This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.
Testing the association between copy number variation 71 focal events and 14 molecular subtypes across 579 patients, 76 significant findings detected with P value < 0.05 and Q value < 0.25.
-
amp_1p34.3 cnv correlated to 'CN_CNMF'.
-
amp_1q21.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
-
amp_1q42.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
-
amp_2p23.2 cnv correlated to 'CN_CNMF'.
-
amp_2q31.2 cnv correlated to 'CN_CNMF'.
-
amp_3q26.2 cnv correlated to 'CN_CNMF'.
-
amp_4q13.3 cnv correlated to 'CN_CNMF'.
-
amp_5p15.33 cnv correlated to 'CN_CNMF'.
-
amp_6p22.3 cnv correlated to 'CN_CNMF'.
-
amp_7q36.3 cnv correlated to 'CN_CNMF'.
-
amp_8p11.21 cnv correlated to 'CN_CNMF'.
-
amp_8q24.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'MRNASEQ_CNMF'.
-
amp_10p15.3 cnv correlated to 'CN_CNMF'.
-
amp_11q14.1 cnv correlated to 'CN_CNMF'.
-
amp_12p13.33 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
-
amp_12p12.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
-
amp_12q15 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
-
amp_14q32.33 cnv correlated to 'CN_CNMF'.
-
amp_15q26.3 cnv correlated to 'CN_CNMF'.
-
amp_18q11.2 cnv correlated to 'CN_CNMF'.
-
amp_19p13.12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.
-
amp_19q12 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
-
amp_19q13.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
-
amp_20p13 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
-
amp_20q11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
-
amp_20q13.33 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
-
amp_xp11.23 cnv correlated to 'CN_CNMF'.
-
del_1p36.11 cnv correlated to 'CN_CNMF'.
-
del_1q41 cnv correlated to 'CN_CNMF'.
-
del_2q37.3 cnv correlated to 'CN_CNMF'.
-
del_3p26.2 cnv correlated to 'CN_CNMF'.
-
del_5q12.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
-
del_5q13.2 cnv correlated to 'CN_CNMF'.
-
del_6q27 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
-
del_7p22.1 cnv correlated to 'CN_CNMF'.
-
del_8p23.3 cnv correlated to 'CN_CNMF'.
-
del_8p21.2 cnv correlated to 'CN_CNMF'.
-
del_9p24.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', and 'METHLYATION_CNMF'.
-
del_9q34.13 cnv correlated to 'CN_CNMF'.
-
del_10q24.2 cnv correlated to 'CN_CNMF'.
-
del_11p15.5 cnv correlated to 'CN_CNMF'.
-
del_12q24.33 cnv correlated to 'CN_CNMF'.
-
del_13q14.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
-
del_14q23.3 cnv correlated to 'CN_CNMF'.
-
del_15q11.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
-
del_15q15.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
-
del_16q23.1 cnv correlated to 'CN_CNMF'.
-
del_19q13.33 cnv correlated to 'MRNA_CNMF'.
-
del_19q13.43 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 71 focal events and 14 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 76 significant findings detected.
Clinical Features |
MRNA CNMF |
MRNA CHIERARCHICAL |
MIR CNMF |
MIR CHIERARCHICAL |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
||
nCNV (%) | nWild-Type | 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 | 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 | |
amp 19p13 12 | 315 (54%) | 264 |
0.00019 (0.175) |
0.00025 (0.228) |
0.0371 (1.00) |
0.251 (1.00) |
1e-05 (0.00986) |
1e-05 (0.00986) |
0.00035 (0.318) |
0.0001 (0.0924) |
0.24 (1.00) |
0.465 (1.00) |
0.586 (1.00) |
0.0985 (1.00) |
1 (1.00) |
0.481 (1.00) |
amp 8q24 21 | 461 (80%) | 118 |
1e-05 (0.00986) |
1e-05 (0.00986) |
0.247 (1.00) |
0.00262 (1.00) |
1e-05 (0.00986) |
0.00443 (1.00) |
0.987 (1.00) |
0.325 (1.00) |
1e-05 (0.00986) |
0.00029 (0.264) |
0.161 (1.00) |
0.0976 (1.00) |
0.571 (1.00) |
0.571 (1.00) |
amp 20q11 21 | 348 (60%) | 231 |
0.00271 (1.00) |
0.00303 (1.00) |
0.112 (1.00) |
0.00296 (1.00) |
1e-05 (0.00986) |
1e-05 (0.00986) |
0.13 (1.00) |
0.0193 (1.00) |
0.00019 (0.175) |
0.0474 (1.00) |
0.292 (1.00) |
0.00054 (0.488) |
1 (1.00) |
0.335 (1.00) |
del 6q27 | 380 (66%) | 199 |
0.323 (1.00) |
0.0612 (1.00) |
0.271 (1.00) |
0.103 (1.00) |
1e-05 (0.00986) |
4e-05 (0.0373) |
0.62 (1.00) |
0.56 (1.00) |
2e-05 (0.0188) |
0.0016 (1.00) |
0.561 (1.00) |
0.026 (1.00) |
0.691 (1.00) |
0.436 (1.00) |
del 9p24 3 | 261 (45%) | 318 |
0.00026 (0.237) |
1e-05 (0.00986) |
0.623 (1.00) |
0.0132 (1.00) |
0.0615 (1.00) |
7e-05 (0.065) |
0.321 (1.00) |
0.955 (1.00) |
0.0726 (1.00) |
0.0516 (1.00) |
0.0886 (1.00) |
0.126 (1.00) |
1 (1.00) |
0.514 (1.00) |
amp 1q21 3 | 367 (63%) | 212 |
0.269 (1.00) |
0.163 (1.00) |
0.64 (1.00) |
0.399 (1.00) |
1e-05 (0.00986) |
0.00022 (0.202) |
0.0767 (1.00) |
0.0711 (1.00) |
0.657 (1.00) |
0.371 (1.00) |
0.841 (1.00) |
0.00628 (1.00) |
0.652 (1.00) |
0.695 (1.00) |
amp 1q42 2 | 322 (56%) | 257 |
0.0234 (1.00) |
0.0274 (1.00) |
0.884 (1.00) |
0.00779 (1.00) |
1e-05 (0.00986) |
9e-05 (0.0834) |
0.257 (1.00) |
0.124 (1.00) |
0.506 (1.00) |
0.319 (1.00) |
0.265 (1.00) |
0.00297 (1.00) |
1 (1.00) |
0.51 (1.00) |
amp 12p13 33 | 330 (57%) | 249 |
0.0229 (1.00) |
0.00345 (1.00) |
0.263 (1.00) |
0.0548 (1.00) |
1e-05 (0.00986) |
0.00014 (0.129) |
0.196 (1.00) |
0.151 (1.00) |
0.0146 (1.00) |
0.0311 (1.00) |
0.535 (1.00) |
0.00771 (1.00) |
0.378 (1.00) |
0.529 (1.00) |
amp 12p12 1 | 313 (54%) | 266 |
0.127 (1.00) |
0.306 (1.00) |
0.9 (1.00) |
0.0412 (1.00) |
1e-05 (0.00986) |
3e-05 (0.0281) |
0.615 (1.00) |
0.0905 (1.00) |
0.0117 (1.00) |
0.301 (1.00) |
0.442 (1.00) |
0.00492 (1.00) |
0.391 (1.00) |
0.0414 (1.00) |
amp 12q15 | 222 (38%) | 357 |
0.0028 (1.00) |
0.242 (1.00) |
0.574 (1.00) |
0.0023 (1.00) |
1e-05 (0.00986) |
1e-05 (0.00986) |
0.0731 (1.00) |
0.249 (1.00) |
0.00141 (1.00) |
0.0714 (1.00) |
0.968 (1.00) |
0.101 (1.00) |
0.231 (1.00) |
0.269 (1.00) |
amp 19q12 | 322 (56%) | 257 |
0.125 (1.00) |
