This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.
Testing the association between copy number variation 29 focal events and 8 molecular subtypes across 224 patients, 69 significant findings detected with P value < 0.05 and Q value < 0.25.
-
amp_2p23.2 cnv correlated to 'CN_CNMF'.
-
amp_2q32.1 cnv correlated to 'CN_CNMF'.
-
amp_3p12.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
amp_3q26.31 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
amp_7q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
amp_17q25.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
del_1p36.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
-
del_3p22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
del_4q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
del_5q35.2 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
del_6p12.3 cnv correlated to 'CN_CNMF'.
-
del_6q22.31 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
-
del_6q27 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
-
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
del_10p11.21 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
-
del_11q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
-
del_11q24.2 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
-
del_14q11.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
del_15q13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
-
del_16q24.1 cnv correlated to 'METHLYATION_CNMF'.
-
del_21q22.3 cnv correlated to 'CN_CNMF'.
-
del_22q12.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
del_xp11.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
-
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 29 focal events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 69 significant findings detected.
|
Clinical Features |
CN CNMF |
METHLYATION CNMF |
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 | |
| amp 7q22 1 | 135 (60%) | 89 |
1e-05 (0.00232) |
1e-05 (0.00232) |
1e-05 (0.00232) |
1e-05 (0.00232) |
0.116 (1.00) |
0.00779 (1.00) |
0.023 (1.00) |
2e-05 (0.0041) |
| del 9p21 3 | 33 (15%) | 191 |
1e-05 (0.00232) |
1e-05 (0.00232) |
1e-05 (0.00232) |
2e-05 (0.0041) |
0.00626 (0.945) |
0.0102 (1.00) |
0.0822 (1.00) |
8e-05 (0.015) |
| amp 3p12 1 | 64 (29%) | 160 |
1e-05 (0.00232) |
0.00445 (0.681) |
3e-05 (0.00603) |
0.00038 (0.0669) |
0.212 (1.00) |
0.00674 (1.00) |
0.315 (1.00) |
5e-05 (0.0098) |
| amp 17q25 2 | 160 (71%) | 64 |
1e-05 (0.00232) |
0.0001 (0.0185) |
6e-05 (0.0115) |
2e-05 (0.0041) |
0.228 (1.00) |
0.12 (1.00) |
0.215 (1.00) |
0.0201 (1.00) |
| del 3p22 1 | 19 (8%) | 205 |
0.00019 (0.034) |
2e-05 (0.0041) |
1e-05 (0.00232) |
0.00209 (0.334) |
0.0859 (1.00) |
0.113 (1.00) |
0.0707 (1.00) |
1e-05 (0.00232) |
| del 4q34 3 | 26 (12%) | 198 |
0.00013 (0.0237) |
1e-05 (0.00232) |
1e-05 (0.00232) |
0.0109 (1.00) |
0.445 (1.00) |
0.214 (1.00) |
0.932 (1.00) |
3e-05 (0.00603) |
| del 5q35 2 | 11 (5%) | 213 |
0.0107 (1.00) |
3e-05 (0.00603) |
0.00045 (0.0783) |
0.00146 (0.239) |
0.0441 (1.00) |
0.0017 (0.277) |
0.208 (1.00) |
1e-05 (0.00232) |
| del 22q12 2 | 53 (24%) | 171 |
5e-05 (0.0098) |
1e-05 (0.00232) |
1e-05 (0.00232) |
0.0493 (1.00) |
0.904 (1.00) |
0.938 (1.00) |
0.509 (1.00) |
1e-05 (0.00232) |
| amp 3q26 31 | 80 (36%) | 144 |
1e-05 (0.00232) |
0.056 (1.00) |
7e-05 (0.0133) |
0.00312 (0.487) |
0.068 (1.00) |
0.0144 (1.00) |
0.333 (1.00) |
1e-05 (0.00232) |
| del 1p36 32 | 44 (20%) | 180 |
1e-05 (0.00232) |
7e-05 (0.0133) |
1e-05 (0.00232) |
0.0556 (1.00) |
0.891 (1.00) |
0.951 (1.00) |
0.467 (1.00) |
0.00391 (0.602) |
| del 6q27 | 24 (11%) | 200 |
0.00016 (0.0288) |
0.00053 (0.0906) |
7e-05 (0.0133) |
0.0645 (1.00) |
0.545 (1.00) |
0.636 (1.00) |
0.636 (1.00) |
0.00807 (1.00) |
| del 11q22 3 | 23 (10%) | 201 |
