(primary solid tumor cohort)
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 303 patients, 27 significant findings detected with Q value < 0.25.
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4p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
-
4q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
-
5p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
-
5q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
-
7p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
-
7q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
-
12p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
-
12q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
-
14q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
-
16p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
-
16q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
-
17p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
-
17q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
-
19p gain cnv correlated to 'HISTOLOGICAL.TYPE' and 'NUMBER.OF.LYMPH.NODES'.
-
19q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
-
20p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
-
20q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
-
2p loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
-
2q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
-
3q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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9p loss cnv correlated to 'NEOPLASM.DISEASESTAGE'.
-
9q loss cnv correlated to 'NEOPLASM.DISEASESTAGE'.
-
11p loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
-
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%) | 300 |
1 (1.00) |
0.186 (1.00) |
0.575 (1.00) |
0.000248 (0.117) |
1 (1.00) |
1 (1.00) |
0.279 (1.00) |
1 (1.00) |
0.529 (1.00) |
0.222 (1.00) |
3.19e-15 (1.53e-12) |
0.703 (1.00) |
1 (1.00) |
0.558 (1.00) |
|
4p gain | 4 (1%) | 299 |
0.00468 (1.00) |
0.118 (1.00) |
1 (1.00) |
0.371 (1.00) |
0.173 (1.00) |
1 (1.00) |
0.17 (1.00) |
1 (1.00) |
0.374 (1.00) |
0.292 (1.00) |
3.14e-15 (1.52e-12) |
0.502 (1.00) |
0.623 (1.00) |
0.43 (1.00) |
|
4q gain | 4 (1%) | 299 |
0.00468 (1.00) |
0.118 (1.00) |
1 (1.00) |
0.371 (1.00) |
0.173 (1.00) |
1 (1.00) |
0.17 (1.00) |
1 (1.00) |
0.374 (1.00) |
0.292 (1.00) |
3.14e-15 (1.52e-12) |
0.502 (1.00) |
0.623 (1.00) |
0.43 (1.00) |
|
5p gain | 9 (3%) | 294 |
0.00468 (1.00) |
0.0351 (1.00) |
1 (1.00) |
0.0215 (1.00) |
0.351 (1.00) |
1 (1.00) |
0.0112 (1.00) |
0.746 (1.00) |
0.153 (1.00) |
0.585 (1.00) |
2.97e-15 (1.47e-12) |
0.0112 (1.00) |
0.501 (1.00) |
0.0739 (1.00) |
|
5q gain | 9 (3%) | 294 |
0.00468 (1.00) |
0.0351 (1.00) |
1 (1.00) |
0.0215 (1.00) |
0.351 (1.00) |
1 (1.00) |
0.0112 (1.00) |
0.746 (1.00) |
0.153 (1.00) |
0.585 (1.00) |
2.97e-15 (1.47e-12) |
0.0112 (1.00) |
0.501 (1.00) |
0.0739 (1.00) |
|
7p gain | 11 (4%) | 292 |
1 (1.00) |
0.0361 (1.00) |
0.737 (1.00) |
0.0296 (1.00) |
1 (1.00) |
1 (1.00) |
0.0236 (1.00) |
0.451 (1.00) |
0.0947 (1.00) |
0.301 (1.00) |
2.86e-15 (1.42e-12) |
0.00371 (1.00) |
0.541 (1.00) |
0.171 (1.00) |
|
7q gain | 13 (4%) | 290 |