0.00619 (1.00) |
0.0295 (1.00) |
0.513 (1.00) |
1e-05 (0.00986) |
1e-05 (0.00986) |
0.0471 (1.00) |
0.213 (1.00) |
0.552 (1.00) |
0.375 (1.00) |
0.346 (1.00) |
0.06 (1.00) |
1 (1.00) |
0.782 (1.00) |
amp 19q13 2 | 245 (42%) | 334 |
0.945 (1.00) |
0.537 (1.00) |
0.665 (1.00) |
0.39 (1.00) |
1e-05 (0.00986) |
0.00011 (0.102) |
0.447 (1.00) |
0.146 (1.00) |
0.382 (1.00) |
0.0869 (1.00) |
0.977 (1.00) |
0.552 (1.00) |
0.675 (1.00) |
0.612 (1.00) |
amp 20p13 | 317 (55%) | 262 |
0.188 (1.00) |
0.00571 (1.00) |
0.207 (1.00) |
0.0332 (1.00) |
1e-05 (0.00986) |
1e-05 (0.00986) |
0.321 (1.00) |
0.573 (1.00) |
0.0165 (1.00) |
0.348 (1.00) |
0.248 (1.00) |
0.00082 (0.736) |
1 (1.00) |
0.936 (1.00) |
amp 20q13 33 | 402 (69%) | 177 |
0.0107 (1.00) |
0.00088 (0.789) |
0.683 (1.00) |
0.00125 (1.00) |
1e-05 (0.00986) |
1e-05 (0.00986) |
0.851 (1.00) |
0.279 (1.00) |
0.00841 (1.00) |
0.00475 (1.00) |
0.477 (1.00) |
0.0491 (1.00) |
0.624 (1.00) |
0.0139 (1.00) |
del 5q12 1 | 355 (61%) | 224 |
0.883 (1.00) |
0.874 (1.00) |
0.577 (1.00) |
0.0558 (1.00) |
1e-05 (0.00986) |
0.0002 (0.183) |
0.685 (1.00) |
0.863 (1.00) |
0.295 (1.00) |
0.0541 (1.00) |
0.162 (1.00) |
0.253 (1.00) |
1 (1.00) |
0.263 (1.00) |
del 13q14 2 | 364 (63%) | 215 |
0.0105 (1.00) |
0.0155 (1.00) |
0.613 (1.00) |
0.0429 (1.00) |
0.00024 (0.219) |
1e-05 (0.00986) |
0.00219 (1.00) |
0.052 (1.00) |
0.0991 (1.00) |
0.677 (1.00) |
0.377 (1.00) |
0.367 (1.00) |
0.675 (1.00) |
0.249 (1.00) |
del 15q11 2 | 299 (52%) | 280 |
0.00546 (1.00) |
0.0354 (1.00) |
0.0106 (1.00) |
0.0062 (1.00) |
1e-05 (0.00986) |
3e-05 (0.0281) |
0.468 (1.00) |
0.766 (1.00) |
0.00509 (1.00) |
0.159 (1.00) |
0.0258 (1.00) |
0.00973 (1.00) |
1 (1.00) |
0.372 (1.00) |
del 15q15 1 | 363 (63%) | 216 |
0.0259 (1.00) |
0.0596 (1.00) |
0.0211 (1.00) |
0.00285 (1.00) |
1e-05 (0.00986) |
1e-05 (0.00986) |
0.156 (1.00) |
0.152 (1.00) |
0.0115 (1.00) |
0.5 (1.00) |
0.395 (1.00) |
0.00184 (1.00) |
0.204 (1.00) |
0.144 (1.00) |
del 19q13 43 | 285 (49%) | 294 |
0.0167 (1.00) |
0.0817 (1.00) |
0.0799 (1.00) |
0.386 (1.00) |
0.00011 (0.102) |
5e-05 (0.0466) |
0.161 (1.00) |
0.488 (1.00) |
0.564 (1.00) |
0.985 (1.00) |
0.518 (1.00) |
0.121 (1.00) |
0.0427 (1.00) |
0.0214 (1.00) |
amp 1p34 3 | 292 (50%) | 287 |
0.431 (1.00) |
0.0813 (1.00) |
0.125 (1.00) |
0.0851 (1.00) |
1e-05 (0.00986) |
0.195 (1.00) |
0.112 (1.00) |
0.388 (1.00) |
0.555 (1.00) |
0.184 (1.00) |
0.0882 (1.00) |
0.163 (1.00) |
0.0743 (1.00) |
0.927 (1.00) |
amp 2p23 2 | 252 (44%) | 327 |
0.326 (1.00) |
0.0135 (1.00) |
0.759 (1.00) |
0.171 (1.00) |
1e-05 (0.00986) |
0.00441 (1.00) |
0.145 (1.00) |
0.213 (1.00) |
0.0317 (1.00) |
0.0202 (1.00) |
0.92 (1.00) |
0.202 (1.00) |
1 (1.00) |
0.671 (1.00) |
amp 2q31 2 | 262 (45%) | 317 |
0.114 (1.00) |
0.173 (1.00) |
0.0341 (1.00) |
0.0298 (1.00) |
1e-05 (0.00986) |
0.00754 (1.00) |
0.0491 (1.00) |
0.321 (1.00) |
0.151 (1.00) |
0.271 (1.00) |
0.286 (1.00) |
0.0869 (1.00) |
0.67 (1.00) |
0.888 (1.00) |
amp 3q26 2 | 485 (84%) | 94 |
0.00906 (1.00) |
0.0255 (1.00) |
0.818 (1.00) |
0.28 (1.00) |
1e-05 (0.00986) |
0.0356 (1.00) |
0.405 (1.00) |
0.28 (1.00) |
0.00703 (1.00) |
0.0114 (1.00) |
0.125 (1.00) |
0.0679 (1.00) |
1 (1.00) |
0.578 (1.00) |
amp 4q13 3 | 113 (20%) | 466 |
0.905 (1.00) |
0.465 (1.00) |
0.387 (1.00) |
0.986 (1.00) |
0.00025 (0.228) |
0.522 (1.00) |
0.617 (1.00) |
0.539 (1.00) |
0.182 (1.00) |
0.484 (1.00) |
0.966 (1.00) |
0.693 (1.00) |
0.323 (1.00) |
0.696 (1.00) |
amp 5p15 33 | 309 (53%) | 270 |
1 (1.00) |
0.0553 (1.00) |
0.626 (1.00) |
0.25 (1.00) |
1e-05 (0.00986) |
0.0972 (1.00) |
0.981 (1.00) |
0.237 (1.00) |
0.243 (1.00) |
0.391 (1.00) |
0.0245 (1.00) |
0.148 (1.00) |
0.231 (1.00) |
0.268 (1.00) |
amp 6p22 3 | 306 (53%) | 273 |
0.176 (1.00) |
0.0301 (1.00) |
0.275 (1.00) |
0.0728 (1.00) |
1e-05 (0.00986) |
0.012 (1.00) |
0.0736 (1.00) |
0.0566 (1.00) |
0.867 (1.00) |
0.213 (1.00) |
0.378 (1.00) |
0.614 (1.00) |
1 (1.00) |
0.254 (1.00) |
amp 7q36 3 | 320 (55%) | 259 |
0.106 (1.00) |
0.178 (1.00) |
0.36 (1.00) |
0.989 (1.00) |
3e-05 (0.0281) |
0.455 (1.00) |
0.0319 (1.00) |
0.201 (1.00) |
0.845 (1.00) |
0.97 (1.00) |
0.211 (1.00) |
0.502 (1.00) |
0.198 (1.00) |
0.263 (1.00) |
amp 8p11 21 | 211 (36%) | 368 |
0.11 (1.00) |
0.352 (1.00) |
0.102 (1.00) |
0.533 (1.00) |
1e-05 (0.00986) |
0.0161 (1.00) |
0.011 (1.00) |
0.42 (1.00) |
0.279 (1.00) |
0.172 (1.00) |
0.769 (1.00) |
0.326 (1.00) |
0.231 (1.00) |
0.858 (1.00) |
amp 10p15 3 | 252 (44%) | 327 |
0.823 (1.00) |
0.102 (1.00) |
0.0536 (1.00) |
0.165 (1.00) |
1e-05 (0.00986) |
0.00043 (0.39) |
0.488 (1.00) |
0.501 (1.00) |
0.242 (1.00) |
0.121 (1.00) |
0.378 (1.00) |
0.0675 (1.00) |
1 (1.00) |
0.608 (1.00) |
amp 11q14 1 | 257 (44%) | 322 |
0.00528 (1.00) |
0.00385 (1.00) |
0.773 (1.00) |
0.31 (1.00) |
1e-05 (0.00986) |
0.00263 (1.00) |
0.38 (1.00) |
0.228 (1.00) |
0.00457 (1.00) |
0.0268 (1.00) |
0.131 (1.00) |
0.923 (1.00) |
0.0427 (1.00) |
0.435 (1.00) |
amp 14q32 33 | 156 (27%) | 423 |
0.437 (1.00) |
0.653 (1.00) |
0.198 (1.00) |
0.0172 (1.00) |
5e-05 (0.0466) |
0.289 (1.00) |
1 (1.00) |
0.203 (1.00) |
0.166 (1.00) |
0.241 (1.00) |
0.373 (1.00) |
0.423 (1.00) |
0.0964 (1.00) |
0.139 (1.00) |
amp 15q26 3 | 163 (28%) | 416 |
0.084 (1.00) |
0.426 (1.00) |
0.507 (1.00) |
0.426 (1.00) |
1e-05 (0.00986) |
0.805 (1.00) |
0.978 (1.00) |
0.18 (1.00) |
0.203 (1.00) |
0.548 (1.00) |
0.155 (1.00) |
0.0648 (1.00) |
0.675 (1.00) |
0.785 (1.00) |
amp 18q11 2 | 143 (25%) | 436 |
0.823 (1.00) |
0.782 (1.00) |
0.953 (1.00) |
0.222 (1.00) |
1e-05 (0.00986) |
0.00386 (1.00) |
0.156 (1.00) |
0.42 (1.00) |
0.0422 (1.00) |
0.0761 (1.00) |
0.148 (1.00) |
0.511 (1.00) |
0.381 (1.00) |
0.093 (1.00) |
amp xp11 23 | 159 (27%) | 420 |
0.664 (1.00) |
0.867 (1.00) |
0.418 (1.00) |
0.632 (1.00) |
1e-05 (0.00986) |
0.00169 (1.00) |
