This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.
Testing the association between copy number variation 30 focal events and 10 molecular subtypes across 494 patients, 88 significant findings detected with P value < 0.05 and Q value < 0.25.
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amp_xq22.3 cnv correlated to 'CN_CNMF'.
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del_1q24.2 cnv correlated to 'CN_CNMF'.
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del_2p23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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del_2q35 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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del_6q22.31 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
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del_8p23.2 cnv correlated to 'CN_CNMF'.
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del_8p22 cnv correlated to 'CN_CNMF'.
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del_8p12 cnv correlated to 'CN_CNMF'.
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del_8q24.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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del_9q21.13 cnv correlated to 'CN_CNMF'.
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del_10q21.2 cnv correlated to 'CN_CNMF'.
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del_10q23.31 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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del_11p15.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
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del_13q12.3 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
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del_13q21.31 cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
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del_15q25.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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del_18p11.21 cnv correlated to 'CN_CNMF'.
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del_19p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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del_21q21.1 cnv correlated to 'CN_CNMF'.
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del_22q13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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del_22q13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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del_22q13.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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del_22q13.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 30 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 88 significant findings detected.
|
Clinical Features |
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 | |
| del 2p23 1 | 12 (2%) | 482 |
1e-05 (0.00288) |
1e-05 (0.00288) |
0.77 (1.00) |
0.0921 (1.00) |
3e-05 (0.00744) |
3e-05 (0.00744) |
1e-05 (0.00288) |
1e-05 (0.00288) |
2e-05 (0.0051) |
1e-05 (0.00288) |
| del 2q35 | 12 (2%) | 482 |
1e-05 (0.00288) |
1e-05 (0.00288) |
0.539 (1.00) |
0.023 (1.00) |
3e-05 (0.00744) |
1e-05 (0.00288) |
1e-05 (0.00288) |
2e-05 (0.0051) |
1e-05 (0.00288) |
1e-05 (0.00288) |
| del 22q13 1 | 86 (17%) | 408 |
1e-05 (0.00288) |
1e-05 (0.00288) |
0.119 (1.00) |
0.504 (1.00) |
1e-05 (0.00288) |
1e-05 (0.00288) |
0.00081 (0.168) |
0.00013 (0.0305) |
1e-05 (0.00288) |
2e-05 (0.0051) |
| del 22q13 2 | 86 (17%) | 408 |
1e-05 (0.00288) |
2e-05 (0.0051) |
0.119 (1.00) |
0.504 (1.00) |
1e-05 (0.00288) |
1e-05 (0.00288) |
0.0011 (0.222) |
0.00011 (0.026) |
1e-05 (0.00288) |
3e-05 (0.00744) |
| del 22q13 31 | 86 (17%) | 408 |
1e-05 (0.00288) |
3e-05 (0.00744) |
0.118 (1.00) |
0.501 (1.00) |
1e-05 (0.00288) |
1e-05 (0.00288) |
0.00089 (0.184) |
0.00017 (0.0393) |
2e-05 (0.0051) |
1e-05 (0.00288) |
| del 22q13 32 | 87 (18%) | 407 |
1e-05 (0.00288) |
1e-05 (0.00288) |
0.118 (1.00) |
0.502 (1.00) |
1e-05 (0.00288) |
1e-05 (0.00288) |
0.00051 (0.111) |
8e-05 (0.019) |
2e-05 (0.0051) |
1e-05 (0.00288) |
| del 8q24 22 | 7 (1%) | 487 |
7e-05 (0.0167) |
0.00046 (0.101) |
0.838 (1.00) |
0.172 (1.00) |
0.00172 (0.335) |
0.00045 (0.0994) |
0.0002 (0.046) |
0.00173 (0.336) |
0.00068 (0.145) |
0.00014 (0.0328) |
| del 10q23 31 | 12 (2%) | 482 |
1e-05 (0.00288) |
0.0023 (0.435) |
0.0515 (1.00) |
0.149 (1.00) |
0.00066 (0.141) |
0.00071 (0.15) |
0.00458 (0.82) |
0.00043 (0.0955) |
0.00042 (0.0937) |
0.0008 (0.167) |
| del 19p13 2 | 7 (1%) | 487 |
0.00071 (0.15) |
0.00048 (0.105) |
0.856 (1.00) |
0.299 (1.00) |
0.00171 (0.335) |
0.00027 (0.0607) |
0.00022 (0.0499) |
