Correlation between copy number variation genes and molecular subtypes
Prostate Adenocarcinoma (Primary solid tumor)
22 February 2013 | analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1639MZC
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 variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1639MZC
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.

Summary

Testing the association between copy number variation of 44 peak regions and 6 molecular subtypes across 177 patients, 35 significant findings detected with Q value < 0.25.

- Amp Peak 4(8p11.22) cnvs correlated to 'CN_CNMF'.

- Amp Peak 5(8q21.13) cnvs correlated to 'CN_CNMF'.

- Amp Peak 7(12q24.32) cnvs correlated to 'CN_CNMF'.

- Del Peak 5(2q22.1) cnvs correlated to 'CN_CNMF'.

- Del Peak 6(2q22.3) cnvs correlated to 'CN_CNMF'.

- Del Peak 10(5q11.2) cnvs correlated to 'CN_CNMF'.

- Del Peak 11(5q21.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Del Peak 12(6q15) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

- Del Peak 14(8p21.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Del Peak 15(8p11.21) cnvs correlated to 'METHLYATION_CNMF'.

- Del Peak 16(10q23.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

- Del Peak 18(12p13.2) cnvs correlated to 'CN_CNMF'.

- Del Peak 19(13q14.13) cnvs correlated to 'CN_CNMF'.

- Del Peak 20(16q22.3) cnvs correlated to 'CN_CNMF'.

- Del Peak 21(16q24.1) cnvs correlated to 'CN_CNMF'.

- Del Peak 22(17p13.1) cnvs correlated to 'CN_CNMF'.

- Del Peak 23(17q21.31) cnvs correlated to 'METHLYATION_CNMF'.

- Del Peak 24(18q22.1) cnvs correlated to 'CN_CNMF'.

- Del Peak 25(18q23) cnvs correlated to 'CN_CNMF'.

- Del Peak 26(21q22.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- Del Peak 27(21q22.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 44 regions and 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 35 significant findings detected.

