This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 69 focal events and 12 clinical features across 1080 patients, 229 significant findings detected with Q value < 0.25.
-
amp_1p22.3 cnv correlated to 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'NUMBER_OF_LYMPH_NODES', and 'RACE'.
-
amp_1q21.3 cnv correlated to 'PATHOLOGY_T_STAGE'.
-
amp_1q44 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
-
amp_3p25.1 cnv correlated to 'Time to Death', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', and 'HISTOLOGICAL_TYPE'.
-
amp_3q26.32 cnv correlated to 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
-
amp_4q13.3 cnv correlated to 'HISTOLOGICAL_TYPE'.
-
amp_5p15.33 cnv correlated to 'Time to Death', 'PATHOLOGY_N_STAGE', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
-
amp_6p23 cnv correlated to 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
-
amp_6q21 cnv correlated to 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.
-
amp_8p11.23 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_N_STAGE', and 'NUMBER_OF_LYMPH_NODES'.
-
amp_8p11.21 cnv correlated to 'HISTOLOGICAL_TYPE'.
-
amp_8q24.21 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
-
amp_10p15.1 cnv correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.
-
amp_10q22.3 cnv correlated to 'HISTOLOGICAL_TYPE'.
-
amp_11p13 cnv correlated to 'HISTOLOGICAL_TYPE'.
-
amp_11q13.3 cnv correlated to 'PATHOLOGY_T_STAGE' and 'GENDER'.
-
amp_11q14.1 cnv correlated to 'PATHOLOGY_T_STAGE' and 'HISTOLOGICAL_TYPE'.
-
amp_12p13.33 cnv correlated to 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', 'RACE', and 'ETHNICITY'.
-
amp_12q15 cnv correlated to 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.
-
amp_13q34 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'RADIATION_THERAPY', 'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.
-
amp_14q21.1 cnv correlated to 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.
-
amp_15q26.3 cnv correlated to 'YEARS_TO_BIRTH', 'HISTOLOGICAL_TYPE', and 'RACE'.
-
amp_17q12 cnv correlated to 'PATHOLOGY_N_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', and 'RACE'.
-
amp_17q23.1 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'GENDER', and 'HISTOLOGICAL_TYPE'.
-
amp_19p13.12 cnv correlated to 'PATHOLOGY_M_STAGE', 'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.
-
amp_19q12 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', 'NUMBER_OF_LYMPH_NODES', and 'RACE'.
-
amp_19q13.42 cnv correlated to 'HISTOLOGICAL_TYPE'.
-
amp_20q13.2 cnv correlated to 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'GENDER', and 'HISTOLOGICAL_TYPE'.
-
del_1p36.13 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.
-
del_1p22.1 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', and 'NUMBER_OF_LYMPH_NODES'.
-
del_2q37.3 cnv correlated to 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
-
del_3p21.31 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'RADIATION_THERAPY', 'HISTOLOGICAL_TYPE', and 'RACE'.
-
del_4p16.3 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
-
del_4q35.1 cnv correlated to 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
-
del_5q11.2 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', and 'RACE'.
-
del_5q21.3 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', 'NUMBER_OF_LYMPH_NODES', and 'RACE'.
-
del_6p25.3 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', and 'HISTOLOGICAL_TYPE'.
-
del_6q15 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_N_STAGE', and 'NUMBER_OF_LYMPH_NODES'.
-
del_6q27 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_N_STAGE', and 'RADIATION_THERAPY'.
-
del_7p22.3 cnv correlated to 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.
-
del_7q36.1 cnv correlated to 'HISTOLOGICAL_TYPE'.
-
del_8p23.2 cnv correlated to 'Time to Death', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
-
del_8p11.21 cnv correlated to 'HISTOLOGICAL_TYPE'.
-
del_9p23 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.
-
del_9p21.3 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.
-
del_9q21.11 cnv correlated to 'GENDER', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
-
del_9q34.2 cnv correlated to 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', and 'RACE'.
-
del_10q23.31 cnv correlated to 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
-
del_10q26.3 cnv correlated to 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
-
del_11p15.5 cnv correlated to 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
-
del_11q13.1 cnv correlated to 'RACE'.
-
del_11q23.3 cnv correlated to 'PATHOLOGY_T_STAGE', 'GENDER', and 'RACE'.
-
del_11q25 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', and 'RACE'.
-
del_12p13.1 cnv correlated to 'HISTOLOGICAL_TYPE'.
-
del_12q23.1 cnv correlated to 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
-
del_12q24.31 cnv correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.
-
del_13q14.2 cnv correlated to 'HISTOLOGICAL_TYPE'.
-
del_14q24.1 cnv correlated to 'Time to Death', 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
-
del_15q13.1 cnv correlated to 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', 'NUMBER_OF_LYMPH_NODES', and 'RACE'.
-
del_16q24.3 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
-
del_17p12 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
-
del_17q21.31 cnv correlated to 'YEARS_TO_BIRTH', 'HISTOLOGICAL_TYPE', and 'RACE'.
-
del_18q23 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', and 'HISTOLOGICAL_TYPE'.
-
del_19p13.3 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
-
del_19q13.32 cnv correlated to 'PATHOLOGY_N_STAGE' and 'HISTOLOGICAL_TYPE'.
-
del_20p13 cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.
-
del_21q11.2 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', and 'HISTOLOGICAL_TYPE'.
-
del_22q13.32 cnv correlated to 'RADIATION_THERAPY' and 'HISTOLOGICAL_TYPE'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 69 focal events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 229 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 |
HISTOLOGICAL TYPE |
NUMBER OF LYMPH NODES |
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 | Fisher's exact test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
del 1p36 13 | 452 (42%) | 628 |
0.0218 (0.117) |
0.0183 (0.101) |
0.00064 (0.00768) |
1e-05 (0.00023) |
0.00056 (0.00703) |
0.127 (0.359) |
0.0346 (0.164) |
0.186 (0.447) |
0.00278 (0.0245) |
0.00101 (0.0109) |
0.805 (0.939) |
0.743 (0.908) |
del 9p23 | 325 (30%) | 755 |
0.0133 (0.0824) |
0.278 (0.546) |
0.00558 (0.0405) |
0.00032 (0.00469) |
0.0007 (0.00816) |
0.0641 (0.238) |
0.201 (0.457) |
0.479 (0.715) |
1e-05 (0.00023) |
0.0369 (0.17) |
0.35 (0.61) |
1 (1.00) |
del 11q25 | 513 (48%) | 567 |
0.95 (1.00) |
0.0265 (0.134) |
0.0238 (0.125) |
0.00246 (0.0221) |
0.0677 (0.245) |
0.83 (0.943) |
0.0171 (0.1) |
0.896 (0.973) |
0.0111 (0.07) |
0.277 (0.546) |
0.00063 (0.00767) |
1 (1.00) |
del 1p22 1 | 362 (34%) | 718 |
0.000661 (0.00782) |
0.0412 (0.184) |
0.0104 (0.067) |
4e-05 (0.00077) |
0.00766 (0.0529) |
0.498 (0.732) |
0.232 (0.499) |
0.333 (0.606) |
0.118 (0.343) |
0.000895 (0.00988) |
0.667 (0.865) |
0.117 (0.343) |
amp 12q15 | 276 (26%) | 804 |
0.258 (0.524) |
0.235 (0.501) |
0.407 (0.655) |
0.0179 (0.101) |
0.0145 (0.0876) |
0.81 (0.939) |
0.00307 (0.0262) |
0.551 (0.77) |
0.0011 (0.0114) |
0.0179 (0.101) |
0.415 (0.659) |
0.251 (0.521) |
amp 13q34 | 179 (17%) | 901 |
0.394 (0.653) |
0.0539 (0.213) |
0.153 (0.398) |
0.00529 (0.0388) |
0.253 (0.521) |
0.573 (0.793) |
0.702 (0.886) |
0.0444 (0.195) |
0.00121 (0.0122) |
0.0645 (0.238) |
0.605 (0.82) |
0.83 (0.943) |
amp 19q12 | 284 (26%) | 796 |
0.777 (0.926) |
0.488 (0.724) |
0.00939 (0.0627) |
0.546 (0.768) |
0.0359 (0.169) |
0.468 (0.71) |
0.526 (0.755) |
0.941 (1.00) |
1e-05 (0.00023) |
0.00508 (0.0376) |
0.0369 (0.17) |
0.853 (0.954) |
del 3p21 31 | 347 (32%) | 733 |
0.0851 (0.284) |
0.00267 (0.0237) |
0.139 (0.38) |
3e-05 (0.000606) |
0.455 (0.698) |
0.65 (0.853) |
1 (1.00) |
0.0586 (0.226) |
2e-05 (0.000436) |
0.266 (0.536) |
0.0113 (0.0709) |
0.605 (0.82) |
del 5q11 2 | 280 (26%) | 800 |
0.431 (0.677) |
4.3e-06 (0.00023) |
0.201 (0.457) |
0.00037 (0.00502) |
0.284 (0.548) |
0.34 (0.61) |
0.0436 (0.194) |
0.553 (0.772) |
1e-05 (0.00023) |
0.163 (0.413) |
6e-05 (0.00108) |
1 (1.00) |
del 5q21 3 | 272 (25%) | 808 |
0.92 (0.99) |
0.000324 (0.00469) |
0.105 (0.325) |
0.00021 (0.00328) |
0.108 (0.333) |
0.811 (0.939) |
0.314 (0.58) |
0.5 (0.733) |
1e-05 (0.00023) |
0.00312 (0.0263) |
9e-05 (0.00159) |
0.852 (0.954) |
del 8p23 2 | 558 (52%) | 522 |
0.0521 (0.208) |
0.633 (0.845) |
0.978 (1.00) |
0.00387 (0.0312) |
0.061 (0.233) |
0.831 (0.943) |
0.388 (0.649) |
0.472 (0.712) |
1e-05 (0.00023) |
0.783 (0.926) |
0.00118 (0.0121) |
0.745 (0.909) |
del 9p21 3 | 364 (34%) | 716 |
0.188 (0.447) |
0.378 (0.639) |
0.0172 (0.1) |
0.00284 (0.0245) |
0.00408 (0.0322) |
0.172 (0.424) |
0.119 (0.344) |
0.68 (0.866) |
1e-05 (0.00023) |
0.0624 (0.234) |
0.2 (0.457) |
0.863 (0.957) |
del 9q34 2 | 297 (28%) | 783 |
0.577 (0.795) |
0.92 (0.99) |
0.118 (0.343) |
0.0197 (0.107) |
0.0669 (0.243) |
0.81 (0.939) |
0.00508 (0.0376) |
0.305 (0.571) |
1e-05 (0.00023) |
0.189 (0.447) |
0.0472 (0.2) |
0.363 (0.622) |
del 15q13 1 | 375 (35%) | 705 |
0.539 (0.768) |
0.347 (0.61) |
0.146 (0.39) |
0.0014 (0.014) |
0.0221 (0.117) |
0.369 (0.629) |
0.761 (0.916) |
0.411 (0.659) |
1e-05 (0.00023) |
0.037 (0.17) |
0.0239 (0.125) |
0.866 (0.958) |
amp 1p22 3 | 250 (23%) | 830 |
0.818 (0.943) |
0.28 (0.547) |
0.419 (0.66) |
0.0259 (0.132) |
0.0177 (0.101) |
0.61 (0.824) |
0.743 (0.908) |
0.54 (0.768) |
0.303 (0.567) |
0.0152 (0.091) |
0.0477 (0.2) |
0.847 (0.954) |
amp 1q44 | 789 (73%) | 291 |
0.114 (0.339) |
0.32 (0.589) |
0.0521 (0.208) |
0.00332 (0.0275) |
0.214 (0.475) |
0.342 (0.61) |
1 (1.00) |
0.505 (0.737) |
0.00406 (0.0322) |
0.602 (0.82) |
0.0455 (0.198) |
0.141 (0.382) |
amp 3p25 1 | 198 (18%) | 882 |
0.0307 (0.153) |
0.152 (0.397) |
0.0851 (0.284) |
0.00045 (0.00591) |
0.0459 (0.198) |
0.423 (0.666) |
0.706 (0.889) |
0.737 (0.908) |
1e-05 (0.00023) |
0.353 (0.612) |
0.503 (0.734) |
1 (1.00) |
amp 5p15 33 | 394 (36%) | 686 |
0.0586 (0.226) |
0.197 (0.456) |
0.806 (0.939) |
0.151 (0.397) |
0.0182 (0.101) |
0.825 (0.943) |
0.766 (0.92) |
0.0584 (0.226) |
0.00624 (0.0443) |
0.859 (0.956) |
0.236 (0.502) |
0.501 (0.733) |
amp 8p11 23 | 412 (38%) | 668 |
0.0243 (0.126) |
0.12 (0.345) |
0.0506 (0.208) |
0.589 (0.804) |
0.063 (0.235) |
0.182 (0.443) |
1 (1.00) |
0.893 (0.971) |
0.301 (0.566) |
0.00487 (0.037) |
0.667 (0.865) |
0.401 (0.655) |
amp 8q24 21 | 678 (63%) | 402 |
0.101 (0.322) |
0.0555 (0.219) |
0.405 (0.655) |
0.0521 (0.208) |
0.253 (0.521) |
0.653 (0.853) |
0.228 (0.497) |
0.459 (0.704) |
1e-05 (0.00023) |
0.761 (0.916) |
0.00151 (0.0149) |
0.239 (0.506) |
amp 12p13 33 | 282 (26%) | 798 |
0.728 (0.901) |
0.446 (0.692) |
0.514 (0.745) |
0.00192 (0.0177) |
0.64 (0.849) |
0.81 (0.939) |
0.202 (0.457) |
0.101 (0.322) |
1e-05 (0.00023) |
0.292 (0.556) |
0.0222 (0.117) |
0.0616 (0.233) |
amp 14q21 1 | 220 (20%) | 860 |
0.474 (0.712) |
0.188 (0.447) |
0.284 (0.548) |
0.0161 (0.0962) |
0.0321 (0.155) |
0.437 (0.683) |
0.718 (0.893) |
0.471 (0.712) |
0.00685 (0.0481) |
0.0103 (0.0666) |
0.569 (0.788) |
0.311 (0.577) |
amp 17q12 | 333 (31%) | 747 |
0.103 (0.323) |
0.932 (0.998) |
0.434 (0.679) |
0.0824 (0.281) |
0.0616 (0.233) |
0.818 (0.943) |
0.011 (0.0698) |
0.723 (0.898) |
0.0005 (0.00637) |
0.359 (0.617) |
0.00169 (0.0159) |
1 (1.00) |
amp 17q23 1 | 426 (39%) | 654 |
0.13 (0.364) |
0.214 (0.475) |
0.0291 (0.146) |
0.00034 (0.00469) |
0.265 (0.536) |
0.828 (0.943) |
1.29e-05 (0.000289) |
0.789 (0.93) |
1e-05 (0.00023) |
0.397 (0.653) |
0.144 (0.387) |
0.739 (0.908) |
amp 20q13 2 | 548 (51%) | 532 |
0.648 (0.853) |
0.671 (0.865) |
0.184 (0.445) |
0.00109 (0.0114) |
0.00105 (0.0111) |
1 (1.00) |
0.0378 (0.172) |
0.171 (0.423) |
1e-05 (0.00023) |
0.169 (0.419) |
0.225 (0.494) |
0.417 (0.659) |
del 4p16 3 | 339 (31%) | 741 |
0.984 (1.00) |
0.0561 (0.22) |
0.102 (0.323) |
0.00015 (0.00259) |
0.607 (0.821) |
0.65 (0.853) |
0.763 (0.917) |
0.674 (0.865) |
1e-05 (0.00023) |
0.535 (0.766) |
0.018 (0.101) |
0.727 (0.901) |
del 14q24 1 | 353 (33%) | 727 |
0.0509 (0.208) |
0.2 (0.457) |
0.222 (0.489) |
0.00017 (0.00287) |
0.394 (0.653) |
0.653 (0.853) |
0.542 (0.768) |
0.147 (0.39) |
1e-05 (0.00023) |
0.372 (0.633) |
0.00033 (0.00469) |
0.863 (0.957) |
del 16q24 3 | 693 (64%) | 387 |
0.95 (1.00) |
0.000319 (0.00469) |
0.377 (0.638) |
0.0602 (0.231) |
0.432 (0.677) |
0.114 (0.339) |
1 (1.00) |
0.684 (0.869) |
1e-05 (0.00023) |
0.309 (0.574) |
0.00765 (0.0529) |
0.239 (0.506) |
del 17p12 | 650 (60%) | 430 |
0.334 (0.606) |
0.0024 (0.0218) |
0.461 (0.704) |
0.047 (0.2) |
0.875 (0.96) |
0.829 (0.943) |
0.382 (0.641) |
0.947 (1.00) |
0.00428 (0.0331) |
0.743 (0.908) |
0.0457 (0.198) |
0.868 (0.958) |
del 18q23 | 354 (33%) | 726 |
0.084 (0.284) |
0.253 (0.521) |
0.0662 (0.243) |
0.0178 (0.101) |
0.0578 (0.226) |
0.653 (0.853) |
0.543 (0.768) |
0.237 (0.502) |
0.00021 (0.00328) |
0.461 (0.704) |
0.0818 (0.281) |
0.863 (0.957) |
del 19p13 3 | 363 (34%) | 717 |
0.269 (0.538) |
0.00162 (0.0156) |
0.928 (0.996) |
0.0473 (0.2) |
0.894 (0.971) |
0.824 (0.943) |
0.356 (0.616) |
0.783 (0.926) |
1e-05 (0.00023) |
0.21 (0.471) |
0.00021 (0.00328) |
1 (1.00) |
del 21q11 2 | 217 (20%) | 863 |
0.581 (0.797) |
0.402 (0.655) |
0.00928 (0.0625) |
0.00997 (0.065) |
0.0139 (0.0847) |
0.103 (0.323) |
1 (1.00) |
0.38 (0.639) |
0.00086 (0.00973) |
0.142 (0.382) |
0.181 (0.442) |
0.544 (0.768) |
amp 3q26 32 | 340 (31%) | 740 |
0.957 (1.00) |
0.448 (0.693) |
0.112 (0.338) |
0.0002 (0.00328) |
0.358 (0.617) |
0.82 (0.943) |
1 (1.00) |