0.00186 (0.357) |
0.0009 (0.185) |
0.00021 (0.0481) |
| del 15q25 3 | 9 (2%) | 485 |
0.00021 (0.0481) |
0.0014 (0.279) |
0.243 (1.00) |
0.0618 (1.00) |
0.0049 (0.862) |
0.00106 (0.216) |
0.00069 (0.146) |
0.00016 (0.0371) |
0.00153 (0.303) |
0.00045 (0.0994) |
| del 6q22 31 | 7 (1%) | 487 |
6e-05 (0.0144) |
0.00222 (0.422) |
0.0126 (1.00) |
0.574 (1.00) |
0.0321 (1.00) |
0.0138 (1.00) |
0.00327 (0.605) |
0.00092 (0.189) |
0.00971 (1.00) |
0.00181 (0.349) |
| del 11p15 1 | 7 (1%) | 487 |
1e-05 (0.00288) |
0.0115 (1.00) |
0.494 (1.00) |
0.958 (1.00) |
0.00657 (1.00) |
0.0138 (1.00) |
0.00312 (0.583) |
0.00117 (0.235) |
0.00982 (1.00) |
0.00312 (0.583) |
| del 13q12 3 | 16 (3%) | 478 |
0.00606 (1.00) |
0.0006 (0.129) |
0.184 (1.00) |
0.085 (1.00) |
0.00051 (0.111) |
0.0104 (1.00) |
0.0349 (1.00) |
0.00537 (0.934) |
0.0118 (1.00) |
0.0066 (1.00) |
| del 13q21 31 | 18 (4%) | 476 |
0.00528 (0.924) |
0.0167 (1.00) |
0.0553 (1.00) |
0.186 (1.00) |
0.00106 (0.216) |
0.00159 (0.313) |
0.00452 (0.814) |
0.00015 (0.0349) |
0.00485 (0.858) |
0.00469 (0.835) |
| amp xq22 3 | 15 (3%) | 479 |
2e-05 (0.0051) |
0.717 (1.00) |
0.841 (1.00) |
0.504 (1.00) |
0.774 (1.00) |
0.988 (1.00) |
1 (1.00) |
0.713 (1.00) |
0.945 (1.00) |
0.902 (1.00) |
| del 1q24 2 | 3 (1%) | 491 |
0.00037 (0.0829) |
0.0488 (1.00) |
0.0959 (1.00) |
0.111 (1.00) |
0.0281 (1.00) |
0.0164 (1.00) |
0.0701 (1.00) |
0.0283 (1.00) |
||
| del 8p23 2 | 4 (1%) | 490 |
1e-05 (0.00288) |
0.0187 (1.00) |
0.0421 (1.00) |
0.0355 (1.00) |
0.00858 (1.00) |
0.0037 (0.681) |
0.0229 (1.00) |
0.00973 (1.00) |
||
| del 8p22 | 4 (1%) | 490 |
3e-05 (0.00744) |
0.0182 (1.00) |
0.0431 (1.00) |
0.0376 (1.00) |
0.00818 (1.00) |
0.00379 (0.694) |
0.0228 (1.00) |
0.00942 (1.00) |
||
| del 8p12 | 4 (1%) | 490 |
3e-05 (0.00744) |
0.0187 (1.00) |
0.0437 (1.00) |
0.0368 (1.00) |
0.00861 (1.00) |
0.00396 (0.721) |
0.0224 (1.00) |
0.00918 (1.00) |
||
| del 9q21 13 | 24 (5%) | 470 |
1e-05 (0.00288) |
0.0567 (1.00) |
0.174 (1.00) |
0.115 (1.00) |
0.104 (1.00) |
0.0397 (1.00) |
0.00909 (1.00) |
0.00441 (0.798) |
0.0123 (1.00) |
0.00246 (0.462) |
| del 10q21 2 | 12 (2%) | 482 |
5e-05 (0.012) |
0.0654 (1.00) |
0.157 (1.00) |
0.675 (1.00) |
0.0185 (1.00) |
0.0153 (1.00) |
0.136 (1.00) |
0.174 (1.00) |
0.0352 (1.00) |
0.18 (1.00) |
| del 18p11 21 | 4 (1%) | 490 |
0.00023 (0.052) |
0.183 (1.00) |
1 (1.00) |
0.386 (1.00) |
0.238 (1.00) |
0.161 (1.00) |
0.113 (1.00) |
0.0642 (1.00) |
0.0229 (1.00) |
0.207 (1.00) |
| del 21q21 1 | 9 (2%) | 485 |
6e-05 (0.0144) |
0.31 (1.00) |
0.147 (1.00) |
0.323 (1.00) |
0.739 (1.00) |
0.709 (1.00) |
0.0536 (1.00) |
0.119 (1.00) |
0.0536 (1.00) |
0.0212 (1.00) |
| del 5p15 2 | 4 (1%) | 490 |
0.347 (1.00) |
0.366 (1.00) |
0.413 (1.00) |
0.541 (1.00) |
0.556 (1.00) |
0.689 (1.00) |
0.48 (1.00) |
0.164 (1.00) |
||
| del 7q34 | 4 (1%) | 490 |
0.639 (1.00) |
0.794 (1.00) |
0.737 (1.00) |
0.816 (1.00) |
0.689 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||
| del 16q23 3 | 6 (1%) | 488 |
0.0489 (1.00) |
0.12 (1.00) |
0.444 (1.00) |
0.445 (1.00) |
0.287 (1.00) |
0.101 (1.00) |
0.198 (1.00) |
0.211 (1.00) |
0.295 (1.00) |
0.26 (1.00) |
| del 17p13 1 | 8 (2%) | 486 |
0.00186 (0.357) |
0.416 (1.00) |
1 (1.00) |
0.389 (1.00) |
0.651 (1.00) |
0.647 (1.00) |
0.329 (1.00) |
0.141 (1.00) |
0.674 (1.00) |
0.192 (1.00) |
| del 18q22 2 | 5 (1%) | 489 |
0.00135 (0.27) |
0.0593 (1.00) |
1 (1.00) |
0.505 (1.00) |
0.116 (1.00) |
0.0615 (1.00) |
0.041 (1.00) |
0.0188 (1.00) |
0.0077 (1.00) |
0.0642 (1.00) |
| del xq22 1 | 6 (1%) | 488 |
0.0741 (1.00) |
0.421 (1.00) |
0.0983 (1.00) |
0.228 (1.00) |
0.59 (1.00) |
0.557 (1.00) |
0.528 (1.00) |
0.446 (1.00) |
0.701 (1.00) |
0.472 (1.00) |
| del xq22 3 | 4 (1%) | 490 |
0.054 (1.00) |
0.0459 (1.00) |
0.276 (1.00) |
0.195 (1.00) |
0.092 (1.00) |
0.279 (1.00) |
0.114 (1.00) |
0.0645 (1.00) |
0.227 (1.00) |
0.207 (1.00) |
P value = 2e-05 (Fisher's exact test), Q value = 0.0051
Table S1. Gene #1: 'amp_xq22.3' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 34 | 383 | 77 |
| AMP PEAK 1(XQ22.3) MUTATED | 7 | 8 | 0 |
| AMP PEAK 1(XQ22.3) WILD-TYPE | 27 | 375 | 77 |
Figure S1. Get High-res Image Gene #1: 'amp_xq22.3' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00037 (Fisher's exact test), Q value = 0.083
Table S2. Gene #2: 'del_1q24.2' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 34 | 383 | 77 |
| DEL PEAK 1(1Q24.2) MUTATED | 3 | 0 | 0 |
| DEL PEAK 1(1Q24.2) WILD-TYPE | 31 | 383 | 77 |
Figure S2. Get High-res Image Gene #2: 'del_1q24.2' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S3. Gene #3: 'del_2p23.1' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 34 | 383 | 77 |
| DEL PEAK 2(2P23.1) MUTATED | 9 | 1 | 2 |