0.718 (1.00) |
0.902 (1.00) |
0.448 (1.00) |
0.929 (1.00) |
0.277 (1.00) |
0.0318 (1.00) |
0.675 (1.00) |
0.634 (1.00) |
del 1p36 11 | 269 (46%) | 310 |
0.738 (1.00) |
0.0687 (1.00) |
0.0294 (1.00) |
0.117 (1.00) |
6e-05 (0.0558) |
0.0889 (1.00) |
0.125 (1.00) |
0.392 (1.00) |
0.852 (1.00) |
0.42 (1.00) |
0.22 (1.00) |
0.171 (1.00) |
0.675 (1.00) |
0.978 (1.00) |
del 1q41 | 97 (17%) | 482 |
0.0884 (1.00) |
0.625 (1.00) |
0.299 (1.00) |
0.837 (1.00) |
1e-05 (0.00986) |
0.135 (1.00) |
0.487 (1.00) |
0.0179 (1.00) |
0.282 (1.00) |
0.246 (1.00) |
0.921 (1.00) |
0.97 (1.00) |
0.455 (1.00) |
|
del 2q37 3 | 175 (30%) | 404 |
0.0159 (1.00) |
0.464 (1.00) |
0.635 (1.00) |
0.0269 (1.00) |
2e-05 (0.0188) |
0.0882 (1.00) |
0.748 (1.00) |
0.588 (1.00) |
0.014 (1.00) |
0.00236 (1.00) |
0.0229 (1.00) |
0.0192 (1.00) |
0.323 (1.00) |
0.966 (1.00) |
del 3p26 2 | 209 (36%) | 370 |
0.156 (1.00) |
0.00057 (0.515) |
0.00582 (1.00) |
0.00437 (1.00) |
9e-05 (0.0834) |
0.00057 (0.515) |
0.97 (1.00) |
0.24 (1.00) |
0.00293 (1.00) |
0.00982 (1.00) |
0.63 (1.00) |
0.123 (1.00) |
0.415 (1.00) |
0.94 (1.00) |
del 5q13 2 | 419 (72%) | 160 |
0.747 (1.00) |
0.623 (1.00) |
0.9 (1.00) |
0.257 (1.00) |
1e-05 (0.00986) |
0.104 (1.00) |
0.791 (1.00) |
0.831 (1.00) |
0.517 (1.00) |
0.0924 (1.00) |
0.155 (1.00) |
0.107 (1.00) |
1 (1.00) |
0.723 (1.00) |
del 7p22 1 | 253 (44%) | 326 |
0.394 (1.00) |
0.514 (1.00) |
0.771 (1.00) |
0.0614 (1.00) |
1e-05 (0.00986) |
0.626 (1.00) |
0.818 (1.00) |
0.602 (1.00) |
0.347 (1.00) |
0.127 (1.00) |
0.349 (1.00) |
0.905 (1.00) |
0.231 (1.00) |
0.784 (1.00) |
del 8p23 3 | 388 (67%) | 191 |
0.0448 (1.00) |
0.152 (1.00) |
0.572 (1.00) |
0.0115 (1.00) |
1e-05 (0.00986) |
0.0515 (1.00) |
0.892 (1.00) |
0.449 (1.00) |
0.895 (1.00) |
0.912 (1.00) |
0.247 (1.00) |
0.249 (1.00) |
1 (1.00) |
|
del 8p21 2 | 406 (70%) | 173 |
0.0425 (1.00) |
0.0919 (1.00) |
0.183 (1.00) |
0.00522 (1.00) |
1e-05 (0.00986) |
0.147 (1.00) |
0.875 (1.00) |
0.994 (1.00) |
0.458 (1.00) |
0.701 (1.00) |
0.58 (1.00) |
0.518 (1.00) |
1 (1.00) |
|
del 9q34 13 | 342 (59%) | 237 |
0.017 (1.00) |
0.00089 (0.797) |
0.698 (1.00) |
0.41 (1.00) |
1e-05 (0.00986) |
0.0183 (1.00) |
0.675 (1.00) |
0.163 (1.00) |
0.0774 (1.00) |
0.0806 (1.00) |
0.0503 (1.00) |
0.1 (1.00) |
1 (1.00) |
0.793 (1.00) |
del 10q24 2 | 251 (43%) | 328 |
0.00318 (1.00) |
0.00276 (1.00) |
0.0073 (1.00) |
0.236 (1.00) |
9e-05 (0.0834) |
0.00196 (1.00) |
0.0162 (1.00) |
0.00243 (1.00) |
0.532 (1.00) |
0.365 (1.00) |
0.00187 (1.00) |
0.368 (1.00) |
1 (1.00) |
0.784 (1.00) |
del 11p15 5 | 346 (60%) | 233 |
0.111 (1.00) |
0.971 (1.00) |
0.619 (1.00) |
0.0855 (1.00) |
1e-05 (0.00986) |
0.00758 (1.00) |
0.946 (1.00) |
0.711 (1.00) |
0.7 (1.00) |
0.506 (1.00) |
0.106 (1.00) |
0.00864 (1.00) |
0.204 (1.00) |
0.927 (1.00) |
del 12q24 33 | 220 (38%) | 359 |
0.00112 (1.00) |
0.0992 (1.00) |
0.163 (1.00) |
0.0146 (1.00) |
1e-05 (0.00986) |
0.0198 (1.00) |
0.292 (1.00) |
0.224 (1.00) |
0.0503 (1.00) |
0.0321 (1.00) |
0.0155 (1.00) |
0.00464 (1.00) |
0.646 (1.00) |
1 (1.00) |
del 14q23 3 | 305 (53%) | 274 |
0.0656 (1.00) |
0.506 (1.00) |
0.651 (1.00) |
0.609 (1.00) |
6e-05 (0.0558) |
0.737 (1.00) |
0.23 (1.00) |
0.508 (1.00) |
0.856 (1.00) |
0.282 (1.00) |
0.9 (1.00) |
0.595 (1.00) |
0.666 (1.00) |
0.14 (1.00) |
del 16q23 1 | 452 (78%) | 127 |
0.108 (1.00) |
0.243 (1.00) |
0.103 (1.00) |
0.0606 (1.00) |
0.00015 (0.138) |
0.538 (1.00) |
0.812 (1.00) |
0.227 (1.00) |
0.274 (1.00) |
0.169 (1.00) |
0.0568 (1.00) |
0.0484 (1.00) |
1 (1.00) |
0.902 (1.00) |
del 19q13 33 | 299 (52%) | 280 |
0.00023 (0.21) |
0.00229 (1.00) |
0.0457 (1.00) |
0.0199 (1.00) |
0.0143 (1.00) |
0.00278 (1.00) |
0.0289 (1.00) |
0.301 (1.00) |
0.00628 (1.00) |
0.123 (1.00) |
0.321 (1.00) |
0.13 (1.00) |
0.391 (1.00) |
0.112 (1.00) |
amp 4p16 3 | 160 (28%) | 419 |
1 (1.00) |
0.32 (1.00) |
0.0293 (1.00) |
0.479 (1.00) |
0.00042 (0.381) |
0.0277 (1.00) |
0.27 (1.00) |
0.688 (1.00) |
0.687 (1.00) |
0.983 (1.00) |
0.629 (1.00) |
0.0187 (1.00) |
0.652 (1.00) |
0.579 (1.00) |
amp 10q22 3 | 184 (32%) | 395 |
0.371 (1.00) |
0.265 (1.00) |
0.608 (1.00) |
0.949 (1.00) |
0.0788 (1.00) |
0.843 (1.00) |
0.772 (1.00) |
0.82 (1.00) |
0.342 (1.00) |
0.898 (1.00) |
0.228 (1.00) |
0.648 (1.00) |
0.67 (1.00) |
0.303 (1.00) |
amp 14q11 2 | 148 (26%) | 431 |
0.0168 (1.00) |
0.0592 (1.00) |
0.29 (1.00) |
0.00669 (1.00) |
0.0687 (1.00) |
0.193 (1.00) |
0.532 (1.00) |
0.47 (1.00) |
0.34 (1.00) |
0.411 (1.00) |
0.3 (1.00) |
0.822 (1.00) |
0.323 (1.00) |
0.277 (1.00) |
amp 17q25 3 | 215 (37%) | 364 |
0.468 (1.00) |
0.0561 (1.00) |
0.982 (1.00) |
0.665 (1.00) |
0.00382 (1.00) |
0.774 (1.00) |
0.0727 (1.00) |
0.128 (1.00) |
0.0119 (1.00) |
0.0259 (1.00) |
0.326 (1.00) |
0.129 (1.00) |
1 (1.00) |
0.709 (1.00) |
amp 22q12 2 | 91 (16%) | 488 |
0.623 (1.00) |
0.157 (1.00) |
0.0698 (1.00) |
0.0359 (1.00) |
0.00762 (1.00) |
0.00061 (0.55) |
0.983 (1.00) |
0.0911 (1.00) |
0.0591 (1.00) |
0.0595 (1.00) |
0.108 (1.00) |
0.0144 (1.00) |
1 (1.00) |
0.0865 (1.00) |
amp xq28 | 220 (38%) | 359 |
0.245 (1.00) |
0.848 (1.00) |
0.555 (1.00) |
0.123 (1.00) |
0.00047 (0.425) |
0.178 (1.00) |
0.456 (1.00) |
0.444 (1.00) |
0.627 (1.00) |
0.939 (1.00) |
0.878 (1.00) |
0.802 (1.00) |
0.0427 (1.00) |
0.624 (1.00) |
del 2p25 3 | 120 (21%) | 459 |
0.881 (1.00) |
0.267 (1.00) |
0.422 (1.00) |
0.159 (1.00) |
0.401 (1.00) |
0.638 (1.00) |
0.261 (1.00) |
0.542 (1.00) |
0.0632 (1.00) |
0.239 (1.00) |
0.876 (1.00) |
0.95 (1.00) |
0.381 (1.00) |
0.426 (1.00) |
del 2q22 1 | 137 (24%) | 442 |
0.106 (1.00) |
0.273 (1.00) |
0.568 (1.00) |
0.00388 (1.00) |
0.0767 (1.00) |
0.665 (1.00) |
0.604 (1.00) |
0.719 (1.00) |
0.919 (1.00) |
0.301 (1.00) |
0.479 (1.00) |
0.603 (1.00) |
1 (1.00) |
0.266 (1.00) |
del 3q13 31 | 84 (15%) | 495 |
0.328 (1.00) |
0.227 (1.00) |
0.568 (1.00) |
