This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.
Testing the association between copy number variation 40 focal events and 10 molecular subtypes across 48 patients, 6 significant findings detected with P value < 0.05 and Q value < 0.25.
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amp_2p16.1 cnv correlated to 'METHLYATION_CNMF'.
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amp_3q29 cnv correlated to 'CN_CNMF'.
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amp_7p22.3 cnv correlated to 'CN_CNMF'.
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amp_7q21.3 cnv correlated to 'CN_CNMF'.
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del_6q14.1 cnv correlated to 'MIRSEQ_MATURE_CNMF'.
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del_17p13.1 cnv correlated to 'CN_CNMF'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 40 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 6 significant findings detected.
Clinical Features |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
||
nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
amp 2p16 1 | 16 (33%) | 32 |
0.124 (0.728) |
0.000509 (0.0678) |
0.266 (0.97) |
0.272 (0.97) |
0.686 (1.00) |
0.75 (1.00) |
0.0581 (0.581) |
0.012 (0.37) |
0.335 (0.977) |
0.471 (1.00) |
amp 3q29 | 15 (31%) | 33 |
0.00324 (0.216) |
0.212 (0.919) |
0.697 (1.00) |
0.109 (0.727) |
0.655 (1.00) |
1 (1.00) |
0.882 (1.00) |
0.296 (0.977) |
1 (1.00) |
0.205 (0.919) |
amp 7p22 3 | 16 (33%) | 32 |
7.62e-05 (0.0152) |
0.359 (0.982) |
0.699 (1.00) |
0.762 (1.00) |
1 (1.00) |
0.654 (1.00) |
0.926 (1.00) |
0.886 (1.00) |
1 (1.00) |
0.123 (0.728) |
amp 7q21 3 | 15 (31%) | 33 |
1.04e-05 (0.00416) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.67 (1.00) |
0.121 (0.728) |
0.514 (1.00) |
0.888 (1.00) |
0.742 (1.00) |
0.444 (1.00) |
del 6q14 1 | 17 (35%) | 31 |
0.221 (0.919) |
0.547 (1.00) |
0.469 (1.00) |
0.519 (1.00) |
0.435 (1.00) |
0.326 (0.977) |
0.195 (0.904) |
0.176 (0.868) |
0.00321 (0.216) |
0.119 (0.728) |
del 17p13 1 | 13 (27%) | 35 |
0.00227 (0.216) |
0.517 (1.00) |
0.697 (1.00) |
0.885 (1.00) |
1 (1.00) |
1 (1.00) |
0.647 (1.00) |
0.509 (1.00) |
1 (1.00) |
0.61 (1.00) |
amp 1q24 2 | 16 (33%) | 32 |
0.00524 (0.297) |
1 (1.00) |
0.697 (1.00) |
0.507 (1.00) |
0.41 (1.00) |
0.226 (0.929) |
0.775 (1.00) |
0.459 (1.00) |
1 (1.00) |
1 (1.00) |
amp 3q27 3 | 14 (29%) | 34 |
0.008 (0.297) |
0.341 (0.977) |
1 (1.00) |
0.252 (0.959) |
0.396 (1.00) |
0.718 (1.00) |
0.712 (1.00) |
0.292 (0.977) |
0.516 (1.00) |
0.373 (0.982) |
amp 5p13 1 | 8 (17%) | 40 |
1 (1.00) |
0.701 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.452 (1.00) |
0.587 (1.00) |
0.673 (1.00) |
0.187 (0.896) |
|
amp 8q24 23 | 14 (29%) | 34 |
1 (1.00) |
0.752 (1.00) |
