This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.
Testing the association between copy number variation of 70 peak regions and 12 molecular subtypes across 559 patients, 82 significant findings detected with Q value < 0.25.
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Amp Peak 1(1p34.3) cnvs correlated to 'CN_CNMF'.
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Amp Peak 2(1q21.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 3(1q42.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 4(2p23.2) cnvs correlated to 'CN_CNMF'.
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Amp Peak 5(2q31.2) cnvs correlated to 'CN_CNMF'.
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Amp Peak 6(3q26.2) cnvs correlated to 'CN_CNMF'.
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Amp Peak 8(4q13.3) cnvs correlated to 'CN_CNMF'.
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Amp Peak 9(5p15.33) cnvs correlated to 'CN_CNMF'.
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Amp Peak 10(6p22.3) cnvs correlated to 'CN_CNMF'.
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Amp Peak 11(7q36.3) cnvs correlated to 'CN_CNMF'.
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Amp Peak 12(8p11.21) cnvs correlated to 'CN_CNMF'.
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Amp Peak 13(8q24.21) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'MRNASEQ_CNMF'.
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Amp Peak 14(10p15.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 16(11q14.1) cnvs correlated to 'CN_CNMF'.
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Amp Peak 17(12p13.33) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 18(12p12.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 20(15q26.3) cnvs correlated to 'CN_CNMF'.
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Amp Peak 22(18q11.2) cnvs correlated to 'CN_CNMF'.
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Amp Peak 23(19p13.12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', and 'RPPA_CHIERARCHICAL'.
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Amp Peak 24(19q12) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 25(19q13.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 26(20p13) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'METHLYATION_CNMF'.
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Amp Peak 27(20q11.21) cnvs correlated to 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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Amp Peak 28(20q13.33) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'METHLYATION_CNMF'.
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Amp Peak 29(22q12.2) cnvs correlated to 'CN_CNMF'.
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Amp Peak 30(Xp11.23) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 31(Xq28) cnvs correlated to 'CN_CNMF'.
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Del Peak 1(1p36.11) cnvs correlated to 'CN_CNMF'.
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Del Peak 2(1q32.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 5(2q37.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 6(3p26.2) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'METHLYATION_CNMF'.
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Del Peak 9(5q11.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 10(5q13.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 11(6q27) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 12(7p22.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 13(8p23.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 14(8p21.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 15(9p24.3) cnvs correlated to 'MRNA_CNMF'.
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Del Peak 16(9q21.11) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 17(9q34.13) cnvs correlated to 'CN_CNMF'.
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Del Peak 20(10q26.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 21(11p15.5) cnvs correlated to 'CN_CNMF'.
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Del Peak 23(12q23.1) cnvs correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.
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Del Peak 24(12q24.33) cnvs correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.
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Del Peak 25(13q14.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CNMF'.
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Del Peak 27(15q15.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 29(16q22.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 30(16q23.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 32(17q11.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 36(19q13.43) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 70 regions and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 82 significant findings detected.
Molecular subtypes |
MRNA CNMF |
MRNA CHIERARCHICAL |
MIR CNMF |
MIR CHIERARCHICAL |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
||
nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Chi-square 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 Peak 27(20q11 21) | 326 (58%) | 233 |
0.00553 (1.00) |
3.68e-08 (2.97e-05) |
0.185 (1.00) |
0.000105 (0.0808) |
1.01e-22 (8.5e-20) |
8.1e-13 (6.74e-10) |
0.18 (1.00) |
0.0246 (1.00) |
0.000329 (0.25) |
0.0458 (1.00) |
0.551 (1.00) |
0.897 (1.00) |
Amp Peak 13(8q24 21) | 439 (79%) | 120 |
1.05e-07 (8.43e-05) |
1.24e-05 (0.00981) |
0.229 (1.00) |
0.00313 (1.00) |
2.87e-19 (2.41e-16) |
0.0047 (1.00) |
0.918 (1.00) |
0.631 (1.00) |
1.62e-06 (0.00129) |
0.00146 (1.00) |
0.204 (1.00) |
0.0269 (1.00) |
Amp Peak 23(19p13 12) | 301 (54%) | 258 |
0.000624 (0.468) |
0.000463 (0.349) |
0.0461 (1.00) |
0.052 (1.00) |
1.97e-14 (1.64e-11) |
3.88e-06 (0.00308) |
4.82e-05 (0.0376) |
0.000193 (0.148) |
0.184 (1.00) |
0.162 (1.00) |
0.587 (1.00) |
0.761 (1.00) |
Amp Peak 26(20p13) | 300 (54%) | 259 |
0.186 (1.00) |
0.000126 (0.0967) |
0.201 (1.00) |
0.0141 (1.00) |
9.8e-12 (8.13e-09) |
2.23e-09 (1.83e-06) |
0.569 (1.00) |
0.448 (1.00) |
0.0317 (1.00) |
0.0785 (1.00) |
0.248 (1.00) |
0.845 (1.00) |
Amp Peak 28(20q13 33) | 387 (69%) | 172 |
0.00761 (1.00) |
3.75e-05 (0.0294) |
0.599 (1.00) |
0.00326 (1.00) |
1.21e-15 (1.01e-12) |
2.8e-08 (2.26e-05) |
0.62 (1.00) |
0.347 (1.00) |
0.0247 (1.00) |
0.0702 (1.00) |
0.432 (1.00) |
0.416 (1.00) |
Del Peak 6(3p26 2) | 206 (37%) | 353 |
0.083 (1.00) |
6.13e-05 (0.0477) |
0.00412 (1.00) |
0.0222 (1.00) |
9.31e-05 (0.0719) |
5.51e-05 (0.0429) |
0.728 (1.00) |
0.238 (1.00) |
