Kidney Renal Papillary Cell Carcinoma: Correlation between copy number variation genes and molecular subtypes
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
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 33 peak regions and 8 molecular subtypes across 127 patients, 33 significant findings detected with Q value < 0.25.

- Amp Peak 1(2q32.1) cnvs correlated to 'CN_CNMF'.

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

- Amp Peak 3(3q26.31) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- Amp Peak 4(5q35.2) cnvs correlated to 'CN_CNMF'.

- Amp Peak 6(7q22.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- Amp Peak 7(17q25.2) cnvs correlated to 'CN_CNMF'.

- Amp Peak 8(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(4q33) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Del Peak 7(5q15) cnvs correlated to 'CN_CNMF'.

- Del Peak 8(5q35.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- Del Peak 9(6p12.3) cnvs correlated to 'CN_CNMF'.

- Del Peak 11(6q26) cnvs correlated to 'CN_CNMF'.

- Del Peak 12(9p21.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

- Del Peak 16(14q11.2) cnvs correlated to 'CN_CNMF'.

- Del Peak 17(14q23.3) cnvs correlated to 'CN_CNMF'.

- Del Peak 18(14q32.2) cnvs correlated to 'CN_CNMF'.

- Del Peak 23(22q12.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Del Peak 24(Xq21.31) cnvs correlated to 'CN_CNMF'.