| DEL PEAK 2(2P23.1) WILD-TYPE | 25 | 382 | 75 |
Figure S3. Get High-res Image Gene #3: 'del_2p23.1' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S4. Gene #3: 'del_2p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 273 | 151 | 70 |
| DEL PEAK 2(2P23.1) MUTATED | 0 | 11 | 1 |
| DEL PEAK 2(2P23.1) WILD-TYPE | 273 | 140 | 69 |
Figure S4. Get High-res Image Gene #3: 'del_2p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.0074
Table S5. Gene #3: 'del_2p23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 154 | 55 | 116 | 167 |
| DEL PEAK 2(2P23.1) MUTATED | 12 | 0 | 0 | 0 |
| DEL PEAK 2(2P23.1) WILD-TYPE | 142 | 55 | 116 | 167 |
Figure S5. Get High-res Image Gene #3: 'del_2p23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.0074
Table S6. Gene #3: 'del_2p23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 126 | 100 | 73 | 115 | 78 |
| DEL PEAK 2(2P23.1) MUTATED | 11 | 1 | 0 | 0 | 0 |
| DEL PEAK 2(2P23.1) WILD-TYPE | 115 | 99 | 73 | 115 | 78 |
Figure S6. Get High-res Image Gene #3: 'del_2p23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S7. Gene #3: 'del_2p23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 150 | 173 | 170 |
| DEL PEAK 2(2P23.1) MUTATED | 12 | 0 | 0 |
| DEL PEAK 2(2P23.1) WILD-TYPE | 138 | 173 | 170 |
Figure S7. Get High-res Image Gene #3: 'del_2p23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S8. Gene #3: 'del_2p23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 125 | 205 | 163 |
| DEL PEAK 2(2P23.1) MUTATED | 11 | 1 | 0 |
| DEL PEAK 2(2P23.1) WILD-TYPE | 114 | 204 | 163 |
Figure S8. Get High-res Image Gene #3: 'del_2p23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 2e-05 (Fisher's exact test), Q value = 0.0051
Table S9. Gene #3: 'del_2p23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 163 | 169 | 161 |
| DEL PEAK 2(2P23.1) MUTATED | 12 | 0 | 0 |
| DEL PEAK 2(2P23.1) WILD-TYPE | 151 | 169 | 161 |
Figure S9. Get High-res Image Gene #3: 'del_2p23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S10. Gene #3: 'del_2p23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 123 | 187 | 105 | 78 |
| DEL PEAK 2(2P23.1) MUTATED | 12 | 0 | 0 | 0 |
| DEL PEAK 2(2P23.1) WILD-TYPE | 111 | 187 | 105 | 78 |
Figure S10. Get High-res Image Gene #3: 'del_2p23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S11. Gene #4: 'del_2q35' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 34 | 383 | 77 |
| DEL PEAK 3(2Q35) MUTATED | 11 | 1 | 0 |
| DEL PEAK 3(2Q35) WILD-TYPE | 23 | 382 | 77 |
Figure S11. Get High-res Image Gene #4: 'del_2q35' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S12. Gene #4: 'del_2q35' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 273 | 151 | 70 |
| DEL PEAK 3(2Q35) MUTATED | 0 | 12 | 0 |
| DEL PEAK 3(2Q35) WILD-TYPE | 273 | 139 | 70 |
Figure S12. Get High-res Image Gene #4: 'del_2q35' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.0074
Table S13. Gene #4: 'del_2q35' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 154 | 55 | 116 | 167 |
| DEL PEAK 3(2Q35) MUTATED | 12 | 0 | 0 | 0 |
| DEL PEAK 3(2Q35) WILD-TYPE | 142 | 55 | 116 | 167 |
Figure S13. Get High-res Image Gene #4: 'del_2q35' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S14. Gene #4: 'del_2q35' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 126 | 100 | 73 | 115 | 78 |
| DEL PEAK 3(2Q35) MUTATED | 12 | 0 | 0 | 0 | 0 |
| DEL PEAK 3(2Q35) WILD-TYPE | 114 | 100 | 73 | 115 | 78 |
Figure S14. Get High-res Image Gene #4: 'del_2q35' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S15. Gene #4: 'del_2q35' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 150 | 173 | 170 |
| DEL PEAK 3(2Q35) MUTATED | 12 | 0 | 0 |
| DEL PEAK 3(2Q35) WILD-TYPE | 138 | 173 | 170 |
Figure S15. Get High-res Image Gene #4: 'del_2q35' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 2e-05 (Fisher's exact test), Q value = 0.0051
Table S16. Gene #4: 'del_2q35' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 125 | 205 | 163 |
| DEL PEAK 3(2Q35) MUTATED | 11 | 1 | 0 |
| DEL PEAK 3(2Q35) WILD-TYPE | 114 | 204 | 163 |
Figure S16. Get High-res Image Gene #4: 'del_2q35' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S17. Gene #4: 'del_2q35' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 163 | 169 | 161 |
| DEL PEAK 3(2Q35) MUTATED | 12 | 0 | 0 |
| DEL PEAK 3(2Q35) WILD-TYPE | 151 | 169 | 161 |
Figure S17. Get High-res Image Gene #4: 'del_2q35' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S18. Gene #4: 'del_2q35' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 123 | 187 | 105 | 78 |
| DEL PEAK 3(2Q35) MUTATED | 12 | 0 | 0 | 0 |
| DEL PEAK 3(2Q35) WILD-TYPE | 111 | 187 | 105 | 78 |
