This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.
Testing the association between copy number variation 32 arm-level events and 6 molecular subtypes across 191 patients, 79 significant findings detected with P value < 0.05 and Q value < 0.25.
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1p gain cnv correlated to 'CN_CNMF'.
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4p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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4q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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8p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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8q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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10q gain cnv correlated to 'CN_CNMF'.
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11p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
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11q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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13q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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17q gain cnv correlated to 'CN_CNMF'.
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19p gain cnv correlated to 'CN_CNMF'.
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19q gain cnv correlated to 'CN_CNMF'.
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21q gain cnv correlated to 'CN_CNMF'.
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22q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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xp gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
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xq gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
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3p loss cnv correlated to 'CN_CNMF'.
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3q loss cnv correlated to 'CN_CNMF'.
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5q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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7p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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7q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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12p loss cnv correlated to 'CN_CNMF'.
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15q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
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16q loss cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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17p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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17q loss cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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18p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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18q loss cnv correlated to 'CN_CNMF'.
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19p loss cnv correlated to 'CN_CNMF'.
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19q loss cnv correlated to 'CN_CNMF'.
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xp loss cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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xq loss cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 32 arm-level events and 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 79 significant findings detected.
Clinical Features |
CN CNMF |
METHLYATION CNMF |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ 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 | |
8p gain | 22 (12%) | 169 |
0.00091 (0.00793) |
0.00025 (0.0032) |
0.0287 (0.0795) |
0.00084 (0.00793) |
0.00981 (0.0349) |
0.0163 (0.0497) |
8q gain | 23 (12%) | 168 |
0.00147 (0.0101) |
0.00039 (0.00452) |
0.0135 (0.0454) |
0.00184 (0.0112) |
0.00711 (0.0268) |
0.0145 (0.0462) |
7p loss | 17 (9%) | 174 |
4e-05 (0.000698) |
0.00016 (0.00236) |
0.00095 (0.00793) |
1e-05 (0.00024) |
0.00358 (0.0181) |
