This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 99 focal events and 12 clinical features across 625 patients, 65 significant findings detected with Q value < 0.25.
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amp_1p36.22 cnv correlated to 'GENDER'.
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amp_1p34.2 cnv correlated to 'RADIATION_THERAPY'.
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amp_1q42.3 cnv correlated to 'YEARS_TO_BIRTH'.
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amp_2q12.2 cnv correlated to 'PATHOLOGIC_STAGE'.
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amp_3q26.2 cnv correlated to 'PATHOLOGIC_STAGE' and 'RACE'.
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amp_5p15.33 cnv correlated to 'PATHOLOGY_T_STAGE'.
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amp_5p13.1 cnv correlated to 'PATHOLOGY_T_STAGE'.
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amp_6q21 cnv correlated to 'Time to Death'.
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amp_7p22.3 cnv correlated to 'GENDER'.
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amp_7p11.2 cnv correlated to 'PATHOLOGY_T_STAGE' and 'GENDER'.
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amp_7q21.2 cnv correlated to 'GENDER'.
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amp_8p23.1 cnv correlated to 'YEARS_TO_BIRTH' and 'GENDER'.
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amp_12p12.1 cnv correlated to 'PATHOLOGY_T_STAGE'.
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amp_14q13.3 cnv correlated to 'GENDER'.
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amp_17q12 cnv correlated to 'PATHOLOGY_M_STAGE', 'GENDER', and 'RACE'.
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amp_20q13.2 cnv correlated to 'GENDER'.
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del_4p16.3 cnv correlated to 'GENDER'.
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del_4q34.3 cnv correlated to 'YEARS_TO_BIRTH' and 'PATHOLOGIC_STAGE'.
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del_7q31.1 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', and 'GENDER'.
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del_7q36.3 cnv correlated to 'PATHOLOGIC_STAGE'.
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del_8p23.2 cnv correlated to 'GENDER'.
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del_9p21.3 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'GENDER'.
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del_9q21.11 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.
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del_10p15.3 cnv correlated to 'Time to Death'.
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del_10p11.21 cnv correlated to 'PATHOLOGY_T_STAGE' and 'RACE'.
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del_10q21.1 cnv correlated to 'RACE'.
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del_10q22.3 cnv correlated to 'RACE'.
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del_10q23.31 cnv correlated to 'PATHOLOGY_T_STAGE'.
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del_11p15.5 cnv correlated to 'GENDER' and 'RADIATION_THERAPY'.
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del_12q23.1 cnv correlated to 'PATHOLOGY_T_STAGE'.
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del_13q12.11 cnv correlated to 'GENDER'.
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del_13q14.2 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'GENDER', 'RADIATION_THERAPY', and 'RACE'.
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del_13q21.31 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'RADIATION_THERAPY'.
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del_14q32.32 cnv correlated to 'PATHOLOGY_M_STAGE'.
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del_15q11.2 cnv correlated to 'PATHOLOGY_T_STAGE'.
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del_16p13.3 cnv correlated to 'PATHOLOGY_T_STAGE'.
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del_17p12 cnv correlated to 'GENDER'.
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del_18q12.2 cnv correlated to 'PATHOLOGY_T_STAGE'.
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del_18q21.2 cnv correlated to 'PATHOLOGY_T_STAGE'.
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del_19p13.3 cnv correlated to 'GENDER'.
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del_22q11.1 cnv correlated to 'PATHOLOGY_T_STAGE'.
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del_xp22.2 cnv correlated to 'GENDER'.
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del_xp21.1 cnv correlated to 'GENDER'.
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del_xp11.3 cnv correlated to 'GENDER'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 99 focal events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 65 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 |
NUMBER PACK YEARS SMOKED |
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 | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
del 13q14 2 | 125 (20%) | 500 |
0.987 (1.00) |
0.00395 (0.144) |
4e-05 (0.0155) |
0.0033 (0.14) |
0.00959 (0.215) |
0.146 (0.575) |
0.00208 (0.11) |
0.0136 (0.249) |
0.0905 (0.495) |
0.305 (0.739) |
0.00933 (0.213) |
1 (1.00) |
del 7q31 1 | 127 (20%) | 498 |
0.248 (0.702) |
0.0412 (0.387) |
0.00092 (0.0729) |
0.00549 (0.166) |
0.00877 (0.209) |
0.304 (0.739) |
0.0015 (0.0992) |
0.898 (1.00) |
1 (1.00) |
0.105 (0.529) |
0.364 (0.781) |
0.699 (0.951) |
amp 17q12 | 222 (36%) | 403 |
0.279 (0.724) |
0.444 (0.821) |
0.0492 (0.433) |
0.716 (0.954) |
0.776 (0.969) |
0.00809 (0.209) |
0.00448 (0.152) |
0.325 (0.748) |
0.691 (0.944) |
0.221 (0.68) |
0.0131 (0.249) |
1 (1.00) |
del 9p21 3 | 334 (53%) | 291 |
0.518 (0.859) |
0.887 (1.00) |
0.0115 (0.24) |
0.00203 (0.11) |
0.105 (0.529) |
0.87 (1.00) |
0.0037 (0.142) |
0.0943 (0.509) |
0.171 (0.611) |
0.25 (0.704) |
0.215 (0.668) |
0.221 (0.68) |
del 13q21 31 | 126 (20%) | 499 |
0.914 (1.00) |
0.0811 (0.465) |
0.0122 (0.245) |
0.0132 (0.249) |
0.318 (0.742) |
0.147 (0.575) |
0.0286 (0.34) |
0.00471 (0.155) |
0.163 (0.6) |
0.57 (0.879) |
0.0519 (0.443) |
0.445 (0.821) |
amp 3q26 2 | 287 (46%) | 338 |
0.986 (1.00) |
0.0146 (0.259) |
0.00664 (0.183) |
0.968 (1.00) |
0.688 (0.944) |
0.739 (0.957) |
0.0647 (0.447) |
0.0158 (0.261) |
0.197 (0.651) |
0.0964 (0.515) |
0.00134 (0.0936) |
0.0655 (0.447) |
amp 7p11 2 | 340 (54%) | 285 |
0.433 (0.818) |
0.0742 (0.455) |
0.2 (0.655) |
0.0113 (0.24) |
