This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.
Testing the association between copy number variation 28 focal events and 10 molecular subtypes across 162 patients, 93 significant findings detected with P value < 0.05 and Q value < 0.25.
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amp_1q21.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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amp_4q31.1 cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CNMF'.
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amp_11p15.2 cnv correlated to 'CN_CNMF'.
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amp_12q13.3 cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_MATURE_CNMF'.
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amp_17q21.31 cnv correlated to 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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del_1p12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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del_3p24.1 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_3q26.1 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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del_4q34.2 cnv correlated to 'CN_CNMF'.
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del_6p12.3 cnv correlated to 'MRNASEQ_CNMF'.
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del_6q16.1 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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del_8p22 cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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del_8q23.3 cnv correlated to 'MIRSEQ_CNMF'.
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del_9q21.12 cnv correlated to 'RPPA_CNMF'.
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del_11p15.4 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_11q22.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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del_16q21 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
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del_17p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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del_17q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 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', and 'MIRSEQ_MATURE_CNMF'.
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del_xp21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 28 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, 93 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 1p12 | 113 (70%) | 49 |
1e-05 (0.000215) |
1e-05 (0.000215) |
0.305 (0.466) |
0.00137 (0.00984) |
1e-05 (0.000215) |
3e-05 (0.000467) |
0.0016 (0.0112) |
0.0167 (0.0678) |
0.0159 (0.0668) |
0.00125 (0.00921) |
| del 3q26 1 | 93 (57%) | 69 |
1e-05 (0.000215) |
0.643 (0.757) |
0.0162 (0.0668) |
0.0145 (0.0644) |
0.0283 (0.101) |
1e-05 (0.000215) |
0.00253 (0.0168) |
0.0092 (0.0452) |
0.00193 (0.0132) |
0.00011 (0.0014) |
| del 3p24 1 | 64 (40%) | 98 |
0.00845 (0.043) |
0.0422 (0.136) |
0.225 (0.396) |
0.0859 (0.202) |
3e-05 (0.000467) |
2e-05 (0.00035) |
2e-05 (0.00035) |
0.00024 (0.0028) |
1e-05 (0.000215) |
1e-05 (0.000215) |
| del 11p15 4 | 58 (36%) | 104 |
0.0148 (0.0644) |
4e-05 (0.00056) |
0.0943 (0.218) |
0.113 (0.25) |
0.0008 (0.00659) |
1e-05 (0.000215) |
6e-05 (8e-04) |
1e-05 (0.000215) |
1e-05 (0.000215) |
1e-05 (0.000215) |
| del xp21 1 | 46 (28%) | 116 |
0.0003 (0.00321) |
0.00074 (0.00659) |
0.0469 (0.143) |
0.243 (0.418) |
0.036 (0.121) |
0.00358 (0.0228) |
0.00027 (0.00302) |
0.0462 (0.143) |
0.311 (0.474) |
0.0184 (0.0735) |
| del 6q16 1 | 24 (15%) | 138 |
0.0446 (0.142) |
0.066 (0.172) |
0.04 (0.13) |
0.217 (0.39) |
0.0313 (0.108) |
0.00769 (0.0421) |
0.016 (0.0668) |
0.00587 (0.0357) |
0.0573 (0.162) |
0.0206 (0.0789) |
| del 11q22 1 | 50 (31%) | 112 |
2e-05 (0.00035) |
0.139 (0.289) |
0.182 (0.342) |
0.0608 (0.162) |
0.0002 (0.00243) |
0.00465 (0.0289) |
0.00094 (0.00731) |
0.00079 (0.00659) |
0.0006 (0.0056) |
4e-05 (0.00056) |
| del 17p13 2 | 64 (40%) | 98 |
0.00031 (0.00321) |
0.00097 (0.00734) |
0.409 (0.566) |
0.0664 (0.172) |
0.00884 (0.0442) |
0.00627 (0.0366) |
0.0203 (0.0789) |
0.00821 (0.043) |
0.169 (0.329) |
0.0295 (0.103) |
| del 22q13 31 | 65 (40%) | 97 |
1e-05 (0.000215) |
0.0107 (0.0509) |
0.729 (0.814) |
0.0583 (0.162) |
0.0107 (0.0509) |
0.00052 (0.0052) |
0.0067 (0.0383) |
0.0272 (0.1) |
0.047 (0.143) |
0.0654 (0.172) |
| del 17q11 2 | 42 (26%) | 120 |
0.0008 (0.00659) |
0.00622 (0.0366) |
0.0245 (0.0923) |
0.131 (0.279) |
0.0329 (0.112) |
0.00258 (0.0168) |
0.103 (0.235) |
0.0705 (0.176) |
0.188 (0.348) |
0.00782 (0.0421) |
| amp 17q21 31 | 16 (10%) | 146 |
0.0674 (0.172) |
1 (1.00) |
0.407 (0.566) |
0.353 (0.512) |
0.518 (0.671) |
0.00056 (0.00541) |
0.948 (0.983) |
0.143 (0.295) |
0.0123 (0.0566) |
0.0131 (0.059) |
| amp 1q21 3 | 30 (19%) | 132 |
1e-05 (0.000215) |
0.0389 (0.128) |
0.91 (0.956) |
0.799 (0.874) |
0.72 (0.806) |
0.941 (0.98) |
0.714 (0.805) |