0.0004 (0.07) |
0.00056 (0.0952) |
0.00046 (0.0796) |
0.028 (1.00) |
0.203 (1.00) |
0.238 (1.00) |
0.258 (1.00) |
0.229 (1.00) |
| del 14q11 2 | 44 (20%) | 180 |
1e-05 (0.00232) |
0.0341 (1.00) |
0.00058 (0.098) |
0.00134 (0.222) |
0.575 (1.00) |
0.498 (1.00) |
0.619 (1.00) |
0.0868 (1.00) |
| del 15q13 3 | 29 (13%) | 195 |
5e-05 (0.0098) |
0.0001 (0.0185) |
3e-05 (0.00603) |
0.00184 (0.296) |
0.11 (1.00) |
0.145 (1.00) |
0.203 (1.00) |
0.0032 (0.496) |
| del xp11 22 | 21 (9%) | 203 |
9e-05 (0.0167) |
1e-05 (0.00232) |
1e-05 (0.00232) |
0.0123 (1.00) |
0.198 (1.00) |
0.223 (1.00) |
0.39 (1.00) |
0.0251 (1.00) |
| del xq28 | 20 (9%) | 204 |
0.00012 (0.022) |
0.00071 (0.119) |
0.00024 (0.0427) |
0.266 (1.00) |
0.36 (1.00) |
0.685 (1.00) |
0.466 (1.00) |
0.0537 (1.00) |
| del 6q22 31 | 21 (9%) | 203 |
0.00049 (0.0843) |
0.0211 (1.00) |
0.00031 (0.0549) |
0.146 (1.00) |
0.655 (1.00) |
0.421 (1.00) |
0.651 (1.00) |
0.00225 (0.358) |
| del 10p11 21 | 13 (6%) | 211 |
0.00447 (0.681) |
0.00136 (0.224) |
5e-05 (0.0098) |
0.12 (1.00) |
0.147 (1.00) |
0.872 (1.00) |
0.456 (1.00) |
0.0694 (1.00) |
| del 11q24 2 | 23 (10%) | 201 |
0.00293 (0.46) |
5e-05 (0.0098) |
0.00014 (0.0253) |
0.0279 (1.00) |
0.203 (1.00) |
0.216 (1.00) |
0.259 (1.00) |
0.0154 (1.00) |
| amp 2p23 2 | 41 (18%) | 183 |
1e-05 (0.00232) |
0.00712 (1.00) |
0.0446 (1.00) |
0.165 (1.00) |
0.0163 (1.00) |
0.854 (1.00) |
0.0587 (1.00) |
0.121 (1.00) |
| amp 2q32 1 | 48 (21%) | 176 |
1e-05 (0.00232) |
0.057 (1.00) |
0.0629 (1.00) |
0.14 (1.00) |
0.255 (1.00) |
0.674 (1.00) |
0.0824 (1.00) |
0.658 (1.00) |
| del 6p12 3 | 19 (8%) | 205 |
0.00079 (0.132) |
0.0307 (1.00) |
0.00629 (0.945) |
0.429 (1.00) |
0.321 (1.00) |
0.448 (1.00) |
0.123 (1.00) |
0.142 (1.00) |
| del 16q24 1 | 9 (4%) | 215 |
0.0196 (1.00) |
1e-05 (0.00232) |
0.0108 (1.00) |
0.111 (1.00) |
0.842 (1.00) |
0.153 (1.00) |
0.912 (1.00) |
0.00227 (0.359) |
| del 21q22 3 | 36 (16%) | 188 |
4e-05 (0.00788) |
0.387 (1.00) |
0.267 (1.00) |
0.866 (1.00) |
0.218 (1.00) |
0.34 (1.00) |
0.32 (1.00) |
0.093 (1.00) |
| amp 19p13 2 | 24 (11%) | 200 |
0.0845 (1.00) |
0.028 (1.00) |
0.0181 (1.00) |
0.0371 (1.00) |
0.36 (1.00) |
1 (1.00) |
0.224 (1.00) |
0.00943 (1.00) |
| del 2q37 3 | 11 (5%) | 213 |
0.00966 (1.00) |
0.00183 (0.296) |
0.173 (1.00) |
0.0141 (1.00) |
0.0713 (1.00) |
0.186 (1.00) |
0.0294 (1.00) |
0.0101 (1.00) |
| del 5p14 2 | 10 (4%) | 214 |
0.416 (1.00) |
0.0108 (1.00) |
0.126 (1.00) |
0.163 (1.00) |
0.166 (1.00) |
0.191 (1.00) |
0.257 (1.00) |
0.0683 (1.00) |
| del 19p13 3 | 17 (8%) | 207 |
0.0571 (1.00) |
0.0343 (1.00) |
0.0255 (1.00) |
0.485 (1.00) |
0.157 (1.00) |
0.576 (1.00) |
0.195 (1.00) |
0.33 (1.00) |
| del 19q13 42 | 16 (7%) | 208 |
0.158 (1.00) |
0.0333 (1.00) |
0.00791 (1.00) |
0.465 (1.00) |
0.19 (1.00) |
0.746 (1.00) |
0.0608 (1.00) |
0.0549 (1.00) |
P value = 1e-05 (Fisher's exact test), Q value = 0.0023
Table S1. Gene #1: 'amp_2p23.2' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 84 | 107 | 33 |
| AMP PEAK 1(2P23.2) MUTATED | 1 | 16 | 24 |
| AMP PEAK 1(2P23.2) WILD-TYPE | 83 | 91 | 9 |
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 = 0.0023
Table S2. Gene #2: 'amp_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 84 | 107 | 33 |
| AMP PEAK 2(2Q32.1) MUTATED | 1 | 22 | 25 |
| AMP PEAK 2(2Q32.1) WILD-TYPE | 83 | 85 | 8 |
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 = 0.0023
Table S3. Gene #3: 'amp_3p12.1' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 84 | 107 | 33 |
| AMP PEAK 3(3P12.1) MUTATED | 29 | 9 | 26 |
| AMP PEAK 3(3P12.1) WILD-TYPE | 55 | 98 | 7 |
Figure S3. Get High-res Image Gene #3: 'amp_3p12.1' versus Molecular Subtype #1: 'CN_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.006