1 (1.00) |
0.0201 (1.00) |
0.529 (1.00) |
0.00532 (1.00) |
1 (1.00) |
1 (1.00) |
0.0503 (1.00) |
0.804 (1.00) |
0.0152 (1.00) |
0.116 (1.00) |
2.86e-15 (1.42e-12) |
0.0116 (1.00) |
0.573 (1.00) |
0.162 (1.00) |
|
12p gain | 10 (3%) | 293 |
1 (1.00) |
0.141 (1.00) |
0.461 (1.00) |
0.0155 (1.00) |
1 (1.00) |
1 (1.00) |
0.00495 (1.00) |
0.563 (1.00) |
0.0579 (1.00) |
0.63 (1.00) |
2.97e-15 (1.47e-12) |
0.0481 (1.00) |
0.75 (1.00) |
0.369 (1.00) |
|
12q gain | 10 (3%) | 293 |
1 (1.00) |
0.141 (1.00) |
0.461 (1.00) |
0.0155 (1.00) |
1 (1.00) |
1 (1.00) |
0.00495 (1.00) |
0.563 (1.00) |
0.0579 (1.00) |
0.63 (1.00) |
2.97e-15 (1.47e-12) |
0.0481 (1.00) |
0.75 (1.00) |
0.369 (1.00) |
|
14q gain | 6 (2%) | 297 |
1 (1.00) |
0.257 (1.00) |
0.343 (1.00) |
0.0949 (1.00) |
1 (1.00) |
1 (1.00) |
0.0589 (1.00) |
1 (1.00) |
0.192 (1.00) |
0.422 (1.00) |
3.14e-15 (1.52e-12) |
0.043 (1.00) |
0.214 (1.00) |
0.47 (1.00) |
|
16p gain | 8 (3%) | 295 |
1 (1.00) |
0.252 (1.00) |
0.208 (1.00) |
0.212 (1.00) |
1 (1.00) |
1 (1.00) |
0.361 (1.00) |
1 (1.00) |
0.0468 (1.00) |
0.174 (1.00) |
3.08e-15 (1.5e-12) |
0.151 (1.00) |
1 (1.00) |
0.477 (1.00) |
|
16q gain | 6 (2%) | 297 |
1 (1.00) |
0.152 (1.00) |
0.343 (1.00) |
0.503 (1.00) |
1 (1.00) |
1 (1.00) |
0.279 (1.00) |
1 (1.00) |
0.192 (1.00) |
0.422 (1.00) |
3.14e-15 (1.52e-12) |
0.043 (1.00) |
0.684 (1.00) |
0.426 (1.00) |
|
17p gain | 8 (3%) | 295 |
1 (1.00) |
0.307 (1.00) |
0.208 (1.00) |
0.0224 (1.00) |
1 (1.00) |
1 (1.00) |
0.165 (1.00) |
0.33 (1.00) |
0.18 (1.00) |
0.535 (1.00) |
3.02e-15 (1.47e-12) |
0.0104 (1.00) |
0.723 (1.00) |
0.478 (1.00) |
|
17q gain | 9 (3%) | 294 |
1 (1.00) |
0.467 (1.00) |
0.118 (1.00) |
0.0467 (1.00) |
1 (1.00) |
1 (1.00) |
0.0705 (1.00) |
0.273 (1.00) |
0.153 (1.00) |
0.585 (1.00) |
2.97e-15 (1.47e-12) |
0.0242 (1.00) |
1 (1.00) |
0.752 (1.00) |
|
19q gain | 4 (1%) | 299 |
0.00468 (1.00) |
0.0697 (1.00) |
1 (1.00) |
0.00151 (0.705) |
0.173 (1.00) |
1 (1.00) |
0.17 (1.00) |
0.61 (1.00) |
0.374 (1.00) |
0.292 (1.00) |
3.14e-15 (1.52e-12) |
0.502 (1.00) |
1 (1.00) |
0.312 (1.00) |
|
20p gain | 5 (2%) | 298 |
1 (1.00) |
0.279 (1.00) |
0.336 (1.00) |
0.0333 (1.00) |
1 (1.00) |
1 (1.00) |
0.123 (1.00) |
0.406 (1.00) |
0.158 (1.00) |
1 (1.00) |
3.19e-15 (1.53e-12) |
0.0115 (1.00) |
1 (1.00) |
0.149 (1.00) |
|
20q gain | 5 (2%) | 298 |
1 (1.00) |
0.279 (1.00) |
0.336 (1.00) |
0.0333 (1.00) |
1 (1.00) |
1 (1.00) |
0.123 (1.00) |
0.406 (1.00) |
0.158 (1.00) |
1 (1.00) |
3.19e-15 (1.53e-12) |
0.0115 (1.00) |
1 (1.00) |
0.149 (1.00) |
|
2p loss | 7 (2%) | 296 |
1 (1.00) |
0.189 (1.00) |
0.684 (1.00) |
0.0496 (1.00) |
1 (1.00) |
1 (1.00) |
0.203 (1.00) |
0.311 (1.00) |
0.112 (1.00) |
0.48 (1.00) |
2.97e-15 (1.47e-12) |
0.0031 (1.00) |
1 (1.00) |
0.9 (1.00) |
|
2q loss | 6 (2%) | 297 |
1 (1.00) |
0.0373 (1.00) |
1 (1.00) |
0.0186 (1.00) |
1 (1.00) |
1 (1.00) |
0.279 (1.00) |
0.42 (1.00) |
0.171 (1.00) |
0.422 (1.00) |
3.02e-15 (1.47e-12) |
0.000534 (0.251) |
0.684 (1.00) |
0.325 (1.00) |
|
3q loss | 3 (1%) | 300 |
1 (1.00) |
0.2 (1.00) |
1 (1.00) |
0.0585 (1.00) |
1 (1.00) |
1 (1.00) |
0.279 (1.00) |