- Del Peak 25(Xq28) 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 33 regions and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 33 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 | Chi-square 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) | 32 (25%) | 95 | 1 (1.00) | 0.537 (1.00) | 4.19e-15 (9.84e-13) | 0.0294 (1.00) | 0.00279 (0.545) | 1.79e-06 (0.000404) | 0.00534 (1.00) | 0.000228 (0.0487)
Amp Peak 6(7q22 1) | 71 (56%) | 56 | 1 (1.00) | 0.808 (1.00) | 9.68e-07 (0.00022) | 6.15e-05 (0.0135) | 0.00172 (0.344) | 0.000515 (0.109) | 0.0134 (1.00) | 0.0157 (1.00)
Del Peak 8(5q35 2) | 9 (7%) | 118 | 1 (1.00) |  | 0.000165 (0.0356) | 0.00157 (0.315) | 0.000616 (0.129) | 0.00116 (0.235) | 0.394 (1.00) | 0.12 (1.00)
Del Peak 12(9p21 3) | 19 (15%) | 108 | 1 (1.00) | 0.75 (1.00) | 0.000476 (0.101) | 1.18e-05 (0.00265) | 3.4e-05 (0.00752) | 0.00182 (0.362) | 0.0341 (1.00) | 0.0922 (1.00)
Amp Peak 3(3q26 31) | 42 (33%) | 85 | 0.302 (1.00) | 0.0559 (1.00) | 1.33e-10 (3.06e-08) | 0.155 (1.00) | 0.0313 (1.00) | 0.00114 (0.232) | 0.0588 (1.00) | 0.00149 (0.302)
Del Peak 4(3p22 1) | 10 (8%) | 117 | 0.438 (1.00) |  | 0.000437 (0.093) | 8.4e-05 (0.0182) | 0.0206 (1.00) | 0.00417 (0.801) | 0.0159 (1.00) | 0.111 (1.00)
Del Peak 5(4q33) | 16 (13%) | 111 | 1 (1.00) | 0.75 (1.00) | 0.000736 (0.153) | 0.000168 (0.036) | 0.00217 (0.429) | 0.0162 (1.00) | 0.446 (1.00) | 0.598 (1.00)
Del Peak 23(22q12 2) | 34 (27%) | 93 | 0.55 (1.00) | 0.75 (1.00) | 0.000694 (0.145) | 0.000756 (0.156) | 0.519 (1.00) | 0.0314 (1.00) | 0.0652 (1.00) | 0.384 (1.00)
Amp Peak 1(2q32 1) | 23 (18%) | 104 | 0.55 (1.00) | 0.75 (1.00) | 0.000867 (0.179) | 0.0974 (1.00) | 0.942 (1.00) | 1 (1.00) | 0.832 (1.00) | 0.439 (1.00)
Amp Peak 4(5q35 2) | 19 (15%) | 108 | 0.0625 (1.00) | 0.141 (1.00) | 1.8e-13 (4.2e-11) | 0.0267 (1.00) | 0.678 (1.00) | 0.0565 (1.00) | 0.566 (1.00) | 0.0452 (1.00)
Amp Peak 7(17q25 2) | 87 (69%) | 40 | 0.585 (1.00) | 1 (1.00) | 0.00112 (0.229) | 0.0949 (1.00) | 0.28 (1.00) | 0.0388 (1.00) | 0.826 (1.00) | 0.477 (1.00)
Amp Peak 8(19p13 2) | 14 (11%) | 113 | 0.0885 (1.00) | 0.615 (1.00) | 3.65e-08 (8.35e-06) | 0.132 (1.00) | 0.0683 (1.00) | 0.765 (1.00) | 0.722 (1.00) | 0.682 (1.00)
Del Peak 1(1p36 31) | 27 (21%) | 100 | 1 (1.00) | 0.75 (1.00) | 3.09e-07 (7.05e-05) | 0.009 (1.00) | 0.0725 (1.00) | 0.0861 (1.00) | 0.418 (1.00) | 0.172 (1.00)
Del Peak 7(5q15) | 10 (8%) | 117 |  |  | 2.07e-05 (0.00462) | 0.053 (1.00) | 0.0129 (1.00) | 0.0506 (1.00) | 0.96 (1.00) | 0.315 (1.00)
Del Peak 9(6p12 3) | 12 (9%) | 115 | 1 (1.00) |  | 6.35e-05 (0.0139) | 0.0263 (1.00) | 0.697 (1.00) | 0.675 (1.00) | 0.411 (1.00) | 0.77 (1.00)
Del Peak 11(6q26) | 15 (12%) | 112 | 1 (1.00) |  | 7.23e-05 (0.0158) | 0.00303 (0.588) | 0.399 (1.00) | 0.303 (1.00) | 0.913 (1.00) | 0.597 (1.00)
Del Peak 16(14q11 2) | 29 (23%) | 98 | 0.596 (1.00) | 0.167 (1.00) | 1.86e-10 (4.27e-08) | 0.276 (1.00) | 0.0934 (1.00) | 0.177 (1.00) | 0.835 (1.00) | 0.953 (1.00)
Del Peak 17(14q23 3) | 28 (22%) | 99 | 1 (1.00) | 0.385 (1.00) | 6.82e-13 (1.58e-10) | 0.122 (1.00) | 0.0351 (1.00) | 0.0295 (1.00) | 0.719 (1.00) | 0.886 (1.00)
Del Peak 18(14q32 2) | 28 (22%) | 99 | 1 (1.00) | 0.385 (1.00) | 6.48e-13 (1.51e-10) | 0.23 (1.00) | 0.0775 (1.00) | 0.0648 (1.00) | 0.719 (1.00) | 0.886 (1.00)
Del Peak 24(Xq21 31) | 18 (14%) | 109 | 1 (1.00) |  | 7.17e-06 (0.00161) | 0.00341 (0.658) | 0.00278 (0.545) | 0.0354 (1.00) | 0.768 (1.00) | 0.806 (1.00)
Del Peak 25(Xq28) | 17 (13%) | 110 | 1 (1.00) |  | 2.93e-05 (0.0065) | 0.0608 (1.00) | 0.0436 (1.00) | 0.253 (1.00) | 0.713 (1.00) | 0.941 (1.00)
Amp Peak 5(6p12 3) | 4 (3%) | 123 |  |  | 0.0634 (1.00) | 0.137 (1.00) | 0.114 (1.00) | 0.35 (1.00) | 0.165 (1.00) | 0.186 (1.00)
Amp Peak 9(19q13 11) | 4 (3%) | 123 |  |  | 0.927 (1.00) | 0.137 (1.00) | 0.201 (1.00) | 0.13 (1.00) | 0.331 (1.00) | 0.473 (1.00)
Del Peak 2(2p11 2) | 3 (2%) | 124 |  |  | 0.613 (1.00) | 0.8 (1.00) |  |  | 0.028 (1.00) | 0.0273 (1.00)
Del Peak 3(2q37 3) | 5 (4%) | 122 | 1 (1.00) |  | 0.959 (1.00) | 0.139 (1.00) | 0.684 (1.00) | 0.35 (1.00) | 0.704 (1.00) | 0.84 (1.00)
Del Peak 6(5p15 2) | 7 (6%) | 120 |  |  | 0.00642 (1.00) | 0.0362 (1.00) | 0.0395 (1.00) | 0.017 (1.00) | 0.447 (1.00) | 0.444 (1.00)
Del Peak 10(6q22 31) | 14 (11%) | 113 | 1 (1.00) |  | 0.00555 (1.00) | 0.0212 (1.00) | 0.0976 (1.00) | 0.175 (1.00) | 0.787 (1.00) | 0.337 (1.00)
Del Peak 13(10p15 3) | 8 (6%) | 119 |  |  | 0.0609 (1.00) | 0.0111 (1.00) | 0.435 (1.00) | 0.232 (1.00) | 0.293 (1.00) | 0.106 (1.00)
Del Peak 14(11q22 3) | 14 (11%) | 113 | 1 (1.00) |  | 0.00848 (1.00) | 0.00257 (0.506) | 0.0772 (1.00) | 0.0114 (1.00) | 0.903 (1.00) | 0.568 (1.00)
Del Peak 19(15q14) | 16 (13%) | 111 | 1 (1.00) |  | 0.00506 (0.967) | 0.00849 (1.00) | 0.112 (1.00) | 0.301 (1.00) | 0.288 (1.00) | 0.438 (1.00)
Del Peak 20(19p13 3) | 13 (10%) | 114 | 0.438 (1.00) |  | 0.00729 (1.00) | 0.231 (1.00) | 0.43 (1.00) | 0.0871 (1.00) | 0.801 (1.00) | 0.731 (1.00)
Del Peak 21(19q13 2) | 11 (9%) | 116 |  |  | 0.179 (1.00) | 0.136 (1.00) | 0.732 (1.00) | 0.0493 (1.00) | 0.419 (1.00) | 0.595 (1.00)
Del Peak 22(19q13 42) | 12 (9%) | 115 |  |  | 0.186 (1.00) | 0.3 (1.00) | 0.732 (1.00) | 0.232 (1.00) | 0.471 (1.00) | 0.438 (1.00)