0.00138 (1.00) |
0.0109 (1.00) |
0.579 (1.00) |
0.796 (1.00) |
Del Peak 25(13q14 2) | 348 (62%) | 211 |
0.0259 (1.00) |
0.516 (1.00) |
0.723 (1.00) |
0.683 (1.00) |
1.11e-06 (0.000885) |
9.8e-06 (0.00777) |
0.000301 (0.229) |
0.00813 (1.00) |
0.0309 (1.00) |
0.247 (1.00) |
0.221 (1.00) |
1 (1.00) |
Amp Peak 2(1q21 3) | 350 (63%) | 209 |
0.211 (1.00) |
0.0621 (1.00) |
0.687 (1.00) |
0.15 (1.00) |
7.18e-12 (5.96e-09) |
4.81e-05 (0.0376) |
0.0483 (1.00) |
0.0541 (1.00) |
0.658 (1.00) |
0.126 (1.00) |
0.907 (1.00) |
0.86 (1.00) |
Amp Peak 3(1q42 2) | 304 (54%) | 255 |
0.023 (1.00) |
0.0325 (1.00) |
0.941 (1.00) |
0.0063 (1.00) |
3.15e-10 (2.59e-07) |
9.54e-05 (0.0735) |
0.102 (1.00) |
0.11 (1.00) |
0.426 (1.00) |
0.62 (1.00) |
0.177 (1.00) |
0.439 (1.00) |
Amp Peak 14(10p15 3) | 239 (43%) | 320 |
0.758 (1.00) |
0.092 (1.00) |
0.0698 (1.00) |
0.255 (1.00) |
4.44e-11 (3.67e-08) |
0.000103 (0.0794) |
0.368 (1.00) |
0.316 (1.00) |
0.285 (1.00) |
0.378 (1.00) |
0.671 (1.00) |
0.475 (1.00) |
Amp Peak 17(12p13 33) | 311 (56%) | 248 |
0.0361 (1.00) |
0.00326 (1.00) |
0.29 (1.00) |
0.0108 (1.00) |
1.1e-09 (8.99e-07) |
1.36e-05 (0.0107) |
0.148 (1.00) |
0.288 (1.00) |
0.00977 (1.00) |
0.054 (1.00) |
0.523 (1.00) |
0.612 (1.00) |
Amp Peak 18(12p12 1) | 294 (53%) | 265 |
0.273 (1.00) |
0.013 (1.00) |
0.843 (1.00) |
0.0968 (1.00) |
2.05e-12 (1.71e-09) |
1.01e-06 (0.000812) |
0.766 (1.00) |
0.0386 (1.00) |
0.0267 (1.00) |
0.0935 (1.00) |
0.177 (1.00) |
0.133 (1.00) |
Amp Peak 24(19q12) | 309 (55%) | 250 |
0.0736 (1.00) |
0.0235 (1.00) |
0.0402 (1.00) |
0.147 (1.00) |
2.89e-26 (2.43e-23) |
3.63e-10 (2.98e-07) |
0.0574 (1.00) |
0.771 (1.00) |
0.409 (1.00) |
0.391 (1.00) |
0.361 (1.00) |
0.784 (1.00) |
Amp Peak 25(19q13 2) | 235 (42%) | 324 |
0.957 (1.00) |
0.0425 (1.00) |
0.654 (1.00) |
0.307 (1.00) |
6.25e-10 (5.12e-07) |
0.000201 (0.153) |
0.609 (1.00) |
0.376 (1.00) |
0.473 (1.00) |
0.774 (1.00) |
0.977 (1.00) |
0.611 (1.00) |
Amp Peak 30(Xp11 23) | 162 (29%) | 397 |
0.759 (1.00) |
0.257 (1.00) |
0.298 (1.00) |
0.308 (1.00) |
3.27e-06 (0.0026) |
1.46e-05 (0.0115) |
0.808 (1.00) |
0.106 (1.00) |
0.34 (1.00) |
0.402 (1.00) |
0.205 (1.00) |
0.0203 (1.00) |
Del Peak 11(6q27) | 362 (65%) | 197 |
0.509 (1.00) |
0.0229 (1.00) |
0.216 (1.00) |
0.0651 (1.00) |
8e-09 (6.52e-06) |
1.62e-05 (0.0128) |
0.849 (1.00) |
0.748 (1.00) |
0.000522 (0.393) |
0.0556 (1.00) |
0.598 (1.00) |
0.075 (1.00) |
Del Peak 16(9q21 11) | 268 (48%) | 291 |
0.0107 (1.00) |
0.00136 (1.00) |
0.139 (1.00) |
0.00112 (0.836) |
4.16e-15 (3.48e-12) |
3.98e-07 (0.00032) |
0.0737 (1.00) |
0.79 (1.00) |
0.00135 (1.00) |
0.568 (1.00) |
0.074 (1.00) |
0.507 (1.00) |
Del Peak 23(12q23 1) | 193 (35%) | 366 |
0.0032 (1.00) |
0.000204 (0.156) |
0.0409 (1.00) |
0.0174 (1.00) |
4.4e-08 (3.55e-05) |
0.0261 (1.00) |
0.603 (1.00) |
0.518 (1.00) |
0.0912 (1.00) |
0.0166 (1.00) |
0.132 (1.00) |
0.0221 (1.00) |
Del Peak 24(12q24 33) | 213 (38%) | 346 |
0.00195 (1.00) |
2.63e-06 (0.00209) |
0.216 (1.00) |
0.0891 (1.00) |
1.14e-11 (9.42e-09) |
0.0505 (1.00) |
0.299 (1.00) |
0.214 (1.00) |
0.208 (1.00) |
0.0189 (1.00) |
0.0175 (1.00) |
0.0162 (1.00) |
Del Peak 27(15q15 1) | 351 (63%) | 208 |
0.0423 (1.00) |
0.000469 (0.353) |
0.0111 (1.00) |
0.00626 (1.00) |
1.75e-10 (1.44e-07) |
7.64e-05 (0.0593) |
0.0265 (1.00) |
0.162 (1.00) |
0.0219 (1.00) |
0.0736 (1.00) |
0.246 (1.00) |
0.407 (1.00) |
Del Peak 36(19q13 43) | 277 (50%) | 282 |
0.0199 (1.00) |
0.0612 (1.00) |
0.0603 (1.00) |
0.164 (1.00) |
0.000298 (0.227) |
0.000107 (0.0821) |
0.17 (1.00) |
0.328 (1.00) |
0.517 (1.00) |
0.182 (1.00) |
0.472 (1.00) |
0.18 (1.00) |
Amp Peak 1(1p34 3) | 277 (50%) | 282 |
0.179 (1.00) |
0.84 (1.00) |
0.148 (1.00) |
0.134 (1.00) |
1.18e-06 (0.000944) |
0.119 (1.00) |
0.149 (1.00) |
0.846 (1.00) |
0.455 (1.00) |
0.386 (1.00) |
0.0286 (1.00) |
0.423 (1.00) |
Amp Peak 4(2p23 2) | 235 (42%) | 324 |
0.341 (1.00) |
0.0263 (1.00) |
0.582 (1.00) |
0.0135 (1.00) |
2.67e-08 (2.16e-05) |
0.00279 (1.00) |
0.315 (1.00) |
0.463 (1.00) |
0.0855 (1.00) |
0.333 (1.00) |
0.939 (1.00) |
0.611 (1.00) |
Amp Peak 5(2q31 2) | 245 (44%) | 314 |
0.0779 (1.00) |
0.00222 (1.00) |
0.0744 (1.00) |
0.052 (1.00) |
9.18e-10 (7.52e-07) |
0.000382 (0.289) |
0.0604 (1.00) |
0.776 (1.00) |
0.184 (1.00) |
0.136 (1.00) |
0.522 (1.00) |
0.346 (1.00) |
Amp Peak 6(3q26 2) | 465 (83%) | 94 |
0.00679 (1.00) |
0.00101 (0.756) |
0.989 (1.00) |
0.454 (1.00) |
1.02e-08 (8.31e-06) |
0.108 (1.00) |
0.969 (1.00) |
0.115 (1.00) |
0.0435 (1.00) |
0.133 (1.00) |
0.163 (1.00) |
0.302 (1.00) |
Amp Peak 8(4q13 3) | 105 (19%) | 454 |
0.914 (1.00) |
0.133 (1.00) |
0.354 (1.00) |
0.175 (1.00) |
1.59e-05 (0.0125) |
0.125 (1.00) |
0.567 (1.00) |
0.115 (1.00) |
0.459 (1.00) |
0.717 (1.00) |
0.804 (1.00) |
0.948 (1.00) |
Amp Peak 9(5p15 33) | 295 (53%) | 264 |
0.884 (1.00) |
0.485 (1.00) |
0.625 (1.00) |
0.54 (1.00) |
4.22e-07 (0.000338) |
0.341 (1.00) |
0.581 (1.00) |
0.376 (1.00) |
0.162 (1.00) |
0.608 (1.00) |
0.00672 (1.00) |
0.425 (1.00) |
Amp Peak 10(6p22 3) | 287 (51%) | 272 |
0.132 (1.00) |
0.0154 (1.00) |
0.249 (1.00) |
0.156 (1.00) |
1.67e-07 (0.000134) |
0.0327 (1.00) |
0.0249 (1.00) |
0.0142 (1.00) |
0.793 (1.00) |
0.662 (1.00) |
0.176 (1.00) |
0.74 (1.00) |
Amp Peak 11(7q36 3) | 300 (54%) | 259 |
0.0439 (1.00) |
0.515 (1.00) |
0.262 (1.00) |
0.588 (1.00) |
1.65e-06 (0.00132) |
0.211 (1.00) |
0.164 (1.00) |
0.528 (1.00) |
0.987 (1.00) |
1 (1.00) |
0.103 (1.00) |
0.325 (1.00) |
Amp Peak 12(8p11 21) | 196 (35%) | 363 |
0.105 (1.00) |
0.00242 (1.00) |
0.102 (1.00) |
0.292 (1.00) |
2.11e-05 (0.0166) |
0.0122 (1.00) |
0.131 (1.00) |
0.598 (1.00) |
0.271 (1.00) |
0.105 (1.00) |
0.844 (1.00) |
0.385 (1.00) |
Amp Peak 16(11q14 1) | 247 (44%) | 312 |
0.00682 (1.00) |
0.0904 (1.00) |
0.847 (1.00) |
0.294 (1.00) |
9.58e-09 (7.8e-06) |
0.021 (1.00) |
0.319 (1.00) |
0.125 (1.00) |
0.013 (1.00) |
0.0644 (1.00) |
0.125 (1.00) |
0.968 (1.00) |
Amp Peak 20(15q26 3) | 156 (28%) | 403 |
0.0786 (1.00) |
0.955 (1.00) |
0.503 (1.00) |
0.689 (1.00) |
5.92e-10 (4.86e-07) |
0.646 (1.00) |
0.851 (1.00) |
0.0803 (1.00) |
0.233 (1.00) |
0.673 (1.00) |
0.0967 (1.00) |
0.173 (1.00) |
Amp Peak 22(18q11 2) | 137 (25%) | 422 |
0.952 (1.00) |
0.198 (1.00) |
0.976 (1.00) |
0.527 (1.00) |
2.9e-06 (0.0023) |
0.000456 (0.345) |
0.109 (1.00) |
0.341 (1.00) |
0.103 (1.00) |
0.0226 (1.00) |
0.282 (1.00) |
0.397 (1.00) |
Amp Peak 29(22q12 2) | 88 (16%) | 471 |
0.602 (1.00) |
0.739 (1.00) |
0.0836 (1.00) |
0.359 (1.00) |
8.03e-05 (0.0622) |
0.00187 (1.00) |
0.983 (1.00) |
0.108 (1.00) |
0.275 (1.00) |
0.289 (1.00) |
0.0839 (1.00) |
0.0166 (1.00) |
Amp Peak 31(Xq28) | 222 (40%) | 337 |
0.241 (1.00) |
0.392 (1.00) |