1 (1.00) |
0.529 (1.00) |
1 (1.00) |
3.19e-15 (1.53e-12) |
0.0285 (1.00) |
1 (1.00) |
0.147 (1.00) |
|
9p loss | 5 (2%) | 298 |
1 (1.00) |
0.922 (1.00) |
0.336 (1.00) |
0.559 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.406 (1.00) |
0.55 (1.00) |
1 (1.00) |
0.456 (1.00) |
4.92e-05 (0.0232) |
0.681 (1.00) |
0.477 (1.00) |
|
9q loss | 7 (2%) | 296 |
1 (1.00) |
0.34 (1.00) |
0.684 (1.00) |
0.163 (1.00) |
0.284 (1.00) |
0.298 (1.00) |
0.502 (1.00) |
0.311 (1.00) |
0.513 (1.00) |
1 (1.00) |
0.745 (1.00) |
1.14e-05 (0.00541) |
0.72 (1.00) |
0.5 (1.00) |
|
11p loss | 4 (1%) | 299 |
0.00468 (1.00) |
0.0307 (1.00) |
0.262 (1.00) |
0.171 (1.00) |
0.173 (1.00) |
1 (1.00) |
0.17 (1.00) |
0.61 (1.00) |
0.374 (1.00) |
0.292 (1.00) |
3.14e-15 (1.52e-12) |
0.502 (1.00) |
0.623 (1.00) |
0.204 (1.00) |
|
11q loss | 5 (2%) | 298 |
0.00468 (1.00) |
0.0185 (1.00) |
0.103 (1.00) |
0.0977 (1.00) |
0.212 (1.00) |
1 (1.00) |
0.123 (1.00) |
0.406 (1.00) |
0.256 (1.00) |
0.359 (1.00) |
3.08e-15 (1.5e-12) |
0.169 (1.00) |
1 (1.00) |
0.204 (1.00) |
|
13q loss | 9 (3%) | 294 |
0.00468 (1.00) |
0.0329 (1.00) |
0.236 (1.00) |
0.0753 (1.00) |
0.351 (1.00) |
0.00442 (1.00) |
0.273 (1.00) |
0.746 (1.00) |
0.144 (1.00) |
0.407 (1.00) |
2.91e-15 (1.44e-12) |
0.154 (1.00) |
0.501 (1.00) |
0.404 (1.00) |
|
15q loss | 3 (1%) | 300 |
1 (1.00) |
0.405 (1.00) |
0.575 (1.00) |
0.0437 (1.00) |
1 (1.00) |
1 (1.00) |
0.279 (1.00) |
1 (1.00) |
0.529 (1.00) |
1 (1.00) |
3.19e-15 (1.53e-12) |
0.0285 (1.00) |
1 (1.00) |
0.355 (1.00) |
|
1q gain | 8 (3%) | 295 |
1 (1.00) |
0.161 (1.00) |
0.419 (1.00) |
0.307 (1.00) |
0.318 (1.00) |
1 (1.00) |
0.754 (1.00) |
0.0035 (1.00) |
0.3 (1.00) |
0.289 (1.00) |
0.438 (1.00) |
0.0803 (1.00) |
0.169 (1.00) |
0.61 (1.00) |
|
11p gain | 3 (1%) | 300 |
1 (1.00) |
0.718 (1.00) |
1 (1.00) |
0.0218 (1.00) |
1 (1.00) |
1 (1.00) |
0.279 (1.00) |
1 (1.00) |
0.555 (1.00) |
1 (1.00) |
0.445 (1.00) |
0.619 (1.00) |
0.013 (1.00) |
||
1p loss | 3 (1%) | 300 |
1 (1.00) |
0.181 (1.00) |
0.575 (1.00) |
0.541 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.529 (1.00) |
1 (1.00) |
0.0285 (1.00) |
0.619 (1.00) |
|||
10p loss | 3 (1%) | 300 |
1 (1.00) |
0.0335 (1.00) |
1 (1.00) |
0.541 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.529 (1.00) |
1 (1.00) |
0.0285 (1.00) |
1 (1.00) |
|||
10q loss | 3 (1%) | 300 |
1 (1.00) |
0.0335 (1.00) |
1 (1.00) |
0.541 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.529 (1.00) |
1 (1.00) |
0.0285 (1.00) |
1 (1.00) |
|||
17p loss | 4 (1%) | 299 |
1 (1.00) |
0.526 (1.00) |
0.575 (1.00) |
0.799 (1.00) |
0.0113 (1.00) |
1 (1.00) |
0.644 (1.00) |
0.05 (1.00) |
0.274 (1.00) |
1 (1.00) |
0.573 (1.00) |
0.075 (1.00) |
0.366 (1.00) |
0.227 (1.00) |
|
18p loss | 3 (1%) | 300 |
1 (1.00) |
0.97 (1.00) |
0.575 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.862 (1.00) |
1 (1.00) |
0.0615 (1.00) |
0.0425 (1.00) |
0.619 (1.00) |
0.665 (1.00) |
|
18q loss | 3 (1%) | 300 |
1 (1.00) |
0.97 (1.00) |
0.575 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.862 (1.00) |
1 (1.00) |
0.0615 (1.00) |
0.0425 (1.00) |
0.619 (1.00) |