0.626 (1.00) |
0.11 (1.00) |
0.0825 (1.00) |
0.25 (1.00) |
0.453 (1.00) |
0.407 (1.00) |
0.396 (1.00) |
0.519 (1.00) |
0.523 (1.00) |
1 (1.00) |
|
del 4q22 1 | 394 (68%) | 185 |
0.0535 (1.00) |
0.0237 (1.00) |
1 (1.00) |
0.166 (1.00) |
0.0155 (1.00) |
0.225 (1.00) |
0.191 (1.00) |
0.0615 (1.00) |
0.071 (1.00) |
0.388 (1.00) |
0.303 (1.00) |
0.255 (1.00) |
0.675 (1.00) |
0.413 (1.00) |
del 4q34 3 | 421 (73%) | 158 |
0.0533 (1.00) |
0.00075 (0.674) |
0.0626 (1.00) |
0.0281 (1.00) |
0.184 (1.00) |
0.58 (1.00) |
0.669 (1.00) |
0.199 (1.00) |
0.0839 (1.00) |
0.0193 (1.00) |
0.42 (1.00) |
0.53 (1.00) |
1 (1.00) |
0.56 (1.00) |
del 10p15 3 | 120 (21%) | 459 |
0.179 (1.00) |
0.709 (1.00) |
0.087 (1.00) |
0.319 (1.00) |
0.0972 (1.00) |
0.351 (1.00) |
0.29 (1.00) |
0.0409 (1.00) |
0.0143 (1.00) |
0.0889 (1.00) |
0.253 (1.00) |
0.266 (1.00) |
0.594 (1.00) |
0.105 (1.00) |
del 11q25 | 201 (35%) | 378 |
0.623 (1.00) |
0.652 (1.00) |
0.209 (1.00) |
0.0532 (1.00) |
0.273 (1.00) |
0.417 (1.00) |
0.322 (1.00) |
0.267 (1.00) |
0.931 (1.00) |
0.454 (1.00) |
0.708 (1.00) |
0.274 (1.00) |
1 (1.00) |
0.768 (1.00) |
del 16p13 3 | 313 (54%) | 266 |
0.602 (1.00) |
0.0718 (1.00) |
0.274 (1.00) |
0.0295 (1.00) |
0.108 (1.00) |
0.419 (1.00) |
0.84 (1.00) |
0.821 (1.00) |
0.37 (1.00) |
0.426 (1.00) |
0.224 (1.00) |
0.485 (1.00) |
0.675 (1.00) |
0.787 (1.00) |
del 16q22 1 | 461 (80%) | 118 |
0.499 (1.00) |
0.706 (1.00) |
0.0319 (1.00) |
0.449 (1.00) |
0.00089 (0.797) |
0.64 (1.00) |
0.694 (1.00) |
0.143 (1.00) |
0.221 (1.00) |
0.285 (1.00) |
0.313 (1.00) |
0.0482 (1.00) |
1 (1.00) |
0.385 (1.00) |
del 17p12 | 491 (85%) | 88 |
0.143 (1.00) |
0.336 (1.00) |
0.595 (1.00) |
0.69 (1.00) |
0.709 (1.00) |
0.322 (1.00) |
0.907 (1.00) |
0.371 (1.00) |
0.154 (1.00) |
0.194 (1.00) |
0.504 (1.00) |
0.21 (1.00) |
1 (1.00) |
|
del 17q11 2 | 472 (82%) | 107 |
0.921 (1.00) |
0.19 (1.00) |
0.734 (1.00) |
0.217 (1.00) |
0.00072 (0.648) |
0.00276 (1.00) |
0.767 (1.00) |
0.0359 (1.00) |
0.373 (1.00) |
0.439 (1.00) |
0.151 (1.00) |
0.164 (1.00) |
1 (1.00) |
0.339 (1.00) |
del 18q23 | 381 (66%) | 198 |
0.883 (1.00) |
0.854 (1.00) |
0.369 (1.00) |
0.957 (1.00) |
0.00275 (1.00) |
0.587 (1.00) |
0.48 (1.00) |
0.185 (1.00) |
0.152 (1.00) |
0.362 (1.00) |
0.66 (1.00) |
0.492 (1.00) |
0.646 (1.00) |
0.794 (1.00) |
del 19p13 3 | 512 (88%) | 67 |
0.158 (1.00) |
0.091 (1.00) |
0.839 (1.00) |
0.547 (1.00) |
0.00034 (0.309) |
0.0181 (1.00) |
0.622 (1.00) |
0.405 (1.00) |
0.335 (1.00) |
0.517 (1.00) |
0.477 (1.00) |
0.732 (1.00) |
1 (1.00) |
|
del 21q22 3 | 227 (39%) | 352 |
0.371 (1.00) |
0.0417 (1.00) |
0.693 (1.00) |
0.205 (1.00) |
0.795 (1.00) |
0.263 (1.00) |
0.659 (1.00) |
0.714 (1.00) |
0.246 (1.00) |
0.127 (1.00) |
0.82 (1.00) |
0.727 (1.00) |
0.162 (1.00) |
0.928 (1.00) |
del 22q13 32 | 503 (87%) | 76 |
0.209 (1.00) |
0.123 (1.00) |
0.0352 (1.00) |
0.285 (1.00) |
0.0175 (1.00) |
0.159 (1.00) |
0.122 (1.00) |
0.0447 (1.00) |
0.169 (1.00) |
0.0136 (1.00) |
0.0366 (1.00) |
0.577 (1.00) |
||
del xp21 1 | 355 (61%) | 224 |
0.405 (1.00) |
0.644 (1.00) |
0.0998 (1.00) |
0.8 (1.00) |
0.167 (1.00) |
0.0203 (1.00) |
0.461 (1.00) |
0.108 (1.00) |
0.885 (1.00) |
0.238 (1.00) |
0.976 (1.00) |
0.716 (1.00) |
0.594 (1.00) |
0.282 (1.00) |
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S1. Gene #1: 'amp_1p34.3' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
AMP PEAK 1(1P34.3) MUTATED | 58 | 114 | 120 |
AMP PEAK 1(1P34.3) WILD-TYPE | 113 | 92 | 82 |
Figure S1. Get High-res Image Gene #1: 'amp_1p34.3' versus Molecular Subtype #5: 'CN_CNMF'
![](D1V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S2. Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
AMP PEAK 2(1Q21.3) MUTATED | 86 | 114 | 167 |
AMP PEAK 2(1Q21.3) WILD-TYPE | 85 | 92 | 35 |
Figure S2. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'CN_CNMF'
![](D2V5.png)
P value = 0.00022 (Fisher's exact test), Q value = 0.2
Table S3. Gene #2: 'amp_1q21.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
AMP PEAK 2(1Q21.3) MUTATED | 128 | 92 | 141 |
AMP PEAK 2(1Q21.3) WILD-TYPE | 44 | 83 | 80 |
Figure S3. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'
![](D2V6.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S4. Gene #3: 'amp_1q42.2' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
AMP PEAK 3(1Q42.2) MUTATED | 88 | 87 | 147 |
AMP PEAK 3(1Q42.2) WILD-TYPE | 83 | 119 | 55 |
Figure S4. Get High-res Image Gene #3: 'amp_1q42.2' versus Molecular Subtype #5: 'CN_CNMF'
![](D3V5.png)
P value = 9e-05 (Fisher's exact test), Q value = 0.083
Table S5. Gene #3: 'amp_1q42.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
AMP PEAK 3(1Q42.2) MUTATED | 119 | 87 | 108 |
AMP PEAK 3(1Q42.2) WILD-TYPE | 53 | 88 | 113 |
Figure S5. Get High-res Image Gene #3: 'amp_1q42.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'
![](D3V6.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S6. Gene #4: 'amp_2p23.2' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
AMP PEAK 4(2P23.2) MUTATED | 47 | 87 | 118 |
AMP PEAK 4(2P23.2) WILD-TYPE | 124 | 119 | 84 |
Figure S6. Get High-res Image Gene #4: 'amp_2p23.2' versus Molecular Subtype #5: 'CN_CNMF'
![](D4V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S7. Gene #5: 'amp_2q31.2' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
AMP PEAK 5(2Q31.2) MUTATED | 46 | 102 | 114 |
AMP PEAK 5(2Q31.2) WILD-TYPE | 125 | 104 | 88 |
Figure S7. Get High-res Image Gene #5: 'amp_2q31.2' versus Molecular Subtype #5: 'CN_CNMF'
![](D5V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S8. Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
AMP PEAK 6(3Q26.2) MUTATED | 113 | 181 | 191 |
AMP PEAK 6(3Q26.2) WILD-TYPE | 58 | 25 | 11 |
Figure S8. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'CN_CNMF'
![](D6V5.png)