Figure S18. Get High-res Image Gene #4: 'del_2q35' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 6e-05 (Fisher's exact test), Q value = 0.014
Table S19. Gene #6: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 34 | 383 | 77 |
| DEL PEAK 6(6Q22.31) MUTATED | 5 | 2 | 0 |
| DEL PEAK 6(6Q22.31) WILD-TYPE | 29 | 381 | 77 |
Figure S19. Get High-res Image Gene #6: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00092 (Fisher's exact test), Q value = 0.19
Table S20. Gene #6: 'del_6q22.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 125 | 205 | 163 |
| DEL PEAK 6(6Q22.31) MUTATED | 6 | 0 | 1 |
| DEL PEAK 6(6Q22.31) WILD-TYPE | 119 | 205 | 162 |
Figure S20. Get High-res Image Gene #6: 'del_6q22.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S21. Gene #8: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 34 | 383 | 77 |
| DEL PEAK 9(8P23.2) MUTATED | 4 | 0 | 0 |
| DEL PEAK 9(8P23.2) WILD-TYPE | 30 | 383 | 77 |
Figure S21. Get High-res Image Gene #8: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.0074
Table S22. Gene #9: 'del_8p22' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 34 | 383 | 77 |
| DEL PEAK 10(8P22) MUTATED | 4 | 0 | 0 |
| DEL PEAK 10(8P22) WILD-TYPE | 30 | 383 | 77 |
Figure S22. Get High-res Image Gene #9: 'del_8p22' versus Molecular Subtype #1: 'CN_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.0074
Table S23. Gene #10: 'del_8p12' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 34 | 383 | 77 |
| DEL PEAK 11(8P12) MUTATED | 4 | 0 | 0 |
| DEL PEAK 11(8P12) WILD-TYPE | 30 | 383 | 77 |
Figure S23. Get High-res Image Gene #10: 'del_8p12' versus Molecular Subtype #1: 'CN_CNMF'
P value = 7e-05 (Fisher's exact test), Q value = 0.017
Table S24. Gene #11: 'del_8q24.22' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 34 | 383 | 77 |
| DEL PEAK 12(8Q24.22) MUTATED | 5 | 2 | 0 |
| DEL PEAK 12(8Q24.22) WILD-TYPE | 29 | 381 | 77 |
Figure S24. Get High-res Image Gene #11: 'del_8q24.22' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00046 (Fisher's exact test), Q value = 0.1
Table S25. Gene #11: 'del_8q24.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 273 | 151 | 70 |
| DEL PEAK 12(8Q24.22) MUTATED | 0 | 7 | 0 |
| DEL PEAK 12(8Q24.22) WILD-TYPE | 273 | 144 | 70 |
Figure S25. Get High-res Image Gene #11: 'del_8q24.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.00045 (Fisher's exact test), Q value = 0.099
Table S26. Gene #11: 'del_8q24.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 126 | 100 | 73 | 115 | 78 |
| DEL PEAK 12(8Q24.22) MUTATED | 7 | 0 | 0 | 0 | 0 |
| DEL PEAK 12(8Q24.22) WILD-TYPE | 119 | 100 | 73 | 115 | 78 |
Figure S26. Get High-res Image Gene #11: 'del_8q24.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 2e-04 (Fisher's exact test), Q value = 0.046
Table S27. Gene #11: 'del_8q24.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 150 | 173 | 170 |
| DEL PEAK 12(8Q24.22) MUTATED | 7 | 0 | 0 |
| DEL PEAK 12(8Q24.22) WILD-TYPE | 143 | 173 | 170 |
Figure S27. Get High-res Image Gene #11: 'del_8q24.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.00068 (Fisher's exact test), Q value = 0.14
Table S28. Gene #11: 'del_8q24.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 163 | 169 | 161 |
| DEL PEAK 12(8Q24.22) MUTATED | 7 | 0 | 0 |
| DEL PEAK 12(8Q24.22) WILD-TYPE | 156 | 169 | 161 |
Figure S28. Get High-res Image Gene #11: 'del_8q24.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.00014 (Fisher's exact test), Q value = 0.033
Table S29. Gene #11: 'del_8q24.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 123 | 187 | 105 | 78 |
| DEL PEAK 12(8Q24.22) MUTATED | 7 | 0 | 0 | 0 |
| DEL PEAK 12(8Q24.22) WILD-TYPE | 116 | 187 | 105 | 78 |
Figure S29. Get High-res Image Gene #11: 'del_8q24.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S30. Gene #12: 'del_9q21.13' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 34 | 383 | 77 |
| DEL PEAK 13(9Q21.13) MUTATED | 16 | 7 | 1 |
| DEL PEAK 13(9Q21.13) WILD-TYPE | 18 | 376 | 76 |
Figure S30. Get High-res Image Gene #12: 'del_9q21.13' versus Molecular Subtype #1: 'CN_CNMF'
P value = 5e-05 (Fisher's exact test), Q value = 0.012
Table S31. Gene #13: 'del_10q21.2' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 34 | 383 | 77 |
| DEL PEAK 14(10Q21.2) MUTATED | 6 | 6 | 0 |
| DEL PEAK 14(10Q21.2) WILD-TYPE | 28 | 377 | 77 |
Figure S31. Get High-res Image Gene #13: 'del_10q21.2' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S32. Gene #14: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 34 | 383 | 77 |
| DEL PEAK 15(10Q23.31) MUTATED | 7 | 5 | 0 |
| DEL PEAK 15(10Q23.31) WILD-TYPE | 27 | 378 | 77 |