0.445 (0.608) |
0.0587 (0.162) |
0.211 (0.381) |
| amp 4q31 1 | 15 (9%) | 147 |
0.0594 (0.162) |
0.227 (0.397) |
0.619 (0.738) |
0.0503 (0.15) |
0.29 (0.46) |
0.00088 (0.00704) |
0.62 (0.738) |
0.256 (0.434) |
0.0118 (0.0553) |
0.0691 (0.174) |
| amp 12q13 3 | 16 (10%) | 146 |
0.126 (0.27) |
0.135 (0.284) |
0.756 (0.837) |
0.322 (0.483) |
0.827 (0.894) |
0.622 (0.738) |
0.0286 (0.101) |
0.275 (0.45) |
0.015 (0.0644) |
0.108 (0.241) |
| del 8p22 | 25 (15%) | 137 |
0.0526 (0.155) |
0.206 (0.375) |
0.57 (0.716) |
0.646 (0.757) |
0.0078 (0.0421) |
0.00841 (0.043) |
0.121 (0.264) |
0.24 (0.418) |
0.175 (0.334) |
0.293 (0.46) |
| amp 11p15 2 | 8 (5%) | 154 |
0.0467 (0.143) |
0.06 (0.162) |
0.344 (0.504) |
0.224 (0.396) |
0.329 (0.487) |
0.101 (0.232) |
0.305 (0.466) |
0.395 (0.559) |
0.0676 (0.172) |
0.139 (0.289) |
| del 4q34 2 | 13 (8%) | 149 |
0.0478 (0.144) |
0.293 (0.46) |
0.516 (0.671) |
0.316 (0.478) |
0.055 (0.159) |
0.493 (0.654) |
0.509 (0.669) |
0.899 (0.95) |
0.295 (0.46) |
0.346 (0.504) |
| del 6p12 3 | 10 (6%) | 152 |
0.505 (0.666) |
0.269 (0.446) |
0.02 (0.0789) |
0.0869 (0.203) |
0.29 (0.46) |
0.164 (0.324) |
0.668 (0.776) |
0.2 (0.368) |
||
| del 8q23 3 | 13 (8%) | 149 |
0.0853 (0.202) |
1 (1.00) |
0.481 (0.648) |
1 (1.00) |
0.265 (0.444) |
0.522 (0.671) |
0.0372 (0.124) |
0.465 (0.629) |
0.753 (0.836) |
0.328 (0.487) |
| del 9q21 12 | 14 (9%) | 148 |
0.519 (0.671) |
0.157 (0.316) |
0.0247 (0.0923) |
0.0601 (0.162) |
0.397 (0.559) |
0.391 (0.559) |
0.529 (0.673) |
0.113 (0.25) |
0.432 (0.593) |
0.395 (0.559) |
| del 16q21 | 5 (3%) | 157 |
0.528 (0.673) |
0.716 (0.805) |
0.696 (0.801) |
0.788 (0.866) |
0.547 (0.693) |
0.0276 (0.1) |
0.261 (0.441) |
0.591 (0.729) |
0.333 (0.491) |
0.645 (0.757) |
| amp 14q24 3 | 10 (6%) | 152 |
0.28 (0.453) |
0.582 (0.725) |
0.71 (0.805) |
0.162 (0.324) |
1 (1.00) |
0.175 (0.334) |
0.458 (0.623) |
0.714 (0.805) |
0.271 (0.447) |
0.933 (0.975) |
| del 1q44 | 21 (13%) | 141 |
0.587 (0.728) |
0.57 (0.716) |
0.0832 (0.199) |
0.153 (0.312) |
0.219 (0.39) |
0.277 (0.451) |
0.406 (0.566) |
0.705 (0.805) |
0.173 (0.334) |
0.652 (0.761) |
| del 4q22 1 | 13 (8%) | 149 |
0.296 (0.46) |
0.611 (0.737) |
0.202 (0.37) |
0.597 (0.732) |
0.0543 (0.158) |
0.269 (0.446) |
0.355 (0.513) |
0.492 (0.654) |
0.492 (0.654) |
0.169 (0.329) |
| del 5q15 | 12 (7%) | 150 |
0.076 (0.187) |
0.683 (0.79) |
0.0602 (0.162) |
0.804 (0.876) |
1 (1.00) |
1 (1.00) |
0.869 (0.932) |
0.186 (0.347) |
0.286 (0.46) |
0.243 (0.418) |
| del 9p24 2 | 15 (9%) | 147 |
0.132 (0.279) |
0.0746 (0.185) |
0.083 (0.199) |
0.163 (0.324) |
0.107 (0.241) |
0.177 (0.334) |
0.521 (0.671) |
0.0779 (0.19) |
0.154 (0.312) |
0.125 (0.27) |
| del 12q21 33 | 8 (5%) | 154 |
0.255 (0.434) |
0.582 (0.725) |
0.616 (0.738) |
0.606 (0.737) |
0.912 (0.956) |
0.876 (0.937) |
0.598 (0.732) |
0.698 (0.801) |
0.844 (0.909) |
0.884 (0.941) |
| del 13q22 3 | 8 (5%) | 154 |
1 (1.00) |
0.812 (0.881) |
0.323 (0.483) |
0.788 (0.866) |
0.297 (0.46) |
0.429 (0.592) |
1 (1.00) |
0.61 (0.737) |
0.395 (0.559) |
0.9 (0.95) |
P value = 1e-05 (Fisher's exact test), Q value = 0.00022
Table S1. Gene #1: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 37 | 40 | 10 | 50 | 25 |
| AMP PEAK 1(1Q21.3) MUTATED | 17 | 0 | 0 | 11 | 2 |
| AMP PEAK 1(1Q21.3) WILD-TYPE | 20 | 40 | 10 | 39 | 23 |
Figure S1. Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.0389 (Fisher's exact test), Q value = 0.13
Table S2. Gene #1: 'amp_1q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 40 | 77 | 45 |
| AMP PEAK 1(1Q21.3) MUTATED | 10 | 17 | 3 |
| AMP PEAK 1(1Q21.3) WILD-TYPE | 30 | 60 | 42 |
Figure S2. Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.00088 (Fisher's exact test), Q value = 0.007
Table S3. Gene #2: 'amp_4q31.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 34 | 64 | 43 | 21 |
| AMP PEAK 2(4Q31.1) MUTATED | 9 | 5 | 0 | 1 |
| AMP PEAK 2(4Q31.1) WILD-TYPE | 25 | 59 | 43 | 20 |
Figure S3. Get High-res Image Gene #2: 'amp_4q31.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0118 (Fisher's exact test), Q value = 0.055
Table S4. Gene #2: 'amp_4q31.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 33 | 50 | 16 | 33 | 29 |
| AMP PEAK 2(4Q31.1) MUTATED | 6 | 4 | 4 | 1 | 0 |
| AMP PEAK 2(4Q31.1) WILD-TYPE | 27 | 46 | 12 | 32 | 29 |
Figure S4. Get High-res Image Gene #2: 'amp_4q31.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.0467 (Fisher's exact test), Q value = 0.14
Table S5. Gene #3: 'amp_11p15.2' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 37 | 40 | 10 | 50 | 25 |
| AMP PEAK 3(11P15.2) MUTATED | 3 | 0 | 2 | 3 | 0 |
| AMP PEAK 3(11P15.2) WILD-TYPE | 34 | 40 | 8 | 47 | 25 |
Figure S5. Get High-res Image Gene #3: 'amp_11p15.2' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.0286 (Fisher's exact test), Q value = 0.1
Table S6. Gene #4: 'amp_12q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 63 | 44 | 55 |
| AMP PEAK 4(12Q13.3) MUTATED | 11 | 1 | 4 |
| AMP PEAK 4(12Q13.3) WILD-TYPE | 52 | 43 | 51 |