'Amp Peak 1(2q32.1) mutation analysis' versus 'CN_CNMF'

P value = 0.000867 (Chi-square test), Q value = 0.18

Table S1. Gene #1: 'Amp Peak 1(2q32.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 24 | 44 | 13 | 26 | 20
AMP PEAK 1(2Q32.1) MUTATED | 10 | 1 | 1 | 7 | 4
AMP PEAK 1(2Q32.1) WILD-TYPE | 14 | 43 | 12 | 19 | 16

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(2q32.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 4.19e-15 (Chi-square test), Q value = 9.8e-13

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 24 | 44 | 13 | 26 | 20
AMP PEAK 2(3P14.1) MUTATED | 2 | 2 | 3 | 5 | 20
AMP PEAK 2(3P14.1) WILD-TYPE | 22 | 42 | 10 | 21 | 0

Figure S2. 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 = 4e-04

Table S3. 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 S3. 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 = 0.049

Table S4. 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 S4. Get High-res Image Gene #2: 'Amp Peak 2(3p14.1) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 3(3q26.31) mutation analysis' versus 'CN_CNMF'

P value = 1.33e-10 (Chi-square test), Q value = 3.1e-08

Table S5. Gene #3: 'Amp Peak 3(3q26.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 24 | 44 | 13 | 26 | 20
AMP PEAK 3(3Q26.31) MUTATED | 5 | 5 | 3 | 9 | 20
AMP PEAK 3(3Q26.31) WILD-TYPE | 19 | 39 | 10 | 17 | 0

Figure S5. Get High-res Image Gene #3: 'Amp Peak 3(3q26.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 3(3q26.31) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00114 (Fisher's exact test), Q value = 0.23

Table S6. Gene #3: 'Amp Peak 3(3q26.31) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 37 | 21
AMP PEAK 3(3Q26.31) MUTATED | 4 | 20 | 2
AMP PEAK 3(3Q26.31) WILD-TYPE | 14 | 17 | 19

Figure S6. Get High-res Image Gene #3: 'Amp Peak 3(3q26.31) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 4(5q35.2) mutation analysis' versus 'CN_CNMF'

P value = 1.8e-13 (Chi-square test), Q value = 4.2e-11

Table S7. Gene #4: 'Amp Peak 4(5q35.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 24 | 44 | 13 | 26 | 20
AMP PEAK 4(5Q35.2) MUTATED | 0 | 2 | 0 | 17 | 0
AMP PEAK 4(5Q35.2) WILD-TYPE | 24 | 42 | 13 | 9 | 20

