This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and subtypes.
Testing the association between copy number variation 22 arm-level results and 6 molecular subtypes across 191 patients, 20 significant findings detected with 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'.
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4q gain cnv correlated to 'CN_CNMF'.
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8p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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8q gain cnv correlated to 'CN_CNMF'.
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10q gain cnv correlated to 'CN_CNMF'.
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11p gain cnv correlated to 'CN_CNMF'.
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11q gain cnv correlated to 'CN_CNMF'.
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17q gain cnv correlated to 'CN_CNMF'.
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21q gain cnv correlated to 'CN_CNMF'.
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5q loss cnv correlated to 'CN_CNMF'.
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7p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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7q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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17p loss cnv correlated to 'CN_CNMF'.
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17q loss cnv correlated to 'CN_CNMF'.
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18p loss cnv correlated to 'CN_CNMF'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 22 arm-level results and 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 20 significant findings detected.
Molecular subtypes |
CN CNMF |
METHLYATION CNMF |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
||
nCNV (%) | nWild-Type | Chi-square test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
7q loss | 0 (0%) | 173 |
6.33e-08 (7.86e-06) |
9.23e-05 (0.0109) |
0.0272 (1.00) |
0.0211 (1.00) |
0.0122 (1.00) |
0.00099 (0.113) |
8p gain | 0 (0%) | 171 |
2.44e-05 (0.00295) |
0.00189 (0.21) |
0.0674 (1.00) |
0.0126 (1.00) |
0.0124 (1.00) |
0.157 (1.00) |
7p loss | 0 (0%) | 176 |
1.61e-06 (0.000198) |
0.0017 (0.191) |
0.00277 (0.297) |
0.00279 (0.297) |
0.0269 (1.00) |
0.00265 (0.286) |
1p gain | 0 (0%) | 188 |
0.00135 (0.153) |
0.185 (1.00) |
0.186 (1.00) |
0.552 (1.00) |
0.0923 (1.00) |
0.0481 (1.00) |
4p gain | 0 (0%) | 187 |
9.82e-05 (0.0115) |
0.0502 (1.00) |
0.55 (1.00) |
0.343 (1.00) |
0.831 (1.00) |
|
4q gain | 0 (0%) | 187 |
9.82e-05 (0.0115) |
0.0502 (1.00) |
0.55 (1.00) |
0.343 (1.00) |
0.831 (1.00) |
|
8q gain | 0 (0%) | 170 |
6.42e-05 (0.00764) |
0.00509 (0.509) |
0.0434 (1.00) |
0.0125 (1.00) |
0.00717 (0.695) |
0.223 (1.00) |
10q gain | 0 (0%) | 188 |
0.000979 (0.113) |
0.185 (1.00) |
0.186 (1.00) |
0.552 (1.00) |
0.552 (1.00) |
0.222 (1.00) |
11p gain | 0 (0%) | 187 |
3.32e-15 (4.29e-13) |
0.0808 (1.00) |
0.467 (1.00) |
1 (1.00) |
0.523 (1.00) |
0.0704 (1.00) |
11q gain | 0 (0%) | 184 |
9.42e-12 (1.21e-09) |
0.00516 (0.511) |
0.0668 (1.00) |
0.425 (1.00) |
0.291 (1.00) |
0.271 (1.00) |
17q gain | 0 (0%) | 188 |
6.81e-06 (0.000831) |
0.38 (1.00) |
1 (1.00) |
0.552 (1.00) |
0.482 (1.00) |
0.222 (1.00) |
21q gain | 0 (0%) | 183 |
2.62e-15 (3.41e-13) |
0.203 (1.00) |
0.124 (1.00) |
1 (1.00) |
0.0814 (1.00) |
0.198 (1.00) |
5q loss | 0 (0%) | 185 |
6.1e-11 (7.75e-09) |
0.0134 (1.00) |
0.224 (1.00) |
0.664 (1.00) |
0.0318 (1.00) |
0.0205 (1.00) |
17p loss | 0 (0%) | 181 |
2.2e-10 (2.77e-08) |
0.00255 (0.281) |
0.0752 (1.00) |
0.167 (1.00) |
0.00541 (0.53) |
0.00451 (0.456) |
17q loss | 0 (0%) | 186 |
4.94e-10 (6.18e-08) |
0.0335 (1.00) |
0.224 (1.00) |
0.664 (1.00) |
0.00335 (0.352) |
0.00258 (0.281) |
18p loss | 0 (0%) | 186 |