|  | Molecular subtypes | 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
Del Peak 27(21q22 3) | 57 (32%) | 120 | 6.11e-08 (1.53e-05) | 8.77e-11 (2.29e-08) | 1.26e-09 (3.21e-07) | 2.38e-07 (5.9e-05) | 0.0567 (1.00) | 0.00017 (0.0402)
Del Peak 12(6q15) | 56 (32%) | 121 | 5.01e-16 (1.32e-13) | 7.81e-10 (2e-07) | 0.000903 (0.208) | 0.00209 (0.466) | 0.000276 (0.0647) | 0.824 (1.00)
Del Peak 26(21q22 2) | 58 (33%) | 119 | 2.8e-08 (7.05e-06) | 2.5e-12 (6.54e-10) | 5.24e-09 (1.33e-06) | 2.68e-07 (6.61e-05) | 0.138 (1.00) | 0.00284 (0.629)
Del Peak 16(10q23 31) | 63 (36%) | 114 | 1.59e-07 (3.95e-05) | 1.88e-05 (0.00457) | 6.89e-05 (0.0165) | 0.0214 (1.00) | 0.0408 (1.00) | 0.0472 (1.00)
Del Peak 11(5q21 1) | 31 (18%) | 146 | 1.7e-10 (4.41e-08) | 7.32e-06 (0.00179) | 0.149 (1.00) | 0.47 (1.00) | 0.299 (1.00) | 0.538 (1.00)
Del Peak 14(8p21 3) | 106 (60%) | 71 | 2.84e-08 (7.12e-06) | 4.63e-05 (0.0112) | 0.0474 (1.00) | 0.0594 (1.00) | 0.00184 (0.415) | 0.0562 (1.00)
Amp Peak 4(8p11 22) | 16 (9%) | 161 | 0.000449 (0.105) | 0.481 (1.00) | 0.286 (1.00) | 0.491 (1.00) | 0.587 (1.00) | 0.454 (1.00)
Amp Peak 5(8q21 13) | 44 (25%) | 133 | 3.78e-10 (9.71e-08) | 0.0101 (1.00) | 0.0655 (1.00) | 0.04 (1.00) | 0.372 (1.00) | 0.313 (1.00)
Amp Peak 7(12q24 32) | 7 (4%) | 170 | 0.000749 (0.173) | 0.264 (1.00) | 0.675 (1.00) | 1 (1.00) | 0.456 (1.00) | 0.864 (1.00)
Del Peak 5(2q22 1) | 21 (12%) | 156 | 9.66e-05 (0.0231) | 0.00421 (0.914) | 0.586 (1.00) | 0.313 (1.00) | 0.0121 (1.00) | 0.00772 (1.00)
Del Peak 6(2q22 3) | 23 (13%) | 154 | 4.5e-05 (0.0109) | 0.0319 (1.00) | 0.0398 (1.00) | 0.0112 (1.00) | 0.0038 (0.832) | 0.0855 (1.00)
Del Peak 10(5q11 2) | 29 (16%) | 148 | 2.4e-06 (0.000587) | 0.0294 (1.00) | 0.798 (1.00) | 0.956 (1.00) | 0.599 (1.00) | 0.68 (1.00)
Del Peak 15(8p11 21) | 59 (33%) | 118 | 0.0116 (1.00) | 0.000204 (0.048) | 0.0647 (1.00) | 0.0193 (1.00) | 0.281 (1.00) | 0.207 (1.00)
Del Peak 18(12p13 2) | 38 (21%) | 139 | 0.000529 (0.123) | 0.031 (1.00) | 0.702 (1.00) | 0.651 (1.00) | 0.0527 (1.00) | 0.856 (1.00)
Del Peak 19(13q14 13) | 81 (46%) | 96 | 0.000113 (0.0269) | 0.00503 (1.00) | 0.0245 (1.00) | 0.0251 (1.00) | 0.306 (1.00) | 0.363 (1.00)
Del Peak 20(16q22 3) | 57 (32%) | 120 | 6.54e-07 (0.000161) | 0.0146 (1.00) | 0.015 (1.00) | 0.154 (1.00) | 0.0185 (1.00) | 0.0792 (1.00)
Del Peak 21(16q24 1) | 72 (41%) | 105 | 2.18e-10 (5.61e-08) | 0.00797 (1.00) | 0.0605 (1.00) | 0.373 (1.00) | 0.0395 (1.00) | 0.0325 (1.00)
Del Peak 22(17p13 1) | 45 (25%) | 132 | 3.97e-09 (1.01e-06) | 0.216 (1.00) | 0.0694 (1.00) | 0.00328 (0.723) | 0.286 (1.00) | 0.0611 (1.00)
Del Peak 23(17q21 31) | 34 (19%) | 143 | 0.00156 (0.357) | 0.000275 (0.0645) | 0.00426 (0.921) | 0.00464 (0.993) | 0.533 (1.00) | 0.289 (1.00)
Del Peak 24(18q22 1) | 44 (25%) | 133 | 9.08e-11 (2.36e-08) | 0.625 (1.00) | 0.667 (1.00) | 0.108 (1.00) | 0.0534 (1.00) | 0.152 (1.00)
Del Peak 25(18q23) | 50 (28%) | 127 | 1.2e-13 (3.16e-11) | 0.525 (1.00) | 0.423 (1.00) | 0.13 (1.00) | 0.104 (1.00) | 0.447 (1.00)
