Correlation between copy number variations of arm-level result and molecular subtypes
Prostate Adenocarcinoma (Primary solid tumor)
23 September 2013 | analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1PG1Q3H
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1PG1Q3H
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and subtypes.

Summary

Testing the association between copy number variation 32 arm-level results and 10 molecular subtypes across 197 patients, 23 significant findings detected with Q value < 0.25.

- 7p gain cnv correlated to 'CN_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

- 7q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

- 8p gain cnv correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.

- 8q gain cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

- 6q loss cnv correlated to 'CN_CNMF'.

- 8p loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

- 13q loss cnv correlated to 'CN_CNMF'.

- 16q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

- 17p loss cnv correlated to 'CN_CNMF'.

- 18q loss cnv correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 32 arm-level results and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 23 significant findings detected.

|  | Molecular subtypes | 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 | Chi-square test | Fisher's exact test | Chi-square test | Fisher's exact test
8q gain | 0 (0%) | 173 | 2.28e-08 (7.14e-06) | 0.129 (1.00) | 0.00025 (0.0747) | 0.000107 (0.0323) | 0.00976 (1.00) | 0.00615 (1.00) | 0.000351 (0.104) | 1.01e-05 (0.00308) | 4.53e-06 (0.00139) | 0.061 (1.00)
8p loss | 0 (0%) | 149 | 0.00345 (0.98) | 4.24e-06 (0.0013) | 0.556 (1.00) | 0.824 (1.00) | 0.000407 (0.12) | 0.000413 (0.122) | 1.66e-05 (0.00504) | 0.482 (1.00) | 0.0092 (1.00) | 0.0842 (1.00)
7p gain | 0 (0%) | 180 | 9.28e-08 (2.9e-05) | 0.0299 (1.00) | 0.0455 (1.00) | 0.115 (1.00) | 0.041 (1.00) | 0.0349 (1.00) | 0.0141 (1.00) | 0.000276 (0.0821) | 0.000205 (0.0614) | 0.139 (1.00)
7q gain | 0 (0%) | 181 | 4.16e-07 (0.000129) | 0.0247 (1.00) | 0.0866 (1.00) | 0.219 (1.00) | 0.0626 (1.00) | 0.124 (1.00) | 0.0107 (1.00) | 0.00177 (0.511) | 0.000104 (0.0313) | 0.316 (1.00)
8p gain | 0 (0%) | 186 | 1.93e-06 (0.000596) | 0.109 (1.00) | 0.000875 (0.255) | 0.000425 (0.125) | 0.0403 (1.00) | 0.0688 (1.00) | 0.00748 (1.00) | 0.00609 (1.00) | 0.00366 (1.00) | 0.32 (1.00)
16q loss | 0 (0%) | 169 | 8.64e-09 (2.71e-06) | 0.00343 (0.976) | 0.415 (1.00) | 0.109 (1.00) | 0.0304 (1.00) | 0.00252 (0.721) | 0.00917 (1.00) | 0.000463 (0.136) | 0.0357 (1.00) | 0.243 (1.00)
6q loss | 0 (0%) | 188 | 0.000736 (0.215) | 0.0656 (1.00) | 0.488 (1.00) | 0.629 (1.00) | 0.0824 (1.00) | 0.0149 (1.00) | 0.306 (1.00) | 0.15 (1.00) | 0.386 (1.00) | 0.722 (1.00)
13q loss | 0 (0%) | 182 | 3.11e-06 (0.000957) | 0.0541 (1.00) | 0.00606 (1.00) | 0.0194 (1.00) | 0.0098 (1.00) | 0.0211 (1.00) | 0.243 (1.00) | 0.144 (1.00) | 0.262 (1.00) | 0.543 (1.00)
17p loss | 0 (0%) | 173 | 6.49e-07 (0.000201) | 0.00999 (1.00) | 0.0175 (1.00) | 0.0282 (1.00) | 0.0187 (1.00) | 0.00155 (0.449) | 0.0383 (1.00) | 0.043 (1.00) | 0.0242 (1.00) | 0.322 (1.00)
18q loss | 0 (0%) | 171 | 7.98e-05 (0.0242) | 0.233 (1.00) | 0.0059 (1.00) | 0.00786 (1.00) | 0.113 (1.00) | 0.0341 (1.00) | 0.383 (1.00) | 0.0304 (1.00) | 0.133 (1.00) | 0.334 (1.00)
1p gain | 0 (0%) | 194 | 0.0497 (1.00) | 0.0233 (1.00) | 0.781 (1.00) | 0.636 (1.00) | 0.109 (1.00) | 0.185 (1.00) | 0.566 (1.00) | 0.267 (1.00) | 0.00368 (1.00) | 0.736 (1.00)