0.944 (1.00) |
1e-05 (0.00023) |
0.107 (0.331) |
0.00315 (0.0263) |
0.109 (0.333) |
amp 6p23 | 299 (28%) | 781 |
0.914 (0.986) |
0.201 (0.457) |
0.337 (0.61) |
0.00281 (0.0245) |
0.234 (0.501) |
0.81 (0.939) |
0.196 (0.456) |
0.308 (0.574) |
1e-05 (0.00023) |
0.998 (1.00) |
0.00164 (0.0156) |
0.585 (0.8) |
amp 6q21 | 202 (19%) | 878 |
0.115 (0.339) |
0.29 (0.554) |
0.0809 (0.279) |
0.00059 (0.00729) |
0.141 (0.382) |
1 (1.00) |
0.707 (0.889) |
0.933 (0.998) |
1e-05 (0.00023) |
0.046 (0.198) |
0.0983 (0.319) |
0.676 (0.866) |
amp 15q26 3 | 194 (18%) | 886 |
0.19 (0.447) |
0.00973 (0.0639) |
0.807 (0.939) |
0.297 (0.561) |
0.902 (0.977) |
1 (1.00) |
0.245 (0.513) |
1 (1.00) |
1e-05 (0.00023) |
0.647 (0.853) |
0.0504 (0.208) |
0.284 (0.548) |
amp 19p13 12 | 230 (21%) | 850 |
0.121 (0.346) |
0.634 (0.846) |
0.343 (0.61) |
0.404 (0.655) |
0.159 (0.407) |
0.0623 (0.234) |
0.145 (0.388) |
0.181 (0.442) |
0.0313 (0.155) |
0.000495 (0.00637) |
0.172 (0.424) |
1 (1.00) |
del 2q37 3 | 317 (29%) | 763 |
0.612 (0.826) |
0.544 (0.768) |
0.35 (0.61) |
0.00158 (0.0154) |
0.416 (0.659) |
0.246 (0.513) |
1 (1.00) |
0.52 (0.75) |
1e-05 (0.00023) |
0.289 (0.554) |
0.0319 (0.155) |
0.468 (0.71) |
del 4q35 1 | 345 (32%) | 735 |
0.085 (0.284) |
0.55 (0.77) |
0.345 (0.61) |
0.00182 (0.0169) |
0.777 (0.926) |
0.497 (0.732) |
0.761 (0.916) |
0.673 (0.865) |
1e-05 (0.00023) |
0.75 (0.913) |
0.00599 (0.0431) |
0.0772 (0.271) |
del 6p25 3 | 204 (19%) | 876 |
0.887 (0.966) |
0.0526 (0.209) |
0.231 (0.499) |
0.0096 (0.0636) |
0.111 (0.336) |
1 (1.00) |
0.256 (0.523) |
0.136 (0.375) |
0.0258 (0.132) |
0.587 (0.802) |
0.472 (0.712) |
0.679 (0.866) |
del 6q15 | 358 (33%) | 722 |
0.79 (0.93) |
0.0399 (0.18) |
0.209 (0.468) |
0.375 (0.637) |
0.0335 (0.159) |
0.494 (0.73) |
0.76 (0.916) |
0.0977 (0.319) |
0.14 (0.382) |
0.0204 (0.11) |
0.135 (0.374) |
0.604 (0.82) |
del 6q27 | 375 (35%) | 705 |
0.101 (0.322) |
6.42e-06 (0.00023) |
0.246 (0.513) |
0.684 (0.869) |
0.0265 (0.134) |
1 (1.00) |
0.235 (0.501) |
0.00504 (0.0376) |
0.278 (0.546) |
0.289 (0.554) |
0.62 (0.834) |
0.302 (0.567) |
del 7p22 3 | 137 (13%) | 943 |
0.742 (0.908) |
0.345 (0.61) |
0.36 (0.619) |
0.192 (0.45) |
0.0521 (0.208) |
1 (1.00) |
1 (1.00) |
0.771 (0.923) |
1e-05 (0.00023) |
0.0137 (0.0839) |
0.658 (0.856) |
1 (1.00) |
del 9q21 11 | 294 (27%) | 786 |
0.38 (0.639) |
0.957 (1.00) |
0.273 (0.543) |
0.0718 (0.259) |
0.213 (0.475) |
0.342 (0.61) |
0.0222 (0.117) |
0.0477 (0.2) |
1e-05 (0.00023) |
0.516 (0.747) |
0.19 (0.447) |
0.353 (0.612) |
del 10q23 31 | 320 (30%) | 760 |
0.711 (0.89) |
0.0787 (0.273) |
0.231 (0.499) |
0.0165 (0.0975) |
0.115 (0.339) |
0.819 (0.943) |
0.123 (0.352) |
0.671 (0.865) |
3e-05 (0.000606) |
0.267 (0.536) |
0.28 (0.547) |
0.0486 (0.202) |
del 10q26 3 | 319 (30%) | 761 |
0.083 (0.282) |
0.388 (0.649) |
0.165 (0.413) |
0.0332 (0.159) |
0.189 (0.447) |
0.347 (0.61) |
0.526 (0.755) |
0.943 (1.00) |
1e-05 (0.00023) |
0.348 (0.61) |
0.114 (0.339) |
0.019 (0.104) |
del 11p15 5 | 309 (29%) | 771 |
0.203 (0.457) |
0.751 (0.913) |
0.241 (0.508) |
0.00413 (0.0323) |
0.414 (0.659) |
0.344 (0.61) |
0.34 (0.61) |
0.943 (1.00) |
1e-05 (0.00023) |
0.827 (0.943) |
0.0048 (0.0368) |
0.364 (0.623) |
del 11q23 3 | 547 (51%) | 533 |
0.944 (1.00) |
0.212 (0.473) |
0.1 (0.322) |
0.033 (0.159) |
0.111 (0.336) |
0.395 (0.653) |
0.0377 (0.172) |
0.794 (0.934) |
0.0778 (0.271) |
0.165 (0.413) |
0.0183 (0.101) |
0.871 (0.958) |
del 12q23 1 | 201 (19%) | 879 |
0.872 (0.958) |
0.0897 (0.293) |
0.565 (0.783) |
0.0316 (0.155) |
0.829 (0.943) |
0.403 (0.655) |
1 (1.00) |
0.451 (0.695) |
0.00099 (0.0108) |
0.484 (0.72) |
0.00626 (0.0443) |
1 (1.00) |
del 17q21 31 | 371 (34%) | 709 |
0.477 (0.715) |
0.000386 (0.00515) |
0.488 (0.724) |
0.0727 (0.261) |
0.145 (0.388) |
0.367 (0.626) |
0.761 (0.916) |
1 (1.00) |
1e-05 (0.00023) |
0.823 (0.943) |
5e-05 (0.00092) |
1 (1.00) |
amp 10p15 1 | 304 (28%) | 776 |
0.155 (0.4) |
0.632 (0.845) |
0.226 (0.494) |
0.0748 (0.264) |
0.461 (0.704) |
0.478 (0.715) |
1 (1.00) |
0.562 (0.78) |
1e-05 (0.00023) |
0.192 (0.45) |
3e-05 (0.000606) |
0.713 (0.892) |
amp 11q13 3 | 398 (37%) | 682 |
0.406 (0.655) |
0.267 (0.536) |
0.656 (0.855) |
0.0319 (0.155) |
0.672 (0.865) |
0.267 (0.536) |
0.0382 (0.173) |
0.417 (0.659) |
0.254 (0.522) |
0.779 (0.926) |
0.342 (0.61) |
0.501 (0.733) |
amp 11q14 1 | 267 (25%) | 813 |
0.29 (0.554) |
0.276 (0.546) |
0.439 (0.684) |
0.0668 (0.243) |
0.111 (0.336) |
0.467 (0.71) |
0.183 (0.444) |
0.281 (0.547) |
0.00849 (0.0576) |
0.853 (0.954) |
0.116 (0.339) |
0.446 (0.692) |
del 12q24 31 | 211 (20%) | 869 |
0.113 (0.339) |
0.125 (0.355) |
0.848 (0.954) |
0.0779 (0.271) |
0.64 (0.849) |
1 (1.00) |
0.479 (0.715) |
0.869 (0.958) |
0.0442 (0.195) |
0.329 (0.6) |
0.0509 (0.208) |
0.545 (0.768) |
del 19q13 32 | 216 (20%) | 864 |
0.118 (0.343) |
0.312 (0.578) |
0.452 (0.695) |
0.323 (0.593) |
0.0664 (0.243) |
0.412 (0.659) |
0.715 (0.892) |
0.517 (0.747) |
1e-05 (0.00023) |
0.831 (0.943) |
0.0895 (0.293) |
0.544 (0.768) |
del 20p13 | 160 (15%) | 920 |
0.197 (0.456) |
0.0472 (0.2) |
0.63 (0.844) |
0.413 (0.659) |
0.981 (1.00) |
0.129 (0.363) |
0.402 (0.655) |
0.167 (0.416) |
4e-05 (0.00077) |
0.886 (0.966) |
0.165 (0.413) |
0.64 (0.849) |
del 22q13 32 | 492 (46%) | 588 |
0.955 (1.00) |
0.399 (0.654) |
0.805 (0.939) |
0.159 (0.407) |
0.858 (0.956) |
0.396 (0.653) |
0.398 (0.653) |
0.0362 (0.169) |
0.00034 (0.00469) |
0.987 (1.00) |
0.416 (0.659) |
0.626 (0.84) |
amp 1q21 3 | 781 (72%) | 299 |
0.985 (1.00) |
0.902 (0.977) |
0.193 (0.452) |
0.0115 (0.0716) |
0.349 (0.61) |
1 (1.00) |
0.103 (0.323) |
0.715 (0.892) |
0.0746 (0.264) |
0.68 (0.866) |
0.198 (0.456) |
0.0997 (0.321) |
amp 4q13 3 | 163 (15%) | 917 |
0.114 (0.339) |
0.257 (0.523) |
0.872 (0.958) |
0.178 (0.435) |
0.71 (0.89) |
0.768 (0.921) |
0.406 (0.655) |
0.27 (0.538) |
1e-05 (0.00023) |
0.754 (0.915) |
0.149 (0.391) |
0.16 (0.408) |
amp 8p11 21 | 421 (39%) | 659 |
0.836 (0.945) |
0.162 (0.413) |
0.346 (0.61) |
0.879 (0.963) |
0.687 (0.871) |
0.274 (0.544) |
0.774 (0.925) |
0.203 (0.457) |
0.00087 (0.00973) |
0.394 (0.653) |
0.131 (0.367) |
0.508 (0.739) |
amp 10q22 3 | 150 (14%) | 930 |
0.153 (0.397) |
0.936 (1) |
0.3 (0.565) |
0.148 (0.391) |
0.198 (0.456) |
1 (1.00) |
0.678 (0.866) |
0.707 (0.889) |
0.00022 (0.00337) |
0.198 (0.456) |
0.169 (0.419) |
1 (1.00) |
amp 11p13 | 223 (21%) | 857 |
0.558 (0.776) |
0.251 (0.521) |
0.883 (0.965) |
0.392 (0.653) |
0.958 (1.00) |
0.44 (0.684) |
0.283 (0.548) |
0.295 (0.56) |
1e-05 (0.00023) |
0.492 (0.727) |
0.329 (0.6) |
0.84 (0.949) |
amp 19q13 42 | 276 (26%) | 804 |
0.885 (0.966) |
0.647 (0.853) |
0.854 (0.954) |
0.257 (0.523) |
0.558 (0.776) |
0.223 (0.491) |
0.0873 (0.289) |
0.94 (1.00) |
0.00774 (0.053) |
0.0887 (0.292) |
0.853 (0.954) |
0.45 (0.695) |
del 7q36 1 | 200 (19%) | 880 |
0.23 (0.498) |
0.912 (0.984) |
0.789 (0.93) |
0.186 (0.447) |
0.338 (0.61) |
0.406 (0.655) |
0.473 (0.712) |
0.867 (0.958) |
5e-05 (0.00092) |
0.859 (0.956) |
0.624 (0.839) |
0.523 (0.754) |
del 8p11 21 | 200 (19%) | 880 |
0.0748 (0.264) |
0.296 (0.56) |
0.809 (0.939) |
0.154 (0.399) |
0.228 (0.497) |
0.165 (0.413) |
0.138 (0.379) |
0.933 (0.998) |
0.00388 (0.0312) |
0.126 (0.357) |
0.134 (0.373) |
0.832 (0.943) |
del 11q13 1 | 241 (22%) | 839 |
0.54 (0.768) |
0.717 (0.892) |
0.395 (0.653) |
0.0857 (0.285) |
0.546 (0.768) |
0.799 (0.938) |
0.736 (0.908) |
0.641 (0.849) |
0.698 (0.884) |
0.49 (0.726) |
0.00346 (0.0284) |
0.842 (0.95) |
del 12p13 1 | 188 (17%) | 892 |
0.347 (0.61) |
0.327 (0.598) |
0.242 (0.508) |
0.147 (0.39) |
0.903 (0.977) |
0.782 (0.926) |
0.14 (0.382) |
1 (1.00) |
0.00085 (0.00973) |
0.579 (0.796) |
0.702 (0.886) |
0.665 (0.864) |
del 13q14 2 | 495 (46%) | 585 |
0.275 (0.544) |
0.547 (0.768) |
0.577 (0.795) |
0.0826 (0.281) |
0.255 (0.523) |
0.669 (0.865) |
0.78 (0.926) |
0.132 (0.367) |
1e-05 (0.00023) |
0.734 (0.907) |
0.0737 (0.263) |
0.0992 (0.321) |
amp 17p11 2 | 147 (14%) | 933 |
0.283 (0.548) |
0.355 (0.616) |
0.739 (0.908) |
0.16 (0.408) |
0.65 (0.853) |
0.756 (0.916) |
0.217 (0.478) |
0.104 (0.325) |
0.509 (0.74) |
0.314 (0.58) |
0.578 (0.795) |
1 (1.00) |
P value = 0.0259 (Fisher's exact test), Q value = 0.13
Table S1. Gene #1: 'amp_1p22.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
AMP PEAK 1(1P22.3) MUTATED | 46 | 155 | 36 | 11 |
AMP PEAK 1(1P22.3) WILD-TYPE | 230 | 469 | 100 | 29 |
Figure S1. Get High-res Image Gene #1: 'amp_1p22.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D1V4.png)
P value = 0.0177 (Fisher's exact test), Q value = 0.1
Table S2. Gene #1: 'amp_1p22.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 507 | 358 | 119 | 77 |
AMP PEAK 1(1P22.3) MUTATED | 137 | 68 | 21 | 20 |
AMP PEAK 1(1P22.3) WILD-TYPE | 370 | 290 | 98 | 57 |
Figure S2. Get High-res Image Gene #1: 'amp_1p22.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D1V5.png)
P value = 0.0152 (Wilcoxon-test), Q value = 0.091
Table S3. Gene #1: 'amp_1p22.3' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 914 | 2.4 (4.7) |
AMP PEAK 1(1P22.3) MUTATED | 221 | 2.0 (4.1) |
AMP PEAK 1(1P22.3) WILD-TYPE | 693 | 2.5 (4.8) |
Figure S3. Get High-res Image Gene #1: 'amp_1p22.3' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
![](D1V10.png)
P value = 0.0477 (Fisher's exact test), Q value = 0.2
Table S4. Gene #1: 'amp_1p22.3' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
AMP PEAK 1(1P22.3) MUTATED | 0 | 9 | 54 | 166 |
AMP PEAK 1(1P22.3) WILD-TYPE | 1 | 51 | 127 | 579 |
Figure S4. Get High-res Image Gene #1: 'amp_1p22.3' versus Clinical Feature #11: 'RACE'
![](D1V11.png)
P value = 0.0115 (Fisher's exact test), Q value = 0.072
Table S5. Gene #2: 'amp_1q21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
AMP PEAK 2(1Q21.3) MUTATED | 182 | 460 | 101 | 35 |
AMP PEAK 2(1Q21.3) WILD-TYPE | 94 | 164 | 35 | 5 |
Figure S5. Get High-res Image Gene #2: 'amp_1q21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D2V4.png)
P value = 0.0521 (Fisher's exact test), Q value = 0.21
Table S6. Gene #3: 'amp_1q44' 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 TIS | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 89 | 85 | 6 | 6 | 353 | 252 | 2 | 154 | 29 | 65 | 20 | 1 | 13 |
AMP PEAK 3(1Q44) MUTATED | 56 | 56 | 3 | 6 | 266 | 187 | 1 | 109 | 25 | 53 | 13 | 1 | 8 |
AMP PEAK 3(1Q44) WILD-TYPE | 33 | 29 | 3 | 0 | 87 | 65 | 1 | 45 | 4 | 12 | 7 | 0 | 5 |
Figure S6. Get High-res Image Gene #3: 'amp_1q44' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D3V3.png)
P value = 0.00332 (Fisher's exact test), Q value = 0.027
Table S7. Gene #3: 'amp_1q44' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
AMP PEAK 3(1Q44) MUTATED | 179 | 474 | 100 | 33 |
AMP PEAK 3(1Q44) WILD-TYPE | 97 | 150 | 36 | 7 |
Figure S7. Get High-res Image Gene #3: 'amp_1q44' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D3V4.png)
P value = 0.00406 (Fisher's exact test), Q value = 0.032
Table S8. Gene #3: 'amp_1q44' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
AMP PEAK 3(1Q44) MUTATED | 1 | 549 | 167 | 5 | 5 | 20 | 9 | 33 |
AMP PEAK 3(1Q44) WILD-TYPE | 0 | 221 | 33 | 1 | 4 | 9 | 8 | 14 |
Figure S8. Get High-res Image Gene #3: 'amp_1q44' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D3V9.png)
P value = 0.0455 (Fisher's exact test), Q value = 0.2
Table S9. Gene #3: 'amp_1q44' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
AMP PEAK 3(1Q44) MUTATED | 1 | 35 | 133 | 554 |
AMP PEAK 3(1Q44) WILD-TYPE | 0 | 25 | 48 | 191 |
Figure S9. Get High-res Image Gene #3: 'amp_1q44' versus Clinical Feature #11: 'RACE'
![](D3V11.png)
P value = 0.0307 (logrank test), Q value = 0.15
Table S10. Gene #4: 'amp_3p25.1' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 1064 | 147 | 0.0 - 282.9 (27.9) |
AMP PEAK 4(3P25.1) MUTATED | 196 | 35 | 0.3 - 282.9 (26.8) |
AMP PEAK 4(3P25.1) WILD-TYPE | 868 | 112 | 0.0 - 281.3 (28.2) |
Figure S10. Get High-res Image Gene #4: 'amp_3p25.1' versus Clinical Feature #1: 'Time to Death'
![](D4V1.png)
P value = 0.00045 (Fisher's exact test), Q value = 0.0059
Table S11. Gene #4: 'amp_3p25.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
AMP PEAK 4(3P25.1) MUTATED | 37 | 132 | 15 | 13 |
AMP PEAK 4(3P25.1) WILD-TYPE | 239 | 492 | 121 | 27 |
Figure S11. Get High-res Image Gene #4: 'amp_3p25.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D4V4.png)
P value = 0.0459 (Fisher's exact test), Q value = 0.2
Table S12. Gene #4: 'amp_3p25.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 507 | 358 | 119 | 77 |
AMP PEAK 4(3P25.1) MUTATED | 95 | 55 | 32 | 12 |
AMP PEAK 4(3P25.1) WILD-TYPE | 412 | 303 | 87 | 65 |
Figure S12. Get High-res Image Gene #4: 'amp_3p25.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D4V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S13. Gene #4: 'amp_3p25.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
AMP PEAK 4(3P25.1) MUTATED | 1 | 168 | 14 | 1 | 2 | 5 | 1 | 6 |
AMP PEAK 4(3P25.1) WILD-TYPE | 0 | 602 | 186 | 5 | 7 | 24 | 16 | 41 |
Figure S13. Get High-res Image Gene #4: 'amp_3p25.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D4V9.png)
P value = 2e-04 (Fisher's exact test), Q value = 0.0033
Table S14. Gene #5: 'amp_3q26.32' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
AMP PEAK 5(3Q26.32) MUTATED | 66 | 225 | 31 | 17 |
AMP PEAK 5(3Q26.32) WILD-TYPE | 210 | 399 | 105 | 23 |
Figure S14. Get High-res Image Gene #5: 'amp_3q26.32' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D5V4.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S15. Gene #5: 'amp_3q26.32' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
AMP PEAK 5(3Q26.32) MUTATED | 1 | 293 | 16 | 5 | 7 | 6 | 1 | 10 |
AMP PEAK 5(3Q26.32) WILD-TYPE | 0 | 477 | 184 | 1 | 2 | 23 | 16 | 37 |
Figure S15. Get High-res Image Gene #5: 'amp_3q26.32' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D5V9.png)