Amp Peak 1(1q21 3) | 10 (6%) | 167 | 0.0731 (1.00) | 0.361 (1.00) | 0.534 (1.00) | 0.726 (1.00) | 0.0787 (1.00) | 1 (1.00)
Amp Peak 2(3q26 2) | 25 (14%) | 152 | 0.00195 (0.437) | 0.267 (1.00) | 0.73 (1.00) | 0.631 (1.00) | 0.932 (1.00) | 0.377 (1.00)
Amp Peak 3(7p15 3) | 33 (19%) | 144 | 0.00185 (0.417) | 0.107 (1.00) | 0.0633 (1.00) | 0.113 (1.00) | 0.87 (1.00) | 0.55 (1.00)
Amp Peak 6(10q21 2) | 10 (6%) | 167 | 0.00948 (1.00) | 0.434 (1.00) | 0.119 (1.00) | 0.0962 (1.00) | 0.278 (1.00) | 1 (1.00)
Amp Peak 8(14q21 1) | 8 (5%) | 169 | 0.107 (1.00) | 0.543 (1.00) | 0.132 (1.00) | 0.298 (1.00) | 0.828 (1.00) | 0.265 (1.00)
Amp Peak 9(Xp22 11) | 5 (3%) | 172 | 0.325 (1.00) | 0.863 (1.00) | 0.858 (1.00) | 0.863 (1.00) | 0.21 (1.00) | 0.396 (1.00)
Amp Peak 10(Xp22 11) | 5 (3%) | 172 | 0.62 (1.00) | 0.619 (1.00) | 0.551 (1.00) | 0.688 (1.00) | 0.755 (1.00) | 0.325 (1.00)
Amp Peak 11(Xp21 1) | 4 (2%) | 173 | 0.693 (1.00) | 0.387 (1.00) | 0.839 (1.00) | 1 (1.00) | 0.266 (1.00) | 0.666 (1.00)
Amp Peak 12(Xq21 1) | 7 (4%) | 170 | 0.351 (1.00) | 0.203 (1.00) | 0.212 (1.00) | 0.438 (1.00) | 0.406 (1.00) | 0.771 (1.00)
Amp Peak 13(Xq21 1) | 5 (3%) | 172 | 0.0712 (1.00) | 0.00434 (0.934) | 0.51 (1.00) | 0.377 (1.00) | 0.869 (1.00) | 0.845 (1.00)
Amp Peak 14(Xq21 31) | 5 (3%) | 172 | 0.0904 (1.00) | 0.275 (1.00) | 0.551 (1.00) | 0.234 (1.00) | 0.703 (1.00) | 1 (1.00)
Amp Peak 15(Xq25) | 4 (2%) | 173 | 0.0327 (1.00) | 0.237 (1.00) | 0.29 (1.00) | 0.631 (1.00) | 0.404 (1.00) | 0.133 (1.00)
Amp Peak 16(Xq25) | 6 (3%) | 171 | 1 (1.00) | 0.322 (1.00) | 0.193 (1.00) | 0.327 (1.00) | 0.197 (1.00) | 0.405 (1.00)
Amp Peak 17(Xq27 1) | 9 (5%) | 168 | 0.00408 (0.89) | 0.434 (1.00) | 1 (1.00) | 0.815 (1.00) | 0.0648 (1.00) | 0.0234 (1.00)
Del Peak 1(1p31 3) | 21 (12%) | 156 | 0.0431 (1.00) | 0.00225 (0.499) | 0.0189 (1.00) | 0.00182 (0.412) | 0.187 (1.00) | 0.152 (1.00)
Del Peak 2(1p21 3) | 17 (10%) | 160 | 0.00593 (1.00) | 0.745 (1.00) | 0.867 (1.00) | 0.518 (1.00) | 0.0741 (1.00) | 0.89 (1.00)
Del Peak 3(1q23 1) | 8 (5%) | 169 | 0.0635 (1.00) | 0.127 (1.00) | 0.212 (1.00) | 0.043 (1.00) | 0.0579 (1.00) | 0.707 (1.00)
Del Peak 4(1q42 13) | 17 (10%) | 160 | 0.114 (1.00) | 0.0123 (1.00) | 0.875 (1.00) | 0.713 (1.00) | 0.27 (1.00) | 0.791 (1.00)
Del Peak 7(3p13) | 28 (16%) | 149 | 0.387 (1.00) | 0.087 (1.00) | 0.48 (1.00) | 0.885 (1.00) | 0.195 (1.00) | 0.117 (1.00)
Del Peak 8(3q29) | 12 (7%) | 165 | 0.406 (1.00) | 0.212 (1.00) | 0.0981 (1.00) | 0.15 (1.00) | 0.579 (1.00) | 1 (1.00)
Del Peak 9(4q28 1) | 12 (7%) | 165 | 0.0172 (1.00) | 0.00141 (0.324) | 0.189 (1.00) | 0.622 (1.00) | 0.263 (1.00) | 0.181 (1.00)
Del Peak 13(7q36 1) | 8 (5%) | 169 | 0.538 (1.00) | 0.348 (1.00) | 0.534 (1.00) | 0.726 (1.00) | 0.69 (1.00) | 0.564 (1.00)
Del Peak 17(11q23 2) | 20 (11%) | 157 | 0.121 (1.00) | 0.222 (1.00) | 0.754 (1.00) | 0.753 (1.00) | 0.387 (1.00) | 0.602 (1.00)

