This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.
Testing the association between copy number variation 31 focal events and 10 molecular subtypes across 288 patients, 100 significant findings detected with P value < 0.05 and Q value < 0.25.
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amp_2p23.2 cnv correlated to 'CN_CNMF'.
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amp_2q32.1 cnv correlated to 'CN_CNMF'.
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amp_3q27.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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amp_5q35.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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amp_7q31.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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amp_17q25.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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amp_19p13.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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del_1p36.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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del_2q22.1 cnv correlated to 'MRNASEQ_CNMF'.
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del_3p22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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del_4q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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del_5q35.2 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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del_6p12.3 cnv correlated to 'CN_CNMF'.
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del_6q22.31 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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del_6q25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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del_10q21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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del_11q22.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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del_11q23.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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del_14q11.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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del_14q24.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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del_15q13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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del_16q24.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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del_19p13.3 cnv correlated to 'CN_CNMF'.
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del_19q13.42 cnv correlated to 'CN_CNMF'.
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del_22q12.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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del_xp11.4 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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del_xq28 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 31 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, 100 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 | |
| amp 7q31 2 | 177 (61%) | 111 |
1e-05 (0.0031) |
1e-05 (0.0031) |
0.0134 (1.00) |
5e-05 (0.0121) |
1e-05 (0.0031) |
1e-05 (0.0031) |
0.0508 (1.00) |
1e-05 (0.0031) |
3e-05 (0.00756) |
1e-05 (0.0031) |
| del 9p21 3 | 40 (14%) | 248 |
1e-05 (0.0031) |
1e-05 (0.0031) |
0.37 (1.00) |
0.00073 (0.159) |
1e-05 (0.0031) |
1e-05 (0.0031) |
0.00038 (0.0844) |
0.0302 (1.00) |
0.0001 (0.0233) |
3e-05 (0.00756) |
| amp 17q25 2 | 201 (70%) | 87 |
1e-05 (0.0031) |
3e-05 (0.00756) |
0.0804 (1.00) |
0.00011 (0.0255) |
1e-05 (0.0031) |
1e-05 (0.0031) |
0.0702 (1.00) |
0.00103 (0.218) |
0.00161 (0.328) |
0.00105 (0.222) |
| del 4q34 3 | 32 (11%) | 256 |
1e-05 (0.0031) |
1e-05 (0.0031) |
0.572 (1.00) |
0.00593 (1.00) |
1e-05 (0.0031) |
5e-05 (0.0121) |
0.423 (1.00) |
0.367 (1.00) |
0.00893 (1.00) |
3e-05 (0.00756) |
| del xp11 4 | 34 (12%) | 254 |
1e-05 (0.0031) |
1e-05 (0.0031) |
0.373 (1.00) |
0.00274 (0.535) |
1e-05 (0.0031) |
2e-05 (0.00508) |
0.704 (1.00) |
0.264 (1.00) |
0.00138 (0.286) |
0.0004 (0.0884) |
| amp 3q27 1 | 100 (35%) | 188 |
1e-05 (0.0031) |
0.0576 (1.00) |
0.256 (1.00) |
0.0117 (1.00) |
1e-05 (0.0031) |
0.00085 (0.184) |
0.0336 (1.00) |
0.00019 (0.0431) |
0.761 (1.00) |
0.0174 (1.00) |
| amp 5q35 2 | 37 (13%) | 251 |
1e-05 (0.0031) |
0.00016 (0.0365) |
0.256 (1.00) |
0.321 (1.00) |
0.00065 (0.142) |
8e-05 (0.0188) |
0.051 (1.00) |
0.00537 (0.967) |
0.41 (1.00) |
0.0548 (1.00) |
| del 1p36 31 | 55 (19%) | 233 |
1e-05 (0.0031) |
6e-05 (0.0144) |
0.662 (1.00) |
0.0521 (1.00) |
1e-05 (0.0031) |
1e-05 (0.0031) |
0.771 (1.00) |
0.855 (1.00) |
0.0244 (1.00) |
0.00554 (0.988) |
| del 3p22 1 | 25 (9%) | 263 |
1e-05 (0.0031) |
1e-05 (0.0031) |
0.472 (1.00) |
0.00168 (0.339) |
1e-05 (0.0031) |
1e-05 (0.0031) |
0.202 (1.00) |
0.00572 (1.00) |
0.0256 (1.00) |