0.947 (1.00) |
0.183 (0.631) |
0.00372 (0.142) |
0.347 (0.766) |
0.535 (0.866) |
0.506 (0.852) |
0.0656 (0.447) |
1 (1.00) |
amp 8p23 1 | 229 (37%) | 396 |
0.406 (0.796) |
0.00428 (0.15) |
0.408 (0.796) |
0.38 (0.787) |
0.746 (0.957) |
1 (1.00) |
0.00055 (0.0683) |
0.663 (0.932) |
0.444 (0.821) |
0.279 (0.724) |
0.44 (0.821) |
0.532 (0.864) |
del 4q34 3 | 300 (48%) | 325 |
0.136 (0.565) |
0.0102 (0.221) |
0.00631 (0.178) |
0.179 (0.625) |
0.484 (0.837) |
0.32 (0.742) |
0.54 (0.869) |
0.465 (0.827) |
0.924 (1.00) |
0.881 (1.00) |
0.85 (1.00) |
1 (1.00) |
del 10p11 21 | 102 (16%) | 523 |
0.0841 (0.467) |
0.53 (0.864) |
0.034 (0.372) |
0.00401 (0.144) |
0.911 (1.00) |
1 (1.00) |
0.345 (0.766) |
0.21 (0.663) |
0.407 (0.796) |
0.0561 (0.444) |
0.00067 (0.0683) |
0.396 (0.789) |
del 11p15 5 | 175 (28%) | 450 |
0.876 (1.00) |
0.271 (0.717) |
0.144 (0.575) |
0.0237 (0.303) |
0.616 (0.904) |
0.853 (1.00) |
0.00827 (0.209) |
0.0102 (0.221) |
0.152 (0.581) |
0.447 (0.821) |
0.142 (0.575) |
0.481 (0.837) |
amp 1p36 22 | 101 (16%) | 524 |
0.962 (1.00) |
0.911 (1.00) |
0.334 (0.758) |
0.092 (0.501) |
0.968 (1.00) |
0.82 (0.994) |
0.00079 (0.0722) |
0.117 (0.555) |
0.238 (0.688) |
0.143 (0.575) |
0.215 (0.668) |
0.393 (0.788) |
amp 1p34 2 | 95 (15%) | 530 |
0.892 (1.00) |
0.149 (0.576) |
0.101 (0.518) |
0.178 (0.625) |
0.451 (0.823) |
0.34 (0.763) |
0.145 (0.575) |
0.000689 (0.0683) |
0.884 (1.00) |
0.681 (0.94) |
0.381 (0.787) |
0.673 (0.935) |
amp 1q42 3 | 244 (39%) | 381 |
0.307 (0.739) |
0.00269 (0.128) |
0.459 (0.827) |
0.0533 (0.443) |
0.947 (1.00) |
0.734 (0.957) |
0.0195 (0.29) |
0.0682 (0.447) |
0.522 (0.859) |
0.839 (0.999) |
0.022 (0.297) |
1 (1.00) |
amp 2q12 2 | 155 (25%) | 470 |
0.871 (1.00) |
0.372 (0.787) |
0.00573 (0.166) |
0.0189 (0.285) |
0.501 (0.852) |
0.556 (0.874) |
0.128 (0.563) |
1 (1.00) |
0.777 (0.97) |
0.926 (1.00) |
0.196 (0.651) |
1 (1.00) |
amp 5p15 33 | 228 (36%) | 397 |
0.994 (1.00) |
0.723 (0.956) |
0.215 (0.668) |
1e-05 (0.00594) |
0.88 (1.00) |
1 (1.00) |
0.0232 (0.303) |
0.196 (0.651) |
0.167 (0.608) |
0.602 (0.899) |
0.0232 (0.303) |
0.754 (0.957) |
amp 5p13 1 | 216 (35%) | 409 |
0.812 (0.994) |
0.779 (0.97) |
0.667 (0.934) |
0.00848 (0.209) |
0.443 (0.821) |
0.486 (0.837) |
0.231 (0.684) |
0.827 (0.995) |
0.919 (1.00) |
0.915 (1.00) |
0.286 (0.727) |
1 (1.00) |
amp 6q21 | 111 (18%) | 514 |
0.00568 (0.166) |
0.565 (0.877) |
0.0243 (0.304) |
0.559 (0.874) |
0.415 (0.802) |
0.0149 (0.26) |
0.423 (0.81) |
1 (1.00) |
0.337 (0.763) |
0.57 (0.879) |
0.0566 (0.444) |
1 (1.00) |
amp 7p22 3 | 353 (56%) | 272 |
0.557 (0.874) |
0.285 (0.726) |
0.12 (0.558) |
0.0392 (0.385) |
0.82 (0.994) |
1 (1.00) |
0.000393 (0.0668) |
0.463 (0.827) |
0.851 (1.00) |
0.459 (0.827) |
0.575 (0.883) |
0.23 (0.684) |
amp 7q21 2 | 317 (51%) | 308 |
0.967 (1.00) |
0.942 (1.00) |
0.929 (1.00) |
0.0725 (0.451) |
0.515 (0.859) |
0.741 (0.957) |
0.00213 (0.11) |
0.348 (0.766) |
0.178 (0.625) |
0.262 (0.708) |
0.0979 (0.517) |
0.764 (0.963) |
amp 12p12 1 | 207 (33%) | 418 |
0.209 (0.66) |
0.234 (0.688) |
0.0464 (0.412) |
0.0019 (0.11) |
0.867 (1.00) |
0.723 (0.956) |
0.0405 (0.387) |
0.224 (0.68) |
0.0587 (0.444) |
0.381 (0.787) |
0.141 (0.573) |
1 (1.00) |
amp 14q13 3 | 113 (18%) | 512 |
0.083 (0.465) |
0.101 (0.518) |
0.171 (0.611) |
0.327 (0.748) |
0.747 (0.957) |
1 (1.00) |
0.00881 (0.209) |
0.0612 (0.447) |
0.664 (0.932) |
0.75 (0.957) |
0.303 (0.739) |
0.118 (0.558) |
amp 20q13 2 | 416 (67%) | 209 |
0.105 (0.529) |
0.0374 (0.378) |
0.487 (0.837) |
0.193 (0.651) |
0.0399 (0.387) |
0.863 (1.00) |
0.00301 (0.132) |
0.271 (0.717) |
0.964 (1.00) |
0.208 (0.66) |
0.967 (1.00) |
1 (1.00) |
del 4p16 3 | 271 (43%) | 354 |
0.239 (0.688) |
0.537 (0.867) |
0.401 (0.794) |
0.13 (0.563) |
0.202 (0.655) |
0.131 (0.563) |
0.0133 (0.249) |
0.6 (0.899) |
0.928 (1.00) |
0.375 (0.787) |
0.388 (0.788) |
1 (1.00) |
del 7q36 3 | 163 (26%) | 462 |
0.303 (0.739) |
0.392 (0.788) |
0.00069 (0.0683) |
0.0695 (0.447) |
0.133 (0.563) |
0.455 (0.827) |
0.232 (0.684) |
0.724 (0.956) |
0.669 (0.934) |
0.544 (0.873) |
0.592 (0.896) |
1 (1.00) |
del 8p23 2 | 212 (34%) | 413 |
0.757 (0.957) |
0.26 (0.706) |
0.238 (0.688) |
0.0552 (0.444) |
0.373 (0.787) |
0.382 (0.787) |
0.000291 (0.0668) |
0.189 (0.641) |
0.651 (0.928) |
0.0834 (0.465) |
0.13 (0.563) |
0.328 (0.75) |
del 9q21 11 | 176 (28%) | 449 |
0.269 (0.717) |
0.824 (0.995) |
0.256 (0.706) |
0.259 (0.706) |
0.878 (1.00) |
0.855 (1.00) |
0.0802 (0.462) |
0.909 (1.00) |
1 (1.00) |
0.0121 (0.245) |
0.183 (0.631) |
1 (1.00) |
del 10p15 3 | 131 (21%) | 494 |
0.005 (0.16) |
0.956 (1.00) |
0.245 (0.695) |
0.357 (0.778) |
0.327 (0.748) |
0.838 (0.999) |
0.0406 (0.387) |
0.899 (1.00) |
0.294 (0.729) |
0.514 (0.859) |
0.0311 (0.359) |
0.704 (0.953) |
del 10q21 1 | 112 (18%) | 513 |
0.754 (0.957) |
0.53 (0.864) |
0.65 (0.927) |
0.202 (0.655) |
0.958 (1.00) |
0.385 (0.787) |
0.82 (0.994) |
0.417 (0.803) |
0.293 (0.729) |
0.507 (0.852) |
0.00343 (0.141) |
0.426 (0.812) |
del 10q22 3 | 135 (22%) | 490 |
0.197 (0.651) |
0.117 (0.555) |
0.633 (0.916) |
0.0168 (0.269) |
0.885 (1.00) |
0.842 (0.999) |
0.241 (0.691) |
0.9 (1.00) |
0.122 (0.558) |
0.318 (0.742) |
0.00128 (0.0936) |
0.256 (0.706) |
del 10q23 31 | 183 (29%) | 442 |
0.125 (0.561) |
0.0436 (0.397) |
0.98 (1.00) |
0.0078 (0.206) |
0.896 (1.00) |
0.717 (0.954) |
0.565 (0.877) |
0.567 (0.878) |
0.083 (0.465) |
0.857 (1.00) |
0.0146 (0.259) |
0.506 (0.852) |
del 12q23 1 | 109 (17%) | 516 |
0.982 (1.00) |
0.256 (0.706) |
0.619 (0.904) |
0.00211 (0.11) |
0.88 (1.00) |
0.657 (0.93) |
1 (1.00) |
0.135 (0.565) |
0.329 (0.75) |
0.304 (0.739) |
0.36 (0.779) |
0.653 (0.929) |
del 13q12 11 | 138 (22%) | 487 |
0.742 (0.957) |
0.106 (0.529) |
0.0566 (0.444) |
0.0156 (0.261) |
0.261 (0.706) |
0.689 (0.944) |
5.21e-05 (0.0155) |
0.0831 (0.465) |
0.559 (0.874) |
0.202 (0.655) |
0.268 (0.717) |
0.26 (0.706) |
del 14q32 32 | 190 (30%) | 435 |
0.795 (0.982) |
0.506 (0.852) |
0.148 (0.575) |
0.529 (0.864) |
0.431 (0.818) |
0.00564 (0.166) |
0.447 (0.821) |
0.91 (1.00) |
0.772 (0.965) |
0.639 (0.919) |
0.718 (0.954) |
0.0385 (0.385) |
del 15q11 2 | 183 (29%) | 442 |
0.45 (0.822) |
0.621 (0.904) |
0.461 (0.827) |
0.0134 (0.249) |
0.53 (0.864) |
0.855 (1.00) |
0.443 (0.821) |
0.209 (0.66) |
0.876 (1.00) |
0.423 (0.81) |
0.688 (0.944) |
0.736 (0.957) |
del 16p13 3 | 178 (28%) | 447 |
0.2 (0.655) |
0.109 (0.541) |
0.0366 (0.378) |
0.00921 (0.213) |
0.15 (0.577) |
0.359 (0.779) |
0.0255 (0.316) |
0.908 (1.00) |
0.626 (0.908) |
0.458 (0.827) |
0.853 (1.00) |
1 (1.00) |
del 17p12 | 267 (43%) | 358 |
0.583 (0.89) |
0.171 (0.611) |