0.832 (1.00) |
0.117 (1.00) |
2.43e-05 (0.019) |
0.15 (1.00) |
0.521 (1.00) |
0.425 (1.00) |
0.476 (1.00) |
0.621 (1.00) |
0.799 (1.00) |
0.569 (1.00) |
Del Peak 1(1p36 11) | 264 (47%) | 295 |
0.952 (1.00) |
0.804 (1.00) |
0.0385 (1.00) |
0.326 (1.00) |
5.76e-05 (0.0448) |
0.182 (1.00) |
0.189 (1.00) |
0.486 (1.00) |
0.936 (1.00) |
0.81 (1.00) |
0.324 (1.00) |
0.0681 (1.00) |
Del Peak 2(1q32 3) | 92 (16%) | 467 |
0.0848 (1.00) |
0.518 (1.00) |
0.477 (1.00) |
0.11 (1.00) |
6.56e-09 (5.35e-06) |
0.284 (1.00) |
0.982 (1.00) |
0.104 (1.00) |
0.244 (1.00) |
0.372 (1.00) |
0.848 (1.00) |
0.877 (1.00) |
Del Peak 5(2q37 3) | 172 (31%) | 387 |
0.0103 (1.00) |
0.00158 (1.00) |
0.716 (1.00) |
0.00146 (1.00) |
3.05e-05 (0.0239) |
0.0428 (1.00) |
0.562 (1.00) |
0.667 (1.00) |
0.0276 (1.00) |
0.0296 (1.00) |
0.00457 (1.00) |
0.0106 (1.00) |
Del Peak 9(5q11 2) | 335 (60%) | 224 |
0.694 (1.00) |
0.144 (1.00) |
0.425 (1.00) |
0.206 (1.00) |
2.74e-08 (2.21e-05) |
0.000791 (0.592) |
0.897 (1.00) |
0.881 (1.00) |
0.209 (1.00) |
0.424 (1.00) |
0.0328 (1.00) |
0.0145 (1.00) |
Del Peak 10(5q13 2) | 398 (71%) | 161 |
0.702 (1.00) |
0.738 (1.00) |
0.888 (1.00) |
0.809 (1.00) |
7.51e-13 (6.25e-10) |
0.0601 (1.00) |
0.956 (1.00) |
0.821 (1.00) |
0.407 (1.00) |
0.135 (1.00) |
0.134 (1.00) |
0.032 (1.00) |
Del Peak 12(7p22 1) | 243 (43%) | 316 |
0.569 (1.00) |
0.0224 (1.00) |
0.678 (1.00) |
0.66 (1.00) |
2.92e-14 (2.43e-11) |
0.854 (1.00) |
0.756 (1.00) |
0.744 (1.00) |
0.37 (1.00) |
0.115 (1.00) |
0.788 (1.00) |
0.904 (1.00) |
Del Peak 13(8p23 3) | 375 (67%) | 184 |
0.0571 (1.00) |
0.00845 (1.00) |
0.629 (1.00) |
0.0185 (1.00) |
1.1e-10 (9.09e-08) |
0.0567 (1.00) |
0.831 (1.00) |
0.665 (1.00) |
0.925 (1.00) |
0.417 (1.00) |
0.309 (1.00) |
0.174 (1.00) |
Del Peak 14(8p21 2) | 392 (70%) | 167 |
0.0388 (1.00) |
0.0146 (1.00) |
0.233 (1.00) |
0.00956 (1.00) |
1.05e-08 (8.49e-06) |
0.37 (1.00) |
0.432 (1.00) |
0.978 (1.00) |
0.321 (1.00) |
0.615 (1.00) |
0.84 (1.00) |
1 (1.00) |
Del Peak 15(9p24 3) | 247 (44%) | 312 |
0.000117 (0.0896) |
0.0803 (1.00) |
0.772 (1.00) |
0.00914 (1.00) |
0.0119 (1.00) |
0.000361 (0.273) |
0.732 (1.00) |
0.338 (1.00) |
0.0629 (1.00) |
0.392 (1.00) |
0.0638 (1.00) |
0.0232 (1.00) |
Del Peak 17(9q34 13) | 330 (59%) | 229 |
0.0193 (1.00) |
0.0144 (1.00) |
1 (1.00) |
0.0188 (1.00) |
1.15e-08 (9.36e-06) |
0.00984 (1.00) |
0.448 (1.00) |
0.277 (1.00) |
0.229 (1.00) |
0.284 (1.00) |
0.0578 (1.00) |
0.155 (1.00) |
Del Peak 20(10q26 3) | 186 (33%) | 373 |
0.00841 (1.00) |
0.0553 (1.00) |
0.25 (1.00) |
0.405 (1.00) |
8.82e-05 (0.0682) |
0.104 (1.00) |
0.317 (1.00) |
0.0113 (1.00) |
0.0636 (1.00) |
0.055 (1.00) |
0.00607 (1.00) |
0.094 (1.00) |
Del Peak 21(11p15 5) | 334 (60%) | 225 |
0.0499 (1.00) |
0.306 (1.00) |
0.729 (1.00) |
0.0477 (1.00) |
2.91e-11 (2.4e-08) |
0.0167 (1.00) |
0.916 (1.00) |
0.792 (1.00) |
0.9 (1.00) |
0.334 (1.00) |
0.0763 (1.00) |
0.00977 (1.00) |
Del Peak 29(16q22 1) | 441 (79%) | 118 |
0.363 (1.00) |
0.319 (1.00) |
0.0303 (1.00) |
0.925 (1.00) |
9.04e-05 (0.0698) |
0.454 (1.00) |
0.482 (1.00) |
0.306 (1.00) |
0.528 (1.00) |
0.0792 (1.00) |
0.505 (1.00) |
0.188 (1.00) |
Del Peak 30(16q23 1) | 434 (78%) | 125 |
0.11 (1.00) |
0.105 (1.00) |
0.143 (1.00) |
0.32 (1.00) |
3.93e-05 (0.0307) |
0.49 (1.00) |
0.434 (1.00) |
0.397 (1.00) |
0.563 (1.00) |
0.231 (1.00) |
0.101 (1.00) |
0.0265 (1.00) |
Del Peak 32(17q11 2) | 456 (82%) | 103 |
0.95 (1.00) |
0.0627 (1.00) |
0.735 (1.00) |
0.477 (1.00) |
0.000195 (0.149) |
0.000733 (0.549) |
0.671 (1.00) |
0.103 (1.00) |
0.705 (1.00) |
0.315 (1.00) |
0.077 (1.00) |
0.294 (1.00) |
Amp Peak 7(4p16 3) | 152 (27%) | 407 |
0.955 (1.00) |
0.0338 (1.00) |
0.0518 (1.00) |
0.694 (1.00) |
0.00123 (0.913) |
0.00705 (1.00) |
0.335 (1.00) |
0.888 (1.00) |
0.348 (1.00) |
0.35 (1.00) |
0.444 (1.00) |
0.179 (1.00) |
Amp Peak 15(10q22 3) | 175 (31%) | 384 |
0.443 (1.00) |
0.327 (1.00) |
0.607 (1.00) |
0.0601 (1.00) |
0.227 (1.00) |
0.973 (1.00) |
0.704 (1.00) |
0.955 (1.00) |
0.219 (1.00) |
0.403 (1.00) |
0.0934 (1.00) |
0.576 (1.00) |
Amp Peak 19(14q11 2) | 142 (25%) | 417 |
0.00478 (1.00) |
0.0765 (1.00) |
0.323 (1.00) |
0.00145 (1.00) |
0.0909 (1.00) |
0.14 (1.00) |
0.229 (1.00) |
0.169 (1.00) |
0.422 (1.00) |
0.159 (1.00) |
0.305 (1.00) |
0.31 (1.00) |
Amp Peak 21(17q25 3) | 205 (37%) | 354 |
0.453 (1.00) |
0.261 (1.00) |
0.913 (1.00) |
0.123 (1.00) |
0.0162 (1.00) |
0.944 (1.00) |
0.214 (1.00) |
0.211 (1.00) |
0.0216 (1.00) |
0.0427 (1.00) |
0.508 (1.00) |
0.148 (1.00) |
Del Peak 3(2p25 3) | 117 (21%) | 442 |
0.973 (1.00) |
0.982 (1.00) |
0.454 (1.00) |
0.489 (1.00) |
0.306 (1.00) |
0.587 (1.00) |
0.0516 (1.00) |
0.109 (1.00) |
0.269 (1.00) |
0.799 (1.00) |
0.914 (1.00) |
1 (1.00) |
Del Peak 4(2q22 1) | 132 (24%) | 427 |
0.0722 (1.00) |
0.13 (1.00) |
0.867 (1.00) |
0.15 (1.00) |
0.0526 (1.00) |
0.251 (1.00) |
0.368 (1.00) |
0.697 (1.00) |
0.723 (1.00) |
0.235 (1.00) |
0.618 (1.00) |
0.106 (1.00) |
Del Peak 7(4q22 1) | 373 (67%) | 186 |
0.0283 (1.00) |
0.328 (1.00) |
0.927 (1.00) |
0.00966 (1.00) |
0.0279 (1.00) |
0.521 (1.00) |
0.0172 (1.00) |
0.0581 (1.00) |
0.131 (1.00) |
0.42 (1.00) |
0.0797 (1.00) |
0.0697 (1.00) |
Del Peak 8(4q34 3) | 404 (72%) | 155 |
0.0165 (1.00) |
0.135 (1.00) |
0.0222 (1.00) |
0.0134 (1.00) |
0.183 (1.00) |
0.475 (1.00) |
0.592 (1.00) |
0.296 (1.00) |
0.0313 (1.00) |
0.0911 (1.00) |
0.37 (1.00) |
0.241 (1.00) |
Del Peak 18(10p15 3) | 118 (21%) | 441 |
0.138 (1.00) |
0.0407 (1.00) |
0.0968 (1.00) |
0.0865 (1.00) |
0.0994 (1.00) |
0.412 (1.00) |
0.372 (1.00) |
0.0779 (1.00) |
0.0834 (1.00) |
0.0149 (1.00) |
0.267 (1.00) |
0.118 (1.00) |
Del Peak 19(10q23 31) | 215 (38%) | 344 |
0.238 (1.00) |
0.981 (1.00) |
0.000556 (0.418) |
0.0125 (1.00) |
0.0019 (1.00) |
0.00115 (0.86) |
0.197 (1.00) |
0.0155 (1.00) |
0.865 (1.00) |
0.103 (1.00) |
0.0405 (1.00) |
0.351 (1.00) |
Del Peak 22(11q25) | 193 (35%) | 366 |
0.81 (1.00) |
0.211 (1.00) |
0.175 (1.00) |
0.38 (1.00) |
0.141 (1.00) |
0.483 (1.00) |
0.468 (1.00) |
0.56 (1.00) |
0.635 (1.00) |
0.367 (1.00) |
0.732 (1.00) |
0.199 (1.00) |
Del Peak 26(14q23 2) | 292 (52%) | 267 |
0.109 (1.00) |
0.6 (1.00) |
0.823 (1.00) |
0.802 (1.00) |
0.00227 (1.00) |
0.381 (1.00) |
0.202 (1.00) |
0.499 (1.00) |
0.891 (1.00) |
0.133 (1.00) |
0.483 (1.00) |
0.423 (1.00) |
Del Peak 28(16p13 3) | 297 (53%) | 262 |
0.542 (1.00) |
0.0773 (1.00) |
0.167 (1.00) |
0.462 (1.00) |
0.0856 (1.00) |
0.685 (1.00) |
0.645 (1.00) |
0.0862 (1.00) |
0.772 (1.00) |
0.634 (1.00) |
0.148 (1.00) |
0.636 (1.00) |
Del Peak 31(17p12) | 472 (84%) | 87 |
0.322 (1.00) |
0.719 (1.00) |
0.619 (1.00) |
0.591 (1.00) |
0.697 (1.00) |
0.332 (1.00) |
0.967 (1.00) |
0.355 (1.00) |
0.205 (1.00) |