Figure S6. Get High-res Image Gene #4: 'amp_12q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.015 (Fisher's exact test), Q value = 0.064
Table S7. Gene #4: 'amp_12q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 33 | 50 | 16 | 33 | 29 |
| AMP PEAK 4(12Q13.3) MUTATED | 3 | 5 | 0 | 8 | 0 |
| AMP PEAK 4(12Q13.3) WILD-TYPE | 30 | 45 | 16 | 25 | 29 |
Figure S7. Get High-res Image Gene #4: 'amp_12q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.00056 (Fisher's exact test), Q value = 0.0054
Table S8. Gene #6: 'amp_17q21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 34 | 64 | 43 | 21 |
| AMP PEAK 6(17Q21.31) MUTATED | 10 | 5 | 1 | 0 |
| AMP PEAK 6(17Q21.31) WILD-TYPE | 24 | 59 | 42 | 21 |
Figure S8. Get High-res Image Gene #6: 'amp_17q21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0123 (Fisher's exact test), Q value = 0.057
Table S9. Gene #6: 'amp_17q21.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 33 | 50 | 16 | 33 | 29 |
| AMP PEAK 6(17Q21.31) MUTATED | 6 | 5 | 4 | 0 | 1 |
| AMP PEAK 6(17Q21.31) WILD-TYPE | 27 | 45 | 12 | 33 | 28 |
Figure S9. Get High-res Image Gene #6: 'amp_17q21.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.0131 (Fisher's exact test), Q value = 0.059
Table S10. Gene #6: 'amp_17q21.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 18 | 41 | 27 | 15 | 23 | 18 | 19 |
| AMP PEAK 6(17Q21.31) MUTATED | 2 | 3 | 8 | 1 | 0 | 2 | 0 |
| AMP PEAK 6(17Q21.31) WILD-TYPE | 16 | 38 | 19 | 14 | 23 | 16 | 19 |
Figure S10. Get High-res Image Gene #6: 'amp_17q21.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00022
Table S11. Gene #7: 'del_1p12' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 37 | 40 | 10 | 50 | 25 |
| DEL PEAK 1(1P12) MUTATED | 28 | 14 | 8 | 40 | 23 |
| DEL PEAK 1(1P12) WILD-TYPE | 9 | 26 | 2 | 10 | 2 |
Figure S11. Get High-res Image Gene #7: 'del_1p12' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00022
Table S12. Gene #7: 'del_1p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 40 | 77 | 45 |
| DEL PEAK 1(1P12) MUTATED | 25 | 67 | 21 |
| DEL PEAK 1(1P12) WILD-TYPE | 15 | 10 | 24 |
Figure S12. Get High-res Image Gene #7: 'del_1p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.00137 (Fisher's exact test), Q value = 0.0098
Table S13. Gene #7: 'del_1p12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 31 | 18 | 28 |
| DEL PEAK 1(1P12) MUTATED | 15 | 17 | 22 |
| DEL PEAK 1(1P12) WILD-TYPE | 16 | 1 | 6 |
Figure S13. Get High-res Image Gene #7: 'del_1p12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00022
Table S14. Gene #7: 'del_1p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 32 | 65 | 44 | 21 |
| DEL PEAK 1(1P12) MUTATED | 23 | 59 | 21 | 10 |
| DEL PEAK 1(1P12) WILD-TYPE | 9 | 6 | 23 | 11 |
Figure S14. Get High-res Image Gene #7: 'del_1p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.00047
Table S15. Gene #7: 'del_1p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 34 | 64 | 43 | 21 |
| DEL PEAK 1(1P12) MUTATED | 19 | 58 | 27 | 9 |
| DEL PEAK 1(1P12) WILD-TYPE | 15 | 6 | 16 | 12 |
Figure S15. Get High-res Image Gene #7: 'del_1p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0016 (Fisher's exact test), Q value = 0.011
Table S16. Gene #7: 'del_1p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 63 | 44 | 55 |
| DEL PEAK 1(1P12) MUTATED | 38 | 27 | 48 |
| DEL PEAK 1(1P12) WILD-TYPE | 25 | 17 | 7 |
Figure S16. Get High-res Image Gene #7: 'del_1p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.0167 (Fisher's exact test), Q value = 0.068
Table S17. Gene #7: 'del_1p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 66 | 54 | 18 | 24 |
| DEL PEAK 1(1P12) MUTATED | 41 | 46 | 12 | 14 |
| DEL PEAK 1(1P12) WILD-TYPE | 25 | 8 | 6 | 10 |
Figure S17. Get High-res Image Gene #7: 'del_1p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0159 (Fisher's exact test), Q value = 0.067
Table S18. Gene #7: 'del_1p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 33 | 50 | 16 | 33 | 29 |
| DEL PEAK 1(1P12) MUTATED | 20 | 43 | 13 | 20 | 17 |
| DEL PEAK 1(1P12) WILD-TYPE | 13 | 7 | 3 | 13 | 12 |
Figure S18. Get High-res Image Gene #7: 'del_1p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.00125 (Fisher's exact test), Q value = 0.0092
Table S19. Gene #7: 'del_1p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 18 | 41 | 27 | 15 | 23 | 18 | 19 |
| DEL PEAK 1(1P12) MUTATED | 11 | 35 | 19 | 15 | 12 | 12 | 9 |
| DEL PEAK 1(1P12) WILD-TYPE | 7 | 6 | 8 | 0 | 11 | 6 | 10 |
Figure S19. Get High-res Image Gene #7: 'del_1p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.00845 (Fisher's exact test), Q value = 0.043
Table S20. Gene #9: 'del_3p24.1' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 37 | 40 | 10 | 50 | 25 |
| DEL PEAK 3(3P24.1) MUTATED | 13 | 15 | 1 | 29 | 6 |
| DEL PEAK 3(3P24.1) WILD-TYPE | 24 | 25 | 9 | 21 | 19 |
Figure S20. Get High-res Image Gene #9: 'del_3p24.1' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.0422 (Fisher's exact test), Q value = 0.14
Table S21. Gene #9: 'del_3p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 40 | 77 | 45 |