Table S4. Gene #3: 'amp_3p12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 47 | 70 | 62 | 32 |
| AMP PEAK 3(3P12.1) MUTATED | 23 | 8 | 24 | 7 |
| AMP PEAK 3(3P12.1) WILD-TYPE | 24 | 62 | 38 | 25 |
Figure S4. Get High-res Image Gene #3: 'amp_3p12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
P value = 0.00038 (Fisher's exact test), Q value = 0.067
Table S5. Gene #3: 'amp_3p12.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 73 | 72 | 66 |
| AMP PEAK 3(3P12.1) MUTATED | 23 | 10 | 29 |
| AMP PEAK 3(3P12.1) WILD-TYPE | 50 | 62 | 37 |
Figure S5. Get High-res Image Gene #3: 'amp_3p12.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
P value = 5e-05 (Fisher's exact test), Q value = 0.0098
Table S6. Gene #3: 'amp_3p12.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 27 | 34 | 36 | 32 | 35 | 40 | 20 |
| AMP PEAK 3(3P12.1) MUTATED | 13 | 2 | 11 | 7 | 6 | 21 | 4 |
| AMP PEAK 3(3P12.1) WILD-TYPE | 14 | 32 | 25 | 25 | 29 | 19 | 16 |
Figure S6. Get High-res Image Gene #3: 'amp_3p12.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0023
Table S7. Gene #4: 'amp_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 84 | 107 | 33 |
| AMP PEAK 4(3Q26.31) MUTATED | 35 | 16 | 29 |
| AMP PEAK 4(3Q26.31) WILD-TYPE | 49 | 91 | 4 |
Figure S7. Get High-res Image Gene #4: 'amp_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'
P value = 7e-05 (Fisher's exact test), Q value = 0.013
Table S8. Gene #4: 'amp_3q26.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 47 | 70 | 62 | 32 |
| AMP PEAK 4(3Q26.31) MUTATED | 26 | 11 | 26 | 14 |
| AMP PEAK 4(3Q26.31) WILD-TYPE | 21 | 59 | 36 | 18 |
Figure S8. Get High-res Image Gene #4: 'amp_3q26.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0023
Table S9. Gene #4: 'amp_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 27 | 34 | 36 | 32 | 35 | 40 | 20 |
| AMP PEAK 4(3Q26.31) MUTATED | 16 | 4 | 13 | 9 | 7 | 26 | 5 |
| AMP PEAK 4(3Q26.31) WILD-TYPE | 11 | 30 | 23 | 23 | 28 | 14 | 15 |
Figure S9. Get High-res Image Gene #4: 'amp_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0023
Table S10. Gene #5: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 84 | 107 | 33 |
| AMP PEAK 5(7Q22.1) MUTATED | 79 | 29 | 27 |
| AMP PEAK 5(7Q22.1) WILD-TYPE | 5 | 78 | 6 |
Figure S10. Get High-res Image Gene #5: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0023
Table S11. Gene #5: 'amp_7q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 56 | 56 | 96 |
| AMP PEAK 5(7Q22.1) MUTATED | 28 | 18 | 78 |
| AMP PEAK 5(7Q22.1) WILD-TYPE | 28 | 38 | 18 |
Figure S11. Get High-res Image Gene #5: 'amp_7q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0023
Table S12. Gene #5: 'amp_7q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 47 | 70 | 62 | 32 |
| AMP PEAK 5(7Q22.1) MUTATED | 27 | 22 | 55 | 25 |
| AMP PEAK 5(7Q22.1) WILD-TYPE | 20 | 48 | 7 | 7 |
Figure S12. Get High-res Image Gene #5: 'amp_7q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0023
Table S13. Gene #5: 'amp_7q22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 73 | 72 | 66 |
| AMP PEAK 5(7Q22.1) MUTATED | 32 | 37 | 60 |
| AMP PEAK 5(7Q22.1) WILD-TYPE | 41 | 35 | 6 |
Figure S13. Get High-res Image Gene #5: 'amp_7q22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
P value = 2e-05 (Fisher's exact test), Q value = 0.0041
Table S14. Gene #5: 'amp_7q22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 27 | 34 | 36 | 32 | 35 | 40 | 20 |
| AMP PEAK 5(7Q22.1) MUTATED | 15 | 10 | 28 | 24 | 20 | 32 | 6 |
| AMP PEAK 5(7Q22.1) WILD-TYPE | 12 | 24 | 8 | 8 | 15 | 8 | 14 |
Figure S14. Get High-res Image Gene #5: 'amp_7q22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0023
Table S15. Gene #6: 'amp_17q25.2' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 84 | 107 | 33 |