0.921 (1.00) |
0.232 (0.684) |
0.761 (0.96) |
0.315 (0.742) |
0.0133 (0.249) |
0.171 (0.611) |
0.163 (0.6) |
0.781 (0.97) |
0.305 (0.739) |
0.344 (0.766) |
del 18q12 2 | 292 (47%) | 333 |
0.188 (0.641) |
0.362 (0.779) |
0.393 (0.788) |
1e-05 (0.00594) |
0.829 (0.997) |
0.868 (1.00) |
0.114 (0.55) |
0.601 (0.899) |
1 (1.00) |
0.125 (0.561) |
0.46 (0.827) |
0.222 (0.68) |
del 18q21 2 | 323 (52%) | 302 |
0.549 (0.874) |
0.548 (0.874) |
0.594 (0.896) |
0.00043 (0.0668) |
0.785 (0.974) |
0.869 (1.00) |
0.0661 (0.447) |
0.347 (0.766) |
0.914 (1.00) |
0.235 (0.688) |
0.319 (0.742) |
0.0342 (0.372) |
del 19p13 3 | 249 (40%) | 376 |
0.0674 (0.447) |
0.942 (1.00) |
0.691 (0.944) |
0.0544 (0.443) |
0.485 (0.837) |
1 (1.00) |
0.000905 (0.0729) |
0.165 (0.606) |
0.268 (0.717) |
0.433 (0.818) |
0.0336 (0.372) |
1 (1.00) |
del 22q11 1 | 230 (37%) | 395 |
0.148 (0.575) |
0.149 (0.575) |
0.0661 (0.447) |
0.00045 (0.0668) |
0.806 (0.991) |
0.734 (0.957) |
0.277 (0.724) |
0.104 (0.529) |
0.684 (0.942) |
0.82 (0.994) |
0.254 (0.706) |
1 (1.00) |
del xp22 2 | 150 (24%) | 475 |
0.489 (0.838) |
0.0781 (0.46) |
0.312 (0.742) |
0.44 (0.821) |
0.361 (0.779) |
0.7 (0.951) |
0.00291 (0.132) |
0.546 (0.873) |
0.542 (0.871) |
0.115 (0.554) |
0.0373 (0.378) |
0.479 (0.835) |
del xp21 1 | 143 (23%) | 482 |
0.558 (0.874) |
0.415 (0.802) |
0.311 (0.742) |
0.742 (0.957) |
0.272 (0.717) |
0.226 (0.68) |
0.00249 (0.123) |
0.711 (0.954) |
0.839 (0.999) |
0.758 (0.957) |
0.611 (0.903) |
0.0716 (0.451) |
del xp11 3 | 146 (23%) | 479 |
0.841 (0.999) |
0.228 (0.681) |
0.0578 (0.444) |
0.252 (0.704) |
0.238 (0.688) |
0.324 (0.748) |
0.00693 (0.187) |
0.175 (0.623) |
0.183 (0.631) |
0.684 (0.942) |
0.155 (0.585) |
0.283 (0.726) |
amp 1q21 3 | 249 (40%) | 376 |
0.393 (0.788) |
0.0704 (0.447) |
0.252 (0.704) |
0.0241 (0.304) |
0.702 (0.952) |
0.61 (0.903) |
0.129 (0.563) |
0.109 (0.541) |
0.892 (1.00) |
0.87 (1.00) |
0.12 (0.558) |
1 (1.00) |
amp 6p21 1 | 192 (31%) | 433 |
0.396 (0.789) |
0.0207 (0.296) |
0.0664 (0.447) |
0.0459 (0.41) |
0.117 (0.555) |
0.468 (0.83) |
0.106 (0.531) |
0.734 (0.957) |
0.135 (0.565) |
0.757 (0.957) |
0.0776 (0.46) |
1 (1.00) |
amp 6q12 | 141 (23%) | 484 |
0.0407 (0.387) |
0.691 (0.944) |
0.0531 (0.443) |
0.474 (0.834) |
0.341 (0.763) |
0.315 (0.742) |
0.464 (0.827) |
0.707 (0.953) |
0.113 (0.549) |
0.661 (0.932) |
0.358 (0.779) |
0.472 (0.833) |
amp 8p11 21 | 272 (44%) | 353 |
0.388 (0.788) |
0.465 (0.827) |
0.067 (0.447) |
0.445 (0.821) |
0.153 (0.581) |
0.506 (0.852) |
0.077 (0.46) |
0.753 (0.957) |
0.412 (0.799) |
0.98 (1.00) |
0.769 (0.965) |
0.765 (0.963) |
amp 8q24 21 | 454 (73%) | 171 |
0.769 (0.965) |
0.386 (0.787) |
0.642 (0.92) |
0.259 (0.706) |
0.241 (0.691) |
0.711 (0.954) |
0.116 (0.554) |
1 (1.00) |
0.128 (0.563) |
0.392 (0.788) |
0.298 (0.733) |
1 (1.00) |
amp 9p24 1 | 91 (15%) | 534 |
0.84 (0.999) |
0.706 (0.953) |
0.882 (1.00) |
0.677 (0.935) |
0.298 (0.733) |
1 (1.00) |
0.385 (0.787) |
0.462 (0.827) |
0.948 (1.00) |
0.603 (0.899) |
0.203 (0.656) |
0.677 (0.935) |
amp 9p13 3 | 132 (21%) | 493 |
0.647 (0.925) |
0.839 (0.999) |
0.133 (0.563) |
0.446 (0.821) |
0.674 (0.935) |
0.838 (0.999) |
0.592 (0.896) |
0.38 (0.787) |
0.796 (0.982) |
0.223 (0.68) |
0.911 (1.00) |
0.237 (0.688) |
amp 9q34 3 | 185 (30%) | 440 |
0.0347 (0.372) |
0.021 (0.297) |
0.755 (0.957) |
0.364 (0.781) |
0.253 (0.706) |
0.717 (0.954) |
0.0438 (0.397) |
0.0292 (0.344) |
0.52 (0.859) |
0.022 (0.297) |
0.588 (0.893) |
0.516 (0.859) |
amp 10p11 22 | 169 (27%) | 456 |
0.853 (1.00) |
0.665 (0.933) |
0.181 (0.631) |
0.0616 (0.447) |
0.983 (1.00) |
0.573 (0.88) |
0.622 (0.904) |
0.56 (0.874) |
0.0454 (0.409) |
0.121 (0.558) |
0.146 (0.575) |
0.735 (0.957) |
amp 10q22 2 | 125 (20%) | 500 |
0.612 (0.903) |
0.524 (0.861) |
0.0761 (0.459) |
0.132 (0.563) |
0.503 (0.852) |
0.675 (0.935) |
0.743 (0.957) |
0.3 (0.735) |
0.0328 (0.372) |
0.0376 (0.378) |
0.138 (0.568) |
0.131 (0.563) |
amp 10q26 13 | 119 (19%) | 506 |
0.383 (0.787) |
0.887 (1.00) |
0.0213 (0.297) |
0.157 (0.587) |
0.877 (1.00) |
0.519 (0.859) |
0.911 (1.00) |
0.791 (0.978) |
0.734 (0.957) |
0.069 (0.447) |
0.243 (0.692) |
0.227 (0.68) |
amp 11p13 | 138 (22%) | 487 |
0.0541 (0.443) |
0.525 (0.861) |
0.251 (0.704) |
0.031 (0.359) |
0.491 (0.839) |
0.0699 (0.447) |
0.0262 (0.321) |
0.38 (0.787) |
0.0968 (0.515) |
0.0992 (0.517) |
0.0726 (0.451) |
1 (1.00) |
amp 11q13 3 | 218 (35%) | 407 |
0.875 (1.00) |
0.56 (0.874) |
0.12 (0.558) |
0.924 (1.00) |
0.17 (0.611) |
0.486 (0.837) |
0.0542 (0.443) |
0.101 (0.518) |
0.81 (0.992) |
0.273 (0.717) |
0.0275 (0.33) |
0.754 (0.957) |
amp 12q15 | 161 (26%) | 464 |
0.0745 (0.455) |
0.228 (0.681) |
0.314 (0.742) |
0.552 (0.874) |
0.393 (0.788) |
0.058 (0.444) |
0.194 (0.651) |
1 (1.00) |
0.346 (0.766) |
0.877 (1.00) |
0.134 (0.565) |
1 (1.00) |
amp 13q12 3 | 216 (35%) | 409 |
0.889 (1.00) |
0.11 (0.544) |
0.405 (0.796) |
0.898 (1.00) |
0.184 (0.632) |
0.382 (0.787) |
0.927 (1.00) |
0.381 (0.787) |
0.42 (0.806) |
0.019 (0.285) |
0.145 (0.575) |
0.755 (0.957) |
amp 13q22 1 | 243 (39%) | 382 |
0.449 (0.822) |
0.801 (0.985) |
0.619 (0.904) |
0.819 (0.994) |
0.198 (0.652) |
1 (1.00) |
0.0589 (0.444) |
0.592 (0.896) |
0.0968 (0.515) |
0.204 (0.656) |
0.306 (0.739) |
0.113 (0.549) |
amp 15q26 1 | 168 (27%) | 457 |
0.56 (0.874) |
0.992 (1.00) |
0.52 (0.859) |
0.169 (0.611) |
0.288 (0.728) |
0.131 (0.563) |
0.0932 (0.505) |
0.291 (0.729) |
0.571 (0.879) |
0.0349 (0.372) |
0.131 (0.563) |
0.292 (0.729) |
amp 18p11 32 | 178 (28%) | 447 |
0.34 (0.763) |
0.634 (0.916) |
0.0586 (0.444) |
0.275 (0.72) |
0.359 (0.779) |
0.459 (0.827) |
0.208 (0.66) |
0.729 (0.957) |
0.414 (0.802) |
0.577 (0.885) |
0.123 (0.561) |
0.308 (0.739) |
amp 18q11 2 | 198 (32%) | 427 |
0.596 (0.896) |
0.127 (0.563) |
0.548 (0.874) |
0.476 (0.834) |
0.716 (0.954) |
0.477 (0.835) |
0.925 (1.00) |
1 (1.00) |
0.379 (0.787) |
0.699 (0.951) |
0.272 (0.717) |
0.746 (0.957) |
amp 19p13 2 | 79 (13%) | 546 |
0.0368 (0.378) |
0.842 (0.999) |
0.157 (0.587) |
0.39 (0.788) |
0.282 (0.726) |
0.446 (0.821) |
0.292 (0.729) |
0.641 (0.919) |
0.237 (0.688) |
0.42 (0.806) |
0.224 (0.68) |
0.373 (0.787) |
amp 19q12 | 185 (30%) | 440 |
0.886 (1.00) |
0.617 (0.904) |
0.919 (1.00) |
0.154 (0.582) |
0.381 (0.787) |
1 (1.00) |
0.292 (0.729) |
0.733 (0.957) |
0.35 (0.768) |
0.468 (0.83) |
0.0792 (0.461) |
1 (1.00) |
amp 19q13 43 | 164 (26%) | 461 |
0.659 (0.93) |
0.849 (1.00) |
0.556 (0.874) |
0.317 (0.742) |
0.378 (0.787) |
0.848 (1.00) |
0.319 (0.742) |
1 (1.00) |
0.809 (0.992) |
0.231 (0.684) |
0.0528 (0.443) |
0.736 (0.957) |
amp xq28 | 154 (25%) | 471 |
0.798 (0.982) |
