This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.
Testing the association between copy number variation 29 focal events and 12 molecular subtypes across 527 patients, 139 significant findings detected with P value < 0.05 and Q value < 0.25.
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amp_1q24.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
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amp_1q32.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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amp_3q26.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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amp_4q32.1 cnv correlated to 'MIRSEQ_CNMF'.
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amp_5q35.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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amp_7q36.3 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', and 'MRNASEQ_CNMF'.
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amp_8q24.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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amp_10p14 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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amp_xp22.2 cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.
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amp_xp11.4 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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del_1p36.23 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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del_1p31.1 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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del_1q43 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
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del_2q37.3 cnv correlated to 'MRNA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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del_3p25.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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del_3p12.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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del_3p11.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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del_3q11.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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del_4q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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del_6q26 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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del_6q26 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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del_8p23.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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del_9p23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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del_10q23.31 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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del_13q13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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del_14q31.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 29 focal events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 139 significant findings detected.
|
Clinical Features |
MRNA CNMF |
MRNA 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 | |
| del 1p36 23 | 103 (20%) | 424 |
0.00015 (0.0363) |
0.0009 (0.194) |
1e-05 (0.00348) |
0.0783 (1.00) |
3e-05 (0.00786) |
8e-05 (0.0198) |
4e-05 (0.0104) |
1e-05 (0.00348) |
1e-05 (0.00348) |
2e-05 (0.00546) |
0.00056 (0.124) |
0.00013 (0.0316) |
| del 3p25 3 | 462 (88%) | 65 |
1e-05 (0.00348) |
1e-05 (0.00348) |
1e-05 (0.00348) |
1e-05 (0.00348) |
4e-05 (0.0104) |
0.0222 (1.00) |
1e-05 (0.00348) |
1e-05 (0.00348) |
2e-05 (0.00546) |
3e-05 (0.00786) |
0.00093 (0.2) |
1e-05 (0.00348) |
| del 14q31 1 | 228 (43%) | 299 |
8e-05 (0.0198) |
0.00041 (0.0922) |
1e-05 (0.00348) |
1e-05 (0.00348) |
1e-05 (0.00348) |
4e-05 (0.0104) |
1e-05 (0.00348) |
1e-05 (0.00348) |
1e-05 (0.00348) |
1e-05 (0.00348) |
2e-05 (0.00546) |
0.00365 (0.712) |
| amp 8q24 22 | 79 (15%) | 448 |
0.225 (1.00) |
0.104 (1.00) |
1e-05 (0.00348) |
2e-05 (0.00546) |
1e-05 (0.00348) |
0.00065 (0.143) |
1e-05 (0.00348) |
1e-05 (0.00348) |
1e-05 (0.00348) |
1e-05 (0.00348) |
1e-05 (0.00348) |
6e-05 (0.0151) |
| del 9p23 | 152 (29%) | 375 |
0.0037 (0.714) |
0.0358 (1.00) |
1e-05 (0.00348) |
1e-05 (0.00348) |
1e-05 (0.00348) |
0.00018 (0.0425) |
1e-05 (0.00348) |
1e-05 (0.00348) |
1e-05 (0.00348) |
1e-05 (0.00348) |
1e-05 (0.00348) |
3e-05 (0.00786) |
| del 9p21 3 | 159 (30%) | 368 |
0.00122 (0.255) |
0.0163 (1.00) |
1e-05 (0.00348) |
1e-05 (0.00348) |
1e-05 (0.00348) |
4e-05 (0.0104) |
1e-05 (0.00348) |
1e-05 (0.00348) |
1e-05 (0.00348) |
1e-05 (0.00348) |
1e-05 (0.00348) |
1e-05 (0.00348) |
| amp 3q26 32 | 87 (17%) | 440 |
0.0576 (1.00) |
0.121 (1.00) |
1e-05 (0.00348) |
2e-05 (0.00546) |
0.00294 (0.579) |
1e-05 (0.00348) |
1e-05 (0.00348) |
1e-05 (0.00348) |
1e-05 (0.00348) |
0.00021 (0.0489) |
0.00131 (0.271) |
0.0432 (1.00) |
| del 6q26 | 151 (29%) | 376 |
0.0149 (1.00) |
0.098 (1.00) |
1e-05 (0.00348) |
0.0133 (1.00) |
2e-05 (0.00546) |
0.00033 (0.0752) |
0.00044 (0.0986) |
0.00113 (0.237) |
1e-05 (0.00348) |
0.00548 (0.986) |
0.00017 (0.0405) |
0.0838 (1.00) |
| del 6q26 | 151 (29%) | 376 |
0.0151 (1.00) |
0.099 (1.00) |
1e-05 (0.00348) |
0.0124 (1.00) |
1e-05 (0.00348) |
0.0003 (0.0687) |
0.00018 (0.0425) |
0.00077 (0.167) |
1e-05 (0.00348) |
0.00515 (0.932) |
1e-05 (0.00348) |
0.0849 (1.00) |
| del 13q13 3 | 81 (15%) | 446 |
0.0143 (1.00) |
0.0847 (1.00) |
1e-05 (0.00348) |
0.00021 (0.0489) |
1e-05 (0.00348) |
0.00361 (0.708) |
2e-05 (0.00546) |
1e-05 (0.00348) |
1e-05 (0.00348) |
1e-05 (0.00348) |
0.0535 (1.00) |
0.00138 (0.284) |
| del 1p31 1 | 77 (15%) | 450 |
0.00168 (0.341) |
0.00674 (1.00) |
1e-05 (0.00348) |
0.102 (1.00) |
0.0001 (0.0245) |
0.00108 (0.23) |
0.00944 (1.00) |
8e-05 (0.0198) |
1e-05 (0.00348) |
0.00016 (0.0386) |
0.0112 (1.00) |
0.00504 (0.917) |
| amp 1q32 1 | 62 (12%) | 465 |
0.41 (1.00) |
0.899 (1.00) |
1e-05 (0.00348) |
0.0381 (1.00) |
0.161 (1.00) |
0.146 (1.00) |
1e-05 (0.00348) |
0.00556 (0.995) |
4e-05 (0.0104) |
0.28 (1.00) |
0.00038 (0.0859) |
0.304 (1.00) |
| del 3p12 3 | 334 (63%) | 193 |
0.00384 (0.726) |
0.0187 (1.00) |
1e-05 (0.00348) |
0.0002 (0.0468) |
0.494 (1.00) |
0.498 (1.00) |
6e-05 (0.0151) |
1e-05 (0.00348) |
0.095 (1.00) |
0.258 (1.00) |
0.0347 (1.00) |
0.157 (1.00) |
| del 4q34 3 | 78 (15%) | 449 |
0.24 (1.00) |
0.495 (1.00) |
1e-05 (0.00348) |
1e-05 (0.00348) |
0.0109 (1.00) |