0.00446 (0.834) |
| del 5q35 2 | 11 (4%) | 277 |
0.028 (1.00) |
4e-05 (0.00984) |
0.414 (1.00) |
0.00632 (1.00) |
6e-05 (0.0144) |
6e-05 (0.0144) |
0.00712 (1.00) |
0.00301 (0.581) |
0.00166 (0.337) |
1e-05 (0.0031) |
| del 6q25 3 | 32 (11%) | 256 |
1e-05 (0.0031) |
0.00044 (0.0968) |
0.857 (1.00) |
0.104 (1.00) |
1e-05 (0.0031) |
6e-05 (0.0144) |
0.342 (1.00) |
0.743 (1.00) |
0.0414 (1.00) |
0.0653 (1.00) |
| del 10q21 1 | 19 (7%) | 269 |
1e-05 (0.0031) |
4e-05 (0.00984) |
0.332 (1.00) |
0.00408 (0.767) |
8e-05 (0.0188) |
0.00078 (0.169) |
0.636 (1.00) |
0.975 (1.00) |
0.0374 (1.00) |
0.00616 (1.00) |
| del 11q23 3 | 29 (10%) | 259 |
1e-05 (0.0031) |
0.00015 (0.0345) |
0.418 (1.00) |
0.192 (1.00) |
6e-05 (0.0144) |
0.00028 (0.0627) |
0.323 (1.00) |
0.333 (1.00) |
0.00598 (1.00) |
0.00513 (0.939) |
| del 15q13 3 | 35 (12%) | 253 |
1e-05 (0.0031) |
4e-05 (0.00984) |
0.135 (1.00) |
0.00947 (1.00) |
1e-05 (0.0031) |
1e-05 (0.0031) |
0.0766 (1.00) |
0.601 (1.00) |
0.0409 (1.00) |
0.0033 (0.634) |
| del 22q12 2 | 63 (22%) | 225 |
1e-05 (0.0031) |
1e-05 (0.0031) |
0.742 (1.00) |
0.00595 (1.00) |
1e-05 (0.0031) |
1e-05 (0.0031) |
1 (1.00) |
0.4 (1.00) |
0.0379 (1.00) |
0.00525 (0.95) |
| amp 19p13 2 | 31 (11%) | 257 |
1e-05 (0.0031) |
0.00816 (1.00) |
0.00467 (0.864) |
0.00448 (0.834) |
0.0009 (0.193) |
0.00096 (0.204) |
0.122 (1.00) |
0.564 (1.00) |
0.0612 (1.00) |
0.0078 (1.00) |
| del 6q22 31 | 29 (10%) | 259 |
1e-05 (0.0031) |
0.00755 (1.00) |
0.96 (1.00) |
0.0379 (1.00) |
2e-05 (0.00508) |
3e-05 (0.00756) |
0.418 (1.00) |
0.266 (1.00) |
0.0138 (1.00) |
0.0376 (1.00) |
| del 11q22 3 | 31 (11%) | 257 |
1e-05 (0.0031) |
0.00144 (0.297) |
0.738 (1.00) |
0.234 (1.00) |
0.00015 (0.0345) |
0.0002 (0.0452) |
0.239 (1.00) |
0.191 (1.00) |
0.00281 (0.545) |
0.0024 (0.475) |
| del 14q11 2 | 51 (18%) | 237 |
1e-05 (0.0031) |
0.0141 (1.00) |
0.0777 (1.00) |
0.00398 (0.752) |
1e-05 (0.0031) |
1e-05 (0.0031) |
0.523 (1.00) |
0.561 (1.00) |
0.0238 (1.00) |
0.0286 (1.00) |
| del 14q24 2 | 50 (17%) | 238 |
1e-05 (0.0031) |
0.00134 (0.279) |
0.0384 (1.00) |
0.00266 (0.524) |
1e-05 (0.0031) |
1e-05 (0.0031) |
0.54 (1.00) |
0.573 (1.00) |
0.00657 (1.00) |
0.0081 (1.00) |
| del 16q24 1 | 12 (4%) | 276 |
0.00026 (0.0585) |
4e-05 (0.00984) |
0.307 (1.00) |
0.548 (1.00) |
0.00089 (0.191) |
0.0183 (1.00) |
1 (1.00) |
0.054 (1.00) |
0.0103 (1.00) |
0.0499 (1.00) |
| del xq28 | 28 (10%) | 260 |
1e-05 (0.0031) |
0.00012 (0.0277) |
0.903 (1.00) |
0.078 (1.00) |
1e-05 (0.0031) |
0.0017 (0.342) |
0.75 (1.00) |
0.794 (1.00) |
0.00725 (1.00) |
0.00509 (0.937) |
| amp 2p23 2 | 45 (16%) | 243 |
1e-05 (0.0031) |
0.0109 (1.00) |
0.804 (1.00) |
0.051 (1.00) |
0.66 (1.00) |
0.0655 (1.00) |
0.152 (1.00) |
0.062 (1.00) |
0.437 (1.00) |
0.079 (1.00) |
| amp 2q32 1 | 53 (18%) | 235 |
1e-05 (0.0031) |
0.0645 (1.00) |
0.811 (1.00) |
0.0839 (1.00) |
0.435 (1.00) |
0.029 (1.00) |
0.302 (1.00) |
0.127 (1.00) |
0.975 (1.00) |
0.511 (1.00) |
| del 2q22 1 | 10 (3%) | 278 |
0.0033 (0.634) |
0.00552 (0.988) |
0.541 (1.00) |
0.313 (1.00) |
0.00031 (0.0691) |
0.0518 (1.00) |
0.671 (1.00) |
0.808 (1.00) |
0.178 (1.00) |
0.426 (1.00) |
| del 6p12 3 | 26 (9%) | 262 |
1e-05 (0.0031) |
0.00905 (1.00) |
1 (1.00) |
0.631 (1.00) |
0.00133 (0.278) |
0.00124 (0.26) |
0.131 (1.00) |
0.506 (1.00) |
0.264 (1.00) |
0.22 (1.00) |
| del 19p13 3 | 23 (8%) | 265 |
1e-05 (0.0031) |
0.0449 (1.00) |
0.779 (1.00) |
0.294 (1.00) |
0.0376 (1.00) |
0.00519 (0.945) |
0.238 (1.00) |
0.313 (1.00) |
0.0873 (1.00) |
0.0363 (1.00) |
| del 19q13 42 | 19 (7%) | 269 |
3e-05 (0.00756) |
0.0453 (1.00) |
0.888 (1.00) |
0.134 (1.00) |
0.01 (1.00) |
0.00273 (0.535) |
0.398 (1.00) |
0.304 (1.00) |
0.229 (1.00) |
0.346 (1.00) |
| del 2p12 | 8 (3%) | 280 |
0.0844 (1.00) |
0.122 (1.00) |
0.129 (1.00) |
0.103 (1.00) |
0.25 (1.00) |
0.238 (1.00) |
0.176 (1.00) |
0.283 (1.00) |
0.694 (1.00) |
1 (1.00) |
| del 2q37 3 | 12 (4%) | 276 |
0.0947 (1.00) |
0.00188 (0.376) |
0.00727 (1.00) |
0.0478 (1.00) |
0.00706 (1.00) |
0.0214 (1.00) |
0.144 (1.00) |
0.151 (1.00) |
0.0455 (1.00) |
0.235 (1.00) |
| del 5p15 33 | 13 (5%) | 275 |
0.26 (1.00) |
0.00233 (0.464) |
0.854 (1.00) |
0.0138 (1.00) |
0.0198 (1.00) |
0.00352 (0.669) |
0.559 (1.00) |
0.203 (1.00) |
0.332 (1.00) |
0.00159 (0.326) |
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S1. Gene #1: 'amp_2p23.2' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 114 | 76 | 46 | 52 |
| AMP PEAK 1(2P23.2) MUTATED | 2 | 3 | 14 | 26 |
| AMP PEAK 1(2P23.2) WILD-TYPE | 112 | 73 | 32 | 26 |
Figure S1. Get High-res Image Gene #1: 'amp_2p23.2' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S2. Gene #2: 'amp_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 114 | 76 | 46 | 52 |
| AMP PEAK 2(2Q32.1) MUTATED | 4 | 4 | 15 | 30 |
| AMP PEAK 2(2Q32.1) WILD-TYPE | 110 | 72 | 31 | 22 |
Figure S2. Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S3. Gene #3: 'amp_3q27.1' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 114 | 76 | 46 | 52 |
| AMP PEAK 3(3Q27.1) MUTATED | 20 | 17 | 45 | 18 |
| AMP PEAK 3(3Q27.1) WILD-TYPE | 94 | 59 | 1 | 34 |