Figure S7. Get High-res Image Gene #4: 'Amp Peak 4(5q35.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 6(7q22.1) mutation analysis' versus 'CN_CNMF'

P value = 9.68e-07 (Chi-square test), Q value = 0.00022

Table S8. Gene #6: 'Amp Peak 6(7q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 24 | 44 | 13 | 26 | 20
AMP PEAK 6(7Q22.1) MUTATED | 7 | 22 | 13 | 10 | 19
AMP PEAK 6(7Q22.1) WILD-TYPE | 17 | 22 | 0 | 16 | 1

Figure S8. Get High-res Image Gene #6: 'Amp Peak 6(7q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 6(7q22.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.15e-05 (Fisher's exact test), Q value = 0.014

Table S9. Gene #6: 'Amp Peak 6(7q22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 27 | 53 | 31
AMP PEAK 6(7Q22.1) MUTATED | 10 | 40 | 10
AMP PEAK 6(7Q22.1) WILD-TYPE | 17 | 13 | 21

Figure S9. Get High-res Image Gene #6: 'Amp Peak 6(7q22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 6(7q22.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000515 (Fisher's exact test), Q value = 0.11

Table S10. Gene #6: 'Amp Peak 6(7q22.1) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S10. Get High-res Image Gene #6: 'Amp Peak 6(7q22.1) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 7(17q25.2) mutation analysis' versus 'CN_CNMF'

P value = 0.00112 (Chi-square test), Q value = 0.23

Table S11. Gene #7: 'Amp Peak 7(17q25.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 24 | 44 | 13 | 26 | 20
AMP PEAK 7(17Q25.2) MUTATED | 12 | 26 | 13 | 17 | 19
AMP PEAK 7(17Q25.2) WILD-TYPE | 12 | 18 | 0 | 9 | 1

Figure S11. Get High-res Image Gene #7: 'Amp Peak 7(17q25.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 8(19p13.2) mutation analysis' versus 'CN_CNMF'

P value = 3.65e-08 (Chi-square test), Q value = 8.4e-06

Table S12. Gene #8: 'Amp Peak 8(19p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 24 | 44 | 13 | 26 | 20
AMP PEAK 8(19P13.2) MUTATED | 3 | 0 | 8 | 2 | 1
AMP PEAK 8(19P13.2) WILD-TYPE | 21 | 44 | 5 | 24 | 19

Figure S12. Get High-res Image Gene #8: 'Amp Peak 8(19p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 3.09e-07 (Chi-square test), Q value = 7.1e-05

Table S13. Gene #10: 'Del Peak 1(1p36.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 24 | 44 | 13 | 26 | 20
DEL PEAK 1(1P36.31) MUTATED | 12 | 3 | 0 | 12 | 0
DEL PEAK 1(1P36.31) WILD-TYPE | 12 | 41 | 13 | 14 | 20

Figure S13. Get High-res Image Gene #10: '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 = 0.000437 (Chi-square test), Q value = 0.093

Table S14. Gene #13: 'Del Peak 4(3p22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 24 | 44 | 13 | 26 | 20
DEL PEAK 4(3P22.1) MUTATED | 3 | 0 | 0 | 7 | 0
DEL PEAK 4(3P22.1) WILD-TYPE | 21 | 44 | 13 | 19 | 20

Figure S14. Get High-res Image Gene #13: '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 = 8.4e-05 (Fisher's exact test), Q value = 0.018

Table S15. Gene #13: 'Del Peak 4(3p22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 27 | 53 | 31
DEL PEAK 4(3P22.1) MUTATED | 1 | 0 | 8
DEL PEAK 4(3P22.1) WILD-TYPE | 26 | 53 | 23

Figure S15. Get High-res Image Gene #13: 'Del Peak 4(3p22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 5(4q33) mutation analysis' versus 'CN_CNMF'

P value = 0.000736 (Chi-square test), Q value = 0.15

Table S16. Gene #14: 'Del Peak 5(4q33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 24 | 44 | 13 | 26 | 20
DEL PEAK 5(4Q33) MUTATED | 8 | 1 | 0 | 6 | 1
DEL PEAK 5(4Q33) WILD-TYPE | 16 | 43 | 13 | 20 | 19