0.448 (1.00) |
0.783 (1.00) |
0.639 (1.00) |
0.679 (1.00) |
0.491 (1.00) |
0.197 (0.904) |
0.726 (1.00) |
0.344 (0.977) |
amp 12q21 1 | 14 (29%) | 34 |
0.517 (1.00) |
0.0243 (0.471) |
1 (1.00) |
0.717 (1.00) |
1 (1.00) |
0.123 (0.728) |
0.682 (1.00) |
0.0726 (0.618) |
0.323 (0.977) |
0.726 (1.00) |
amp 16p12 2 | 10 (21%) | 38 |
0.00818 (0.297) |
0.0723 (0.618) |
1 (1.00) |
0.861 (1.00) |
0.173 (0.867) |
0.343 (0.977) |
0.0685 (0.618) |
0.0486 (0.549) |
1 (1.00) |
0.614 (1.00) |
amp 18q21 2 | 16 (33%) | 32 |
0.0306 (0.471) |
0.76 (1.00) |
0.266 (0.97) |
0.719 (1.00) |
0.655 (1.00) |
1 (1.00) |
0.216 (0.919) |
0.0287 (0.471) |
0.335 (0.977) |
0.113 (0.727) |
amp 19q13 43 | 10 (21%) | 38 |
1 (1.00) |
0.286 (0.977) |
1 (1.00) |
1 (1.00) |
0.583 (1.00) |
1 (1.00) |
0.267 (0.97) |
0.278 (0.976) |
0.709 (1.00) |
0.0551 (0.575) |
amp xq27 3 | 7 (15%) | 41 |
0.0967 (0.694) |
0.0971 (0.694) |
0.665 (1.00) |
0.442 (1.00) |
0.655 (1.00) |
0.704 (1.00) |
0.329 (0.977) |
0.0805 (0.644) |
0.682 (1.00) |
0.33 (0.977) |
del 1p36 32 | 11 (23%) | 37 |
0.0155 (0.414) |
1 (1.00) |
0.674 (1.00) |
0.547 (1.00) |
1 (1.00) |
0.515 (1.00) |
0.551 (1.00) |
0.703 (1.00) |
1 (1.00) |
0.436 (1.00) |
del 1p13 1 | 12 (25%) | 36 |
0.501 (1.00) |
0.74 (1.00) |
0.674 (1.00) |
0.345 (0.977) |
0.67 (1.00) |
0.274 (0.97) |
0.56 (1.00) |
0.765 (1.00) |
1 (1.00) |
0.575 (1.00) |
del 1q43 | 10 (21%) | 38 |
0.0363 (0.519) |
0.724 (1.00) |
0.101 (0.712) |
0.0468 (0.549) |
1 (1.00) |
1 (1.00) |
0.714 (1.00) |
0.842 (1.00) |
1 (1.00) |
0.611 (1.00) |
del 2q23 1 | 8 (17%) | 40 |
0.236 (0.929) |
1 (1.00) |
0.152 (0.817) |
0.133 (0.76) |
1 (1.00) |
0.516 (1.00) |
0.779 (1.00) |
0.524 (1.00) |
0.673 (1.00) |
0.619 (1.00) |
del 3p21 31 | 8 (17%) | 40 |
0.451 (1.00) |
0.701 (1.00) |
1 (1.00) |
0.709 (1.00) |
0.484 (1.00) |
0.237 (0.929) |
0.777 (1.00) |
0.214 (0.919) |
0.443 (1.00) |
|
del 4q35 1 | 10 (21%) | 38 |
0.487 (1.00) |
0.724 (1.00) |
0.674 (1.00) |
0.349 (0.977) |
0.639 (1.00) |
0.545 (1.00) |
0.346 (0.977) |
0.153 (0.817) |
0.149 (0.817) |
0.37 (0.982) |
del 5q33 3 | 4 (8%) | 44 |
0.286 (0.977) |
0.609 (1.00) |
0.489 (1.00) |
1 (1.00) |
0.0341 (0.505) |
0.257 (0.963) |
0.00778 (0.297) |
0.313 (0.977) |
0.743 (1.00) |
|
del 6p21 32 | 6 (12%) | 42 |
1 (1.00) |
1 (1.00) |
0.308 (0.977) |
0.219 (0.919) |
0.583 (1.00) |
0.76 (1.00) |
0.698 (1.00) |
0.523 (1.00) |
0.644 (1.00) |
0.329 (0.977) |
del 6q22 32 | 16 (33%) | 32 |
0.759 (1.00) |
0.0305 (0.471) |
0.722 (1.00) |
0.889 (1.00) |
0.396 (1.00) |
0.388 (1.00) |
0.372 (0.982) |
0.369 (0.982) |
0.0494 (0.549) |
0.11 (0.727) |
del 6q23 3 | 16 (33%) | 32 |
1 (1.00) |
0.0305 (0.471) |
0.0696 (0.618) |
0.0767 (0.64) |
0.0836 (0.655) |
0.0221 (0.471) |
0.173 (0.867) |
0.167 (0.859) |