P value = 0.00315 (Fisher's exact test), Q value = 0.026
Table S16. Gene #5: 'amp_3q26.32' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
AMP PEAK 5(3Q26.32) MUTATED | 1 | 27 | 65 | 208 |
AMP PEAK 5(3Q26.32) WILD-TYPE | 0 | 33 | 116 | 537 |
Figure S16. Get High-res Image Gene #5: 'amp_3q26.32' versus Clinical Feature #11: 'RACE'
![](D5V11.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S17. Gene #6: 'amp_4q13.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
AMP PEAK 6(4Q13.3) MUTATED | 0 | 142 | 7 | 2 | 3 | 2 | 1 | 6 |
AMP PEAK 6(4Q13.3) WILD-TYPE | 1 | 628 | 193 | 4 | 6 | 27 | 16 | 41 |
Figure S17. Get High-res Image Gene #6: 'amp_4q13.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D6V9.png)
P value = 0.0586 (logrank test), Q value = 0.23
Table S18. Gene #7: 'amp_5p15.33' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 1064 | 147 | 0.0 - 282.9 (27.9) |
AMP PEAK 7(5P15.33) MUTATED | 390 | 59 | 0.0 - 255.7 (25.0) |
AMP PEAK 7(5P15.33) WILD-TYPE | 674 | 88 | 0.0 - 282.9 (29.2) |
Figure S18. Get High-res Image Gene #7: 'amp_5p15.33' versus Clinical Feature #1: 'Time to Death'
![](D7V1.png)
P value = 0.0182 (Fisher's exact test), Q value = 0.1
Table S19. Gene #7: 'amp_5p15.33' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 507 | 358 | 119 | 77 |
AMP PEAK 7(5P15.33) MUTATED | 197 | 111 | 54 | 27 |
AMP PEAK 7(5P15.33) WILD-TYPE | 310 | 247 | 65 | 50 |
Figure S19. Get High-res Image Gene #7: 'amp_5p15.33' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D7V5.png)
P value = 0.0584 (Fisher's exact test), Q value = 0.23
Table S20. Gene #7: 'amp_5p15.33' versus Clinical Feature #8: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 429 | 518 |
AMP PEAK 7(5P15.33) MUTATED | 144 | 205 |
AMP PEAK 7(5P15.33) WILD-TYPE | 285 | 313 |
Figure S20. Get High-res Image Gene #7: 'amp_5p15.33' versus Clinical Feature #8: 'RADIATION_THERAPY'
![](D7V8.png)
P value = 0.00624 (Fisher's exact test), Q value = 0.044
Table S21. Gene #7: 'amp_5p15.33' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
AMP PEAK 7(5P15.33) MUTATED | 1 | 297 | 61 | 2 | 7 | 9 | 2 | 14 |
AMP PEAK 7(5P15.33) WILD-TYPE | 0 | 473 | 139 | 4 | 2 | 20 | 15 | 33 |
Figure S21. Get High-res Image Gene #7: 'amp_5p15.33' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D7V9.png)
P value = 0.00281 (Fisher's exact test), Q value = 0.024
Table S22. Gene #8: 'amp_6p23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
AMP PEAK 8(6P23) MUTATED | 55 | 197 | 34 | 12 |
AMP PEAK 8(6P23) WILD-TYPE | 221 | 427 | 102 | 28 |
Figure S22. Get High-res Image Gene #8: 'amp_6p23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D8V4.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S23. Gene #8: 'amp_6p23' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
AMP PEAK 8(6P23) MUTATED | 0 | 247 | 26 | 4 | 4 | 5 | 2 | 10 |
AMP PEAK 8(6P23) WILD-TYPE | 1 | 523 | 174 | 2 | 5 | 24 | 15 | 37 |
Figure S23. Get High-res Image Gene #8: 'amp_6p23' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D8V9.png)
P value = 0.00164 (Fisher's exact test), Q value = 0.016
Table S24. Gene #8: 'amp_6p23' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
AMP PEAK 8(6P23) MUTATED | 0 | 15 | 70 | 185 |
AMP PEAK 8(6P23) WILD-TYPE | 1 | 45 | 111 | 560 |
Figure S24. Get High-res Image Gene #8: 'amp_6p23' versus Clinical Feature #11: 'RACE'
![](D8V11.png)
P value = 0.00059 (Fisher's exact test), Q value = 0.0073
Table S25. Gene #9: 'amp_6q21' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
AMP PEAK 9(6Q21) MUTATED | 34 | 142 | 22 | 4 |
AMP PEAK 9(6Q21) WILD-TYPE | 242 | 482 | 114 | 36 |
Figure S25. Get High-res Image Gene #9: 'amp_6q21' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D9V4.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S26. Gene #9: 'amp_6q21' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
AMP PEAK 9(6Q21) MUTATED | 1 | 171 | 15 | 3 | 5 | 1 | 0 | 6 |
AMP PEAK 9(6Q21) WILD-TYPE | 0 | 599 | 185 | 3 | 4 | 28 | 17 | 41 |
Figure S26. Get High-res Image Gene #9: 'amp_6q21' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D9V9.png)
P value = 0.046 (Wilcoxon-test), Q value = 0.2
Table S27. Gene #9: 'amp_6q21' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 914 | 2.4 (4.7) |
AMP PEAK 9(6Q21) MUTATED | 173 | 2.0 (4.4) |
AMP PEAK 9(6Q21) WILD-TYPE | 741 | 2.5 (4.7) |
Figure S27. Get High-res Image Gene #9: 'amp_6q21' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
![](D9V10.png)
P value = 0.0243 (logrank test), Q value = 0.13
Table S28. Gene #10: 'amp_8p11.23' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 1064 | 147 | 0.0 - 282.9 (27.9) |
AMP PEAK 10(8P11.23) MUTATED | 406 | 69 | 0.0 - 281.3 (26.2) |
AMP PEAK 10(8P11.23) WILD-TYPE | 658 | 78 | 0.0 - 282.9 (28.9) |
Figure S28. Get High-res Image Gene #10: 'amp_8p11.23' versus Clinical Feature #1: 'Time to Death'
![](D10V1.png)
P value = 0.0506 (Fisher's exact test), Q value = 0.21
Table S29. Gene #10: 'amp_8p11.23' 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 TIS | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 89 | 85 | 6 | 6 | 353 | 252 | 2 | 154 | 29 | 65 | 20 | 1 | 13 |
AMP PEAK 10(8P11.23) MUTATED | 24 | 29 | 4 | 1 | 135 | 94 | 2 | 57 | 16 | 30 | 11 | 0 | 6 |
AMP PEAK 10(8P11.23) WILD-TYPE | 65 | 56 | 2 | 5 | 218 | 158 | 0 | 97 | 13 | 35 | 9 | 1 | 7 |
Figure S29. Get High-res Image Gene #10: 'amp_8p11.23' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D10V3.png)
P value = 0.063 (Fisher's exact test), Q value = 0.24
Table S30. Gene #10: 'amp_8p11.23' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 507 | 358 | 119 | 77 |
AMP PEAK 10(8P11.23) MUTATED | 173 | 146 | 48 | 36 |
AMP PEAK 10(8P11.23) WILD-TYPE | 334 | 212 | 71 | 41 |
Figure S30. Get High-res Image Gene #10: 'amp_8p11.23' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D10V5.png)
P value = 0.00487 (Wilcoxon-test), Q value = 0.037
Table S31. Gene #10: 'amp_8p11.23' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 914 | 2.4 (4.7) |
AMP PEAK 10(8P11.23) MUTATED | 346 | 2.9 (5.3) |
AMP PEAK 10(8P11.23) WILD-TYPE | 568 | 2.1 (4.2) |
Figure S31. Get High-res Image Gene #10: 'amp_8p11.23' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
![](D10V10.png)
P value = 0.00087 (Fisher's exact test), Q value = 0.0097
Table S32. Gene #11: 'amp_8p11.21' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
AMP PEAK 11(8P11.21) MUTATED | 1 | 322 | 55 | 5 | 4 | 10 | 4 | 19 |
AMP PEAK 11(8P11.21) WILD-TYPE | 0 | 448 | 145 | 1 | 5 | 19 | 13 | 28 |
Figure S32. Get High-res Image Gene #11: 'amp_8p11.21' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D11V9.png)
P value = 0.0555 (Wilcoxon-test), Q value = 0.22
Table S33. Gene #12: 'amp_8q24.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1065 | 58.6 (13.2) |
AMP PEAK 12(8Q24.21) MUTATED | 670 | 58.0 (13.1) |
AMP PEAK 12(8Q24.21) WILD-TYPE | 395 | 59.7 (13.3) |
Figure S33. Get High-res Image Gene #12: 'amp_8q24.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D12V2.png)
P value = 0.0521 (Fisher's exact test), Q value = 0.21
Table S34. Gene #12: 'amp_8q24.21' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
AMP PEAK 12(8Q24.21) MUTATED | 158 | 412 | 79 | 25 |
AMP PEAK 12(8Q24.21) WILD-TYPE | 118 | 212 | 57 | 15 |
Figure S34. Get High-res Image Gene #12: 'amp_8q24.21' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D12V4.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S35. Gene #12: 'amp_8q24.21' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
AMP PEAK 12(8Q24.21) MUTATED | 1 | 546 | 70 | 6 | 7 | 17 | 5 | 25 |
AMP PEAK 12(8Q24.21) WILD-TYPE | 0 | 224 | 130 | 0 | 2 | 12 | 12 | 22 |
Figure S35. Get High-res Image Gene #12: 'amp_8q24.21' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D12V9.png)
P value = 0.00151 (Fisher's exact test), Q value = 0.015
Table S36. Gene #12: 'amp_8q24.21' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
AMP PEAK 12(8Q24.21) MUTATED | 1 | 41 | 131 | 435 |
AMP PEAK 12(8Q24.21) WILD-TYPE | 0 | 19 | 50 | 310 |
Figure S36. Get High-res Image Gene #12: 'amp_8q24.21' versus Clinical Feature #11: 'RACE'
![](D12V11.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S37. Gene #13: 'amp_10p15.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
AMP PEAK 13(10P15.1) MUTATED | 1 | 262 | 20 | 5 | 1 | 5 | 0 | 9 |
AMP PEAK 13(10P15.1) WILD-TYPE | 0 | 508 | 180 | 1 | 8 | 24 | 17 | 38 |
Figure S37. Get High-res Image Gene #13: 'amp_10p15.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D13V9.png)
P value = 3e-05 (Fisher's exact test), Q value = 0.00061
Table S38. Gene #13: 'amp_10p15.1' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
AMP PEAK 13(10P15.1) MUTATED | 1 | 14 | 75 | 185 |
AMP PEAK 13(10P15.1) WILD-TYPE | 0 | 46 | 106 | 560 |
Figure S38. Get High-res Image Gene #13: 'amp_10p15.1' versus Clinical Feature #11: 'RACE'
![](D13V11.png)
P value = 0.00022 (Fisher's exact test), Q value = 0.0034
Table S39. Gene #14: 'amp_10q22.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
AMP PEAK 14(10Q22.3) MUTATED | 0 | 125 | 11 | 3 | 1 | 4 | 0 | 6 |
AMP PEAK 14(10Q22.3) WILD-TYPE | 1 | 645 | 189 | 3 | 8 | 25 | 17 | 41 |
Figure S39. Get High-res Image Gene #14: 'amp_10q22.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D14V9.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S40. Gene #15: 'amp_11p13' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
AMP PEAK 15(11P13) MUTATED | 1 | 187 | 18 | 3 | 2 | 2 | 2 | 8 |
AMP PEAK 15(11P13) WILD-TYPE | 0 | 583 | 182 | 3 | 7 | 27 | 15 | 39 |
Figure S40. Get High-res Image Gene #15: 'amp_11p13' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D15V9.png)
P value = 0.0319 (Fisher's exact test), Q value = 0.16
Table S41. Gene #16: 'amp_11q13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
AMP PEAK 16(11Q13.3) MUTATED | 86 | 246 | 44 | 19 |
AMP PEAK 16(11Q13.3) WILD-TYPE | 190 | 378 | 92 | 21 |
Figure S41. Get High-res Image Gene #16: 'amp_11q13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D16V4.png)
P value = 0.0382 (Fisher's exact test), Q value = 0.17
Table S42. Gene #16: 'amp_11q13.3' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 1068 | 12 |
AMP PEAK 16(11Q13.3) MUTATED | 390 | 8 |
AMP PEAK 16(11Q13.3) WILD-TYPE | 678 | 4 |
Figure S42. Get High-res Image Gene #16: 'amp_11q13.3' versus Clinical Feature #7: 'GENDER'
![](D16V7.png)
P value = 0.0668 (Fisher's exact test), Q value = 0.24
Table S43. Gene #17: 'amp_11q14.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
AMP PEAK 17(11Q14.1) MUTATED | 60 | 170 | 24 | 10 |
AMP PEAK 17(11Q14.1) WILD-TYPE | 216 | 454 | 112 | 30 |
Figure S43. Get High-res Image Gene #17: 'amp_11q14.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D17V4.png)
P value = 0.00849 (Fisher's exact test), Q value = 0.058
Table S44. Gene #17: 'amp_11q14.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
AMP PEAK 17(11Q14.1) MUTATED | 1 | 212 | 34 | 2 | 2 | 3 | 2 | 11 |
AMP PEAK 17(11Q14.1) WILD-TYPE | 0 | 558 | 166 | 4 | 7 | 26 | 15 | 36 |
Figure S44. Get High-res Image Gene #17: 'amp_11q14.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D17V9.png)
P value = 0.00192 (Fisher's exact test), Q value = 0.018
Table S45. Gene #18: 'amp_12p13.33' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
AMP PEAK 18(12P13.33) MUTATED | 49 | 184 | 35 | 12 |
AMP PEAK 18(12P13.33) WILD-TYPE | 227 | 440 | 101 | 28 |
Figure S45. Get High-res Image Gene #18: 'amp_12p13.33' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D18V4.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S46. Gene #18: 'amp_12p13.33' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
AMP PEAK 18(12P13.33) MUTATED | 1 | 230 | 28 | 4 | 2 | 10 | 1 | 6 |
AMP PEAK 18(12P13.33) WILD-TYPE | 0 | 540 | 172 | 2 | 7 | 19 | 16 | 41 |
Figure S46. Get High-res Image Gene #18: 'amp_12p13.33' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D18V9.png)
P value = 0.0222 (Fisher's exact test), Q value = 0.12
Table S47. Gene #18: 'amp_12p13.33' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
AMP PEAK 18(12P13.33) MUTATED | 0 | 13 | 62 | 178 |
AMP PEAK 18(12P13.33) WILD-TYPE | 1 | 47 | 119 | 567 |
Figure S47. Get High-res Image Gene #18: 'amp_12p13.33' versus Clinical Feature #11: 'RACE'
![](D18V11.png)
P value = 0.0616 (Fisher's exact test), Q value = 0.23
Table S48. Gene #18: 'amp_12p13.33' versus Clinical Feature #12: 'ETHNICITY'
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 39 | 875 |
AMP PEAK 18(12P13.33) MUTATED | 5 | 234 |
AMP PEAK 18(12P13.33) WILD-TYPE | 34 | 641 |
Figure S48. Get High-res Image Gene #18: 'amp_12p13.33' versus Clinical Feature #12: 'ETHNICITY'
![](D18V12.png)
P value = 0.0179 (Fisher's exact test), Q value = 0.1
Table S49. Gene #19: 'amp_12q15' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
AMP PEAK 19(12Q15) MUTATED | 55 | 174 | 31 | 15 |
AMP PEAK 19(12Q15) WILD-TYPE | 221 | 450 | 105 | 25 |
Figure S49. Get High-res Image Gene #19: 'amp_12q15' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D19V4.png)
P value = 0.0145 (Fisher's exact test), Q value = 0.088
Table S50. Gene #19: 'amp_12q15' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 507 | 358 | 119 | 77 |
AMP PEAK 19(12Q15) MUTATED | 115 | 88 | 44 | 22 |
AMP PEAK 19(12Q15) WILD-TYPE | 392 | 270 | 75 | 55 |
Figure S50. Get High-res Image Gene #19: 'amp_12q15' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D19V5.png)
P value = 0.00307 (Fisher's exact test), Q value = 0.026
Table S51. Gene #19: 'amp_12q15' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 1068 | 12 |
AMP PEAK 19(12Q15) MUTATED | 268 | 8 |
AMP PEAK 19(12Q15) WILD-TYPE | 800 | 4 |
Figure S51. Get High-res Image Gene #19: 'amp_12q15' versus Clinical Feature #7: 'GENDER'
![](D19V7.png)
P value = 0.0011 (Fisher's exact test), Q value = 0.011
