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 8 molecular subtypes across 171 patients, 10 significant findings detected with P value < 0.05 and Q value < 0.25.
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4p cnv correlated to 'CN_CNMF'.
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4q cnv correlated to 'CN_CNMF'.
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5p cnv correlated to 'CN_CNMF'.
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5q cnv correlated to 'CN_CNMF'.
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7q cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_MATURE_CNMF'.
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16q cnv correlated to 'MIRSEQ_CHIERARCHICAL'.
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17p cnv correlated to 'CN_CNMF'.
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19p cnv correlated to 'CN_CNMF'.
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19q cnv correlated to 'CN_CNMF'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 40 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, 10 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 | Chi-square test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
7q | 43 (25%) | 128 |
0.0123 (1.00) |
0.684 (1.00) |
0.416 (1.00) |
0.821 (1.00) |
0.000572 (0.178) |
0.399 (1.00) |
0.000326 (0.102) |
0.533 (1.00) |
4p | 73 (43%) | 98 |
1.47e-05 (0.00463) |
0.231 (1.00) |
0.704 (1.00) |
0.00218 (0.671) |
0.34 (1.00) |
0.335 (1.00) |
0.329 (1.00) |
0.183 (1.00) |
4q | 52 (30%) | 119 |
1.86e-05 (0.00587) |
0.501 (1.00) |
0.361 (1.00) |
0.141 (1.00) |
0.698 (1.00) |
0.0608 (1.00) |
0.377 (1.00) |
0.53 (1.00) |
5p | 69 (40%) | 102 |
7.6e-09 (2.43e-06) |
0.0584 (1.00) |
0.82 (1.00) |
0.223 (1.00) |
0.189 (1.00) |
0.438 (1.00) |
0.31 (1.00) |
0.598 (1.00) |
5q | 57 (33%) | 114 |
1.78e-08 (5.68e-06) |
0.0201 (1.00) |
0.946 (1.00) |
1 (1.00) |
0.191 (1.00) |
0.178 (1.00) |
0.219 (1.00) |
0.826 (1.00) |
16q | 44 (26%) | 127 |
0.289 (1.00) |
0.00863 (1.00) |
0.0813 (1.00) |
0.0188 (1.00) |
0.00975 (1.00) |
0.000267 (0.0835) |
0.0433 (1.00) |
0.00898 (1.00) |
17p | 60 (35%) | 111 |
6.59e-07 (0.00021) |
0.674 (1.00) |
0.532 (1.00) |
0.742 (1.00) |
0.61 (1.00) |
0.62 (1.00) |
0.259 (1.00) |
0.208 (1.00) |
19p | 56 (33%) | 115 |
3.94e-05 (0.0124) |
0.178 (1.00) |
0.251 (1.00) |
0.273 (1.00) |
0.0148 (1.00) |
0.109 (1.00) |
0.0266 (1.00) |
0.119 (1.00) |
19q | 55 (32%) | 116 |
4.45e-06 (0.00141) |
0.175 (1.00) |
0.693 (1.00) |
0.686 (1.00) |
0.0015 (0.463) |
0.272 (1.00) |
0.0143 (1.00) |
0.148 (1.00) |
1p | 61 (36%) | 110 |
0.382 (1.00) |
0.0952 (1.00) |
0.108 (1.00) |
0.167 (1.00) |
0.799 (1.00) |
0.693 (1.00) |
0.858 (1.00) |
0.532 (1.00) |
1q | 87 (51%) | 84 |
0.0341 (1.00) |
0.049 (1.00) |
0.268 (1.00) |
0.381 (1.00) |
1 (1.00) |
0.425 (1.00) |
0.724 (1.00) |
0.874 (1.00) |
2p | 45 (26%) | 126 |
0.00203 (0.624) |
0.0573 (1.00) |
0.384 (1.00) |
0.318 (1.00) |
0.118 (1.00) |
0.0283 (1.00) |
0.637 (1.00) |
0.294 (1.00) |
2q | 40 (23%) | 131 |
0.026 (1.00) |
0.123 (1.00) |
0.787 (1.00) |
0.852 (1.00) |
0.323 (1.00) |
0.27 (1.00) |
0.711 (1.00) |
0.729 (1.00) |
3p | 81 (47%) | 90 |
0.351 (1.00) |
0.346 (1.00) |
0.815 (1.00) |
0.0506 (1.00) |
0.107 (1.00) |
0.434 (1.00) |
0.00359 (1.00) |
0.0296 (1.00) |
3q | 108 (63%) | 63 |
0.0032 (0.972) |
0.0127 (1.00) |
0.0329 (1.00) |
0.00445 (1.00) |
0.363 (1.00) |
0.00487 (1.00) |
0.185 (1.00) |
0.00695 (1.00) |
6p | 55 (32%) | 116 |
0.275 (1.00) |
0.25 (1.00) |
0.315 (1.00) |
0.671 (1.00) |
0.932 (1.00) |
0.338 (1.00) |
0.738 (1.00) |
0.458 (1.00) |
6q | 59 (35%) | 112 |
0.149 (1.00) |
0.23 (1.00) |
0.346 (1.00) |
0.892 (1.00) |
0.795 (1.00) |
0.451 (1.00) |
0.476 (1.00) |
0.807 (1.00) |
7p | 34 (20%) | 137 |
0.0848 (1.00) |
0.6 (1.00) |
0.434 (1.00) |
0.712 (1.00) |