0.223 (0.68) |
0.447 (0.821) |
0.552 (0.874) |
0.826 (0.995) |
1 (1.00) |
0.0538 (0.443) |
0.717 (0.954) |
0.374 (0.787) |
0.316 (0.742) |
0.0602 (0.447) |
0.158 (0.588) |
del 1p36 11 | 210 (34%) | 415 |
0.26 (0.706) |
0.954 (1.00) |
0.257 (0.706) |
0.278 (0.724) |
0.469 (0.831) |
1 (1.00) |
0.138 (0.569) |
0.438 (0.821) |
0.0202 (0.296) |
0.78 (0.97) |
0.441 (0.821) |
1 (1.00) |
del 1p13 2 | 156 (25%) | 469 |
0.133 (0.563) |
0.82 (0.994) |
0.0902 (0.495) |
0.0662 (0.447) |
0.0973 (0.516) |
1 (1.00) |
0.0429 (0.397) |
0.81 (0.992) |
0.856 (1.00) |
0.401 (0.794) |
0.289 (0.728) |
0.47 (0.831) |
del 1q44 | 46 (7%) | 579 |
0.261 (0.706) |
0.0218 (0.297) |
0.667 (0.934) |
0.538 (0.867) |
0.565 (0.877) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.143 (0.575) |
0.553 (0.874) |
0.271 (0.717) |
1 (1.00) |
del 1q44 | 43 (7%) | 582 |
0.611 (0.903) |
0.744 (0.957) |
0.153 (0.581) |
0.819 (0.994) |
0.453 (0.825) |
0.504 (0.852) |
0.729 (0.957) |
0.838 (0.999) |
0.133 (0.563) |
0.886 (1.00) |
0.65 (0.927) |
1 (1.00) |
del 2q22 1 | 126 (20%) | 499 |
0.521 (0.859) |
0.139 (0.569) |
0.668 (0.934) |
0.613 (0.903) |
0.617 (0.904) |
1 (1.00) |
1 (1.00) |
0.252 (0.704) |
0.0233 (0.303) |
0.603 (0.899) |
0.757 (0.957) |
0.128 (0.563) |
del 2q32 1 | 87 (14%) | 538 |
0.407 (0.796) |
0.571 (0.879) |
0.919 (1.00) |
0.512 (0.858) |
0.162 (0.6) |
0.339 (0.763) |
1 (1.00) |
0.65 (0.927) |
0.294 (0.729) |
0.386 (0.787) |
1 (1.00) |
0.373 (0.787) |
del 2q33 3 | 85 (14%) | 540 |
0.718 (0.954) |
0.459 (0.827) |
0.798 (0.982) |
0.224 (0.68) |
0.788 (0.976) |
0.338 (0.763) |
0.612 (0.903) |
1 (1.00) |
0.592 (0.896) |
0.341 (0.763) |
0.476 (0.834) |
1 (1.00) |
del 2q37 2 | 122 (20%) | 503 |
0.953 (1.00) |
0.136 (0.565) |
0.875 (1.00) |
0.837 (0.999) |
0.708 (0.953) |
0.0591 (0.444) |
0.826 (0.995) |
0.517 (0.859) |
0.895 (1.00) |
0.162 (0.6) |
0.51 (0.856) |
0.227 (0.68) |
del 3p26 2 | 250 (40%) | 375 |
0.818 (0.994) |
0.489 (0.838) |
0.524 (0.861) |
0.489 (0.838) |
0.354 (0.774) |
0.402 (0.795) |
0.0746 (0.455) |
0.596 (0.896) |
0.817 (0.994) |
0.749 (0.957) |
0.406 (0.796) |
0.756 (0.957) |
del 3p14 2 | 282 (45%) | 343 |
0.0816 (0.465) |
0.374 (0.787) |
0.0205 (0.296) |
0.0652 (0.447) |
0.0354 (0.372) |
0.317 (0.742) |
0.481 (0.837) |
1 (1.00) |
0.385 (0.787) |
0.671 (0.935) |
0.0235 (0.303) |
0.545 (0.873) |
del 3q11 1 | 98 (16%) | 527 |
0.294 (0.729) |
0.14 (0.573) |
0.722 (0.956) |
0.284 (0.726) |
0.348 (0.766) |
0.656 (0.93) |
0.399 (0.794) |
0.313 (0.742) |
0.0688 (0.447) |
0.739 (0.957) |
0.951 (1.00) |
1 (1.00) |
del 3q26 31 | 63 (10%) | 562 |
0.635 (0.916) |
0.487 (0.837) |
0.771 (0.965) |
0.303 (0.739) |
0.427 (0.812) |
0.786 (0.975) |
0.771 (0.965) |
0.485 (0.837) |
0.558 (0.874) |
0.264 (0.71) |
0.61 (0.903) |
|
del 4p15 2 | 269 (43%) | 356 |
0.034 (0.372) |
0.366 (0.783) |
0.254 (0.706) |
0.127 (0.563) |
0.826 (0.995) |
0.243 (0.692) |
0.0271 (0.329) |
0.4 (0.794) |
0.705 (0.953) |
0.201 (0.655) |
0.197 (0.651) |
1 (1.00) |
del 4q22 1 | 298 (48%) | 327 |
0.0997 (0.517) |
0.207 (0.66) |
0.057 (0.444) |
0.0187 (0.285) |
0.327 (0.748) |
1 (1.00) |
0.0796 (0.461) |
0.347 (0.766) |
0.824 (0.995) |
0.505 (0.852) |
0.338 (0.763) |
0.56 (0.874) |
del 5q12 1 | 282 (45%) | 343 |
0.771 (0.965) |
0.609 (0.903) |
0.0567 (0.444) |
0.0668 (0.447) |
0.319 (0.742) |
0.868 (1.00) |
0.0526 (0.443) |
0.531 (0.864) |
0.484 (0.837) |
0.928 (1.00) |
0.384 (0.787) |
1 (1.00) |
del 6p25 3 | 188 (30%) | 437 |
0.269 (0.717) |
0.284 (0.726) |
0.537 (0.867) |
0.121 (0.558) |
0.988 (1.00) |
0.357 (0.778) |
0.634 (0.916) |
0.427 (0.812) |
0.597 (0.897) |
0.989 (1.00) |
1 (1.00) |
0.19 (0.642) |
del 6q16 3 | 147 (24%) | 478 |
0.794 (0.982) |
0.908 (1.00) |
0.581 (0.889) |
0.0695 (0.447) |
0.462 (0.827) |
0.072 (0.451) |
0.0176 (0.276) |
0.214 (0.668) |
0.663 (0.932) |
0.0697 (0.447) |
0.316 (0.742) |
0.72 (0.954) |
del 6q26 | 152 (24%) | 473 |
0.657 (0.93) |
0.596 (0.896) |
0.187 (0.637) |
0.0164 (0.267) |
0.857 (1.00) |
1 (1.00) |
0.0671 (0.447) |
0.46 (0.827) |
0.148 (0.575) |
0.238 (0.688) |
0.479 (0.835) |
0.718 (0.954) |
del 9p23 | 302 (48%) | 323 |
0.836 (0.999) |
0.562 (0.875) |
0.0639 (0.447) |
0.0413 (0.387) |
0.166 (0.606) |
0.408 (0.796) |
0.0352 (0.372) |
0.211 (0.664) |
0.177 (0.625) |
0.616 (0.904) |
0.781 (0.97) |
0.362 (0.779) |
del 11q25 | 178 (28%) | 447 |
0.124 (0.561) |
0.318 (0.742) |
0.0626 (0.447) |
0.0657 (0.447) |
0.365 (0.781) |
0.709 (0.953) |
0.0151 (0.26) |
0.0644 (0.447) |
0.297 (0.733) |
0.207 (0.66) |
0.618 (0.904) |
0.0861 (0.476) |
del 12p13 1 | 113 (18%) | 512 |
0.581 (0.889) |
0.0771 (0.46) |
0.27 (0.717) |
0.0986 (0.517) |
0.961 (1.00) |
0.661 (0.932) |
0.91 (1.00) |
0.42 (0.806) |
0.56 (0.874) |
0.113 (0.549) |
0.378 (0.787) |
0.677 (0.935) |
del 14q23 3 | 187 (30%) | 438 |
0.715 (0.954) |
0.517 (0.859) |
0.289 (0.728) |
0.599 (0.898) |
0.0392 (0.385) |
0.275 (0.72) |
0.444 (0.821) |
0.733 (0.957) |
0.747 (0.957) |
0.904 (1.00) |
0.502 (0.852) |
0.735 (0.957) |
del 16p13 3 | 148 (24%) | 477 |
0.45 (0.822) |
0.206 (0.66) |
0.0329 (0.372) |
0.065 (0.447) |
0.0517 (0.443) |
0.325 (0.748) |
0.122 (0.558) |
1 (1.00) |
0.588 (0.893) |
0.475 (0.834) |
0.439 (0.821) |
0.709 (0.953) |
del 16q23 1 | 265 (42%) | 360 |
0.913 (1.00) |
0.429 (0.816) |
0.0817 (0.465) |
0.617 (0.904) |
0.189 (0.641) |
0.0177 (0.276) |
0.0761 (0.459) |
0.834 (0.999) |
0.967 (1.00) |
0.69 (0.944) |
0.702 (0.952) |
0.353 (0.774) |
del 17q24 3 | 103 (16%) | 522 |
0.654 (0.929) |
0.0541 (0.443) |
0.403 (0.796) |
0.0993 (0.517) |
0.283 (0.726) |
0.658 (0.93) |
0.41 (0.798) |
0.0778 (0.46) |
0.176 (0.625) |
0.745 (0.957) |
0.186 (0.637) |
0.7 (0.951) |
del 19q13 11 | 120 (19%) | 505 |
0.64 (0.919) |
0.834 (0.999) |
0.973 (1.00) |
0.28 (0.726) |
0.534 (0.865) |
0.146 (0.575) |
0.182 (0.631) |
1 (1.00) |
0.677 (0.935) |
0.227 (0.68) |
0.368 (0.784) |
1 (1.00) |
del 20p12 1 | 72 (12%) | 553 |
0.913 (1.00) |
0.935 (1.00) |
0.902 (1.00) |
0.432 (0.818) |
0.94 (1.00) |
1 (1.00) |
0.585 (0.89) |
0.112 (0.549) |
0.471 (0.832) |
0.753 (0.957) |
0.906 (1.00) |
0.287 (0.727) |
del 21q11 2 | 290 (46%) | 335 |
0.583 (0.89) |
0.0735 (0.455) |
0.911 (1.00) |
0.285 (0.726) |
0.308 (0.739) |
0.621 (0.904) |
0.93 (1.00) |
0.464 (0.827) |
0.707 (0.953) |
0.551 (0.874) |
0.623 (0.904) |
0.214 (0.668) |
del 21q22 13 | 305 (49%) | 320 |
0.612 (0.903) |
0.285 (0.726) |
0.865 (1.00) |
0.533 (0.865) |
0.906 (1.00) |
0.409 (0.796) |
0.726 (0.957) |
0.531 (0.864) |
0.0435 (0.397) |
0.145 (0.575) |
0.195 (0.651) |
0.222 (0.68) |
del 22q13 31 | 235 (38%) | 390 |
0.152 (0.581) |
0.521 (0.859) |
0.0158 (0.261) |
0.167 (0.608) |