Figure S32. Get High-res Image Gene #14: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00066 (Fisher's exact test), Q value = 0.14
Table S33. Gene #14: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 154 | 55 | 116 | 167 |
| DEL PEAK 15(10Q23.31) MUTATED | 10 | 0 | 2 | 0 |
| DEL PEAK 15(10Q23.31) WILD-TYPE | 144 | 55 | 114 | 167 |
Figure S33. Get High-res Image Gene #14: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.00071 (Fisher's exact test), Q value = 0.15
Table S34. Gene #14: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 126 | 100 | 73 | 115 | 78 |
| DEL PEAK 15(10Q23.31) MUTATED | 9 | 3 | 0 | 0 | 0 |
| DEL PEAK 15(10Q23.31) WILD-TYPE | 117 | 97 | 73 | 115 | 78 |
Figure S34. Get High-res Image Gene #14: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00043 (Fisher's exact test), Q value = 0.095
Table S35. Gene #14: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 125 | 205 | 163 |
| DEL PEAK 15(10Q23.31) MUTATED | 9 | 1 | 2 |
| DEL PEAK 15(10Q23.31) WILD-TYPE | 116 | 204 | 161 |
Figure S35. Get High-res Image Gene #14: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00042 (Fisher's exact test), Q value = 0.094
Table S36. Gene #14: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 163 | 169 | 161 |
| DEL PEAK 15(10Q23.31) MUTATED | 10 | 0 | 2 |
| DEL PEAK 15(10Q23.31) WILD-TYPE | 153 | 169 | 159 |
Figure S36. Get High-res Image Gene #14: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 8e-04 (Fisher's exact test), Q value = 0.17
Table S37. Gene #14: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 123 | 187 | 105 | 78 |
| DEL PEAK 15(10Q23.31) MUTATED | 9 | 1 | 2 | 0 |
| DEL PEAK 15(10Q23.31) WILD-TYPE | 114 | 186 | 103 | 78 |
Figure S37. Get High-res Image Gene #14: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S38. Gene #15: 'del_11p15.1' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 34 | 383 | 77 |
| DEL PEAK 16(11P15.1) MUTATED | 6 | 0 | 1 |
| DEL PEAK 16(11P15.1) WILD-TYPE | 28 | 383 | 76 |
Figure S38. Get High-res Image Gene #15: 'del_11p15.1' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00117 (Fisher's exact test), Q value = 0.24
Table S39. Gene #15: 'del_11p15.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 125 | 205 | 163 |
| DEL PEAK 16(11P15.1) MUTATED | 6 | 0 | 1 |
| DEL PEAK 16(11P15.1) WILD-TYPE | 119 | 205 | 162 |
Figure S39. Get High-res Image Gene #15: 'del_11p15.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 6e-04 (Fisher's exact test), Q value = 0.13
Table S40. Gene #16: 'del_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 273 | 151 | 70 |
| DEL PEAK 17(13Q12.3) MUTATED | 2 | 11 | 3 |
| DEL PEAK 17(13Q12.3) WILD-TYPE | 271 | 140 | 67 |
Figure S40. Get High-res Image Gene #16: 'del_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.00051 (Fisher's exact test), Q value = 0.11
Table S41. Gene #16: 'del_13q12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 154 | 55 | 116 | 167 |
| DEL PEAK 17(13Q12.3) MUTATED | 11 | 3 | 2 | 0 |
| DEL PEAK 17(13Q12.3) WILD-TYPE | 143 | 52 | 114 | 167 |
Figure S41. Get High-res Image Gene #16: 'del_13q12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.00106 (Fisher's exact test), Q value = 0.22
Table S42. Gene #17: 'del_13q21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 154 | 55 | 116 | 167 |
| DEL PEAK 18(13Q21.31) MUTATED | 11 | 2 | 5 | 0 |
| DEL PEAK 18(13Q21.31) WILD-TYPE | 143 | 53 | 111 | 167 |
Figure S42. Get High-res Image Gene #17: 'del_13q21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.00015 (Fisher's exact test), Q value = 0.035
Table S43. Gene #17: 'del_13q21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 125 | 205 | 163 |
| DEL PEAK 18(13Q21.31) MUTATED | 11 | 7 | 0 |
| DEL PEAK 18(13Q21.31) WILD-TYPE | 114 | 198 | 163 |
Figure S43. Get High-res Image Gene #17: 'del_13q21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00021 (Fisher's exact test), Q value = 0.048
Table S44. Gene #18: 'del_15q25.3' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 34 | 383 | 77 |
| DEL PEAK 19(15Q25.3) MUTATED | 5 | 3 | 1 |
| DEL PEAK 19(15Q25.3) WILD-TYPE | 29 | 380 | 76 |
Figure S44. Get High-res Image Gene #18: 'del_15q25.3' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00106 (Fisher's exact test), Q value = 0.22
Table S45. Gene #18: 'del_15q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 126 | 100 | 73 | 115 | 78 |
| DEL PEAK 19(15Q25.3) MUTATED | 8 | 0 | 0 | 1 | 0 |
| DEL PEAK 19(15Q25.3) WILD-TYPE | 118 | 100 | 73 | 114 | 78 |
Figure S45. Get High-res Image Gene #18: 'del_15q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00069 (Fisher's exact test), Q value = 0.15
Table S46. Gene #18: 'del_15q25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 150 | 173 | 170 |