Figure S3. Get High-res Image Gene #3: 'amp_3q27.1' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S4. Gene #3: 'amp_3q27.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 78 | 114 | 95 |
| AMP PEAK 3(3Q27.1) MUTATED | 39 | 48 | 13 |
| AMP PEAK 3(3Q27.1) WILD-TYPE | 39 | 66 | 82 |
Figure S4. Get High-res Image Gene #3: 'amp_3q27.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.00085 (Fisher's exact test), Q value = 0.18
Table S5. Gene #3: 'amp_3q27.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 125 | 72 | 44 | 46 |
| AMP PEAK 3(3Q27.1) MUTATED | 39 | 39 | 12 | 10 |
| AMP PEAK 3(3Q27.1) WILD-TYPE | 86 | 33 | 32 | 36 |
Figure S5. Get High-res Image Gene #3: 'amp_3q27.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00019 (Fisher's exact test), Q value = 0.043
Table S6. Gene #3: 'amp_3q27.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 55 | 66 | 81 | 86 |
| AMP PEAK 3(3Q27.1) MUTATED | 20 | 18 | 43 | 19 |
| AMP PEAK 3(3Q27.1) WILD-TYPE | 35 | 48 | 38 | 67 |
Figure S6. Get High-res Image Gene #3: 'amp_3q27.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S7. Gene #4: 'amp_5q35.2' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 114 | 76 | 46 | 52 |
| AMP PEAK 4(5Q35.2) MUTATED | 19 | 2 | 0 | 16 |
| AMP PEAK 4(5Q35.2) WILD-TYPE | 95 | 74 | 46 | 36 |
Figure S7. Get High-res Image Gene #4: 'amp_5q35.2' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00016 (Fisher's exact test), Q value = 0.036
Table S8. Gene #4: 'amp_5q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 63 | 58 | 103 |
| AMP PEAK 4(5Q35.2) MUTATED | 11 | 15 | 4 |
| AMP PEAK 4(5Q35.2) WILD-TYPE | 52 | 43 | 99 |
Figure S8. Get High-res Image Gene #4: 'amp_5q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.00065 (Fisher's exact test), Q value = 0.14
Table S9. Gene #4: 'amp_5q35.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 78 | 114 | 95 |
| AMP PEAK 4(5Q35.2) MUTATED | 12 | 5 | 20 |
| AMP PEAK 4(5Q35.2) WILD-TYPE | 66 | 109 | 75 |
Figure S9. Get High-res Image Gene #4: 'amp_5q35.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 8e-05 (Fisher's exact test), Q value = 0.019
Table S10. Gene #4: 'amp_5q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 125 | 72 | 44 | 46 |
| AMP PEAK 4(5Q35.2) MUTATED | 29 | 3 | 1 | 4 |
| AMP PEAK 4(5Q35.2) WILD-TYPE | 96 | 69 | 43 | 42 |
Figure S10. Get High-res Image Gene #4: 'amp_5q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S11. Gene #5: 'amp_7q31.2' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 114 | 76 | 46 | 52 |
| AMP PEAK 5(7Q31.2) MUTATED | 32 | 75 | 43 | 27 |
| AMP PEAK 5(7Q31.2) WILD-TYPE | 82 | 1 | 3 | 25 |
Figure S11. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S12. Gene #5: 'amp_7q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 63 | 58 | 103 |
| AMP PEAK 5(7Q31.2) MUTATED | 34 | 19 | 85 |
| AMP PEAK 5(7Q31.2) WILD-TYPE | 29 | 39 | 18 |
Figure S12. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 5e-05 (Fisher's exact test), Q value = 0.012
Table S13. Gene #5: 'amp_7q31.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
|---|---|---|---|---|---|---|---|---|
| ALL | 17 | 22 | 29 | 22 | 27 | 39 | 25 | 25 |
| AMP PEAK 5(7Q31.2) MUTATED | 14 | 17 | 27 | 9 | 12 | 18 | 18 | 14 |
| AMP PEAK 5(7Q31.2) WILD-TYPE | 3 | 5 | 2 | 13 | 15 | 21 | 7 | 11 |
Figure S13. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S14. Gene #5: 'amp_7q31.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 78 | 114 | 95 |
| AMP PEAK 5(7Q31.2) MUTATED | 50 | 97 | 29 |
| AMP PEAK 5(7Q31.2) WILD-TYPE | 28 | 17 | 66 |
Figure S14. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S15. Gene #5: 'amp_7q31.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 125 | 72 | 44 | 46 |
| AMP PEAK 5(7Q31.2) MUTATED | 59 | 68 | 32 | 17 |
| AMP PEAK 5(7Q31.2) WILD-TYPE | 66 | 4 | 12 | 29 |
Figure S15. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S16. Gene #5: 'amp_7q31.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 55 | 66 | 81 | 86 |
| AMP PEAK 5(7Q31.2) MUTATED | 23 | 41 | 67 | 46 |
| AMP PEAK 5(7Q31.2) WILD-TYPE | 32 | 25 | 14 | 40 |
Figure S16. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 3e-05 (Fisher's exact test), Q value = 0.0076
Table S17. Gene #5: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 69 | 81 | 71 |
| AMP PEAK 5(7Q31.2) MUTATED | 33 | 64 | 35 |
| AMP PEAK 5(7Q31.2) WILD-TYPE | 36 | 17 | 36 |
Figure S17. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S18. Gene #5: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 98 | 77 | 16 | 30 |
| AMP PEAK 5(7Q31.2) MUTATED | 67 | 35 | 4 | 26 |
| AMP PEAK 5(7Q31.2) WILD-TYPE | 31 | 42 | 12 | 4 |
Figure S18. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S19. Gene #6: 'amp_17q25.2' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 114 | 76 | 46 | 52 |
| AMP PEAK 6(17Q25.2) MUTATED | 43 | 76 | 45 | 37 |
| AMP PEAK 6(17Q25.2) WILD-TYPE | 71 | 0 | 1 | 15 |
Figure S19. Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #1: 'CN_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.0076
Table S20. Gene #6: 'amp_17q25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 63 | 58 | 103 |
| AMP PEAK 6(17Q25.2) MUTATED | 38 | 34 | 89 |
| AMP PEAK 6(17Q25.2) WILD-TYPE | 25 | 24 | 14 |