| DEL PEAK 3(3P24.1) MUTATED | 21 | 23 | 20 |
| DEL PEAK 3(3P24.1) WILD-TYPE | 19 | 54 | 25 |
Figure S21. Get High-res Image Gene #9: 'del_3p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.00047
Table S22. Gene #9: 'del_3p24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 32 | 65 | 44 | 21 |
| DEL PEAK 3(3P24.1) MUTATED | 18 | 15 | 27 | 4 |
| DEL PEAK 3(3P24.1) WILD-TYPE | 14 | 50 | 17 | 17 |
Figure S22. Get High-res Image Gene #9: 'del_3p24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 2e-05 (Fisher's exact test), Q value = 0.00035
Table S23. Gene #9: 'del_3p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 34 | 64 | 43 | 21 |
| DEL PEAK 3(3P24.1) MUTATED | 12 | 17 | 31 | 4 |
| DEL PEAK 3(3P24.1) WILD-TYPE | 22 | 47 | 12 | 17 |
Figure S23. Get High-res Image Gene #9: 'del_3p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 2e-05 (Fisher's exact test), Q value = 0.00035
Table S24. Gene #9: 'del_3p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 63 | 44 | 55 |
| DEL PEAK 3(3P24.1) MUTATED | 38 | 7 | 19 |
| DEL PEAK 3(3P24.1) WILD-TYPE | 25 | 37 | 36 |
Figure S24. Get High-res Image Gene #9: 'del_3p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.00024 (Fisher's exact test), Q value = 0.0028
Table S25. Gene #9: 'del_3p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 66 | 54 | 18 | 24 |
| DEL PEAK 3(3P24.1) MUTATED | 39 | 15 | 6 | 4 |
| DEL PEAK 3(3P24.1) WILD-TYPE | 27 | 39 | 12 | 20 |
Figure S25. Get High-res Image Gene #9: 'del_3p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00022
Table S26. Gene #9: 'del_3p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 33 | 50 | 16 | 33 | 29 |
| DEL PEAK 3(3P24.1) MUTATED | 11 | 15 | 3 | 27 | 8 |
| DEL PEAK 3(3P24.1) WILD-TYPE | 22 | 35 | 13 | 6 | 21 |
Figure S26. Get High-res Image Gene #9: 'del_3p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00022
Table S27. Gene #9: 'del_3p24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 18 | 41 | 27 | 15 | 23 | 18 | 19 |
| DEL PEAK 3(3P24.1) MUTATED | 6 | 15 | 13 | 1 | 20 | 6 | 3 |
| DEL PEAK 3(3P24.1) WILD-TYPE | 12 | 26 | 14 | 14 | 3 | 12 | 16 |
Figure S27. Get High-res Image Gene #9: 'del_3p24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00022
Table S28. Gene #10: 'del_3q26.1' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 37 | 40 | 10 | 50 | 25 |
| DEL PEAK 4(3Q26.1) MUTATED | 9 | 12 | 6 | 45 | 21 |
| DEL PEAK 4(3Q26.1) WILD-TYPE | 28 | 28 | 4 | 5 | 4 |
Figure S28. Get High-res Image Gene #10: 'del_3q26.1' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.0162 (Fisher's exact test), Q value = 0.067
Table S29. Gene #10: 'del_3q26.1' versus Molecular Subtype #3: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 16 | 20 | 23 | 18 |
| DEL PEAK 4(3Q26.1) MUTATED | 10 | 15 | 16 | 5 |
| DEL PEAK 4(3Q26.1) WILD-TYPE | 6 | 5 | 7 | 13 |
Figure S29. Get High-res Image Gene #10: 'del_3q26.1' versus Molecular Subtype #3: 'RPPA_CNMF'
P value = 0.0145 (Fisher's exact test), Q value = 0.064
Table S30. Gene #10: 'del_3q26.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 31 | 18 | 28 |
| DEL PEAK 4(3Q26.1) MUTATED | 13 | 15 | 18 |
| DEL PEAK 4(3Q26.1) WILD-TYPE | 18 | 3 | 10 |
Figure S30. Get High-res Image Gene #10: 'del_3q26.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
P value = 0.0283 (Fisher's exact test), Q value = 0.1
Table S31. Gene #10: 'del_3q26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 32 | 65 | 44 | 21 |
| DEL PEAK 4(3Q26.1) MUTATED | 20 | 44 | 22 | 7 |
| DEL PEAK 4(3Q26.1) WILD-TYPE | 12 | 21 | 22 | 14 |
Figure S31. Get High-res Image Gene #10: 'del_3q26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00022
Table S32. Gene #10: 'del_3q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 34 | 64 | 43 | 21 |
| DEL PEAK 4(3Q26.1) MUTATED | 6 | 47 | 33 | 7 |
| DEL PEAK 4(3Q26.1) WILD-TYPE | 28 | 17 | 10 | 14 |
Figure S32. Get High-res Image Gene #10: 'del_3q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00253 (Fisher's exact test), Q value = 0.017
Table S33. Gene #10: 'del_3q26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 63 | 44 | 55 |
| DEL PEAK 4(3Q26.1) MUTATED | 38 | 16 | 39 |
| DEL PEAK 4(3Q26.1) WILD-TYPE | 25 | 28 | 16 |
Figure S33. Get High-res Image Gene #10: 'del_3q26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.0092 (Fisher's exact test), Q value = 0.045
Table S34. Gene #10: 'del_3q26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 66 | 54 | 18 | 24 |
| DEL PEAK 4(3Q26.1) MUTATED | 39 | 38 | 5 | 11 |
| DEL PEAK 4(3Q26.1) WILD-TYPE | 27 | 16 | 13 | 13 |
Figure S34. Get High-res Image Gene #10: 'del_3q26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.00193 (Fisher's exact test), Q value = 0.013
Table S35. Gene #10: 'del_3q26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 33 | 50 | 16 | 33 | 29 |
| DEL PEAK 4(3Q26.1) MUTATED | 10 | 36 | 8 | 23 | 16 |
| DEL PEAK 4(3Q26.1) WILD-TYPE | 23 | 14 | 8 | 10 | 13 |
Figure S35. Get High-res Image Gene #10: 'del_3q26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.00011 (Fisher's exact test), Q value = 0.0014