0.178 (0.625) |
0.394 (0.788) |
0.322 (0.745) |
0.239 (0.688) |
0.507 (0.852) |
0.899 (1.00) |
0.137 (0.568) |
0.754 (0.957) |
del xq11 2 | 103 (16%) | 522 |
0.91 (1.00) |
0.918 (1.00) |
0.965 (1.00) |
0.57 (0.879) |
0.826 (0.995) |
0.25 (0.704) |
0.156 (0.587) |
0.12 (0.558) |
0.346 (0.766) |
0.968 (1.00) |
1 (1.00) |
0.677 (0.935) |
del xq21 33 | 96 (15%) | 529 |
0.439 (0.821) |
0.747 (0.957) |
0.636 (0.916) |
0.551 (0.874) |
0.394 (0.788) |
0.635 (0.916) |
0.331 (0.754) |
0.0796 (0.461) |
0.0704 (0.447) |
0.502 (0.852) |
1 (1.00) |
1 (1.00) |
P value = 0.00079 (Fisher's exact test), Q value = 0.072
Table S1. Gene #1: 'amp_1p36.22' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
AMP PEAK 1(1P36.22) MUTATED | 16 | 85 |
AMP PEAK 1(1P36.22) WILD-TYPE | 169 | 355 |
Figure S1. Get High-res Image Gene #1: 'amp_1p36.22' versus Clinical Feature #7: 'GENDER'
![](D1V7.png)
P value = 0.000689 (Fisher's exact test), Q value = 0.068
Table S2. Gene #2: 'amp_1p34.2' versus Clinical Feature #8: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 438 | 116 |
AMP PEAK 2(1P34.2) MUTATED | 54 | 30 |
AMP PEAK 2(1P34.2) WILD-TYPE | 384 | 86 |
Figure S2. Get High-res Image Gene #2: 'amp_1p34.2' versus Clinical Feature #8: 'RADIATION_THERAPY'
![](D2V8.png)
P value = 0.00269 (Wilcoxon-test), Q value = 0.13
Table S3. Gene #4: 'amp_1q42.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 616 | 64.8 (11.2) |
AMP PEAK 4(1Q42.3) MUTATED | 240 | 63.2 (10.4) |
AMP PEAK 4(1Q42.3) WILD-TYPE | 376 | 65.7 (11.6) |
Figure S3. Get High-res Image Gene #4: 'amp_1q42.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D4V2.png)
P value = 0.00573 (Fisher's exact test), Q value = 0.17
Table S4. Gene #5: 'amp_2q12.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 11 | 20 | 47 | 33 | 87 | 88 | 29 | 97 | 73 | 46 | 51 | 4 |
AMP PEAK 5(2Q12.2) MUTATED | 1 | 9 | 10 | 7 | 27 | 30 | 8 | 15 | 12 | 11 | 6 | 2 |
AMP PEAK 5(2Q12.2) WILD-TYPE | 10 | 11 | 37 | 26 | 60 | 58 | 21 | 82 | 61 | 35 | 45 | 2 |
Figure S4. Get High-res Image Gene #5: 'amp_2q12.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D5V3.png)
P value = 0.00664 (Fisher's exact test), Q value = 0.18
Table S5. Gene #6: 'amp_3q26.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 11 | 20 | 47 | 33 | 87 | 88 | 29 | 97 | 73 | 46 | 51 | 4 |
AMP PEAK 6(3Q26.2) MUTATED | 3 | 9 | 18 | 12 | 47 | 43 | 23 | 39 | 29 | 25 | 20 | 3 |
AMP PEAK 6(3Q26.2) WILD-TYPE | 8 | 11 | 29 | 21 | 40 | 45 | 6 | 58 | 44 | 21 | 31 | 1 |
Figure S5. Get High-res Image Gene #6: 'amp_3q26.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D6V3.png)
P value = 0.00134 (Fisher's exact test), Q value = 0.094
Table S6. Gene #6: 'amp_3q26.2' versus Clinical Feature #11: 'RACE'
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER | WHITE |
---|---|---|---|---|
ALL | 134 | 17 | 1 | 392 |
AMP PEAK 6(3Q26.2) MUTATED | 79 | 10 | 0 | 162 |
AMP PEAK 6(3Q26.2) WILD-TYPE | 55 | 7 | 1 | 230 |
Figure S6. Get High-res Image Gene #6: 'amp_3q26.2' versus Clinical Feature #11: 'RACE'
![](D6V11.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0059
Table S7. Gene #7: 'amp_5p15.33' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 55 | 136 | 283 | 124 |
AMP PEAK 7(5P15.33) MUTATED | 12 | 53 | 127 | 26 |
AMP PEAK 7(5P15.33) WILD-TYPE | 43 | 83 | 156 | 98 |
Figure S7. Get High-res Image Gene #7: 'amp_5p15.33' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D7V4.png)
P value = 0.00848 (Fisher's exact test), Q value = 0.21
Table S8. Gene #8: 'amp_5p13.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 55 | 136 | 283 | 124 |
AMP PEAK 8(5P13.1) MUTATED | 12 | 50 | 112 | 32 |
AMP PEAK 8(5P13.1) WILD-TYPE | 43 | 86 | 171 | 92 |
Figure S8. Get High-res Image Gene #8: 'amp_5p13.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D8V4.png)
P value = 0.00568 (logrank test), Q value = 0.17
Table S9. Gene #11: 'amp_6q21' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 590 | 235 | 0.0 - 122.3 (13.5) |
AMP PEAK 11(6Q21) MUTATED | 103 | 52 | 0.7 - 68.0 (12.9) |
AMP PEAK 11(6Q21) WILD-TYPE | 487 | 183 | 0.0 - 122.3 (13.8) |
Figure S9. Get High-res Image Gene #11: 'amp_6q21' versus Clinical Feature #1: 'Time to Death'
![](D11V1.png)
P value = 0.000393 (Fisher's exact test), Q value = 0.067
Table S10. Gene #12: 'amp_7p22.3' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
AMP PEAK 12(7P22.3) MUTATED | 84 | 269 |
AMP PEAK 12(7P22.3) WILD-TYPE | 101 | 171 |
Figure S10. Get High-res Image Gene #12: 'amp_7p22.3' versus Clinical Feature #7: 'GENDER'
![](D12V7.png)
P value = 0.0113 (Fisher's exact test), Q value = 0.24
Table S11. Gene #13: 'amp_7p11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 55 | 136 | 283 | 124 |
AMP PEAK 13(7P11.2) MUTATED | 36 | 61 | 162 | 58 |
AMP PEAK 13(7P11.2) WILD-TYPE | 19 | 75 | 121 | 66 |
Figure S11. Get High-res Image Gene #13: 'amp_7p11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D13V4.png)
P value = 0.00372 (Fisher's exact test), Q value = 0.14
Table S12. Gene #13: 'amp_7p11.2' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
AMP PEAK 13(7P11.2) MUTATED | 84 | 256 |
AMP PEAK 13(7P11.2) WILD-TYPE | 101 | 184 |
Figure S12. Get High-res Image Gene #13: 'amp_7p11.2' versus Clinical Feature #7: 'GENDER'
![](D13V7.png)
P value = 0.00213 (Fisher's exact test), Q value = 0.11
Table S13. Gene #14: 'amp_7q21.2' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
AMP PEAK 14(7Q21.2) MUTATED | 76 | 241 |
AMP PEAK 14(7Q21.2) WILD-TYPE | 109 | 199 |
Figure S13. Get High-res Image Gene #14: 'amp_7q21.2' versus Clinical Feature #7: 'GENDER'
![](D14V7.png)
P value = 0.00428 (Wilcoxon-test), Q value = 0.15
Table S14. Gene #15: 'amp_8p23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 616 | 64.8 (11.2) |
AMP PEAK 15(8P23.1) MUTATED | 225 | 66.4 (11.1) |
AMP PEAK 15(8P23.1) WILD-TYPE | 391 | 63.9 (11.2) |
Figure S14. Get High-res Image Gene #15: 'amp_8p23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D15V2.png)
P value = 0.00055 (Fisher's exact test), Q value = 0.068
Table S15. Gene #15: 'amp_8p23.1' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
AMP PEAK 15(8P23.1) MUTATED | 87 | 142 |
AMP PEAK 15(8P23.1) WILD-TYPE | 98 | 298 |
Figure S15. Get High-res Image Gene #15: 'amp_8p23.1' versus Clinical Feature #7: 'GENDER'
![](D15V7.png)
P value = 0.0019 (Fisher's exact test), Q value = 0.11
Table S16. Gene #26: 'amp_12p12.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 55 | 136 | 283 | 124 |
AMP PEAK 26(12P12.1) MUTATED | 14 | 40 | 115 | 29 |
AMP PEAK 26(12P12.1) WILD-TYPE | 41 | 96 | 168 | 95 |