0.556 (1.00) |
0.491 (1.00) |
0.237 (1.00) |
Del Peak 33(18q23) | 364 (65%) | 195 |
0.666 (1.00) |
0.82 (1.00) |
0.566 (1.00) |
0.379 (1.00) |
0.0022 (1.00) |
0.673 (1.00) |
0.465 (1.00) |
0.786 (1.00) |
0.139 (1.00) |
0.104 (1.00) |
0.637 (1.00) |
0.336 (1.00) |
Del Peak 34(19p13 3) | 492 (88%) | 67 |
0.257 (1.00) |
0.00399 (1.00) |
0.943 (1.00) |
0.462 (1.00) |
0.0096 (1.00) |
0.0228 (1.00) |
0.619 (1.00) |
0.179 (1.00) |
0.314 (1.00) |
0.00187 (1.00) |
0.403 (1.00) |
0.28 (1.00) |
Del Peak 35(19q13 33) | 290 (52%) | 269 |
0.000675 (0.506) |
0.0101 (1.00) |
0.0634 (1.00) |
0.138 (1.00) |
0.0362 (1.00) |
0.00165 (1.00) |
0.156 (1.00) |
0.0548 (1.00) |
0.0045 (1.00) |
0.0316 (1.00) |
0.408 (1.00) |
0.454 (1.00) |
Del Peak 37(21q22 3) | 218 (39%) | 341 |
0.235 (1.00) |
0.359 (1.00) |
0.705 (1.00) |
0.241 (1.00) |
0.855 (1.00) |
0.306 (1.00) |
0.858 (1.00) |
0.901 (1.00) |
0.14 (1.00) |
0.233 (1.00) |
0.458 (1.00) |
0.861 (1.00) |
Del Peak 38(22q13 32) | 483 (86%) | 76 |
0.125 (1.00) |
0.0621 (1.00) |
0.0229 (1.00) |
0.0717 (1.00) |
0.0592 (1.00) |
0.102 (1.00) |
0.0288 (1.00) |
0.356 (1.00) |
0.0956 (1.00) |
0.0272 (1.00) |
0.0286 (1.00) |
0.503 (1.00) |
Del Peak 39(Xp21 1) | 356 (64%) | 203 |
0.296 (1.00) |
0.98 (1.00) |
0.12 (1.00) |
0.643 (1.00) |
0.051 (1.00) |
0.0126 (1.00) |
0.119 (1.00) |
0.0349 (1.00) |
0.577 (1.00) |
0.803 (1.00) |
0.943 (1.00) |
0.222 (1.00) |
P value = 1.18e-06 (Fisher's exact test), Q value = 0.00094
Table S1. Gene #1: 'Amp Peak 1(1p34.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
AMP PEAK 1(1P34.3) MUTATED | 53 | 116 | 108 |
AMP PEAK 1(1P34.3) WILD-TYPE | 110 | 93 | 79 |
Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1p34.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D1V5.png)
P value = 7.18e-12 (Fisher's exact test), Q value = 6e-09
Table S2. Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
AMP PEAK 2(1Q21.3) MUTATED | 80 | 116 | 154 |
AMP PEAK 2(1Q21.3) WILD-TYPE | 83 | 93 | 33 |
Figure S2. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D2V5.png)
P value = 4.81e-05 (Fisher's exact test), Q value = 0.038
Table S3. Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 167 | 171 | 220 |
AMP PEAK 2(1Q21.3) MUTATED | 124 | 87 | 139 |
AMP PEAK 2(1Q21.3) WILD-TYPE | 43 | 84 | 81 |
Figure S3. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
![](D2V6.png)
P value = 3.15e-10 (Fisher's exact test), Q value = 2.6e-07
Table S4. Gene #3: 'Amp Peak 3(1q42.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
AMP PEAK 3(1Q42.2) MUTATED | 84 | 84 | 136 |
AMP PEAK 3(1Q42.2) WILD-TYPE | 79 | 125 | 51 |
Figure S4. Get High-res Image Gene #3: 'Amp Peak 3(1q42.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D3V5.png)
P value = 9.54e-05 (Fisher's exact test), Q value = 0.074
Table S5. Gene #3: 'Amp Peak 3(1q42.2) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 167 | 171 | 220 |
AMP PEAK 3(1Q42.2) MUTATED | 114 | 83 | 107 |
AMP PEAK 3(1Q42.2) WILD-TYPE | 53 | 88 | 113 |
Figure S5. Get High-res Image Gene #3: 'Amp Peak 3(1q42.2) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
![](D3V6.png)
P value = 2.67e-08 (Fisher's exact test), Q value = 2.2e-05
Table S6. Gene #4: 'Amp Peak 4(2p23.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
AMP PEAK 4(2P23.2) MUTATED | 44 | 83 | 108 |
AMP PEAK 4(2P23.2) WILD-TYPE | 119 | 126 | 79 |
Figure S6. Get High-res Image Gene #4: 'Amp Peak 4(2p23.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D4V5.png)
P value = 9.18e-10 (Fisher's exact test), Q value = 7.5e-07
Table S7. Gene #5: 'Amp Peak 5(2q31.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
AMP PEAK 5(2Q31.2) MUTATED | 39 | 100 | 106 |
AMP PEAK 5(2Q31.2) WILD-TYPE | 124 | 109 | 81 |
Figure S7. Get High-res Image Gene #5: 'Amp Peak 5(2q31.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D5V5.png)
P value = 1.02e-08 (Fisher's exact test), Q value = 8.3e-06
Table S8. Gene #6: 'Amp Peak 6(3q26.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
AMP PEAK 6(3Q26.2) MUTATED | 111 | 182 | 172 |
AMP PEAK 6(3Q26.2) WILD-TYPE | 52 | 27 | 15 |
Figure S8. Get High-res Image Gene #6: 'Amp Peak 6(3q26.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D6V5.png)
P value = 1.59e-05 (Fisher's exact test), Q value = 0.013
Table S9. Gene #8: 'Amp Peak 8(4q13.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
AMP PEAK 8(4Q13.3) MUTATED | 13 | 55 | 37 |
AMP PEAK 8(4Q13.3) WILD-TYPE | 150 | 154 | 150 |
Figure S9. Get High-res Image Gene #8: 'Amp Peak 8(4q13.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D8V5.png)
P value = 4.22e-07 (Fisher's exact test), Q value = 0.00034
Table S10. Gene #9: 'Amp Peak 9(5p15.33) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
AMP PEAK 9(5P15.33) MUTATED | 57 | 125 | 113 |
AMP PEAK 9(5P15.33) WILD-TYPE | 106 | 84 | 74 |
Figure S10. Get High-res Image Gene #9: 'Amp Peak 9(5p15.33) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D9V5.png)
P value = 1.67e-07 (Fisher's exact test), Q value = 0.00013
Table S11. Gene #10: 'Amp Peak 10(6p22.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
AMP PEAK 10(6P22.3) MUTATED | 54 | 126 | 107 |
AMP PEAK 10(6P22.3) WILD-TYPE | 109 | 83 | 80 |
Figure S11. Get High-res Image Gene #10: 'Amp Peak 10(6p22.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D10V5.png)
P value = 1.65e-06 (Fisher's exact test), Q value = 0.0013
Table S12. Gene #11: 'Amp Peak 11(7q36.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
AMP PEAK 11(7Q36.3) MUTATED | 60 | 124 | 116 |
AMP PEAK 11(7Q36.3) WILD-TYPE | 103 | 85 | 71 |
Figure S12. Get High-res Image Gene #11: 'Amp Peak 11(7q36.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D11V5.png)
P value = 2.11e-05 (Fisher's exact test), Q value = 0.017
Table S13. Gene #12: 'Amp Peak 12(8p11.21) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
AMP PEAK 12(8P11.21) MUTATED | 40 | 67 | 89 |
AMP PEAK 12(8P11.21) WILD-TYPE | 123 | 142 | 98 |
Figure S13. Get High-res Image Gene #12: 'Amp Peak 12(8p11.21) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D12V5.png)
P value = 1.05e-07 (Fisher's exact test), Q value = 8.4e-05
Table S14. Gene #13: 'Amp Peak 13(8q24.21) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 215 | 213 | 129 |
AMP PEAK 13(8Q24.21) MUTATED | 142 | 183 | 113 |
AMP PEAK 13(8Q24.21) WILD-TYPE | 73 | 30 | 16 |
Figure S14. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'
![](D13V1.png)
P value = 1.24e-05 (Fisher's exact test), Q value = 0.0098
Table S15. Gene #13: 'Amp Peak 13(8q24.21) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 233 | 199 | 125 |
AMP PEAK 13(8Q24.21) MUTATED | 205 | 140 | 93 |
AMP PEAK 13(8Q24.21) WILD-TYPE | 28 | 59 | 32 |