| AMP PEAK 6(17Q25.2) MUTATED | 83 | 47 | 30 |
| AMP PEAK 6(17Q25.2) WILD-TYPE | 1 | 60 | 3 |
Figure S15. Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-04 (Fisher's exact test), Q value = 0.018
Table S16. Gene #6: 'amp_17q25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 56 | 56 | 96 |
| AMP PEAK 6(17Q25.2) MUTATED | 33 | 33 | 82 |
| AMP PEAK 6(17Q25.2) WILD-TYPE | 23 | 23 | 14 |
Figure S16. Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 6e-05 (Fisher's exact test), Q value = 0.011
Table S17. Gene #6: 'amp_17q25.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 47 | 70 | 62 | 32 |
| AMP PEAK 6(17Q25.2) MUTATED | 37 | 38 | 56 | 23 |
| AMP PEAK 6(17Q25.2) WILD-TYPE | 10 | 32 | 6 | 9 |
Figure S17. Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
P value = 2e-05 (Fisher's exact test), Q value = 0.0041
Table S18. Gene #6: 'amp_17q25.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 73 | 72 | 66 |
| AMP PEAK 6(17Q25.2) MUTATED | 49 | 44 | 61 |
| AMP PEAK 6(17Q25.2) WILD-TYPE | 24 | 28 | 5 |
Figure S18. Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0023
Table S19. Gene #8: 'del_1p36.32' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 84 | 107 | 33 |
| DEL PEAK 1(1P36.32) MUTATED | 1 | 34 | 9 |
| DEL PEAK 1(1P36.32) WILD-TYPE | 83 | 73 | 24 |
Figure S19. Get High-res Image Gene #8: 'del_1p36.32' versus Molecular Subtype #1: 'CN_CNMF'
P value = 7e-05 (Fisher's exact test), Q value = 0.013
Table S20. Gene #8: 'del_1p36.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 56 | 56 | 96 |
| DEL PEAK 1(1P36.32) MUTATED | 10 | 22 | 9 |
| DEL PEAK 1(1P36.32) WILD-TYPE | 46 | 34 | 87 |
Figure S20. Get High-res Image Gene #8: 'del_1p36.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0023
Table S21. Gene #8: 'del_1p36.32' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 47 | 70 | 62 | 32 |
| DEL PEAK 1(1P36.32) MUTATED | 5 | 31 | 5 | 0 |
| DEL PEAK 1(1P36.32) WILD-TYPE | 42 | 39 | 57 | 32 |
Figure S21. Get High-res Image Gene #8: 'del_1p36.32' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
P value = 0.00019 (Fisher's exact test), Q value = 0.034
Table S22. Gene #10: 'del_3p22.1' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 84 | 107 | 33 |
| DEL PEAK 3(3P22.1) MUTATED | 0 | 16 | 3 |
| DEL PEAK 3(3P22.1) WILD-TYPE | 84 | 91 | 30 |
Figure S22. Get High-res Image Gene #10: 'del_3p22.1' versus Molecular Subtype #1: 'CN_CNMF'
P value = 2e-05 (Fisher's exact test), Q value = 0.0041
Table S23. Gene #10: 'del_3p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 56 | 56 | 96 |
| DEL PEAK 3(3P22.1) MUTATED | 3 | 14 | 1 |
| DEL PEAK 3(3P22.1) WILD-TYPE | 53 | 42 | 95 |
Figure S23. Get High-res Image Gene #10: 'del_3p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0023
Table S24. Gene #10: 'del_3p22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 47 | 70 | 62 | 32 |
| DEL PEAK 3(3P22.1) MUTATED | 1 | 16 | 0 | 0 |
| DEL PEAK 3(3P22.1) WILD-TYPE | 46 | 54 | 62 | 32 |
Figure S24. Get High-res Image Gene #10: 'del_3p22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0023
Table S25. Gene #10: 'del_3p22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 27 | 34 | 36 | 32 | 35 | 40 | 20 |
| DEL PEAK 3(3P22.1) MUTATED | 0 | 10 | 1 | 0 | 5 | 0 | 3 |
| DEL PEAK 3(3P22.1) WILD-TYPE | 27 | 24 | 35 | 32 | 30 | 40 | 17 |
Figure S25. Get High-res Image Gene #10: 'del_3p22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.00013 (Fisher's exact test), Q value = 0.024
Table S26. Gene #11: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 84 | 107 | 33 |
| DEL PEAK 4(4Q34.3) MUTATED | 1 | 20 | 5 |
| DEL PEAK 4(4Q34.3) WILD-TYPE | 83 | 87 | 28 |
Figure S26. Get High-res Image Gene #11: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0023