0.665 (1.00) |
|
21q loss | 5 (2%) | 298 |
1 (1.00) |
0.0267 (1.00) |
0.602 (1.00) |
0.317 (1.00) |
1 (1.00) |
1 (1.00) |
0.415 (1.00) |
0.406 (1.00) |
0.55 (1.00) |
0.556 (1.00) |
0.993 (1.00) |
0.00498 (1.00) |
0.371 (1.00) |
0.686 (1.00) |
|
22q loss | 39 (13%) | 264 |
1 (1.00) |
0.327 (1.00) |
1 (1.00) |
0.000578 (0.271) |
0.229 (1.00) |
0.7 (1.00) |
0.552 (1.00) |
0.161 (1.00) |
0.119 (1.00) |
0.632 (1.00) |
0.448 (1.00) |
0.458 (1.00) |
0.304 (1.00) |
0.739 (1.00) |
P value = 3.14e-15 (t-test), Q value = 1.5e-12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 242 | 2.8 (5.1) |
4P GAIN MUTATED | 4 | 0.0 (0.0) |
4P GAIN WILD-TYPE | 238 | 2.8 (5.2) |
P value = 3.14e-15 (t-test), Q value = 1.5e-12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 242 | 2.8 (5.1) |
4Q GAIN MUTATED | 4 | 0.0 (0.0) |
4Q GAIN WILD-TYPE | 238 | 2.8 (5.2) |
P value = 2.97e-15 (t-test), Q value = 1.5e-12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 242 | 2.8 (5.1) |
5P GAIN MUTATED | 7 | 0.0 (0.0) |
5P GAIN WILD-TYPE | 235 | 2.9 (5.2) |
P value = 2.97e-15 (t-test), Q value = 1.5e-12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 242 | 2.8 (5.1) |
5Q GAIN MUTATED | 7 | 0.0 (0.0) |
5Q GAIN WILD-TYPE | 235 | 2.9 (5.2) |
P value = 2.86e-15 (t-test), Q value = 1.4e-12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 242 | 2.8 (5.1) |
7P GAIN MUTATED | 9 | 0.0 (0.0) |
7P GAIN WILD-TYPE | 233 | 2.9 (5.2) |
P value = 2.86e-15 (t-test), Q value = 1.4e-12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 242 | 2.8 (5.1) |
7Q GAIN MUTATED | 9 | 0.0 (0.0) |
7Q GAIN WILD-TYPE | 233 | 2.9 (5.2) |
P value = 2.97e-15 (t-test), Q value = 1.5e-12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 242 | 2.8 (5.1) |
12P GAIN MUTATED | 7 | 0.0 (0.0) |
12P GAIN WILD-TYPE | 235 | 2.9 (5.2) |
P value = 2.97e-15 (t-test), Q value = 1.5e-12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 242 | 2.8 (5.1) |
12Q GAIN MUTATED | 7 | 0.0 (0.0) |
12Q GAIN WILD-TYPE | 235 | 2.9 (5.2) |
P value = 3.14e-15 (t-test), Q value = 1.5e-12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 242 | 2.8 (5.1) |
14Q GAIN MUTATED | 4 | 0.0 (0.0) |
14Q GAIN WILD-TYPE | 238 | 2.8 (5.2) |
P value = 3.08e-15 (t-test), Q value = 1.5e-12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 242 | 2.8 (5.1) |
16P GAIN MUTATED | 5 | 0.0 (0.0) |
16P GAIN WILD-TYPE | 237 | 2.8 (5.2) |
P value = 3.14e-15 (t-test), Q value = 1.5e-12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 242 | 2.8 (5.1) |
16Q GAIN MUTATED | 4 | 0.0 (0.0) |
16Q GAIN WILD-TYPE | 238 | 2.8 (5.2) |
P value = 3.02e-15 (t-test), Q value = 1.5e-12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 242 | 2.8 (5.1) |
17P GAIN MUTATED | 6 | 0.0 (0.0) |
17P GAIN WILD-TYPE | 236 | 2.8 (5.2) |
P value = 2.97e-15 (t-test), Q value = 1.5e-12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 242 | 2.8 (5.1) |
17Q GAIN MUTATED | 7 | 0.0 (0.0) |
17Q GAIN WILD-TYPE | 235 | 2.9 (5.2) |
P value = 0.000248 (Fisher's exact test), Q value = 0.12