Figure S15. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'
![](D13V2.png)
P value = 2.87e-19 (Fisher's exact test), Q value = 2.4e-16
Table S16. Gene #13: 'Amp Peak 13(8q24.21) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
AMP PEAK 13(8Q24.21) MUTATED | 106 | 203 | 130 |
AMP PEAK 13(8Q24.21) WILD-TYPE | 57 | 6 | 57 |
Figure S16. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D13V5.png)
P value = 1.62e-06 (Fisher's exact test), Q value = 0.0013
Table S17. Gene #13: 'Amp Peak 13(8q24.21) mutation analysis' versus Clinical Feature #9: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 70 | 91 |
AMP PEAK 13(8Q24.21) MUTATED | 87 | 64 | 57 |
AMP PEAK 13(8Q24.21) WILD-TYPE | 11 | 6 | 34 |
Figure S17. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21) mutation analysis' versus Clinical Feature #9: 'MRNASEQ_CNMF'
![](D13V9.png)
P value = 4.44e-11 (Fisher's exact test), Q value = 3.7e-08
Table S18. Gene #14: 'Amp Peak 14(10p15.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
AMP PEAK 14(10P15.3) MUTATED | 46 | 76 | 117 |
AMP PEAK 14(10P15.3) WILD-TYPE | 117 | 133 | 70 |
Figure S18. Get High-res Image Gene #14: 'Amp Peak 14(10p15.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D14V5.png)
P value = 0.000103 (Fisher's exact test), Q value = 0.079
Table S19. Gene #14: 'Amp Peak 14(10p15.3) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 167 | 171 | 220 |
AMP PEAK 14(10P15.3) MUTATED | 94 | 60 | 84 |
AMP PEAK 14(10P15.3) WILD-TYPE | 73 | 111 | 136 |
Figure S19. Get High-res Image Gene #14: 'Amp Peak 14(10p15.3) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
![](D14V6.png)
P value = 9.58e-09 (Fisher's exact test), Q value = 7.8e-06
Table S20. Gene #16: 'Amp Peak 16(11q14.1) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
AMP PEAK 16(11Q14.1) MUTATED | 48 | 125 | 74 |
AMP PEAK 16(11Q14.1) WILD-TYPE | 115 | 84 | 113 |
Figure S20. Get High-res Image Gene #16: 'Amp Peak 16(11q14.1) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D16V5.png)
P value = 1.1e-09 (Fisher's exact test), Q value = 9e-07
Table S21. Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
AMP PEAK 17(12P13.33) MUTATED | 64 | 111 | 136 |
AMP PEAK 17(12P13.33) WILD-TYPE | 99 | 98 | 51 |
Figure S21. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D17V5.png)
P value = 1.36e-05 (Fisher's exact test), Q value = 0.011
Table S22. Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 167 | 171 | 220 |
AMP PEAK 17(12P13.33) MUTATED | 117 | 92 | 102 |
AMP PEAK 17(12P13.33) WILD-TYPE | 50 | 79 | 118 |
Figure S22. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
![](D17V6.png)
P value = 2.05e-12 (Fisher's exact test), Q value = 1.7e-09
Table S23. Gene #18: 'Amp Peak 18(12p12.1) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
AMP PEAK 18(12P12.1) MUTATED | 59 | 98 | 137 |
AMP PEAK 18(12P12.1) WILD-TYPE | 104 | 111 | 50 |
Figure S23. Get High-res Image Gene #18: 'Amp Peak 18(12p12.1) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D18V5.png)
P value = 1.01e-06 (Fisher's exact test), Q value = 0.00081
Table S24. Gene #18: 'Amp Peak 18(12p12.1) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 167 | 171 | 220 |
AMP PEAK 18(12P12.1) MUTATED | 116 | 80 | 98 |
AMP PEAK 18(12P12.1) WILD-TYPE | 51 | 91 | 122 |
Figure S24. Get High-res Image Gene #18: 'Amp Peak 18(12p12.1) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
![](D18V6.png)
P value = 5.92e-10 (Fisher's exact test), Q value = 4.9e-07
Table S25. Gene #20: 'Amp Peak 20(15q26.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
AMP PEAK 20(15Q26.3) MUTATED | 27 | 92 | 37 |
AMP PEAK 20(15Q26.3) WILD-TYPE | 136 | 117 | 150 |
Figure S25. Get High-res Image Gene #20: 'Amp Peak 20(15q26.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D20V5.png)
P value = 2.9e-06 (Fisher's exact test), Q value = 0.0023
Table S26. Gene #22: 'Amp Peak 22(18q11.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
AMP PEAK 22(18Q11.2) MUTATED | 22 | 47 | 68 |
AMP PEAK 22(18Q11.2) WILD-TYPE | 141 | 162 | 119 |
Figure S26. Get High-res Image Gene #22: 'Amp Peak 22(18q11.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D22V5.png)
P value = 1.97e-14 (Fisher's exact test), Q value = 1.6e-11
Table S27. Gene #23: 'Amp Peak 23(19p13.12) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
AMP PEAK 23(19P13.12) MUTATED | 68 | 89 | 144 |
AMP PEAK 23(19P13.12) WILD-TYPE | 95 | 120 | 43 |
Figure S27. Get High-res Image Gene #23: 'Amp Peak 23(19p13.12) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D23V5.png)
P value = 3.88e-06 (Fisher's exact test), Q value = 0.0031
Table S28. Gene #23: 'Amp Peak 23(19p13.12) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 167 | 171 | 220 |
AMP PEAK 23(19P13.12) MUTATED | 114 | 71 | 115 |
AMP PEAK 23(19P13.12) WILD-TYPE | 53 | 100 | 105 |
Figure S28. Get High-res Image Gene #23: 'Amp Peak 23(19p13.12) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
![](D23V6.png)
P value = 4.82e-05 (Fisher's exact test), Q value = 0.038
Table S29. Gene #23: 'Amp Peak 23(19p13.12) mutation analysis' versus Clinical Feature #7: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 124 | 204 | 70 |
AMP PEAK 23(19P13.12) MUTATED | 57 | 131 | 26 |
AMP PEAK 23(19P13.12) WILD-TYPE | 67 | 73 | 44 |
Figure S29. Get High-res Image Gene #23: 'Amp Peak 23(19p13.12) mutation analysis' versus Clinical Feature #7: 'RPPA_CNMF'
![](D23V7.png)
P value = 0.000193 (Fisher's exact test), Q value = 0.15
Table S30. Gene #23: 'Amp Peak 23(19p13.12) mutation analysis' versus Clinical Feature #8: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 98 | 65 | 141 | 94 |
AMP PEAK 23(19P13.12) MUTATED | 56 | 36 | 57 | 65 |
AMP PEAK 23(19P13.12) WILD-TYPE | 42 | 29 | 84 | 29 |
Figure S30. Get High-res Image Gene #23: 'Amp Peak 23(19p13.12) mutation analysis' versus Clinical Feature #8: 'RPPA_CHIERARCHICAL'
![](D23V8.png)
P value = 2.89e-26 (Fisher's exact test), Q value = 2.4e-23
Table S31. Gene #24: 'Amp Peak 24(19q12) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
AMP PEAK 24(19Q12) MUTATED | 62 | 86 | 161 |
AMP PEAK 24(19Q12) WILD-TYPE | 101 | 123 | 26 |
Figure S31. Get High-res Image Gene #24: 'Amp Peak 24(19q12) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D24V5.png)
P value = 3.63e-10 (Fisher's exact test), Q value = 3e-07
Table S32. Gene #24: 'Amp Peak 24(19q12) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 167 | 171 | 220 |
AMP PEAK 24(19Q12) MUTATED | 124 | 67 | 118 |
AMP PEAK 24(19Q12) WILD-TYPE | 43 | 104 | 102 |
Figure S32. Get High-res Image Gene #24: 'Amp Peak 24(19q12) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
![](D24V6.png)
P value = 6.25e-10 (Fisher's exact test), Q value = 5.1e-07