0.00538 (1.00) |
0.709 (1.00) |
0.00281 (0.861) |
0.618 (1.00) |
8p | 71 (42%) | 100 |
0.0193 (1.00) |
0.082 (1.00) |
0.501 (1.00) |
0.742 (1.00) |
0.889 (1.00) |
0.681 (1.00) |
1 (1.00) |
0.497 (1.00) |
8q | 59 (35%) | 112 |
0.0386 (1.00) |
0.308 (1.00) |
0.565 (1.00) |
0.244 (1.00) |
0.304 (1.00) |
0.0975 (1.00) |
0.535 (1.00) |
0.286 (1.00) |
9p | 58 (34%) | 113 |
0.0459 (1.00) |
0.953 (1.00) |
0.557 (1.00) |
0.704 (1.00) |
0.97 (1.00) |
0.453 (1.00) |
0.77 (1.00) |
1 (1.00) |
9q | 53 (31%) | 118 |
0.0555 (1.00) |
0.977 (1.00) |
0.305 (1.00) |
0.335 (1.00) |
0.897 (1.00) |
0.435 (1.00) |
0.706 (1.00) |
0.422 (1.00) |
10p | 50 (29%) | 121 |
0.026 (1.00) |
0.642 (1.00) |
0.39 (1.00) |
0.412 (1.00) |
0.545 (1.00) |
0.117 (1.00) |
0.706 (1.00) |
0.531 (1.00) |
10q | 51 (30%) | 120 |
0.0362 (1.00) |
0.465 (1.00) |
0.142 (1.00) |
0.221 (1.00) |
0.401 (1.00) |
0.0497 (1.00) |
0.329 (1.00) |
0.355 (1.00) |
11p | 58 (34%) | 113 |
0.0271 (1.00) |
0.361 (1.00) |
0.378 (1.00) |
0.421 (1.00) |
0.73 (1.00) |
0.231 (1.00) |
0.356 (1.00) |
0.675 (1.00) |
11q | 71 (42%) | 100 |
0.0038 (1.00) |
0.609 (1.00) |
0.852 (1.00) |
0.752 (1.00) |
0.57 (1.00) |
0.939 (1.00) |
0.582 (1.00) |
0.279 (1.00) |
12p | 51 (30%) | 120 |
0.00778 (1.00) |
0.601 (1.00) |
0.834 (1.00) |
0.51 (1.00) |
0.449 (1.00) |
0.69 (1.00) |
0.462 (1.00) |
0.746 (1.00) |
12q | 34 (20%) | 137 |
0.0453 (1.00) |
0.405 (1.00) |
0.0888 (1.00) |
0.636 (1.00) |
0.129 (1.00) |
0.607 (1.00) |
0.354 (1.00) |
0.67 (1.00) |
13q | 58 (34%) | 113 |
0.168 (1.00) |
0.296 (1.00) |
0.39 (1.00) |
0.122 (1.00) |
0.228 (1.00) |
0.556 (1.00) |
0.0626 (1.00) |
0.329 (1.00) |
14q | 44 (26%) | 127 |
0.0198 (1.00) |
0.458 (1.00) |
0.175 (1.00) |
0.0878 (1.00) |
0.101 (1.00) |
0.015 (1.00) |
0.069 (1.00) |
0.0786 (1.00) |
15q | 52 (30%) | 119 |
0.077 (1.00) |
0.576 (1.00) |
0.979 (1.00) |
0.219 (1.00) |
0.228 (1.00) |
0.164 (1.00) |
0.297 (1.00) |
0.859 (1.00) |
16p | 42 (25%) | 129 |
0.0916 (1.00) |
0.0762 (1.00) |
0.302 (1.00) |
0.181 (1.00) |
0.0077 (1.00) |
0.0143 (1.00) |
0.0416 (1.00) |
0.0862 (1.00) |
17q | 42 (25%) | 129 |
0.00525 (1.00) |
0.627 (1.00) |
0.375 (1.00) |
0.509 (1.00) |
0.453 (1.00) |
0.726 (1.00) |
0.736 (1.00) |
0.611 (1.00) |
18p | 53 (31%) | 118 |
0.0555 (1.00) |
0.966 (1.00) |
0.34 (1.00) |
1 (1.00) |
0.698 (1.00) |
0.673 (1.00) |
0.715 (1.00) |
1 (1.00) |
18q | 55 (32%) | 116 |
0.0429 (1.00) |
0.239 (1.00) |
0.00496 (1.00) |
0.151 (1.00) |
0.512 (1.00) |
0.0536 (1.00) |
0.476 (1.00) |
0.212 (1.00) |
20p | 67 (39%) | 104 |
0.00135 (0.418) |
0.0598 (1.00) |
0.204 (1.00) |
0.0476 (1.00) |
0.572 (1.00) |
0.0731 (1.00) |
0.428 (1.00) |
0.249 (1.00) |
20q | 67 (39%) | 104 |
0.0175 (1.00) |
0.0582 (1.00) |
0.404 (1.00) |
0.212 (1.00) |
0.809 (1.00) |
0.182 (1.00) |
0.645 (1.00) |
0.563 (1.00) |
21q | 51 (30%) | 120 |
0.0443 (1.00) |
0.823 (1.00) |
0.128 (1.00) |
0.39 (1.00) |
0.906 (1.00) |
1 (1.00) |
0.77 (1.00) |
0.887 (1.00) |
22q | 59 (35%) | 112 |
0.00721 (1.00) |
0.248 (1.00) |
0.273 (1.00) |
0.73 (1.00) |
0.0241 (1.00) |
0.128 (1.00) |
0.0487 (1.00) |
0.215 (1.00) |
xq | 59 (35%) | 112 |
0.533 (1.00) |
0.0192 (1.00) |
0.207 (1.00) |
0.0242 (1.00) |
0.00444 (1.00) |
0.118 (1.00) |
0.00298 (0.908) |
0.00974 (1.00) |
P value = 1.47e-05 (Fisher's exact test), Q value = 0.0046
Table S1. Gene #7: '4p' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 36 | 77 |
4P MUTATED | 27 | 26 | 20 |
4P WILD-TYPE | 31 | 10 | 57 |
Figure S1. Get High-res Image Gene #7: '4p' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1.86e-05 (Fisher's exact test), Q value = 0.0059
Table S2. Gene #8: '4q' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 36 | 77 |
4Q MUTATED | 17 | 22 | 13 |
4Q WILD-TYPE | 41 | 14 | 64 |
Figure S2. Get High-res Image Gene #8: '4q' versus Molecular Subtype #1: 'CN_CNMF'

P value = 7.6e-09 (Fisher's exact test), Q value = 2.4e-06
Table S3. Gene #9: '5p' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 36 | 77 |
5P MUTATED | 24 | 29 | 16 |
5P WILD-TYPE | 34 | 7 | 61 |
Figure S3. Get High-res Image Gene #9: '5p' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1.78e-08 (Fisher's exact test), Q value = 5.7e-06
Table S4. Gene #10: '5q' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 36 | 77 |
5Q MUTATED | 16 | 27 | 14 |
5Q WILD-TYPE | 42 | 9 | 63 |
Figure S4. Get High-res Image Gene #10: '5q' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.000572 (Fisher's exact test), Q value = 0.18
Table S5. Gene #14: '7q' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 57 | 44 | 54 |
7Q MUTATED | 22 | 3 | 16 |
7Q WILD-TYPE | 35 | 41 | 38 |
Figure S5. Get High-res Image Gene #14: '7q' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

P value = 0.000326 (Fisher's exact test), Q value = 0.1
Table S6. Gene #14: '7q' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 57 | 47 | 51 |
7Q MUTATED | 21 | 3 | 17 |
7Q WILD-TYPE | 36 | 44 | 34 |
Figure S6. Get High-res Image Gene #14: '7q' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

P value = 0.000267 (Fisher's exact test), Q value = 0.084
Table S7. Gene #29: '16q' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 48 | 20 | 37 | 50 |
16Q MUTATED | 5 | 7 | 19 | 11 |
16Q WILD-TYPE | 43 | 13 | 18 | 39 |
Figure S7. Get High-res Image Gene #29: '16q' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

P value = 6.59e-07 (Fisher's exact test), Q value = 0.00021
Table S8. Gene #30: '17p' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 36 | 77 |
17P MUTATED | 25 | 23 | 12 |
17P WILD-TYPE | 33 | 13 | 65 |
Figure S8. Get High-res Image Gene #30: '17p' versus Molecular Subtype #1: 'CN_CNMF'

P value = 3.94e-05 (Fisher's exact test), Q value = 0.012
Table S9. Gene #34: '19p' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 36 | 77 |
19P MUTATED | 17 | 23 | 16 |
19P WILD-TYPE | 41 | 13 | 61 |
Figure S9. Get High-res Image Gene #34: '19p' versus Molecular Subtype #1: 'CN_CNMF'

P value = 4.45e-06 (Fisher's exact test), Q value = 0.0014
Table S10. Gene #35: '19q' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 36 | 77 |
19Q MUTATED | 16 | 24 | 15 |
19Q WILD-TYPE | 42 | 12 | 62 |
Figure S10. Get High-res Image Gene #35: '19q' versus Molecular Subtype #1: 'CN_CNMF'

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Copy number data file = transformed.cor.cli.txt
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Molecular subtype file = CESC-TP.transferedmergedcluster.txt
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Number of patients = 171
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Number of significantly focal cnvs = 40
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Number of molecular subtypes = 8
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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 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 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.