nPatients | OTHER | THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL | THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) | THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES) |
---|---|---|---|---|
ALL | 20 | 178 | 75 | 30 |
19P GAIN MUTATED | 3 | 0 | 0 | 0 |
19P GAIN WILD-TYPE | 17 | 178 | 75 | 30 |
P value = 3.19e-15 (t-test), Q value = 1.5e-12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 242 | 2.8 (5.1) |
19P GAIN MUTATED | 3 | 0.0 (0.0) |
19P GAIN WILD-TYPE | 239 | 2.8 (5.1) |
P value = 3.14e-15 (t-test), Q value = 1.5e-12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 242 | 2.8 (5.1) |
19Q GAIN MUTATED | 4 | 0.0 (0.0) |
19Q GAIN WILD-TYPE | 238 | 2.8 (5.2) |
P value = 3.19e-15 (t-test), Q value = 1.5e-12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 242 | 2.8 (5.1) |
20P GAIN MUTATED | 3 | 0.0 (0.0) |
20P GAIN WILD-TYPE | 239 | 2.8 (5.1) |
P value = 3.19e-15 (t-test), Q value = 1.5e-12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 242 | 2.8 (5.1) |
20Q GAIN MUTATED | 3 | 0.0 (0.0) |
20Q GAIN WILD-TYPE | 239 | 2.8 (5.1) |
P value = 2.97e-15 (t-test), Q value = 1.5e-12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 242 | 2.8 (5.1) |
2P LOSS MUTATED | 7 | 0.0 (0.0) |
2P LOSS WILD-TYPE | 235 | 2.9 (5.2) |
P value = 3.02e-15 (t-test), Q value = 1.5e-12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 242 | 2.8 (5.1) |
2Q LOSS MUTATED | 6 | 0.0 (0.0) |
2Q LOSS WILD-TYPE | 236 | 2.8 (5.2) |
P value = 3.19e-15 (t-test), Q value = 1.5e-12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 242 | 2.8 (5.1) |
3Q LOSS MUTATED | 3 | 0.0 (0.0) |
3Q LOSS WILD-TYPE | 239 | 2.8 (5.1) |
P value = 4.92e-05 (Chi-square test), Q value = 0.023
nPatients | STAGE I | STAGE II | STAGE III | STAGE IVA | STAGE IVC |
---|---|---|---|---|---|
ALL | 173 | 33 | 66 | 27 | 3 |
9P LOSS MUTATED | 1 | 4 | 0 | 0 | 0 |
9P LOSS WILD-TYPE | 172 | 29 | 66 | 27 | 3 |
P value = 1.14e-05 (Chi-square test), Q value = 0.0054
nPatients | STAGE I | STAGE II | STAGE III | STAGE IVA | STAGE IVC |
---|---|---|---|---|---|
ALL | 173 | 33 | 66 | 27 | 3 |
9Q LOSS MUTATED | 1 | 5 | 0 | 1 | 0 |
9Q LOSS WILD-TYPE | 172 | 28 | 66 | 26 | 3 |
P value = 3.14e-15 (t-test), Q value = 1.5e-12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 242 | 2.8 (5.1) |
11P LOSS MUTATED | 4 | 0.0 (0.0) |
11P LOSS WILD-TYPE | 238 | 2.8 (5.2) |
P value = 3.08e-15 (t-test), Q value = 1.5e-12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 242 | 2.8 (5.1) |
11Q LOSS MUTATED | 5 | 0.0 (0.0) |
11Q LOSS WILD-TYPE | 237 | 2.8 (5.2) |
P value = 2.91e-15 (t-test), Q value = 1.4e-12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 242 | 2.8 (5.1) |
13Q LOSS MUTATED | 8 | 0.0 (0.0) |
13Q LOSS WILD-TYPE | 234 | 2.9 (5.2) |
P value = 3.19e-15 (t-test), Q value = 1.5e-12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 242 | 2.8 (5.1) |
15Q LOSS MUTATED | 3 | 0.0 (0.0) |
15Q LOSS WILD-TYPE | 239 | 2.8 (5.1) |
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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 = 303
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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.