Table S52. Gene #19: 'amp_12q15' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
AMP PEAK 19(12Q15) MUTATED | 0 | 224 | 34 | 1 | 1 | 9 | 2 | 5 |
AMP PEAK 19(12Q15) WILD-TYPE | 1 | 546 | 166 | 5 | 8 | 20 | 15 | 42 |
Figure S52. Get High-res Image Gene #19: 'amp_12q15' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D19V9.png)
P value = 0.0179 (Wilcoxon-test), Q value = 0.1
Table S53. Gene #19: 'amp_12q15' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 914 | 2.4 (4.7) |
AMP PEAK 19(12Q15) MUTATED | 218 | 2.7 (4.6) |
AMP PEAK 19(12Q15) WILD-TYPE | 696 | 2.3 (4.7) |
Figure S53. Get High-res Image Gene #19: 'amp_12q15' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
![](D19V10.png)
P value = 0.0539 (Wilcoxon-test), Q value = 0.21
Table S54. Gene #20: 'amp_13q34' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1065 | 58.6 (13.2) |
AMP PEAK 20(13Q34) MUTATED | 177 | 56.9 (12.7) |
AMP PEAK 20(13Q34) WILD-TYPE | 888 | 59.0 (13.3) |
Figure S54. Get High-res Image Gene #20: 'amp_13q34' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D20V2.png)
P value = 0.00529 (Fisher's exact test), Q value = 0.039
Table S55. Gene #20: 'amp_13q34' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
AMP PEAK 20(13Q34) MUTATED | 30 | 124 | 18 | 6 |
AMP PEAK 20(13Q34) WILD-TYPE | 246 | 500 | 118 | 34 |
Figure S55. Get High-res Image Gene #20: 'amp_13q34' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D20V4.png)
P value = 0.0444 (Fisher's exact test), Q value = 0.2
Table S56. Gene #20: 'amp_13q34' versus Clinical Feature #8: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 429 | 518 |
AMP PEAK 20(13Q34) MUTATED | 84 | 75 |
AMP PEAK 20(13Q34) WILD-TYPE | 345 | 443 |
Figure S56. Get High-res Image Gene #20: 'amp_13q34' versus Clinical Feature #8: 'RADIATION_THERAPY'
![](D20V8.png)
P value = 0.00121 (Fisher's exact test), Q value = 0.012
Table S57. Gene #20: 'amp_13q34' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
AMP PEAK 20(13Q34) MUTATED | 0 | 146 | 14 | 1 | 3 | 4 | 2 | 9 |
AMP PEAK 20(13Q34) WILD-TYPE | 1 | 624 | 186 | 5 | 6 | 25 | 15 | 38 |
Figure S57. Get High-res Image Gene #20: 'amp_13q34' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D20V9.png)
P value = 0.0645 (Wilcoxon-test), Q value = 0.24
Table S58. Gene #20: 'amp_13q34' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 914 | 2.4 (4.7) |
AMP PEAK 20(13Q34) MUTATED | 154 | 1.9 (4.4) |
AMP PEAK 20(13Q34) WILD-TYPE | 760 | 2.5 (4.7) |
Figure S58. Get High-res Image Gene #20: 'amp_13q34' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
![](D20V10.png)
P value = 0.0161 (Fisher's exact test), Q value = 0.096
Table S59. Gene #21: 'amp_14q21.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
AMP PEAK 21(14Q21.1) MUTATED | 43 | 148 | 21 | 8 |
AMP PEAK 21(14Q21.1) WILD-TYPE | 233 | 476 | 115 | 32 |
Figure S59. Get High-res Image Gene #21: 'amp_14q21.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D21V4.png)
P value = 0.0321 (Fisher's exact test), Q value = 0.16
Table S60. Gene #21: 'amp_14q21.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 507 | 358 | 119 | 77 |
AMP PEAK 21(14Q21.1) MUTATED | 87 | 75 | 32 | 21 |
AMP PEAK 21(14Q21.1) WILD-TYPE | 420 | 283 | 87 | 56 |
Figure S60. Get High-res Image Gene #21: 'amp_14q21.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D21V5.png)
P value = 0.00685 (Fisher's exact test), Q value = 0.048
Table S61. Gene #21: 'amp_14q21.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
AMP PEAK 21(14Q21.1) MUTATED | 0 | 174 | 23 | 0 | 3 | 9 | 2 | 9 |
AMP PEAK 21(14Q21.1) WILD-TYPE | 1 | 596 | 177 | 6 | 6 | 20 | 15 | 38 |
Figure S61. Get High-res Image Gene #21: 'amp_14q21.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D21V9.png)
P value = 0.0103 (Wilcoxon-test), Q value = 0.067
Table S62. Gene #21: 'amp_14q21.1' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 914 | 2.4 (4.7) |
AMP PEAK 21(14Q21.1) MUTATED | 177 | 2.9 (4.8) |
AMP PEAK 21(14Q21.1) WILD-TYPE | 737 | 2.3 (4.6) |
Figure S62. Get High-res Image Gene #21: 'amp_14q21.1' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
![](D21V10.png)
P value = 0.00973 (Wilcoxon-test), Q value = 0.064
Table S63. Gene #22: 'amp_15q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1065 | 58.6 (13.2) |
AMP PEAK 22(15Q26.3) MUTATED | 190 | 56.4 (12.9) |
AMP PEAK 22(15Q26.3) WILD-TYPE | 875 | 59.1 (13.2) |
Figure S63. Get High-res Image Gene #22: 'amp_15q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D22V2.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S64. Gene #22: 'amp_15q26.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
AMP PEAK 22(15Q26.3) MUTATED | 0 | 167 | 11 | 3 | 1 | 4 | 3 | 4 |
AMP PEAK 22(15Q26.3) WILD-TYPE | 1 | 603 | 189 | 3 | 8 | 25 | 14 | 43 |
Figure S64. Get High-res Image Gene #22: 'amp_15q26.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D22V9.png)
P value = 0.0504 (Fisher's exact test), Q value = 0.21
Table S65. Gene #22: 'amp_15q26.3' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
AMP PEAK 22(15Q26.3) MUTATED | 0 | 16 | 39 | 118 |
AMP PEAK 22(15Q26.3) WILD-TYPE | 1 | 44 | 142 | 627 |
Figure S65. Get High-res Image Gene #22: 'amp_15q26.3' versus Clinical Feature #11: 'RACE'
![](D22V11.png)
P value = 0.0616 (Fisher's exact test), Q value = 0.23
Table S66. Gene #24: 'amp_17q12' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 507 | 358 | 119 | 77 |
AMP PEAK 24(17Q12) MUTATED | 138 | 128 | 35 | 22 |
AMP PEAK 24(17Q12) WILD-TYPE | 369 | 230 | 84 | 55 |
Figure S66. Get High-res Image Gene #24: 'amp_17q12' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D24V5.png)
P value = 0.011 (Fisher's exact test), Q value = 0.07
Table S67. Gene #24: 'amp_17q12' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 1068 | 12 |
AMP PEAK 24(17Q12) MUTATED | 325 | 8 |
AMP PEAK 24(17Q12) WILD-TYPE | 743 | 4 |
Figure S67. Get High-res Image Gene #24: 'amp_17q12' versus Clinical Feature #7: 'GENDER'
![](D24V7.png)
P value = 5e-04 (Fisher's exact test), Q value = 0.0064
Table S68. Gene #24: 'amp_17q12' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
AMP PEAK 24(17Q12) MUTATED | 0 | 270 | 38 | 1 | 3 | 6 | 4 | 11 |
AMP PEAK 24(17Q12) WILD-TYPE | 1 | 500 | 162 | 5 | 6 | 23 | 13 | 36 |
Figure S68. Get High-res Image Gene #24: 'amp_17q12' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D24V9.png)
P value = 0.00169 (Fisher's exact test), Q value = 0.016
Table S69. Gene #24: 'amp_17q12' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
AMP PEAK 24(17Q12) MUTATED | 1 | 30 | 52 | 210 |
AMP PEAK 24(17Q12) WILD-TYPE | 0 | 30 | 129 | 535 |
Figure S69. Get High-res Image Gene #24: 'amp_17q12' versus Clinical Feature #11: 'RACE'
![](D24V11.png)
P value = 0.0291 (Fisher's exact test), Q value = 0.15
Table S70. Gene #25: 'amp_17q23.1' 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 TIS | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 89 | 85 | 6 | 6 | 353 | 252 | 2 | 154 | 29 | 65 | 20 | 1 | 13 |
AMP PEAK 25(17Q23.1) MUTATED | 27 | 25 | 1 | 2 | 152 | 102 | 1 | 68 | 16 | 20 | 9 | 1 | 2 |
AMP PEAK 25(17Q23.1) WILD-TYPE | 62 | 60 | 5 | 4 | 201 | 150 | 1 | 86 | 13 | 45 | 11 | 0 | 11 |
Figure S70. Get High-res Image Gene #25: 'amp_17q23.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D25V3.png)
P value = 0.00034 (Fisher's exact test), Q value = 0.0047
Table S71. Gene #25: 'amp_17q23.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
AMP PEAK 25(17Q23.1) MUTATED | 81 | 276 | 49 | 18 |
AMP PEAK 25(17Q23.1) WILD-TYPE | 195 | 348 | 87 | 22 |
Figure S71. Get High-res Image Gene #25: 'amp_17q23.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D25V4.png)
P value = 1.29e-05 (Fisher's exact test), Q value = 0.00029
Table S72. Gene #25: 'amp_17q23.1' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 1068 | 12 |
AMP PEAK 25(17Q23.1) MUTATED | 414 | 12 |
AMP PEAK 25(17Q23.1) WILD-TYPE | 654 | 0 |
Figure S72. Get High-res Image Gene #25: 'amp_17q23.1' versus Clinical Feature #7: 'GENDER'
![](D25V7.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S73. Gene #25: 'amp_17q23.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
AMP PEAK 25(17Q23.1) MUTATED | 1 | 341 | 44 | 3 | 6 | 12 | 5 | 13 |
AMP PEAK 25(17Q23.1) WILD-TYPE | 0 | 429 | 156 | 3 | 3 | 17 | 12 | 34 |
Figure S73. Get High-res Image Gene #25: 'amp_17q23.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D25V9.png)
P value = 0.0623 (Fisher's exact test), Q value = 0.23
Table S74. Gene #26: 'amp_19p13.12' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
nPatients | 0 | 1 |
---|---|---|
ALL | 889 | 22 |
AMP PEAK 26(19P13.12) MUTATED | 192 | 1 |
AMP PEAK 26(19P13.12) WILD-TYPE | 697 | 21 |
Figure S74. Get High-res Image Gene #26: 'amp_19p13.12' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
![](D26V6.png)
P value = 0.0313 (Fisher's exact test), Q value = 0.16
Table S75. Gene #26: 'amp_19p13.12' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
AMP PEAK 26(19P13.12) MUTATED | 1 | 169 | 33 | 4 | 3 | 6 | 2 | 12 |
AMP PEAK 26(19P13.12) WILD-TYPE | 0 | 601 | 167 | 2 | 6 | 23 | 15 | 35 |
Figure S75. Get High-res Image Gene #26: 'amp_19p13.12' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D26V9.png)
P value = 0.000495 (Wilcoxon-test), Q value = 0.0064
Table S76. Gene #26: 'amp_19p13.12' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 914 | 2.4 (4.7) |
AMP PEAK 26(19P13.12) MUTATED | 207 | 1.9 (4.5) |
AMP PEAK 26(19P13.12) WILD-TYPE | 707 | 2.5 (4.7) |
Figure S76. Get High-res Image Gene #26: 'amp_19p13.12' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
![](D26V10.png)
P value = 0.00939 (Fisher's exact test), Q value = 0.063
Table S77. Gene #27: 'amp_19q12' 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 TIS | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 89 | 85 | 6 | 6 | 353 | 252 | 2 | 154 | 29 | 65 | 20 | 1 | 13 |
AMP PEAK 27(19Q12) MUTATED | 23 | 18 | 2 | 2 | 121 | 56 | 0 | 36 | 8 | 12 | 3 | 0 | 0 |
AMP PEAK 27(19Q12) WILD-TYPE | 66 | 67 | 4 | 4 | 232 | 196 | 2 | 118 | 21 | 53 | 17 | 1 | 13 |
Figure S77. Get High-res Image Gene #27: 'amp_19q12' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D27V3.png)
P value = 0.0359 (Fisher's exact test), Q value = 0.17
Table S78. Gene #27: 'amp_19q12' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 507 | 358 | 119 | 77 |
AMP PEAK 27(19Q12) MUTATED | 155 | 86 | 28 | 14 |
AMP PEAK 27(19Q12) WILD-TYPE | 352 | 272 | 91 | 63 |
Figure S78. Get High-res Image Gene #27: 'amp_19q12' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D27V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S79. Gene #27: 'amp_19q12' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
AMP PEAK 27(19Q12) MUTATED | 0 | 226 | 30 | 6 | 3 | 6 | 2 | 11 |
AMP PEAK 27(19Q12) WILD-TYPE | 1 | 544 | 170 | 0 | 6 | 23 | 15 | 36 |
Figure S79. Get High-res Image Gene #27: 'amp_19q12' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D27V9.png)
P value = 0.00508 (Wilcoxon-test), Q value = 0.038
Table S80. Gene #27: 'amp_19q12' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 914 | 2.4 (4.7) |
AMP PEAK 27(19Q12) MUTATED | 246 | 2.0 (4.6) |
AMP PEAK 27(19Q12) WILD-TYPE | 668 | 2.5 (4.7) |
Figure S80. Get High-res Image Gene #27: 'amp_19q12' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
![](D27V10.png)
P value = 0.0369 (Fisher's exact test), Q value = 0.17
Table S81. Gene #27: 'amp_19q12' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
AMP PEAK 27(19Q12) MUTATED | 0 | 13 | 63 | 188 |
AMP PEAK 27(19Q12) WILD-TYPE | 1 | 47 | 118 | 557 |
Figure S81. Get High-res Image Gene #27: 'amp_19q12' versus Clinical Feature #11: 'RACE'
![](D27V11.png)
P value = 0.00774 (Fisher's exact test), Q value = 0.053
Table S82. Gene #28: 'amp_19q13.42' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
AMP PEAK 28(19Q13.42) MUTATED | 1 | 217 | 33 | 2 | 3 | 5 | 2 | 13 |
AMP PEAK 28(19Q13.42) WILD-TYPE | 0 | 553 | 167 | 4 | 6 | 24 | 15 | 34 |
Figure S82. Get High-res Image Gene #28: 'amp_19q13.42' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D28V9.png)
P value = 0.00109 (Fisher's exact test), Q value = 0.011
Table S83. Gene #29: 'amp_20q13.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
AMP PEAK 29(20Q13.2) MUTATED | 120 | 346 | 57 | 22 |
AMP PEAK 29(20Q13.2) WILD-TYPE | 156 | 278 | 79 | 18 |
Figure S83. Get High-res Image Gene #29: 'amp_20q13.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D29V4.png)
P value = 0.00105 (Fisher's exact test), Q value = 0.011
Table S84. Gene #29: 'amp_20q13.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 507 | 358 | 119 | 77 |
AMP PEAK 29(20Q13.2) MUTATED | 248 | 179 | 79 | 31 |
AMP PEAK 29(20Q13.2) WILD-TYPE | 259 | 179 | 40 | 46 |
Figure S84. Get High-res Image Gene #29: 'amp_20q13.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D29V5.png)
P value = 0.0378 (Fisher's exact test), Q value = 0.17
Table S85. Gene #29: 'amp_20q13.2' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 1068 | 12 |
AMP PEAK 29(20Q13.2) MUTATED | 538 | 10 |
AMP PEAK 29(20Q13.2) WILD-TYPE | 530 | 2 |
Figure S85. Get High-res Image Gene #29: 'amp_20q13.2' versus Clinical Feature #7: 'GENDER'
![](D29V7.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S86. Gene #29: 'amp_20q13.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
AMP PEAK 29(20Q13.2) MUTATED | 1 | 452 | 55 | 1 | 7 | 11 | 1 | 20 |
AMP PEAK 29(20Q13.2) WILD-TYPE | 0 | 318 | 145 | 5 | 2 | 18 | 16 | 27 |
Figure S86. Get High-res Image Gene #29: 'amp_20q13.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D29V9.png)
P value = 0.0218 (logrank test), Q value = 0.12
Table S87. Gene #30: 'del_1p36.13' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 1064 | 147 | 0.0 - 282.9 (27.9) |
DEL PEAK 1(1P36.13) MUTATED | 448 | 68 | 0.2 - 282.9 (25.0) |