5.17e-05 (0.00621) |
0.0335 (1.00) |
1 (1.00) |
1 (1.00) |
0.248 (1.00) |
0.329 (1.00) |
13q gain | 0 (0%) | 188 |
0.00355 (0.369) |
0.185 (1.00) |
0.186 (1.00) |
0.552 (1.00) |
0.552 (1.00) |
0.222 (1.00) |
19p gain | 0 (0%) | 186 |
0.0342 (1.00) |
0.633 (1.00) |
1 (1.00) |
1 (1.00) |
0.651 (1.00) |
0.607 (1.00) |
19q gain | 0 (0%) | 186 |
0.0342 (1.00) |
0.633 (1.00) |
1 (1.00) |
1 (1.00) |
0.651 (1.00) |
0.607 (1.00) |
22q gain | 0 (0%) | 183 |
0.00406 (0.414) |
0.0206 (1.00) |
0.0349 (1.00) |
0.269 (1.00) |
0.0651 (1.00) |
0.0493 (1.00) |
12p loss | 0 (0%) | 188 |
0.0191 (1.00) |
0.0326 (1.00) |
0.618 (1.00) |
0.552 (1.00) |
0.793 (1.00) |
0.222 (1.00) |
18q loss | 0 (0%) | 188 |
0.00355 (0.369) |
0.185 (1.00) |
0.786 (1.00) |
1 (1.00) |
0.0618 (1.00) |
0.0481 (1.00) |
P value = 0.00135 (Chi-square test), Q value = 0.15
Table S1. Gene #1: '1p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
1P GAIN CNV | 0 | 2 | 0 | 1 | 0 |
1P GAIN WILD-TYPE | 142 | 13 | 15 | 17 | 1 |
Figure S1. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D1V1.png)
P value = 9.82e-05 (Chi-square test), Q value = 0.011
Table S2. Gene #2: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
4P GAIN CNV | 0 | 0 | 1 | 3 | 0 |
4P GAIN WILD-TYPE | 142 | 15 | 14 | 15 | 1 |
Figure S2. Get High-res Image Gene #2: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D2V1.png)
P value = 9.82e-05 (Chi-square test), Q value = 0.011
Table S3. Gene #3: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
4Q GAIN CNV | 0 | 0 | 1 | 3 | 0 |
4Q GAIN WILD-TYPE | 142 | 15 | 14 | 15 | 1 |
Figure S3. Get High-res Image Gene #3: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D3V1.png)
P value = 2.44e-05 (Chi-square test), Q value = 0.003
Table S4. Gene #4: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
8P GAIN CNV | 8 | 1 | 4 | 6 | 1 |
8P GAIN WILD-TYPE | 134 | 14 | 11 | 12 | 0 |
Figure S4. Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D4V1.png)
P value = 0.00189 (Chi-square test), Q value = 0.21
Table S5. Gene #4: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 46 | 44 | 61 | 14 | 20 |
8P GAIN CNV | 2 | 1 | 14 | 0 | 2 |
8P GAIN WILD-TYPE | 44 | 43 | 47 | 14 | 18 |
Figure S5. Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D4V2.png)
P value = 6.42e-05 (Chi-square test), Q value = 0.0076
Table S6. Gene #5: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
8Q GAIN CNV | 9 | 1 | 4 | 6 | 1 |
8Q GAIN WILD-TYPE | 133 | 14 | 11 | 12 | 0 |
Figure S6. Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D5V1.png)
P value = 0.000979 (Chi-square test), Q value = 0.11
Table S7. Gene #6: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
10Q GAIN CNV | 0 | 1 | 2 | 0 | 0 |
10Q GAIN WILD-TYPE | 142 | 14 | 13 | 18 | 1 |
Figure S7. Get High-res Image Gene #6: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D6V1.png)
P value = 3.32e-15 (Chi-square test), Q value = 4.3e-13
Table S8. Gene #7: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
11P GAIN CNV | 0 | 3 | 0 | 0 | 1 |
11P GAIN WILD-TYPE | 142 | 12 | 15 | 18 | 0 |
Figure S8. Get High-res Image Gene #7: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D7V1.png)
P value = 9.42e-12 (Chi-square test), Q value = 1.2e-09
Table S9. Gene #8: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
11Q GAIN CNV | 0 | 4 | 0 | 2 | 1 |
11Q GAIN WILD-TYPE | 142 | 11 | 15 | 16 | 0 |
Figure S9. Get High-res Image Gene #8: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D8V1.png)
P value = 6.81e-06 (Chi-square test), Q value = 0.00083
Table S10. Gene #10: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
17Q GAIN CNV | 0 | 0 | 0 | 3 | 0 |
17Q GAIN WILD-TYPE | 142 | 15 | 15 | 15 | 1 |
Figure S10. Get High-res Image Gene #10: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D10V1.png)
P value = 2.62e-15 (Chi-square test), Q value = 3.4e-13