Table S33. Gene #25: 'Amp Peak 25(19q13.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
AMP PEAK 25(19Q13.2) MUTATED | 48 | 73 | 114 |
AMP PEAK 25(19Q13.2) WILD-TYPE | 115 | 136 | 73 |
Figure S33. Get High-res Image Gene #25: 'Amp Peak 25(19q13.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D25V5.png)
P value = 0.000201 (Fisher's exact test), Q value = 0.15
Table S34. Gene #25: 'Amp Peak 25(19q13.2) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 167 | 171 | 220 |
AMP PEAK 25(19Q13.2) MUTATED | 91 | 56 | 88 |
AMP PEAK 25(19Q13.2) WILD-TYPE | 76 | 115 | 132 |
Figure S34. Get High-res Image Gene #25: 'Amp Peak 25(19q13.2) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
![](D25V6.png)
P value = 0.000126 (Fisher's exact test), Q value = 0.097
Table S35. Gene #26: 'Amp Peak 26(20p13) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 233 | 199 | 125 |
AMP PEAK 26(20P13) MUTATED | 120 | 128 | 51 |
AMP PEAK 26(20P13) WILD-TYPE | 113 | 71 | 74 |
Figure S35. Get High-res Image Gene #26: 'Amp Peak 26(20p13) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'
![](D26V2.png)
P value = 9.8e-12 (Fisher's exact test), Q value = 8.1e-09
Table S36. Gene #26: 'Amp Peak 26(20p13) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
AMP PEAK 26(20P13) MUTATED | 66 | 95 | 139 |
AMP PEAK 26(20P13) WILD-TYPE | 97 | 114 | 48 |
Figure S36. Get High-res Image Gene #26: 'Amp Peak 26(20p13) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D26V5.png)
P value = 2.23e-09 (Fisher's exact test), Q value = 1.8e-06
Table S37. Gene #26: 'Amp Peak 26(20p13) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 167 | 171 | 220 |
AMP PEAK 26(20P13) MUTATED | 123 | 78 | 98 |
AMP PEAK 26(20P13) WILD-TYPE | 44 | 93 | 122 |
Figure S37. Get High-res Image Gene #26: 'Amp Peak 26(20p13) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
![](D26V6.png)
P value = 3.68e-08 (Fisher's exact test), Q value = 3e-05
Table S38. Gene #27: 'Amp Peak 27(20q11.21) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 233 | 199 | 125 |
AMP PEAK 27(20Q11.21) MUTATED | 132 | 143 | 49 |
AMP PEAK 27(20Q11.21) WILD-TYPE | 101 | 56 | 76 |
Figure S38. Get High-res Image Gene #27: 'Amp Peak 27(20q11.21) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'
![](D27V2.png)
P value = 0.000105 (Chi-square test), Q value = 0.081
Table S39. Gene #27: 'Amp Peak 27(20q11.21) mutation analysis' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 65 | 115 | 125 | 99 | 57 | 94 |
AMP PEAK 27(20Q11.21) MUTATED | 37 | 54 | 71 | 50 | 39 | 73 |
AMP PEAK 27(20Q11.21) WILD-TYPE | 28 | 61 | 54 | 49 | 18 | 21 |
Figure S39. Get High-res Image Gene #27: 'Amp Peak 27(20q11.21) mutation analysis' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'
![](D27V4.png)
P value = 1.01e-22 (Fisher's exact test), Q value = 8.5e-20
Table S40. Gene #27: 'Amp Peak 27(20q11.21) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
AMP PEAK 27(20Q11.21) MUTATED | 72 | 92 | 162 |
AMP PEAK 27(20Q11.21) WILD-TYPE | 91 | 117 | 25 |
Figure S40. Get High-res Image Gene #27: 'Amp Peak 27(20q11.21) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D27V5.png)
P value = 8.1e-13 (Fisher's exact test), Q value = 6.7e-10
Table S41. Gene #27: 'Amp Peak 27(20q11.21) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 167 | 171 | 220 |
AMP PEAK 27(20Q11.21) MUTATED | 136 | 86 | 104 |
AMP PEAK 27(20Q11.21) WILD-TYPE | 31 | 85 | 116 |
Figure S41. Get High-res Image Gene #27: 'Amp Peak 27(20q11.21) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
![](D27V6.png)
P value = 0.000329 (Fisher's exact test), Q value = 0.25
Table S42. Gene #27: 'Amp Peak 27(20q11.21) mutation analysis' versus Clinical Feature #9: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 70 | 91 |
AMP PEAK 27(20Q11.21) MUTATED | 60 | 29 | 66 |
AMP PEAK 27(20Q11.21) WILD-TYPE | 38 | 41 | 25 |
Figure S42. Get High-res Image Gene #27: 'Amp Peak 27(20q11.21) mutation analysis' versus Clinical Feature #9: 'MRNASEQ_CNMF'
![](D27V9.png)
P value = 3.75e-05 (Fisher's exact test), Q value = 0.029
Table S43. Gene #28: 'Amp Peak 28(20q13.33) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 233 | 199 | 125 |
AMP PEAK 28(20Q13.33) MUTATED | 157 | 158 | 70 |
AMP PEAK 28(20Q13.33) WILD-TYPE | 76 | 41 | 55 |
Figure S43. Get High-res Image Gene #28: 'Amp Peak 28(20q13.33) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'
![](D28V2.png)
P value = 1.21e-15 (Fisher's exact test), Q value = 1e-12
Table S44. Gene #28: 'Amp Peak 28(20q13.33) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
AMP PEAK 28(20Q13.33) MUTATED | 82 | 138 | 167 |
AMP PEAK 28(20Q13.33) WILD-TYPE | 81 | 71 | 20 |
Figure S44. Get High-res Image Gene #28: 'Amp Peak 28(20q13.33) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D28V5.png)
P value = 2.8e-08 (Fisher's exact test), Q value = 2.3e-05
Table S45. Gene #28: 'Amp Peak 28(20q13.33) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 167 | 171 | 220 |
AMP PEAK 28(20Q13.33) MUTATED | 144 | 106 | 137 |
AMP PEAK 28(20Q13.33) WILD-TYPE | 23 | 65 | 83 |
Figure S45. Get High-res Image Gene #28: 'Amp Peak 28(20q13.33) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
![](D28V6.png)
P value = 8.03e-05 (Fisher's exact test), Q value = 0.062
Table S46. Gene #29: 'Amp Peak 29(22q12.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
AMP PEAK 29(22Q12.2) MUTATED | 10 | 44 | 34 |
AMP PEAK 29(22Q12.2) WILD-TYPE | 153 | 165 | 153 |
Figure S46. Get High-res Image Gene #29: 'Amp Peak 29(22q12.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D29V5.png)
P value = 3.27e-06 (Fisher's exact test), Q value = 0.0026
Table S47. Gene #30: 'Amp Peak 30(Xp11.23) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
AMP PEAK 30(XP11.23) MUTATED | 29 | 55 | 78 |
AMP PEAK 30(XP11.23) WILD-TYPE | 134 | 154 | 109 |
Figure S47. Get High-res Image Gene #30: 'Amp Peak 30(Xp11.23) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D30V5.png)
P value = 1.46e-05 (Fisher's exact test), Q value = 0.011
Table S48. Gene #30: 'Amp Peak 30(Xp11.23) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 167 | 171 | 220 |
AMP PEAK 30(XP11.23) MUTATED | 72 | 37 | 53 |
AMP PEAK 30(XP11.23) WILD-TYPE | 95 | 134 | 167 |
Figure S48. Get High-res Image Gene #30: 'Amp Peak 30(Xp11.23) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
![](D30V6.png)
P value = 2.43e-05 (Fisher's exact test), Q value = 0.019
Table S49. Gene #31: 'Amp Peak 31(Xq28) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
AMP PEAK 31(XQ28) MUTATED | 42 | 102 | 78 |
AMP PEAK 31(XQ28) WILD-TYPE | 121 | 107 | 109 |
Figure S49. Get High-res Image Gene #31: 'Amp Peak 31(Xq28) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D31V5.png)
