This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 68 focal events and 15 clinical features across 515 patients, 21 significant findings detected with Q value < 0.25.
-
amp_1p22.3 cnv correlated to 'YEARS_TO_BIRTH'.
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amp_6p21.1 cnv correlated to 'RACE'.
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amp_7p11.2 cnv correlated to 'PATHOLOGY_N_STAGE'.
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amp_7q31.2 cnv correlated to 'YEARS_TO_BIRTH'.
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amp_8q24.21 cnv correlated to 'HISTOLOGICAL_TYPE'.
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amp_11q13.3 cnv correlated to 'YEARS_TO_BIRTH'.
-
amp_12q14.1 cnv correlated to 'YEAR_OF_TOBACCO_SMOKING_ONSET'.
-
amp_17q12 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.
-
del_2q22.1 cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.
-
del_5q31.1 cnv correlated to 'YEARS_TO_BIRTH'.
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del_6q11.1 cnv correlated to 'PATHOLOGY_N_STAGE'.
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del_9p23 cnv correlated to 'PATHOLOGY_N_STAGE'.
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del_9p21.3 cnv correlated to 'PATHOLOGY_N_STAGE'.
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del_12p13.2 cnv correlated to 'GENDER'.
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del_13q12.11 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.
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del_14q32.12 cnv correlated to 'PATHOLOGY_N_STAGE'.
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del_15q11.2 cnv correlated to 'YEARS_TO_BIRTH'.
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del_19p13.2 cnv correlated to 'GENDER'.
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del_21q11.2 cnv correlated to 'YEAR_OF_TOBACCO_SMOKING_ONSET'.
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del_22q13.32 cnv correlated to 'YEARS_TO_BIRTH' and 'YEAR_OF_TOBACCO_SMOKING_ONSET'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 68 focal events and 15 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 21 significant findings detected.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
PATHOLOGIC STAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
RADIATION THERAPY |
KARNOFSKY PERFORMANCE SCORE |
HISTOLOGICAL TYPE |
NUMBER PACK YEARS SMOKED |
YEAR OF TOBACCO SMOKING ONSET |
RESIDUAL TUMOR |
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 | Wilcoxon-test | Fisher's exact test | Wilcoxon-test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
del 22q13 32 | 254 (49%) | 261 |
0.986 (1.00) |
0.000533 (0.103) |
0.911 (1.00) |
0.98 (1.00) |
0.928 (1.00) |
0.538 (0.933) |
0.0425 (0.438) |
0.191 (0.718) |
0.0193 (0.318) |
0.133 (0.641) |
0.395 (0.893) |
0.00203 (0.188) |
0.882 (1.00) |
0.121 (0.638) |
0.449 (0.904) |
amp 1p22 3 | 141 (27%) | 374 |
0.706 (0.976) |
0.000371 (0.103) |
0.383 (0.886) |
0.643 (0.969) |
0.0775 (0.523) |
1 (1.00) |
0.921 (1.00) |
0.869 (1.00) |
0.891 (1.00) |
0.68 (0.969) |
0.86 (1.00) |
0.735 (0.985) |
0.695 (0.973) |
0.133 (0.641) |
0.682 (0.969) |
amp 6p21 1 | 190 (37%) | 325 |
0.414 (0.897) |
0.941 (1.00) |
0.575 (0.955) |
0.632 (0.969) |
0.437 (0.901) |
0.201 (0.737) |
0.855 (1.00) |
1 (1.00) |
0.26 (0.806) |
0.165 (0.692) |
0.765 (0.985) |
0.471 (0.905) |
0.4 (0.893) |
0.00115 (0.147) |
0.117 (0.629) |
amp 7p11 2 | 271 (53%) | 244 |
0.0216 (0.339) |
0.00871 (0.306) |
0.0711 (0.505) |
0.24 (0.789) |
0.00034 (0.103) |
1 (1.00) |
0.289 (0.812) |
0.467 (0.905) |
0.195 (0.728) |
0.0691 (0.505) |
0.227 (0.78) |
0.107 (0.615) |
0.894 (1.00) |
0.27 (0.81) |
1 (1.00) |