Table S11. Gene #13: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
21Q GAIN CNV | 0 | 0 | 7 | 1 | 0 |
21Q GAIN WILD-TYPE | 142 | 15 | 8 | 17 | 1 |
Figure S11. Get High-res Image Gene #13: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D13V1.png)
P value = 6.1e-11 (Chi-square test), Q value = 7.7e-09
Table S12. Gene #15: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
5Q LOSS CNV | 0 | 0 | 3 | 2 | 1 |
5Q LOSS WILD-TYPE | 142 | 15 | 12 | 16 | 0 |
Figure S12. Get High-res Image Gene #15: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D15V1.png)
P value = 1.61e-06 (Chi-square test), Q value = 2e-04
Table S13. Gene #16: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
7P LOSS CNV | 6 | 0 | 2 | 6 | 1 |
7P LOSS WILD-TYPE | 136 | 15 | 13 | 12 | 0 |
Figure S13. Get High-res Image Gene #16: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D16V1.png)
P value = 0.0017 (Chi-square test), Q value = 0.19
Table S14. Gene #16: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 46 | 44 | 61 | 14 | 20 |
7P LOSS CNV | 1 | 0 | 12 | 1 | 1 |
7P LOSS WILD-TYPE | 45 | 44 | 49 | 13 | 19 |
Figure S14. Get High-res Image Gene #16: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D16V2.png)
P value = 6.33e-08 (Chi-square test), Q value = 7.9e-06
Table S15. Gene #17: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
7Q LOSS CNV | 6 | 0 | 4 | 7 | 1 |
7Q LOSS WILD-TYPE | 136 | 15 | 11 | 11 | 0 |
Figure S15. Get High-res Image Gene #17: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D17V1.png)
P value = 9.23e-05 (Chi-square test), Q value = 0.011
Table S16. Gene #17: '7q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 46 | 44 | 61 | 14 | 20 |
7Q LOSS CNV | 1 | 0 | 15 | 1 | 1 |
7Q LOSS WILD-TYPE | 45 | 44 | 46 | 13 | 19 |
Figure S16. Get High-res Image Gene #17: '7q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D17V2.png)
P value = 0.00099 (Fisher's exact test), Q value = 0.11
Table S17. Gene #17: '7q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 35 | 79 | 65 |
7Q LOSS CNV | 9 | 2 | 6 |
7Q LOSS WILD-TYPE | 26 | 77 | 59 |
Figure S17. Get High-res Image Gene #17: '7q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D17V6.png)
P value = 2.2e-10 (Chi-square test), Q value = 2.8e-08
Table S18. Gene #19: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
17P LOSS CNV | 0 | 1 | 3 | 5 | 1 |
17P LOSS WILD-TYPE | 142 | 14 | 12 | 13 | 0 |
Figure S18. Get High-res Image Gene #19: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D19V1.png)
P value = 4.94e-10 (Chi-square test), Q value = 6.2e-08
Table S19. Gene #20: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
17Q LOSS CNV | 0 | 1 | 2 | 1 | 1 |
17Q LOSS WILD-TYPE | 142 | 14 | 13 | 17 | 0 |
Figure S19. Get High-res Image Gene #20: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D20V1.png)
P value = 5.17e-05 (Chi-square test), Q value = 0.0062
Table S20. Gene #21: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 142 | 15 | 15 | 18 | 1 |
18P LOSS CNV | 0 | 0 | 2 | 3 | 0 |
18P LOSS WILD-TYPE | 142 | 15 | 13 | 15 | 1 |
Figure S20. Get High-res Image Gene #21: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D21V1.png)
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Mutation data file = broad_values_by_arm.mutsig.cluster.txt
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Molecular subtypes file = LAML-TB.transferedmergedcluster.txt
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Number of patients = 191
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Number of significantly arm-level cnvs = 22
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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 multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R
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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.