DEL PEAK 1(1P36.13) WILD-TYPE | 616 | 79 | 0.0 - 281.3 (30.0) |
Figure S87. Get High-res Image Gene #30: 'del_1p36.13' versus Clinical Feature #1: 'Time to Death'
![](D30V1.png)
P value = 0.0183 (Wilcoxon-test), Q value = 0.1
Table S88. Gene #30: 'del_1p36.13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1065 | 58.6 (13.2) |
DEL PEAK 1(1P36.13) MUTATED | 446 | 59.5 (13.1) |
DEL PEAK 1(1P36.13) WILD-TYPE | 619 | 58.0 (13.3) |
Figure S88. Get High-res Image Gene #30: 'del_1p36.13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D30V2.png)
P value = 0.00064 (Fisher's exact test), Q value = 0.0077
Table S89. Gene #30: 'del_1p36.13' 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 TIS | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 89 | 85 | 6 | 6 | 353 | 252 | 2 | 154 | 29 | 65 | 20 | 1 | 13 |
DEL PEAK 1(1P36.13) MUTATED | 28 | 24 | 0 | 3 | 136 | 117 | 1 | 74 | 18 | 33 | 12 | 0 | 5 |
DEL PEAK 1(1P36.13) WILD-TYPE | 61 | 61 | 6 | 3 | 217 | 135 | 1 | 80 | 11 | 32 | 8 | 1 | 8 |
Figure S89. Get High-res Image Gene #30: 'del_1p36.13' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D30V3.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S90. Gene #30: 'del_1p36.13' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
DEL PEAK 1(1P36.13) MUTATED | 83 | 287 | 55 | 26 |
DEL PEAK 1(1P36.13) WILD-TYPE | 193 | 337 | 81 | 14 |
Figure S90. Get High-res Image Gene #30: 'del_1p36.13' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D30V4.png)
P value = 0.00056 (Fisher's exact test), Q value = 0.007
Table S91. Gene #30: 'del_1p36.13' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 507 | 358 | 119 | 77 |
DEL PEAK 1(1P36.13) MUTATED | 180 | 166 | 57 | 41 |
DEL PEAK 1(1P36.13) WILD-TYPE | 327 | 192 | 62 | 36 |
Figure S91. Get High-res Image Gene #30: 'del_1p36.13' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D30V5.png)
P value = 0.0346 (Fisher's exact test), Q value = 0.16
Table S92. Gene #30: 'del_1p36.13' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 1068 | 12 |
DEL PEAK 1(1P36.13) MUTATED | 443 | 9 |
DEL PEAK 1(1P36.13) WILD-TYPE | 625 | 3 |
Figure S92. Get High-res Image Gene #30: 'del_1p36.13' versus Clinical Feature #7: 'GENDER'
![](D30V7.png)
P value = 0.00278 (Fisher's exact test), Q value = 0.024
Table S93. Gene #30: 'del_1p36.13' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 1(1P36.13) MUTATED | 1 | 347 | 74 | 1 | 0 | 8 | 4 | 17 |
DEL PEAK 1(1P36.13) WILD-TYPE | 0 | 423 | 126 | 5 | 9 | 21 | 13 | 30 |
Figure S93. Get High-res Image Gene #30: 'del_1p36.13' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D30V9.png)
P value = 0.00101 (Wilcoxon-test), Q value = 0.011
Table S94. Gene #30: 'del_1p36.13' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 914 | 2.4 (4.7) |
DEL PEAK 1(1P36.13) MUTATED | 372 | 2.9 (5.1) |
DEL PEAK 1(1P36.13) WILD-TYPE | 542 | 2.1 (4.3) |
Figure S94. Get High-res Image Gene #30: 'del_1p36.13' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
![](D30V10.png)
P value = 0.000661 (logrank test), Q value = 0.0078
Table S95. Gene #31: 'del_1p22.1' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 1064 | 147 | 0.0 - 282.9 (27.9) |
DEL PEAK 2(1P22.1) MUTATED | 357 | 62 | 0.2 - 165.8 (25.2) |
DEL PEAK 2(1P22.1) WILD-TYPE | 707 | 85 | 0.0 - 282.9 (29.1) |
Figure S95. Get High-res Image Gene #31: 'del_1p22.1' versus Clinical Feature #1: 'Time to Death'
![](D31V1.png)
P value = 0.0412 (Wilcoxon-test), Q value = 0.18
Table S96. Gene #31: 'del_1p22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1065 | 58.6 (13.2) |
DEL PEAK 2(1P22.1) MUTATED | 356 | 59.7 (13.0) |
DEL PEAK 2(1P22.1) WILD-TYPE | 709 | 58.1 (13.3) |
Figure S96. Get High-res Image Gene #31: 'del_1p22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D31V2.png)
P value = 0.0104 (Fisher's exact test), Q value = 0.067
Table S97. Gene #31: 'del_1p22.1' 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 TIS | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 89 | 85 | 6 | 6 | 353 | 252 | 2 | 154 | 29 | 65 | 20 | 1 | 13 |
DEL PEAK 2(1P22.1) MUTATED | 20 | 21 | 0 | 1 | 115 | 84 | 1 | 60 | 16 | 28 | 9 | 0 | 5 |
DEL PEAK 2(1P22.1) WILD-TYPE | 69 | 64 | 6 | 5 | 238 | 168 | 1 | 94 | 13 | 37 | 11 | 1 | 8 |
Figure S97. Get High-res Image Gene #31: 'del_1p22.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D31V3.png)
P value = 4e-05 (Fisher's exact test), Q value = 0.00077
Table S98. Gene #31: 'del_1p22.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
DEL PEAK 2(1P22.1) MUTATED | 67 | 226 | 45 | 24 |
DEL PEAK 2(1P22.1) WILD-TYPE | 209 | 398 | 91 | 16 |
Figure S98. Get High-res Image Gene #31: 'del_1p22.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D31V4.png)
P value = 0.00766 (Fisher's exact test), Q value = 0.053
Table S99. Gene #31: 'del_1p22.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 507 | 358 | 119 | 77 |
DEL PEAK 2(1P22.1) MUTATED | 146 | 127 | 50 | 32 |
DEL PEAK 2(1P22.1) WILD-TYPE | 361 | 231 | 69 | 45 |
Figure S99. Get High-res Image Gene #31: 'del_1p22.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D31V5.png)
P value = 0.000895 (Wilcoxon-test), Q value = 0.0099
Table S100. Gene #31: 'del_1p22.1' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 914 | 2.4 (4.7) |
DEL PEAK 2(1P22.1) MUTATED | 291 | 3.0 (5.3) |
DEL PEAK 2(1P22.1) WILD-TYPE | 623 | 2.1 (4.3) |
Figure S100. Get High-res Image Gene #31: 'del_1p22.1' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
![](D31V10.png)
P value = 0.00158 (Fisher's exact test), Q value = 0.015
Table S101. Gene #32: 'del_2q37.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
DEL PEAK 3(2Q37.3) MUTATED | 61 | 197 | 38 | 19 |
DEL PEAK 3(2Q37.3) WILD-TYPE | 215 | 427 | 98 | 21 |
Figure S101. Get High-res Image Gene #32: 'del_2q37.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D32V4.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S102. Gene #32: 'del_2q37.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 3(2Q37.3) MUTATED | 0 | 261 | 26 | 3 | 5 | 10 | 3 | 8 |
DEL PEAK 3(2Q37.3) WILD-TYPE | 1 | 509 | 174 | 3 | 4 | 19 | 14 | 39 |
Figure S102. Get High-res Image Gene #32: 'del_2q37.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D32V9.png)
P value = 0.0319 (Fisher's exact test), Q value = 0.16
Table S103. Gene #32: 'del_2q37.3' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
DEL PEAK 3(2Q37.3) MUTATED | 0 | 25 | 58 | 197 |
DEL PEAK 3(2Q37.3) WILD-TYPE | 1 | 35 | 123 | 548 |
Figure S103. Get High-res Image Gene #32: 'del_2q37.3' versus Clinical Feature #11: 'RACE'
![](D32V11.png)
P value = 0.00267 (Wilcoxon-test), Q value = 0.024
Table S104. Gene #33: 'del_3p21.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1065 | 58.6 (13.2) |
DEL PEAK 4(3P21.31) MUTATED | 341 | 56.8 (13.1) |
DEL PEAK 4(3P21.31) WILD-TYPE | 724 | 59.5 (13.2) |
Figure S104. Get High-res Image Gene #33: 'del_3p21.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D33V2.png)
P value = 3e-05 (Fisher's exact test), Q value = 0.00061
Table S105. Gene #33: 'del_3p21.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
DEL PEAK 4(3P21.31) MUTATED | 60 | 236 | 39 | 10 |
DEL PEAK 4(3P21.31) WILD-TYPE | 216 | 388 | 97 | 30 |
Figure S105. Get High-res Image Gene #33: 'del_3p21.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D33V4.png)
P value = 0.0586 (Fisher's exact test), Q value = 0.23
Table S106. Gene #33: 'del_3p21.31' versus Clinical Feature #8: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 429 | 518 |
DEL PEAK 4(3P21.31) MUTATED | 123 | 179 |
DEL PEAK 4(3P21.31) WILD-TYPE | 306 | 339 |
Figure S106. Get High-res Image Gene #33: 'del_3p21.31' versus Clinical Feature #8: 'RADIATION_THERAPY'
![](D33V8.png)
P value = 2e-05 (Fisher's exact test), Q value = 0.00044
Table S107. Gene #33: 'del_3p21.31' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 4(3P21.31) MUTATED | 1 | 285 | 41 | 1 | 2 | 6 | 1 | 10 |
DEL PEAK 4(3P21.31) WILD-TYPE | 0 | 485 | 159 | 5 | 7 | 23 | 16 | 37 |
Figure S107. Get High-res Image Gene #33: 'del_3p21.31' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D33V9.png)
P value = 0.0113 (Fisher's exact test), Q value = 0.071
Table S108. Gene #33: 'del_3p21.31' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
DEL PEAK 4(3P21.31) MUTATED | 0 | 26 | 72 | 224 |
DEL PEAK 4(3P21.31) WILD-TYPE | 1 | 34 | 109 | 521 |
Figure S108. Get High-res Image Gene #33: 'del_3p21.31' versus Clinical Feature #11: 'RACE'
![](D33V11.png)
P value = 0.0561 (Wilcoxon-test), Q value = 0.22
Table S109. Gene #34: 'del_4p16.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1065 | 58.6 (13.2) |
DEL PEAK 5(4P16.3) MUTATED | 332 | 57.6 (12.7) |
DEL PEAK 5(4P16.3) WILD-TYPE | 733 | 59.1 (13.4) |
Figure S109. Get High-res Image Gene #34: 'del_4p16.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D34V2.png)
P value = 0.00015 (Fisher's exact test), Q value = 0.0026
Table S110. Gene #34: 'del_4p16.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
DEL PEAK 5(4P16.3) MUTATED | 59 | 226 | 39 | 13 |
DEL PEAK 5(4P16.3) WILD-TYPE | 217 | 398 | 97 | 27 |
Figure S110. Get High-res Image Gene #34: 'del_4p16.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D34V4.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S111. Gene #34: 'del_4p16.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 5(4P16.3) MUTATED | 1 | 281 | 32 | 4 | 3 | 6 | 0 | 12 |
DEL PEAK 5(4P16.3) WILD-TYPE | 0 | 489 | 168 | 2 | 6 | 23 | 17 | 35 |
Figure S111. Get High-res Image Gene #34: 'del_4p16.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D34V9.png)
P value = 0.018 (Fisher's exact test), Q value = 0.1
Table S112. Gene #34: 'del_4p16.3' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
DEL PEAK 5(4P16.3) MUTATED | 1 | 17 | 73 | 225 |
DEL PEAK 5(4P16.3) WILD-TYPE | 0 | 43 | 108 | 520 |
Figure S112. Get High-res Image Gene #34: 'del_4p16.3' versus Clinical Feature #11: 'RACE'
![](D34V11.png)
P value = 0.00182 (Fisher's exact test), Q value = 0.017
Table S113. Gene #35: 'del_4q35.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
DEL PEAK 6(4Q35.1) MUTATED | 66 | 223 | 38 | 16 |
DEL PEAK 6(4Q35.1) WILD-TYPE | 210 | 401 | 98 | 24 |
Figure S113. Get High-res Image Gene #35: 'del_4q35.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D35V4.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S114. Gene #35: 'del_4q35.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 6(4Q35.1) MUTATED | 1 | 287 | 36 | 4 | 4 | 4 | 0 | 8 |
DEL PEAK 6(4Q35.1) WILD-TYPE | 0 | 483 | 164 | 2 | 5 | 25 | 17 | 39 |
Figure S114. Get High-res Image Gene #35: 'del_4q35.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D35V9.png)
P value = 0.00599 (Fisher's exact test), Q value = 0.043
Table S115. Gene #35: 'del_4q35.1' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
DEL PEAK 6(4Q35.1) MUTATED | 1 | 23 | 73 | 218 |
DEL PEAK 6(4Q35.1) WILD-TYPE | 0 | 37 | 108 | 527 |
Figure S115. Get High-res Image Gene #35: 'del_4q35.1' versus Clinical Feature #11: 'RACE'
![](D35V11.png)
P value = 4.3e-06 (Wilcoxon-test), Q value = 0.00023
Table S116. Gene #36: 'del_5q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1065 | 58.6 (13.2) |
DEL PEAK 7(5Q11.2) MUTATED | 277 | 55.6 (13.2) |
DEL PEAK 7(5Q11.2) WILD-TYPE | 788 | 59.7 (13.0) |
Figure S116. Get High-res Image Gene #36: 'del_5q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D36V2.png)
P value = 0.00037 (Fisher's exact test), Q value = 0.005
Table S117. Gene #36: 'del_5q11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
DEL PEAK 7(5Q11.2) MUTATED | 60 | 187 | 20 | 12 |
DEL PEAK 7(5Q11.2) WILD-TYPE | 216 | 437 | 116 | 28 |
Figure S117. Get High-res Image Gene #36: 'del_5q11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D36V4.png)
P value = 0.0436 (Fisher's exact test), Q value = 0.19
Table S118. Gene #36: 'del_5q11.2' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 1068 | 12 |
DEL PEAK 7(5Q11.2) MUTATED | 280 | 0 |
DEL PEAK 7(5Q11.2) WILD-TYPE | 788 | 12 |
Figure S118. Get High-res Image Gene #36: 'del_5q11.2' versus Clinical Feature #7: 'GENDER'
![](D36V7.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S119. Gene #36: 'del_5q11.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 7(5Q11.2) MUTATED | 1 | 244 | 12 | 5 | 1 | 6 | 1 | 9 |
DEL PEAK 7(5Q11.2) WILD-TYPE | 0 | 526 | 188 | 1 | 8 | 23 | 16 | 38 |
Figure S119. Get High-res Image Gene #36: 'del_5q11.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D36V9.png)
P value = 6e-05 (Fisher's exact test), Q value = 0.0011
Table S120. Gene #36: 'del_5q11.2' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
DEL PEAK 7(5Q11.2) MUTATED | 1 | 20 | 68 | 170 |
DEL PEAK 7(5Q11.2) WILD-TYPE | 0 | 40 | 113 | 575 |
Figure S120. Get High-res Image Gene #36: 'del_5q11.2' versus Clinical Feature #11: 'RACE'
![](D36V11.png)
P value = 0.000324 (Wilcoxon-test), Q value = 0.0047
Table S121. Gene #37: 'del_5q21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1065 | 58.6 (13.2) |
DEL PEAK 8(5Q21.3) MUTATED | 269 | 56.2 (13.4) |
DEL PEAK 8(5Q21.3) WILD-TYPE | 796 | 59.5 (13.1) |
Figure S121. Get High-res Image Gene #37: 'del_5q21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D37V2.png)
P value = 0.00021 (Fisher's exact test), Q value = 0.0033
Table S122. Gene #37: 'del_5q21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
DEL PEAK 8(5Q21.3) MUTATED | 54 | 184 | 20 | 12 |
DEL PEAK 8(5Q21.3) WILD-TYPE | 222 | 440 | 116 | 28 |
Figure S122. Get High-res Image Gene #37: 'del_5q21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D37V4.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S123. Gene #37: 'del_5q21.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 8(5Q21.3) MUTATED | 1 | 243 | 6 | 6 | 1 | 6 | 0 | 8 |
DEL PEAK 8(5Q21.3) WILD-TYPE | 0 | 527 | 194 | 0 | 8 | 23 | 17 | 39 |