Table S36. Gene #10: 'del_3q26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 18 | 41 | 27 | 15 | 23 | 18 | 19 |
| DEL PEAK 4(3Q26.1) MUTATED | 5 | 31 | 16 | 9 | 19 | 5 | 8 |
| DEL PEAK 4(3Q26.1) WILD-TYPE | 13 | 10 | 11 | 6 | 4 | 13 | 11 |
Figure S36. Get High-res Image Gene #10: 'del_3q26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.0478 (Fisher's exact test), Q value = 0.14
Table S37. Gene #12: 'del_4q34.2' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 37 | 40 | 10 | 50 | 25 |
| DEL PEAK 6(4Q34.2) MUTATED | 0 | 7 | 1 | 4 | 1 |
| DEL PEAK 6(4Q34.2) WILD-TYPE | 37 | 33 | 9 | 46 | 24 |
Figure S37. Get High-res Image Gene #12: 'del_4q34.2' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.02 (Fisher's exact test), Q value = 0.079
Table S38. Gene #14: 'del_6p12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 32 | 65 | 44 | 21 |
| DEL PEAK 8(6P12.3) MUTATED | 1 | 1 | 4 | 4 |
| DEL PEAK 8(6P12.3) WILD-TYPE | 31 | 64 | 40 | 17 |
Figure S38. Get High-res Image Gene #14: 'del_6p12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.0446 (Fisher's exact test), Q value = 0.14
Table S39. Gene #15: 'del_6q16.1' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 37 | 40 | 10 | 50 | 25 |
| DEL PEAK 9(6Q16.1) MUTATED | 3 | 3 | 4 | 11 | 3 |
| DEL PEAK 9(6Q16.1) WILD-TYPE | 34 | 37 | 6 | 39 | 22 |
Figure S39. Get High-res Image Gene #15: 'del_6q16.1' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.04 (Fisher's exact test), Q value = 0.13
Table S40. Gene #15: 'del_6q16.1' versus Molecular Subtype #3: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 16 | 20 | 23 | 18 |
| DEL PEAK 9(6Q16.1) MUTATED | 2 | 2 | 7 | 0 |
| DEL PEAK 9(6Q16.1) WILD-TYPE | 14 | 18 | 16 | 18 |
Figure S40. Get High-res Image Gene #15: 'del_6q16.1' versus Molecular Subtype #3: 'RPPA_CNMF'
P value = 0.0313 (Fisher's exact test), Q value = 0.11
Table S41. Gene #15: 'del_6q16.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 32 | 65 | 44 | 21 |
| DEL PEAK 9(6Q16.1) MUTATED | 1 | 15 | 4 | 4 |
| DEL PEAK 9(6Q16.1) WILD-TYPE | 31 | 50 | 40 | 17 |
Figure S41. Get High-res Image Gene #15: 'del_6q16.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.00769 (Fisher's exact test), Q value = 0.042
Table S42. Gene #15: 'del_6q16.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 34 | 64 | 43 | 21 |
| DEL PEAK 9(6Q16.1) MUTATED | 1 | 16 | 3 | 4 |
| DEL PEAK 9(6Q16.1) WILD-TYPE | 33 | 48 | 40 | 17 |
Figure S42. Get High-res Image Gene #15: 'del_6q16.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.016 (Fisher's exact test), Q value = 0.067
Table S43. Gene #15: 'del_6q16.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 63 | 44 | 55 |
| DEL PEAK 9(6Q16.1) MUTATED | 4 | 6 | 14 |
| DEL PEAK 9(6Q16.1) WILD-TYPE | 59 | 38 | 41 |
Figure S43. Get High-res Image Gene #15: 'del_6q16.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.00587 (Fisher's exact test), Q value = 0.036
Table S44. Gene #15: 'del_6q16.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 66 | 54 | 18 | 24 |
| DEL PEAK 9(6Q16.1) MUTATED | 4 | 15 | 1 | 4 |
| DEL PEAK 9(6Q16.1) WILD-TYPE | 62 | 39 | 17 | 20 |
Figure S44. Get High-res Image Gene #15: 'del_6q16.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0206 (Fisher's exact test), Q value = 0.079
Table S45. Gene #15: 'del_6q16.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 18 | 41 | 27 | 15 | 23 | 18 | 19 |
| DEL PEAK 9(6Q16.1) MUTATED | 0 | 11 | 1 | 4 | 3 | 1 | 4 |
| DEL PEAK 9(6Q16.1) WILD-TYPE | 18 | 30 | 26 | 11 | 20 | 17 | 15 |
Figure S45. Get High-res Image Gene #15: 'del_6q16.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.0078 (Fisher's exact test), Q value = 0.042
Table S46. Gene #16: 'del_8p22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 32 | 65 | 44 | 21 |
| DEL PEAK 10(8P22) MUTATED | 3 | 18 | 3 | 1 |
| DEL PEAK 10(8P22) WILD-TYPE | 29 | 47 | 41 | 20 |
Figure S46. Get High-res Image Gene #16: 'del_8p22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.00841 (Fisher's exact test), Q value = 0.043
Table S47. Gene #16: 'del_8p22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 34 | 64 | 43 | 21 |
| DEL PEAK 10(8P22) MUTATED | 5 | 17 | 2 | 1 |
| DEL PEAK 10(8P22) WILD-TYPE | 29 | 47 | 41 | 20 |
Figure S47. Get High-res Image Gene #16: 'del_8p22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0372 (Fisher's exact test), Q value = 0.12
Table S48. Gene #17: 'del_8q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 63 | 44 | 55 |
| DEL PEAK 11(8Q23.3) MUTATED | 6 | 0 | 7 |
| DEL PEAK 11(8Q23.3) WILD-TYPE | 57 | 44 | 48 |
Figure S48. Get High-res Image Gene #17: 'del_8q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.0247 (Fisher's exact test), Q value = 0.092
Table S49. Gene #19: 'del_9q21.12' versus Molecular Subtype #3: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 16 | 20 | 23 | 18 |
| DEL PEAK 13(9Q21.12) MUTATED | 0 | 0 | 5 | 1 |
| DEL PEAK 13(9Q21.12) WILD-TYPE | 16 | 20 | 18 | 17 |