'Amp Peak 4(8p11.22) mutation analysis' versus 'CN_CNMF'

P value = 0.000449 (Fisher's exact test), Q value = 0.1

Table S1. Gene #4: 'Amp Peak 4(8p11.22) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 83 | 54 | 1
AMP PEAK 4(8P11.22) MUTATED | 4 | 1 | 11 | 0
AMP PEAK 4(8P11.22) WILD-TYPE | 35 | 82 | 43 | 1

Figure S1. Get High-res Image Gene #4: 'Amp Peak 4(8p11.22) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 5(8q21.13) mutation analysis' versus 'CN_CNMF'

P value = 3.78e-10 (Fisher's exact test), Q value = 9.7e-08

Table S2. Gene #5: 'Amp Peak 5(8q21.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 83 | 54 | 1
AMP PEAK 5(8Q21.13) MUTATED | 9 | 5 | 30 | 0
AMP PEAK 5(8Q21.13) WILD-TYPE | 30 | 78 | 24 | 1

Figure S2. Get High-res Image Gene #5: 'Amp Peak 5(8q21.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 7(12q24.32) mutation analysis' versus 'CN_CNMF'

P value = 0.000749 (Fisher's exact test), Q value = 0.17

Table S3. Gene #7: 'Amp Peak 7(12q24.32) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 83 | 54 | 1
AMP PEAK 7(12Q24.32) MUTATED | 0 | 0 | 7 | 0
AMP PEAK 7(12Q24.32) WILD-TYPE | 39 | 83 | 47 | 1

Figure S3. Get High-res Image Gene #7: 'Amp Peak 7(12q24.32) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 5(2q22.1) mutation analysis' versus 'CN_CNMF'

P value = 9.66e-05 (Fisher's exact test), Q value = 0.023

Table S4. Gene #22: 'Del Peak 5(2q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 83 | 54 | 1
DEL PEAK 5(2Q22.1) MUTATED | 9 | 2 | 9 | 1
DEL PEAK 5(2Q22.1) WILD-TYPE | 30 | 81 | 45 | 0

Figure S4. Get High-res Image Gene #22: 'Del Peak 5(2q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 6(2q22.3) mutation analysis' versus 'CN_CNMF'

P value = 4.5e-05 (Fisher's exact test), Q value = 0.011

Table S5. Gene #23: 'Del Peak 6(2q22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 83 | 54 | 1
DEL PEAK 6(2Q22.3) MUTATED | 8 | 2 | 12 | 1
DEL PEAK 6(2Q22.3) WILD-TYPE | 31 | 81 | 42 | 0

Figure S5. Get High-res Image Gene #23: 'Del Peak 6(2q22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 10(5q11.2) mutation analysis' versus 'CN_CNMF'

P value = 2.4e-06 (Fisher's exact test), Q value = 0.00059

Table S6. Gene #27: 'Del Peak 10(5q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 83 | 54 | 1
DEL PEAK 10(5Q11.2) MUTATED | 12 | 2 | 15 | 0
DEL PEAK 10(5Q11.2) WILD-TYPE | 27 | 81 | 39 | 1

Figure S6. Get High-res Image Gene #27: 'Del Peak 10(5q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 11(5q21.1) mutation analysis' versus 'CN_CNMF'

P value = 1.7e-10 (Fisher's exact test), Q value = 4.4e-08

Table S7. Gene #28: 'Del Peak 11(5q21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 83 | 54 | 1
DEL PEAK 11(5Q21.1) MUTATED | 16 | 0 | 15 | 0
DEL PEAK 11(5Q21.1) WILD-TYPE | 23 | 83 | 39 | 1

Figure S7. Get High-res Image Gene #28: 'Del Peak 11(5q21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 11(5q21.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.32e-06 (Fisher's exact test), Q value = 0.0018

Table S8. Gene #28: 'Del Peak 11(5q21.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 53 | 50 | 68
DEL PEAK 11(5Q21.1) MUTATED | 20 | 3 | 5
DEL PEAK 11(5Q21.1) WILD-TYPE | 33 | 47 | 63

Figure S8. Get High-res Image Gene #28: 'Del Peak 11(5q21.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 12(6q15) mutation analysis' versus 'CN_CNMF'

P value = 5.01e-16 (Fisher's exact test), Q value = 1.3e-13

Table S9. Gene #29: 'Del Peak 12(6q15) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 83 | 54 | 1
DEL PEAK 12(6Q15) MUTATED | 29 | 4 | 22 | 1
DEL PEAK 12(6Q15) WILD-TYPE | 10 | 79 | 32 | 0