| DEL PEAK 19(15Q25.3) MUTATED | 8 | 1 | 0 |
| DEL PEAK 19(15Q25.3) WILD-TYPE | 142 | 172 | 170 |
Figure S46. Get High-res Image Gene #18: 'del_15q25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.00016 (Fisher's exact test), Q value = 0.037
Table S47. Gene #18: 'del_15q25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 125 | 205 | 163 |
| DEL PEAK 19(15Q25.3) MUTATED | 8 | 1 | 0 |
| DEL PEAK 19(15Q25.3) WILD-TYPE | 117 | 204 | 163 |
Figure S47. Get High-res Image Gene #18: 'del_15q25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00045 (Fisher's exact test), Q value = 0.099
Table S48. Gene #18: 'del_15q25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 123 | 187 | 105 | 78 |
| DEL PEAK 19(15Q25.3) MUTATED | 8 | 1 | 0 | 0 |
| DEL PEAK 19(15Q25.3) WILD-TYPE | 115 | 186 | 105 | 78 |
Figure S48. Get High-res Image Gene #18: 'del_15q25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.00023 (Fisher's exact test), Q value = 0.052
Table S49. Gene #21: 'del_18p11.21' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 34 | 383 | 77 |
| DEL PEAK 23(18P11.21) MUTATED | 3 | 0 | 1 |
| DEL PEAK 23(18P11.21) WILD-TYPE | 31 | 383 | 76 |
Figure S49. Get High-res Image Gene #21: 'del_18p11.21' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00071 (Fisher's exact test), Q value = 0.15
Table S50. Gene #23: 'del_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 34 | 383 | 77 |
| DEL PEAK 25(19P13.2) MUTATED | 4 | 2 | 1 |
| DEL PEAK 25(19P13.2) WILD-TYPE | 30 | 381 | 76 |
Figure S50. Get High-res Image Gene #23: 'del_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00048 (Fisher's exact test), Q value = 0.1
Table S51. Gene #23: 'del_19p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 273 | 151 | 70 |
| DEL PEAK 25(19P13.2) MUTATED | 0 | 7 | 0 |
| DEL PEAK 25(19P13.2) WILD-TYPE | 273 | 144 | 70 |
Figure S51. Get High-res Image Gene #23: 'del_19p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.00027 (Fisher's exact test), Q value = 0.061
Table S52. Gene #23: 'del_19p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 126 | 100 | 73 | 115 | 78 |
| DEL PEAK 25(19P13.2) MUTATED | 7 | 0 | 0 | 0 | 0 |
| DEL PEAK 25(19P13.2) WILD-TYPE | 119 | 100 | 73 | 115 | 78 |
Figure S52. Get High-res Image Gene #23: 'del_19p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00022 (Fisher's exact test), Q value = 0.05
Table S53. Gene #23: 'del_19p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 150 | 173 | 170 |
| DEL PEAK 25(19P13.2) MUTATED | 7 | 0 | 0 |
| DEL PEAK 25(19P13.2) WILD-TYPE | 143 | 173 | 170 |
Figure S53. Get High-res Image Gene #23: 'del_19p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 9e-04 (Fisher's exact test), Q value = 0.19
Table S54. Gene #23: 'del_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 163 | 169 | 161 |
| DEL PEAK 25(19P13.2) MUTATED | 7 | 0 | 0 |
| DEL PEAK 25(19P13.2) WILD-TYPE | 156 | 169 | 161 |
Figure S54. Get High-res Image Gene #23: 'del_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.00021 (Fisher's exact test), Q value = 0.048
Table S55. Gene #23: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 123 | 187 | 105 | 78 |
| DEL PEAK 25(19P13.2) MUTATED | 7 | 0 | 0 | 0 |
| DEL PEAK 25(19P13.2) WILD-TYPE | 116 | 187 | 105 | 78 |
Figure S55. Get High-res Image Gene #23: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 6e-05 (Fisher's exact test), Q value = 0.014
Table S56. Gene #24: 'del_21q21.1' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 34 | 383 | 77 |
| DEL PEAK 28(21Q21.1) MUTATED | 5 | 2 | 2 |
| DEL PEAK 28(21Q21.1) WILD-TYPE | 29 | 381 | 75 |
Figure S56. Get High-res Image Gene #24: 'del_21q21.1' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S57. Gene #25: 'del_22q13.1' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 34 | 383 | 77 |
| DEL PEAK 29(22Q13.1) MUTATED | 9 | 0 | 77 |
| DEL PEAK 29(22Q13.1) WILD-TYPE | 25 | 383 | 0 |
Figure S57. Get High-res Image Gene #25: 'del_22q13.1' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S58. Gene #25: 'del_22q13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 273 | 151 | 70 |
| DEL PEAK 29(22Q13.1) MUTATED | 35 | 45 | 6 |
| DEL PEAK 29(22Q13.1) WILD-TYPE | 238 | 106 | 64 |
Figure S58. Get High-res Image Gene #25: 'del_22q13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S59. Gene #25: 'del_22q13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 154 | 55 | 116 | 167 |
| DEL PEAK 29(22Q13.1) MUTATED | 45 | 8 | 26 | 7 |
| DEL PEAK 29(22Q13.1) WILD-TYPE | 109 | 47 | 90 | 160 |
Figure S59. Get High-res Image Gene #25: 'del_22q13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S60. Gene #25: 'del_22q13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 126 | 100 | 73 | 115 | 78 |