Figure S20. Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.00011 (Fisher's exact test), Q value = 0.026
Table S21. Gene #6: 'amp_17q25.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
|---|---|---|---|---|---|---|---|---|
| ALL | 17 | 22 | 29 | 22 | 27 | 39 | 25 | 25 |
| AMP PEAK 6(17Q25.2) MUTATED | 15 | 20 | 26 | 11 | 13 | 23 | 21 | 17 |
| AMP PEAK 6(17Q25.2) WILD-TYPE | 2 | 2 | 3 | 11 | 14 | 16 | 4 | 8 |
Figure S21. Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S22. Gene #6: 'amp_17q25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 78 | 114 | 95 |
| AMP PEAK 6(17Q25.2) MUTATED | 54 | 101 | 45 |
| AMP PEAK 6(17Q25.2) WILD-TYPE | 24 | 13 | 50 |
Figure S22. Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S23. Gene #6: 'amp_17q25.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 125 | 72 | 44 | 46 |
| AMP PEAK 6(17Q25.2) MUTATED | 79 | 68 | 35 | 18 |
| AMP PEAK 6(17Q25.2) WILD-TYPE | 46 | 4 | 9 | 28 |
Figure S23. Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00103 (Fisher's exact test), Q value = 0.22
Table S24. Gene #6: 'amp_17q25.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 55 | 66 | 81 | 86 |
| AMP PEAK 6(17Q25.2) MUTATED | 30 | 46 | 69 | 56 |
| AMP PEAK 6(17Q25.2) WILD-TYPE | 25 | 20 | 12 | 30 |
Figure S24. Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00105 (Fisher's exact test), Q value = 0.22
Table S25. Gene #6: 'amp_17q25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 98 | 77 | 16 | 30 |
| AMP PEAK 6(17Q25.2) MUTATED | 72 | 45 | 7 | 27 |
| AMP PEAK 6(17Q25.2) WILD-TYPE | 26 | 32 | 9 | 3 |
Figure S25. Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S26. Gene #7: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 114 | 76 | 46 | 52 |
| AMP PEAK 7(19P13.2) MUTATED | 1 | 22 | 0 | 8 |
| AMP PEAK 7(19P13.2) WILD-TYPE | 113 | 54 | 46 | 44 |
Figure S26. Get High-res Image Gene #7: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'
P value = 9e-04 (Fisher's exact test), Q value = 0.19
Table S27. Gene #7: 'amp_19p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 78 | 114 | 95 |
| AMP PEAK 7(19P13.2) MUTATED | 3 | 22 | 6 |
| AMP PEAK 7(19P13.2) WILD-TYPE | 75 | 92 | 89 |
Figure S27. Get High-res Image Gene #7: 'amp_19p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.00096 (Fisher's exact test), Q value = 0.2
Table S28. Gene #7: 'amp_19p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 125 | 72 | 44 | 46 |
| AMP PEAK 7(19P13.2) MUTATED | 4 | 11 | 9 | 7 |
| AMP PEAK 7(19P13.2) WILD-TYPE | 121 | 61 | 35 | 39 |
Figure S28. Get High-res Image Gene #7: 'amp_19p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S29. Gene #8: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 114 | 76 | 46 | 52 |
| DEL PEAK 1(1P36.31) MUTATED | 21 | 0 | 2 | 32 |
| DEL PEAK 1(1P36.31) WILD-TYPE | 93 | 76 | 44 | 20 |
Figure S29. Get High-res Image Gene #8: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'
P value = 6e-05 (Fisher's exact test), Q value = 0.014
Table S30. Gene #8: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 63 | 58 | 103 |
| DEL PEAK 1(1P36.31) MUTATED | 11 | 22 | 9 |
| DEL PEAK 1(1P36.31) WILD-TYPE | 52 | 36 | 94 |
Figure S30. Get High-res Image Gene #8: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S31. Gene #8: 'del_1p36.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 78 | 114 | 95 |
| DEL PEAK 1(1P36.31) MUTATED | 11 | 6 | 38 |
| DEL PEAK 1(1P36.31) WILD-TYPE | 67 | 108 | 57 |
Figure S31. Get High-res Image Gene #8: 'del_1p36.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S32. Gene #8: 'del_1p36.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 125 | 72 | 44 | 46 |
| DEL PEAK 1(1P36.31) MUTATED | 29 | 6 | 1 | 19 |
| DEL PEAK 1(1P36.31) WILD-TYPE | 96 | 66 | 43 | 27 |
Figure S32. Get High-res Image Gene #8: 'del_1p36.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00031 (Fisher's exact test), Q value = 0.069
Table S33. Gene #10: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 78 | 114 | 95 |
| DEL PEAK 3(2Q22.1) MUTATED | 1 | 0 | 9 |
| DEL PEAK 3(2Q22.1) WILD-TYPE | 77 | 114 | 86 |
Figure S33. Get High-res Image Gene #10: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S34. Gene #12: 'del_3p22.1' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 114 | 76 | 46 | 52 |
| DEL PEAK 5(3P22.1) MUTATED | 6 | 0 | 0 | 19 |
| DEL PEAK 5(3P22.1) WILD-TYPE | 108 | 76 | 46 | 33 |
Figure S34. Get High-res Image Gene #12: 'del_3p22.1' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S35. Gene #12: 'del_3p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 63 | 58 | 103 |
| DEL PEAK 5(3P22.1) MUTATED | 3 | 14 | 1 |
| DEL PEAK 5(3P22.1) WILD-TYPE | 60 | 44 | 102 |
Figure S35. Get High-res Image Gene #12: 'del_3p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S36. Gene #12: 'del_3p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 78 | 114 | 95 |
| DEL PEAK 5(3P22.1) MUTATED | 5 | 0 | 20 |
| DEL PEAK 5(3P22.1) WILD-TYPE | 73 | 114 | 75 |
Figure S36. Get High-res Image Gene #12: 'del_3p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S37. Gene #12: 'del_3p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 125 | 72 | 44 | 46 |