Figure S9. Get High-res Image Gene #29: 'Del Peak 12(6q15) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 12(6q15) mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.81e-10 (Fisher's exact test), Q value = 2e-07

Table S10. Gene #29: 'Del Peak 12(6q15) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 53 | 50 | 68
DEL PEAK 12(6Q15) MUTATED | 32 | 2 | 19
DEL PEAK 12(6Q15) WILD-TYPE | 21 | 48 | 49

Figure S10. Get High-res Image Gene #29: 'Del Peak 12(6q15) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 12(6q15) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000903 (Fisher's exact test), Q value = 0.21

Table S11. Gene #29: 'Del Peak 12(6q15) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 50 | 41 | 49
DEL PEAK 12(6Q15) MUTATED | 24 | 5 | 14
DEL PEAK 12(6Q15) WILD-TYPE | 26 | 36 | 35

Figure S11. Get High-res Image Gene #29: 'Del Peak 12(6q15) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

'Del Peak 12(6q15) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000276 (Fisher's exact test), Q value = 0.065

Table S12. Gene #29: 'Del Peak 12(6q15) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 45 | 46 | 25 | 60
DEL PEAK 12(6Q15) MUTATED | 23 | 5 | 6 | 21
DEL PEAK 12(6Q15) WILD-TYPE | 22 | 41 | 19 | 39

Figure S12. Get High-res Image Gene #29: 'Del Peak 12(6q15) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

'Del Peak 14(8p21.3) mutation analysis' versus 'CN_CNMF'

P value = 2.84e-08 (Fisher's exact test), Q value = 7.1e-06

Table S13. Gene #31: 'Del Peak 14(8p21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 83 | 54 | 1
DEL PEAK 14(8P21.3) MUTATED | 18 | 38 | 49 | 1
DEL PEAK 14(8P21.3) WILD-TYPE | 21 | 45 | 5 | 0

Figure S13. Get High-res Image Gene #31: 'Del Peak 14(8p21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 14(8p21.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.63e-05 (Fisher's exact test), Q value = 0.011

Table S14. Gene #31: 'Del Peak 14(8p21.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 53 | 50 | 68
DEL PEAK 14(8P21.3) MUTATED | 29 | 19 | 53
DEL PEAK 14(8P21.3) WILD-TYPE | 24 | 31 | 15

Figure S14. Get High-res Image Gene #31: 'Del Peak 14(8p21.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 15(8p11.21) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000204 (Fisher's exact test), Q value = 0.048

Table S15. Gene #32: 'Del Peak 15(8p11.21) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 53 | 50 | 68
DEL PEAK 15(8P11.21) MUTATED | 17 | 6 | 32
DEL PEAK 15(8P11.21) WILD-TYPE | 36 | 44 | 36

Figure S15. Get High-res Image Gene #32: 'Del Peak 15(8p11.21) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 16(10q23.31) mutation analysis' versus 'CN_CNMF'

P value = 1.59e-07 (Fisher's exact test), Q value = 3.9e-05

Table S16. Gene #33: 'Del Peak 16(10q23.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 83 | 54 | 1
DEL PEAK 16(10Q23.31) MUTATED | 6 | 21 | 35 | 1
DEL PEAK 16(10Q23.31) WILD-TYPE | 33 | 62 | 19 | 0

Figure S16. Get High-res Image Gene #33: 'Del Peak 16(10q23.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 16(10q23.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.88e-05 (Fisher's exact test), Q value = 0.0046

Table S17. Gene #33: 'Del Peak 16(10q23.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 53 | 50 | 68
DEL PEAK 16(10Q23.31) MUTATED | 13 | 10 | 39
DEL PEAK 16(10Q23.31) WILD-TYPE | 40 | 40 | 29

Figure S17. Get High-res Image Gene #33: 'Del Peak 16(10q23.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 16(10q23.31) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.89e-05 (Fisher's exact test), Q value = 0.017

Table S18. Gene #33: 'Del Peak 16(10q23.31) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 50 | 41 | 49
DEL PEAK 16(10Q23.31) MUTATED | 12 | 11 | 31
DEL PEAK 16(10Q23.31) WILD-TYPE | 38 | 30 | 18

Figure S18. Get High-res Image Gene #33: 'Del Peak 16(10q23.31) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