amp 7q31 2 | 214 (42%) | 301 |
0.694 (0.973) |
0.00318 (0.217) |
0.15 (0.675) |
0.156 (0.688) |
0.0305 (0.411) |
0.402 (0.893) |
0.72 (0.978) |
0.235 (0.789) |
0.925 (1.00) |
0.127 (0.641) |
0.0679 (0.505) |
0.442 (0.904) |
0.531 (0.933) |
0.744 (0.985) |
0.246 (0.794) |
amp 8q24 21 | 321 (62%) | 194 |
0.147 (0.673) |
0.0232 (0.349) |
0.715 (0.976) |
0.0358 (0.419) |
0.767 (0.985) |
0.518 (0.933) |
0.274 (0.81) |
0.765 (0.985) |
0.28 (0.811) |
0.00071 (0.103) |
0.389 (0.888) |
0.634 (0.969) |
0.0792 (0.525) |
0.131 (0.641) |
1 (1.00) |
amp 11q13 3 | 170 (33%) | 345 |
0.159 (0.692) |
0.00512 (0.249) |
0.712 (0.976) |
0.464 (0.905) |
0.648 (0.969) |
0.19 (0.718) |
0.925 (1.00) |
0.639 (0.969) |
0.532 (0.933) |
0.0522 (0.475) |
0.315 (0.824) |
0.38 (0.883) |
1 (1.00) |
0.0647 (0.505) |
1 (1.00) |
amp 12q14 1 | 168 (33%) | 347 |
0.0361 (0.419) |
0.0407 (0.437) |
0.328 (0.831) |
0.34 (0.846) |
0.625 (0.969) |
0.269 (0.81) |
0.301 (0.816) |
0.755 (0.985) |
0.455 (0.905) |
0.871 (1.00) |
0.971 (1.00) |
0.00417 (0.232) |
0.287 (0.812) |
0.494 (0.926) |
0.438 (0.901) |
amp 17q12 | 226 (44%) | 289 |
0.837 (1.00) |
0.15 (0.675) |
0.489 (0.923) |
0.343 (0.849) |
0.306 (0.817) |
0.536 (0.933) |
0.534 (0.933) |
0.239 (0.789) |
0.0558 (0.486) |
0.117 (0.629) |
0.00331 (0.217) |
0.586 (0.956) |
0.155 (0.688) |
0.183 (0.718) |
1 (1.00) |
del 2q22 1 | 46 (9%) | 469 |
0.457 (0.905) |
0.372 (0.875) |
0.653 (0.969) |
0.676 (0.969) |
0.736 (0.985) |
0.253 (0.805) |
0.757 (0.985) |
0.804 (0.998) |
0.00498 (0.249) |
0.594 (0.96) |
0.0736 (0.51) |
0.663 (0.969) |
0.922 (1.00) |
0.277 (0.81) |
0.465 (0.905) |
del 5q31 1 | 207 (40%) | 308 |
0.182 (0.718) |
0.00341 (0.217) |
0.959 (1.00) |
0.916 (1.00) |
0.63 (0.969) |
1 (1.00) |
0.178 (0.715) |
0.658 (0.969) |
0.809 (0.998) |
0.0692 (0.505) |
0.00644 (0.283) |
0.204 (0.744) |
0.364 (0.875) |
0.0828 (0.541) |
0.0164 (0.307) |
del 6q11 1 | 134 (26%) | 381 |
0.125 (0.641) |
0.461 (0.905) |
0.00811 (0.295) |
0.89 (1.00) |
0.0029 (0.217) |
0.638 (0.969) |
0.227 (0.78) |
0.187 (0.718) |
0.82 (0.999) |
0.92 (1.00) |
0.217 (0.761) |
0.474 (0.905) |
0.541 (0.933) |
0.824 (1.00) |
0.686 (0.97) |
del 9p23 | 284 (55%) | 231 |
0.117 (0.629) |
0.421 (0.897) |
0.601 (0.962) |
0.882 (1.00) |
0.00385 (0.231) |
0.683 (0.969) |
0.33 (0.831) |
0.0402 (0.436) |
0.162 (0.692) |
0.691 (0.972) |
0.65 (0.969) |
0.782 (0.986) |
0.377 (0.883) |
0.881 (1.00) |
1 (1.00) |
del 9p21 3 | 290 (56%) | 225 |
0.114 (0.629) |
0.159 (0.692) |
0.271 (0.81) |
0.753 (0.985) |
0.00433 (0.232) |
0.837 (1.00) |
0.0259 (0.368) |
0.307 (0.817) |
0.437 (0.901) |
0.599 (0.962) |
0.926 (1.00) |
0.669 (0.969) |
0.569 (0.955) |
0.835 (1.00) |
1 (1.00) |
del 12p13 2 | 138 (27%) | 377 |
0.767 (0.985) |
0.679 (0.969) |
0.131 (0.641) |
0.558 (0.944) |
0.636 (0.969) |
0.639 (0.969) |
0.000314 (0.103) |
0.871 (1.00) |
0.784 (0.986) |
0.598 (0.962) |
0.0393 (0.436) |
0.259 (0.806) |
0.448 (0.904) |
0.0632 (0.505) |
0.679 (0.969) |
del 13q12 11 | 293 (57%) | 222 |
0.731 (0.985) |
0.18 (0.718) |
0.985 (1.00) |
0.326 (0.831) |
0.99 (1.00) |
0.683 (0.969) |
0.0744 (0.51) |
0.558 (0.944) |
0.979 (1.00) |
0.136 (0.646) |
0.00132 (0.15) |
0.306 (0.817) |
0.812 (0.998) |
0.648 (0.969) |
1 (1.00) |
del 14q32 12 | 144 (28%) | 371 |
0.15 (0.675) |
0.0637 (0.505) |
0.0129 (0.307) |
0.143 (0.664) |
0.00294 (0.217) |
0.369 (0.875) |
0.623 (0.969) |
0.633 (0.969) |
0.188 (0.718) |
0.737 (0.985) |
0.253 (0.805) |
0.0423 (0.438) |
0.105 (0.608) |
0.0211 (0.336) |
1 (1.00) |
del 15q11 2 | 262 (51%) | 253 |
0.507 (0.932) |
0.000685 (0.103) |
0.386 (0.888) |
0.708 (0.976) |
0.746 (0.985) |
1 (1.00) |
0.378 (0.883) |
0.307 (0.817) |
0.404 (0.893) |
0.0478 (0.464) |
0.582 (0.956) |
0.391 (0.888) |