| DEL PEAK 5(3P22.1) MUTATED | 21 | 0 | 0 | 4 |
| DEL PEAK 5(3P22.1) WILD-TYPE | 104 | 72 | 44 | 42 |
Figure S37. Get High-res Image Gene #12: 'del_3p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S38. Gene #13: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 114 | 76 | 46 | 52 |
| DEL PEAK 6(4Q34.3) MUTATED | 8 | 1 | 1 | 22 |
| DEL PEAK 6(4Q34.3) WILD-TYPE | 106 | 75 | 45 | 30 |
Figure S38. Get High-res Image Gene #13: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S39. Gene #13: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 63 | 58 | 103 |
| DEL PEAK 6(4Q34.3) MUTATED | 4 | 20 | 2 |
| DEL PEAK 6(4Q34.3) WILD-TYPE | 59 | 38 | 101 |
Figure S39. Get High-res Image Gene #13: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S40. Gene #13: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 78 | 114 | 95 |
| DEL PEAK 6(4Q34.3) MUTATED | 4 | 2 | 26 |
| DEL PEAK 6(4Q34.3) WILD-TYPE | 74 | 112 | 69 |
Figure S40. Get High-res Image Gene #13: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 5e-05 (Fisher's exact test), Q value = 0.012
Table S41. Gene #13: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 125 | 72 | 44 | 46 |
| DEL PEAK 6(4Q34.3) MUTATED | 18 | 1 | 1 | 12 |
| DEL PEAK 6(4Q34.3) WILD-TYPE | 107 | 71 | 43 | 34 |
Figure S41. Get High-res Image Gene #13: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 3e-05 (Fisher's exact test), Q value = 0.0076
Table S42. Gene #13: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 98 | 77 | 16 | 30 |
| DEL PEAK 6(4Q34.3) MUTATED | 7 | 11 | 8 | 0 |
| DEL PEAK 6(4Q34.3) WILD-TYPE | 91 | 66 | 8 | 30 |
Figure S42. Get High-res Image Gene #13: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 4e-05 (Fisher's exact test), Q value = 0.0098
Table S43. Gene #15: 'del_5q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 63 | 58 | 103 |
| DEL PEAK 8(5Q35.2) MUTATED | 1 | 9 | 0 |
| DEL PEAK 8(5Q35.2) WILD-TYPE | 62 | 49 | 103 |
Figure S43. Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 6e-05 (Fisher's exact test), Q value = 0.014
Table S44. Gene #15: 'del_5q35.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 78 | 114 | 95 |
| DEL PEAK 8(5Q35.2) MUTATED | 1 | 0 | 10 |
| DEL PEAK 8(5Q35.2) WILD-TYPE | 77 | 114 | 85 |
Figure S44. Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 6e-05 (Fisher's exact test), Q value = 0.014
Table S45. Gene #15: 'del_5q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 125 | 72 | 44 | 46 |
| DEL PEAK 8(5Q35.2) MUTATED | 3 | 0 | 0 | 8 |
| DEL PEAK 8(5Q35.2) WILD-TYPE | 122 | 72 | 44 | 38 |
Figure S45. Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S46. Gene #15: 'del_5q35.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 98 | 77 | 16 | 30 |
| DEL PEAK 8(5Q35.2) MUTATED | 1 | 1 | 8 | 0 |
| DEL PEAK 8(5Q35.2) WILD-TYPE | 97 | 76 | 8 | 30 |
Figure S46. Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S47. Gene #16: 'del_6p12.3' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 114 | 76 | 46 | 52 |
| DEL PEAK 9(6P12.3) MUTATED | 8 | 0 | 1 | 17 |
| DEL PEAK 9(6P12.3) WILD-TYPE | 106 | 76 | 45 | 35 |
Figure S47. Get High-res Image Gene #16: 'del_6p12.3' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S48. Gene #17: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 114 | 76 | 46 | 52 |
| DEL PEAK 10(6Q22.31) MUTATED | 8 | 0 | 1 | 20 |
| DEL PEAK 10(6Q22.31) WILD-TYPE | 106 | 76 | 45 | 32 |
Figure S48. Get High-res Image Gene #17: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'
P value = 2e-05 (Fisher's exact test), Q value = 0.0051
Table S49. Gene #17: 'del_6q22.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 78 | 114 | 95 |
| DEL PEAK 10(6Q22.31) MUTATED | 5 | 3 | 21 |
| DEL PEAK 10(6Q22.31) WILD-TYPE | 73 | 111 | 74 |
Figure S49. Get High-res Image Gene #17: 'del_6q22.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.0076
Table S50. Gene #17: 'del_6q22.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 125 | 72 | 44 | 46 |
| DEL PEAK 10(6Q22.31) MUTATED | 14 | 2 | 0 | 13 |
| DEL PEAK 10(6Q22.31) WILD-TYPE | 111 | 70 | 44 | 33 |
Figure S50. Get High-res Image Gene #17: 'del_6q22.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S51. Gene #18: 'del_6q25.3' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 114 | 76 | 46 | 52 |
| DEL PEAK 11(6Q25.3) MUTATED | 7 | 0 | 1 | 24 |
| DEL PEAK 11(6Q25.3) WILD-TYPE | 107 | 76 | 45 | 28 |
Figure S51. Get High-res Image Gene #18: 'del_6q25.3' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00044 (Fisher's exact test), Q value = 0.097
Table S52. Gene #18: 'del_6q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 63 | 58 | 103 |
| DEL PEAK 11(6Q25.3) MUTATED | 5 | 14 | 4 |
| DEL PEAK 11(6Q25.3) WILD-TYPE | 58 | 44 | 99 |
Figure S52. Get High-res Image Gene #18: 'del_6q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S53. Gene #18: 'del_6q25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 78 | 114 | 95 |
| DEL PEAK 11(6Q25.3) MUTATED | 6 | 3 | 23 |
| DEL PEAK 11(6Q25.3) WILD-TYPE | 72 | 111 | 72 |
Figure S53. Get High-res Image Gene #18: 'del_6q25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 6e-05 (Fisher's exact test), Q value = 0.014