Table S27. Gene #11: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 56 | 56 | 96 |
| DEL PEAK 4(4Q34.3) MUTATED | 3 | 19 | 2 |
| DEL PEAK 4(4Q34.3) WILD-TYPE | 53 | 37 | 94 |
Figure S27. Get High-res Image Gene #11: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0023
Table S28. Gene #11: 'del_4q34.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 47 | 70 | 62 | 32 |
| DEL PEAK 4(4Q34.3) MUTATED | 2 | 22 | 1 | 0 |
| DEL PEAK 4(4Q34.3) WILD-TYPE | 45 | 48 | 61 | 32 |
Figure S28. Get High-res Image Gene #11: 'del_4q34.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.006
Table S29. Gene #11: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 27 | 34 | 36 | 32 | 35 | 40 | 20 |
| DEL PEAK 4(4Q34.3) MUTATED | 2 | 8 | 3 | 0 | 2 | 2 | 9 |
| DEL PEAK 4(4Q34.3) WILD-TYPE | 25 | 26 | 33 | 32 | 33 | 38 | 11 |
Figure S29. Get High-res Image Gene #11: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 3e-05 (Fisher's exact test), Q value = 0.006
Table S30. Gene #13: 'del_5q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 56 | 56 | 96 |
| DEL PEAK 6(5Q35.2) MUTATED | 1 | 9 | 0 |
| DEL PEAK 6(5Q35.2) WILD-TYPE | 55 | 47 | 96 |
Figure S30. Get High-res Image Gene #13: 'del_5q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.00045 (Fisher's exact test), Q value = 0.078
Table S31. Gene #13: 'del_5q35.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 47 | 70 | 62 | 32 |
| DEL PEAK 6(5Q35.2) MUTATED | 1 | 10 | 0 | 0 |
| DEL PEAK 6(5Q35.2) WILD-TYPE | 46 | 60 | 62 | 32 |
Figure S31. Get High-res Image Gene #13: 'del_5q35.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
P value = 0.00146 (Fisher's exact test), Q value = 0.24
Table S32. Gene #13: 'del_5q35.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 73 | 72 | 66 |
| DEL PEAK 6(5Q35.2) MUTATED | 2 | 9 | 0 |
| DEL PEAK 6(5Q35.2) WILD-TYPE | 71 | 63 | 66 |
Figure S32. Get High-res Image Gene #13: 'del_5q35.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
P value = 1e-05 (Fisher's exact test), Q value = 0.0023
Table S33. Gene #13: 'del_5q35.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 27 | 34 | 36 | 32 | 35 | 40 | 20 |
| DEL PEAK 6(5Q35.2) MUTATED | 0 | 2 | 0 | 0 | 0 | 1 | 8 |
| DEL PEAK 6(5Q35.2) WILD-TYPE | 27 | 32 | 36 | 32 | 35 | 39 | 12 |
Figure S33. Get High-res Image Gene #13: 'del_5q35.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.00079 (Fisher's exact test), Q value = 0.13
Table S34. Gene #14: 'del_6p12.3' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 84 | 107 | 33 |
| DEL PEAK 7(6P12.3) MUTATED | 1 | 11 | 7 |
| DEL PEAK 7(6P12.3) WILD-TYPE | 83 | 96 | 26 |
Figure S34. Get High-res Image Gene #14: 'del_6p12.3' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00049 (Fisher's exact test), Q value = 0.084
Table S35. Gene #15: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 84 | 107 | 33 |
| DEL PEAK 8(6Q22.31) MUTATED | 1 | 13 | 7 |
| DEL PEAK 8(6Q22.31) WILD-TYPE | 83 | 94 | 26 |
Figure S35. Get High-res Image Gene #15: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00031 (Fisher's exact test), Q value = 0.055
Table S36. Gene #15: 'del_6q22.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 47 | 70 | 62 | 32 |
| DEL PEAK 8(6Q22.31) MUTATED | 2 | 16 | 3 | 0 |
| DEL PEAK 8(6Q22.31) WILD-TYPE | 45 | 54 | 59 | 32 |
Figure S36. Get High-res Image Gene #15: 'del_6q22.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
P value = 0.00016 (Fisher's exact test), Q value = 0.029
Table S37. Gene #16: 'del_6q27' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 84 | 107 | 33 |
| DEL PEAK 9(6Q27) MUTATED | 1 | 15 | 8 |
| DEL PEAK 9(6Q27) WILD-TYPE | 83 | 92 | 25 |