Figure S49. Get High-res Image Gene #19: 'del_9q21.12' versus Molecular Subtype #3: 'RPPA_CNMF'
P value = 0.0148 (Fisher's exact test), Q value = 0.064
Table S50. Gene #20: 'del_11p15.4' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 37 | 40 | 10 | 50 | 25 |
| DEL PEAK 14(11P15.4) MUTATED | 10 | 21 | 0 | 18 | 9 |
| DEL PEAK 14(11P15.4) WILD-TYPE | 27 | 19 | 10 | 32 | 16 |
Figure S50. Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #1: 'CN_CNMF'
P value = 4e-05 (Fisher's exact test), Q value = 0.00056
Table S51. Gene #20: 'del_11p15.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 40 | 77 | 45 |
| DEL PEAK 14(11P15.4) MUTATED | 22 | 14 | 22 |
| DEL PEAK 14(11P15.4) WILD-TYPE | 18 | 63 | 23 |
Figure S51. Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 8e-04 (Fisher's exact test), Q value = 0.0066
Table S52. Gene #20: 'del_11p15.4' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 32 | 65 | 44 | 21 |
| DEL PEAK 14(11P15.4) MUTATED | 12 | 14 | 26 | 6 |
| DEL PEAK 14(11P15.4) WILD-TYPE | 20 | 51 | 18 | 15 |
Figure S52. Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00022
Table S53. Gene #20: 'del_11p15.4' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 34 | 64 | 43 | 21 |
| DEL PEAK 14(11P15.4) MUTATED | 11 | 10 | 31 | 6 |
| DEL PEAK 14(11P15.4) WILD-TYPE | 23 | 54 | 12 | 15 |
Figure S53. Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 6e-05 (Fisher's exact test), Q value = 8e-04
Table S54. Gene #20: 'del_11p15.4' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 63 | 44 | 55 |
| DEL PEAK 14(11P15.4) MUTATED | 36 | 10 | 12 |
| DEL PEAK 14(11P15.4) WILD-TYPE | 27 | 34 | 43 |
Figure S54. Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00022
Table S55. Gene #20: 'del_11p15.4' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 66 | 54 | 18 | 24 |
| DEL PEAK 14(11P15.4) MUTATED | 39 | 8 | 5 | 6 |
| DEL PEAK 14(11P15.4) WILD-TYPE | 27 | 46 | 13 | 18 |
Figure S55. Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00022
Table S56. Gene #20: 'del_11p15.4' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 33 | 50 | 16 | 33 | 29 |
| DEL PEAK 14(11P15.4) MUTATED | 10 | 8 | 3 | 23 | 13 |
| DEL PEAK 14(11P15.4) WILD-TYPE | 23 | 42 | 13 | 10 | 16 |
Figure S56. Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.00022
Table S57. Gene #20: 'del_11p15.4' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 18 | 41 | 27 | 15 | 23 | 18 | 19 |
| DEL PEAK 14(11P15.4) MUTATED | 9 | 7 | 8 | 2 | 21 | 5 | 5 |
| DEL PEAK 14(11P15.4) WILD-TYPE | 9 | 34 | 19 | 13 | 2 | 13 | 14 |
Figure S57. Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 2e-05 (Fisher's exact test), Q value = 0.00035
Table S58. Gene #21: 'del_11q22.1' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 37 | 40 | 10 | 50 | 25 |
| DEL PEAK 15(11Q22.1) MUTATED | 8 | 22 | 1 | 19 | 0 |
| DEL PEAK 15(11Q22.1) WILD-TYPE | 29 | 18 | 9 | 31 | 25 |
Figure S58. Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #1: 'CN_CNMF'
P value = 2e-04 (Fisher's exact test), Q value = 0.0024
Table S59. Gene #21: 'del_11q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 32 | 65 | 44 | 21 |
| DEL PEAK 15(11Q22.1) MUTATED | 8 | 11 | 25 | 6 |
| DEL PEAK 15(11Q22.1) WILD-TYPE | 24 | 54 | 19 | 15 |
Figure S59. Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.00465 (Fisher's exact test), Q value = 0.029
Table S60. Gene #21: 'del_11q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 34 | 64 | 43 | 21 |
| DEL PEAK 15(11Q22.1) MUTATED | 11 | 12 | 22 | 5 |
| DEL PEAK 15(11Q22.1) WILD-TYPE | 23 | 52 | 21 | 16 |
Figure S60. Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00094 (Fisher's exact test), Q value = 0.0073
Table S61. Gene #21: 'del_11q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 63 | 44 | 55 |
| DEL PEAK 15(11Q22.1) MUTATED | 29 | 13 | 8 |
| DEL PEAK 15(11Q22.1) WILD-TYPE | 34 | 31 | 47 |
Figure S61. Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.00079 (Fisher's exact test), Q value = 0.0066
Table S62. Gene #21: 'del_11q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 66 | 54 | 18 | 24 |
| DEL PEAK 15(11Q22.1) MUTATED | 31 | 8 | 3 | 8 |
| DEL PEAK 15(11Q22.1) WILD-TYPE | 35 | 46 | 15 | 16 |
Figure S62. Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 6e-04 (Fisher's exact test), Q value = 0.0056
Table S63. Gene #21: 'del_11q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 33 | 50 | 16 | 33 | 29 |
| DEL PEAK 15(11Q22.1) MUTATED | 9 | 8 | 3 | 20 | 10 |
| DEL PEAK 15(11Q22.1) WILD-TYPE | 24 | 42 | 13 | 13 | 19 |
Figure S63. Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 4e-05 (Fisher's exact test), Q value = 0.00056
Table S64. Gene #21: 'del_11q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 18 | 41 | 27 | 15 | 23 | 18 | 19 |
| DEL PEAK 15(11Q22.1) MUTATED | 8 | 8 | 7 | 1 | 17 | 3 | 6 |
| DEL PEAK 15(11Q22.1) WILD-TYPE | 10 | 33 | 20 | 14 | 6 | 15 | 13 |
Figure S64. Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.0276 (Fisher's exact test), Q value = 0.1
Table S65. Gene #24: 'del_16q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 34 | 64 | 43 | 21 |