Figure S16. Get High-res Image Gene #14: 'Del Peak 5(4q33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 5(4q33) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000168 (Fisher's exact test), Q value = 0.036

Table S17. Gene #14: 'Del Peak 5(4q33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 27 | 53 | 31
DEL PEAK 5(4Q33) MUTATED | 2 | 1 | 10
DEL PEAK 5(4Q33) WILD-TYPE | 25 | 52 | 21

Figure S17. Get High-res Image Gene #14: 'Del Peak 5(4q33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 7(5q15) mutation analysis' versus 'CN_CNMF'

P value = 2.07e-05 (Chi-square test), Q value = 0.0046

Table S18. Gene #16: 'Del Peak 7(5q15) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 24 | 44 | 13 | 26 | 20
DEL PEAK 7(5Q15) MUTATED | 8 | 1 | 0 | 0 | 1
DEL PEAK 7(5Q15) WILD-TYPE | 16 | 43 | 13 | 26 | 19

Figure S18. Get High-res Image Gene #16: 'Del Peak 7(5q15) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 8(5q35.2) mutation analysis' versus 'CN_CNMF'

P value = 0.000165 (Chi-square test), Q value = 0.036

Table S19. Gene #17: 'Del Peak 8(5q35.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 24 | 44 | 13 | 26 | 20
DEL PEAK 8(5Q35.2) MUTATED | 7 | 1 | 0 | 0 | 1
DEL PEAK 8(5Q35.2) WILD-TYPE | 17 | 43 | 13 | 26 | 19

Figure S19. Get High-res Image Gene #17: 'Del Peak 8(5q35.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 8(5q35.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000616 (Fisher's exact test), Q value = 0.13

Table S20. Gene #17: 'Del Peak 8(5q35.2) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 27 | 24 | 25
DEL PEAK 8(5Q35.2) MUTATED | 0 | 6 | 0
DEL PEAK 8(5Q35.2) WILD-TYPE | 27 | 18 | 25

Figure S20. Get High-res Image Gene #17: 'Del Peak 8(5q35.2) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 8(5q35.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00116 (Fisher's exact test), Q value = 0.23

Table S21. Gene #17: 'Del Peak 8(5q35.2) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 37 | 21
DEL PEAK 8(5Q35.2) MUTATED | 5 | 0 | 1
DEL PEAK 8(5Q35.2) WILD-TYPE | 13 | 37 | 20

Figure S21. Get High-res Image Gene #17: 'Del Peak 8(5q35.2) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 9(6p12.3) mutation analysis' versus 'CN_CNMF'

P value = 6.35e-05 (Chi-square test), Q value = 0.014

Table S22. Gene #18: 'Del Peak 9(6p12.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 24 | 44 | 13 | 26 | 20
DEL PEAK 9(6P12.3) MUTATED | 1 | 1 | 0 | 9 | 1
DEL PEAK 9(6P12.3) WILD-TYPE | 23 | 43 | 13 | 17 | 19

Figure S22. Get High-res Image Gene #18: 'Del Peak 9(6p12.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 11(6q26) mutation analysis' versus 'CN_CNMF'

P value = 7.23e-05 (Chi-square test), Q value = 0.016

Table S23. Gene #20: 'Del Peak 11(6q26) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 24 | 44 | 13 | 26 | 20
DEL PEAK 11(6Q26) MUTATED | 3 | 1 | 0 | 10 | 1
DEL PEAK 11(6Q26) WILD-TYPE | 21 | 43 | 13 | 16 | 19

Figure S23. Get High-res Image Gene #20: 'Del Peak 11(6q26) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 12(9p21.3) mutation analysis' versus 'CN_CNMF'

P value = 0.000476 (Chi-square test), Q value = 0.1

Table S24. Gene #21: 'Del Peak 12(9p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 24 | 44 | 13 | 26 | 20
DEL PEAK 12(9P21.3) MUTATED | 9 | 2 | 0 | 7 | 1
DEL PEAK 12(9P21.3) WILD-TYPE | 15 | 42 | 13 | 19 | 19

Figure S24. Get High-res Image Gene #21: 'Del Peak 12(9p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 12(9p21.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.18e-05 (Fisher's exact test), Q value = 0.0027

Table S25. Gene #21: 'Del Peak 12(9p21.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 27 | 53 | 31
DEL PEAK 12(9P21.3) MUTATED | 6 | 0 | 10
DEL PEAK 12(9P21.3) WILD-TYPE | 21 | 53 | 21