P value = 0.00025 (Fisher's exact test), Q value = 0.23
Table S9. Gene #8: 'amp_4q13.3' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
AMP PEAK 8(4Q13.3) MUTATED | 17 | 54 | 42 |
AMP PEAK 8(4Q13.3) WILD-TYPE | 154 | 152 | 160 |
Figure S9. Get High-res Image Gene #8: 'amp_4q13.3' versus Molecular Subtype #5: 'CN_CNMF'
![](D8V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S10. Gene #9: 'amp_5p15.33' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
AMP PEAK 9(5P15.33) MUTATED | 60 | 123 | 126 |
AMP PEAK 9(5P15.33) WILD-TYPE | 111 | 83 | 76 |
Figure S10. Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #5: 'CN_CNMF'
![](D9V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S11. Gene #10: 'amp_6p22.3' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
AMP PEAK 10(6P22.3) MUTATED | 59 | 124 | 123 |
AMP PEAK 10(6P22.3) WILD-TYPE | 112 | 82 | 79 |
Figure S11. Get High-res Image Gene #10: 'amp_6p22.3' versus Molecular Subtype #5: 'CN_CNMF'
![](D10V5.png)
P value = 3e-05 (Fisher's exact test), Q value = 0.028
Table S12. Gene #11: 'amp_7q36.3' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
AMP PEAK 11(7Q36.3) MUTATED | 69 | 124 | 127 |
AMP PEAK 11(7Q36.3) WILD-TYPE | 102 | 82 | 75 |
Figure S12. Get High-res Image Gene #11: 'amp_7q36.3' versus Molecular Subtype #5: 'CN_CNMF'
![](D11V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S13. Gene #12: 'amp_8p11.21' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
AMP PEAK 12(8P11.21) MUTATED | 42 | 70 | 99 |
AMP PEAK 12(8P11.21) WILD-TYPE | 129 | 136 | 103 |
Figure S13. Get High-res Image Gene #12: 'amp_8p11.21' versus Molecular Subtype #5: 'CN_CNMF'
![](D12V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S14. Gene #13: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 215 | 216 | 126 |
AMP PEAK 13(8Q24.21) MUTATED | 144 | 188 | 110 |
AMP PEAK 13(8Q24.21) WILD-TYPE | 71 | 28 | 16 |
Figure S14. Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D13V1.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S15. Gene #13: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 310 | 158 | 89 |
AMP PEAK 13(8Q24.21) MUTATED | 245 | 144 | 53 |
AMP PEAK 13(8Q24.21) WILD-TYPE | 65 | 14 | 36 |
Figure S15. Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D13V2.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S16. Gene #13: 'amp_8q24.21' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
AMP PEAK 13(8Q24.21) MUTATED | 113 | 200 | 148 |
AMP PEAK 13(8Q24.21) WILD-TYPE | 58 | 6 | 54 |
Figure S16. Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #5: 'CN_CNMF'
![](D13V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S17. Gene #13: 'amp_8q24.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 100 | 67 | 91 |
AMP PEAK 13(8Q24.21) MUTATED | 90 | 61 | 56 |
AMP PEAK 13(8Q24.21) WILD-TYPE | 10 | 6 | 35 |
Figure S17. Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
![](D13V9.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S18. Gene #14: 'amp_10p15.3' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
AMP PEAK 14(10P15.3) MUTATED | 45 | 81 | 126 |
AMP PEAK 14(10P15.3) WILD-TYPE | 126 | 125 | 76 |
Figure S18. Get High-res Image Gene #14: 'amp_10p15.3' versus Molecular Subtype #5: 'CN_CNMF'
![](D14V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S19. Gene #16: 'amp_11q14.1' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
AMP PEAK 16(11Q14.1) MUTATED | 54 | 117 | 86 |
AMP PEAK 16(11Q14.1) WILD-TYPE | 117 | 89 | 116 |
Figure S19. Get High-res Image Gene #16: 'amp_11q14.1' versus Molecular Subtype #5: 'CN_CNMF'
![](D16V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S20. Gene #17: 'amp_12p13.33' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
AMP PEAK 17(12P13.33) MUTATED | 71 | 111 | 148 |
AMP PEAK 17(12P13.33) WILD-TYPE | 100 | 95 | 54 |
Figure S20. Get High-res Image Gene #17: 'amp_12p13.33' versus Molecular Subtype #5: 'CN_CNMF'
![](D17V5.png)
P value = 0.00014 (Fisher's exact test), Q value = 0.13
Table S21. Gene #17: 'amp_12p13.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
AMP PEAK 17(12P13.33) MUTATED | 119 | 96 | 108 |
AMP PEAK 17(12P13.33) WILD-TYPE | 53 | 79 | 113 |
Figure S21. Get High-res Image Gene #17: 'amp_12p13.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'
![](D17V6.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S22. Gene #18: 'amp_12p12.1' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
AMP PEAK 18(12P12.1) MUTATED | 66 | 98 | 149 |
AMP PEAK 18(12P12.1) WILD-TYPE | 105 | 108 | 53 |
Figure S22. Get High-res Image Gene #18: 'amp_12p12.1' versus Molecular Subtype #5: 'CN_CNMF'
![](D18V5.png)
P value = 3e-05 (Fisher's exact test), Q value = 0.028
Table S23. Gene #18: 'amp_12p12.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
AMP PEAK 18(12P12.1) MUTATED | 117 | 87 | 102 |
AMP PEAK 18(12P12.1) WILD-TYPE | 55 | 88 | 119 |
Figure S23. Get High-res Image Gene #18: 'amp_12p12.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'
![](D18V6.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S24. Gene #19: 'amp_12q15' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
AMP PEAK 19(12Q15) MUTATED | 52 | 58 | 112 |
AMP PEAK 19(12Q15) WILD-TYPE | 119 | 148 | 90 |
Figure S24. Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #5: 'CN_CNMF'
![](D19V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S25. Gene #19: 'amp_12q15' versus Molecular Subtype #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
AMP PEAK 19(12Q15) MUTATED | 90 | 62 | 65 |
AMP PEAK 19(12Q15) WILD-TYPE | 82 | 113 | 156 |
Figure S25. Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #6: 'METHLYATION_CNMF'
![](D19V6.png)
P value = 5e-05 (Fisher's exact test), Q value = 0.047
Table S26. Gene #21: 'amp_14q32.33' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
AMP PEAK 21(14Q32.33) MUTATED | 41 | 77 | 38 |