| DEL PEAK 18(16Q21) MUTATED | 4 | 1 | 0 | 0 |
| DEL PEAK 18(16Q21) WILD-TYPE | 30 | 63 | 43 | 21 |
Figure S65. Get High-res Image Gene #24: 'del_16q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00031 (Fisher's exact test), Q value = 0.0032
Table S66. Gene #25: 'del_17p13.2' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 37 | 40 | 10 | 50 | 25 |
| DEL PEAK 19(17P13.2) MUTATED | 12 | 12 | 8 | 28 | 4 |
| DEL PEAK 19(17P13.2) WILD-TYPE | 25 | 28 | 2 | 22 | 21 |
Figure S66. Get High-res Image Gene #25: 'del_17p13.2' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00097 (Fisher's exact test), Q value = 0.0073
Table S67. Gene #25: 'del_17p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 40 | 77 | 45 |
| DEL PEAK 19(17P13.2) MUTATED | 9 | 42 | 13 |
| DEL PEAK 19(17P13.2) WILD-TYPE | 31 | 35 | 32 |
Figure S67. Get High-res Image Gene #25: 'del_17p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.00884 (Fisher's exact test), Q value = 0.044
Table S68. Gene #25: 'del_17p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 32 | 65 | 44 | 21 |
| DEL PEAK 19(17P13.2) MUTATED | 9 | 36 | 14 | 5 |
| DEL PEAK 19(17P13.2) WILD-TYPE | 23 | 29 | 30 | 16 |
Figure S68. Get High-res Image Gene #25: 'del_17p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.00627 (Fisher's exact test), Q value = 0.037
Table S69. Gene #25: 'del_17p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 34 | 64 | 43 | 21 |
| DEL PEAK 19(17P13.2) MUTATED | 10 | 36 | 13 | 5 |
| DEL PEAK 19(17P13.2) WILD-TYPE | 24 | 28 | 30 | 16 |
Figure S69. Get High-res Image Gene #25: 'del_17p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0203 (Fisher's exact test), Q value = 0.079
Table S70. Gene #25: 'del_17p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 63 | 44 | 55 |
| DEL PEAK 19(17P13.2) MUTATED | 21 | 13 | 30 |
| DEL PEAK 19(17P13.2) WILD-TYPE | 42 | 31 | 25 |
Figure S70. Get High-res Image Gene #25: 'del_17p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.00821 (Fisher's exact test), Q value = 0.043
Table S71. Gene #25: 'del_17p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 66 | 54 | 18 | 24 |
| DEL PEAK 19(17P13.2) MUTATED | 18 | 30 | 9 | 7 |
| DEL PEAK 19(17P13.2) WILD-TYPE | 48 | 24 | 9 | 17 |
Figure S71. Get High-res Image Gene #25: 'del_17p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0295 (Fisher's exact test), Q value = 0.1
Table S72. Gene #25: 'del_17p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 18 | 41 | 27 | 15 | 23 | 18 | 19 |
| DEL PEAK 19(17P13.2) MUTATED | 8 | 20 | 4 | 9 | 9 | 9 | 5 |
| DEL PEAK 19(17P13.2) WILD-TYPE | 10 | 21 | 23 | 6 | 14 | 9 | 14 |
Figure S72. Get High-res Image Gene #25: 'del_17p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 8e-04 (Fisher's exact test), Q value = 0.0066
Table S73. Gene #26: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 37 | 40 | 10 | 50 | 25 |
| DEL PEAK 20(17Q11.2) MUTATED | 6 | 7 | 4 | 23 | 2 |
| DEL PEAK 20(17Q11.2) WILD-TYPE | 31 | 33 | 6 | 27 | 23 |
Figure S73. Get High-res Image Gene #26: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00622 (Fisher's exact test), Q value = 0.037
Table S74. Gene #26: 'del_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 40 | 77 | 45 |
| DEL PEAK 20(17Q11.2) MUTATED | 4 | 28 | 10 |
| DEL PEAK 20(17Q11.2) WILD-TYPE | 36 | 49 | 35 |
Figure S74. Get High-res Image Gene #26: 'del_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.0245 (Fisher's exact test), Q value = 0.092
Table S75. Gene #26: 'del_17q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 16 | 20 | 23 | 18 |
| DEL PEAK 20(17Q11.2) MUTATED | 4 | 6 | 8 | 0 |
| DEL PEAK 20(17Q11.2) WILD-TYPE | 12 | 14 | 15 | 18 |
Figure S75. Get High-res Image Gene #26: 'del_17q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'
P value = 0.0329 (Fisher's exact test), Q value = 0.11
Table S76. Gene #26: 'del_17q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 32 | 65 | 44 | 21 |
| DEL PEAK 20(17Q11.2) MUTATED | 5 | 25 | 9 | 3 |
| DEL PEAK 20(17Q11.2) WILD-TYPE | 27 | 40 | 35 | 18 |
Figure S76. Get High-res Image Gene #26: 'del_17q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.00258 (Fisher's exact test), Q value = 0.017
Table S77. Gene #26: 'del_17q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 34 | 64 | 43 | 21 |
| DEL PEAK 20(17Q11.2) MUTATED | 6 | 27 | 6 | 3 |
| DEL PEAK 20(17Q11.2) WILD-TYPE | 28 | 37 | 37 | 18 |
Figure S77. Get High-res Image Gene #26: 'del_17q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00782 (Fisher's exact test), Q value = 0.042
Table S78. Gene #26: 'del_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 18 | 41 | 27 | 15 | 23 | 18 | 19 |
| DEL PEAK 20(17Q11.2) MUTATED | 6 | 18 | 1 | 3 | 7 | 4 | 3 |
| DEL PEAK 20(17Q11.2) WILD-TYPE | 12 | 23 | 26 | 12 | 16 | 14 | 16 |
Figure S78. Get High-res Image Gene #26: 'del_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.00022
Table S79. Gene #27: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 37 | 40 | 10 | 50 | 25 |
| DEL PEAK 21(22Q13.31) MUTATED | 18 | 5 | 9 | 29 | 4 |