P value = 5.76e-05 (Fisher's exact test), Q value = 0.045
Table S50. Gene #32: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
DEL PEAK 1(1P36.11) MUTATED | 85 | 115 | 64 |
DEL PEAK 1(1P36.11) WILD-TYPE | 78 | 94 | 123 |
Figure S50. Get High-res Image Gene #32: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D32V5.png)
P value = 6.56e-09 (Fisher's exact test), Q value = 5.4e-06
Table S51. Gene #33: 'Del Peak 2(1q32.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
DEL PEAK 2(1Q32.3) MUTATED | 14 | 61 | 17 |
DEL PEAK 2(1Q32.3) WILD-TYPE | 149 | 148 | 170 |
Figure S51. Get High-res Image Gene #33: 'Del Peak 2(1q32.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D33V5.png)
P value = 3.05e-05 (Fisher's exact test), Q value = 0.024
Table S52. Gene #36: 'Del Peak 5(2q37.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
DEL PEAK 5(2Q37.3) MUTATED | 35 | 88 | 49 |
DEL PEAK 5(2Q37.3) WILD-TYPE | 128 | 121 | 138 |
Figure S52. Get High-res Image Gene #36: 'Del Peak 5(2q37.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D36V5.png)
P value = 6.13e-05 (Fisher's exact test), Q value = 0.048
Table S53. Gene #37: 'Del Peak 6(3p26.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 233 | 199 | 125 |
DEL PEAK 6(3P26.2) MUTATED | 88 | 90 | 27 |
DEL PEAK 6(3P26.2) WILD-TYPE | 145 | 109 | 98 |
Figure S53. Get High-res Image Gene #37: 'Del Peak 6(3p26.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'
![](D37V2.png)
P value = 9.31e-05 (Fisher's exact test), Q value = 0.072
Table S54. Gene #37: 'Del Peak 6(3p26.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
DEL PEAK 6(3P26.2) MUTATED | 44 | 71 | 91 |
DEL PEAK 6(3P26.2) WILD-TYPE | 119 | 138 | 96 |
Figure S54. Get High-res Image Gene #37: 'Del Peak 6(3p26.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D37V5.png)
P value = 5.51e-05 (Fisher's exact test), Q value = 0.043
Table S55. Gene #37: 'Del Peak 6(3p26.2) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 167 | 171 | 220 |
DEL PEAK 6(3P26.2) MUTATED | 84 | 48 | 73 |
DEL PEAK 6(3P26.2) WILD-TYPE | 83 | 123 | 147 |
Figure S55. Get High-res Image Gene #37: 'Del Peak 6(3p26.2) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
![](D37V6.png)
P value = 2.74e-08 (Fisher's exact test), Q value = 2.2e-05
Table S56. Gene #40: 'Del Peak 9(5q11.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
DEL PEAK 9(5Q11.2) MUTATED | 67 | 147 | 121 |
DEL PEAK 9(5Q11.2) WILD-TYPE | 96 | 62 | 66 |
Figure S56. Get High-res Image Gene #40: 'Del Peak 9(5q11.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D40V5.png)
P value = 7.51e-13 (Fisher's exact test), Q value = 6.3e-10
Table S57. Gene #41: 'Del Peak 10(5q13.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
DEL PEAK 10(5Q13.2) MUTATED | 84 | 181 | 133 |
DEL PEAK 10(5Q13.2) WILD-TYPE | 79 | 28 | 54 |
Figure S57. Get High-res Image Gene #41: 'Del Peak 10(5q13.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D41V5.png)
P value = 8e-09 (Fisher's exact test), Q value = 6.5e-06
Table S58. Gene #42: 'Del Peak 11(6q27) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
DEL PEAK 11(6Q27) MUTATED | 114 | 159 | 89 |
DEL PEAK 11(6Q27) WILD-TYPE | 49 | 50 | 98 |
Figure S58. Get High-res Image Gene #42: 'Del Peak 11(6q27) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D42V5.png)
P value = 1.62e-05 (Fisher's exact test), Q value = 0.013
Table S59. Gene #42: 'Del Peak 11(6q27) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 167 | 171 | 220 |
DEL PEAK 11(6Q27) MUTATED | 85 | 128 | 148 |
DEL PEAK 11(6Q27) WILD-TYPE | 82 | 43 | 72 |
Figure S59. Get High-res Image Gene #42: 'Del Peak 11(6q27) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
![](D42V6.png)
P value = 2.92e-14 (Fisher's exact test), Q value = 2.4e-11
Table S60. Gene #43: 'Del Peak 12(7p22.1) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
DEL PEAK 12(7P22.1) MUTATED | 45 | 135 | 63 |
DEL PEAK 12(7P22.1) WILD-TYPE | 118 | 74 | 124 |
Figure S60. Get High-res Image Gene #43: 'Del Peak 12(7p22.1) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D43V5.png)
P value = 1.1e-10 (Fisher's exact test), Q value = 9.1e-08
Table S61. Gene #44: 'Del Peak 13(8p23.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
DEL PEAK 13(8P23.3) MUTATED | 75 | 163 | 137 |
DEL PEAK 13(8P23.3) WILD-TYPE | 88 | 46 | 50 |
Figure S61. Get High-res Image Gene #44: 'Del Peak 13(8p23.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D44V5.png)
P value = 1.05e-08 (Fisher's exact test), Q value = 8.5e-06
Table S62. Gene #45: 'Del Peak 14(8p21.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
DEL PEAK 14(8P21.2) MUTATED | 84 | 165 | 143 |
DEL PEAK 14(8P21.2) WILD-TYPE | 79 | 44 | 44 |
Figure S62. Get High-res Image Gene #45: 'Del Peak 14(8p21.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D45V5.png)
P value = 0.000117 (Fisher's exact test), Q value = 0.09
Table S63. Gene #46: 'Del Peak 15(9p24.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 215 | 213 | 129 |
DEL PEAK 15(9P24.3) MUTATED | 110 | 70 | 66 |
DEL PEAK 15(9P24.3) WILD-TYPE | 105 | 143 | 63 |
Figure S63. Get High-res Image Gene #46: 'Del Peak 15(9p24.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'
![](D46V1.png)
P value = 4.16e-15 (Fisher's exact test), Q value = 3.5e-12
Table S64. Gene #47: 'Del Peak 16(9q21.11) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
DEL PEAK 16(9Q21.11) MUTATED | 69 | 66 | 133 |
DEL PEAK 16(9Q21.11) WILD-TYPE | 94 | 143 | 54 |
Figure S64. Get High-res Image Gene #47: 'Del Peak 16(9q21.11) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D47V5.png)
P value = 3.98e-07 (Fisher's exact test), Q value = 0.00032
Table S65. Gene #47: 'Del Peak 16(9q21.11) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 167 | 171 | 220 |
DEL PEAK 16(9Q21.11) MUTATED | 109 | 65 | 94 |
DEL PEAK 16(9Q21.11) WILD-TYPE | 58 | 106 | 126 |
Figure S65. Get High-res Image Gene #47: 'Del Peak 16(9q21.11) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
![](D47V6.png)
P value = 1.15e-08 (Fisher's exact test), Q value = 9.4e-06
Table S66. Gene #48: 'Del Peak 17(9q34.13) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
DEL PEAK 17(9Q34.13) MUTATED | 82 | 105 | 143 |
DEL PEAK 17(9Q34.13) WILD-TYPE | 81 | 104 | 44 |
Figure S66. Get High-res Image Gene #48: 'Del Peak 17(9q34.13) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D48V5.png)
P value = 8.82e-05 (Fisher's exact test), Q value = 0.068
Table S67. Gene #51: 'Del Peak 20(10q26.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
DEL PEAK 20(10Q26.3) MUTATED | 34 | 87 | 65 |
DEL PEAK 20(10Q26.3) WILD-TYPE | 129 | 122 | 122 |