0.00339 (0.0181) |
7q loss | 20 (10%) | 171 |
1e-05 (0.00024) |
2e-05 (0.000427) |
0.00585 (0.0252) |
1e-05 (0.00024) |
0.00143 (0.0101) |
0.00084 (0.00793) |
22q gain | 9 (5%) | 182 |
0.00095 (0.00793) |
0.00425 (0.0204) |
0.137 (0.258) |
0.0168 (0.0504) |
0.0562 (0.132) |
0.0132 (0.0452) |
5q loss | 6 (3%) | 185 |
1e-05 (0.00024) |
0.00682 (0.0262) |
0.226 (0.364) |
0.633 (0.769) |
0.0312 (0.082) |
0.0327 (0.0848) |
17p loss | 13 (7%) | 178 |
1e-05 (0.00024) |
0.00187 (0.0112) |
0.157 (0.292) |
0.00138 (0.0101) |
0.161 (0.296) |
0.00385 (0.019) |
11q gain | 7 (4%) | 184 |
1e-05 (0.00024) |
0.0298 (0.0795) |
0.0667 (0.147) |
0.0736 (0.159) |
0.291 (0.443) |
0.0149 (0.0462) |
16q loss | 4 (2%) | 187 |
0.00108 (0.00864) |
0.0556 (0.132) |
0.785 (0.923) |
1 (1.00) |
0.0145 (0.0462) |
0.0224 (0.0643) |
17q loss | 7 (4%) | 184 |
1e-05 (0.00024) |
0.112 (0.218) |
0.0667 (0.147) |
0.234 (0.375) |
0.0375 (0.0959) |
0.0491 (0.119) |
xp loss | 5 (3%) | 186 |
0.00012 (0.00192) |
0.199 (0.345) |
0.224 (0.364) |
0.631 (0.769) |
0.00353 (0.0181) |
0.00501 (0.0224) |
xq loss | 5 (3%) | 186 |
4e-05 (0.000698) |
0.201 (0.345) |
0.224 (0.364) |
0.631 (0.769) |
0.0033 (0.0181) |
0.0048 (0.0219) |
4p gain | 4 (2%) | 187 |
0.0294 (0.0795) |
0.00755 (0.0274) |
0.342 (0.501) |
0.837 (0.962) |
||
4q gain | 4 (2%) | 187 |
0.0292 (0.0795) |
0.0074 (0.0273) |
0.342 (0.501) |
0.833 (0.962) |
||
11p gain | 4 (2%) | 187 |
0.0007 (0.00747) |
0.43 (0.597) |
0.465 (0.625) |
0.369 (0.533) |
0.523 (0.682) |
0.0221 (0.0643) |
13q gain | 6 (3%) | 185 |
0.0418 (0.106) |
0.00655 (0.0259) |
0.124 (0.238) |
0.0845 (0.178) |
0.801 (0.932) |
0.0736 (0.159) |
xp gain | 3 (2%) | 188 |
0.00183 (0.0112) |
0.699 (0.837) |
0.892 (0.978) |
0.0468 (0.115) |
||
xq gain | 3 (2%) | 188 |
0.00159 (0.0105) |
0.701 (0.837) |
0.891 (0.978) |
0.0469 (0.115) |
||
15q loss | 4 (2%) | 187 |
0.0004 (0.00452) |
0.55 (0.707) |
0.0662 (0.147) |
0.369 (0.533) |
0.0228 (0.0645) |
0.186 (0.326) |
18p loss | 5 (3%) | 186 |
0.00018 (0.00247) |
0.0207 (0.0613) |
1 (1.00) |
0.864 (0.962) |
0.249 (0.386) |
0.185 (0.326) |
1p gain | 3 (2%) | 188 |
0.00441 (0.0207) |
0.209 (0.349) |
0.185 (0.326) |
0.592 (0.733) |
0.0911 (0.185) |
0.0927 (0.185) |
10q gain | 3 (2%) | 188 |
0.0148 (0.0462) |
0.21 (0.349) |
0.184 (0.326) |
0.59 (0.733) |
0.552 (0.707) |
0.0924 (0.185) |
17q gain | 3 (2%) | 188 |
0.00626 (0.0257) |
0.702 (0.837) |
1 (1.00) |
0.591 (0.733) |
0.482 (0.634) |
0.304 (0.459) |
19p gain | 5 (3%) | 186 |
0.0141 (0.0462) |
0.249 (0.386) |
1 (1.00) |
0.867 (0.962) |
0.581 (0.733) |
1 (1.00) |
19q gain | 5 (3%) | 186 |
0.0126 (0.0441) |
0.248 (0.386) |
1 (1.00) |
0.864 (0.962) |
0.578 (0.733) |
1 (1.00) |
21q gain | 8 (4%) | 183 |
1e-05 (0.00024) |
0.112 (0.218) |
0.125 (0.239) |
0.525 (0.682) |
0.0829 (0.177) |
0.412 (0.582) |
3p loss | 3 (2%) | 188 |
0.00662 (0.0259) |
0.211 (0.349) |
0.788 (0.923) |
1 (1.00) |
0.0611 (0.141) |
0.0926 (0.185) |
3q loss | 3 (2%) | 188 |
0.0063 (0.0257) |
0.21 (0.349) |
0.788 (0.923) |
1 (1.00) |
0.0622 (0.142) |
0.0922 (0.185) |
12p loss | 4 (2%) | 187 |
0.00591 (0.0252) |
0.431 (0.597) |
0.376 (0.538) |
0.39 (0.554) |
0.481 (0.634) |
0.186 (0.326) |
18q loss | 4 (2%) | 187 |
0.00118 (0.00906) |
0.0566 (0.132) |
0.467 (0.625) |
0.865 (0.962) |
0.101 (0.2) |
0.183 (0.326) |
19p loss | 4 (2%) | 187 |
0.00318 (0.018) |
0.432 (0.597) |
0.469 (0.625) |
0.864 (0.962) |
0.31 (0.464) |
0.246 (0.386) |
19q loss | 4 (2%) | 187 |
0.003 (0.0175) |
0.436 (0.598) |
0.468 (0.625) |
0.863 (0.962) |
0.311 (0.464) |
0.252 (0.386) |
P value = 0.00441 (Fisher's exact test), Q value = 0.021
Table S1. Gene #1: '1p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
1P GAIN MUTATED | 0 | 2 | 1 | 0 |
1P GAIN WILD-TYPE | 148 | 12 | 26 | 2 |
Figure S1. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D1V1.png)
P value = 0.0294 (Fisher's exact test), Q value = 0.08
Table S2. Gene #2: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
4P GAIN MUTATED | 1 | 0 | 3 | 0 |
4P GAIN WILD-TYPE | 147 | 14 | 24 | 2 |
Figure S2. Get High-res Image Gene #2: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D2V1.png)
P value = 0.00755 (Fisher's exact test), Q value = 0.027
