Correlation between copy number variation genes and molecular subtypes
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
22 February 2013 | analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1PC30KT
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/C1PC30KT
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 22 peak regions and 8 molecular subtypes across 117 patients, 21 significant findings detected with Q value < 0.25.

- Amp Peak 2(3p14.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

- Amp Peak 5(7q22.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- Amp Peak 6(17q25.2) cnvs correlated to 'CN_CNMF'.

- Amp Peak 7(19p13.2) cnvs correlated to 'CN_CNMF'.

- Del Peak 1(1p36.31) cnvs correlated to 'CN_CNMF'.

- Del Peak 4(3p22.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Del Peak 5(4q31.22) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Del Peak 6(5q35.2) cnvs correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- Del Peak 8(9p21.3) cnvs correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

- Del Peak 9(14q11.2) cnvs correlated to 'CN_CNMF'.

- Del Peak 10(14q23.3) cnvs correlated to 'CN_CNMF'.

- Del Peak 11(14q32.2) cnvs correlated to 'CN_CNMF'.

- Del Peak 13(Xq21.31) cnvs correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 22 regions and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 21 significant findings detected.

|  | Molecular subtypes | MRNA CNMF | MRNA CHIERARCHICAL | 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 | Fisher's exact test | Fisher's exact test
Amp Peak 2(3p14 1) | 31 (26%) | 86 | 1 (1.00) | 0.537 (1.00) | 2.36e-17 (3.76e-15) | 0.0858 (1.00) | 0.00279 (0.373) | 1.79e-06 (0.000274) | 0.00534 (0.688) | 0.000228 (0.0335)
Amp Peak 5(7q22 1) | 68 (58%) | 49 | 1 (1.00) | 0.808 (1.00) | 3.56e-09 (5.52e-07) | 0.00792 (1.00) | 0.00172 (0.239) | 0.000515 (0.0746) | 0.0134 (1.00) | 0.0157 (1.00)
Del Peak 4(3p22 1) | 8 (7%) | 109 | 0.438 (1.00) |  | 0.000862 (0.122) | 0.000694 (0.0985) | 0.0206 (1.00) | 0.00417 (0.547) | 0.0159 (1.00) | 0.111 (1.00)
Del Peak 5(4q31 22) | 13 (11%) | 104 | 1 (1.00) |  | 0.000304 (0.0444) | 0.000543 (0.0782) | 0.00681 (0.872) | 0.024 (1.00) | 0.582 (1.00) | 0.61 (1.00)
Del Peak 6(5q35 2) | 8 (7%) | 109 | 1 (1.00) |  | 0.319 (1.00) | 0.00185 (0.253) | 0.000616 (0.088) | 0.00116 (0.162) | 0.394 (1.00) | 0.12 (1.00)
Del Peak 8(9p21 3) | 18 (15%) | 99 | 1 (1.00) | 0.75 (1.00) | 0.00471 (0.612) | 4.27e-05 (0.00636) | 3.4e-05 (0.0051) | 0.00182 (0.251) | 0.0341 (1.00) | 0.0922 (1.00)
Amp Peak 6(17q25 2) | 80 (68%) | 37 | 0.585 (1.00) | 1 (1.00) | 2.9e-06 (0.000438) | 0.233 (1.00) | 0.28 (1.00) | 0.0388 (1.00) | 0.826 (1.00) | 0.477 (1.00)
Amp Peak 7(19p13 2) | 14 (12%) | 103 | 0.0885 (1.00) | 0.615 (1.00) | 4.94e-09 (7.61e-07) | 0.161 (1.00) | 0.0683 (1.00) | 0.765 (1.00) | 0.722 (1.00) | 0.682 (1.00)
Del Peak 1(1p36 31) | 25 (21%) | 92 | 0.585 (1.00) | 1 (1.00) | 2.27e-06 (0.000346) | 0.172 (1.00) | 0.0316 (1.00) | 0.0382 (1.00) | 0.255 (1.00) | 0.124 (1.00)
Del Peak 9(14q11 2) | 26 (22%) | 91 | 0.596 (1.00) | 0.167 (1.00) | 2.56e-10 (3.99e-08) | 0.3 (1.00) | 0.0934 (1.00) | 0.177 (1.00) | 0.835 (1.00) | 0.953 (1.00)
Del Peak 10(14q23 3) | 25 (21%) | 92 | 1 (1.00) | 0.385 (1.00) | 2.2e-12 (3.48e-10) | 0.139 (1.00) | 0.0351 (1.00) | 0.0295 (1.00) | 0.719 (1.00) | 0.886 (1.00)
Del Peak 11(14q32 2) | 25 (21%) | 92 | 1 (1.00) | 0.385 (1.00) | 1.29e-11 (2.02e-09) | 0.3 (1.00) | 0.0775 (1.00) | 0.0648 (1.00) | 0.719 (1.00) | 0.886 (1.00)
Del Peak 13(Xq21 31) | 17 (15%) | 100 | 1 (1.00) |  | 0.000118 (0.0175) | 0.00263 (0.355) | 0.00278 (0.373) | 0.0354 (1.00) | 0.768 (1.00) | 0.806 (1.00)
Amp Peak 1(2q32 1) | 20 (17%) | 97 | 0.55 (1.00) | 0.75 (1.00) | 0.00237 (0.322) | 0.397 (1.00) | 0.942 (1.00) | 1 (1.00) | 0.832 (1.00) | 0.439 (1.00)
Amp Peak 3(5q35 2) | 15 (13%) | 102 | 0.0625 (1.00) | 0.141 (1.00) | 0.2 (1.00) | 0.0369 (1.00) | 0.678 (1.00) | 0.0565 (1.00) | 0.566 (1.00) | 0.0452 (1.00)
Amp Peak 4(6p12 3) | 4 (3%) | 113 |  |  | 0.438 (1.00) | 0.199 (1.00) | 0.114 (1.00) | 0.35 (1.00) | 0.165 (1.00) | 0.186 (1.00)
Amp Peak 8(19q13 11) | 4 (3%) | 113 |  |  | 0.69 (1.00) | 0.199 (1.00) | 0.201 (1.00) | 0.13 (1.00) | 0.331 (1.00) | 0.473 (1.00)
Del Peak 2(2p11 2) | 3 (3%) | 114 |  |  | 0.884 (1.00) | 0.791 (1.00) |  |  | 0.028 (1.00) | 0.0273 (1.00)
Del Peak 3(2q37 3) | 5 (4%) | 112 | 1 (1.00) |  | 0.331 (1.00) | 0.163 (1.00) | 0.684 (1.00) | 0.35 (1.00) | 0.704 (1.00) | 0.84 (1.00)
Del Peak 7(6q22 31) | 13 (11%) | 104 | 1 (1.00) |  | 0.0489 (1.00) | 0.114 (1.00) | 0.0976 (1.00) | 0.175 (1.00) | 0.787 (1.00) | 0.337 (1.00)
Del Peak 12(19q13 42) | 10 (9%) | 107 |  |  | 0.163 (1.00) | 0.885 (1.00) | 0.732 (1.00) | 0.232 (1.00) | 0.471 (1.00) | 0.438 (1.00)
Del Peak 14(Xq28) | 16 (14%) | 101 | 1 (1.00) |  | 0.00368 (0.486) | 0.045 (1.00) | 0.0436 (1.00) | 0.253 (1.00) | 0.713 (1.00) | 0.941 (1.00)