Figure S123. Get High-res Image Gene #37: 'del_5q21.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D37V9.png)
P value = 0.00312 (Wilcoxon-test), Q value = 0.026
Table S124. Gene #37: 'del_5q21.3' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 914 | 2.4 (4.7) |
DEL PEAK 8(5Q21.3) MUTATED | 232 | 1.7 (3.7) |
DEL PEAK 8(5Q21.3) WILD-TYPE | 682 | 2.6 (4.9) |
Figure S124. Get High-res Image Gene #37: 'del_5q21.3' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
![](D37V10.png)
P value = 9e-05 (Fisher's exact test), Q value = 0.0016
Table S125. Gene #37: 'del_5q21.3' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
DEL PEAK 8(5Q21.3) MUTATED | 0 | 18 | 70 | 163 |
DEL PEAK 8(5Q21.3) WILD-TYPE | 1 | 42 | 111 | 582 |
Figure S125. Get High-res Image Gene #37: 'del_5q21.3' versus Clinical Feature #11: 'RACE'
![](D37V11.png)
P value = 0.0526 (Wilcoxon-test), Q value = 0.21
Table S126. Gene #38: 'del_6p25.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1065 | 58.6 (13.2) |
DEL PEAK 9(6P25.3) MUTATED | 201 | 56.9 (13.0) |
DEL PEAK 9(6P25.3) WILD-TYPE | 864 | 59.0 (13.2) |
Figure S126. Get High-res Image Gene #38: 'del_6p25.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D38V2.png)
P value = 0.0096 (Fisher's exact test), Q value = 0.064
Table S127. Gene #38: 'del_6p25.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
DEL PEAK 9(6P25.3) MUTATED | 45 | 138 | 15 | 6 |
DEL PEAK 9(6P25.3) WILD-TYPE | 231 | 486 | 121 | 34 |
Figure S127. Get High-res Image Gene #38: 'del_6p25.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D38V4.png)
P value = 0.0258 (Fisher's exact test), Q value = 0.13
Table S128. Gene #38: 'del_6p25.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 9(6P25.3) MUTATED | 1 | 161 | 24 | 2 | 0 | 5 | 3 | 8 |
DEL PEAK 9(6P25.3) WILD-TYPE | 0 | 609 | 176 | 4 | 9 | 24 | 14 | 39 |
Figure S128. Get High-res Image Gene #38: 'del_6p25.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D38V9.png)
P value = 0.0399 (Wilcoxon-test), Q value = 0.18
Table S129. Gene #39: 'del_6q15' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1065 | 58.6 (13.2) |
DEL PEAK 10(6Q15) MUTATED | 355 | 57.4 (13.2) |
DEL PEAK 10(6Q15) WILD-TYPE | 710 | 59.3 (13.2) |
Figure S129. Get High-res Image Gene #39: 'del_6q15' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D39V2.png)
P value = 0.0335 (Fisher's exact test), Q value = 0.16
Table S130. Gene #39: 'del_6q15' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 507 | 358 | 119 | 77 |
DEL PEAK 10(6Q15) MUTATED | 149 | 130 | 49 | 23 |
DEL PEAK 10(6Q15) WILD-TYPE | 358 | 228 | 70 | 54 |
Figure S130. Get High-res Image Gene #39: 'del_6q15' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D39V5.png)
P value = 0.0204 (Wilcoxon-test), Q value = 0.11
Table S131. Gene #39: 'del_6q15' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 914 | 2.4 (4.7) |
DEL PEAK 10(6Q15) MUTATED | 293 | 2.5 (4.6) |
DEL PEAK 10(6Q15) WILD-TYPE | 621 | 2.3 (4.7) |
Figure S131. Get High-res Image Gene #39: 'del_6q15' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
![](D39V10.png)
P value = 6.42e-06 (Wilcoxon-test), Q value = 0.00023
Table S132. Gene #40: 'del_6q27' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1065 | 58.6 (13.2) |
DEL PEAK 11(6Q27) MUTATED | 371 | 56.0 (12.7) |
DEL PEAK 11(6Q27) WILD-TYPE | 694 | 60.0 (13.3) |
Figure S132. Get High-res Image Gene #40: 'del_6q27' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D40V2.png)
P value = 0.0265 (Fisher's exact test), Q value = 0.13
Table S133. Gene #40: 'del_6q27' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 507 | 358 | 119 | 77 |
DEL PEAK 11(6Q27) MUTATED | 168 | 138 | 46 | 17 |
DEL PEAK 11(6Q27) WILD-TYPE | 339 | 220 | 73 | 60 |
Figure S133. Get High-res Image Gene #40: 'del_6q27' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D40V5.png)
P value = 0.00504 (Fisher's exact test), Q value = 0.038
Table S134. Gene #40: 'del_6q27' versus Clinical Feature #8: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 429 | 518 |
DEL PEAK 11(6Q27) MUTATED | 130 | 203 |
DEL PEAK 11(6Q27) WILD-TYPE | 299 | 315 |
Figure S134. Get High-res Image Gene #40: 'del_6q27' versus Clinical Feature #8: 'RADIATION_THERAPY'
![](D40V8.png)
P value = 0.0521 (Fisher's exact test), Q value = 0.21
Table S135. Gene #41: 'del_7p22.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 507 | 358 | 119 | 77 |
DEL PEAK 12(7P22.3) MUTATED | 76 | 36 | 17 | 5 |
DEL PEAK 12(7P22.3) WILD-TYPE | 431 | 322 | 102 | 72 |
Figure S135. Get High-res Image Gene #41: 'del_7p22.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D41V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S136. Gene #41: 'del_7p22.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 12(7P22.3) MUTATED | 0 | 121 | 4 | 1 | 2 | 4 | 0 | 5 |
DEL PEAK 12(7P22.3) WILD-TYPE | 1 | 649 | 196 | 5 | 7 | 25 | 17 | 42 |
Figure S136. Get High-res Image Gene #41: 'del_7p22.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D41V9.png)
P value = 0.0137 (Wilcoxon-test), Q value = 0.084
Table S137. Gene #41: 'del_7p22.3' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 914 | 2.4 (4.7) |
DEL PEAK 12(7P22.3) MUTATED | 109 | 1.6 (3.5) |
DEL PEAK 12(7P22.3) WILD-TYPE | 805 | 2.5 (4.8) |
Figure S137. Get High-res Image Gene #41: 'del_7p22.3' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
![](D41V10.png)
P value = 5e-05 (Fisher's exact test), Q value = 0.00092
Table S138. Gene #42: 'del_7q36.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 13(7Q36.1) MUTATED | 0 | 166 | 15 | 0 | 2 | 7 | 0 | 10 |
DEL PEAK 13(7Q36.1) WILD-TYPE | 1 | 604 | 185 | 6 | 7 | 22 | 17 | 37 |
Figure S138. Get High-res Image Gene #42: 'del_7q36.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D42V9.png)
P value = 0.0521 (logrank test), Q value = 0.21
Table S139. Gene #43: 'del_8p23.2' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 1064 | 147 | 0.0 - 282.9 (27.9) |
DEL PEAK 14(8P23.2) MUTATED | 553 | 91 | 0.2 - 282.9 (27.2) |
DEL PEAK 14(8P23.2) WILD-TYPE | 511 | 56 | 0.0 - 281.3 (28.2) |
Figure S139. Get High-res Image Gene #43: 'del_8p23.2' versus Clinical Feature #1: 'Time to Death'
![](D43V1.png)
P value = 0.00387 (Fisher's exact test), Q value = 0.031
Table S140. Gene #43: 'del_8p23.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
DEL PEAK 14(8P23.2) MUTATED | 157 | 324 | 52 | 23 |
DEL PEAK 14(8P23.2) WILD-TYPE | 119 | 300 | 84 | 17 |
Figure S140. Get High-res Image Gene #43: 'del_8p23.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D43V4.png)
P value = 0.061 (Fisher's exact test), Q value = 0.23
Table S141. Gene #43: 'del_8p23.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 507 | 358 | 119 | 77 |
DEL PEAK 14(8P23.2) MUTATED | 247 | 186 | 74 | 37 |
DEL PEAK 14(8P23.2) WILD-TYPE | 260 | 172 | 45 | 40 |
Figure S141. Get High-res Image Gene #43: 'del_8p23.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D43V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S142. Gene #43: 'del_8p23.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 14(8P23.2) MUTATED | 1 | 446 | 64 | 3 | 3 | 10 | 4 | 26 |
DEL PEAK 14(8P23.2) WILD-TYPE | 0 | 324 | 136 | 3 | 6 | 19 | 13 | 21 |
Figure S142. Get High-res Image Gene #43: 'del_8p23.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D43V9.png)
P value = 0.00118 (Fisher's exact test), Q value = 0.012
Table S143. Gene #43: 'del_8p23.2' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
DEL PEAK 14(8P23.2) MUTATED | 1 | 41 | 105 | 357 |
DEL PEAK 14(8P23.2) WILD-TYPE | 0 | 19 | 76 | 388 |
Figure S143. Get High-res Image Gene #43: 'del_8p23.2' versus Clinical Feature #11: 'RACE'
![](D43V11.png)
P value = 0.00388 (Fisher's exact test), Q value = 0.031
Table S144. Gene #44: 'del_8p11.21' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 15(8P11.21) MUTATED | 0 | 166 | 20 | 0 | 2 | 5 | 1 | 6 |
DEL PEAK 15(8P11.21) WILD-TYPE | 1 | 604 | 180 | 6 | 7 | 24 | 16 | 41 |
Figure S144. Get High-res Image Gene #44: 'del_8p11.21' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D44V9.png)
P value = 0.0133 (logrank test), Q value = 0.082
Table S145. Gene #45: 'del_9p23' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 1064 | 147 | 0.0 - 282.9 (27.9) |
DEL PEAK 16(9P23) MUTATED | 320 | 50 | 0.0 - 165.8 (24.6) |
DEL PEAK 16(9P23) WILD-TYPE | 744 | 97 | 0.0 - 282.9 (30.0) |
Figure S145. Get High-res Image Gene #45: 'del_9p23' versus Clinical Feature #1: 'Time to Death'
![](D45V1.png)
P value = 0.00558 (Fisher's exact test), Q value = 0.041
Table S146. Gene #45: 'del_9p23' 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 TIS | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 89 | 85 | 6 | 6 | 353 | 252 | 2 | 154 | 29 | 65 | 20 | 1 | 13 |
DEL PEAK 16(9P23) MUTATED | 21 | 19 | 1 | 1 | 98 | 71 | 1 | 62 | 16 | 19 | 10 | 0 | 4 |
DEL PEAK 16(9P23) WILD-TYPE | 68 | 66 | 5 | 5 | 255 | 181 | 1 | 92 | 13 | 46 | 10 | 1 | 9 |
Figure S146. Get High-res Image Gene #45: 'del_9p23' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D45V3.png)
P value = 0.00032 (Fisher's exact test), Q value = 0.0047
Table S147. Gene #45: 'del_9p23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
DEL PEAK 16(9P23) MUTATED | 60 | 207 | 38 | 19 |
DEL PEAK 16(9P23) WILD-TYPE | 216 | 417 | 98 | 21 |
Figure S147. Get High-res Image Gene #45: 'del_9p23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D45V4.png)
P value = 7e-04 (Fisher's exact test), Q value = 0.0082
Table S148. Gene #45: 'del_9p23' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 507 | 358 | 119 | 77 |
DEL PEAK 16(9P23) MUTATED | 137 | 103 | 55 | 24 |
DEL PEAK 16(9P23) WILD-TYPE | 370 | 255 | 64 | 53 |
Figure S148. Get High-res Image Gene #45: 'del_9p23' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D45V5.png)
P value = 0.0641 (Fisher's exact test), Q value = 0.24
Table S149. Gene #45: 'del_9p23' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
nPatients | 0 | 1 |
---|---|---|
ALL | 889 | 22 |
DEL PEAK 16(9P23) MUTATED | 274 | 11 |
DEL PEAK 16(9P23) WILD-TYPE | 615 | 11 |
Figure S149. Get High-res Image Gene #45: 'del_9p23' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
![](D45V6.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S150. Gene #45: 'del_9p23' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 16(9P23) MUTATED | 0 | 269 | 26 | 3 | 5 | 9 | 5 | 8 |
DEL PEAK 16(9P23) WILD-TYPE | 1 | 501 | 174 | 3 | 4 | 20 | 12 | 39 |
Figure S150. Get High-res Image Gene #45: 'del_9p23' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D45V9.png)
P value = 0.0369 (Wilcoxon-test), Q value = 0.17
Table S151. Gene #45: 'del_9p23' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 914 | 2.4 (4.7) |
DEL PEAK 16(9P23) MUTATED | 263 | 2.7 (4.9) |
DEL PEAK 16(9P23) WILD-TYPE | 651 | 2.3 (4.5) |
Figure S151. Get High-res Image Gene #45: 'del_9p23' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
![](D45V10.png)
P value = 0.0172 (Fisher's exact test), Q value = 0.1
Table S152. Gene #46: '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 TIS | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 89 | 85 | 6 | 6 | 353 | 252 | 2 | 154 | 29 | 65 | 20 | 1 | 13 |
DEL PEAK 17(9P21.3) MUTATED | 24 | 22 | 3 | 1 | 114 | 78 | 1 | 64 | 17 | 23 | 10 | 0 | 6 |
DEL PEAK 17(9P21.3) WILD-TYPE | 65 | 63 | 3 | 5 | 239 | 174 | 1 | 90 | 12 | 42 | 10 | 1 | 7 |
Figure S152. Get High-res Image Gene #46: 'del_9p21.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D46V3.png)
P value = 0.00284 (Fisher's exact test), Q value = 0.024
Table S153. Gene #46: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
DEL PEAK 17(9P21.3) MUTATED | 73 | 228 | 42 | 20 |
DEL PEAK 17(9P21.3) WILD-TYPE | 203 | 396 | 94 | 20 |
Figure S153. Get High-res Image Gene #46: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D46V4.png)
P value = 0.00408 (Fisher's exact test), Q value = 0.032
Table S154. Gene #46: 'del_9p21.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 507 | 358 | 119 | 77 |
DEL PEAK 17(9P21.3) MUTATED | 161 | 111 | 57 | 30 |
DEL PEAK 17(9P21.3) WILD-TYPE | 346 | 247 | 62 | 47 |
Figure S154. Get High-res Image Gene #46: 'del_9p21.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D46V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S155. Gene #46: 'del_9p21.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 17(9P21.3) MUTATED | 1 | 302 | 24 | 4 | 6 | 12 | 5 | 10 |
DEL PEAK 17(9P21.3) WILD-TYPE | 0 | 468 | 176 | 2 | 3 | 17 | 12 | 37 |
Figure S155. Get High-res Image Gene #46: 'del_9p21.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D46V9.png)
P value = 0.0624 (Wilcoxon-test), Q value = 0.23
Table S156. Gene #46: 'del_9p21.3' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 914 | 2.4 (4.7) |
DEL PEAK 17(9P21.3) MUTATED | 295 | 2.6 (4.5) |
DEL PEAK 17(9P21.3) WILD-TYPE | 619 | 2.3 (4.8) |
Figure S156. Get High-res Image Gene #46: 'del_9p21.3' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
![](D46V10.png)
P value = 0.0222 (Fisher's exact test), Q value = 0.12
Table S157. Gene #47: 'del_9q21.11' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 1068 | 12 |
DEL PEAK 18(9Q21.11) MUTATED | 287 | 7 |
DEL PEAK 18(9Q21.11) WILD-TYPE | 781 | 5 |
Figure S157. Get High-res Image Gene #47: 'del_9q21.11' versus Clinical Feature #7: 'GENDER'
![](D47V7.png)
P value = 0.0477 (Fisher's exact test), Q value = 0.2
Table S158. Gene #47: 'del_9q21.11' versus Clinical Feature #8: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 429 | 518 |
DEL PEAK 18(9Q21.11) MUTATED | 103 | 155 |
DEL PEAK 18(9Q21.11) WILD-TYPE | 326 | 363 |
Figure S158. Get High-res Image Gene #47: 'del_9q21.11' versus Clinical Feature #8: 'RADIATION_THERAPY'
![](D47V8.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S159. Gene #47: 'del_9q21.11' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 18(9Q21.11) MUTATED | 0 | 245 | 23 | 2 | 4 | 10 | 3 | 7 |