1q gain | 0 (0%) | 192 | 0.00405 (1.00) | 0.227 (1.00) | 0.189 (1.00) | 0.129 (1.00) | 0.376 (1.00) | 0.118 (1.00) | 0.405 (1.00) | 0.272 (1.00) | 0.0807 (1.00) | 0.693 (1.00)
3p gain | 0 (0%) | 192 | 0.553 (1.00) | 0.445 (1.00) | 0.189 (1.00) | 0.129 (1.00) | 0.131 (1.00) | 0.118 (1.00) | 0.0404 (1.00) | 0.0242 (1.00) | 0.459 (1.00) | 0.693 (1.00)
3q gain | 0 (0%) | 190 | 0.2 (1.00) | 0.299 (1.00) | 0.0748 (1.00) | 0.0499 (1.00) | 0.0186 (1.00) | 0.0482 (1.00) | 0.162 (1.00) | 0.00242 (0.695) | 0.0164 (1.00) | 0.413 (1.00)
9p gain | 0 (0%) | 194 | 0.0497 (1.00) | 0.384 (1.00) |  |  | 0.775 (1.00) | 0.0572 (1.00) | 0.26 (1.00) | 0.501 (1.00) | 0.867 (1.00) | 1 (1.00)
9q gain | 0 (0%) | 189 | 0.00404 (1.00) | 0.0854 (1.00) | 0.0479 (1.00) | 0.0638 (1.00) | 0.134 (1.00) | 0.176 (1.00) | 0.389 (1.00) | 0.0915 (1.00) | 0.0231 (1.00) | 0.535 (1.00)
10q gain | 0 (0%) | 193 | 0.187 (1.00) | 0.462 (1.00) | 0.113 (1.00) | 0.11 (1.00) | 0.328 (1.00) | 0.131 (1.00) | 0.65 (1.00) | 0.0572 (1.00) | 0.874 (1.00) | 0.625 (1.00)
12q gain | 0 (0%) | 194 | 0.556 (1.00) | 0.195 (1.00) | 0.484 (1.00) | 1 (1.00) | 0.528 (1.00) | 1 (1.00) | 0.935 (1.00) | 0.585 (1.00) | 0.535 (1.00) | 0.736 (1.00)
16p gain | 0 (0%) | 194 | 0.0497 (1.00) | 0.384 (1.00) | 0.781 (1.00) | 0.636 (1.00) | 0.775 (1.00) | 0.0572 (1.00) | 0.566 (1.00) | 0.585 (1.00) | 0.837 (1.00) | 0.736 (1.00)
16q gain | 0 (0%) | 194 | 0.0497 (1.00) | 0.384 (1.00) | 0.781 (1.00) | 0.636 (1.00) | 0.775 (1.00) | 0.0572 (1.00) | 0.566 (1.00) | 0.585 (1.00) | 0.837 (1.00) | 0.736 (1.00)
5q loss | 0 (0%) | 192 | 0.00405 (1.00) | 0.0362 (1.00) | 0.452 (1.00) | 0.318 (1.00) | 0.131 (1.00) | 0.0472 (1.00) | 0.405 (1.00) | 0.0104 (1.00) | 0.602 (1.00) | 1 (1.00)
8q loss | 0 (0%) | 193 | 0.187 (1.00) | 0.317 (1.00) | 0.561 (1.00) | 1 (1.00) | 0.328 (1.00) | 0.131 (1.00) | 0.263 (1.00) | 0.448 (1.00) | 0.605 (1.00) | 0.362 (1.00)
10p loss | 0 (0%) | 190 | 0.0109 (1.00) | 0.0897 (1.00) | 0.0748 (1.00) | 0.0499 (1.00) | 0.181 (1.00) | 0.0401 (1.00) | 0.22 (1.00) | 0.0268 (1.00) | 0.246 (1.00) | 0.413 (1.00)
10q loss | 0 (0%) | 190 | 0.0109 (1.00) | 0.562 (1.00) | 0.189 (1.00) | 0.129 (1.00) | 0.511 (1.00) | 0.15 (1.00) | 0.254 (1.00) | 0.446 (1.00) | 0.246 (1.00) | 0.413 (1.00)
12p loss | 0 (0%) | 186 | 0.011 (1.00) | 0.0644 (1.00) | 0.231 (1.00) | 0.629 (1.00) | 0.034 (1.00) | 0.0208 (1.00) | 0.241 (1.00) | 0.271 (1.00) | 0.348 (1.00) | 0.691 (1.00)
15q loss | 0 (0%) | 194 | 0.0497 (1.00) | 0.0233 (1.00) | 0.781 (1.00) | 0.636 (1.00) | 0.109 (1.00) | 0.185 (1.00) | 0.553 (1.00) | 0.0452 (1.00) | 0.00377 (1.00) | 0.512 (1.00)
16p loss | 0 (0%) | 193 | 0.018 (1.00) | 0.00649 (1.00) |  |  | 0.0353 (1.00) | 0.178 (1.00) | 0.00923 (1.00) | 0.0452 (1.00) | 0.00377 (1.00) | 0.0468 (1.00)
18p loss | 0 (0%) | 178 | 0.00197 (0.568) | 0.177 (1.00) | 0.0263 (1.00) | 0.0279 (1.00) | 0.47 (1.00) | 0.117 (1.00) | 0.166 (1.00) | 0.129 (1.00) | 0.0274 (1.00) | 0.0638 (1.00)
20p loss | 0 (0%) | 192 | 0.553 (1.00) | 0.0362 (1.00) | 0.537 (1.00) | 0.736 (1.00) | 0.131 (1.00) | 0.304 (1.00) | 0.263 (1.00) | 0.0283 (1.00) | 0.459 (1.00) | 0.268 (1.00)
21q loss | 0 (0%) | 192 | 0.0598 (1.00) | 0.273 (1.00) | 0.484 (1.00) | 0.777 (1.00) | 0.131 (1.00) | 0.147 (1.00) | 0.753 (1.00) | 0.187 (1.00) | 0.769 (1.00) | 0.835 (1.00)
22q loss | 0 (0%) | 192 | 0.0186 (1.00) | 0.273 (1.00) | 0.837 (1.00) | 0.684 (1.00) | 0.376 (1.00) | 0.118 (1.00) | 0.787 (1.00) | 1 (1.00) | 0.491 (1.00) | 1 (1.00)
Xq loss | 0 (0%) | 194 | 0.123 (1.00) | 0.0233 (1.00) |  |  | 0.109 (1.00) | 0.185 (1.00) | 0.349 (1.00) | 0.585 (1.00) | 0.311 (1.00) | 0.26 (1.00)