AMP PEAK 21(14Q32.33) WILD-TYPE | 130 | 129 | 164 |
Figure S26. Get High-res Image Gene #21: 'amp_14q32.33' versus Molecular Subtype #5: 'CN_CNMF'
![](D21V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S27. Gene #22: 'amp_15q26.3' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
AMP PEAK 22(15Q26.3) MUTATED | 34 | 90 | 39 |
AMP PEAK 22(15Q26.3) WILD-TYPE | 137 | 116 | 163 |
Figure S27. Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #5: 'CN_CNMF'
![](D22V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S28. Gene #24: 'amp_18q11.2' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
AMP PEAK 24(18Q11.2) MUTATED | 25 | 44 | 74 |
AMP PEAK 24(18Q11.2) WILD-TYPE | 146 | 162 | 128 |
Figure S28. Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #5: 'CN_CNMF'
![](D24V5.png)
P value = 0.00019 (Fisher's exact test), Q value = 0.17
Table S29. Gene #25: 'amp_19p13.12' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 215 | 216 | 126 |
AMP PEAK 25(19P13.12) MUTATED | 136 | 115 | 51 |
AMP PEAK 25(19P13.12) WILD-TYPE | 79 | 101 | 75 |
Figure S29. Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D25V1.png)
P value = 0.00025 (Fisher's exact test), Q value = 0.23
Table S30. Gene #25: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 310 | 158 | 89 |
AMP PEAK 25(19P13.12) MUTATED | 186 | 64 | 52 |
AMP PEAK 25(19P13.12) WILD-TYPE | 124 | 94 | 37 |
Figure S30. Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D25V2.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S31. Gene #25: 'amp_19p13.12' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
AMP PEAK 25(19P13.12) MUTATED | 72 | 92 | 151 |
AMP PEAK 25(19P13.12) WILD-TYPE | 99 | 114 | 51 |
Figure S31. Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #5: 'CN_CNMF'
![](D25V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S32. Gene #25: 'amp_19p13.12' versus Molecular Subtype #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
AMP PEAK 25(19P13.12) MUTATED | 118 | 73 | 116 |
AMP PEAK 25(19P13.12) WILD-TYPE | 54 | 102 | 105 |
Figure S32. Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #6: 'METHLYATION_CNMF'
![](D25V6.png)
P value = 1e-04 (Fisher's exact test), Q value = 0.092
Table S33. Gene #25: 'amp_19p13.12' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 116 | 96 | 128 | 58 |
AMP PEAK 25(19P13.12) MUTATED | 44 | 55 | 86 | 31 |
AMP PEAK 25(19P13.12) WILD-TYPE | 72 | 41 | 42 | 27 |
Figure S33. Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'
![](D25V8.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S34. Gene #26: 'amp_19q12' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
AMP PEAK 26(19Q12) MUTATED | 67 | 83 | 172 |
AMP PEAK 26(19Q12) WILD-TYPE | 104 | 123 | 30 |
Figure S34. Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #5: 'CN_CNMF'
![](D26V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S35. Gene #26: 'amp_19q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
AMP PEAK 26(19Q12) MUTATED | 128 | 70 | 121 |
AMP PEAK 26(19Q12) WILD-TYPE | 44 | 105 | 100 |
Figure S35. Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'
![](D26V6.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S36. Gene #27: 'amp_19q13.2' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
AMP PEAK 27(19Q13.2) MUTATED | 51 | 71 | 123 |
AMP PEAK 27(19Q13.2) WILD-TYPE | 120 | 135 | 79 |
Figure S36. Get High-res Image Gene #27: 'amp_19q13.2' versus Molecular Subtype #5: 'CN_CNMF'
![](D27V5.png)
P value = 0.00011 (Fisher's exact test), Q value = 0.1
Table S37. Gene #27: 'amp_19q13.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
AMP PEAK 27(19Q13.2) MUTATED | 94 | 56 | 91 |
AMP PEAK 27(19Q13.2) WILD-TYPE | 78 | 119 | 130 |
Figure S37. Get High-res Image Gene #27: 'amp_19q13.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'
![](D27V6.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S38. Gene #28: 'amp_20p13' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
AMP PEAK 28(20P13) MUTATED | 69 | 97 | 151 |
AMP PEAK 28(20P13) WILD-TYPE | 102 | 109 | 51 |
Figure S38. Get High-res Image Gene #28: 'amp_20p13' versus Molecular Subtype #5: 'CN_CNMF'
![](D28V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S39. Gene #28: 'amp_20p13' versus Molecular Subtype #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
AMP PEAK 28(20P13) MUTATED | 123 | 81 | 103 |
AMP PEAK 28(20P13) WILD-TYPE | 49 | 94 | 118 |
Figure S39. Get High-res Image Gene #28: 'amp_20p13' versus Molecular Subtype #6: 'METHLYATION_CNMF'
![](D28V6.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S40. Gene #29: 'amp_20q11.21' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
AMP PEAK 29(20Q11.21) MUTATED | 79 | 95 | 174 |
AMP PEAK 29(20Q11.21) WILD-TYPE | 92 | 111 | 28 |
Figure S40. Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #5: 'CN_CNMF'
![](D29V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S41. Gene #29: 'amp_20q11.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
AMP PEAK 29(20Q11.21) MUTATED | 140 | 91 | 109 |
AMP PEAK 29(20Q11.21) WILD-TYPE | 32 | 84 | 112 |
Figure S41. Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'
![](D29V6.png)
P value = 0.00019 (Fisher's exact test), Q value = 0.17
Table S42. Gene #29: 'amp_20q11.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 100 | 67 | 91 |
AMP PEAK 29(20Q11.21) MUTATED | 63 | 28 | 67 |
AMP PEAK 29(20Q11.21) WILD-TYPE | 37 | 39 | 24 |
Figure S42. Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
![](D29V9.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S43. Gene #30: 'amp_20q13.33' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
AMP PEAK 30(20Q13.33) MUTATED | 87 | 132 | 183 |
AMP PEAK 30(20Q13.33) WILD-TYPE | 84 | 74 | 19 |
Figure S43. Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #5: 'CN_CNMF'