DEL PEAK 18(9Q21.11) WILD-TYPE | 1 | 525 | 177 | 4 | 5 | 19 | 14 | 40 |
Figure S159. Get High-res Image Gene #47: 'del_9q21.11' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D47V9.png)
P value = 0.0197 (Fisher's exact test), Q value = 0.11
Table S160. Gene #48: 'del_9q34.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
DEL PEAK 19(9Q34.2) MUTATED | 60 | 188 | 32 | 15 |
DEL PEAK 19(9Q34.2) WILD-TYPE | 216 | 436 | 104 | 25 |
Figure S160. Get High-res Image Gene #48: 'del_9q34.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D48V4.png)
P value = 0.0669 (Fisher's exact test), Q value = 0.24
Table S161. Gene #48: 'del_9q34.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 507 | 358 | 119 | 77 |
DEL PEAK 19(9Q34.2) MUTATED | 149 | 83 | 41 | 21 |
DEL PEAK 19(9Q34.2) WILD-TYPE | 358 | 275 | 78 | 56 |
Figure S161. Get High-res Image Gene #48: 'del_9q34.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D48V5.png)
P value = 0.00508 (Fisher's exact test), Q value = 0.038
Table S162. Gene #48: 'del_9q34.2' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 1068 | 12 |
DEL PEAK 19(9Q34.2) MUTATED | 289 | 8 |
DEL PEAK 19(9Q34.2) WILD-TYPE | 779 | 4 |
Figure S162. Get High-res Image Gene #48: 'del_9q34.2' versus Clinical Feature #7: 'GENDER'
![](D48V7.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S163. Gene #48: 'del_9q34.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 19(9Q34.2) MUTATED | 0 | 251 | 22 | 4 | 3 | 7 | 3 | 6 |
DEL PEAK 19(9Q34.2) WILD-TYPE | 1 | 519 | 178 | 2 | 6 | 22 | 14 | 41 |
Figure S163. Get High-res Image Gene #48: 'del_9q34.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D48V9.png)
P value = 0.0472 (Fisher's exact test), Q value = 0.2
Table S164. Gene #48: 'del_9q34.2' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
DEL PEAK 19(9Q34.2) MUTATED | 0 | 17 | 63 | 187 |
DEL PEAK 19(9Q34.2) WILD-TYPE | 1 | 43 | 118 | 558 |
Figure S164. Get High-res Image Gene #48: 'del_9q34.2' versus Clinical Feature #11: 'RACE'
![](D48V11.png)
P value = 0.0165 (Fisher's exact test), Q value = 0.097
Table S165. Gene #49: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
DEL PEAK 20(10Q23.31) MUTATED | 70 | 190 | 38 | 20 |
DEL PEAK 20(10Q23.31) WILD-TYPE | 206 | 434 | 98 | 20 |
Figure S165. Get High-res Image Gene #49: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D49V4.png)
P value = 3e-05 (Fisher's exact test), Q value = 0.00061
Table S166. Gene #49: 'del_10q23.31' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 20(10Q23.31) MUTATED | 0 | 246 | 41 | 5 | 7 | 8 | 1 | 11 |
DEL PEAK 20(10Q23.31) WILD-TYPE | 1 | 524 | 159 | 1 | 2 | 21 | 16 | 36 |
Figure S166. Get High-res Image Gene #49: 'del_10q23.31' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D49V9.png)
P value = 0.0486 (Fisher's exact test), Q value = 0.2
Table S167. Gene #49: 'del_10q23.31' versus Clinical Feature #12: 'ETHNICITY'
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 39 | 875 |
DEL PEAK 20(10Q23.31) MUTATED | 6 | 267 |
DEL PEAK 20(10Q23.31) WILD-TYPE | 33 | 608 |
Figure S167. Get High-res Image Gene #49: 'del_10q23.31' versus Clinical Feature #12: 'ETHNICITY'
![](D49V12.png)
P value = 0.0332 (Fisher's exact test), Q value = 0.16
Table S168. Gene #50: 'del_10q26.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
DEL PEAK 21(10Q26.3) MUTATED | 67 | 192 | 40 | 18 |
DEL PEAK 21(10Q26.3) WILD-TYPE | 209 | 432 | 96 | 22 |
Figure S168. Get High-res Image Gene #50: 'del_10q26.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D50V4.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S169. Gene #50: 'del_10q26.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 21(10Q26.3) MUTATED | 0 | 255 | 32 | 5 | 7 | 8 | 2 | 9 |
DEL PEAK 21(10Q26.3) WILD-TYPE | 1 | 515 | 168 | 1 | 2 | 21 | 15 | 38 |
Figure S169. Get High-res Image Gene #50: 'del_10q26.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D50V9.png)
P value = 0.019 (Fisher's exact test), Q value = 0.1
Table S170. Gene #50: 'del_10q26.3' versus Clinical Feature #12: 'ETHNICITY'
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 39 | 875 |
DEL PEAK 21(10Q26.3) MUTATED | 5 | 265 |
DEL PEAK 21(10Q26.3) WILD-TYPE | 34 | 610 |
Figure S170. Get High-res Image Gene #50: 'del_10q26.3' versus Clinical Feature #12: 'ETHNICITY'
![](D50V12.png)
P value = 0.00413 (Fisher's exact test), Q value = 0.032
Table S171. Gene #51: 'del_11p15.5' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
DEL PEAK 22(11P15.5) MUTATED | 60 | 200 | 33 | 15 |
DEL PEAK 22(11P15.5) WILD-TYPE | 216 | 424 | 103 | 25 |
Figure S171. Get High-res Image Gene #51: 'del_11p15.5' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D51V4.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S172. Gene #51: 'del_11p15.5' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 22(11P15.5) MUTATED | 0 | 250 | 30 | 4 | 2 | 12 | 2 | 9 |
DEL PEAK 22(11P15.5) WILD-TYPE | 1 | 520 | 170 | 2 | 7 | 17 | 15 | 38 |
Figure S172. Get High-res Image Gene #51: 'del_11p15.5' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D51V9.png)
P value = 0.0048 (Fisher's exact test), Q value = 0.037
Table S173. Gene #51: 'del_11p15.5' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
DEL PEAK 22(11P15.5) MUTATED | 0 | 19 | 69 | 190 |
DEL PEAK 22(11P15.5) WILD-TYPE | 1 | 41 | 112 | 555 |
Figure S173. Get High-res Image Gene #51: 'del_11p15.5' versus Clinical Feature #11: 'RACE'
![](D51V11.png)
P value = 0.00346 (Fisher's exact test), Q value = 0.028
Table S174. Gene #52: 'del_11q13.1' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
DEL PEAK 23(11Q13.1) MUTATED | 0 | 21 | 50 | 143 |
DEL PEAK 23(11Q13.1) WILD-TYPE | 1 | 39 | 131 | 602 |
Figure S174. Get High-res Image Gene #52: 'del_11q13.1' versus Clinical Feature #11: 'RACE'
![](D52V11.png)
P value = 0.033 (Fisher's exact test), Q value = 0.16
Table S175. Gene #53: 'del_11q23.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
DEL PEAK 24(11Q23.3) MUTATED | 120 | 327 | 77 | 22 |
DEL PEAK 24(11Q23.3) WILD-TYPE | 156 | 297 | 59 | 18 |
Figure S175. Get High-res Image Gene #53: 'del_11q23.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D53V4.png)
P value = 0.0377 (Fisher's exact test), Q value = 0.17
Table S176. Gene #53: 'del_11q23.3' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 1068 | 12 |
DEL PEAK 24(11Q23.3) MUTATED | 537 | 10 |
DEL PEAK 24(11Q23.3) WILD-TYPE | 531 | 2 |
Figure S176. Get High-res Image Gene #53: 'del_11q23.3' versus Clinical Feature #7: 'GENDER'
![](D53V7.png)
P value = 0.0183 (Fisher's exact test), Q value = 0.1
Table S177. Gene #53: 'del_11q23.3' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
DEL PEAK 24(11Q23.3) MUTATED | 1 | 33 | 106 | 353 |
DEL PEAK 24(11Q23.3) WILD-TYPE | 0 | 27 | 75 | 392 |
Figure S177. Get High-res Image Gene #53: 'del_11q23.3' versus Clinical Feature #11: 'RACE'
![](D53V11.png)
P value = 0.0265 (Wilcoxon-test), Q value = 0.13
Table S178. Gene #54: 'del_11q25' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1065 | 58.6 (13.2) |
DEL PEAK 25(11Q25) MUTATED | 506 | 57.6 (13.5) |
DEL PEAK 25(11Q25) WILD-TYPE | 559 | 59.6 (12.9) |
Figure S178. Get High-res Image Gene #54: 'del_11q25' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D54V2.png)
P value = 0.0238 (Fisher's exact test), Q value = 0.12
Table S179. Gene #54: 'del_11q25' 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 TIS | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 89 | 85 | 6 | 6 | 353 | 252 | 2 | 154 | 29 | 65 | 20 | 1 | 13 |
DEL PEAK 25(11Q25) MUTATED | 31 | 33 | 2 | 2 | 162 | 137 | 1 | 86 | 12 | 27 | 10 | 0 | 8 |
DEL PEAK 25(11Q25) WILD-TYPE | 58 | 52 | 4 | 4 | 191 | 115 | 1 | 68 | 17 | 38 | 10 | 1 | 5 |
Figure S179. Get High-res Image Gene #54: 'del_11q25' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D54V3.png)
P value = 0.00246 (Fisher's exact test), Q value = 0.022
Table S180. Gene #54: 'del_11q25' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
DEL PEAK 25(11Q25) MUTATED | 106 | 316 | 73 | 17 |
DEL PEAK 25(11Q25) WILD-TYPE | 170 | 308 | 63 | 23 |
Figure S180. Get High-res Image Gene #54: 'del_11q25' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D54V4.png)
P value = 0.0677 (Fisher's exact test), Q value = 0.24
Table S181. Gene #54: 'del_11q25' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 507 | 358 | 119 | 77 |
DEL PEAK 25(11Q25) MUTATED | 226 | 181 | 65 | 31 |
DEL PEAK 25(11Q25) WILD-TYPE | 281 | 177 | 54 | 46 |
Figure S181. Get High-res Image Gene #54: 'del_11q25' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D54V5.png)
P value = 0.0171 (Fisher's exact test), Q value = 0.1
Table S182. Gene #54: 'del_11q25' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 1068 | 12 |
DEL PEAK 25(11Q25) MUTATED | 503 | 10 |
DEL PEAK 25(11Q25) WILD-TYPE | 565 | 2 |
Figure S182. Get High-res Image Gene #54: 'del_11q25' versus Clinical Feature #7: 'GENDER'
![](D54V7.png)
P value = 0.0111 (Fisher's exact test), Q value = 0.07
Table S183. Gene #54: 'del_11q25' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 25(11Q25) MUTATED | 1 | 377 | 92 | 5 | 4 | 16 | 5 | 12 |
DEL PEAK 25(11Q25) WILD-TYPE | 0 | 393 | 108 | 1 | 5 | 13 | 12 | 35 |
Figure S183. Get High-res Image Gene #54: 'del_11q25' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D54V9.png)
P value = 0.00063 (Fisher's exact test), Q value = 0.0077
Table S184. Gene #54: 'del_11q25' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
DEL PEAK 25(11Q25) MUTATED | 1 | 29 | 107 | 323 |
DEL PEAK 25(11Q25) WILD-TYPE | 0 | 31 | 74 | 422 |
Figure S184. Get High-res Image Gene #54: 'del_11q25' versus Clinical Feature #11: 'RACE'
![](D54V11.png)
P value = 0.00085 (Fisher's exact test), Q value = 0.0097
Table S185. Gene #55: 'del_12p13.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 26(12P13.1) MUTATED | 0 | 157 | 19 | 1 | 3 | 3 | 1 | 3 |
DEL PEAK 26(12P13.1) WILD-TYPE | 1 | 613 | 181 | 5 | 6 | 26 | 16 | 44 |
Figure S185. Get High-res Image Gene #55: 'del_12p13.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D55V9.png)
P value = 0.0316 (Fisher's exact test), Q value = 0.16
Table S186. Gene #56: 'del_12q23.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
DEL PEAK 27(12Q23.1) MUTATED | 37 | 130 | 22 | 10 |
DEL PEAK 27(12Q23.1) WILD-TYPE | 239 | 494 | 114 | 30 |
Figure S186. Get High-res Image Gene #56: 'del_12q23.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D56V4.png)
P value = 0.00099 (Fisher's exact test), Q value = 0.011
Table S187. Gene #56: 'del_12q23.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 27(12Q23.1) MUTATED | 0 | 162 | 21 | 3 | 3 | 4 | 0 | 8 |
DEL PEAK 27(12Q23.1) WILD-TYPE | 1 | 608 | 179 | 3 | 6 | 25 | 17 | 39 |
Figure S187. Get High-res Image Gene #56: 'del_12q23.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D56V9.png)
P value = 0.00626 (Fisher's exact test), Q value = 0.044
Table S188. Gene #56: 'del_12q23.1' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
DEL PEAK 27(12Q23.1) MUTATED | 0 | 13 | 50 | 125 |
DEL PEAK 27(12Q23.1) WILD-TYPE | 1 | 47 | 131 | 620 |
Figure S188. Get High-res Image Gene #56: 'del_12q23.1' versus Clinical Feature #11: 'RACE'
![](D56V11.png)
P value = 0.0442 (Fisher's exact test), Q value = 0.2
Table S189. Gene #57: 'del_12q24.31' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 28(12Q24.31) MUTATED | 0 | 161 | 30 | 3 | 3 | 6 | 0 | 8 |
DEL PEAK 28(12Q24.31) WILD-TYPE | 1 | 609 | 170 | 3 | 6 | 23 | 17 | 39 |
Figure S189. Get High-res Image Gene #57: 'del_12q24.31' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D57V9.png)
P value = 0.0509 (Fisher's exact test), Q value = 0.21
Table S190. Gene #57: 'del_12q24.31' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
DEL PEAK 28(12Q24.31) MUTATED | 0 | 11 | 49 | 136 |
DEL PEAK 28(12Q24.31) WILD-TYPE | 1 | 49 | 132 | 609 |
Figure S190. Get High-res Image Gene #57: 'del_12q24.31' versus Clinical Feature #11: 'RACE'
![](D57V11.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S191. Gene #58: 'del_13q14.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 29(13Q14.2) MUTATED | 0 | 389 | 67 | 5 | 5 | 13 | 2 | 13 |
DEL PEAK 29(13Q14.2) WILD-TYPE | 1 | 381 | 133 | 1 | 4 | 16 | 15 | 34 |
Figure S191. Get High-res Image Gene #58: 'del_13q14.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D58V9.png)
P value = 0.0509 (logrank test), Q value = 0.21
Table S192. Gene #59: 'del_14q24.1' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 1064 | 147 | 0.0 - 282.9 (27.9) |
DEL PEAK 30(14Q24.1) MUTATED | 349 | 60 | 0.0 - 255.7 (28.2) |
DEL PEAK 30(14Q24.1) WILD-TYPE | 715 | 87 | 0.0 - 282.9 (27.0) |
Figure S192. Get High-res Image Gene #59: 'del_14q24.1' versus Clinical Feature #1: 'Time to Death'
![](D59V1.png)
P value = 0.00017 (Fisher's exact test), Q value = 0.0029
Table S193. Gene #59: 'del_14q24.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
DEL PEAK 30(14Q24.1) MUTATED | 66 | 237 | 37 | 11 |
DEL PEAK 30(14Q24.1) WILD-TYPE | 210 | 387 | 99 | 29 |
Figure S193. Get High-res Image Gene #59: 'del_14q24.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D59V4.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S194. Gene #59: 'del_14q24.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 30(14Q24.1) MUTATED | 1 | 296 | 34 | 4 | 4 | 4 | 1 | 8 |
DEL PEAK 30(14Q24.1) WILD-TYPE | 0 | 474 | 166 | 2 | 5 | 25 | 16 | 39 |
Figure S194. Get High-res Image Gene #59: 'del_14q24.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D59V9.png)
P value = 0.00033 (Fisher's exact test), Q value = 0.0047
Table S195. Gene #59: 'del_14q24.1' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
DEL PEAK 30(14Q24.1) MUTATED | 0 | 18 | 83 | 220 |
DEL PEAK 30(14Q24.1) WILD-TYPE | 1 | 42 | 98 | 525 |
Figure S195. Get High-res Image Gene #59: 'del_14q24.1' versus Clinical Feature #11: 'RACE'
![](D59V11.png)
P value = 0.0014 (Fisher's exact test), Q value = 0.014
Table S196. Gene #60: 'del_15q13.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
DEL PEAK 31(15Q13.1) MUTATED | 73 | 246 | 43 | 12 |
DEL PEAK 31(15Q13.1) WILD-TYPE | 203 | 378 | 93 | 28 |
Figure S196. Get High-res Image Gene #60: 'del_15q13.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D60V4.png)
P value = 0.0221 (Fisher's exact test), Q value = 0.12
Table S197. Gene #60: 'del_15q13.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 507 | 358 | 119 | 77 |
DEL PEAK 31(15Q13.1) MUTATED | 193 | 110 | 49 | 20 |
DEL PEAK 31(15Q13.1) WILD-TYPE | 314 | 248 | 70 | 57 |
Figure S197. Get High-res Image Gene #60: 'del_15q13.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D60V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S198. Gene #60: 'del_15q13.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 31(15Q13.1) MUTATED | 1 | 305 | 39 | 4 | 3 | 10 | 1 | 11 |
DEL PEAK 31(15Q13.1) WILD-TYPE | 0 | 465 | 161 | 2 | 6 | 19 | 16 | 36 |
Figure S198. Get High-res Image Gene #60: 'del_15q13.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D60V9.png)
P value = 0.037 (Wilcoxon-test), Q value = 0.17
Table S199. Gene #60: 'del_15q13.1' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 914 | 2.4 (4.7) |
DEL PEAK 31(15Q13.1) MUTATED | 319 | 2.2 (4.8) |
DEL PEAK 31(15Q13.1) WILD-TYPE | 595 | 2.5 (4.6) |
Figure S199. Get High-res Image Gene #60: 'del_15q13.1' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'
![](D60V10.png)
P value = 0.0239 (Fisher's exact test), Q value = 0.12
Table S200. Gene #60: 'del_15q13.1' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
DEL PEAK 31(15Q13.1) MUTATED | 0 | 23 | 79 | 243 |
DEL PEAK 31(15Q13.1) WILD-TYPE | 1 | 37 | 102 | 502 |
Figure S200. Get High-res Image Gene #60: 'del_15q13.1' versus Clinical Feature #11: 'RACE'
![](D60V11.png)
P value = 0.000319 (Wilcoxon-test), Q value = 0.0047
Table S201. Gene #61: 'del_16q24.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1065 | 58.6 (13.2) |
DEL PEAK 32(16Q24.3) MUTATED | 684 | 59.8 (13.0) |
DEL PEAK 32(16Q24.3) WILD-TYPE | 381 | 56.6 (13.3) |
Figure S201. Get High-res Image Gene #61: 'del_16q24.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D61V2.png)
P value = 0.0602 (Fisher's exact test), Q value = 0.23
Table S202. Gene #61: 'del_16q24.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
DEL PEAK 32(16Q24.3) MUTATED | 182 | 392 | 97 | 20 |
DEL PEAK 32(16Q24.3) WILD-TYPE | 94 | 232 | 39 | 20 |
Figure S202. Get High-res Image Gene #61: 'del_16q24.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D61V4.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S203. Gene #61: 'del_16q24.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 32(16Q24.3) MUTATED | 0 | 464 | 180 | 3 | 1 | 21 | 3 | 21 |
DEL PEAK 32(16Q24.3) WILD-TYPE | 1 | 306 | 20 | 3 | 8 | 8 | 14 | 26 |
Figure S203. Get High-res Image Gene #61: 'del_16q24.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D61V9.png)
P value = 0.00765 (Fisher's exact test), Q value = 0.053
Table S204. Gene #61: 'del_16q24.3' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
DEL PEAK 32(16Q24.3) MUTATED | 1 | 34 | 97 | 490 |
DEL PEAK 32(16Q24.3) WILD-TYPE | 0 | 26 | 84 | 255 |
Figure S204. Get High-res Image Gene #61: 'del_16q24.3' versus Clinical Feature #11: 'RACE'
![](D61V11.png)
P value = 0.0024 (Wilcoxon-test), Q value = 0.022
Table S205. Gene #62: 'del_17p12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1065 | 58.6 (13.2) |
DEL PEAK 33(17P12) MUTATED | 640 | 57.7 (13.1) |
DEL PEAK 33(17P12) WILD-TYPE | 425 | 60.1 (13.3) |
Figure S205. Get High-res Image Gene #62: 'del_17p12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D62V2.png)
P value = 0.047 (Fisher's exact test), Q value = 0.2
Table S206. Gene #62: 'del_17p12' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
DEL PEAK 33(17P12) MUTATED | 148 | 395 | 82 | 22 |
DEL PEAK 33(17P12) WILD-TYPE | 128 | 229 | 54 | 18 |
Figure S206. Get High-res Image Gene #62: 'del_17p12' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D62V4.png)
P value = 0.00428 (Fisher's exact test), Q value = 0.033
Table S207. Gene #62: 'del_17p12' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 33(17P12) MUTATED | 0 | 489 | 103 | 5 | 5 | 18 | 6 | 23 |
DEL PEAK 33(17P12) WILD-TYPE | 1 | 281 | 97 | 1 | 4 | 11 | 11 | 24 |
Figure S207. Get High-res Image Gene #62: 'del_17p12' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D62V9.png)
P value = 0.0457 (Fisher's exact test), Q value = 0.2
Table S208. Gene #62: 'del_17p12' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
DEL PEAK 33(17P12) MUTATED | 1 | 44 | 115 | 433 |
DEL PEAK 33(17P12) WILD-TYPE | 0 | 16 | 66 | 312 |
Figure S208. Get High-res Image Gene #62: 'del_17p12' versus Clinical Feature #11: 'RACE'
![](D62V11.png)
P value = 0.000386 (Wilcoxon-test), Q value = 0.0052
Table S209. Gene #63: 'del_17q21.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1065 | 58.6 (13.2) |
DEL PEAK 34(17Q21.31) MUTATED | 363 | 56.8 (13.4) |
DEL PEAK 34(17Q21.31) WILD-TYPE | 702 | 59.6 (13.0) |
Figure S209. Get High-res Image Gene #63: 'del_17q21.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D63V2.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S210. Gene #63: 'del_17q21.31' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 34(17Q21.31) MUTATED | 0 | 297 | 39 | 4 | 5 | 11 | 1 | 13 |
DEL PEAK 34(17Q21.31) WILD-TYPE | 1 | 473 | 161 | 2 | 4 | 18 | 16 | 34 |
Figure S210. Get High-res Image Gene #63: 'del_17q21.31' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D63V9.png)
P value = 5e-05 (Fisher's exact test), Q value = 0.00092
Table S211. Gene #63: 'del_17q21.31' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
DEL PEAK 34(17Q21.31) MUTATED | 0 | 34 | 75 | 233 |
DEL PEAK 34(17Q21.31) WILD-TYPE | 1 | 26 | 106 | 512 |
Figure S211. Get High-res Image Gene #63: 'del_17q21.31' versus Clinical Feature #11: 'RACE'
![](D63V11.png)
P value = 0.0662 (Fisher's exact test), Q value = 0.24
Table S212. Gene #64: 'del_18q23' 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 TIS | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 89 | 85 | 6 | 6 | 353 | 252 | 2 | 154 | 29 | 65 | 20 | 1 | 13 |
DEL PEAK 35(18Q23) MUTATED | 23 | 29 | 0 | 0 | 113 | 77 | 0 | 56 | 15 | 29 | 6 | 0 | 3 |
DEL PEAK 35(18Q23) WILD-TYPE | 66 | 56 | 6 | 6 | 240 | 175 | 2 | 98 | 14 | 36 | 14 | 1 | 10 |
Figure S212. Get High-res Image Gene #64: 'del_18q23' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D64V3.png)
P value = 0.0178 (Fisher's exact test), Q value = 0.1
Table S213. Gene #64: 'del_18q23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
DEL PEAK 35(18Q23) MUTATED | 75 | 215 | 43 | 20 |
DEL PEAK 35(18Q23) WILD-TYPE | 201 | 409 | 93 | 20 |
Figure S213. Get High-res Image Gene #64: 'del_18q23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D64V4.png)
P value = 0.0578 (Fisher's exact test), Q value = 0.23
Table S214. Gene #64: 'del_18q23' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 507 | 358 | 119 | 77 |
DEL PEAK 35(18Q23) MUTATED | 160 | 107 | 49 | 31 |
DEL PEAK 35(18Q23) WILD-TYPE | 347 | 251 | 70 | 46 |
Figure S214. Get High-res Image Gene #64: 'del_18q23' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D64V5.png)
P value = 0.00021 (Fisher's exact test), Q value = 0.0033
Table S215. Gene #64: 'del_18q23' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 35(18Q23) MUTATED | 1 | 274 | 54 | 3 | 5 | 8 | 0 | 8 |
DEL PEAK 35(18Q23) WILD-TYPE | 0 | 496 | 146 | 3 | 4 | 21 | 17 | 39 |
Figure S215. Get High-res Image Gene #64: 'del_18q23' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D64V9.png)
P value = 0.00162 (Wilcoxon-test), Q value = 0.016
Table S216. Gene #65: 'del_19p13.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1065 | 58.6 (13.2) |
DEL PEAK 36(19P13.3) MUTATED | 355 | 56.9 (13.6) |
DEL PEAK 36(19P13.3) WILD-TYPE | 710 | 59.5 (12.9) |
Figure S216. Get High-res Image Gene #65: 'del_19p13.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D65V2.png)
P value = 0.0473 (Fisher's exact test), Q value = 0.2
Table S217. Gene #65: 'del_19p13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
DEL PEAK 36(19P13.3) MUTATED | 81 | 230 | 37 | 15 |
DEL PEAK 36(19P13.3) WILD-TYPE | 195 | 394 | 99 | 25 |
Figure S217. Get High-res Image Gene #65: 'del_19p13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D65V4.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S218. Gene #65: 'del_19p13.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 36(19P13.3) MUTATED | 1 | 302 | 24 | 5 | 4 | 9 | 5 | 12 |
DEL PEAK 36(19P13.3) WILD-TYPE | 0 | 468 | 176 | 1 | 5 | 20 | 12 | 35 |
Figure S218. Get High-res Image Gene #65: 'del_19p13.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D65V9.png)
P value = 0.00021 (Fisher's exact test), Q value = 0.0033
Table S219. Gene #65: 'del_19p13.3' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 60 | 181 | 745 |
DEL PEAK 36(19P13.3) MUTATED | 0 | 28 | 79 | 223 |
DEL PEAK 36(19P13.3) WILD-TYPE | 1 | 32 | 102 | 522 |
Figure S219. Get High-res Image Gene #65: 'del_19p13.3' versus Clinical Feature #11: 'RACE'
![](D65V11.png)
P value = 0.0664 (Fisher's exact test), Q value = 0.24
Table S220. Gene #66: 'del_19q13.32' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 507 | 358 | 119 | 77 |
DEL PEAK 37(19Q13.32) MUTATED | 98 | 70 | 35 | 12 |
DEL PEAK 37(19Q13.32) WILD-TYPE | 409 | 288 | 84 | 65 |
Figure S220. Get High-res Image Gene #66: 'del_19q13.32' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D66V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00023
Table S221. Gene #66: 'del_19q13.32' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 37(19Q13.32) MUTATED | 0 | 185 | 10 | 3 | 1 | 6 | 4 | 6 |
DEL PEAK 37(19Q13.32) WILD-TYPE | 1 | 585 | 190 | 3 | 8 | 23 | 13 | 41 |
Figure S221. Get High-res Image Gene #66: 'del_19q13.32' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D66V9.png)
P value = 0.0472 (Wilcoxon-test), Q value = 0.2
Table S222. Gene #67: 'del_20p13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1065 | 58.6 (13.2) |
DEL PEAK 38(20P13) MUTATED | 157 | 56.7 (12.2) |
DEL PEAK 38(20P13) WILD-TYPE | 908 | 59.0 (13.3) |
Figure S222. Get High-res Image Gene #67: 'del_20p13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D67V2.png)
P value = 4e-05 (Fisher's exact test), Q value = 0.00077
Table S223. Gene #67: 'del_20p13' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 38(20P13) MUTATED | 1 | 137 | 11 | 2 | 0 | 2 | 1 | 6 |
DEL PEAK 38(20P13) WILD-TYPE | 0 | 633 | 189 | 4 | 9 | 27 | 16 | 41 |
Figure S223. Get High-res Image Gene #67: 'del_20p13' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D67V9.png)
P value = 0.00928 (Fisher's exact test), Q value = 0.062
Table S224. Gene #68: 'del_21q11.2' 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 TIS | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 89 | 85 | 6 | 6 | 353 | 252 | 2 | 154 | 29 | 65 | 20 | 1 | 13 |
DEL PEAK 39(21Q11.2) MUTATED | 12 | 12 | 0 | 1 | 66 | 54 | 1 | 39 | 12 | 9 | 7 | 1 | 3 |
DEL PEAK 39(21Q11.2) WILD-TYPE | 77 | 73 | 6 | 5 | 287 | 198 | 1 | 115 | 17 | 56 | 13 | 0 | 10 |
Figure S224. Get High-res Image Gene #68: 'del_21q11.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
![](D68V3.png)
P value = 0.00997 (Fisher's exact test), Q value = 0.065
Table S225. Gene #68: 'del_21q11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 276 | 624 | 136 | 40 |
DEL PEAK 39(21Q11.2) MUTATED | 41 | 139 | 23 | 13 |
DEL PEAK 39(21Q11.2) WILD-TYPE | 235 | 485 | 113 | 27 |
Figure S225. Get High-res Image Gene #68: 'del_21q11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D68V4.png)
P value = 0.0139 (Fisher's exact test), Q value = 0.085
Table S226. Gene #68: 'del_21q11.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 507 | 358 | 119 | 77 |
DEL PEAK 39(21Q11.2) MUTATED | 90 | 74 | 37 | 13 |
DEL PEAK 39(21Q11.2) WILD-TYPE | 417 | 284 | 82 | 64 |
Figure S226. Get High-res Image Gene #68: 'del_21q11.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D68V5.png)
P value = 0.00086 (Fisher's exact test), Q value = 0.0097
Table S227. Gene #68: 'del_21q11.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 39(21Q11.2) MUTATED | 0 | 176 | 21 | 2 | 2 | 9 | 2 | 5 |
DEL PEAK 39(21Q11.2) WILD-TYPE | 1 | 594 | 179 | 4 | 7 | 20 | 15 | 42 |
Figure S227. Get High-res Image Gene #68: 'del_21q11.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D68V9.png)
P value = 0.0362 (Fisher's exact test), Q value = 0.17
Table S228. Gene #69: 'del_22q13.32' versus Clinical Feature #8: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 429 | 518 |
DEL PEAK 40(22Q13.32) MUTATED | 183 | 257 |
DEL PEAK 40(22Q13.32) WILD-TYPE | 246 | 261 |
Figure S228. Get High-res Image Gene #69: 'del_22q13.32' versus Clinical Feature #8: 'RADIATION_THERAPY'
![](D69V8.png)
P value = 0.00034 (Fisher's exact test), Q value = 0.0047
Table S229. Gene #69: 'del_22q13.32' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 770 | 200 | 6 | 9 | 29 | 17 | 47 |
DEL PEAK 40(22Q13.32) MUTATED | 1 | 361 | 90 | 3 | 3 | 19 | 1 | 13 |
DEL PEAK 40(22Q13.32) WILD-TYPE | 0 | 409 | 110 | 3 | 6 | 10 | 16 | 34 |
Figure S229. Get High-res Image Gene #69: 'del_22q13.32' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D69V9.png)
-
Copy number data file = all_lesions.txt from GISTIC pipeline
-
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BRCA-TP/19785968/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BRCA-TP/19775058/BRCA-TP.merged_data.txt
-
Number of patients = 1080
-
Number of significantly focal cnvs = 69
-
Number of selected clinical features = 12
-
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.