Figure S67. Get High-res Image Gene #51: 'Del Peak 20(10q26.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D51V5.png)
P value = 2.91e-11 (Fisher's exact test), Q value = 2.4e-08
Table S68. Gene #52: 'Del Peak 21(11p15.5) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
DEL PEAK 21(11P15.5) MUTATED | 72 | 162 | 100 |
DEL PEAK 21(11P15.5) WILD-TYPE | 91 | 47 | 87 |
Figure S68. Get High-res Image Gene #52: 'Del Peak 21(11p15.5) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D52V5.png)
P value = 0.000204 (Fisher's exact test), Q value = 0.16
Table S69. Gene #54: 'Del Peak 23(12q23.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 233 | 199 | 125 |
DEL PEAK 23(12Q23.1) MUTATED | 97 | 47 | 48 |
DEL PEAK 23(12Q23.1) WILD-TYPE | 136 | 152 | 77 |
Figure S69. Get High-res Image Gene #54: 'Del Peak 23(12q23.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'
![](D54V2.png)
P value = 4.4e-08 (Fisher's exact test), Q value = 3.6e-05
Table S70. Gene #54: 'Del Peak 23(12q23.1) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
DEL PEAK 23(12Q23.1) MUTATED | 43 | 104 | 46 |
DEL PEAK 23(12Q23.1) WILD-TYPE | 120 | 105 | 141 |
Figure S70. Get High-res Image Gene #54: 'Del Peak 23(12q23.1) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D54V5.png)
P value = 2.63e-06 (Fisher's exact test), Q value = 0.0021
Table S71. Gene #55: 'Del Peak 24(12q24.33) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 233 | 199 | 125 |
DEL PEAK 24(12Q24.33) MUTATED | 101 | 49 | 62 |
DEL PEAK 24(12Q24.33) WILD-TYPE | 132 | 150 | 63 |
Figure S71. Get High-res Image Gene #55: 'Del Peak 24(12q24.33) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'
![](D55V2.png)
P value = 1.14e-11 (Fisher's exact test), Q value = 9.4e-09
Table S72. Gene #55: 'Del Peak 24(12q24.33) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
DEL PEAK 24(12Q24.33) MUTATED | 47 | 119 | 47 |
DEL PEAK 24(12Q24.33) WILD-TYPE | 116 | 90 | 140 |
Figure S72. Get High-res Image Gene #55: 'Del Peak 24(12q24.33) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D55V5.png)
P value = 1.11e-06 (Fisher's exact test), Q value = 0.00089
Table S73. Gene #56: 'Del Peak 25(13q14.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
DEL PEAK 25(13Q14.2) MUTATED | 79 | 156 | 113 |
DEL PEAK 25(13Q14.2) WILD-TYPE | 84 | 53 | 74 |
Figure S73. Get High-res Image Gene #56: 'Del Peak 25(13q14.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D56V5.png)
P value = 9.8e-06 (Fisher's exact test), Q value = 0.0078
Table S74. Gene #56: 'Del Peak 25(13q14.2) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 167 | 171 | 220 |
DEL PEAK 25(13Q14.2) MUTATED | 106 | 83 | 159 |
DEL PEAK 25(13Q14.2) WILD-TYPE | 61 | 88 | 61 |
Figure S74. Get High-res Image Gene #56: 'Del Peak 25(13q14.2) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
![](D56V6.png)
P value = 0.000301 (Fisher's exact test), Q value = 0.23
Table S75. Gene #56: 'Del Peak 25(13q14.2) mutation analysis' versus Clinical Feature #7: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 124 | 204 | 70 |
DEL PEAK 25(13Q14.2) MUTATED | 64 | 146 | 37 |
DEL PEAK 25(13Q14.2) WILD-TYPE | 60 | 58 | 33 |
Figure S75. Get High-res Image Gene #56: 'Del Peak 25(13q14.2) mutation analysis' versus Clinical Feature #7: 'RPPA_CNMF'
![](D56V7.png)
P value = 1.75e-10 (Fisher's exact test), Q value = 1.4e-07
Table S76. Gene #58: 'Del Peak 27(15q15.1) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
DEL PEAK 27(15Q15.1) MUTATED | 78 | 122 | 151 |
DEL PEAK 27(15Q15.1) WILD-TYPE | 85 | 87 | 36 |
Figure S76. Get High-res Image Gene #58: 'Del Peak 27(15q15.1) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D58V5.png)
P value = 7.64e-05 (Fisher's exact test), Q value = 0.059
Table S77. Gene #58: 'Del Peak 27(15q15.1) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 167 | 171 | 220 |
DEL PEAK 27(15Q15.1) MUTATED | 127 | 94 | 130 |
DEL PEAK 27(15Q15.1) WILD-TYPE | 40 | 77 | 90 |
Figure S77. Get High-res Image Gene #58: 'Del Peak 27(15q15.1) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
![](D58V6.png)
P value = 9.04e-05 (Fisher's exact test), Q value = 0.07
Table S78. Gene #60: 'Del Peak 29(16q22.1) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
DEL PEAK 29(16Q22.1) MUTATED | 110 | 170 | 161 |
DEL PEAK 29(16Q22.1) WILD-TYPE | 53 | 39 | 26 |
Figure S78. Get High-res Image Gene #60: 'Del Peak 29(16q22.1) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D60V5.png)
P value = 3.93e-05 (Fisher's exact test), Q value = 0.031
Table S79. Gene #61: 'Del Peak 30(16q23.1) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
DEL PEAK 30(16Q23.1) MUTATED | 107 | 167 | 160 |
DEL PEAK 30(16Q23.1) WILD-TYPE | 56 | 42 | 27 |
Figure S79. Get High-res Image Gene #61: 'Del Peak 30(16q23.1) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D61V5.png)
P value = 0.000195 (Fisher's exact test), Q value = 0.15
Table S80. Gene #63: 'Del Peak 32(17q11.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
DEL PEAK 32(17Q11.2) MUTATED | 127 | 188 | 141 |
DEL PEAK 32(17Q11.2) WILD-TYPE | 36 | 21 | 46 |
Figure S80. Get High-res Image Gene #63: 'Del Peak 32(17q11.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D63V5.png)
P value = 0.000298 (Fisher's exact test), Q value = 0.23
Table S81. Gene #67: 'Del Peak 36(19q13.43) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 209 | 187 |
DEL PEAK 36(19Q13.43) MUTATED | 80 | 84 | 113 |
DEL PEAK 36(19Q13.43) WILD-TYPE | 83 | 125 | 74 |
Figure S81. Get High-res Image Gene #67: 'Del Peak 36(19q13.43) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'
![](D67V5.png)
P value = 0.000107 (Fisher's exact test), Q value = 0.082
Table S82. Gene #67: 'Del Peak 36(19q13.43) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 167 | 171 | 220 |
DEL PEAK 36(19Q13.43) MUTATED | 101 | 64 | 112 |
DEL PEAK 36(19Q13.43) WILD-TYPE | 66 | 107 | 108 |
Figure S82. Get High-res Image Gene #67: 'Del Peak 36(19q13.43) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'
![](D67V6.png)
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Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
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Molecular subtype file = OV-TP.transferedmergedcluster.txt
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Number of patients = 559
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Number of copy number variation regions = 70
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Number of molecular subtypes = 12
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Exclude regions 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 multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.