![](D30V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S44. Gene #30: 'amp_20q13.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
AMP PEAK 30(20Q13.33) MUTATED | 144 | 109 | 140 |
AMP PEAK 30(20Q13.33) WILD-TYPE | 28 | 66 | 81 |
Figure S44. Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'
![](D30V6.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S45. Gene #32: 'amp_xp11.23' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
AMP PEAK 32(XP11.23) MUTATED | 25 | 55 | 79 |
AMP PEAK 32(XP11.23) WILD-TYPE | 146 | 151 | 123 |
Figure S45. Get High-res Image Gene #32: 'amp_xp11.23' versus Molecular Subtype #5: 'CN_CNMF'
![](D32V5.png)
P value = 6e-05 (Fisher's exact test), Q value = 0.056
Table S46. Gene #34: 'del_1p36.11' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
DEL PEAK 1(1P36.11) MUTATED | 87 | 113 | 69 |
DEL PEAK 1(1P36.11) WILD-TYPE | 84 | 93 | 133 |
Figure S46. Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #5: 'CN_CNMF'
![](D34V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S47. Gene #35: 'del_1q41' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
DEL PEAK 2(1Q41) MUTATED | 14 | 60 | 23 |
DEL PEAK 2(1Q41) WILD-TYPE | 157 | 146 | 179 |
Figure S47. Get High-res Image Gene #35: 'del_1q41' versus Molecular Subtype #5: 'CN_CNMF'
![](D35V5.png)
P value = 2e-05 (Fisher's exact test), Q value = 0.019
Table S48. Gene #38: 'del_2q37.3' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
DEL PEAK 5(2Q37.3) MUTATED | 35 | 86 | 54 |
DEL PEAK 5(2Q37.3) WILD-TYPE | 136 | 120 | 148 |
Figure S48. Get High-res Image Gene #38: 'del_2q37.3' versus Molecular Subtype #5: 'CN_CNMF'
![](D38V5.png)
P value = 9e-05 (Fisher's exact test), Q value = 0.083
Table S49. Gene #39: 'del_3p26.2' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
DEL PEAK 6(3P26.2) MUTATED | 47 | 66 | 96 |
DEL PEAK 6(3P26.2) WILD-TYPE | 124 | 140 | 106 |
Figure S49. Get High-res Image Gene #39: 'del_3p26.2' versus Molecular Subtype #5: 'CN_CNMF'
![](D39V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S50. Gene #43: 'del_5q12.1' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
DEL PEAK 10(5Q12.1) MUTATED | 73 | 145 | 137 |
DEL PEAK 10(5Q12.1) WILD-TYPE | 98 | 61 | 65 |
Figure S50. Get High-res Image Gene #43: 'del_5q12.1' versus Molecular Subtype #5: 'CN_CNMF'
![](D43V5.png)
P value = 2e-04 (Fisher's exact test), Q value = 0.18
Table S51. Gene #43: 'del_5q12.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
DEL PEAK 10(5Q12.1) MUTATED | 117 | 85 | 146 |
DEL PEAK 10(5Q12.1) WILD-TYPE | 55 | 90 | 75 |
Figure S51. Get High-res Image Gene #43: 'del_5q12.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'
![](D43V6.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S52. Gene #44: 'del_5q13.2' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
DEL PEAK 11(5Q13.2) MUTATED | 92 | 180 | 147 |
DEL PEAK 11(5Q13.2) WILD-TYPE | 79 | 26 | 55 |
Figure S52. Get High-res Image Gene #44: 'del_5q13.2' versus Molecular Subtype #5: 'CN_CNMF'
![](D44V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S53. Gene #45: 'del_6q27' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
DEL PEAK 12(6Q27) MUTATED | 121 | 162 | 97 |
DEL PEAK 12(6Q27) WILD-TYPE | 50 | 44 | 105 |
Figure S53. Get High-res Image Gene #45: 'del_6q27' versus Molecular Subtype #5: 'CN_CNMF'
![](D45V5.png)
P value = 4e-05 (Fisher's exact test), Q value = 0.037
Table S54. Gene #45: 'del_6q27' versus Molecular Subtype #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
DEL PEAK 12(6Q27) MUTATED | 91 | 132 | 152 |
DEL PEAK 12(6Q27) WILD-TYPE | 81 | 43 | 69 |
Figure S54. Get High-res Image Gene #45: 'del_6q27' versus Molecular Subtype #6: 'METHLYATION_CNMF'
![](D45V6.png)
P value = 2e-05 (Fisher's exact test), Q value = 0.019
Table S55. Gene #45: 'del_6q27' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 100 | 67 | 91 |
DEL PEAK 12(6Q27) MUTATED | 66 | 52 | 38 |
DEL PEAK 12(6Q27) WILD-TYPE | 34 | 15 | 53 |
Figure S55. Get High-res Image Gene #45: 'del_6q27' versus Molecular Subtype #9: 'MRNASEQ_CNMF'
![](D45V9.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S56. Gene #46: 'del_7p22.1' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
DEL PEAK 13(7P22.1) MUTATED | 48 | 135 | 70 |
DEL PEAK 13(7P22.1) WILD-TYPE | 123 | 71 | 132 |
Figure S56. Get High-res Image Gene #46: 'del_7p22.1' versus Molecular Subtype #5: 'CN_CNMF'
![](D46V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S57. Gene #47: 'del_8p23.3' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
DEL PEAK 14(8P23.3) MUTATED | 78 | 162 | 148 |
DEL PEAK 14(8P23.3) WILD-TYPE | 93 | 44 | 54 |
Figure S57. Get High-res Image Gene #47: 'del_8p23.3' versus Molecular Subtype #5: 'CN_CNMF'
![](D47V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S58. Gene #48: 'del_8p21.2' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
DEL PEAK 15(8P21.2) MUTATED | 88 | 166 | 152 |
DEL PEAK 15(8P21.2) WILD-TYPE | 83 | 40 | 50 |
Figure S58. Get High-res Image Gene #48: 'del_8p21.2' versus Molecular Subtype #5: 'CN_CNMF'
![](D48V5.png)
P value = 0.00026 (Fisher's exact test), Q value = 0.24
Table S59. Gene #49: 'del_9p24.3' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 215 | 216 | 126 |
DEL PEAK 16(9P24.3) MUTATED | 109 | 73 | 66 |
DEL PEAK 16(9P24.3) WILD-TYPE | 106 | 143 | 60 |
Figure S59. Get High-res Image Gene #49: 'del_9p24.3' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D49V1.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S60. Gene #49: 'del_9p24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 310 | 158 | 89 |
DEL PEAK 16(9P24.3) MUTATED | 120 | 69 | 59 |
DEL PEAK 16(9P24.3) WILD-TYPE | 190 | 89 | 30 |
Figure S60. Get High-res Image Gene #49: 'del_9p24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D49V2.png)
P value = 7e-05 (Fisher's exact test), Q value = 0.065