Figure S37. Get High-res Image Gene #16: 'del_6q27' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00053 (Fisher's exact test), Q value = 0.091
Table S38. Gene #16: 'del_6q27' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 56 | 56 | 96 |
| DEL PEAK 9(6Q27) MUTATED | 5 | 14 | 4 |
| DEL PEAK 9(6Q27) WILD-TYPE | 51 | 42 | 92 |
Figure S38. Get High-res Image Gene #16: 'del_6q27' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 7e-05 (Fisher's exact test), Q value = 0.013
Table S39. Gene #16: 'del_6q27' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 47 | 70 | 62 | 32 |
| DEL PEAK 9(6Q27) MUTATED | 3 | 18 | 3 | 0 |
| DEL PEAK 9(6Q27) WILD-TYPE | 44 | 52 | 59 | 32 |
Figure S39. Get High-res Image Gene #16: 'del_6q27' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0023
Table S40. Gene #17: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 84 | 107 | 33 |
| DEL PEAK 10(9P21.3) MUTATED | 1 | 25 | 7 |
| DEL PEAK 10(9P21.3) WILD-TYPE | 83 | 82 | 26 |
Figure S40. Get High-res Image Gene #17: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0023
Table S41. Gene #17: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 56 | 56 | 96 |
| DEL PEAK 10(9P21.3) MUTATED | 9 | 19 | 2 |
| DEL PEAK 10(9P21.3) WILD-TYPE | 47 | 37 | 94 |
Figure S41. Get High-res Image Gene #17: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0023
Table S42. Gene #17: 'del_9p21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 47 | 70 | 62 | 32 |
| DEL PEAK 10(9P21.3) MUTATED | 3 | 28 | 0 | 1 |
| DEL PEAK 10(9P21.3) WILD-TYPE | 44 | 42 | 62 | 31 |
Figure S42. Get High-res Image Gene #17: 'del_9p21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
P value = 2e-05 (Fisher's exact test), Q value = 0.0041
Table S43. Gene #17: 'del_9p21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 73 | 72 | 66 |
| DEL PEAK 10(9P21.3) MUTATED | 10 | 21 | 1 |
| DEL PEAK 10(9P21.3) WILD-TYPE | 63 | 51 | 65 |
Figure S43. Get High-res Image Gene #17: 'del_9p21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
P value = 8e-05 (Fisher's exact test), Q value = 0.015
Table S44. Gene #17: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 27 | 34 | 36 | 32 | 35 | 40 | 20 |
| DEL PEAK 10(9P21.3) MUTATED | 0 | 7 | 5 | 0 | 10 | 3 | 8 |
| DEL PEAK 10(9P21.3) WILD-TYPE | 27 | 27 | 31 | 32 | 25 | 37 | 12 |
Figure S44. Get High-res Image Gene #17: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 0.00136 (Fisher's exact test), Q value = 0.22
Table S45. Gene #18: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 56 | 56 | 96 |
| DEL PEAK 11(10P11.21) MUTATED | 1 | 9 | 2 |
| DEL PEAK 11(10P11.21) WILD-TYPE | 55 | 47 | 94 |
Figure S45. Get High-res Image Gene #18: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 5e-05 (Fisher's exact test), Q value = 0.0098
Table S46. Gene #18: 'del_10p11.21' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 47 | 70 | 62 | 32 |
| DEL PEAK 11(10P11.21) MUTATED | 0 | 12 | 1 | 0 |
| DEL PEAK 11(10P11.21) WILD-TYPE | 47 | 58 | 61 | 32 |
Figure S46. Get High-res Image Gene #18: 'del_10p11.21' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
P value = 4e-04 (Fisher's exact test), Q value = 0.07
Table S47. Gene #19: 'del_11q22.3' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 84 | 107 | 33 |
| DEL PEAK 12(11Q22.3) MUTATED | 1 | 16 | 6 |
| DEL PEAK 12(11Q22.3) WILD-TYPE | 83 | 91 | 27 |
Figure S47. Get High-res Image Gene #19: 'del_11q22.3' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00056 (Fisher's exact test), Q value = 0.095
Table S48. Gene #19: 'del_11q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 56 | 56 | 96 |
| DEL PEAK 12(11Q22.3) MUTATED | 6 | 13 | 3 |
| DEL PEAK 12(11Q22.3) WILD-TYPE | 50 | 43 | 93 |
Figure S48. Get High-res Image Gene #19: 'del_11q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.00046 (Fisher's exact test), Q value = 0.08