| DEL PEAK 29(22Q13.1) MUTATED | 40 | 13 | 22 | 9 | 2 |
| DEL PEAK 29(22Q13.1) WILD-TYPE | 86 | 87 | 51 | 106 | 76 |
Figure S60. Get High-res Image Gene #25: 'del_22q13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00081 (Fisher's exact test), Q value = 0.17
Table S61. Gene #25: 'del_22q13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 150 | 173 | 170 |
| DEL PEAK 29(22Q13.1) MUTATED | 41 | 24 | 21 |
| DEL PEAK 29(22Q13.1) WILD-TYPE | 109 | 149 | 149 |
Figure S61. Get High-res Image Gene #25: 'del_22q13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.00013 (Fisher's exact test), Q value = 0.031
Table S62. Gene #25: 'del_22q13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 125 | 205 | 163 |
| DEL PEAK 29(22Q13.1) MUTATED | 38 | 28 | 20 |
| DEL PEAK 29(22Q13.1) WILD-TYPE | 87 | 177 | 143 |
Figure S62. Get High-res Image Gene #25: 'del_22q13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S63. Gene #25: 'del_22q13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 163 | 169 | 161 |
| DEL PEAK 29(22Q13.1) MUTATED | 49 | 18 | 19 |
| DEL PEAK 29(22Q13.1) WILD-TYPE | 114 | 151 | 142 |
Figure S63. Get High-res Image Gene #25: 'del_22q13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 2e-05 (Fisher's exact test), Q value = 0.0051
Table S64. Gene #25: 'del_22q13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 123 | 187 | 105 | 78 |
| DEL PEAK 29(22Q13.1) MUTATED | 38 | 26 | 18 | 4 |
| DEL PEAK 29(22Q13.1) WILD-TYPE | 85 | 161 | 87 | 74 |
Figure S64. Get High-res Image Gene #25: 'del_22q13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S65. Gene #26: 'del_22q13.2' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 34 | 383 | 77 |
| DEL PEAK 30(22Q13.2) MUTATED | 9 | 0 | 77 |
| DEL PEAK 30(22Q13.2) WILD-TYPE | 25 | 383 | 0 |
Figure S65. Get High-res Image Gene #26: 'del_22q13.2' versus Molecular Subtype #1: 'CN_CNMF'
P value = 2e-05 (Fisher's exact test), Q value = 0.0051
Table S66. Gene #26: 'del_22q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 273 | 151 | 70 |
| DEL PEAK 30(22Q13.2) MUTATED | 35 | 45 | 6 |
| DEL PEAK 30(22Q13.2) WILD-TYPE | 238 | 106 | 64 |
Figure S66. Get High-res Image Gene #26: 'del_22q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S67. Gene #26: 'del_22q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 154 | 55 | 116 | 167 |
| DEL PEAK 30(22Q13.2) MUTATED | 45 | 8 | 26 | 7 |
| DEL PEAK 30(22Q13.2) WILD-TYPE | 109 | 47 | 90 | 160 |
Figure S67. Get High-res Image Gene #26: 'del_22q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S68. Gene #26: 'del_22q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 126 | 100 | 73 | 115 | 78 |
| DEL PEAK 30(22Q13.2) MUTATED | 40 | 13 | 22 | 9 | 2 |
| DEL PEAK 30(22Q13.2) WILD-TYPE | 86 | 87 | 51 | 106 | 76 |
Figure S68. Get High-res Image Gene #26: 'del_22q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0011 (Fisher's exact test), Q value = 0.22
Table S69. Gene #26: 'del_22q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 150 | 173 | 170 |
| DEL PEAK 30(22Q13.2) MUTATED | 41 | 24 | 21 |
| DEL PEAK 30(22Q13.2) WILD-TYPE | 109 | 149 | 149 |
Figure S69. Get High-res Image Gene #26: 'del_22q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.00011 (Fisher's exact test), Q value = 0.026
Table S70. Gene #26: 'del_22q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 125 | 205 | 163 |
| DEL PEAK 30(22Q13.2) MUTATED | 38 | 28 | 20 |
| DEL PEAK 30(22Q13.2) WILD-TYPE | 87 | 177 | 143 |
Figure S70. Get High-res Image Gene #26: 'del_22q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S71. Gene #26: 'del_22q13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 163 | 169 | 161 |
| DEL PEAK 30(22Q13.2) MUTATED | 49 | 18 | 19 |
| DEL PEAK 30(22Q13.2) WILD-TYPE | 114 | 151 | 142 |
Figure S71. Get High-res Image Gene #26: 'del_22q13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.0074
Table S72. Gene #26: 'del_22q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 123 | 187 | 105 | 78 |
| DEL PEAK 30(22Q13.2) MUTATED | 38 | 26 | 18 | 4 |
| DEL PEAK 30(22Q13.2) WILD-TYPE | 85 | 161 | 87 | 74 |
Figure S72. Get High-res Image Gene #26: 'del_22q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S73. Gene #27: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 34 | 383 | 77 |
| DEL PEAK 31(22Q13.31) MUTATED | 9 | 0 | 77 |
| DEL PEAK 31(22Q13.31) WILD-TYPE | 25 | 383 | 0 |
Figure S73. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.0074
Table S74. Gene #27: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 273 | 151 | 70 |
| DEL PEAK 31(22Q13.31) MUTATED | 35 | 45 | 6 |
| DEL PEAK 31(22Q13.31) WILD-TYPE | 238 | 106 | 64 |