Table S54. Gene #18: 'del_6q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 125 | 72 | 44 | 46 |
| DEL PEAK 11(6Q25.3) MUTATED | 18 | 2 | 0 | 12 |
| DEL PEAK 11(6Q25.3) WILD-TYPE | 107 | 70 | 44 | 34 |
Figure S54. Get High-res Image Gene #18: 'del_6q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S55. Gene #19: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 114 | 76 | 46 | 52 |
| DEL PEAK 12(9P21.3) MUTATED | 11 | 2 | 1 | 26 |
| DEL PEAK 12(9P21.3) WILD-TYPE | 103 | 74 | 45 | 26 |
Figure S55. Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S56. Gene #19: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 63 | 58 | 103 |
| DEL PEAK 12(9P21.3) MUTATED | 9 | 20 | 2 |
| DEL PEAK 12(9P21.3) WILD-TYPE | 54 | 38 | 101 |
Figure S56. Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.00073 (Fisher's exact test), Q value = 0.16
Table S57. Gene #19: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
|---|---|---|---|---|---|---|---|---|
| ALL | 17 | 22 | 29 | 22 | 27 | 39 | 25 | 25 |
| DEL PEAK 12(9P21.3) MUTATED | 0 | 3 | 0 | 5 | 9 | 3 | 2 | 7 |
| DEL PEAK 12(9P21.3) WILD-TYPE | 17 | 19 | 29 | 17 | 18 | 36 | 23 | 18 |
Figure S57. Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S58. Gene #19: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 78 | 114 | 95 |
| DEL PEAK 12(9P21.3) MUTATED | 6 | 2 | 32 |
| DEL PEAK 12(9P21.3) WILD-TYPE | 72 | 112 | 63 |
Figure S58. Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S59. Gene #19: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 125 | 72 | 44 | 46 |
| DEL PEAK 12(9P21.3) MUTATED | 20 | 0 | 0 | 20 |
| DEL PEAK 12(9P21.3) WILD-TYPE | 105 | 72 | 44 | 26 |
Figure S59. Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00038 (Fisher's exact test), Q value = 0.084
Table S60. Gene #19: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 89 | 103 | 96 |
| DEL PEAK 12(9P21.3) MUTATED | 3 | 16 | 21 |
| DEL PEAK 12(9P21.3) WILD-TYPE | 86 | 87 | 75 |
Figure S60. Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 1e-04 (Fisher's exact test), Q value = 0.023
Table S61. Gene #19: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 69 | 81 | 71 |
| DEL PEAK 12(9P21.3) MUTATED | 8 | 4 | 21 |
| DEL PEAK 12(9P21.3) WILD-TYPE | 61 | 77 | 50 |
Figure S61. Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.0076
Table S62. Gene #19: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 98 | 77 | 16 | 30 |
| DEL PEAK 12(9P21.3) MUTATED | 7 | 19 | 7 | 0 |
| DEL PEAK 12(9P21.3) WILD-TYPE | 91 | 58 | 9 | 30 |
Figure S62. Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S63. Gene #20: 'del_10q21.1' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 114 | 76 | 46 | 52 |
| DEL PEAK 13(10Q21.1) MUTATED | 5 | 0 | 0 | 14 |
| DEL PEAK 13(10Q21.1) WILD-TYPE | 109 | 76 | 46 | 38 |
Figure S63. Get High-res Image Gene #20: 'del_10q21.1' versus Molecular Subtype #1: 'CN_CNMF'
P value = 4e-05 (Fisher's exact test), Q value = 0.0098
Table S64. Gene #20: 'del_10q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 63 | 58 | 103 |
| DEL PEAK 13(10Q21.1) MUTATED | 1 | 12 | 2 |
| DEL PEAK 13(10Q21.1) WILD-TYPE | 62 | 46 | 101 |
Figure S64. Get High-res Image Gene #20: 'del_10q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 8e-05 (Fisher's exact test), Q value = 0.019
Table S65. Gene #20: 'del_10q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 78 | 114 | 95 |
| DEL PEAK 13(10Q21.1) MUTATED | 3 | 1 | 15 |
| DEL PEAK 13(10Q21.1) WILD-TYPE | 75 | 113 | 80 |
Figure S65. Get High-res Image Gene #20: 'del_10q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.00078 (Fisher's exact test), Q value = 0.17
Table S66. Gene #20: 'del_10q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 125 | 72 | 44 | 46 |
| DEL PEAK 13(10Q21.1) MUTATED | 14 | 0 | 0 | 5 |
| DEL PEAK 13(10Q21.1) WILD-TYPE | 111 | 72 | 44 | 41 |
Figure S66. Get High-res Image Gene #20: 'del_10q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S67. Gene #21: 'del_11q22.3' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 114 | 76 | 46 | 52 |
| DEL PEAK 14(11Q22.3) MUTATED | 8 | 4 | 1 | 18 |
| DEL PEAK 14(11Q22.3) WILD-TYPE | 106 | 72 | 45 | 34 |
Figure S67. Get High-res Image Gene #21: 'del_11q22.3' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00015 (Fisher's exact test), Q value = 0.034
Table S68. Gene #21: 'del_11q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 78 | 114 | 95 |
| DEL PEAK 14(11Q22.3) MUTATED | 4 | 6 | 21 |
| DEL PEAK 14(11Q22.3) WILD-TYPE | 74 | 108 | 74 |
Figure S68. Get High-res Image Gene #21: 'del_11q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 2e-04 (Fisher's exact test), Q value = 0.045
Table S69. Gene #21: 'del_11q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 125 | 72 | 44 | 46 |
| DEL PEAK 14(11Q22.3) MUTATED | 18 | 0 | 4 | 9 |
| DEL PEAK 14(11Q22.3) WILD-TYPE | 107 | 72 | 40 | 37 |
Figure S69. Get High-res Image Gene #21: 'del_11q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S70. Gene #22: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 114 | 76 | 46 | 52 |
| DEL PEAK 15(11Q23.3) MUTATED | 6 | 4 | 0 | 19 |