0.0231 (0.471) |
0.258 (0.963) |
del 7q33 | 5 (10%) | 43 |
0.372 (0.982) |
1 (1.00) |
1 (1.00) |
0.464 (1.00) |
0.432 (1.00) |
0.179 (0.875) |
0.644 (1.00) |
0.347 (0.977) |
||
del 8p23 2 | 12 (25%) | 36 |
0.00616 (0.297) |
0.74 (1.00) |
0.239 (0.93) |
0.508 (1.00) |
0.311 (0.977) |
0.358 (0.982) |
0.599 (1.00) |
0.0801 (0.644) |
0.707 (1.00) |
0.926 (1.00) |
del 8q12 1 | 9 (19%) | 39 |
0.127 (0.738) |
0.461 (1.00) |
0.0701 (0.618) |
0.042 (0.549) |
0.311 (0.977) |
0.356 (0.982) |
0.5 (1.00) |
0.408 (1.00) |
1 (1.00) |
0.578 (1.00) |
del 9p21 3 | 17 (35%) | 31 |
0.221 (0.919) |
0.0145 (0.414) |
1 (1.00) |
0.712 (1.00) |
0.114 (0.727) |
0.326 (0.977) |
0.00918 (0.306) |
0.0283 (0.471) |
0.0547 (0.575) |
0.109 (0.727) |
del 10q23 31 | 8 (17%) | 40 |
0.236 (0.929) |
1 (1.00) |
1 (1.00) |
0.769 (1.00) |
0.639 (1.00) |
0.0395 (0.546) |
0.061 (0.595) |
0.678 (1.00) |
0.428 (1.00) |
0.0242 (0.471) |
del 12p13 2 | 8 (17%) | 40 |
0.0446 (0.549) |
0.701 (1.00) |
1 (1.00) |
0.814 (1.00) |
1 (1.00) |
1 (1.00) |
0.66 (1.00) |
0.955 (1.00) |
1 (1.00) |
0.844 (1.00) |
del 13q14 2 | 7 (15%) | 41 |
0.0967 (0.694) |
0.416 (1.00) |
1 (1.00) |
0.274 (0.97) |
1 (1.00) |
0.762 (1.00) |
0.188 (0.896) |
0.251 (0.959) |
1 (1.00) |
0.653 (1.00) |
del 15q21 1 | 13 (27%) | 35 |
0.741 (1.00) |
0.517 (1.00) |
0.413 (1.00) |
0.733 (1.00) |
1 (1.00) |
0.657 (1.00) |
0.489 (1.00) |
0.665 (1.00) |
0.726 (1.00) |
0.33 (0.977) |
del 16p13 13 | 6 (12%) | 42 |
0.197 (0.904) |
0.666 (1.00) |
0.665 (1.00) |
0.15 (0.817) |
0.311 (0.977) |
0.808 (1.00) |
0.325 (0.977) |
0.0291 (0.471) |
0.613 (1.00) |
0.629 (1.00) |
del 16q23 1 | 5 (10%) | 43 |
0.0724 (0.618) |
1 (1.00) |
0.308 (0.977) |
0.365 (0.982) |
0.639 (1.00) |
0.449 (1.00) |
0.0903 (0.694) |
0.166 (0.859) |
0.114 (0.727) |
0.759 (1.00) |
del 17q24 1 | 8 (17%) | 40 |
0.236 (0.929) |
0.0479 (0.549) |
0.346 (0.977) |
0.167 (0.859) |
1 (1.00) |
0.0434 (0.549) |
0.638 (1.00) |
0.0299 (0.471) |
0.214 (0.919) |
0.149 (0.817) |
del 19p13 2 | 4 (8%) | 44 |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.484 (1.00) |
1 (1.00) |
0.43 (1.00) |
1 (1.00) |
0.663 (1.00) |
||
del 19q13 2 | 5 (10%) | 43 |
1 (1.00) |
0.348 (0.977) |
0.489 (1.00) |
0.484 (1.00) |
1 (1.00) |
0.661 (1.00) |
0.581 (1.00) |
0.725 (1.00) |
||
del 22q13 31 | 7 (15%) | 41 |
0.0967 (0.694) |
1 (1.00) |
1 (1.00) |
0.838 (1.00) |
1 (1.00) |
1 (1.00) |
0.949 (1.00) |
0.906 (1.00) |
1 (1.00) |
0.618 (1.00) |
del xq28 | 3 (6%) | 45 |
0.056 (0.575) |
0.234 (0.929) |
0.199 (0.904) |
0.464 (1.00) |
0.477 (1.00) |
0.441 (1.00) |
1 (1.00) |
P value = 0.000509 (Fisher's exact test), Q value = 0.068
Table S1. Gene #2: 'amp_2p16.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 |
---|---|---|
ALL | 24 | 24 |