Figure S74. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S75. Gene #27: 'del_22q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 154 | 55 | 116 | 167 |
| DEL PEAK 31(22Q13.31) MUTATED | 45 | 8 | 26 | 7 |
| DEL PEAK 31(22Q13.31) WILD-TYPE | 109 | 47 | 90 | 160 |
Figure S75. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S76. Gene #27: 'del_22q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 126 | 100 | 73 | 115 | 78 |
| DEL PEAK 31(22Q13.31) MUTATED | 40 | 13 | 22 | 9 | 2 |
| DEL PEAK 31(22Q13.31) WILD-TYPE | 86 | 87 | 51 | 106 | 76 |
Figure S76. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00089 (Fisher's exact test), Q value = 0.18
Table S77. Gene #27: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 150 | 173 | 170 |
| DEL PEAK 31(22Q13.31) MUTATED | 41 | 24 | 21 |
| DEL PEAK 31(22Q13.31) WILD-TYPE | 109 | 149 | 149 |
Figure S77. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.00017 (Fisher's exact test), Q value = 0.039
Table S78. Gene #27: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 125 | 205 | 163 |
| DEL PEAK 31(22Q13.31) MUTATED | 38 | 28 | 20 |
| DEL PEAK 31(22Q13.31) WILD-TYPE | 87 | 177 | 143 |
Figure S78. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 2e-05 (Fisher's exact test), Q value = 0.0051
Table S79. Gene #27: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 163 | 169 | 161 |
| DEL PEAK 31(22Q13.31) MUTATED | 49 | 18 | 19 |
| DEL PEAK 31(22Q13.31) WILD-TYPE | 114 | 151 | 142 |
Figure S79. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S80. Gene #27: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 123 | 187 | 105 | 78 |
| DEL PEAK 31(22Q13.31) MUTATED | 38 | 26 | 18 | 4 |
| DEL PEAK 31(22Q13.31) WILD-TYPE | 85 | 161 | 87 | 74 |
Figure S80. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S81. Gene #28: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 34 | 383 | 77 |
| DEL PEAK 32(22Q13.32) MUTATED | 9 | 1 | 77 |
| DEL PEAK 32(22Q13.32) WILD-TYPE | 25 | 382 | 0 |
Figure S81. Get High-res Image Gene #28: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S82. Gene #28: 'del_22q13.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 273 | 151 | 70 |
| DEL PEAK 32(22Q13.32) MUTATED | 35 | 46 | 6 |
| DEL PEAK 32(22Q13.32) WILD-TYPE | 238 | 105 | 64 |
Figure S82. Get High-res Image Gene #28: 'del_22q13.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S83. Gene #28: 'del_22q13.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 154 | 55 | 116 | 167 |
| DEL PEAK 32(22Q13.32) MUTATED | 46 | 8 | 26 | 7 |
| DEL PEAK 32(22Q13.32) WILD-TYPE | 108 | 47 | 90 | 160 |
Figure S83. Get High-res Image Gene #28: 'del_22q13.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S84. Gene #28: 'del_22q13.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 126 | 100 | 73 | 115 | 78 |
| DEL PEAK 32(22Q13.32) MUTATED | 41 | 13 | 22 | 9 | 2 |
| DEL PEAK 32(22Q13.32) WILD-TYPE | 85 | 87 | 51 | 106 | 76 |
Figure S84. Get High-res Image Gene #28: 'del_22q13.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00051 (Fisher's exact test), Q value = 0.11
Table S85. Gene #28: 'del_22q13.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 150 | 173 | 170 |
| DEL PEAK 32(22Q13.32) MUTATED | 42 | 24 | 21 |
| DEL PEAK 32(22Q13.32) WILD-TYPE | 108 | 149 | 149 |
Figure S85. Get High-res Image Gene #28: 'del_22q13.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 8e-05 (Fisher's exact test), Q value = 0.019
Table S86. Gene #28: 'del_22q13.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 125 | 205 | 163 |
| DEL PEAK 32(22Q13.32) MUTATED | 39 | 28 | 20 |
| DEL PEAK 32(22Q13.32) WILD-TYPE | 86 | 177 | 143 |
Figure S86. Get High-res Image Gene #28: 'del_22q13.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 2e-05 (Fisher's exact test), Q value = 0.0051
Table S87. Gene #28: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 163 | 169 | 161 |
| DEL PEAK 32(22Q13.32) MUTATED | 50 | 18 | 19 |
| DEL PEAK 32(22Q13.32) WILD-TYPE | 113 | 151 | 142 |
Figure S87. Get High-res Image Gene #28: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0029
Table S88. Gene #28: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 123 | 187 | 105 | 78 |
| DEL PEAK 32(22Q13.32) MUTATED | 39 | 26 | 18 | 4 |
| DEL PEAK 32(22Q13.32) WILD-TYPE | 84 | 161 | 87 | 74 |
Figure S88. Get High-res Image Gene #28: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
-
Copy number data file = transformed.cor.cli.txt
-
Molecular subtype file = THCA-TP.transferedmergedcluster.txt
-
Number of patients = 494
-
Number of significantly focal cnvs = 30
-
Number of molecular subtypes = 10
-
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.