0.0427 (1.00) |
0.00026 (0.0598) |
2e-05 (0.00546) |
0.339 (1.00) |
0.00196 (0.392) |
0.0175 (1.00) |
0.0157 (1.00) |
| del 8p23 2 | 154 (29%) | 373 |
0.503 (1.00) |
0.247 (1.00) |
1e-05 (0.00348) |
0.0402 (1.00) |
0.00715 (1.00) |
0.0417 (1.00) |
0.0011 (0.232) |
1e-05 (0.00348) |
0.00057 (0.126) |
0.00122 (0.255) |
0.0581 (1.00) |
0.0125 (1.00) |
| amp 1q24 1 | 62 (12%) | 465 |
0.258 (1.00) |
0.788 (1.00) |
1e-05 (0.00348) |
0.135 (1.00) |
0.289 (1.00) |
0.335 (1.00) |
5e-05 (0.0127) |
0.00406 (0.763) |
1e-05 (0.00348) |
0.245 (1.00) |
0.00246 (0.49) |
0.223 (1.00) |
| amp 7q36 3 | 176 (33%) | 351 |
0.454 (1.00) |
0.859 (1.00) |
1e-05 (0.00348) |
0.00614 (1.00) |
0.00016 (0.0386) |
0.00959 (1.00) |
2e-05 (0.00546) |
0.00371 (0.714) |
0.00251 (0.497) |
0.0283 (1.00) |
0.0337 (1.00) |
0.0452 (1.00) |
| amp xp11 4 | 33 (6%) | 494 |
0.845 (1.00) |
0.797 (1.00) |
0.00016 (0.0386) |
0.113 (1.00) |
0.00075 (0.163) |
0.00365 (0.712) |
0.0294 (1.00) |
0.00045 (0.1) |
0.0321 (1.00) |
0.34 (1.00) |
0.06 (1.00) |
0.105 (1.00) |
| del 2q37 3 | 50 (9%) | 477 |
0.00169 (0.341) |
0.00033 (0.0752) |
0.863 (1.00) |
0.66 (1.00) |
0.14 (1.00) |
0.431 (1.00) |
6e-05 (0.0151) |
1e-05 (0.00348) |
0.0357 (1.00) |
0.011 (1.00) |
0.143 (1.00) |
0.00441 (0.814) |
| amp 5q35 1 | 332 (63%) | 195 |
0.0631 (1.00) |
0.0491 (1.00) |
0.00017 (0.0405) |
0.402 (1.00) |
0.0085 (1.00) |
0.00431 (0.806) |
0.0014 (0.287) |
0.00023 (0.0531) |
0.195 (1.00) |
0.0935 (1.00) |
0.736 (1.00) |
0.0238 (1.00) |
| amp 10p14 | 20 (4%) | 507 |
0.188 (1.00) |
0.774 (1.00) |
2e-05 (0.00546) |
0.178 (1.00) |
0.742 (1.00) |
0.367 (1.00) |
0.00174 (0.35) |
5e-05 (0.0127) |
0.0795 (1.00) |
0.031 (1.00) |
0.828 (1.00) |
0.00803 (1.00) |
| amp xp22 2 | 31 (6%) | 496 |
1 (1.00) |
0.525 (1.00) |
0.00073 (0.16) |
0.236 (1.00) |
0.00109 (0.231) |
0.0316 (1.00) |
0.0538 (1.00) |
0.0073 (1.00) |
0.05 (1.00) |
0.233 (1.00) |
0.117 (1.00) |
0.156 (1.00) |
| del 3p11 2 | 246 (47%) | 281 |
0.169 (1.00) |
0.156 (1.00) |
1e-05 (0.00348) |
0.11 (1.00) |
0.788 (1.00) |
0.338 (1.00) |
0.119 (1.00) |
1e-05 (0.00348) |
0.833 (1.00) |
0.677 (1.00) |
0.0767 (1.00) |
0.985 (1.00) |
| del 3q11 2 | 161 (31%) | 366 |
0.181 (1.00) |
0.167 (1.00) |
1e-05 (0.00348) |
0.0488 (1.00) |
0.867 (1.00) |
0.485 (1.00) |
0.607 (1.00) |
7e-05 (0.0174) |
0.821 (1.00) |
0.732 (1.00) |
0.358 (1.00) |
0.736 (1.00) |
| del 10q23 31 | 96 (18%) | 431 |
0.441 (1.00) |
0.542 (1.00) |
1e-05 (0.00348) |
0.00142 (0.29) |
0.979 (1.00) |
0.00382 (0.726) |
0.0521 (1.00) |
0.00011 (0.0268) |
0.0183 (1.00) |
0.00371 (0.714) |
0.22 (1.00) |
0.0323 (1.00) |
| amp 4q32 1 | 16 (3%) | 511 |
0.19 (1.00) |
0.777 (1.00) |
0.403 (1.00) |
0.704 (1.00) |
0.654 (1.00) |
0.169 (1.00) |
0.0181 (1.00) |
0.0238 (1.00) |
0.00106 (0.227) |
0.477 (1.00) |
0.212 (1.00) |
0.219 (1.00) |
| del 1q43 | 42 (8%) | 485 |
0.0108 (1.00) |
0.0111 (1.00) |
0.00437 (0.813) |
0.369 (1.00) |
0.00585 (1.00) |
0.0498 (1.00) |
0.00448 (0.82) |
2e-05 (0.00546) |
0.0605 (1.00) |
0.0044 (0.814) |
0.955 (1.00) |
0.245 (1.00) |
| amp xq11 2 | 29 (6%) | 498 |
0.17 (1.00) |
0.16 (1.00) |
0.0181 (1.00) |
0.253 (1.00) |
0.0838 (1.00) |
0.072 (1.00) |
0.186 (1.00) |
0.309 (1.00) |
0.101 (1.00) |
0.462 (1.00) |
0.211 (1.00) |
0.243 (1.00) |
| amp xq28 | 37 (7%) | 490 |
0.486 (1.00) |
0.704 (1.00) |
0.0657 (1.00) |
0.641 (1.00) |
0.0369 (1.00) |
0.229 (1.00) |
0.111 (1.00) |
0.0777 (1.00) |
0.106 (1.00) |
0.326 (1.00) |
0.106 (1.00) |
0.457 (1.00) |
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S1. Gene #1: 'amp_1q24.1' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 212 | 152 | 163 |
| AMP PEAK 1(1Q24.1) MUTATED | 9 | 5 | 48 |
| AMP PEAK 1(1Q24.1) WILD-TYPE | 203 | 147 | 115 |
Figure S1. Get High-res Image Gene #1: 'amp_1q24.1' versus Molecular Subtype #3: 'CN_CNMF'
P value = 5e-05 (Fisher's exact test), Q value = 0.013
Table S2. Gene #1: 'amp_1q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 108 | 187 |
| AMP PEAK 1(1Q24.1) MUTATED | 19 | 4 | 37 |
| AMP PEAK 1(1Q24.1) WILD-TYPE | 196 | 104 | 150 |
Figure S2. Get High-res Image Gene #1: 'amp_1q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S3. Gene #1: 'amp_1q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 122 | 206 | 172 |
| AMP PEAK 1(1Q24.1) MUTATED | 4 | 21 | 35 |
| AMP PEAK 1(1Q24.1) WILD-TYPE | 118 | 185 | 137 |
Figure S3. Get High-res Image Gene #1: 'amp_1q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S4. Gene #2: 'amp_1q32.1' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 212 | 152 | 163 |
| AMP PEAK 2(1Q32.1) MUTATED | 7 | 4 | 51 |
| AMP PEAK 2(1Q32.1) WILD-TYPE | 205 | 148 | 112 |
Figure S4. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #3: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S5. Gene #2: 'amp_1q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 108 | 187 |
| AMP PEAK 2(1Q32.1) MUTATED | 19 | 3 | 38 |
| AMP PEAK 2(1Q32.1) WILD-TYPE | 196 | 105 | 149 |
Figure S5. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 4e-05 (Fisher's exact test), Q value = 0.01
Table S6. Gene #2: 'amp_1q32.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 122 | 206 | 172 |
| AMP PEAK 2(1Q32.1) MUTATED | 4 | 20 | 36 |
| AMP PEAK 2(1Q32.1) WILD-TYPE | 118 | 186 | 136 |
Figure S6. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 0.00038 (Fisher's exact test), Q value = 0.086
Table S7. Gene #2: 'amp_1q32.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 57 | 94 | 89 |
| AMP PEAK 2(1Q32.1) MUTATED | 2 | 6 | 20 |
| AMP PEAK 2(1Q32.1) WILD-TYPE | 55 | 88 | 69 |
Figure S7. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S8. Gene #3: 'amp_3q26.32' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 212 | 152 | 163 |
| AMP PEAK 3(3Q26.32) MUTATED | 9 | 24 | 54 |
| AMP PEAK 3(3Q26.32) WILD-TYPE | 203 | 128 | 109 |
Figure S8. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #3: 'CN_CNMF'
P value = 2e-05 (Fisher's exact test), Q value = 0.0055
Table S9. Gene #3: 'amp_3q26.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 128 | 75 | 110 |
| AMP PEAK 3(3Q26.32) MUTATED | 7 | 14 | 30 |
| AMP PEAK 3(3Q26.32) WILD-TYPE | 121 | 61 | 80 |
Figure S9. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S10. Gene #3: 'amp_3q26.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 95 | 198 | 154 |
| AMP PEAK 3(3Q26.32) MUTATED | 12 | 20 | 46 |
| AMP PEAK 3(3Q26.32) WILD-TYPE | 83 | 178 | 108 |
Figure S10. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S11. Gene #3: 'amp_3q26.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 108 | 187 |
| AMP PEAK 3(3Q26.32) MUTATED | 19 | 14 | 54 |
| AMP PEAK 3(3Q26.32) WILD-TYPE | 196 | 94 | 133 |
Figure S11. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S12. Gene #3: 'amp_3q26.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 120 | 176 | 126 | 28 | 32 | 28 |
| AMP PEAK 3(3Q26.32) MUTATED | 14 | 15 | 42 | 3 | 8 | 5 |
| AMP PEAK 3(3Q26.32) WILD-TYPE | 106 | 161 | 84 | 25 | 24 | 23 |
Figure S12. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S13. Gene #3: 'amp_3q26.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 122 | 206 | 172 |
| AMP PEAK 3(3Q26.32) MUTATED | 13 | 16 | 55 |
| AMP PEAK 3(3Q26.32) WILD-TYPE | 109 | 190 | 117 |
Figure S13. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 0.00021 (Fisher's exact test), Q value = 0.049
Table S14. Gene #3: 'amp_3q26.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 159 | 238 | 103 |
| AMP PEAK 3(3Q26.32) MUTATED | 35 | 23 | 26 |
| AMP PEAK 3(3Q26.32) WILD-TYPE | 124 | 215 | 77 |
Figure S14. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00106 (Fisher's exact test), Q value = 0.23
Table S15. Gene #4: 'amp_4q32.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 122 | 206 | 172 |
| AMP PEAK 4(4Q32.1) MUTATED | 3 | 1 | 12 |
| AMP PEAK 4(4Q32.1) WILD-TYPE | 119 | 205 | 160 |
Figure S15. Get High-res Image Gene #4: 'amp_4q32.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 0.00017 (Fisher's exact test), Q value = 0.04
Table S16. Gene #5: 'amp_5q35.1' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 212 | 152 | 163 |
| AMP PEAK 5(5Q35.1) MUTATED | 145 | 74 | 113 |
| AMP PEAK 5(5Q35.1) WILD-TYPE | 67 | 78 | 50 |
Figure S16. Get High-res Image Gene #5: 'amp_5q35.1' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00023 (Fisher's exact test), Q value = 0.053
Table S17. Gene #5: 'amp_5q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 120 | 176 | 126 | 28 | 32 | 28 |
| AMP PEAK 5(5Q35.1) MUTATED | 83 | 118 | 79 | 14 | 25 | 7 |
| AMP PEAK 5(5Q35.1) WILD-TYPE | 37 | 58 | 47 | 14 | 7 | 21 |
Figure S17. Get High-res Image Gene #5: 'amp_5q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S18. Gene #6: 'amp_7q36.3' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 212 | 152 | 163 |
| AMP PEAK 6(7Q36.3) MUTATED | 30 | 57 | 89 |
| AMP PEAK 6(7Q36.3) WILD-TYPE | 182 | 95 | 74 |
Figure S18. Get High-res Image Gene #6: 'amp_7q36.3' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00016 (Fisher's exact test), Q value = 0.039
Table S19. Gene #6: 'amp_7q36.3' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 100 | 88 | 84 | 75 | 43 | 57 |
| AMP PEAK 6(7Q36.3) MUTATED | 22 | 23 | 34 | 33 | 10 | 30 |
| AMP PEAK 6(7Q36.3) WILD-TYPE | 78 | 65 | 50 | 42 | 33 | 27 |
Figure S19. Get High-res Image Gene #6: 'amp_7q36.3' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 2e-05 (Fisher's exact test), Q value = 0.0055
Table S20. Gene #6: 'amp_7q36.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 108 | 187 |
| AMP PEAK 6(7Q36.3) MUTATED | 52 | 34 | 85 |
| AMP PEAK 6(7Q36.3) WILD-TYPE | 163 | 74 | 102 |
Figure S20. Get High-res Image Gene #6: 'amp_7q36.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S21. Gene #7: 'amp_8q24.22' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 212 | 152 | 163 |
| AMP PEAK 7(8Q24.22) MUTATED | 5 | 15 | 59 |
| AMP PEAK 7(8Q24.22) WILD-TYPE | 207 | 137 | 104 |
Figure S21. Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #3: 'CN_CNMF'
P value = 2e-05 (Fisher's exact test), Q value = 0.0055
Table S22. Gene #7: 'amp_8q24.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 128 | 75 | 110 |
| AMP PEAK 7(8Q24.22) MUTATED | 6 | 14 | 33 |
| AMP PEAK 7(8Q24.22) WILD-TYPE | 122 | 61 | 77 |
Figure S22. Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S23. Gene #7: 'amp_8q24.22' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 100 | 88 | 84 | 75 | 43 | 57 |
| AMP PEAK 7(8Q24.22) MUTATED | 6 | 14 | 16 | 12 | 1 | 22 |
| AMP PEAK 7(8Q24.22) WILD-TYPE | 94 | 74 | 68 | 63 | 42 | 35 |
Figure S23. Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 0.00065 (Fisher's exact test), Q value = 0.14
Table S24. Gene #7: 'amp_8q24.22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 95 | 198 | 154 |
| AMP PEAK 7(8Q24.22) MUTATED | 11 | 21 | 39 |
| AMP PEAK 7(8Q24.22) WILD-TYPE | 84 | 177 | 115 |
Figure S24. Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S25. Gene #7: 'amp_8q24.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 108 | 187 |
| AMP PEAK 7(8Q24.22) MUTATED | 9 | 10 | 59 |
| AMP PEAK 7(8Q24.22) WILD-TYPE | 206 | 98 | 128 |
Figure S25. Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S26. Gene #7: 'amp_8q24.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 120 | 176 | 126 | 28 | 32 | 28 |
| AMP PEAK 7(8Q24.22) MUTATED | 10 | 9 | 53 | 2 | 3 | 1 |
| AMP PEAK 7(8Q24.22) WILD-TYPE | 110 | 167 | 73 | 26 | 29 | 27 |
Figure S26. Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S27. Gene #7: 'amp_8q24.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 122 | 206 | 172 |
| AMP PEAK 7(8Q24.22) MUTATED | 13 | 13 | 51 |
| AMP PEAK 7(8Q24.22) WILD-TYPE | 109 | 193 | 121 |
Figure S27. Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S28. Gene #7: 'amp_8q24.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 159 | 238 | 103 |
| AMP PEAK 7(8Q24.22) MUTATED | 40 | 17 | 20 |
| AMP PEAK 7(8Q24.22) WILD-TYPE | 119 | 221 | 83 |
Figure S28. Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S29. Gene #7: 'amp_8q24.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 57 | 94 | 89 |
| AMP PEAK 7(8Q24.22) MUTATED | 4 | 4 | 27 |
| AMP PEAK 7(8Q24.22) WILD-TYPE | 53 | 90 | 62 |
Figure S29. Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
P value = 6e-05 (Fisher's exact test), Q value = 0.015
Table S30. Gene #7: 'amp_8q24.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 93 | 100 | 47 |
| AMP PEAK 7(8Q24.22) MUTATED | 23 | 4 | 8 |
| AMP PEAK 7(8Q24.22) WILD-TYPE | 70 | 96 | 39 |
Figure S30. Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 2e-05 (Fisher's exact test), Q value = 0.0055
Table S31. Gene #8: 'amp_10p14' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 212 | 152 | 163 |
| AMP PEAK 8(10P14) MUTATED | 0 | 6 | 14 |
| AMP PEAK 8(10P14) WILD-TYPE | 212 | 146 | 149 |
Figure S31. Get High-res Image Gene #8: 'amp_10p14' versus Molecular Subtype #3: 'CN_CNMF'
P value = 5e-05 (Fisher's exact test), Q value = 0.013
Table S32. Gene #8: 'amp_10p14' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 120 | 176 | 126 | 28 | 32 | 28 |
| AMP PEAK 8(10P14) MUTATED | 3 | 0 | 13 | 1 | 2 | 1 |
| AMP PEAK 8(10P14) WILD-TYPE | 117 | 176 | 113 | 27 | 30 | 27 |
Figure S32. Get High-res Image Gene #8: 'amp_10p14' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00073 (Fisher's exact test), Q value = 0.16
Table S33. Gene #9: 'amp_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 212 | 152 | 163 |
| AMP PEAK 9(XP22.2) MUTATED | 4 | 9 | 18 |
| AMP PEAK 9(XP22.2) WILD-TYPE | 208 | 143 | 145 |
Figure S33. Get High-res Image Gene #9: 'amp_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00109 (Fisher's exact test), Q value = 0.23
Table S34. Gene #9: 'amp_xp22.2' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 100 | 88 | 84 | 75 | 43 | 57 |
| AMP PEAK 9(XP22.2) MUTATED | 0 | 3 | 7 | 10 | 1 | 4 |
| AMP PEAK 9(XP22.2) WILD-TYPE | 100 | 85 | 77 | 65 | 42 | 53 |
Figure S34. Get High-res Image Gene #9: 'amp_xp22.2' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 0.00016 (Fisher's exact test), Q value = 0.039
Table S35. Gene #10: 'amp_xp11.4' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 212 | 152 | 163 |
| AMP PEAK 10(XP11.4) MUTATED | 4 | 9 | 20 |
| AMP PEAK 10(XP11.4) WILD-TYPE | 208 | 143 | 143 |
Figure S35. Get High-res Image Gene #10: 'amp_xp11.4' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00075 (Fisher's exact test), Q value = 0.16
Table S36. Gene #10: 'amp_xp11.4' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 100 | 88 | 84 | 75 | 43 | 57 |
| AMP PEAK 10(XP11.4) MUTATED | 0 | 5 | 5 | 10 | 0 | 5 |
| AMP PEAK 10(XP11.4) WILD-TYPE | 100 | 83 | 79 | 65 | 43 | 52 |
Figure S36. Get High-res Image Gene #10: 'amp_xp11.4' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 0.00045 (Fisher's exact test), Q value = 0.1
Table S37. Gene #10: 'amp_xp11.4' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 120 | 176 | 126 | 28 | 32 | 28 |
| AMP PEAK 10(XP11.4) MUTATED | 2 | 7 | 19 | 3 | 1 | 1 |
| AMP PEAK 10(XP11.4) WILD-TYPE | 118 | 169 | 107 | 25 | 31 | 27 |
Figure S37. Get High-res Image Gene #10: 'amp_xp11.4' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00015 (Fisher's exact test), Q value = 0.036
Table S38. Gene #13: 'del_1p36.23' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 33 | 24 | 13 |
| DEL PEAK 1(1P36.23) MUTATED | 2 | 8 | 8 |
| DEL PEAK 1(1P36.23) WILD-TYPE | 31 | 16 | 5 |
Figure S38. Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 9e-04 (Fisher's exact test), Q value = 0.19
Table S39. Gene #13: 'del_1p36.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 11 | 12 | 4 | 11 | 13 | 9 | 10 |
| DEL PEAK 1(1P36.23) MUTATED | 0 | 2 | 2 | 5 | 1 | 1 | 7 |
| DEL PEAK 1(1P36.23) WILD-TYPE | 11 | 10 | 2 | 6 | 12 | 8 | 3 |
Figure S39. Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S40. Gene #13: 'del_1p36.23' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 212 | 152 | 163 |
| DEL PEAK 1(1P36.23) MUTATED | 18 | 33 | 52 |
| DEL PEAK 1(1P36.23) WILD-TYPE | 194 | 119 | 111 |
Figure S40. Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #3: 'CN_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.0079
Table S41. Gene #13: 'del_1p36.23' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 100 | 88 | 84 | 75 | 43 | 57 |
| DEL PEAK 1(1P36.23) MUTATED | 9 | 10 | 23 | 24 | 5 | 18 |
| DEL PEAK 1(1P36.23) WILD-TYPE | 91 | 78 | 61 | 51 | 38 | 39 |
Figure S41. Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 8e-05 (Fisher's exact test), Q value = 0.02
Table S42. Gene #13: 'del_1p36.23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 95 | 198 | 154 |
| DEL PEAK 1(1P36.23) MUTATED | 21 | 22 | 46 |
| DEL PEAK 1(1P36.23) WILD-TYPE | 74 | 176 | 108 |
Figure S42. Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 4e-05 (Fisher's exact test), Q value = 0.01
Table S43. Gene #13: 'del_1p36.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 108 | 187 |
| DEL PEAK 1(1P36.23) MUTATED | 25 | 20 | 56 |
| DEL PEAK 1(1P36.23) WILD-TYPE | 190 | 88 | 131 |
Figure S43. Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S44. Gene #13: 'del_1p36.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 120 | 176 | 126 | 28 | 32 | 28 |
| DEL PEAK 1(1P36.23) MUTATED | 15 | 22 | 38 | 3 | 9 | 14 |
| DEL PEAK 1(1P36.23) WILD-TYPE | 105 | 154 | 88 | 25 | 23 | 14 |
Figure S44. Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S45. Gene #13: 'del_1p36.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 122 | 206 | 172 |
| DEL PEAK 1(1P36.23) MUTATED | 19 | 24 | 58 |
| DEL PEAK 1(1P36.23) WILD-TYPE | 103 | 182 | 114 |
Figure S45. Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 2e-05 (Fisher's exact test), Q value = 0.0055
Table S46. Gene #13: 'del_1p36.23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 159 | 238 | 103 |
| DEL PEAK 1(1P36.23) MUTATED | 42 | 27 | 32 |
| DEL PEAK 1(1P36.23) WILD-TYPE | 117 | 211 | 71 |
Figure S46. Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00056 (Fisher's exact test), Q value = 0.12
Table S47. Gene #13: 'del_1p36.23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 57 | 94 | 89 |
| DEL PEAK 1(1P36.23) MUTATED | 10 | 9 | 29 |
| DEL PEAK 1(1P36.23) WILD-TYPE | 47 | 85 | 60 |
Figure S47. Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
P value = 0.00013 (Fisher's exact test), Q value = 0.032
Table S48. Gene #13: 'del_1p36.23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 93 | 100 | 47 |
| DEL PEAK 1(1P36.23) MUTATED | 31 | 9 | 8 |
| DEL PEAK 1(1P36.23) WILD-TYPE | 62 | 91 | 39 |
Figure S48. Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S49. Gene #14: 'del_1p31.1' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 212 | 152 | 163 |
| DEL PEAK 2(1P31.1) MUTATED | 10 | 27 | 40 |
| DEL PEAK 2(1P31.1) WILD-TYPE | 202 | 125 | 123 |
Figure S49. Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #3: 'CN_CNMF'
P value = 1e-04 (Fisher's exact test), Q value = 0.024
Table S50. Gene #14: 'del_1p31.1' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 100 | 88 | 84 | 75 | 43 | 57 |
| DEL PEAK 2(1P31.1) MUTATED | 10 | 4 | 13 | 21 | 4 | 15 |
| DEL PEAK 2(1P31.1) WILD-TYPE | 90 | 84 | 71 | 54 | 39 | 42 |
Figure S50. Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 0.00108 (Fisher's exact test), Q value = 0.23
Table S51. Gene #14: 'del_1p31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 95 | 198 | 154 |
| DEL PEAK 2(1P31.1) MUTATED | 15 | 17 | 35 |
| DEL PEAK 2(1P31.1) WILD-TYPE | 80 | 181 | 119 |
Figure S51. Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 8e-05 (Fisher's exact test), Q value = 0.02
Table S52. Gene #14: 'del_1p31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 120 | 176 | 126 | 28 | 32 | 28 |
| DEL PEAK 2(1P31.1) MUTATED | 13 | 15 | 26 | 4 | 4 | 13 |
| DEL PEAK 2(1P31.1) WILD-TYPE | 107 | 161 | 100 | 24 | 28 | 15 |
Figure S52. Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S53. Gene #14: 'del_1p31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 122 | 206 | 172 |
| DEL PEAK 2(1P31.1) MUTATED | 9 | 21 | 45 |
| DEL PEAK 2(1P31.1) WILD-TYPE | 113 | 185 | 127 |
Figure S53. Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 0.00016 (Fisher's exact test), Q value = 0.039
Table S54. Gene #14: 'del_1p31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 159 | 238 | 103 |
| DEL PEAK 2(1P31.1) MUTATED | 21 | 24 | 30 |
| DEL PEAK 2(1P31.1) WILD-TYPE | 138 | 214 | 73 |
Figure S54. Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 2e-05 (Fisher's exact test), Q value = 0.0055
Table S55. Gene #15: 'del_1q43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 120 | 176 | 126 | 28 | 32 | 28 |
| DEL PEAK 3(1Q43) MUTATED | 6 | 11 | 9 | 0 | 2 | 12 |
| DEL PEAK 3(1Q43) WILD-TYPE | 114 | 165 | 117 | 28 | 30 | 16 |
Figure S55. Get High-res Image Gene #15: 'del_1q43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00033 (Fisher's exact test), Q value = 0.075
Table S56. Gene #16: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 11 | 12 | 4 | 11 | 13 | 9 | 10 |
| DEL PEAK 4(2Q37.3) MUTATED | 0 | 4 | 0 | 0 | 1 | 0 | 6 |
| DEL PEAK 4(2Q37.3) WILD-TYPE | 11 | 8 | 4 | 11 | 12 | 9 | 4 |
Figure S56. Get High-res Image Gene #16: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 6e-05 (Fisher's exact test), Q value = 0.015
Table S57. Gene #16: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 108 | 187 |
| DEL PEAK 4(2Q37.3) MUTATED | 9 | 21 | 19 |
| DEL PEAK 4(2Q37.3) WILD-TYPE | 206 | 87 | 168 |
Figure S57. Get High-res Image Gene #16: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S58. Gene #16: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 120 | 176 | 126 | 28 | 32 | 28 |
| DEL PEAK 4(2Q37.3) MUTATED | 15 | 7 | 16 | 0 | 1 | 10 |
| DEL PEAK 4(2Q37.3) WILD-TYPE | 105 | 169 | 110 | 28 | 31 | 18 |
Figure S58. Get High-res Image Gene #16: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S59. Gene #17: 'del_3p25.3' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 33 | 24 | 13 |
| DEL PEAK 5(3P25.3) MUTATED | 32 | 22 | 3 |
| DEL PEAK 5(3P25.3) WILD-TYPE | 1 | 2 | 10 |
Figure S59. Get High-res Image Gene #17: 'del_3p25.3' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S60. Gene #17: 'del_3p25.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 11 | 12 | 4 | 11 | 13 | 9 | 10 |
| DEL PEAK 5(3P25.3) MUTATED | 11 | 11 | 1 | 11 | 12 | 9 | 2 |
| DEL PEAK 5(3P25.3) WILD-TYPE | 0 | 1 | 3 | 0 | 1 | 0 | 8 |
Figure S60. Get High-res Image Gene #17: 'del_3p25.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S61. Gene #17: 'del_3p25.3' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 212 | 152 | 163 |
| DEL PEAK 5(3P25.3) MUTATED | 211 | 93 | 158 |
| DEL PEAK 5(3P25.3) WILD-TYPE | 1 | 59 | 5 |
Figure S61. Get High-res Image Gene #17: 'del_3p25.3' versus Molecular Subtype #3: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S62. Gene #17: 'del_3p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 128 | 75 | 110 |
| DEL PEAK 5(3P25.3) MUTATED | 120 | 52 | 106 |
| DEL PEAK 5(3P25.3) WILD-TYPE | 8 | 23 | 4 |
Figure S62. Get High-res Image Gene #17: 'del_3p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 4e-05 (Fisher's exact test), Q value = 0.01
Table S63. Gene #17: 'del_3p25.3' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 100 | 88 | 84 | 75 | 43 | 57 |
| DEL PEAK 5(3P25.3) MUTATED | 99 | 74 | 76 | 56 | 40 | 52 |
| DEL PEAK 5(3P25.3) WILD-TYPE | 1 | 14 | 8 | 19 | 3 | 5 |
Figure S63. Get High-res Image Gene #17: 'del_3p25.3' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S64. Gene #17: 'del_3p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 108 | 187 |
| DEL PEAK 5(3P25.3) MUTATED | 208 | 71 | 169 |
| DEL PEAK 5(3P25.3) WILD-TYPE | 7 | 37 | 18 |
Figure S64. Get High-res Image Gene #17: 'del_3p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S65. Gene #17: 'del_3p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 120 | 176 | 126 | 28 | 32 | 28 |
| DEL PEAK 5(3P25.3) MUTATED | 112 | 171 | 110 | 20 | 32 | 3 |
| DEL PEAK 5(3P25.3) WILD-TYPE | 8 | 5 | 16 | 8 | 0 | 25 |
Figure S65. Get High-res Image Gene #17: 'del_3p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 2e-05 (Fisher's exact test), Q value = 0.0055
Table S66. Gene #17: 'del_3p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 122 | 206 | 172 |
| DEL PEAK 5(3P25.3) MUTATED | 104 | 196 | 138 |
| DEL PEAK 5(3P25.3) WILD-TYPE | 18 | 10 | 34 |
Figure S66. Get High-res Image Gene #17: 'del_3p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.0079
Table S67. Gene #17: 'del_3p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 159 | 238 | 103 |
| DEL PEAK 5(3P25.3) MUTATED | 131 | 225 | 82 |
| DEL PEAK 5(3P25.3) WILD-TYPE | 28 | 13 | 21 |
Figure S67. Get High-res Image Gene #17: 'del_3p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00093 (Fisher's exact test), Q value = 0.2
Table S68. Gene #17: 'del_3p25.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 57 | 94 | 89 |
| DEL PEAK 5(3P25.3) MUTATED | 44 | 90 | 73 |
| DEL PEAK 5(3P25.3) WILD-TYPE | 13 | 4 | 16 |
Figure S68. Get High-res Image Gene #17: 'del_3p25.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S69. Gene #17: 'del_3p25.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 93 | 100 | 47 |
| DEL PEAK 5(3P25.3) MUTATED | 68 | 96 | 43 |
| DEL PEAK 5(3P25.3) WILD-TYPE | 25 | 4 | 4 |
Figure S69. Get High-res Image Gene #17: 'del_3p25.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S70. Gene #18: 'del_3p12.3' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 212 | 152 | 163 |
| DEL PEAK 6(3P12.3) MUTATED | 176 | 17 | 141 |
| DEL PEAK 6(3P12.3) WILD-TYPE | 36 | 135 | 22 |
Figure S70. Get High-res Image Gene #18: 'del_3p12.3' versus Molecular Subtype #3: 'CN_CNMF'
P value = 2e-04 (Fisher's exact test), Q value = 0.047
Table S71. Gene #18: 'del_3p12.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 128 | 75 | 110 |
| DEL PEAK 6(3P12.3) MUTATED | 91 | 34 | 79 |
| DEL PEAK 6(3P12.3) WILD-TYPE | 37 | 41 | 31 |
Figure S71. Get High-res Image Gene #18: 'del_3p12.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 6e-05 (Fisher's exact test), Q value = 0.015
Table S72. Gene #18: 'del_3p12.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 108 | 187 |
| DEL PEAK 6(3P12.3) MUTATED | 149 | 48 | 129 |
| DEL PEAK 6(3P12.3) WILD-TYPE | 66 | 60 | 58 |
Figure S72. Get High-res Image Gene #18: 'del_3p12.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S73. Gene #18: 'del_3p12.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 120 | 176 | 126 | 28 | 32 | 28 |
| DEL PEAK 6(3P12.3) MUTATED | 83 | 119 | 87 | 14 | 21 | 2 |
| DEL PEAK 6(3P12.3) WILD-TYPE | 37 | 57 | 39 | 14 | 11 | 26 |
Figure S73. Get High-res Image Gene #18: 'del_3p12.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S74. Gene #19: 'del_3p11.2' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 212 | 152 | 163 |
| DEL PEAK 7(3P11.2) MUTATED | 137 | 7 | 102 |
| DEL PEAK 7(3P11.2) WILD-TYPE | 75 | 145 | 61 |
Figure S74. Get High-res Image Gene #19: 'del_3p11.2' versus Molecular Subtype #3: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S75. Gene #19: 'del_3p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 120 | 176 | 126 | 28 | 32 | 28 |
| DEL PEAK 7(3P11.2) MUTATED | 69 | 81 | 69 | 9 | 11 | 2 |
| DEL PEAK 7(3P11.2) WILD-TYPE | 51 | 95 | 57 | 19 | 21 | 26 |
Figure S75. Get High-res Image Gene #19: 'del_3p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S76. Gene #20: 'del_3q11.2' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 212 | 152 | 163 |
| DEL PEAK 8(3Q11.2) MUTATED | 91 | 6 | 64 |
| DEL PEAK 8(3Q11.2) WILD-TYPE | 121 | 146 | 99 |
Figure S76. Get High-res Image Gene #20: 'del_3q11.2' versus Molecular Subtype #3: 'CN_CNMF'
P value = 7e-05 (Fisher's exact test), Q value = 0.017
Table S77. Gene #20: 'del_3q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 120 | 176 | 126 | 28 | 32 | 28 |
| DEL PEAK 8(3Q11.2) MUTATED | 51 | 49 | 46 | 6 | 5 | 1 |
| DEL PEAK 8(3Q11.2) WILD-TYPE | 69 | 127 | 80 | 22 | 27 | 27 |
Figure S77. Get High-res Image Gene #20: 'del_3q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S78. Gene #21: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 212 | 152 | 163 |
| DEL PEAK 9(4Q34.3) MUTATED | 11 | 15 | 52 |
| DEL PEAK 9(4Q34.3) WILD-TYPE | 201 | 137 | 111 |
Figure S78. Get High-res Image Gene #21: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S79. Gene #21: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 128 | 75 | 110 |
| DEL PEAK 9(4Q34.3) MUTATED | 10 | 9 | 34 |
| DEL PEAK 9(4Q34.3) WILD-TYPE | 118 | 66 | 76 |
Figure S79. Get High-res Image Gene #21: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 0.00026 (Fisher's exact test), Q value = 0.06
Table S80. Gene #21: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 108 | 187 |
| DEL PEAK 9(4Q34.3) MUTATED | 26 | 8 | 44 |
| DEL PEAK 9(4Q34.3) WILD-TYPE | 189 | 100 | 143 |
Figure S80. Get High-res Image Gene #21: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 2e-05 (Fisher's exact test), Q value = 0.0055
Table S81. Gene #21: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 120 | 176 | 126 | 28 | 32 | 28 |
| DEL PEAK 9(4Q34.3) MUTATED | 16 | 18 | 38 | 1 | 5 | 0 |
| DEL PEAK 9(4Q34.3) WILD-TYPE | 104 | 158 | 88 | 27 | 27 | 28 |
Figure S81. Get High-res Image Gene #21: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S82. Gene #22: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 212 | 152 | 163 |
| DEL PEAK 10(6Q26) MUTATED | 33 | 26 | 92 |
| DEL PEAK 10(6Q26) WILD-TYPE | 179 | 126 | 71 |
Figure S82. Get High-res Image Gene #22: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'
P value = 2e-05 (Fisher's exact test), Q value = 0.0055
Table S83. Gene #22: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 100 | 88 | 84 | 75 | 43 | 57 |
| DEL PEAK 10(6Q26) MUTATED | 33 | 10 | 29 | 22 | 8 | 28 |
| DEL PEAK 10(6Q26) WILD-TYPE | 67 | 78 | 55 | 53 | 35 | 29 |
Figure S83. Get High-res Image Gene #22: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 0.00033 (Fisher's exact test), Q value = 0.075
Table S84. Gene #22: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 95 | 198 | 154 |
| DEL PEAK 10(6Q26) MUTATED | 33 | 39 | 58 |
| DEL PEAK 10(6Q26) WILD-TYPE | 62 | 159 | 96 |
Figure S84. Get High-res Image Gene #22: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 0.00044 (Fisher's exact test), Q value = 0.099
Table S85. Gene #22: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 108 | 187 |
| DEL PEAK 10(6Q26) MUTATED | 52 | 21 | 72 |
| DEL PEAK 10(6Q26) WILD-TYPE | 163 | 87 | 115 |
Figure S85. Get High-res Image Gene #22: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 0.00113 (Fisher's exact test), Q value = 0.24
Table S86. Gene #22: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 120 | 176 | 126 | 28 | 32 | 28 |
| DEL PEAK 10(6Q26) MUTATED | 27 | 39 | 53 | 5 | 10 | 11 |
| DEL PEAK 10(6Q26) WILD-TYPE | 93 | 137 | 73 | 23 | 22 | 17 |
Figure S86. Get High-res Image Gene #22: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S87. Gene #22: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 122 | 206 | 172 |
| DEL PEAK 10(6Q26) MUTATED | 22 | 45 | 77 |
| DEL PEAK 10(6Q26) WILD-TYPE | 100 | 161 | 95 |
Figure S87. Get High-res Image Gene #22: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 0.00017 (Fisher's exact test), Q value = 0.04
Table S88. Gene #22: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 57 | 94 | 89 |
| DEL PEAK 10(6Q26) MUTATED | 10 | 18 | 39 |
| DEL PEAK 10(6Q26) WILD-TYPE | 47 | 76 | 50 |
Figure S88. Get High-res Image Gene #22: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S89. Gene #23: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 212 | 152 | 163 |
| DEL PEAK 11(6Q26) MUTATED | 33 | 26 | 92 |
| DEL PEAK 11(6Q26) WILD-TYPE | 179 | 126 | 71 |
Figure S89. Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S90. Gene #23: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 100 | 88 | 84 | 75 | 43 | 57 |
| DEL PEAK 11(6Q26) MUTATED | 32 | 10 | 29 | 22 | 8 | 29 |
| DEL PEAK 11(6Q26) WILD-TYPE | 68 | 78 | 55 | 53 | 35 | 28 |
Figure S90. Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 3e-04 (Fisher's exact test), Q value = 0.069
Table S91. Gene #23: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 95 | 198 | 154 |
| DEL PEAK 11(6Q26) MUTATED | 33 | 39 | 58 |
| DEL PEAK 11(6Q26) WILD-TYPE | 62 | 159 | 96 |
Figure S91. Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 0.00018 (Fisher's exact test), Q value = 0.042
Table S92. Gene #23: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 108 | 187 |
| DEL PEAK 11(6Q26) MUTATED | 52 | 20 | 73 |
| DEL PEAK 11(6Q26) WILD-TYPE | 163 | 88 | 114 |
Figure S92. Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 0.00077 (Fisher's exact test), Q value = 0.17
Table S93. Gene #23: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 120 | 176 | 126 | 28 | 32 | 28 |
| DEL PEAK 11(6Q26) MUTATED | 27 | 39 | 54 | 5 | 9 | 11 |
| DEL PEAK 11(6Q26) WILD-TYPE | 93 | 137 | 72 | 23 | 23 | 17 |
Figure S93. Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S94. Gene #23: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 122 | 206 | 172 |
| DEL PEAK 11(6Q26) MUTATED | 21 | 45 | 78 |
| DEL PEAK 11(6Q26) WILD-TYPE | 101 | 161 | 94 |
Figure S94. Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S95. Gene #23: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 57 | 94 | 89 |
| DEL PEAK 11(6Q26) MUTATED | 9 | 18 | 40 |
| DEL PEAK 11(6Q26) WILD-TYPE | 48 | 76 | 49 |
Figure S95. Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S96. Gene #24: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 212 | 152 | 163 |
| DEL PEAK 12(8P23.2) MUTATED | 38 | 42 | 74 |
| DEL PEAK 12(8P23.2) WILD-TYPE | 174 | 110 | 89 |
Figure S96. Get High-res Image Gene #24: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.0011 (Fisher's exact test), Q value = 0.23
Table S97. Gene #24: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 108 | 187 |
| DEL PEAK 12(8P23.2) MUTATED | 56 | 22 | 73 |
| DEL PEAK 12(8P23.2) WILD-TYPE | 159 | 86 | 114 |
Figure S97. Get High-res Image Gene #24: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S98. Gene #24: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 120 | 176 | 126 | 28 | 32 | 28 |
| DEL PEAK 12(8P23.2) MUTATED | 30 | 49 | 60 | 3 | 4 | 5 |
| DEL PEAK 12(8P23.2) WILD-TYPE | 90 | 127 | 66 | 25 | 28 | 23 |
Figure S98. Get High-res Image Gene #24: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00057 (Fisher's exact test), Q value = 0.13
Table S99. Gene #24: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 122 | 206 | 172 |
| DEL PEAK 12(8P23.2) MUTATED | 36 | 45 | 69 |
| DEL PEAK 12(8P23.2) WILD-TYPE | 86 | 161 | 103 |
Figure S99. Get High-res Image Gene #24: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S100. Gene #25: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 212 | 152 | 163 |
| DEL PEAK 13(9P23) MUTATED | 9 | 30 | 113 |
| DEL PEAK 13(9P23) WILD-TYPE | 203 | 122 | 50 |
Figure S100. Get High-res Image Gene #25: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S101. Gene #25: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 128 | 75 | 110 |
| DEL PEAK 13(9P23) MUTATED | 6 | 21 | 68 |
| DEL PEAK 13(9P23) WILD-TYPE | 122 | 54 | 42 |
Figure S101. Get High-res Image Gene #25: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S102. Gene #25: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 100 | 88 | 84 | 75 | 43 | 57 |
| DEL PEAK 13(9P23) MUTATED | 17 | 23 | 33 | 18 | 10 | 35 |
| DEL PEAK 13(9P23) WILD-TYPE | 83 | 65 | 51 | 57 | 33 | 22 |
Figure S102. Get High-res Image Gene #25: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 0.00018 (Fisher's exact test), Q value = 0.042
Table S103. Gene #25: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 95 | 198 | 154 |
| DEL PEAK 13(9P23) MUTATED | 29 | 42 | 65 |
| DEL PEAK 13(9P23) WILD-TYPE | 66 | 156 | 89 |
Figure S103. Get High-res Image Gene #25: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S104. Gene #25: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 108 | 187 |
| DEL PEAK 13(9P23) MUTATED | 25 | 16 | 106 |
| DEL PEAK 13(9P23) WILD-TYPE | 190 | 92 | 81 |
Figure S104. Get High-res Image Gene #25: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S105. Gene #25: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 120 | 176 | 126 | 28 | 32 | 28 |
| DEL PEAK 13(9P23) MUTATED | 39 | 12 | 79 | 3 | 10 | 4 |
| DEL PEAK 13(9P23) WILD-TYPE | 81 | 164 | 47 | 25 | 22 | 24 |
Figure S105. Get High-res Image Gene #25: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S106. Gene #25: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 122 | 206 | 172 |
| DEL PEAK 13(9P23) MUTATED | 26 | 27 | 91 |
| DEL PEAK 13(9P23) WILD-TYPE | 96 | 179 | 81 |
Figure S106. Get High-res Image Gene #25: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S107. Gene #25: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 159 | 238 | 103 |
| DEL PEAK 13(9P23) MUTATED | 70 | 36 | 38 |
| DEL PEAK 13(9P23) WILD-TYPE | 89 | 202 | 65 |
Figure S107. Get High-res Image Gene #25: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S108. Gene #25: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 57 | 94 | 89 |
| DEL PEAK 13(9P23) MUTATED | 15 | 9 | 47 |
| DEL PEAK 13(9P23) WILD-TYPE | 42 | 85 | 42 |
Figure S108. Get High-res Image Gene #25: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.0079
Table S109. Gene #25: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 93 | 100 | 47 |
| DEL PEAK 13(9P23) MUTATED | 41 | 15 | 15 |
| DEL PEAK 13(9P23) WILD-TYPE | 52 | 85 | 32 |
Figure S109. Get High-res Image Gene #25: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S110. Gene #26: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 212 | 152 | 163 |
| DEL PEAK 14(9P21.3) MUTATED | 12 | 30 | 117 |
| DEL PEAK 14(9P21.3) WILD-TYPE | 200 | 122 | 46 |
Figure S110. Get High-res Image Gene #26: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S111. Gene #26: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 128 | 75 | 110 |
| DEL PEAK 14(9P21.3) MUTATED | 6 | 24 | 68 |
| DEL PEAK 14(9P21.3) WILD-TYPE | 122 | 51 | 42 |
Figure S111. Get High-res Image Gene #26: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S112. Gene #26: 'del_9p21.3' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 100 | 88 | 84 | 75 | 43 | 57 |
| DEL PEAK 14(9P21.3) MUTATED | 18 | 26 | 33 | 19 | 10 | 37 |
| DEL PEAK 14(9P21.3) WILD-TYPE | 82 | 62 | 51 | 56 | 33 | 20 |
Figure S112. Get High-res Image Gene #26: 'del_9p21.3' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 4e-05 (Fisher's exact test), Q value = 0.01
Table S113. Gene #26: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 95 | 198 | 154 |
| DEL PEAK 14(9P21.3) MUTATED | 29 | 44 | 70 |
| DEL PEAK 14(9P21.3) WILD-TYPE | 66 | 154 | 84 |
Figure S113. Get High-res Image Gene #26: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S114. Gene #26: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 108 | 187 |
| DEL PEAK 14(9P21.3) MUTATED | 27 | 18 | 109 |
| DEL PEAK 14(9P21.3) WILD-TYPE | 188 | 90 | 78 |
Figure S114. Get High-res Image Gene #26: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S115. Gene #26: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 120 | 176 | 126 | 28 | 32 | 28 |
| DEL PEAK 14(9P21.3) MUTATED | 39 | 13 | 85 | 2 | 11 | 4 |
| DEL PEAK 14(9P21.3) WILD-TYPE | 81 | 163 | 41 | 26 | 21 | 24 |
Figure S115. Get High-res Image Gene #26: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S116. Gene #26: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 122 | 206 | 172 |
| DEL PEAK 14(9P21.3) MUTATED | 29 | 28 | 93 |
| DEL PEAK 14(9P21.3) WILD-TYPE | 93 | 178 | 79 |
Figure S116. Get High-res Image Gene #26: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S117. Gene #26: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 159 | 238 | 103 |
| DEL PEAK 14(9P21.3) MUTATED | 76 | 36 | 38 |
| DEL PEAK 14(9P21.3) WILD-TYPE | 83 | 202 | 65 |
Figure S117. Get High-res Image Gene #26: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S118. Gene #26: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 57 | 94 | 89 |
| DEL PEAK 14(9P21.3) MUTATED | 16 | 9 | 46 |
| DEL PEAK 14(9P21.3) WILD-TYPE | 41 | 85 | 43 |
Figure S118. Get High-res Image Gene #26: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S119. Gene #26: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 93 | 100 | 47 |
| DEL PEAK 14(9P21.3) MUTATED | 44 | 15 | 12 |
| DEL PEAK 14(9P21.3) WILD-TYPE | 49 | 85 | 35 |
Figure S119. Get High-res Image Gene #26: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S120. Gene #27: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 212 | 152 | 163 |
| DEL PEAK 15(10Q23.31) MUTATED | 20 | 25 | 51 |
| DEL PEAK 15(10Q23.31) WILD-TYPE | 192 | 127 | 112 |
Figure S120. Get High-res Image Gene #27: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00011 (Fisher's exact test), Q value = 0.027
Table S121. Gene #27: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 120 | 176 | 126 | 28 | 32 | 28 |
| DEL PEAK 15(10Q23.31) MUTATED | 23 | 19 | 36 | 2 | 3 | 10 |
| DEL PEAK 15(10Q23.31) WILD-TYPE | 97 | 157 | 90 | 26 | 29 | 18 |
Figure S121. Get High-res Image Gene #27: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S122. Gene #28: 'del_13q13.3' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 212 | 152 | 163 |
| DEL PEAK 16(13Q13.3) MUTATED | 11 | 26 | 44 |
| DEL PEAK 16(13Q13.3) WILD-TYPE | 201 | 126 | 119 |
Figure S122. Get High-res Image Gene #28: 'del_13q13.3' versus Molecular Subtype #3: 'CN_CNMF'
P value = 0.00021 (Fisher's exact test), Q value = 0.049
Table S123. Gene #28: 'del_13q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 128 | 75 | 110 |
| DEL PEAK 16(13Q13.3) MUTATED | 8 | 16 | 26 |
| DEL PEAK 16(13Q13.3) WILD-TYPE | 120 | 59 | 84 |
Figure S123. Get High-res Image Gene #28: 'del_13q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S124. Gene #28: 'del_13q13.3' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 100 | 88 | 84 | 75 | 43 | 57 |
| DEL PEAK 16(13Q13.3) MUTATED | 3 | 11 | 16 | 13 | 6 | 22 |
| DEL PEAK 16(13Q13.3) WILD-TYPE | 97 | 77 | 68 | 62 | 37 | 35 |
Figure S124. Get High-res Image Gene #28: 'del_13q13.3' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 2e-05 (Fisher's exact test), Q value = 0.0055
Table S125. Gene #28: 'del_13q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 108 | 187 |
| DEL PEAK 16(13Q13.3) MUTATED | 19 | 12 | 48 |
| DEL PEAK 16(13Q13.3) WILD-TYPE | 196 | 96 | 139 |
Figure S125. Get High-res Image Gene #28: 'del_13q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S126. Gene #28: 'del_13q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 120 | 176 | 126 | 28 | 32 | 28 |
| DEL PEAK 16(13Q13.3) MUTATED | 7 | 14 | 43 | 1 | 6 | 8 |
| DEL PEAK 16(13Q13.3) WILD-TYPE | 113 | 162 | 83 | 27 | 26 | 20 |
Figure S126. Get High-res Image Gene #28: 'del_13q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S127. Gene #28: 'del_13q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 122 | 206 | 172 |
| DEL PEAK 16(13Q13.3) MUTATED | 13 | 16 | 48 |
| DEL PEAK 16(13Q13.3) WILD-TYPE | 109 | 190 | 124 |
Figure S127. Get High-res Image Gene #28: 'del_13q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S128. Gene #28: 'del_13q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 159 | 238 | 103 |
| DEL PEAK 16(13Q13.3) MUTATED | 32 | 18 | 27 |
| DEL PEAK 16(13Q13.3) WILD-TYPE | 127 | 220 | 76 |
Figure S128. Get High-res Image Gene #28: 'del_13q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 8e-05 (Fisher's exact test), Q value = 0.02
Table S129. Gene #29: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 33 | 24 | 13 |
| DEL PEAK 17(14Q31.1) MUTATED | 10 | 19 | 2 |
| DEL PEAK 17(14Q31.1) WILD-TYPE | 23 | 5 | 11 |
Figure S129. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'
P value = 0.00041 (Fisher's exact test), Q value = 0.092
Table S130. Gene #29: 'del_14q31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 11 | 12 | 4 | 11 | 13 | 9 | 10 |
| DEL PEAK 17(14Q31.1) MUTATED | 4 | 7 | 1 | 11 | 5 | 1 | 2 |
| DEL PEAK 17(14Q31.1) WILD-TYPE | 7 | 5 | 3 | 0 | 8 | 8 | 8 |
Figure S130. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S131. Gene #29: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 212 | 152 | 163 |
| DEL PEAK 17(14Q31.1) MUTATED | 67 | 46 | 115 |
| DEL PEAK 17(14Q31.1) WILD-TYPE | 145 | 106 | 48 |
Figure S131. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S132. Gene #29: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 128 | 75 | 110 |
| DEL PEAK 17(14Q31.1) MUTATED | 32 | 36 | 65 |
| DEL PEAK 17(14Q31.1) WILD-TYPE | 96 | 39 | 45 |
Figure S132. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S133. Gene #29: 'del_14q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 100 | 88 | 84 | 75 | 43 | 57 |
| DEL PEAK 17(14Q31.1) MUTATED | 30 | 30 | 64 | 23 | 13 | 40 |
| DEL PEAK 17(14Q31.1) WILD-TYPE | 70 | 58 | 20 | 52 | 30 | 17 |
Figure S133. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'
P value = 4e-05 (Fisher's exact test), Q value = 0.01
Table S134. Gene #29: 'del_14q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 95 | 198 | 154 |
| DEL PEAK 17(14Q31.1) MUTATED | 58 | 67 | 75 |
| DEL PEAK 17(14Q31.1) WILD-TYPE | 37 | 131 | 79 |
Figure S134. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S135. Gene #29: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 215 | 108 | 187 |
| DEL PEAK 17(14Q31.1) MUTATED | 71 | 19 | 130 |
| DEL PEAK 17(14Q31.1) WILD-TYPE | 144 | 89 | 57 |
Figure S135. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S136. Gene #29: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
|---|---|---|---|---|---|---|
| ALL | 120 | 176 | 126 | 28 | 32 | 28 |
| DEL PEAK 17(14Q31.1) MUTATED | 50 | 54 | 77 | 7 | 30 | 2 |
| DEL PEAK 17(14Q31.1) WILD-TYPE | 70 | 122 | 49 | 21 | 2 | 26 |
Figure S136. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S137. Gene #29: 'del_14q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 122 | 206 | 172 |
| DEL PEAK 17(14Q31.1) MUTATED | 38 | 69 | 112 |
| DEL PEAK 17(14Q31.1) WILD-TYPE | 84 | 137 | 60 |
Figure S137. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0035
Table S138. Gene #29: 'del_14q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 159 | 238 | 103 |
| DEL PEAK 17(14Q31.1) MUTATED | 75 | 79 | 65 |
| DEL PEAK 17(14Q31.1) WILD-TYPE | 84 | 159 | 38 |
Figure S138. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
P value = 2e-05 (Fisher's exact test), Q value = 0.0055
Table S139. Gene #29: 'del_14q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 57 | 94 | 89 |
| DEL PEAK 17(14Q31.1) MUTATED | 19 | 28 | 58 |
| DEL PEAK 17(14Q31.1) WILD-TYPE | 38 | 66 | 31 |
Figure S139. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
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Copy number data file = transformed.cor.cli.txt
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Molecular subtype file = KIRC-TP.transferedmergedcluster.txt
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Number of patients = 527
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Number of significantly focal cnvs = 29
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Number of molecular subtypes = 12
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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.