'Del Peak 18(12p13.2) mutation analysis' versus 'CN_CNMF'

P value = 0.000529 (Fisher's exact test), Q value = 0.12

Table S19. Gene #35: 'Del Peak 18(12p13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 83 | 54 | 1
DEL PEAK 18(12P13.2) MUTATED | 6 | 10 | 22 | 0
DEL PEAK 18(12P13.2) WILD-TYPE | 33 | 73 | 32 | 1

Figure S19. Get High-res Image Gene #35: 'Del Peak 18(12p13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 19(13q14.13) mutation analysis' versus 'CN_CNMF'

P value = 0.000113 (Fisher's exact test), Q value = 0.027

Table S20. Gene #36: 'Del Peak 19(13q14.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 83 | 54 | 1
DEL PEAK 19(13Q14.13) MUTATED | 25 | 24 | 31 | 1
DEL PEAK 19(13Q14.13) WILD-TYPE | 14 | 59 | 23 | 0

Figure S20. Get High-res Image Gene #36: 'Del Peak 19(13q14.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 20(16q22.3) mutation analysis' versus 'CN_CNMF'

P value = 6.54e-07 (Fisher's exact test), Q value = 0.00016

Table S21. Gene #37: 'Del Peak 20(16q22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 83 | 54 | 1
DEL PEAK 20(16Q22.3) MUTATED | 6 | 18 | 33 | 0
DEL PEAK 20(16Q22.3) WILD-TYPE | 33 | 65 | 21 | 1

Figure S21. Get High-res Image Gene #37: 'Del Peak 20(16q22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 21(16q24.1) mutation analysis' versus 'CN_CNMF'

P value = 2.18e-10 (Fisher's exact test), Q value = 5.6e-08

Table S22. Gene #38: 'Del Peak 21(16q24.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 83 | 54 | 1
DEL PEAK 21(16Q24.1) MUTATED | 8 | 22 | 42 | 0
DEL PEAK 21(16Q24.1) WILD-TYPE | 31 | 61 | 12 | 1

Figure S22. Get High-res Image Gene #38: 'Del Peak 21(16q24.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 22(17p13.1) mutation analysis' versus 'CN_CNMF'

P value = 3.97e-09 (Fisher's exact test), Q value = 1e-06

Table S23. Gene #39: 'Del Peak 22(17p13.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 83 | 54 | 1
DEL PEAK 22(17P13.1) MUTATED | 3 | 11 | 30 | 1
DEL PEAK 22(17P13.1) WILD-TYPE | 36 | 72 | 24 | 0

Figure S23. Get High-res Image Gene #39: 'Del Peak 22(17p13.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 23(17q21.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000275 (Fisher's exact test), Q value = 0.065

Table S24. Gene #40: 'Del Peak 23(17q21.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 53 | 50 | 68
DEL PEAK 23(17Q21.31) MUTATED | 4 | 5 | 23
DEL PEAK 23(17Q21.31) WILD-TYPE | 49 | 45 | 45

Figure S24. Get High-res Image Gene #40: 'Del Peak 23(17q21.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 24(18q22.1) mutation analysis' versus 'CN_CNMF'

P value = 9.08e-11 (Fisher's exact test), Q value = 2.4e-08

Table S25. Gene #41: 'Del Peak 24(18q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 83 | 54 | 1
DEL PEAK 24(18Q22.1) MUTATED | 3 | 9 | 32 | 0
DEL PEAK 24(18Q22.1) WILD-TYPE | 36 | 74 | 22 | 1

Figure S25. Get High-res Image Gene #41: 'Del Peak 24(18q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 25(18q23) mutation analysis' versus 'CN_CNMF'

P value = 1.2e-13 (Fisher's exact test), Q value = 3.2e-11

Table S26. Gene #42: 'Del Peak 25(18q23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 83 | 54 | 1
DEL PEAK 25(18Q23) MUTATED | 4 | 9 | 37 | 0
DEL PEAK 25(18Q23) WILD-TYPE | 35 | 74 | 17 | 1

Figure S26. Get High-res Image Gene #42: 'Del Peak 25(18q23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 26(21q22.2) mutation analysis' versus 'CN_CNMF'