AMP PEAK 2(2P16.1) MUTATED | 2 | 14 |
AMP PEAK 2(2P16.1) WILD-TYPE | 22 | 10 |
Figure S1. Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D2V2.png)
P value = 0.00324 (Fisher's exact test), Q value = 0.22
Table S2. Gene #4: 'amp_3q29' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 |
---|---|---|
ALL | 29 | 19 |
AMP PEAK 4(3Q29) MUTATED | 4 | 11 |
AMP PEAK 4(3Q29) WILD-TYPE | 25 | 8 |
Figure S2. Get High-res Image Gene #4: 'amp_3q29' versus Molecular Subtype #1: 'CN_CNMF'
![](D4V1.png)
P value = 7.62e-05 (Fisher's exact test), Q value = 0.015
Table S3. Gene #6: 'amp_7p22.3' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 |
---|---|---|
ALL | 29 | 19 |
AMP PEAK 6(7P22.3) MUTATED | 3 | 13 |
AMP PEAK 6(7P22.3) WILD-TYPE | 26 | 6 |
Figure S3. Get High-res Image Gene #6: 'amp_7p22.3' versus Molecular Subtype #1: 'CN_CNMF'
![](D6V1.png)
P value = 1.04e-05 (Fisher's exact test), Q value = 0.0042
Table S4. Gene #7: 'amp_7q21.3' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 |
---|---|---|
ALL | 29 | 19 |
AMP PEAK 7(7Q21.3) MUTATED | 2 | 13 |
AMP PEAK 7(7Q21.3) WILD-TYPE | 27 | 6 |
Figure S4. Get High-res Image Gene #7: 'amp_7q21.3' versus Molecular Subtype #1: 'CN_CNMF'
![](D7V1.png)
P value = 0.00321 (Fisher's exact test), Q value = 0.22
Table S5. Gene #22: 'del_6q14.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 |
---|---|---|
ALL | 19 | 23 |
DEL PEAK 9(6Q14.1) MUTATED | 11 | 3 |
DEL PEAK 9(6Q14.1) WILD-TYPE | 8 | 20 |
Figure S5. Get High-res Image Gene #22: 'del_6q14.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
![](D22V9.png)
P value = 0.00227 (Fisher's exact test), Q value = 0.22
Table S6. Gene #35: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 |
---|---|---|
ALL | 29 | 19 |
DEL PEAK 22(17P13.1) MUTATED | 3 | 10 |
DEL PEAK 22(17P13.1) WILD-TYPE | 26 | 9 |
Figure S6. Get High-res Image Gene #35: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'
![](D35V1.png)
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Copy number data file = all_lesions.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/DLBC-TP/20146394/transformed.cor.cli.txt
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Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/DLBC-TP/20125263/DLBC-TP.transferedmergedcluster.txt
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Number of patients = 48
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Number of significantly focal cnvs = 40
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Number of molecular subtypes = 10
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Exclude genes that fewer than K tumors have alterations, K = 3
For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.
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.