Table S49. Gene #19: 'del_11q22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 47 | 70 | 62 | 32 |
| DEL PEAK 12(11Q22.3) MUTATED | 2 | 16 | 2 | 1 |
| DEL PEAK 12(11Q22.3) WILD-TYPE | 45 | 54 | 60 | 31 |
Figure S49. Get High-res Image Gene #19: 'del_11q22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
P value = 5e-05 (Fisher's exact test), Q value = 0.0098
Table S50. Gene #20: 'del_11q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 56 | 56 | 96 |
| DEL PEAK 13(11Q24.2) MUTATED | 6 | 14 | 2 |
| DEL PEAK 13(11Q24.2) WILD-TYPE | 50 | 42 | 94 |
Figure S50. Get High-res Image Gene #20: 'del_11q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.00014 (Fisher's exact test), Q value = 0.025
Table S51. Gene #20: 'del_11q24.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 47 | 70 | 62 | 32 |
| DEL PEAK 13(11Q24.2) MUTATED | 2 | 16 | 1 | 2 |
| DEL PEAK 13(11Q24.2) WILD-TYPE | 45 | 54 | 61 | 30 |
Figure S51. Get High-res Image Gene #20: 'del_11q24.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0023
Table S52. Gene #21: 'del_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 84 | 107 | 33 |
| DEL PEAK 14(14Q11.2) MUTATED | 3 | 32 | 9 |
| DEL PEAK 14(14Q11.2) WILD-TYPE | 81 | 75 | 24 |
Figure S52. Get High-res Image Gene #21: 'del_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00058 (Fisher's exact test), Q value = 0.098
Table S53. Gene #21: 'del_14q11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 47 | 70 | 62 | 32 |
| DEL PEAK 14(14Q11.2) MUTATED | 10 | 24 | 5 | 3 |
| DEL PEAK 14(14Q11.2) WILD-TYPE | 37 | 46 | 57 | 29 |
Figure S53. Get High-res Image Gene #21: 'del_14q11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
P value = 0.00134 (Fisher's exact test), Q value = 0.22
Table S54. Gene #21: 'del_14q11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 73 | 72 | 66 |
| DEL PEAK 14(14Q11.2) MUTATED | 14 | 23 | 5 |
| DEL PEAK 14(14Q11.2) WILD-TYPE | 59 | 49 | 61 |
Figure S54. Get High-res Image Gene #21: 'del_14q11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
P value = 5e-05 (Fisher's exact test), Q value = 0.0098
Table S55. Gene #22: 'del_15q13.3' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 84 | 107 | 33 |
| DEL PEAK 15(15Q13.3) MUTATED | 1 | 21 | 7 |
| DEL PEAK 15(15Q13.3) WILD-TYPE | 83 | 86 | 26 |
Figure S55. Get High-res Image Gene #22: 'del_15q13.3' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-04 (Fisher's exact test), Q value = 0.018
Table S56. Gene #22: 'del_15q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 56 | 56 | 96 |
| DEL PEAK 15(15Q13.3) MUTATED | 10 | 14 | 3 |
| DEL PEAK 15(15Q13.3) WILD-TYPE | 46 | 42 | 93 |
Figure S56. Get High-res Image Gene #22: 'del_15q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 3e-05 (Fisher's exact test), Q value = 0.006
Table S57. Gene #22: 'del_15q13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 47 | 70 | 62 | 32 |
| DEL PEAK 15(15Q13.3) MUTATED | 4 | 20 | 2 | 0 |
| DEL PEAK 15(15Q13.3) WILD-TYPE | 43 | 50 | 60 | 32 |
Figure S57. Get High-res Image Gene #22: 'del_15q13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0023
Table S58. Gene #23: 'del_16q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 56 | 56 | 96 |
| DEL PEAK 16(16Q24.1) MUTATED | 0 | 9 | 0 |
| DEL PEAK 16(16Q24.1) WILD-TYPE | 56 | 47 | 96 |
Figure S58. Get High-res Image Gene #23: 'del_16q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 4e-05 (Fisher's exact test), Q value = 0.0079
Table S59. Gene #26: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 84 | 107 | 33 |
| DEL PEAK 19(21Q22.3) MUTATED | 8 | 13 | 15 |
| DEL PEAK 19(21Q22.3) WILD-TYPE | 76 | 94 | 18 |