P value = 2.8e-08 (Fisher's exact test), Q value = 7e-06

Table S27. Gene #43: 'Del Peak 26(21q22.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 83 | 54 | 1
DEL PEAK 26(21Q22.2) MUTATED | 0 | 38 | 19 | 1
DEL PEAK 26(21Q22.2) WILD-TYPE | 39 | 45 | 35 | 0

Figure S27. Get High-res Image Gene #43: 'Del Peak 26(21q22.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 26(21q22.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.5e-12 (Fisher's exact test), Q value = 6.5e-10

Table S28. Gene #43: 'Del Peak 26(21q22.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 53 | 50 | 68
DEL PEAK 26(21Q22.2) MUTATED | 4 | 9 | 44
DEL PEAK 26(21Q22.2) WILD-TYPE | 49 | 41 | 24

Figure S28. Get High-res Image Gene #43: 'Del Peak 26(21q22.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 26(21q22.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.24e-09 (Fisher's exact test), Q value = 1.3e-06

Table S29. Gene #43: 'Del Peak 26(21q22.2) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 50 | 41 | 49
DEL PEAK 26(21Q22.2) MUTATED | 4 | 14 | 32
DEL PEAK 26(21Q22.2) WILD-TYPE | 46 | 27 | 17

Figure S29. Get High-res Image Gene #43: 'Del Peak 26(21q22.2) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

'Del Peak 26(21q22.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.68e-07 (Fisher's exact test), Q value = 6.6e-05

Table S30. Gene #43: 'Del Peak 26(21q22.2) mutation analysis' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 43 | 56
DEL PEAK 26(21Q22.2) MUTATED | 3 | 27 | 20
DEL PEAK 26(21Q22.2) WILD-TYPE | 38 | 16 | 36

Figure S30. Get High-res Image Gene #43: 'Del Peak 26(21q22.2) mutation analysis' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 27(21q22.3) mutation analysis' versus 'CN_CNMF'

P value = 6.11e-08 (Fisher's exact test), Q value = 1.5e-05

Table S31. Gene #44: 'Del Peak 27(21q22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 83 | 54 | 1
DEL PEAK 27(21Q22.3) MUTATED | 0 | 38 | 19 | 0
DEL PEAK 27(21Q22.3) WILD-TYPE | 39 | 45 | 35 | 1

Figure S31. Get High-res Image Gene #44: 'Del Peak 27(21q22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 27(21q22.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.77e-11 (Fisher's exact test), Q value = 2.3e-08

Table S32. Gene #44: 'Del Peak 27(21q22.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 53 | 50 | 68
DEL PEAK 27(21Q22.3) MUTATED | 5 | 8 | 42
DEL PEAK 27(21Q22.3) WILD-TYPE | 48 | 42 | 26

Figure S32. Get High-res Image Gene #44: 'Del Peak 27(21q22.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 27(21q22.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.26e-09 (Fisher's exact test), Q value = 3.2e-07

Table S33. Gene #44: 'Del Peak 27(21q22.3) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 50 | 41 | 49
DEL PEAK 27(21Q22.3) MUTATED | 4 | 12 | 33
DEL PEAK 27(21Q22.3) WILD-TYPE | 46 | 29 | 16

Figure S33. Get High-res Image Gene #44: 'Del Peak 27(21q22.3) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

'Del Peak 27(21q22.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.38e-07 (Fisher's exact test), Q value = 5.9e-05

Table S34. Gene #44: 'Del Peak 27(21q22.3) mutation analysis' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 43 | 56
DEL PEAK 27(21Q22.3) MUTATED | 3 | 27 | 19
DEL PEAK 27(21Q22.3) WILD-TYPE | 38 | 16 | 37

Figure S34. Get High-res Image Gene #44: 'Del Peak 27(21q22.3) mutation analysis' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 27(21q22.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.04

Table S35. Gene #44: 'Del Peak 27(21q22.3) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 30 | 69 | 77
DEL PEAK 27(21Q22.3) MUTATED | 3 | 34 | 20
DEL PEAK 27(21Q22.3) WILD-TYPE | 27 | 35 | 57

Figure S35. Get High-res Image Gene #44: 'Del Peak 27(21q22.3) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

Methods & Data
Input

- Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.

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

- Number of patients = 177

- Number of copy number variation regions = 44

- Number of molecular subtypes = 6

- Exclude regions that fewer than K tumors have alterations, 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

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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

- 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] 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)
[3] GISTIC_version2
Copyright © 2013 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle