08e-14 (t-test), Q value = 1.5e-11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 225 | 2.8 (5.2) |
20Q GAIN MUTATED | 3 | 0.0 (0.0) |
20Q GAIN WILD-TYPE | 222 | 2.9 (5.3) |
P value = 2.86e-14 (t-test), Q value = 1.4e-11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 225 | 2.8 (5.2) |
2P LOSS MUTATED | 7 | 0.0 (0.0) |
2P LOSS WILD-TYPE | 218 | 2.9 (5.3) |
P value = 2.91e-14 (t-test), Q value = 1.4e-11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 225 | 2.8 (5.2) |
2Q LOSS MUTATED | 6 | 0.0 (0.0) |
2Q LOSS WILD-TYPE | 219 | 2.9 (5.3) |
P value = 3.08e-14 (t-test), Q value = 1.5e-11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 225 | 2.8 (5.2) |
3Q LOSS MUTATED | 3 | 0.0 (0.0) |
3Q LOSS WILD-TYPE | 222 | 2.9 (5.3) |
P value = 7.71e-05 (Chi-square test), Q value = 0.036
nPatients | STAGE I | STAGE II | STAGE III | STAGE IVA | STAGE IVC |
---|---|---|---|---|---|
ALL | 161 | 32 | 62 | 25 | 3 |
9P LOSS MUTATED | 1 | 4 | 0 | 0 | 0 |
9P LOSS WILD-TYPE | 160 | 28 | 62 | 25 | 3 |
P value = 1.88e-05 (Chi-square test), Q value = 0.0089
nPatients | STAGE I | STAGE II | STAGE III | STAGE IVA | STAGE IVC |
---|---|---|---|---|---|
ALL | 161 | 32 | 62 | 25 | 3 |
9Q LOSS MUTATED | 1 | 5 | 0 | 1 | 0 |
9Q LOSS WILD-TYPE | 160 | 27 | 62 | 24 | 3 |
P value = 3.02e-14 (t-test), Q value = 1.5e-11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 225 | 2.8 (5.2) |
11P LOSS MUTATED | 4 | 0.0 (0.0) |
11P LOSS WILD-TYPE | 221 | 2.9 (5.3) |
P value = 2.97e-14 (t-test), Q value = 1.4e-11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 225 | 2.8 (5.2) |
11Q LOSS MUTATED | 5 | 0.0 (0.0) |
11Q LOSS WILD-TYPE | 220 | 2.9 (5.3) |
P value = 2.81e-14 (t-test), Q value = 1.4e-11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 225 | 2.8 (5.2) |
13Q LOSS MUTATED | 8 | 0.0 (0.0) |
13Q LOSS WILD-TYPE | 217 | 2.9 (5.3) |
P value = 3.08e-14 (t-test), Q value = 1.5e-11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 225 | 2.8 (5.2) |
15Q LOSS MUTATED | 3 | 0.0 (0.0) |
15Q LOSS WILD-TYPE | 222 | 2.9 (5.3) |
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Mutation data file = broad_values_by_arm.mutsig.cluster.txt
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Clinical data file = THCA-TP.clin.merged.picked.txt
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Number of patients = 284
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Number of significantly arm-level cnvs = 36
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Number of selected clinical features = 15
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Exclude genes 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 continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' 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 multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.