Figure S59. Get High-res Image Gene #26: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'
P value = 5e-05 (Fisher's exact test), Q value = 0.0098
Table S60. Gene #27: 'del_22q12.2' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 84 | 107 | 33 |
| DEL PEAK 20(22Q12.2) MUTATED | 7 | 38 | 8 |
| DEL PEAK 20(22Q12.2) WILD-TYPE | 77 | 69 | 25 |
Figure S60. Get High-res Image Gene #27: 'del_22q12.2' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0023
Table S61. Gene #27: 'del_22q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 56 | 56 | 96 |
| DEL PEAK 20(22Q12.2) MUTATED | 8 | 31 | 11 |
| DEL PEAK 20(22Q12.2) WILD-TYPE | 48 | 25 | 85 |
Figure S61. Get High-res Image Gene #27: 'del_22q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0023
Table S62. Gene #27: 'del_22q12.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 47 | 70 | 62 | 32 |
| DEL PEAK 20(22Q12.2) MUTATED | 8 | 36 | 5 | 2 |
| DEL PEAK 20(22Q12.2) WILD-TYPE | 39 | 34 | 57 | 30 |
Figure S62. Get High-res Image Gene #27: 'del_22q12.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0023
Table S63. Gene #27: 'del_22q12.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 27 | 34 | 36 | 32 | 35 | 40 | 20 |
| DEL PEAK 20(22Q12.2) MUTATED | 2 | 20 | 9 | 1 | 8 | 5 | 8 |
| DEL PEAK 20(22Q12.2) WILD-TYPE | 25 | 14 | 27 | 31 | 27 | 35 | 12 |
Figure S63. Get High-res Image Gene #27: 'del_22q12.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
P value = 9e-05 (Fisher's exact test), Q value = 0.017
Table S64. Gene #28: 'del_xp11.22' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 84 | 107 | 33 |
| DEL PEAK 21(XP11.22) MUTATED | 0 | 15 | 6 |
| DEL PEAK 21(XP11.22) WILD-TYPE | 84 | 92 | 27 |
Figure S64. Get High-res Image Gene #28: 'del_xp11.22' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0023
Table S65. Gene #28: 'del_xp11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 56 | 56 | 96 |
| DEL PEAK 21(XP11.22) MUTATED | 3 | 15 | 1 |
| DEL PEAK 21(XP11.22) WILD-TYPE | 53 | 41 | 95 |
Figure S65. Get High-res Image Gene #28: 'del_xp11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 1e-05 (Fisher's exact test), Q value = 0.0023
Table S66. Gene #28: 'del_xp11.22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 47 | 70 | 62 | 32 |
| DEL PEAK 21(XP11.22) MUTATED | 2 | 18 | 0 | 0 |
| DEL PEAK 21(XP11.22) WILD-TYPE | 45 | 52 | 62 | 32 |
Figure S66. Get High-res Image Gene #28: 'del_xp11.22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
P value = 0.00012 (Fisher's exact test), Q value = 0.022
Table S67. Gene #29: 'del_xq28' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 84 | 107 | 33 |
| DEL PEAK 22(XQ28) MUTATED | 0 | 15 | 5 |
| DEL PEAK 22(XQ28) WILD-TYPE | 84 | 92 | 28 |
Figure S67. Get High-res Image Gene #29: 'del_xq28' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.00071 (Fisher's exact test), Q value = 0.12
Table S68. Gene #29: 'del_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 56 | 56 | 96 |
| DEL PEAK 22(XQ28) MUTATED | 3 | 12 | 3 |
| DEL PEAK 22(XQ28) WILD-TYPE | 53 | 44 | 93 |
Figure S68. Get High-res Image Gene #29: 'del_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.00024 (Fisher's exact test), Q value = 0.043
Table S69. Gene #29: 'del_xq28' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 47 | 70 | 62 | 32 |
| DEL PEAK 22(XQ28) MUTATED | 2 | 15 | 2 | 0 |
| DEL PEAK 22(XQ28) WILD-TYPE | 45 | 55 | 60 | 32 |
Figure S69. Get High-res Image Gene #29: 'del_xq28' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
-
Copy number data file = transformed.cor.cli.txt
-
Molecular subtype file = KIRP-TP.transferedmergedcluster.txt
-
Number of patients = 224
-
Number of significantly focal cnvs = 29
-
Number of molecular subtypes = 8
-
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.