Figure S25. Get High-res Image Gene #21: 'Del Peak 12(9p21.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 12(9p21.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.4e-05 (Fisher's exact test), Q value = 0.0075

Table S26. Gene #21: 'Del Peak 12(9p21.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

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

Figure S26. Get High-res Image Gene #21: 'Del Peak 12(9p21.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 16(14q11.2) mutation analysis' versus 'CN_CNMF'

P value = 1.86e-10 (Chi-square test), Q value = 4.3e-08

Table S27. Gene #24: 'Del Peak 16(14q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 24 | 44 | 13 | 26 | 20
DEL PEAK 16(14Q11.2) MUTATED | 18 | 2 | 0 | 7 | 2
DEL PEAK 16(14Q11.2) WILD-TYPE | 6 | 42 | 13 | 19 | 18

Figure S27. Get High-res Image Gene #24: 'Del Peak 16(14q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 17(14q23.3) mutation analysis' versus 'CN_CNMF'

P value = 6.82e-13 (Chi-square test), Q value = 1.6e-10

Table S28. Gene #25: 'Del Peak 17(14q23.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 24 | 44 | 13 | 26 | 20
DEL PEAK 17(14Q23.3) MUTATED | 19 | 1 | 0 | 7 | 1
DEL PEAK 17(14Q23.3) WILD-TYPE | 5 | 43 | 13 | 19 | 19

Figure S28. Get High-res Image Gene #25: 'Del Peak 17(14q23.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 18(14q32.2) mutation analysis' versus 'CN_CNMF'

P value = 6.48e-13 (Chi-square test), Q value = 1.5e-10

Table S29. Gene #26: 'Del Peak 18(14q32.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 24 | 44 | 13 | 26 | 20
DEL PEAK 18(14Q32.2) MUTATED | 19 | 2 | 0 | 7 | 0
DEL PEAK 18(14Q32.2) WILD-TYPE | 5 | 42 | 13 | 19 | 20

Figure S29. Get High-res Image Gene #26: 'Del Peak 18(14q32.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 23(22q12.2) mutation analysis' versus 'CN_CNMF'

P value = 0.000694 (Chi-square test), Q value = 0.14

Table S30. Gene #31: 'Del Peak 23(22q12.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 24 | 44 | 13 | 26 | 20
DEL PEAK 23(22Q12.2) MUTATED | 9 | 9 | 1 | 14 | 1
DEL PEAK 23(22Q12.2) WILD-TYPE | 15 | 35 | 12 | 12 | 19

Figure S30. Get High-res Image Gene #31: 'Del Peak 23(22q12.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 23(22q12.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000756 (Fisher's exact test), Q value = 0.16

Table S31. Gene #31: 'Del Peak 23(22q12.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 27 | 53 | 31
DEL PEAK 23(22Q12.2) MUTATED | 5 | 9 | 17
DEL PEAK 23(22Q12.2) WILD-TYPE | 22 | 44 | 14

Figure S31. Get High-res Image Gene #31: 'Del Peak 23(22q12.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 24(Xq21.31) mutation analysis' versus 'CN_CNMF'

P value = 7.17e-06 (Chi-square test), Q value = 0.0016

Table S32. Gene #32: 'Del Peak 24(Xq21.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 24 | 44 | 13 | 26 | 20
DEL PEAK 24(XQ21.31) MUTATED | 10 | 0 | 0 | 7 | 1
DEL PEAK 24(XQ21.31) WILD-TYPE | 14 | 44 | 13 | 19 | 19

Figure S32. Get High-res Image Gene #32: 'Del Peak 24(Xq21.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 25(Xq28) mutation analysis' versus 'CN_CNMF'

P value = 2.93e-05 (Chi-square test), Q value = 0.0065

Table S33. Gene #33: 'Del Peak 25(Xq28) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 24 | 44 | 13 | 26 | 20
DEL PEAK 25(XQ28) MUTATED | 9 | 0 | 0 | 7 | 1
DEL PEAK 25(XQ28) WILD-TYPE | 15 | 44 | 13 | 19 | 19

Figure S33. Get High-res Image Gene #33: 'Del Peak 25(Xq28) 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 = 127

- Number of copy number variation regions = 33

- 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

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

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] 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)
[4] GISTIC_version2
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