| DEL PEAK 21(22Q13.31) WILD-TYPE | 19 | 35 | 1 | 21 | 21 |
Figure S79. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.0107 (Fisher's exact test), Q value = 0.051
Table S80. Gene #27: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 40 | 77 | 45 |
| DEL PEAK 21(22Q13.31) MUTATED | 10 | 40 | 15 |
| DEL PEAK 21(22Q13.31) WILD-TYPE | 30 | 37 | 30 |
Figure S80. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.0107 (Fisher's exact test), Q value = 0.051
Table S81. Gene #27: 'del_22q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 32 | 65 | 44 | 21 |
| DEL PEAK 21(22Q13.31) MUTATED | 8 | 36 | 13 | 8 |
| DEL PEAK 21(22Q13.31) WILD-TYPE | 24 | 29 | 31 | 13 |
Figure S81. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.00052 (Fisher's exact test), Q value = 0.0052
Table S82. Gene #27: 'del_22q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 34 | 64 | 43 | 21 |
| DEL PEAK 21(22Q13.31) MUTATED | 13 | 37 | 8 | 7 |
| DEL PEAK 21(22Q13.31) WILD-TYPE | 21 | 27 | 35 | 14 |
Figure S82. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.0067 (Fisher's exact test), Q value = 0.038
Table S83. Gene #27: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 63 | 44 | 55 |
| DEL PEAK 21(22Q13.31) MUTATED | 16 | 20 | 29 |
| DEL PEAK 21(22Q13.31) WILD-TYPE | 47 | 24 | 26 |
Figure S83. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.0272 (Fisher's exact test), Q value = 0.1
Table S84. Gene #27: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 66 | 54 | 18 | 24 |
| DEL PEAK 21(22Q13.31) MUTATED | 18 | 29 | 7 | 11 |
| DEL PEAK 21(22Q13.31) WILD-TYPE | 48 | 25 | 11 | 13 |
Figure S84. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.047 (Fisher's exact test), Q value = 0.14
Table S85. Gene #27: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 33 | 50 | 16 | 33 | 29 |
| DEL PEAK 21(22Q13.31) MUTATED | 11 | 28 | 8 | 9 | 9 |
| DEL PEAK 21(22Q13.31) WILD-TYPE | 22 | 22 | 8 | 24 | 20 |
Figure S85. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
P value = 3e-04 (Fisher's exact test), Q value = 0.0032
Table S86. Gene #28: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 37 | 40 | 10 | 50 | 25 |
| DEL PEAK 22(XP21.1) MUTATED | 6 | 4 | 2 | 24 | 10 |
| DEL PEAK 22(XP21.1) WILD-TYPE | 31 | 36 | 8 | 26 | 15 |
Figure S86. Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00074 (Fisher's exact test), Q value = 0.0066
Table S87. Gene #28: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 40 | 77 | 45 |
| DEL PEAK 22(XP21.1) MUTATED | 9 | 32 | 5 |
| DEL PEAK 22(XP21.1) WILD-TYPE | 31 | 45 | 40 |
Figure S87. Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.0469 (Fisher's exact test), Q value = 0.14
Table S88. Gene #28: 'del_xp21.1' versus Molecular Subtype #3: 'RPPA_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 16 | 20 | 23 | 18 |
| DEL PEAK 22(XP21.1) MUTATED | 7 | 7 | 8 | 1 |
| DEL PEAK 22(XP21.1) WILD-TYPE | 9 | 13 | 15 | 17 |
Figure S88. Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #3: 'RPPA_CNMF'
P value = 0.036 (Fisher's exact test), Q value = 0.12
Table S89. Gene #28: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 32 | 65 | 44 | 21 |
| DEL PEAK 22(XP21.1) MUTATED | 10 | 25 | 9 | 2 |
| DEL PEAK 22(XP21.1) WILD-TYPE | 22 | 40 | 35 | 19 |
Figure S89. Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
P value = 0.00358 (Fisher's exact test), Q value = 0.023
Table S90. Gene #28: 'del_xp21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 34 | 64 | 43 | 21 |
| DEL PEAK 22(XP21.1) MUTATED | 7 | 27 | 11 | 1 |
| DEL PEAK 22(XP21.1) WILD-TYPE | 27 | 37 | 32 | 20 |
Figure S90. Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.00027 (Fisher's exact test), Q value = 0.003
Table S91. Gene #28: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 63 | 44 | 55 |
| DEL PEAK 22(XP21.1) MUTATED | 12 | 7 | 27 |
| DEL PEAK 22(XP21.1) WILD-TYPE | 51 | 37 | 28 |
Figure S91. Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
P value = 0.0462 (Fisher's exact test), Q value = 0.14
Table S92. Gene #28: 'del_xp21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 66 | 54 | 18 | 24 |
| DEL PEAK 22(XP21.1) MUTATED | 15 | 21 | 7 | 3 |
| DEL PEAK 22(XP21.1) WILD-TYPE | 51 | 33 | 11 | 21 |
Figure S92. Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
P value = 0.0184 (Fisher's exact test), Q value = 0.073
Table S93. Gene #28: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 18 | 41 | 27 | 15 | 23 | 18 | 19 |
| DEL PEAK 22(XP21.1) MUTATED | 3 | 19 | 6 | 5 | 5 | 7 | 1 |
| DEL PEAK 22(XP21.1) WILD-TYPE | 15 | 22 | 21 | 10 | 18 | 11 | 18 |
Figure S93. Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
-
Copy number data file = all_lesions.txt from GISTIC pipeline
-
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PCPG-TP/22533877/transformed.cor.cli.txt
-
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PCPG-TP/22542422/PCPG-TP.transferedmergedcluster.txt
-
Number of patients = 162
-
Number of significantly focal cnvs = 28
-
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.