'Amp Peak 2(3p14.1) mutation analysis' versus 'CN_CNMF'

P value = 2.36e-17 (Fisher's exact test), Q value = 3.8e-15

Table S1. Gene #2: 'Amp Peak 2(3p14.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 20 | 28 | 45
AMP PEAK 2(3P14.1) MUTATED | 23 | 4 | 0 | 4
AMP PEAK 2(3P14.1) WILD-TYPE | 1 | 16 | 28 | 41

Figure S1. Get High-res Image Gene #2: 'Amp Peak 2(3p14.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 2(3p14.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.79e-06 (Fisher's exact test), Q value = 0.00027

Table S2. Gene #2: 'Amp Peak 2(3p14.1) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 37 | 21
AMP PEAK 2(3P14.1) MUTATED | 1 | 19 | 0
AMP PEAK 2(3P14.1) WILD-TYPE | 17 | 18 | 21

Figure S2. Get High-res Image Gene #2: 'Amp Peak 2(3p14.1) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 2(3p14.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000228 (Fisher's exact test), Q value = 0.033

Table S3. Gene #2: 'Amp Peak 2(3p14.1) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 27 | 45 | 12 | 33
AMP PEAK 2(3P14.1) MUTATED | 2 | 8 | 8 | 13
AMP PEAK 2(3P14.1) WILD-TYPE | 25 | 37 | 4 | 20

Figure S3. Get High-res Image Gene #2: 'Amp Peak 2(3p14.1) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 5(7q22.1) mutation analysis' versus 'CN_CNMF'