'7p gain' versus 'CN_CNMF'

P value = 9.28e-08 (Fisher's exact test), Q value = 2.9e-05

Table S1. Gene #5: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
7P GAIN CNV | 2 | 0 | 15
7P GAIN WILD-TYPE | 26 | 108 | 46

Figure S1. Get High-res Image Gene #5: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000276 (Fisher's exact test), Q value = 0.082

Table S2. Gene #5: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 21 | 74 | 67
7P GAIN CNV | 1 | 8 | 5 | 3
7P GAIN WILD-TYPE | 33 | 13 | 69 | 64

Figure S2. Get High-res Image Gene #5: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000205 (Chi-square test), Q value = 0.061

Table S3. Gene #5: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 73 | 18 | 12 | 15 | 78
7P GAIN CNV | 6 | 0 | 0 | 6 | 5
7P GAIN WILD-TYPE | 67 | 18 | 12 | 9 | 73

Figure S3. Get High-res Image Gene #5: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 4.16e-07 (Fisher's exact test), Q value = 0.00013

Table S4. Gene #6: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
7Q GAIN CNV | 2 | 0 | 14
7Q GAIN WILD-TYPE | 26 | 108 | 47

Figure S4. Get High-res Image Gene #6: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000104 (Chi-square test), Q value = 0.031

Table S5. Gene #6: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 73 | 18 | 12 | 15 | 78
7Q GAIN CNV | 5 | 0 | 0 | 6 | 5
7Q GAIN WILD-TYPE | 68 | 18 | 12 | 9 | 73

Figure S5. Get High-res Image Gene #6: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 1.93e-06 (Fisher's exact test), Q value = 6e-04

Table S6. Gene #7: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
8P GAIN CNV | 0 | 0 | 11
8P GAIN WILD-TYPE | 28 | 108 | 50

Figure S6. Get High-res Image Gene #7: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.000425 (Fisher's exact test), Q value = 0.12

Table S7. Gene #7: '8p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 51 | 58 | 45
8P GAIN CNV | 0 | 8 | 0
8P GAIN WILD-TYPE | 51 | 50 | 45

Figure S7. Get High-res Image Gene #7: '8p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 2.28e-08 (Fisher's exact test), Q value = 7.1e-06

Table S8. Gene #8: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
8Q GAIN CNV | 2 | 2 | 20
8Q GAIN WILD-TYPE | 26 | 106 | 41

Figure S8. Get High-res Image Gene #8: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.075

Table S9. Gene #8: '8q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 56 | 57
8Q GAIN CNV | 0 | 4 | 14
8Q GAIN WILD-TYPE | 41 | 52 | 43