Table S3. Gene #2: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 33 | 61 | 47 | 44 |
4P GAIN MUTATED | 0 | 0 | 4 | 0 |
4P GAIN WILD-TYPE | 33 | 61 | 43 | 44 |
Figure S3. Get High-res Image Gene #2: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D2V2.png)
P value = 0.0292 (Fisher's exact test), Q value = 0.08
Table S4. Gene #3: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
4Q GAIN MUTATED | 1 | 0 | 3 | 0 |
4Q GAIN WILD-TYPE | 147 | 14 | 24 | 2 |
Figure S4. Get High-res Image Gene #3: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D3V1.png)
P value = 0.0074 (Fisher's exact test), Q value = 0.027
Table S5. Gene #3: '4q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 33 | 61 | 47 | 44 |
4Q GAIN MUTATED | 0 | 0 | 4 | 0 |
4Q GAIN WILD-TYPE | 33 | 61 | 43 | 44 |
Figure S5. Get High-res Image Gene #3: '4q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D3V2.png)
P value = 0.00091 (Fisher's exact test), Q value = 0.0079
Table S6. Gene #4: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
8P GAIN MUTATED | 11 | 1 | 10 | 0 |
8P GAIN WILD-TYPE | 137 | 13 | 17 | 2 |
Figure S6. Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D4V1.png)
P value = 0.00025 (Fisher's exact test), Q value = 0.0032
Table S7. Gene #4: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 33 | 61 | 47 | 44 |
8P GAIN MUTATED | 1 | 16 | 3 | 1 |
8P GAIN WILD-TYPE | 32 | 45 | 44 | 43 |
Figure S7. Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D4V2.png)
P value = 0.0287 (Fisher's exact test), Q value = 0.08
Table S8. Gene #4: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 70 | 52 | 44 |
8P GAIN MUTATED | 13 | 2 | 3 |
8P GAIN WILD-TYPE | 57 | 50 | 41 |
Figure S8. Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D4V3.png)
P value = 0.00084 (Fisher's exact test), Q value = 0.0079
Table S9. Gene #4: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 16 | 13 | 14 | 55 | 26 | 42 |
8P GAIN MUTATED | 1 | 0 | 0 | 15 | 1 | 1 |
8P GAIN WILD-TYPE | 15 | 13 | 14 | 40 | 25 | 41 |
Figure S9. Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
![](D4V4.png)
P value = 0.00981 (Fisher's exact test), Q value = 0.035
Table S10. Gene #4: '8p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 37 | 41 | 43 |
8P GAIN MUTATED | 2 | 9 | 3 | 7 |
8P GAIN WILD-TYPE | 56 | 28 | 38 | 36 |
Figure S10. Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
![](D4V5.png)
P value = 0.0163 (Fisher's exact test), Q value = 0.05
Table S11. Gene #4: '8p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 34 | 78 |
8P GAIN MUTATED | 3 | 8 | 10 |
8P GAIN WILD-TYPE | 64 | 26 | 68 |
Figure S11. Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D4V6.png)
P value = 0.00147 (Fisher's exact test), Q value = 0.01
Table S12. Gene #5: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
8Q GAIN MUTATED | 12 | 1 | 10 | 0 |
8Q GAIN WILD-TYPE | 136 | 13 | 17 | 2 |
Figure S12. Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D5V1.png)
P value = 0.00039 (Fisher's exact test), Q value = 0.0045
Table S13. Gene #5: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 33 | 61 | 47 | 44 |
8Q GAIN MUTATED | 1 | 16 | 4 | 1 |
8Q GAIN WILD-TYPE | 32 | 45 | 43 | 43 |
Figure S13. Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D5V2.png)
P value = 0.0135 (Fisher's exact test), Q value = 0.045
Table S14. Gene #5: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 70 | 52 | 44 |
8Q GAIN MUTATED | 14 | 2 | 3 |
8Q GAIN WILD-TYPE | 56 | 50 | 41 |
Figure S14. Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D5V3.png)
P value = 0.00184 (Fisher's exact test), Q value = 0.011
Table S15. Gene #5: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 16 | 13 | 14 | 55 | 26 | 42 |
8Q GAIN MUTATED | 1 | 0 | 1 | 15 | 1 | 1 |
8Q GAIN WILD-TYPE | 15 | 13 | 13 | 40 | 25 | 41 |
Figure S15. Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
![](D5V4.png)
P value = 0.00711 (Fisher's exact test), Q value = 0.027
Table S16. Gene #5: '8q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 37 | 41 | 43 |
8Q GAIN MUTATED | 2 | 9 | 3 | 8 |
8Q GAIN WILD-TYPE | 56 | 28 | 38 | 35 |
Figure S16. Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
![](D5V5.png)
P value = 0.0145 (Fisher's exact test), Q value = 0.046
Table S17. Gene #5: '8q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 34 | 78 |
8Q GAIN MUTATED | 3 | 8 | 11 |
8Q GAIN WILD-TYPE | 64 | 26 | 67 |
Figure S17. Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D5V6.png)
P value = 0.0148 (Fisher's exact test), Q value = 0.046
Table S18. Gene #6: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
10Q GAIN MUTATED | 0 | 1 | 2 | 0 |
10Q GAIN WILD-TYPE | 148 | 13 | 25 | 2 |
Figure S18. Get High-res Image Gene #6: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D6V1.png)
P value = 7e-04 (Fisher's exact test), Q value = 0.0075
Table S19. Gene #7: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
11P GAIN MUTATED | 0 | 3 | 1 | 0 |
11P GAIN WILD-TYPE | 148 | 11 | 26 | 2 |
Figure S19. Get High-res Image Gene #7: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D7V1.png)
P value = 0.0221 (Fisher's exact test), Q value = 0.064
Table S20. Gene #7: '11p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 34 | 78 |
11P GAIN MUTATED | 0 | 3 | 1 |
11P GAIN WILD-TYPE | 67 | 31 | 77 |
Figure S20. Get High-res Image Gene #7: '11p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D7V6.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00024
Table S21. Gene #8: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
11Q GAIN MUTATED | 0 | 4 | 3 | 0 |
11Q GAIN WILD-TYPE | 148 | 10 | 24 | 2 |
Figure S21. Get High-res Image Gene #8: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D8V1.png)
P value = 0.0298 (Fisher's exact test), Q value = 0.08
Table S22. Gene #8: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 33 | 61 | 47 | 44 |
11Q GAIN MUTATED | 0 | 6 | 1 | 0 |
11Q GAIN WILD-TYPE | 33 | 55 | 46 | 44 |
Figure S22. Get High-res Image Gene #8: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D8V2.png)
P value = 0.0149 (Fisher's exact test), Q value = 0.046
Table S23. Gene #8: '11q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 34 | 78 |
11Q GAIN MUTATED | 0 | 4 | 3 |
11Q GAIN WILD-TYPE | 67 | 30 | 75 |
Figure S23. Get High-res Image Gene #8: '11q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D8V6.png)
P value = 0.0418 (Fisher's exact test), Q value = 0.11
Table S24. Gene #9: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
13Q GAIN MUTATED | 2 | 1 | 3 | 0 |
13Q GAIN WILD-TYPE | 146 | 13 | 24 | 2 |
Figure S24. Get High-res Image Gene #9: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D9V1.png)
P value = 0.00655 (Fisher's exact test), Q value = 0.026
Table S25. Gene #9: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 33 | 61 | 47 | 44 |
13Q GAIN MUTATED | 0 | 6 | 0 | 0 |
13Q GAIN WILD-TYPE | 33 | 55 | 47 | 44 |
Figure S25. Get High-res Image Gene #9: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D9V2.png)
P value = 0.00626 (Fisher's exact test), Q value = 0.026
Table S26. Gene #10: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
17Q GAIN MUTATED | 0 | 0 | 3 | 0 |
17Q GAIN WILD-TYPE | 148 | 14 | 24 | 2 |
Figure S26. Get High-res Image Gene #10: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D10V1.png)
P value = 0.0141 (Fisher's exact test), Q value = 0.046
Table S27. Gene #11: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
19P GAIN MUTATED | 1 | 1 | 3 | 0 |
19P GAIN WILD-TYPE | 147 | 13 | 24 | 2 |
Figure S27. Get High-res Image Gene #11: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D11V1.png)
P value = 0.0126 (Fisher's exact test), Q value = 0.044
Table S28. Gene #12: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
19Q GAIN MUTATED | 1 | 1 | 3 | 0 |
19Q GAIN WILD-TYPE | 147 | 13 | 24 | 2 |
Figure S28. Get High-res Image Gene #12: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D12V1.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00024
Table S29. Gene #13: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
21Q GAIN MUTATED | 0 | 0 | 8 | 0 |
21Q GAIN WILD-TYPE | 148 | 14 | 19 | 2 |
Figure S29. Get High-res Image Gene #13: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D13V1.png)
P value = 0.00095 (Fisher's exact test), Q value = 0.0079
Table S30. Gene #14: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
22Q GAIN MUTATED | 2 | 2 | 5 | 0 |
22Q GAIN WILD-TYPE | 146 | 12 | 22 | 2 |
Figure S30. Get High-res Image Gene #14: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D14V1.png)
P value = 0.00425 (Fisher's exact test), Q value = 0.02
Table S31. Gene #14: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 33 | 61 | 47 | 44 |
22Q GAIN MUTATED | 0 | 8 | 1 | 0 |
22Q GAIN WILD-TYPE | 33 | 53 | 46 | 44 |
Figure S31. Get High-res Image Gene #14: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D14V2.png)
P value = 0.0168 (Fisher's exact test), Q value = 0.05
Table S32. Gene #14: '22q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 16 | 13 | 14 | 55 | 26 | 42 |
22Q GAIN MUTATED | 0 | 1 | 0 | 8 | 0 | 0 |
22Q GAIN WILD-TYPE | 16 | 12 | 14 | 47 | 26 | 42 |
Figure S32. Get High-res Image Gene #14: '22q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
![](D14V4.png)
P value = 0.0132 (Fisher's exact test), Q value = 0.045
Table S33. Gene #14: '22q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 34 | 78 |
22Q GAIN MUTATED | 0 | 4 | 5 |
22Q GAIN WILD-TYPE | 67 | 30 | 73 |
Figure S33. Get High-res Image Gene #14: '22q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D14V6.png)
P value = 0.00183 (Fisher's exact test), Q value = 0.011
Table S34. Gene #15: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
XP GAIN MUTATED | 0 | 1 | 1 | 1 |
XP GAIN WILD-TYPE | 148 | 13 | 26 | 1 |
Figure S34. Get High-res Image Gene #15: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D15V1.png)
P value = 0.0468 (Fisher's exact test), Q value = 0.12
Table S35. Gene #15: 'xp gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 34 | 78 |
XP GAIN MUTATED | 1 | 2 | 0 |
XP GAIN WILD-TYPE | 66 | 32 | 78 |
Figure S35. Get High-res Image Gene #15: 'xp gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D15V6.png)
P value = 0.00159 (Fisher's exact test), Q value = 0.011
Table S36. Gene #16: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
XQ GAIN MUTATED | 0 | 1 | 1 | 1 |
XQ GAIN WILD-TYPE | 148 | 13 | 26 | 1 |
Figure S36. Get High-res Image Gene #16: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D16V1.png)
P value = 0.0469 (Fisher's exact test), Q value = 0.12
Table S37. Gene #16: 'xq gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 34 | 78 |
XQ GAIN MUTATED | 1 | 2 | 0 |
XQ GAIN WILD-TYPE | 66 | 32 | 78 |
Figure S37. Get High-res Image Gene #16: 'xq gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D16V6.png)
P value = 0.00662 (Fisher's exact test), Q value = 0.026
Table S38. Gene #17: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
3P LOSS MUTATED | 0 | 0 | 3 | 0 |
3P LOSS WILD-TYPE | 148 | 14 | 24 | 2 |
Figure S38. Get High-res Image Gene #17: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D17V1.png)
P value = 0.0063 (Fisher's exact test), Q value = 0.026
Table S39. Gene #18: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
3Q LOSS MUTATED | 0 | 0 | 3 | 0 |
3Q LOSS WILD-TYPE | 148 | 14 | 24 | 2 |
Figure S39. Get High-res Image Gene #18: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D18V1.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00024
Table S40. Gene #19: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
5Q LOSS MUTATED | 0 | 0 | 6 | 0 |
5Q LOSS WILD-TYPE | 148 | 14 | 21 | 2 |
Figure S40. Get High-res Image Gene #19: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D19V1.png)
P value = 0.00682 (Fisher's exact test), Q value = 0.026
Table S41. Gene #19: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 33 | 61 | 47 | 44 |
5Q LOSS MUTATED | 0 | 6 | 0 | 0 |
5Q LOSS WILD-TYPE | 33 | 55 | 47 | 44 |
Figure S41. Get High-res Image Gene #19: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D19V2.png)
P value = 0.0312 (Fisher's exact test), Q value = 0.082
Table S42. Gene #19: '5q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 37 | 41 | 43 |
5Q LOSS MUTATED | 0 | 3 | 2 | 0 |
5Q LOSS WILD-TYPE | 58 | 34 | 39 | 43 |
Figure S42. Get High-res Image Gene #19: '5q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
![](D19V5.png)
P value = 0.0327 (Fisher's exact test), Q value = 0.085
Table S43. Gene #19: '5q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 34 | 78 |
5Q LOSS MUTATED | 0 | 3 | 2 |
5Q LOSS WILD-TYPE | 67 | 31 | 76 |
Figure S43. Get High-res Image Gene #19: '5q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D19V6.png)
P value = 4e-05 (Fisher's exact test), Q value = 7e-04
Table S44. Gene #20: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
7P LOSS MUTATED | 7 | 0 | 9 | 1 |
7P LOSS WILD-TYPE | 141 | 14 | 18 | 1 |
Figure S44. Get High-res Image Gene #20: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D20V1.png)
P value = 0.00016 (Fisher's exact test), Q value = 0.0024
Table S45. Gene #20: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 33 | 61 | 47 | 44 |
7P LOSS MUTATED | 0 | 14 | 1 | 2 |
7P LOSS WILD-TYPE | 33 | 47 | 46 | 42 |
Figure S45. Get High-res Image Gene #20: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D20V2.png)
P value = 0.00095 (Fisher's exact test), Q value = 0.0079
Table S46. Gene #20: '7p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 70 | 52 | 44 |
7P LOSS MUTATED | 13 | 0 | 3 |
7P LOSS WILD-TYPE | 57 | 52 | 41 |
Figure S46. Get High-res Image Gene #20: '7p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D20V3.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00024
Table S47. Gene #20: '7p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 16 | 13 | 14 | 55 | 26 | 42 |
7P LOSS MUTATED | 0 | 0 | 0 | 16 | 0 | 0 |
7P LOSS WILD-TYPE | 16 | 13 | 14 | 39 | 26 | 42 |
Figure S47. Get High-res Image Gene #20: '7p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
![](D20V4.png)
P value = 0.00358 (Fisher's exact test), Q value = 0.018
Table S48. Gene #20: '7p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 37 | 41 | 43 |
7P LOSS MUTATED | 1 | 9 | 3 | 4 |
7P LOSS WILD-TYPE | 57 | 28 | 38 | 39 |
Figure S48. Get High-res Image Gene #20: '7p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
![](D20V5.png)
P value = 0.00339 (Fisher's exact test), Q value = 0.018
Table S49. Gene #20: '7p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 34 | 78 |
7P LOSS MUTATED | 1 | 7 | 9 |
7P LOSS WILD-TYPE | 66 | 27 | 69 |
Figure S49. Get High-res Image Gene #20: '7p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D20V6.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00024
Table S50. Gene #21: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
7Q LOSS MUTATED | 8 | 0 | 11 | 1 |
7Q LOSS WILD-TYPE | 140 | 14 | 16 | 1 |
Figure S50. Get High-res Image Gene #21: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D21V1.png)
P value = 2e-05 (Fisher's exact test), Q value = 0.00043
Table S51. Gene #21: '7q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 33 | 61 | 47 | 44 |
7Q LOSS MUTATED | 0 | 17 | 1 | 2 |
7Q LOSS WILD-TYPE | 33 | 44 | 46 | 42 |
Figure S51. Get High-res Image Gene #21: '7q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D21V2.png)
P value = 0.00585 (Fisher's exact test), Q value = 0.025
Table S52. Gene #21: '7q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 70 | 52 | 44 |
7Q LOSS MUTATED | 13 | 1 | 3 |
7Q LOSS WILD-TYPE | 57 | 51 | 41 |
Figure S52. Get High-res Image Gene #21: '7q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D21V3.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00024
Table S53. Gene #21: '7q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 16 | 13 | 14 | 55 | 26 | 42 |
7Q LOSS MUTATED | 0 | 0 | 0 | 17 | 0 | 0 |
7Q LOSS WILD-TYPE | 16 | 13 | 14 | 38 | 26 | 42 |
Figure S53. Get High-res Image Gene #21: '7q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
![](D21V4.png)
P value = 0.00143 (Fisher's exact test), Q value = 0.01
Table S54. Gene #21: '7q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 37 | 41 | 43 |
7Q LOSS MUTATED | 1 | 10 | 4 | 4 |
7Q LOSS WILD-TYPE | 57 | 27 | 37 | 39 |
Figure S54. Get High-res Image Gene #21: '7q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
![](D21V5.png)
P value = 0.00084 (Fisher's exact test), Q value = 0.0079
Table S55. Gene #21: '7q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 34 | 78 |
7Q LOSS MUTATED | 1 | 8 | 10 |
7Q LOSS WILD-TYPE | 66 | 26 | 68 |
Figure S55. Get High-res Image Gene #21: '7q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D21V6.png)
P value = 0.00591 (Fisher's exact test), Q value = 0.025
Table S56. Gene #22: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
12P LOSS MUTATED | 1 | 0 | 2 | 1 |
12P LOSS WILD-TYPE | 147 | 14 | 25 | 1 |
Figure S56. Get High-res Image Gene #22: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D22V1.png)
P value = 4e-04 (Fisher's exact test), Q value = 0.0045
Table S57. Gene #23: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
15Q LOSS MUTATED | 0 | 0 | 3 | 1 |
15Q LOSS WILD-TYPE | 148 | 14 | 24 | 1 |
Figure S57. Get High-res Image Gene #23: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D23V1.png)
P value = 0.0228 (Fisher's exact test), Q value = 0.064
Table S58. Gene #23: '15q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 37 | 41 | 43 |
15Q LOSS MUTATED | 0 | 3 | 0 | 1 |
15Q LOSS WILD-TYPE | 58 | 34 | 41 | 42 |
Figure S58. Get High-res Image Gene #23: '15q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
![](D23V5.png)
P value = 0.00108 (Fisher's exact test), Q value = 0.0086
Table S59. Gene #24: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
16Q LOSS MUTATED | 0 | 0 | 4 | 0 |
16Q LOSS WILD-TYPE | 148 | 14 | 23 | 2 |
Figure S59. Get High-res Image Gene #24: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D24V1.png)
P value = 0.0145 (Fisher's exact test), Q value = 0.046
Table S60. Gene #24: '16q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 37 | 41 | 43 |
16Q LOSS MUTATED | 0 | 3 | 1 | 0 |
16Q LOSS WILD-TYPE | 58 | 34 | 40 | 43 |
Figure S60. Get High-res Image Gene #24: '16q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
![](D24V5.png)
P value = 0.0224 (Fisher's exact test), Q value = 0.064
Table S61. Gene #24: '16q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 34 | 78 |
16Q LOSS MUTATED | 0 | 3 | 1 |
16Q LOSS WILD-TYPE | 67 | 31 | 77 |
Figure S61. Get High-res Image Gene #24: '16q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D24V6.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00024
Table S62. Gene #25: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
17P LOSS MUTATED | 0 | 0 | 13 | 0 |
17P LOSS WILD-TYPE | 148 | 14 | 14 | 2 |
Figure S62. Get High-res Image Gene #25: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D25V1.png)
P value = 0.00187 (Fisher's exact test), Q value = 0.011
Table S63. Gene #25: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 33 | 61 | 47 | 44 |
17P LOSS MUTATED | 0 | 10 | 3 | 0 |
17P LOSS WILD-TYPE | 33 | 51 | 44 | 44 |
Figure S63. Get High-res Image Gene #25: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D25V2.png)
P value = 0.00138 (Fisher's exact test), Q value = 0.01
Table S64. Gene #25: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 16 | 13 | 14 | 55 | 26 | 42 |
17P LOSS MUTATED | 0 | 0 | 0 | 12 | 0 | 1 |
17P LOSS WILD-TYPE | 16 | 13 | 14 | 43 | 26 | 41 |
Figure S64. Get High-res Image Gene #25: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
![](D25V4.png)
P value = 0.00385 (Fisher's exact test), Q value = 0.019
Table S65. Gene #25: '17p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 34 | 78 |
17P LOSS MUTATED | 0 | 4 | 9 |
17P LOSS WILD-TYPE | 67 | 30 | 69 |
Figure S65. Get High-res Image Gene #25: '17p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D25V6.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00024
Table S66. Gene #26: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
17Q LOSS MUTATED | 0 | 0 | 7 | 0 |
17Q LOSS WILD-TYPE | 148 | 14 | 20 | 2 |
Figure S66. Get High-res Image Gene #26: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D26V1.png)
P value = 0.0375 (Fisher's exact test), Q value = 0.096
Table S67. Gene #26: '17q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 37 | 41 | 43 |
17Q LOSS MUTATED | 0 | 4 | 1 | 2 |
17Q LOSS WILD-TYPE | 58 | 33 | 40 | 41 |
Figure S67. Get High-res Image Gene #26: '17q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
![](D26V5.png)
P value = 0.0491 (Fisher's exact test), Q value = 0.12
Table S68. Gene #26: '17q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 34 | 78 |
17Q LOSS MUTATED | 0 | 3 | 4 |
17Q LOSS WILD-TYPE | 67 | 31 | 74 |
Figure S68. Get High-res Image Gene #26: '17q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D26V6.png)
P value = 0.00018 (Fisher's exact test), Q value = 0.0025
Table S69. Gene #27: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
18P LOSS MUTATED | 0 | 0 | 5 | 0 |
18P LOSS WILD-TYPE | 148 | 14 | 22 | 2 |
Figure S69. Get High-res Image Gene #27: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D27V1.png)
P value = 0.0207 (Fisher's exact test), Q value = 0.061
Table S70. Gene #27: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 33 | 61 | 47 | 44 |
18P LOSS MUTATED | 0 | 5 | 0 | 0 |
18P LOSS WILD-TYPE | 33 | 56 | 47 | 44 |
Figure S70. Get High-res Image Gene #27: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D27V2.png)
P value = 0.00118 (Fisher's exact test), Q value = 0.0091
Table S71. Gene #28: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
18Q LOSS MUTATED | 0 | 0 | 4 | 0 |
18Q LOSS WILD-TYPE | 148 | 14 | 23 | 2 |
Figure S71. Get High-res Image Gene #28: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D28V1.png)
P value = 0.00318 (Fisher's exact test), Q value = 0.018
Table S72. Gene #29: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
19P LOSS MUTATED | 0 | 1 | 3 | 0 |
19P LOSS WILD-TYPE | 148 | 13 | 24 | 2 |
Figure S72. Get High-res Image Gene #29: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D29V1.png)
P value = 0.003 (Fisher's exact test), Q value = 0.017
Table S73. Gene #30: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
19Q LOSS MUTATED | 0 | 1 | 3 | 0 |
19Q LOSS WILD-TYPE | 148 | 13 | 24 | 2 |
Figure S73. Get High-res Image Gene #30: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D30V1.png)
P value = 0.00012 (Fisher's exact test), Q value = 0.0019
Table S74. Gene #31: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
XP LOSS MUTATED | 0 | 0 | 4 | 1 |
XP LOSS WILD-TYPE | 148 | 14 | 23 | 1 |
Figure S74. Get High-res Image Gene #31: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D31V1.png)
P value = 0.00353 (Fisher's exact test), Q value = 0.018
Table S75. Gene #31: 'xp loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 37 | 41 | 43 |
XP LOSS MUTATED | 0 | 4 | 1 | 0 |
XP LOSS WILD-TYPE | 58 | 33 | 40 | 43 |
Figure S75. Get High-res Image Gene #31: 'xp loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
![](D31V5.png)
P value = 0.00501 (Fisher's exact test), Q value = 0.022
Table S76. Gene #31: 'xp loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 34 | 78 |
XP LOSS MUTATED | 0 | 4 | 1 |
XP LOSS WILD-TYPE | 67 | 30 | 77 |
Figure S76. Get High-res Image Gene #31: 'xp loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D31V6.png)
P value = 4e-05 (Fisher's exact test), Q value = 7e-04
Table S77. Gene #32: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
XQ LOSS MUTATED | 0 | 0 | 4 | 1 |
XQ LOSS WILD-TYPE | 148 | 14 | 23 | 1 |
Figure S77. Get High-res Image Gene #32: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D32V1.png)
P value = 0.0033 (Fisher's exact test), Q value = 0.018
Table S78. Gene #32: 'xq loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 37 | 41 | 43 |
XQ LOSS MUTATED | 0 | 4 | 1 | 0 |
XQ LOSS WILD-TYPE | 58 | 33 | 40 | 43 |
Figure S78. Get High-res Image Gene #32: 'xq loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
![](D32V5.png)
P value = 0.0048 (Fisher's exact test), Q value = 0.022
Table S79. Gene #32: 'xq loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 34 | 78 |
XQ LOSS MUTATED | 0 | 4 | 1 |
XQ LOSS WILD-TYPE | 67 | 30 | 77 |
Figure S79. Get High-res Image Gene #32: 'xq loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D32V6.png)
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Copy number data file = broad_values_by_arm.txt from GISTIC pipeline
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Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LAML-TB/15087096/transformed.cor.cli.txt
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Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LAML-TB/15098833/LAML-TB.transferedmergedcluster.txt
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Number of patients = 191
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Number of significantly arm-level cnvs = 32
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Number of molecular subtypes = 6
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Exclude genes that fewer than K tumors have mutations, K = 3
For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.