P value = 3.56e-09 (Fisher's exact test), Q value = 5.5e-07

Table S4. Gene #5: 'Amp Peak 5(7q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 20 | 28 | 45
AMP PEAK 5(7Q22.1) MUTATED | 21 | 20 | 9 | 18
AMP PEAK 5(7Q22.1) WILD-TYPE | 3 | 0 | 19 | 27

Figure S4. Get High-res Image Gene #5: 'Amp Peak 5(7q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 5(7q22.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.00172 (Fisher's exact test), Q value = 0.24

Table S5. Gene #5: 'Amp Peak 5(7q22.1) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 27 | 24 | 25
AMP PEAK 5(7Q22.1) MUTATED | 22 | 8 | 13
AMP PEAK 5(7Q22.1) WILD-TYPE | 5 | 16 | 12

Figure S5. Get High-res Image Gene #5: 'Amp Peak 5(7q22.1) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Amp Peak 5(7q22.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000515 (Fisher's exact test), Q value = 0.075

Table S6. Gene #5: 'Amp Peak 5(7q22.1) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 37 | 21
AMP PEAK 5(7Q22.1) MUTATED | 8 | 29 | 6
AMP PEAK 5(7Q22.1) WILD-TYPE | 10 | 8 | 15

Figure S6. Get High-res Image Gene #5: 'Amp Peak 5(7q22.1) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 6(17q25.2) mutation analysis' versus 'CN_CNMF'

P value = 2.9e-06 (Fisher's exact test), Q value = 0.00044

Table S7. Gene #6: 'Amp Peak 6(17q25.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 20 | 28 | 45
AMP PEAK 6(17Q25.2) MUTATED | 22 | 20 | 14 | 24
AMP PEAK 6(17Q25.2) WILD-TYPE | 2 | 0 | 14 | 21

Figure S7. Get High-res Image Gene #6: 'Amp Peak 6(17q25.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 7(19p13.2) mutation analysis' versus 'CN_CNMF'

P value = 4.94e-09 (Fisher's exact test), Q value = 7.6e-07

Table S8. Gene #7: 'Amp Peak 7(19p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 20 | 28 | 45
AMP PEAK 7(19P13.2) MUTATED | 0 | 11 | 3 | 0
AMP PEAK 7(19P13.2) WILD-TYPE | 24 | 9 | 25 | 45

Figure S8. Get High-res Image Gene #7: 'Amp Peak 7(19p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 1(1p36.31) mutation analysis' versus 'CN_CNMF'

P value = 2.27e-06 (Fisher's exact test), Q value = 0.00035

Table S9. Gene #9: 'Del Peak 1(1p36.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 20 | 28 | 45
DEL PEAK 1(1P36.31) MUTATED | 2 | 0 | 16 | 7
DEL PEAK 1(1P36.31) WILD-TYPE | 22 | 20 | 12 | 38

Figure S9. Get High-res Image Gene #9: 'Del Peak 1(1p36.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 4(3p22.1) mutation analysis' versus 'CN_CNMF'

P value = 0.000862 (Fisher's exact test), Q value = 0.12

Table S10. Gene #12: 'Del Peak 4(3p22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 20 | 28 | 45
DEL PEAK 4(3P22.1) MUTATED | 0 | 0 | 7 | 1
DEL PEAK 4(3P22.1) WILD-TYPE | 24 | 20 | 21 | 44

Figure S10. Get High-res Image Gene #12: 'Del Peak 4(3p22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 4(3p22.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000694 (Fisher's exact test), Q value = 0.098

Table S11. Gene #12: 'Del Peak 4(3p22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 21 | 27 | 39
DEL PEAK 4(3P22.1) MUTATED | 0 | 6 | 0
DEL PEAK 4(3P22.1) WILD-TYPE | 21 | 21 | 39

Figure S11. Get High-res Image Gene #12: 'Del Peak 4(3p22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 5(4q31.22) mutation analysis' versus 'CN_CNMF'

P value = 0.000304 (Fisher's exact test), Q value = 0.044

Table S12. Gene #13: 'Del Peak 5(4q31.22) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 20 | 28 | 45
DEL PEAK 5(4Q31.22) MUTATED | 3 | 0 | 9 | 1
DEL PEAK 5(4Q31.22) WILD-TYPE | 21 | 20 | 19 | 44

Figure S12. Get High-res Image Gene #13: 'Del Peak 5(4q31.22) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 5(4q31.22) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000543 (Fisher's exact test), Q value = 0.078