Figure S9. Get High-res Image Gene #8: '8q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'8q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.000107 (Fisher's exact test), Q value = 0.032

Table S10. Gene #8: '8q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 51 | 58 | 45
8Q GAIN CNV | 0 | 14 | 4
8Q GAIN WILD-TYPE | 51 | 44 | 41

Figure S10. Get High-res Image Gene #8: '8q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 0.000351 (Chi-square test), Q value = 0.1

Table S11. Gene #8: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 52 | 39 | 17 | 14 | 74
8Q GAIN CNV | 4 | 1 | 7 | 0 | 11
8Q GAIN WILD-TYPE | 48 | 38 | 10 | 14 | 63

Figure S11. Get High-res Image Gene #8: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.01e-05 (Fisher's exact test), Q value = 0.0031

Table S12. Gene #8: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 21 | 74 | 67
8Q GAIN CNV | 2 | 9 | 11 | 1
8Q GAIN WILD-TYPE | 32 | 12 | 63 | 66

Figure S12. Get High-res Image Gene #8: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.53e-06 (Chi-square test), Q value = 0.0014

Table S13. Gene #8: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 73 | 18 | 12 | 15 | 78
8Q GAIN CNV | 4 | 1 | 0 | 8 | 10
8Q GAIN WILD-TYPE | 69 | 17 | 12 | 7 | 68

Figure S13. Get High-res Image Gene #8: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 0.000736 (Fisher's exact test), Q value = 0.21

Table S14. Gene #16: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
6Q LOSS CNV | 2 | 0 | 7
6Q LOSS WILD-TYPE | 26 | 108 | 54

Figure S14. Get High-res Image Gene #16: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 4.24e-06 (Fisher's exact test), Q value = 0.0013

Table S15. Gene #17: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 57 | 65 | 75
8P LOSS CNV | 11 | 5 | 32
8P LOSS WILD-TYPE | 46 | 60 | 43

Figure S15. Get High-res Image Gene #17: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 0.000407 (Fisher's exact test), Q value = 0.12

Table S16. Gene #17: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 60 | 67
8P LOSS CNV | 12 | 8 | 28
8P LOSS WILD-TYPE | 55 | 52 | 39

Figure S16. Get High-res Image Gene #17: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000413 (Fisher's exact test), Q value = 0.12

Table S17. Gene #17: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 49 | 68 | 77
8P LOSS CNV | 10 | 28 | 10
8P LOSS WILD-TYPE | 39 | 40 | 67

Figure S17. Get High-res Image Gene #17: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 1.66e-05 (Chi-square test), Q value = 0.005

Table S18. Gene #17: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 52 | 39 | 17 | 14 | 74
8P LOSS CNV | 24 | 2 | 2 | 0 | 20
8P LOSS WILD-TYPE | 28 | 37 | 15 | 14 | 54

Figure S18. Get High-res Image Gene #17: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 3.11e-06 (Fisher's exact test), Q value = 0.00096

Table S19. Gene #22: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
13Q LOSS CNV | 3 | 0 | 12
13Q LOSS WILD-TYPE | 25 | 108 | 49

Figure S19. Get High-res Image Gene #22: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 8.64e-09 (Fisher's exact test), Q value = 2.7e-06

Table S20. Gene #25: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
16Q LOSS CNV | 1 | 4 | 23
16Q LOSS WILD-TYPE | 27 | 104 | 38

Figure S20. Get High-res Image Gene #25: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000463 (Fisher's exact test), Q value = 0.14

Table S21. Gene #25: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 21 | 74 | 67
16Q LOSS CNV | 2 | 9 | 12 | 4
16Q LOSS WILD-TYPE | 32 | 12 | 62 | 63

Figure S21. Get High-res Image Gene #25: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 6.49e-07 (Fisher's exact test), Q value = 2e-04

Table S22. Gene #26: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
17P LOSS CNV | 0 | 5 | 19
17P LOSS WILD-TYPE | 28 | 103 | 42

Figure S22. Get High-res Image Gene #26: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 7.98e-05 (Fisher's exact test), Q value = 0.024

Table S23. Gene #28: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
18Q LOSS CNV | 1 | 7 | 18
18Q LOSS WILD-TYPE | 27 | 101 | 43

Figure S23. Get High-res Image Gene #28: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data
Input

- Mutation data file = broad_values_by_arm.mutsig.cluster.txt

- Molecular subtypes file = PRAD-TP.transferedmergedcluster.txt

- Number of patients = 197

- Number of significantly arm-level cnvs = 32

- Number of molecular subtypes = 10

- Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

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

Chi-square test

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

Q value calculation

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.

Download Results

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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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