| DEL PEAK 15(11Q23.3) WILD-TYPE | 108 | 72 | 46 | 33 |
Figure S70. Get High-res Image Gene #22: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00015 (Fisher's exact test), Q value = 0.034
Table S71. Gene #22: 'del_11q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 63 | 58 | 103 |
| DEL PEAK 15(11Q23.3) MUTATED | 6 | 14 | 3 |
| DEL PEAK 15(11Q23.3) WILD-TYPE | 57 | 44 | 100 |
Figure S71. Get High-res Image Gene #22: 'del_11q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 6e-05 (Fisher's exact test), Q value = 0.014
Table S72. Gene #22: 'del_11q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 78 | 114 | 95 |
| DEL PEAK 15(11Q23.3) MUTATED | 3 | 5 | 21 |
| DEL PEAK 15(11Q23.3) WILD-TYPE | 75 | 109 | 74 |
Figure S72. Get High-res Image Gene #22: 'del_11q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.00028 (Fisher's exact test), Q value = 0.063
Table S73. Gene #22: 'del_11q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 125 | 72 | 44 | 46 |
| DEL PEAK 15(11Q23.3) MUTATED | 18 | 0 | 3 | 8 |
| DEL PEAK 15(11Q23.3) WILD-TYPE | 107 | 72 | 41 | 38 |
Figure S73. Get High-res Image Gene #22: 'del_11q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S74. Gene #23: 'del_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 114 | 76 | 46 | 52 |
| DEL PEAK 16(14Q11.2) MUTATED | 20 | 1 | 2 | 28 |
| DEL PEAK 16(14Q11.2) WILD-TYPE | 94 | 75 | 44 | 24 |
Figure S74. Get High-res Image Gene #23: 'del_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S75. Gene #23: 'del_14q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 78 | 114 | 95 |
| DEL PEAK 16(14Q11.2) MUTATED | 13 | 6 | 32 |
| DEL PEAK 16(14Q11.2) WILD-TYPE | 65 | 108 | 63 |
Figure S75. Get High-res Image Gene #23: 'del_14q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S76. Gene #23: 'del_14q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 125 | 72 | 44 | 46 |
| DEL PEAK 16(14Q11.2) MUTATED | 26 | 2 | 4 | 19 |
| DEL PEAK 16(14Q11.2) WILD-TYPE | 99 | 70 | 40 | 27 |
Figure S76. Get High-res Image Gene #23: 'del_14q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S77. Gene #24: 'del_14q24.2' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 114 | 76 | 46 | 52 |
| DEL PEAK 17(14Q24.2) MUTATED | 21 | 0 | 1 | 28 |
| DEL PEAK 17(14Q24.2) WILD-TYPE | 93 | 76 | 45 | 24 |
Figure S77. Get High-res Image Gene #24: 'del_14q24.2' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S78. Gene #24: 'del_14q24.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 78 | 114 | 95 |
| DEL PEAK 17(14Q24.2) MUTATED | 11 | 5 | 34 |
| DEL PEAK 17(14Q24.2) WILD-TYPE | 67 | 109 | 61 |
Figure S78. Get High-res Image Gene #24: 'del_14q24.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S79. Gene #24: 'del_14q24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 125 | 72 | 44 | 46 |
| DEL PEAK 17(14Q24.2) MUTATED | 26 | 2 | 3 | 19 |
| DEL PEAK 17(14Q24.2) WILD-TYPE | 99 | 70 | 41 | 27 |
Figure S79. Get High-res Image Gene #24: 'del_14q24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S80. Gene #25: 'del_15q13.3' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 114 | 76 | 46 | 52 |
| DEL PEAK 18(15Q13.3) MUTATED | 12 | 0 | 3 | 20 |
| DEL PEAK 18(15Q13.3) WILD-TYPE | 102 | 76 | 43 | 32 |
Figure S80. Get High-res Image Gene #25: 'del_15q13.3' versus Molecular Subtype #1: 'CN_CNMF'
P value = 4e-05 (Fisher's exact test), Q value = 0.0098
Table S81. Gene #25: 'del_15q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 63 | 58 | 103 |
| DEL PEAK 18(15Q13.3) MUTATED | 10 | 15 | 3 |
| DEL PEAK 18(15Q13.3) WILD-TYPE | 53 | 43 | 100 |
Figure S81. Get High-res Image Gene #25: 'del_15q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S82. Gene #25: 'del_15q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 78 | 114 | 95 |
| DEL PEAK 18(15Q13.3) MUTATED | 7 | 3 | 25 |
| DEL PEAK 18(15Q13.3) WILD-TYPE | 71 | 111 | 70 |
Figure S82. Get High-res Image Gene #25: 'del_15q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S83. Gene #25: 'del_15q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 125 | 72 | 44 | 46 |
| DEL PEAK 18(15Q13.3) MUTATED | 17 | 2 | 1 | 15 |
| DEL PEAK 18(15Q13.3) WILD-TYPE | 108 | 70 | 43 | 31 |
Figure S83. Get High-res Image Gene #25: 'del_15q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00026 (Fisher's exact test), Q value = 0.058
Table S84. Gene #26: 'del_16q24.1' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 114 | 76 | 46 | 52 |
| DEL PEAK 19(16Q24.1) MUTATED | 4 | 0 | 0 | 8 |
| DEL PEAK 19(16Q24.1) WILD-TYPE | 110 | 76 | 46 | 44 |
Figure S84. Get High-res Image Gene #26: 'del_16q24.1' versus Molecular Subtype #1: 'CN_CNMF'
P value = 4e-05 (Fisher's exact test), Q value = 0.0098
Table S85. Gene #26: 'del_16q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 63 | 58 | 103 |
| DEL PEAK 19(16Q24.1) MUTATED | 1 | 9 | 0 |
| DEL PEAK 19(16Q24.1) WILD-TYPE | 62 | 49 | 103 |
Figure S85. Get High-res Image Gene #26: 'del_16q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.00089 (Fisher's exact test), Q value = 0.19
Table S86. Gene #26: 'del_16q24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 78 | 114 | 95 |
| DEL PEAK 19(16Q24.1) MUTATED | 3 | 0 | 9 |