Table S61. Gene #49: 'del_9p24.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
DEL PEAK 16(9P24.3) MUTATED | 92 | 90 | 75 |
DEL PEAK 16(9P24.3) WILD-TYPE | 80 | 85 | 146 |
Figure S61. Get High-res Image Gene #49: 'del_9p24.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'
![](D49V6.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S62. Gene #50: 'del_9q34.13' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
DEL PEAK 17(9Q34.13) MUTATED | 93 | 98 | 151 |
DEL PEAK 17(9Q34.13) WILD-TYPE | 78 | 108 | 51 |
Figure S62. Get High-res Image Gene #50: 'del_9q34.13' versus Molecular Subtype #5: 'CN_CNMF'
![](D50V5.png)
P value = 9e-05 (Fisher's exact test), Q value = 0.083
Table S63. Gene #52: 'del_10q24.2' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
DEL PEAK 19(10Q24.2) MUTATED | 53 | 111 | 87 |
DEL PEAK 19(10Q24.2) WILD-TYPE | 118 | 95 | 115 |
Figure S63. Get High-res Image Gene #52: 'del_10q24.2' versus Molecular Subtype #5: 'CN_CNMF'
![](D52V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S64. Gene #53: 'del_11p15.5' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
DEL PEAK 20(11P15.5) MUTATED | 77 | 163 | 106 |
DEL PEAK 20(11P15.5) WILD-TYPE | 94 | 43 | 96 |
Figure S64. Get High-res Image Gene #53: 'del_11p15.5' versus Molecular Subtype #5: 'CN_CNMF'
![](D53V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S65. Gene #55: 'del_12q24.33' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
DEL PEAK 22(12Q24.33) MUTATED | 56 | 113 | 51 |
DEL PEAK 22(12Q24.33) WILD-TYPE | 115 | 93 | 151 |
Figure S65. Get High-res Image Gene #55: 'del_12q24.33' versus Molecular Subtype #5: 'CN_CNMF'
![](D55V5.png)
P value = 0.00024 (Fisher's exact test), Q value = 0.22
Table S66. Gene #56: 'del_13q14.2' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
DEL PEAK 23(13Q14.2) MUTATED | 90 | 150 | 124 |
DEL PEAK 23(13Q14.2) WILD-TYPE | 81 | 56 | 78 |
Figure S66. Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #5: 'CN_CNMF'
![](D56V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S67. Gene #56: 'del_13q14.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
DEL PEAK 23(13Q14.2) MUTATED | 109 | 88 | 161 |
DEL PEAK 23(13Q14.2) WILD-TYPE | 63 | 87 | 60 |
Figure S67. Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'
![](D56V6.png)
P value = 6e-05 (Fisher's exact test), Q value = 0.056
Table S68. Gene #57: 'del_14q23.3' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
DEL PEAK 24(14Q23.3) MUTATED | 70 | 104 | 131 |
DEL PEAK 24(14Q23.3) WILD-TYPE | 101 | 102 | 71 |
Figure S68. Get High-res Image Gene #57: 'del_14q23.3' versus Molecular Subtype #5: 'CN_CNMF'
![](D57V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S69. Gene #58: 'del_15q11.2' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
DEL PEAK 25(15Q11.2) MUTATED | 68 | 76 | 155 |
DEL PEAK 25(15Q11.2) WILD-TYPE | 103 | 130 | 47 |
Figure S69. Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #5: 'CN_CNMF'
![](D58V5.png)
P value = 3e-05 (Fisher's exact test), Q value = 0.028
Table S70. Gene #58: 'del_15q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
DEL PEAK 25(15Q11.2) MUTATED | 114 | 82 | 100 |
DEL PEAK 25(15Q11.2) WILD-TYPE | 58 | 93 | 121 |
Figure S70. Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'
![](D58V6.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S71. Gene #59: 'del_15q15.1' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
DEL PEAK 26(15Q15.1) MUTATED | 81 | 115 | 167 |
DEL PEAK 26(15Q15.1) WILD-TYPE | 90 | 91 | 35 |
Figure S71. Get High-res Image Gene #59: 'del_15q15.1' versus Molecular Subtype #5: 'CN_CNMF'
![](D59V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0099
Table S72. Gene #59: 'del_15q15.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
DEL PEAK 26(15Q15.1) MUTATED | 134 | 97 | 129 |
DEL PEAK 26(15Q15.1) WILD-TYPE | 38 | 78 | 92 |
Figure S72. Get High-res Image Gene #59: 'del_15q15.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'
![](D59V6.png)
P value = 0.00015 (Fisher's exact test), Q value = 0.14
Table S73. Gene #62: 'del_16q23.1' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
DEL PEAK 29(16Q23.1) MUTATED | 114 | 168 | 170 |
DEL PEAK 29(16Q23.1) WILD-TYPE | 57 | 38 | 32 |
Figure S73. Get High-res Image Gene #62: 'del_16q23.1' versus Molecular Subtype #5: 'CN_CNMF'
![](D62V5.png)
P value = 0.00023 (Fisher's exact test), Q value = 0.21
Table S74. Gene #67: 'del_19q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 215 | 216 | 126 |
DEL PEAK 34(19Q13.33) MUTATED | 127 | 117 | 46 |
DEL PEAK 34(19Q13.33) WILD-TYPE | 88 | 99 | 80 |
Figure S74. Get High-res Image Gene #67: 'del_19q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D67V1.png)
P value = 0.00011 (Fisher's exact test), Q value = 0.1
Table S75. Gene #68: 'del_19q13.43' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 206 | 202 |
DEL PEAK 35(19Q13.43) MUTATED | 84 | 80 | 121 |
DEL PEAK 35(19Q13.43) WILD-TYPE | 87 | 126 | 81 |
Figure S75. Get High-res Image Gene #68: 'del_19q13.43' versus Molecular Subtype #5: 'CN_CNMF'
![](D68V5.png)
P value = 5e-05 (Fisher's exact test), Q value = 0.047
Table S76. Gene #68: 'del_19q13.43' versus Molecular Subtype #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
DEL PEAK 35(19Q13.43) MUTATED | 105 | 64 | 111 |
DEL PEAK 35(19Q13.43) WILD-TYPE | 67 | 111 | 110 |
Figure S76. Get High-res Image Gene #68: 'del_19q13.43' versus Molecular Subtype #6: 'METHLYATION_CNMF'
![](D68V6.png)
-
Copy number data file = transformed.cor.cli.txt
-
Molecular subtype file = OV-TP.transferedmergedcluster.txt
-
Number of patients = 579
-
Number of significantly focal cnvs = 71
-
Number of molecular subtypes = 14
-
Exclude genes that fewer than K tumors have alterations, K = 3
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.