0.779 (0.986) |
0.983 (1.00) |
1 (1.00) |
del 19p13 2 | 269 (52%) | 246 |
0.491 (0.923) |
0.0362 (0.419) |
0.198 (0.733) |
0.299 (0.815) |
0.066 (0.505) |
0.413 (0.897) |
0.00198 (0.188) |
0.771 (0.985) |
0.555 (0.944) |
0.713 (0.976) |
0.858 (1.00) |
0.308 (0.817) |
0.298 (0.812) |
0.965 (1.00) |
0.122 (0.64) |
del 21q11 2 | 185 (36%) | 330 |
0.753 (0.985) |
0.00672 (0.283) |
0.371 (0.875) |
0.241 (0.789) |
0.736 (0.985) |
0.674 (0.969) |
0.118 (0.629) |
0.0921 (0.569) |
0.0256 (0.368) |
0.0366 (0.419) |
0.884 (1.00) |
0.000608 (0.103) |
0.755 (0.985) |
0.0308 (0.411) |
0.702 (0.976) |
amp 1q21 3 | 371 (72%) | 144 |
0.46 (0.905) |
0.034 (0.419) |
0.286 (0.812) |
0.574 (0.955) |
0.797 (0.996) |
1 (1.00) |
0.116 (0.629) |
1 (1.00) |
0.807 (0.998) |
0.0227 (0.346) |
0.115 (0.629) |
0.172 (0.71) |
0.323 (0.829) |
0.859 (1.00) |
1 (1.00) |
amp 3q26 2 | 170 (33%) | 345 |
0.277 (0.81) |
0.416 (0.897) |
0.818 (0.998) |
0.927 (1.00) |
0.188 (0.718) |
0.267 (0.81) |
0.851 (1.00) |
1 (1.00) |
0.329 (0.831) |
0.447 (0.904) |
0.0115 (0.307) |
0.195 (0.728) |
0.296 (0.812) |
0.468 (0.905) |
0.0387 (0.436) |
amp 5p15 33 | 328 (64%) | 187 |
0.219 (0.761) |
0.0123 (0.307) |
0.498 (0.926) |
0.344 (0.85) |
0.216 (0.761) |
0.833 (1.00) |
0.233 (0.789) |
0.881 (1.00) |
0.577 (0.955) |
0.205 (0.744) |
0.0145 (0.307) |
0.495 (0.926) |
0.696 (0.973) |
0.562 (0.947) |
1 (1.00) |
amp 8p11 21 | 173 (34%) | 342 |
0.296 (0.812) |
0.0555 (0.486) |
0.604 (0.964) |
0.215 (0.761) |
0.275 (0.81) |
1 (1.00) |
0.0247 (0.365) |
0.0898 (0.569) |
0.771 (0.985) |
0.02 (0.324) |
0.524 (0.933) |
0.717 (0.976) |
0.818 (0.998) |
0.801 (0.998) |
0.684 (0.969) |
amp 12p12 1 | 178 (35%) | 337 |
0.034 (0.419) |
0.247 (0.794) |
0.125 (0.641) |
0.235 (0.789) |
0.708 (0.976) |
0.129 (0.641) |
0.579 (0.956) |
0.756 (0.985) |
0.928 (1.00) |
0.515 (0.933) |
0.598 (0.962) |
0.314 (0.824) |
0.0663 (0.505) |
0.55 (0.942) |
1 (1.00) |
amp 12q15 | 171 (33%) | 344 |
0.0163 (0.307) |
0.242 (0.789) |
0.422 (0.897) |
0.516 (0.933) |
0.523 (0.933) |
0.511 (0.933) |
0.261 (0.806) |
1 (1.00) |
0.402 (0.893) |
0.847 (1.00) |
0.699 (0.974) |
0.0133 (0.307) |
0.228 (0.781) |
0.762 (0.985) |
0.208 (0.748) |
amp 14q13 3 | 228 (44%) | 287 |
0.616 (0.969) |
0.22 (0.764) |
0.676 (0.969) |
0.411 (0.896) |
0.903 (1.00) |
0.834 (1.00) |
0.594 (0.96) |
1 (1.00) |
0.0338 (0.419) |
0.0994 (0.593) |
0.354 (0.859) |
0.164 (0.692) |
0.86 (1.00) |
0.429 (0.897) |
0.464 (0.905) |
amp 17q23 1 | 249 (48%) | 266 |
0.35 (0.856) |
0.0905 (0.569) |
0.351 (0.856) |
0.2 (0.737) |
0.183 (0.718) |
0.542 (0.933) |
0.725 (0.98) |
0.563 (0.947) |
0.0365 (0.419) |
0.0155 (0.307) |
0.0113 (0.307) |
0.464 (0.905) |
0.0149 (0.307) |
0.075 (0.51) |
0.26 (0.806) |
amp 18q11 2 | 103 (20%) | 412 |
0.766 (0.985) |
0.537 (0.933) |
0.1 (0.595) |
0.667 (0.969) |
0.947 (1.00) |
0.44 (0.903) |
0.124 (0.641) |
0.365 (0.875) |
0.761 (0.985) |
0.161 (0.692) |
0.213 (0.761) |
0.783 (0.986) |
0.624 (0.969) |
0.324 (0.829) |
1 (1.00) |
amp 19q12 | 136 (26%) | 379 |
0.368 (0.875) |
0.585 (0.956) |
0.368 (0.875) |
0.462 (0.905) |
0.367 (0.875) |
0.348 (0.856) |
0.0357 (0.419) |
0.868 (1.00) |
0.281 (0.811) |
0.279 (0.81) |
0.0521 (0.475) |
0.321 (0.829) |
0.742 (0.985) |
0.968 (1.00) |
1 (1.00) |
amp 20q13 33 | 243 (47%) | 272 |
0.659 (0.969) |
0.035 (0.419) |
0.0605 (0.498) |
0.133 (0.641) |
0.0956 (0.58) |
0.679 (0.969) |
0.93 (1.00) |
0.468 (0.905) |
0.0926 (0.569) |
0.0739 (0.51) |
0.0796 (0.525) |
0.867 (1.00) |
0.809 (0.998) |
0.295 (0.812) |
1 (1.00) |
amp 22q11 22 | 88 (17%) | 427 |
0.48 (0.913) |
0.446 (0.904) |
0.031 (0.411) |
0.278 (0.81) |
0.727 (0.981) |
0.148 (0.675) |
0.162 (0.692) |
0.559 (0.944) |
0.164 (0.692) |
0.29 (0.812) |
0.757 (0.985) |
0.37 (0.875) |
0.775 (0.985) |
1 (1.00) |
1 (1.00) |
amp xq28 | 157 (30%) | 358 |
0.589 (0.957) |
0.477 (0.91) |
0.997 (1.00) |
0.473 (0.905) |
0.279 (0.81) |
0.506 (0.932) |
0.388 (0.888) |
0.873 (1.00) |
0.318 (0.829) |
0.391 (0.888) |
0.109 (0.62) |
0.961 (1.00) |
0.711 (0.976) |
0.824 (1.00) |
0.678 (0.969) |
del 1p36 11 | 124 (24%) | 391 |
0.0496 (0.473) |
0.813 (0.998) |
0.0179 (0.307) |
0.0457 (0.452) |
0.0183 (0.307) |
0.815 (0.998) |
0.216 (0.761) |
0.743 (0.985) |
0.0545 (0.484) |
0.274 (0.81) |
0.601 (0.962) |
0.514 (0.933) |
0.871 (1.00) |
0.53 (0.933) |
0.659 (0.969) |
del 1p13 1 | 148 (29%) | 367 |
0.88 (1.00) |
0.0904 (0.569) |
0.0636 (0.505) |
0.19 (0.718) |
0.163 (0.692) |
0.257 (0.806) |
1 (1.00) |
0.425 (0.897) |
0.883 (1.00) |
0.727 (0.981) |
0.924 (1.00) |
0.496 (0.926) |
0.533 (0.933) |
0.311 (0.824) |
0.679 (0.969) |
del 3p26 2 | 236 (46%) | 279 |
0.337 (0.84) |
0.109 (0.62) |
0.14 (0.658) |
0.0148 (0.307) |
0.0493 (0.473) |
0.408 (0.893) |
0.86 (1.00) |
0.243 (0.789) |
0.949 (1.00) |
0.176 (0.71) |
0.723 (0.979) |
0.0419 (0.438) |
0.285 (0.812) |
0.292 (0.812) |
0.0569 (0.487) |
del 3p21 31 | 245 (48%) | 270 |
0.443 (0.904) |
0.0398 (0.436) |
0.268 (0.81) |
0.0126 (0.307) |
0.00752 (0.295) |
0.837 (1.00) |
0.426 (0.897) |
0.884 (1.00) |
0.715 (0.976) |
0.219 (0.761) |
0.886 (1.00) |
0.0154 (0.307) |
0.292 (0.812) |
0.573 (0.955) |
0.722 (0.979) |
del 3q11 1 | 140 (27%) | 375 |
0.0675 (0.505) |
0.122 (0.64) |
0.7 (0.974) |
0.533 (0.933) |
0.213 (0.761) |
1 (1.00) |
0.552 (0.943) |
0.748 (0.985) |
0.688 (0.971) |
0.783 (0.986) |
0.066 (0.505) |
0.184 (0.718) |
0.851 (1.00) |
0.615 (0.969) |
0.679 (0.969) |
del 3q29 | 135 (26%) | 380 |
0.139 (0.656) |
0.81 (0.998) |
0.908 (1.00) |
0.788 (0.99) |
0.776 (0.985) |
0.247 (0.794) |
1 (1.00) |
1 (1.00) |
0.828 (1.00) |
0.55 (0.942) |
0.17 (0.705) |
0.473 (0.905) |
0.296 (0.812) |
0.35 (0.856) |
0.681 (0.969) |
del 4p16 3 | 130 (25%) | 385 |
0.438 (0.901) |
0.0798 (0.525) |
0.945 (1.00) |
0.818 (0.998) |
0.645 (0.969) |
1 (1.00) |
1 (1.00) |
0.507 (0.932) |
0.00782 (0.295) |
0.162 (0.692) |
0.0414 (0.438) |
0.259 (0.806) |
0.486 (0.92) |
0.708 (0.976) |
0.371 (0.875) |
del 4q34 3 | 187 (36%) | 328 |
0.465 (0.905) |
0.0508 (0.475) |
0.583 (0.956) |
0.387 (0.888) |
0.098 (0.588) |
0.835 (1.00) |
0.168 (0.703) |
0.0676 (0.505) |
0.762 (0.985) |
0.116 (0.629) |
0.323 (0.829) |
0.0537 (0.481) |
0.818 (0.998) |
0.501 (0.93) |
0.104 (0.607) |
del 5q12 1 | 176 (34%) | 339 |
0.444 (0.904) |
0.0184 (0.307) |
0.956 (1.00) |
0.697 (0.974) |
0.198 (0.733) |
1 (1.00) |
0.402 (0.893) |
1 (1.00) |
0.35 (0.856) |
0.0224 (0.346) |
0.00694 (0.283) |
0.442 (0.904) |
0.626 (0.969) |
0.127 (0.641) |
0.0443 (0.443) |
del 6q22 31 | 251 (49%) | 264 |
0.586 (0.956) |
0.437 (0.901) |
0.235 (0.789) |
0.42 (0.897) |
0.401 (0.893) |
0.838 (1.00) |
0.218 (0.761) |
0.884 (1.00) |
0.453 (0.905) |
0.577 (0.955) |
0.0622 (0.505) |
0.186 (0.718) |
0.385 (0.888) |
0.753 (0.985) |
0.266 (0.81) |
del 6q26 | 256 (50%) | 259 |
0.926 (1.00) |
0.527 (0.933) |
0.691 (0.972) |
0.759 (0.985) |
0.46 (0.905) |
0.408 (0.893) |
0.427 (0.897) |
0.772 (0.985) |
0.842 (1.00) |
0.258 (0.806) |
0.353 (0.859) |
0.164 (0.692) |
0.206 (0.746) |
0.796 (0.996) |
0.281 (0.811) |
del 8p23 2 | 256 (50%) | 259 |
0.505 (0.932) |
0.238 (0.789) |
0.515 (0.933) |
0.429 (0.897) |
1 (1.00) |
0.408 (0.893) |
0.034 (0.419) |
0.662 (0.969) |
0.746 (0.985) |
0.0522 (0.475) |
0.62 (0.969) |
0.675 (0.969) |
0.602 (0.963) |
0.627 (0.969) |
0.124 (0.641) |
del 8p11 21 | 122 (24%) | 393 |
0.806 (0.998) |
0.955 (1.00) |
0.409 (0.893) |
0.277 (0.81) |
0.589 (0.957) |
0.807 (0.998) |
0.00926 (0.307) |
0.501 (0.93) |
0.343 (0.849) |
0.289 (0.812) |
0.998 (1.00) |
0.502 (0.93) |
0.0583 (0.492) |
0.0583 (0.492) |
1 (1.00) |
del 9q21 11 | 256 (50%) | 259 |
0.522 (0.933) |
0.666 (0.969) |
0.775 (0.985) |
0.422 (0.897) |
0.661 (0.969) |
0.417 (0.897) |
0.537 (0.933) |
0.664 (0.969) |
0.489 (0.923) |
0.189 (0.718) |
0.141 (0.658) |
0.335 (0.837) |
0.904 (1.00) |
0.571 (0.955) |
1 (1.00) |
del 10p15 3 | 126 (24%) | 389 |
0.0153 (0.307) |
0.971 (1.00) |
0.422 (0.897) |
0.572 (0.955) |
0.239 (0.789) |
0.622 (0.969) |
0.0102 (0.307) |
0.405 (0.893) |
0.183 (0.718) |
0.271 (0.81) |
0.4 (0.893) |
0.743 (0.985) |
0.98 (1.00) |
0.289 (0.812) |
0.0779 (0.523) |
del 10q26 3 | 156 (30%) | 359 |
0.126 (0.641) |
0.174 (0.71) |
0.689 (0.971) |
0.147 (0.673) |
0.898 (1.00) |
0.266 (0.81) |
0.103 (0.605) |
0.112 (0.623) |
0.661 (0.969) |
0.251 (0.802) |
0.184 (0.718) |
0.98 (1.00) |
0.314 (0.824) |
0.189 (0.718) |
0.202 (0.74) |
del 11p15 5 | 143 (28%) | 372 |
0.753 (0.985) |
0.0104 (0.307) |
0.315 (0.824) |
0.429 (0.897) |
0.747 (0.985) |
0.359 (0.87) |
0.0178 (0.307) |
0.0745 (0.51) |
0.856 (1.00) |
0.221 (0.765) |
0.333 (0.835) |
0.011 (0.307) |
0.511 (0.933) |
0.533 (0.933) |
0.434 (0.901) |
del 11q23 2 | 119 (23%) | 396 |
0.778 (0.986) |
0.752 (0.985) |
0.468 (0.905) |
0.971 (1.00) |
0.624 (0.969) |
0.811 (0.998) |
0.0472 (0.463) |
1 (1.00) |
0.914 (1.00) |
0.792 (0.993) |
0.963 (1.00) |
0.176 (0.71) |
0.78 (0.986) |
0.766 (0.985) |
1 (1.00) |
del 11q25 | 116 (23%) | 399 |
0.903 (1.00) |
0.931 (1.00) |
0.323 (0.829) |
0.879 (1.00) |
0.075 (0.51) |
1 (1.00) |
0.0443 (0.443) |
0.599 (0.962) |
0.793 (0.993) |
0.631 (0.969) |
0.592 (0.96) |
0.462 (0.905) |
0.81 (0.998) |
0.642 (0.969) |
1 (1.00) |
del 12q12 | 98 (19%) | 417 |
0.583 (0.956) |
0.258 (0.806) |
0.518 (0.933) |
0.845 (1.00) |
0.434 (0.901) |
0.78 (0.986) |
0.092 (0.569) |
0.707 (0.976) |
0.306 (0.817) |
0.987 (1.00) |
0.0713 (0.505) |
0.708 (0.976) |
0.617 (0.969) |
0.882 (1.00) |
0.653 (0.969) |
del 12q24 33 | 137 (27%) | 378 |
0.54 (0.933) |
0.174 (0.71) |
0.297 (0.812) |
0.29 (0.812) |
0.372 (0.875) |
1 (1.00) |
0.134 (0.641) |
0.626 (0.969) |
0.891 (1.00) |
0.862 (1.00) |
0.0528 (0.476) |
0.629 (0.969) |
0.815 (0.998) |
0.0589 (0.492) |
1 (1.00) |
del 13q12 13 | 292 (57%) | 223 |
0.902 (1.00) |
0.269 (0.81) |
0.972 (1.00) |
0.543 (0.935) |
1 (1.00) |
0.835 (1.00) |
0.13 (0.641) |
0.377 (0.883) |
0.845 (1.00) |
0.0953 (0.58) |
0.0153 (0.307) |
0.315 (0.824) |
0.81 (0.998) |
0.659 (0.969) |
1 (1.00) |
del 13q14 2 | 281 (55%) | 234 |
0.963 (1.00) |
0.246 (0.794) |
0.979 (1.00) |
0.401 (0.893) |
0.646 (0.969) |
0.68 (0.969) |
0.929 (1.00) |
0.883 (1.00) |
0.84 (1.00) |
0.491 (0.923) |
0.0709 (0.505) |
0.744 (0.985) |
0.987 (1.00) |
0.765 (0.985) |
0.471 (0.905) |
del 13q34 | 242 (47%) | 273 |
0.977 (1.00) |
0.269 (0.81) |
0.95 (1.00) |
0.403 (0.893) |
0.93 (1.00) |
1 (1.00) |
1 (1.00) |
0.884 (1.00) |
0.772 (0.985) |
0.449 (0.904) |
0.147 (0.673) |
0.606 (0.964) |
0.484 (0.918) |
0.111 (0.623) |
0.715 (0.976) |
del 15q15 1 | 274 (53%) | 241 |
0.874 (1.00) |
0.00552 (0.256) |
0.523 (0.933) |
0.814 (0.998) |
0.642 (0.969) |
0.679 (0.969) |
0.659 (0.969) |
0.192 (0.719) |
0.0706 (0.505) |
0.0171 (0.307) |
0.151 (0.675) |
0.625 (0.969) |
1 (1.00) |
1 (1.00) |
0.0569 (0.487) |
del 16q23 1 | 169 (33%) | 346 |
0.898 (1.00) |
0.275 (0.81) |
0.283 (0.812) |
0.298 (0.812) |
0.38 (0.883) |
1 (1.00) |
0.573 (0.955) |
0.646 (0.969) |
0.576 (0.955) |
0.695 (0.973) |
0.557 (0.944) |
0.757 (0.985) |
0.618 (0.969) |
0.162 (0.692) |
0.04 (0.436) |
del 17p13 3 | 281 (55%) | 234 |
0.654 (0.969) |
0.0672 (0.505) |
0.773 (0.985) |
0.155 (0.688) |
0.911 (1.00) |
0.683 (0.969) |
0.0918 (0.569) |
0.306 (0.817) |
0.677 (0.969) |
0.0324 (0.419) |
0.169 (0.703) |
0.0126 (0.307) |
0.469 (0.905) |
0.982 (1.00) |
0.454 (0.905) |
del 18q21 32 | 251 (49%) | 264 |
0.0283 (0.396) |
0.0595 (0.493) |
0.0121 (0.307) |
0.327 (0.831) |
0.0119 (0.307) |
0.537 (0.933) |
0.426 (0.897) |
1 (1.00) |
0.996 (1.00) |
0.238 (0.789) |
0.835 (1.00) |
0.103 (0.606) |
0.0154 (0.307) |
0.614 (0.969) |
0.717 (0.976) |
del 19p13 3 | 282 (55%) | 233 |
0.135 (0.642) |
0.0896 (0.569) |
0.321 (0.829) |
0.0645 (0.505) |
0.0972 (0.587) |
0.537 (0.933) |
0.0168 (0.307) |
0.771 (0.985) |
0.747 (0.985) |
0.416 (0.897) |
0.302 (0.817) |
0.13 (0.641) |
0.424 (0.897) |
0.453 (0.905) |
0.0177 (0.307) |
del 19p13 2 | 279 (54%) | 236 |
0.229 (0.781) |
0.0698 (0.505) |
0.241 (0.789) |
0.24 (0.789) |
0.0855 (0.556) |
0.539 (0.933) |
0.0166 (0.307) |
0.884 (1.00) |
0.553 (0.943) |
0.483 (0.918) |
0.847 (1.00) |
0.335 (0.837) |
0.514 (0.933) |
1 (1.00) |
0.129 (0.641) |
del 19q11 | 134 (26%) | 381 |
0.453 (0.905) |
0.0257 (0.368) |
0.397 (0.893) |
0.424 (0.897) |
0.587 (0.956) |
0.647 (0.969) |
0.616 (0.969) |
0.141 (0.658) |
0.847 (1.00) |
0.294 (0.812) |
0.993 (1.00) |
0.295 (0.812) |
0.959 (1.00) |
0.0503 (0.475) |
1 (1.00) |
del 19q13 33 | 194 (38%) | 321 |
0.711 (0.976) |
0.534 (0.933) |
0.645 (0.969) |
0.583 (0.956) |
0.445 (0.904) |
0.404 (0.893) |
0.525 (0.933) |
0.551 (0.942) |
0.99 (1.00) |
0.242 (0.789) |
0.991 (1.00) |
0.85 (1.00) |
0.528 (0.933) |
0.584 (0.956) |
1 (1.00) |
del 20p13 | 131 (25%) | 384 |
0.537 (0.933) |
0.764 (0.985) |
0.119 (0.63) |
0.497 (0.926) |
0.0879 (0.567) |
1 (1.00) |
0.0431 (0.44) |
0.323 (0.829) |
0.188 (0.718) |
0.326 (0.831) |
0.429 (0.897) |
0.175 (0.71) |
0.522 (0.933) |
0.699 (0.974) |
0.683 (0.969) |
del 20q13 12 | 80 (16%) | 435 |
0.361 (0.872) |
0.431 (0.9) |
0.262 (0.808) |
0.366 (0.875) |
0.109 (0.62) |
0.174 (0.71) |
0.33 (0.831) |
0.558 (0.944) |
0.46 (0.905) |
0.112 (0.623) |
0.00953 (0.307) |
0.654 (0.969) |
0.605 (0.964) |
0.662 (0.969) |
0.259 (0.806) |
del xp22 2 | 143 (28%) | 372 |
0.878 (1.00) |
0.382 (0.886) |
0.521 (0.933) |
0.875 (1.00) |
0.134 (0.641) |
1 (1.00) |
0.0299 (0.411) |
0.618 (0.969) |
0.716 (0.976) |
0.402 (0.893) |
0.663 (0.969) |
0.215 (0.761) |
0.927 (1.00) |
0.389 (0.888) |
0.68 (0.969) |
P value = 0.000371 (Wilcoxon-test), Q value = 0.1
Table S1. Gene #1: 'amp_1p22.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 484 | 65.2 (10.0) |
AMP PEAK 1(1P22.3) MUTATED | 134 | 62.6 (10.2) |
AMP PEAK 1(1P22.3) WILD-TYPE | 350 | 66.3 (9.8) |
Figure S1. Get High-res Image Gene #1: 'amp_1p22.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D1V2.png)
P value = 0.00115 (Fisher's exact test), Q value = 0.15
Table S2. Gene #5: 'amp_6p21.1' versus Clinical Feature #14: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 7 | 51 | 389 |
AMP PEAK 5(6P21.1) MUTATED | 1 | 5 | 10 | 159 |
AMP PEAK 5(6P21.1) WILD-TYPE | 0 | 2 | 41 | 230 |
Figure S2. Get High-res Image Gene #5: 'amp_6p21.1' versus Clinical Feature #14: 'RACE'
![](D5V14.png)
P value = 0.00034 (Fisher's exact test), Q value = 0.1
Table S3. Gene #6: 'amp_7p11.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2+N3 |
---|---|---|---|
ALL | 332 | 96 | 76 |
AMP PEAK 6(7P11.2) MUTATED | 158 | 51 | 55 |
AMP PEAK 6(7P11.2) WILD-TYPE | 174 | 45 | 21 |
Figure S3. Get High-res Image Gene #6: 'amp_7p11.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D6V5.png)
P value = 0.00318 (Wilcoxon-test), Q value = 0.22
Table S4. Gene #7: 'amp_7q31.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 484 | 65.2 (10.0) |
AMP PEAK 7(7Q31.2) MUTATED | 202 | 63.7 (10.0) |
AMP PEAK 7(7Q31.2) WILD-TYPE | 282 | 66.3 (9.9) |
Figure S4. Get High-res Image Gene #7: 'amp_7q31.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D7V2.png)
P value = 0.00071 (Fisher's exact test), Q value = 0.1
Table S5. Gene #9: 'amp_8q24.21' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'
nPatients | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG SIGNET RING ADENOCARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 19 | 106 | 320 | 5 | 19 | 2 | 3 | 2 | 23 | 1 | 5 | 10 |
AMP PEAK 9(8Q24.21) MUTATED | 13 | 62 | 210 | 1 | 11 | 1 | 2 | 0 | 16 | 1 | 4 | 0 |
AMP PEAK 9(8Q24.21) WILD-TYPE | 6 | 44 | 110 | 4 | 8 | 1 | 1 | 2 | 7 | 0 | 1 | 10 |
Figure S5. Get High-res Image Gene #9: 'amp_8q24.21' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'
![](D9V10.png)
P value = 0.00512 (Wilcoxon-test), Q value = 0.25
Table S6. Gene #10: 'amp_11q13.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 484 | 65.2 (10.0) |
AMP PEAK 10(11Q13.3) MUTATED | 161 | 63.3 (10.1) |
AMP PEAK 10(11Q13.3) WILD-TYPE | 323 | 66.2 (9.9) |
Figure S6. Get High-res Image Gene #10: 'amp_11q13.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D10V2.png)
P value = 0.00417 (Wilcoxon-test), Q value = 0.23
Table S7. Gene #12: 'amp_12q14.1' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 276 | 1965.0 (12.6) |
AMP PEAK 12(12Q14.1) MUTATED | 91 | 1967.9 (12.5) |
AMP PEAK 12(12Q14.1) WILD-TYPE | 185 | 1963.6 (12.4) |
Figure S7. Get High-res Image Gene #12: 'amp_12q14.1' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'
![](D12V12.png)
P value = 0.00331 (Wilcoxon-test), Q value = 0.22
Table S8. Gene #15: 'amp_17q12' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 355 | 41.6 (27.3) |
AMP PEAK 15(17Q12) MUTATED | 151 | 46.6 (29.3) |
AMP PEAK 15(17Q12) WILD-TYPE | 204 | 37.9 (25.2) |
Figure S8. Get High-res Image Gene #15: 'amp_17q12' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'
![](D15V11.png)
P value = 0.00498 (Wilcoxon-test), Q value = 0.25
Table S9. Gene #24: 'del_2q22.1' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 132 | 78.8 (28.6) |
DEL PEAK 3(2Q22.1) MUTATED | 15 | 62.7 (31.7) |
DEL PEAK 3(2Q22.1) WILD-TYPE | 117 | 80.9 (27.6) |
Figure S9. Get High-res Image Gene #24: 'del_2q22.1' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'
![](D24V9.png)
P value = 0.00341 (Wilcoxon-test), Q value = 0.22
Table S10. Gene #32: 'del_5q31.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 484 | 65.2 (10.0) |
DEL PEAK 11(5Q31.1) MUTATED | 197 | 63.4 (10.5) |
DEL PEAK 11(5Q31.1) WILD-TYPE | 287 | 66.5 (9.5) |
Figure S10. Get High-res Image Gene #32: 'del_5q31.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D32V2.png)
P value = 0.0029 (Fisher's exact test), Q value = 0.22
Table S11. Gene #33: 'del_6q11.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2+N3 |
---|---|---|---|
ALL | 332 | 96 | 76 |
DEL PEAK 12(6Q11.1) MUTATED | 75 | 26 | 32 |
DEL PEAK 12(6Q11.1) WILD-TYPE | 257 | 70 | 44 |
Figure S11. Get High-res Image Gene #33: 'del_6q11.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D33V5.png)
P value = 0.00385 (Fisher's exact test), Q value = 0.23
Table S12. Gene #38: 'del_9p23' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2+N3 |
---|---|---|---|
ALL | 332 | 96 | 76 |
DEL PEAK 17(9P23) MUTATED | 169 | 67 | 43 |
DEL PEAK 17(9P23) WILD-TYPE | 163 | 29 | 33 |
Figure S12. Get High-res Image Gene #38: 'del_9p23' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D38V5.png)
P value = 0.00433 (Fisher's exact test), Q value = 0.23
Table S13. Gene #39: 'del_9p21.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2+N3 |
---|---|---|---|
ALL | 332 | 96 | 76 |
DEL PEAK 18(9P21.3) MUTATED | 173 | 68 | 45 |
DEL PEAK 18(9P21.3) WILD-TYPE | 159 | 28 | 31 |
Figure S13. Get High-res Image Gene #39: 'del_9p21.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D39V5.png)
P value = 0.000314 (Fisher's exact test), Q value = 0.1
Table S14. Gene #46: 'del_12p13.2' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 275 | 240 |
DEL PEAK 25(12P13.2) MUTATED | 92 | 46 |
DEL PEAK 25(12P13.2) WILD-TYPE | 183 | 194 |
Figure S14. Get High-res Image Gene #46: 'del_12p13.2' versus Clinical Feature #7: 'GENDER'
![](D46V7.png)
P value = 0.00132 (Wilcoxon-test), Q value = 0.15
Table S15. Gene #49: 'del_13q12.11' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 355 | 41.6 (27.3) |
DEL PEAK 28(13Q12.11) MUTATED | 195 | 45.6 (28.5) |
DEL PEAK 28(13Q12.11) WILD-TYPE | 160 | 36.8 (25.1) |
Figure S15. Get High-res Image Gene #49: 'del_13q12.11' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'
![](D49V11.png)
P value = 0.00294 (Fisher's exact test), Q value = 0.22
Table S16. Gene #53: 'del_14q32.12' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2+N3 |
---|---|---|---|
ALL | 332 | 96 | 76 |
DEL PEAK 32(14Q32.12) MUTATED | 79 | 40 | 24 |
DEL PEAK 32(14Q32.12) WILD-TYPE | 253 | 56 | 52 |
Figure S16. Get High-res Image Gene #53: 'del_14q32.12' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D53V5.png)
P value = 0.000685 (Wilcoxon-test), Q value = 0.1
Table S17. Gene #54: 'del_15q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 484 | 65.2 (10.0) |
DEL PEAK 33(15Q11.2) MUTATED | 243 | 63.7 (10.5) |
DEL PEAK 33(15Q11.2) WILD-TYPE | 241 | 66.8 (9.3) |
Figure S17. Get High-res Image Gene #54: 'del_15q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D54V2.png)
P value = 0.00198 (Fisher's exact test), Q value = 0.19
Table S18. Gene #61: 'del_19p13.2' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 275 | 240 |
DEL PEAK 40(19P13.2) MUTATED | 126 | 143 |
DEL PEAK 40(19P13.2) WILD-TYPE | 149 | 97 |
Figure S18. Get High-res Image Gene #61: 'del_19p13.2' versus Clinical Feature #7: 'GENDER'
![](D61V7.png)
P value = 0.000608 (Wilcoxon-test), Q value = 0.1
Table S19. Gene #66: 'del_21q11.2' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 276 | 1965.0 (12.6) |
DEL PEAK 45(21Q11.2) MUTATED | 102 | 1968.5 (13.2) |
DEL PEAK 45(21Q11.2) WILD-TYPE | 174 | 1963.0 (11.7) |
Figure S19. Get High-res Image Gene #66: 'del_21q11.2' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'
![](D66V12.png)
P value = 0.000533 (Wilcoxon-test), Q value = 0.1
Table S20. Gene #67: 'del_22q13.32' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 484 | 65.2 (10.0) |
DEL PEAK 46(22Q13.32) MUTATED | 242 | 63.8 (9.8) |
DEL PEAK 46(22Q13.32) WILD-TYPE | 242 | 66.7 (10.0) |
Figure S20. Get High-res Image Gene #67: 'del_22q13.32' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D67V2.png)
P value = 0.00203 (Wilcoxon-test), Q value = 0.19
Table S21. Gene #67: 'del_22q13.32' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 276 | 1965.0 (12.6) |
DEL PEAK 46(22Q13.32) MUTATED | 147 | 1967.2 (12.7) |
DEL PEAK 46(22Q13.32) WILD-TYPE | 129 | 1962.6 (12.0) |
Figure S21. Get High-res Image Gene #67: 'del_22q13.32' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'
![](D67V12.png)
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Copy number data file = all_lesions.txt from GISTIC pipeline
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Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LUAD-TP/19782225/transformed.cor.cli.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LUAD-TP/19775350/LUAD-TP.merged_data.txt
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Number of patients = 515
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Number of significantly focal cnvs = 68
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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 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.