| DEL PEAK 19(16Q24.1) WILD-TYPE | 75 | 114 | 86 |
Figure S86. Get High-res Image Gene #26: 'del_16q24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S87. Gene #27: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 114 | 76 | 46 | 52 |
| DEL PEAK 20(19P13.3) MUTATED | 4 | 4 | 1 | 14 |
| DEL PEAK 20(19P13.3) WILD-TYPE | 110 | 72 | 45 | 38 |
Figure S87. Get High-res Image Gene #27: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.0076
Table S88. Gene #28: 'del_19q13.42' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 114 | 76 | 46 | 52 |
| DEL PEAK 21(19Q13.42) MUTATED | 2 | 3 | 2 | 12 |
| DEL PEAK 21(19Q13.42) WILD-TYPE | 112 | 73 | 44 | 40 |
Figure S88. Get High-res Image Gene #28: 'del_19q13.42' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S89. Gene #29: 'del_22q12.2' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 114 | 76 | 46 | 52 |
| DEL PEAK 22(22Q12.2) MUTATED | 23 | 6 | 2 | 32 |
| DEL PEAK 22(22Q12.2) WILD-TYPE | 91 | 70 | 44 | 20 |
Figure S89. Get High-res Image Gene #29: 'del_22q12.2' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S90. Gene #29: 'del_22q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 63 | 58 | 103 |
| DEL PEAK 22(22Q12.2) MUTATED | 9 | 32 | 11 |
| DEL PEAK 22(22Q12.2) WILD-TYPE | 54 | 26 | 92 |
Figure S90. Get High-res Image Gene #29: 'del_22q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S91. Gene #29: 'del_22q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 78 | 114 | 95 |
| DEL PEAK 22(22Q12.2) MUTATED | 15 | 8 | 40 |
| DEL PEAK 22(22Q12.2) WILD-TYPE | 63 | 106 | 55 |
Figure S91. Get High-res Image Gene #29: 'del_22q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S92. Gene #29: 'del_22q12.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 125 | 72 | 44 | 46 |
| DEL PEAK 22(22Q12.2) MUTATED | 37 | 6 | 2 | 18 |
| DEL PEAK 22(22Q12.2) WILD-TYPE | 88 | 66 | 42 | 28 |
Figure S92. Get High-res Image Gene #29: 'del_22q12.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S93. Gene #30: 'del_xp11.4' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 114 | 76 | 46 | 52 |
| DEL PEAK 23(XP11.4) MUTATED | 12 | 1 | 1 | 20 |
| DEL PEAK 23(XP11.4) WILD-TYPE | 102 | 75 | 45 | 32 |
Figure S93. Get High-res Image Gene #30: 'del_xp11.4' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S94. Gene #30: 'del_xp11.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 63 | 58 | 103 |
| DEL PEAK 23(XP11.4) MUTATED | 4 | 18 | 2 |
| DEL PEAK 23(XP11.4) WILD-TYPE | 59 | 40 | 101 |
Figure S94. Get High-res Image Gene #30: 'del_xp11.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S95. Gene #30: 'del_xp11.4' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 78 | 114 | 95 |
| DEL PEAK 23(XP11.4) MUTATED | 5 | 3 | 26 |
| DEL PEAK 23(XP11.4) WILD-TYPE | 73 | 111 | 69 |
Figure S95. Get High-res Image Gene #30: 'del_xp11.4' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 2e-05 (Fisher's exact test), Q value = 0.0051
Table S96. Gene #30: 'del_xp11.4' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 125 | 72 | 44 | 46 |
| DEL PEAK 23(XP11.4) MUTATED | 19 | 1 | 2 | 12 |
| DEL PEAK 23(XP11.4) WILD-TYPE | 106 | 71 | 42 | 34 |
Figure S96. Get High-res Image Gene #30: 'del_xp11.4' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 4e-04 (Fisher's exact test), Q value = 0.088
Table S97. Gene #30: 'del_xp11.4' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 98 | 77 | 16 | 30 |
| DEL PEAK 23(XP11.4) MUTATED | 5 | 16 | 4 | 0 |
| DEL PEAK 23(XP11.4) WILD-TYPE | 93 | 61 | 12 | 30 |
Figure S97. Get High-res Image Gene #30: 'del_xp11.4' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S98. Gene #31: 'del_xq28' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 114 | 76 | 46 | 52 |
| DEL PEAK 24(XQ28) MUTATED | 10 | 0 | 1 | 17 |
| DEL PEAK 24(XQ28) WILD-TYPE | 104 | 76 | 45 | 35 |
Figure S98. Get High-res Image Gene #31: 'del_xq28' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00012 (Fisher's exact test), Q value = 0.028
Table S99. Gene #31: 'del_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 63 | 58 | 103 |
| DEL PEAK 24(XQ28) MUTATED | 3 | 13 | 3 |
| DEL PEAK 24(XQ28) WILD-TYPE | 60 | 45 | 100 |
Figure S99. Get High-res Image Gene #31: 'del_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
Table S100. Gene #31: 'del_xq28' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 78 | 114 | 95 |
| DEL PEAK 24(XQ28) MUTATED | 4 | 3 | 21 |
| DEL PEAK 24(XQ28) WILD-TYPE | 74 | 111 | 74 |
Figure S100. Get High-res Image Gene #31: 'del_xq28' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
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Copy number data file = transformed.cor.cli.txt
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Molecular subtype file = KIRP-TP.transferedmergedcluster.txt
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Number of patients = 288
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Number of significantly focal cnvs = 31
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Number of molecular subtypes = 10
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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.