Table S13. Gene #13: 'Del Peak 5(4q31.22) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 21 | 27 | 39
DEL PEAK 5(4Q31.22) MUTATED | 0 | 8 | 1
DEL PEAK 5(4Q31.22) WILD-TYPE | 21 | 19 | 38

Figure S13. Get High-res Image Gene #13: 'Del Peak 5(4q31.22) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 6(5q35.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000616 (Fisher's exact test), Q value = 0.088

Table S14. Gene #14: 'Del Peak 6(5q35.2) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 27 | 24 | 25
DEL PEAK 6(5Q35.2) MUTATED | 0 | 6 | 0
DEL PEAK 6(5Q35.2) WILD-TYPE | 27 | 18 | 25

Figure S14. Get High-res Image Gene #14: 'Del Peak 6(5q35.2) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 6(5q35.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00116 (Fisher's exact test), Q value = 0.16

Table S15. Gene #14: 'Del Peak 6(5q35.2) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 37 | 21
DEL PEAK 6(5Q35.2) MUTATED | 5 | 0 | 1
DEL PEAK 6(5Q35.2) WILD-TYPE | 13 | 37 | 20

Figure S15. Get High-res Image Gene #14: 'Del Peak 6(5q35.2) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 8(9p21.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.27e-05 (Fisher's exact test), Q value = 0.0064

Table S16. Gene #16: 'Del Peak 8(9p21.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 21 | 27 | 39
DEL PEAK 8(9P21.3) MUTATED | 4 | 10 | 0
DEL PEAK 8(9P21.3) WILD-TYPE | 17 | 17 | 39

Figure S16. Get High-res Image Gene #16: 'Del Peak 8(9p21.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 8(9p21.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.4e-05 (Fisher's exact test), Q value = 0.0051

Table S17. Gene #16: 'Del Peak 8(9p21.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 27 | 24 | 25
DEL PEAK 8(9P21.3) MUTATED | 1 | 12 | 2
DEL PEAK 8(9P21.3) WILD-TYPE | 26 | 12 | 23

Figure S17. Get High-res Image Gene #16: 'Del Peak 8(9p21.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 9(14q11.2) mutation analysis' versus 'CN_CNMF'

P value = 2.56e-10 (Fisher's exact test), Q value = 4e-08

Table S18. Gene #17: 'Del Peak 9(14q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 20 | 28 | 45
DEL PEAK 9(14Q11.2) MUTATED | 5 | 0 | 19 | 2
DEL PEAK 9(14Q11.2) WILD-TYPE | 19 | 20 | 9 | 43

Figure S18. Get High-res Image Gene #17: 'Del Peak 9(14q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 10(14q23.3) mutation analysis' versus 'CN_CNMF'

P value = 2.2e-12 (Fisher's exact test), Q value = 3.5e-10

Table S19. Gene #18: 'Del Peak 10(14q23.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 20 | 28 | 45
DEL PEAK 10(14Q23.3) MUTATED | 4 | 0 | 20 | 1
DEL PEAK 10(14Q23.3) WILD-TYPE | 20 | 20 | 8 | 44

Figure S19. Get High-res Image Gene #18: 'Del Peak 10(14q23.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 11(14q32.2) mutation analysis' versus 'CN_CNMF'

P value = 1.29e-11 (Fisher's exact test), Q value = 2e-09

Table S20. Gene #19: 'Del Peak 11(14q32.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 20 | 28 | 45
DEL PEAK 11(14Q32.2) MUTATED | 3 | 0 | 20 | 2
DEL PEAK 11(14Q32.2) WILD-TYPE | 21 | 20 | 8 | 43

Figure S20. Get High-res Image Gene #19: 'Del Peak 11(14q32.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 13(Xq21.31) mutation analysis' versus 'CN_CNMF'

P value = 0.000118 (Fisher's exact test), Q value = 0.018

Table S21. Gene #21: 'Del Peak 13(Xq21.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 20 | 28 | 45
DEL PEAK 13(XQ21.31) MUTATED | 4 | 0 | 11 | 2
DEL PEAK 13(XQ21.31) WILD-TYPE | 20 | 20 | 17 | 43

Figure S21. Get High-res Image Gene #21: 'Del Peak 13(Xq21.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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 = KIRP-TP.transferedmergedcluster.txt

- Number of patients = 117

- Number of copy number variation regions = 22

- Number of molecular subtypes = 8

- 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
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