Figure S16. Get High-res Image Gene #26: 'amp_12p12.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D26V4.png)
P value = 0.00881 (Fisher's exact test), Q value = 0.21
Table S17. Gene #30: 'amp_14q13.3' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
AMP PEAK 30(14Q13.3) MUTATED | 22 | 91 |
AMP PEAK 30(14Q13.3) WILD-TYPE | 163 | 349 |
Figure S17. Get High-res Image Gene #30: 'amp_14q13.3' versus Clinical Feature #7: 'GENDER'
![](D30V7.png)
P value = 0.00809 (Fisher's exact test), Q value = 0.21
Table S18. Gene #32: 'amp_17q12' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
nPatients | 0 | 1 |
---|---|---|
ALL | 524 | 39 |
AMP PEAK 32(17Q12) MUTATED | 169 | 21 |
AMP PEAK 32(17Q12) WILD-TYPE | 355 | 18 |
Figure S18. Get High-res Image Gene #32: 'amp_17q12' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
![](D32V6.png)
P value = 0.00448 (Fisher's exact test), Q value = 0.15
Table S19. Gene #32: 'amp_17q12' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
AMP PEAK 32(17Q12) MUTATED | 50 | 172 |
AMP PEAK 32(17Q12) WILD-TYPE | 135 | 268 |
Figure S19. Get High-res Image Gene #32: 'amp_17q12' versus Clinical Feature #7: 'GENDER'
![](D32V7.png)
P value = 0.0131 (Fisher's exact test), Q value = 0.25
Table S20. Gene #32: 'amp_17q12' versus Clinical Feature #11: 'RACE'
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER | WHITE |
---|---|---|---|---|
ALL | 134 | 17 | 1 | 392 |
AMP PEAK 32(17Q12) MUTATED | 40 | 11 | 1 | 137 |
AMP PEAK 32(17Q12) WILD-TYPE | 94 | 6 | 0 | 255 |
Figure S20. Get High-res Image Gene #32: 'amp_17q12' versus Clinical Feature #11: 'RACE'
![](D32V11.png)
P value = 0.00301 (Fisher's exact test), Q value = 0.13
Table S21. Gene #38: 'amp_20q13.2' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
AMP PEAK 38(20Q13.2) MUTATED | 107 | 309 |
AMP PEAK 38(20Q13.2) WILD-TYPE | 78 | 131 |
Figure S21. Get High-res Image Gene #38: 'amp_20q13.2' versus Clinical Feature #7: 'GENDER'
![](D38V7.png)
P value = 0.0133 (Fisher's exact test), Q value = 0.25
Table S22. Gene #52: 'del_4p16.3' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
DEL PEAK 13(4P16.3) MUTATED | 66 | 205 |
DEL PEAK 13(4P16.3) WILD-TYPE | 119 | 235 |
Figure S22. Get High-res Image Gene #52: 'del_4p16.3' versus Clinical Feature #7: 'GENDER'
![](D52V7.png)
P value = 0.0102 (Wilcoxon-test), Q value = 0.22
Table S23. Gene #55: 'del_4q34.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 616 | 64.8 (11.2) |
DEL PEAK 16(4Q34.3) MUTATED | 295 | 66.0 (10.5) |
DEL PEAK 16(4Q34.3) WILD-TYPE | 321 | 63.6 (11.7) |
Figure S23. Get High-res Image Gene #55: 'del_4q34.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D55V2.png)
P value = 0.00631 (Fisher's exact test), Q value = 0.18
Table S24. Gene #55: 'del_4q34.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 11 | 20 | 47 | 33 | 87 | 88 | 29 | 97 | 73 | 46 | 51 | 4 |
DEL PEAK 16(4Q34.3) MUTATED | 2 | 6 | 20 | 22 | 39 | 37 | 20 | 46 | 39 | 26 | 17 | 3 |
DEL PEAK 16(4Q34.3) WILD-TYPE | 9 | 14 | 27 | 11 | 48 | 51 | 9 | 51 | 34 | 20 | 34 | 1 |
Figure S24. Get High-res Image Gene #55: 'del_4q34.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D55V3.png)
P value = 0.00092 (Fisher's exact test), Q value = 0.073
Table S25. Gene #60: 'del_7q31.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 11 | 20 | 47 | 33 | 87 | 88 | 29 | 97 | 73 | 46 | 51 | 4 |
DEL PEAK 21(7Q31.1) MUTATED | 1 | 5 | 4 | 9 | 19 | 21 | 15 | 22 | 9 | 5 | 8 | 2 |
DEL PEAK 21(7Q31.1) WILD-TYPE | 10 | 15 | 43 | 24 | 68 | 67 | 14 | 75 | 64 | 41 | 43 | 2 |
Figure S25. Get High-res Image Gene #60: 'del_7q31.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D60V3.png)
P value = 0.00549 (Fisher's exact test), Q value = 0.17
Table S26. Gene #60: 'del_7q31.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 55 | 136 | 283 | 124 |
DEL PEAK 21(7Q31.1) MUTATED | 14 | 23 | 71 | 14 |
DEL PEAK 21(7Q31.1) WILD-TYPE | 41 | 113 | 212 | 110 |
Figure S26. Get High-res Image Gene #60: 'del_7q31.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D60V4.png)
P value = 0.00877 (Fisher's exact test), Q value = 0.21
Table S27. Gene #60: 'del_7q31.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 207 | 188 | 98 | 96 |
DEL PEAK 21(7Q31.1) MUTATED | 36 | 53 | 21 | 12 |
DEL PEAK 21(7Q31.1) WILD-TYPE | 171 | 135 | 77 | 84 |
Figure S27. Get High-res Image Gene #60: 'del_7q31.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D60V5.png)
P value = 0.0015 (Fisher's exact test), Q value = 0.099
Table S28. Gene #60: 'del_7q31.1' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
DEL PEAK 21(7Q31.1) MUTATED | 23 | 104 |
DEL PEAK 21(7Q31.1) WILD-TYPE | 162 | 336 |
Figure S28. Get High-res Image Gene #60: 'del_7q31.1' versus Clinical Feature #7: 'GENDER'
![](D60V7.png)
P value = 0.00069 (Fisher's exact test), Q value = 0.068
Table S29. Gene #61: 'del_7q36.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 11 | 20 | 47 | 33 | 87 | 88 | 29 | 97 | 73 | 46 | 51 | 4 |
DEL PEAK 22(7Q36.3) MUTATED | 1 | 6 | 5 | 9 | 22 | 33 | 15 | 27 | 12 | 10 | 13 | 3 |
DEL PEAK 22(7Q36.3) WILD-TYPE | 10 | 14 | 42 | 24 | 65 | 55 | 14 | 70 | 61 | 36 | 38 | 1 |
Figure S29. Get High-res Image Gene #61: 'del_7q36.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D61V3.png)
P value = 0.000291 (Fisher's exact test), Q value = 0.067
Table S30. Gene #62: 'del_8p23.2' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
DEL PEAK 23(8P23.2) MUTATED | 43 | 169 |
DEL PEAK 23(8P23.2) WILD-TYPE | 142 | 271 |
Figure S30. Get High-res Image Gene #62: 'del_8p23.2' versus Clinical Feature #7: 'GENDER'
![](D62V7.png)
P value = 0.0115 (Fisher's exact test), Q value = 0.24
Table S31. Gene #64: 'del_9p21.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 11 | 20 | 47 | 33 | 87 | 88 | 29 | 97 | 73 | 46 | 51 | 4 |
DEL PEAK 25(9P21.3) MUTATED | 3 | 12 | 21 | 18 | 54 | 49 | 23 | 48 | 35 | 18 | 27 | 4 |
DEL PEAK 25(9P21.3) WILD-TYPE | 8 | 8 | 26 | 15 | 33 | 39 | 6 | 49 | 38 | 28 | 24 | 0 |
Figure S31. Get High-res Image Gene #64: 'del_9p21.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D64V3.png)
P value = 0.00203 (Fisher's exact test), Q value = 0.11
Table S32. Gene #64: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 55 | 136 | 283 | 124 |
DEL PEAK 25(9P21.3) MUTATED | 31 | 78 | 162 | 47 |
DEL PEAK 25(9P21.3) WILD-TYPE | 24 | 58 | 121 | 77 |
Figure S32. Get High-res Image Gene #64: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D64V4.png)
P value = 0.0037 (Fisher's exact test), Q value = 0.14
Table S33. Gene #64: 'del_9p21.3' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
DEL PEAK 25(9P21.3) MUTATED | 82 | 252 |
DEL PEAK 25(9P21.3) WILD-TYPE | 103 | 188 |
Figure S33. Get High-res Image Gene #64: 'del_9p21.3' versus Clinical Feature #7: 'GENDER'
![](D64V7.png)
P value = 0.0121 (Wilcoxon-test), Q value = 0.25
Table S34. Gene #65: 'del_9q21.11' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 98 | 34.5 (21.5) |
DEL PEAK 26(9Q21.11) MUTATED | 36 | 42.1 (24.2) |
DEL PEAK 26(9Q21.11) WILD-TYPE | 62 | 30.1 (18.6) |
Figure S34. Get High-res Image Gene #65: 'del_9q21.11' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'
![](D65V10.png)
P value = 0.005 (logrank test), Q value = 0.16
Table S35. Gene #66: 'del_10p15.3' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 590 | 235 | 0.0 - 122.3 (13.5) |
DEL PEAK 27(10P15.3) MUTATED | 124 | 58 | 0.1 - 115.7 (12.7) |
DEL PEAK 27(10P15.3) WILD-TYPE | 466 | 177 | 0.0 - 122.3 (14.0) |
Figure S35. Get High-res Image Gene #66: 'del_10p15.3' versus Clinical Feature #1: 'Time to Death'
![](D66V1.png)
P value = 0.00401 (Fisher's exact test), Q value = 0.14
Table S36. Gene #67: 'del_10p11.21' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 55 | 136 | 283 | 124 |
DEL PEAK 28(10P11.21) MUTATED | 6 | 29 | 53 | 9 |
DEL PEAK 28(10P11.21) WILD-TYPE | 49 | 107 | 230 | 115 |
Figure S36. Get High-res Image Gene #67: 'del_10p11.21' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D67V4.png)
P value = 0.00067 (Fisher's exact test), Q value = 0.068
Table S37. Gene #67: 'del_10p11.21' versus Clinical Feature #11: 'RACE'
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER | WHITE |
---|---|---|---|---|
ALL | 134 | 17 | 1 | 392 |
DEL PEAK 28(10P11.21) MUTATED | 32 | 7 | 0 | 51 |
DEL PEAK 28(10P11.21) WILD-TYPE | 102 | 10 | 1 | 341 |
Figure S37. Get High-res Image Gene #67: 'del_10p11.21' versus Clinical Feature #11: 'RACE'
![](D67V11.png)
P value = 0.00343 (Fisher's exact test), Q value = 0.14
Table S38. Gene #68: 'del_10q21.1' versus Clinical Feature #11: 'RACE'
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER | WHITE |
---|---|---|---|---|
ALL | 134 | 17 | 1 | 392 |
DEL PEAK 29(10Q21.1) MUTATED | 31 | 8 | 0 | 61 |
DEL PEAK 29(10Q21.1) WILD-TYPE | 103 | 9 | 1 | 331 |
Figure S38. Get High-res Image Gene #68: 'del_10q21.1' versus Clinical Feature #11: 'RACE'
![](D68V11.png)
P value = 0.00128 (Fisher's exact test), Q value = 0.094
Table S39. Gene #69: 'del_10q22.3' versus Clinical Feature #11: 'RACE'
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER | WHITE |
---|---|---|---|---|
ALL | 134 | 17 | 1 | 392 |
DEL PEAK 30(10Q22.3) MUTATED | 36 | 9 | 0 | 71 |
DEL PEAK 30(10Q22.3) WILD-TYPE | 98 | 8 | 1 | 321 |
Figure S39. Get High-res Image Gene #69: 'del_10q22.3' versus Clinical Feature #11: 'RACE'
![](D69V11.png)
P value = 0.0078 (Fisher's exact test), Q value = 0.21
Table S40. Gene #70: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 55 | 136 | 283 | 124 |
DEL PEAK 31(10Q23.31) MUTATED | 14 | 51 | 83 | 23 |
DEL PEAK 31(10Q23.31) WILD-TYPE | 41 | 85 | 200 | 101 |
Figure S40. Get High-res Image Gene #70: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D70V4.png)
P value = 0.00827 (Fisher's exact test), Q value = 0.21
Table S41. Gene #71: 'del_11p15.5' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
DEL PEAK 32(11P15.5) MUTATED | 38 | 137 |
DEL PEAK 32(11P15.5) WILD-TYPE | 147 | 303 |
Figure S41. Get High-res Image Gene #71: 'del_11p15.5' versus Clinical Feature #7: 'GENDER'
![](D71V7.png)
P value = 0.0102 (Fisher's exact test), Q value = 0.22
Table S42. Gene #71: 'del_11p15.5' versus Clinical Feature #8: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 438 | 116 |
DEL PEAK 32(11P15.5) MUTATED | 109 | 43 |
DEL PEAK 32(11P15.5) WILD-TYPE | 329 | 73 |
Figure S42. Get High-res Image Gene #71: 'del_11p15.5' versus Clinical Feature #8: 'RADIATION_THERAPY'
![](D71V8.png)
P value = 0.00211 (Fisher's exact test), Q value = 0.11
Table S43. Gene #74: 'del_12q23.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 55 | 136 | 283 | 124 |
DEL PEAK 35(12Q23.1) MUTATED | 16 | 17 | 58 | 12 |
DEL PEAK 35(12Q23.1) WILD-TYPE | 39 | 119 | 225 | 112 |
Figure S43. Get High-res Image Gene #74: 'del_12q23.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D74V4.png)
P value = 5.21e-05 (Fisher's exact test), Q value = 0.015
Table S44. Gene #75: 'del_13q12.11' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
DEL PEAK 36(13Q12.11) MUTATED | 22 | 116 |
DEL PEAK 36(13Q12.11) WILD-TYPE | 163 | 324 |
Figure S44. Get High-res Image Gene #75: 'del_13q12.11' versus Clinical Feature #7: 'GENDER'
![](D75V7.png)
P value = 0.00395 (Wilcoxon-test), Q value = 0.14
Table S45. Gene #76: 'del_13q14.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 616 | 64.8 (11.2) |
DEL PEAK 37(13Q14.2) MUTATED | 123 | 62.2 (11.3) |
DEL PEAK 37(13Q14.2) WILD-TYPE | 493 | 65.4 (11.1) |
Figure S45. Get High-res Image Gene #76: 'del_13q14.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D76V2.png)
P value = 4e-05 (Fisher's exact test), Q value = 0.015
Table S46. Gene #76: 'del_13q14.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 11 | 20 | 47 | 33 | 87 | 88 | 29 | 97 | 73 | 46 | 51 | 4 |
DEL PEAK 37(13Q14.2) MUTATED | 4 | 3 | 6 | 5 | 28 | 17 | 15 | 22 | 7 | 5 | 4 | 1 |
DEL PEAK 37(13Q14.2) WILD-TYPE | 7 | 17 | 41 | 28 | 59 | 71 | 14 | 75 | 66 | 41 | 47 | 3 |
Figure S46. Get High-res Image Gene #76: 'del_13q14.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D76V3.png)
P value = 0.0033 (Fisher's exact test), Q value = 0.14
Table S47. Gene #76: 'del_13q14.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 55 | 136 | 283 | 124 |
DEL PEAK 37(13Q14.2) MUTATED | 13 | 32 | 63 | 11 |
DEL PEAK 37(13Q14.2) WILD-TYPE | 42 | 104 | 220 | 113 |
Figure S47. Get High-res Image Gene #76: 'del_13q14.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D76V4.png)
P value = 0.00959 (Fisher's exact test), Q value = 0.21
Table S48. Gene #76: 'del_13q14.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 207 | 188 | 98 | 96 |
DEL PEAK 37(13Q14.2) MUTATED | 50 | 45 | 12 | 12 |
DEL PEAK 37(13Q14.2) WILD-TYPE | 157 | 143 | 86 | 84 |
Figure S48. Get High-res Image Gene #76: 'del_13q14.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D76V5.png)
P value = 0.00208 (Fisher's exact test), Q value = 0.11
Table S49. Gene #76: 'del_13q14.2' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
DEL PEAK 37(13Q14.2) MUTATED | 23 | 102 |
DEL PEAK 37(13Q14.2) WILD-TYPE | 162 | 338 |
Figure S49. Get High-res Image Gene #76: 'del_13q14.2' versus Clinical Feature #7: 'GENDER'
![](D76V7.png)
P value = 0.0136 (Fisher's exact test), Q value = 0.25
Table S50. Gene #76: 'del_13q14.2' versus Clinical Feature #8: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 438 | 116 |
DEL PEAK 37(13Q14.2) MUTATED | 80 | 34 |
DEL PEAK 37(13Q14.2) WILD-TYPE | 358 | 82 |
Figure S50. Get High-res Image Gene #76: 'del_13q14.2' versus Clinical Feature #8: 'RADIATION_THERAPY'
![](D76V8.png)
P value = 0.00933 (Fisher's exact test), Q value = 0.21
Table S51. Gene #76: 'del_13q14.2' versus Clinical Feature #11: 'RACE'
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER | WHITE |
---|---|---|---|---|
ALL | 134 | 17 | 1 | 392 |
DEL PEAK 37(13Q14.2) MUTATED | 41 | 2 | 0 | 70 |
DEL PEAK 37(13Q14.2) WILD-TYPE | 93 | 15 | 1 | 322 |
Figure S51. Get High-res Image Gene #76: 'del_13q14.2' versus Clinical Feature #11: 'RACE'
![](D76V11.png)
P value = 0.0122 (Fisher's exact test), Q value = 0.25
Table S52. Gene #77: 'del_13q21.31' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 11 | 20 | 47 | 33 | 87 | 88 | 29 | 97 | 73 | 46 | 51 | 4 |
DEL PEAK 38(13Q21.31) MUTATED | 3 | 5 | 6 | 6 | 24 | 16 | 13 | 23 | 12 | 6 | 4 | 1 |
DEL PEAK 38(13Q21.31) WILD-TYPE | 8 | 15 | 41 | 27 | 63 | 72 | 16 | 74 | 61 | 40 | 47 | 3 |
Figure S52. Get High-res Image Gene #77: 'del_13q21.31' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D77V3.png)
P value = 0.0132 (Fisher's exact test), Q value = 0.25
Table S53. Gene #77: 'del_13q21.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 55 | 136 | 283 | 124 |
DEL PEAK 38(13Q21.31) MUTATED | 14 | 33 | 60 | 13 |
DEL PEAK 38(13Q21.31) WILD-TYPE | 41 | 103 | 223 | 111 |
Figure S53. Get High-res Image Gene #77: 'del_13q21.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D77V4.png)
P value = 0.00471 (Fisher's exact test), Q value = 0.16
Table S54. Gene #77: 'del_13q21.31' versus Clinical Feature #8: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 438 | 116 |
DEL PEAK 38(13Q21.31) MUTATED | 81 | 36 |
DEL PEAK 38(13Q21.31) WILD-TYPE | 357 | 80 |
Figure S54. Get High-res Image Gene #77: 'del_13q21.31' versus Clinical Feature #8: 'RADIATION_THERAPY'
![](D77V8.png)
P value = 0.00564 (Fisher's exact test), Q value = 0.17
Table S55. Gene #79: 'del_14q32.32' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
nPatients | 0 | 1 |
---|---|---|
ALL | 524 | 39 |
DEL PEAK 40(14Q32.32) MUTATED | 162 | 4 |
DEL PEAK 40(14Q32.32) WILD-TYPE | 362 | 35 |
Figure S55. Get High-res Image Gene #79: 'del_14q32.32' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
![](D79V6.png)
P value = 0.0134 (Fisher's exact test), Q value = 0.25
Table S56. Gene #80: 'del_15q11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 55 | 136 | 283 | 124 |
DEL PEAK 41(15Q11.2) MUTATED | 18 | 41 | 93 | 22 |
DEL PEAK 41(15Q11.2) WILD-TYPE | 37 | 95 | 190 | 102 |
Figure S56. Get High-res Image Gene #80: 'del_15q11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D80V4.png)
P value = 0.00921 (Fisher's exact test), Q value = 0.21
Table S57. Gene #81: 'del_16p13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 55 | 136 | 283 | 124 |
DEL PEAK 42(16P13.3) MUTATED | 20 | 30 | 89 | 23 |
DEL PEAK 42(16P13.3) WILD-TYPE | 35 | 106 | 194 | 101 |
Figure S57. Get High-res Image Gene #81: 'del_16p13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D81V4.png)
P value = 0.0133 (Fisher's exact test), Q value = 0.25
Table S58. Gene #84: 'del_17p12' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
DEL PEAK 45(17P12) MUTATED | 65 | 202 |
DEL PEAK 45(17P12) WILD-TYPE | 120 | 238 |
Figure S58. Get High-res Image Gene #84: 'del_17p12' versus Clinical Feature #7: 'GENDER'
![](D84V7.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0059
Table S59. Gene #86: 'del_18q12.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 55 | 136 | 283 | 124 |
DEL PEAK 47(18Q12.2) MUTATED | 22 | 62 | 158 | 36 |
DEL PEAK 47(18Q12.2) WILD-TYPE | 33 | 74 | 125 | 88 |
Figure S59. Get High-res Image Gene #86: 'del_18q12.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D86V4.png)
P value = 0.00043 (Fisher's exact test), Q value = 0.067
Table S60. Gene #87: 'del_18q21.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 55 | 136 | 283 | 124 |
DEL PEAK 48(18Q21.2) MUTATED | 27 | 69 | 167 | 45 |
DEL PEAK 48(18Q21.2) WILD-TYPE | 28 | 67 | 116 | 79 |
Figure S60. Get High-res Image Gene #87: 'del_18q21.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D87V4.png)
P value = 0.000905 (Fisher's exact test), Q value = 0.073
Table S61. Gene #88: 'del_19p13.3' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
DEL PEAK 49(19P13.3) MUTATED | 55 | 194 |
DEL PEAK 49(19P13.3) WILD-TYPE | 130 | 246 |
Figure S61. Get High-res Image Gene #88: 'del_19p13.3' versus Clinical Feature #7: 'GENDER'
![](D88V7.png)
P value = 0.00045 (Fisher's exact test), Q value = 0.067
Table S62. Gene #93: 'del_22q11.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 55 | 136 | 283 | 124 |
DEL PEAK 54(22Q11.1) MUTATED | 28 | 43 | 119 | 30 |
DEL PEAK 54(22Q11.1) WILD-TYPE | 27 | 93 | 164 | 94 |
Figure S62. Get High-res Image Gene #93: 'del_22q11.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D93V4.png)
P value = 0.00291 (Fisher's exact test), Q value = 0.13
Table S63. Gene #95: 'del_xp22.2' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
DEL PEAK 56(XP22.2) MUTATED | 30 | 120 |
DEL PEAK 56(XP22.2) WILD-TYPE | 155 | 320 |
Figure S63. Get High-res Image Gene #95: 'del_xp22.2' versus Clinical Feature #7: 'GENDER'
![](D95V7.png)
P value = 0.00249 (Fisher's exact test), Q value = 0.12
Table S64. Gene #96: 'del_xp21.1' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
DEL PEAK 57(XP21.1) MUTATED | 28 | 115 |
DEL PEAK 57(XP21.1) WILD-TYPE | 157 | 325 |
Figure S64. Get High-res Image Gene #96: 'del_xp21.1' versus Clinical Feature #7: 'GENDER'
![](D96V7.png)
P value = 0.00693 (Fisher's exact test), Q value = 0.19
Table S65. Gene #97: 'del_xp11.3' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
DEL PEAK 58(XP11.3) MUTATED | 30 | 116 |
DEL PEAK 58(XP11.3) WILD-TYPE | 155 | 324 |
Figure S65. Get High-res Image Gene #97: 'del_xp11.3' versus Clinical Feature #7: 'GENDER'
![](D97V7.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/STES-TP/19785970/transformed.cor.cli.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/STES-TP/19775559/STES-TP.merged_data.txt
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Number of patients = 625
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Number of significantly focal cnvs = 99
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Number of selected clinical features = 12
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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.