Thyroid Adenocarcinoma: 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 27 peak regions and 8 molecular subtypes across 470 patients, 52 significant findings detected with Q value < 0.25.

- Amp Peak 1(Xq22.3) cnvs correlated to 'CN_CNMF'.

- Del Peak 2(2p23.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- Del Peak 3(2q35) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- Del Peak 6(6q22.31) cnvs correlated to 'CN_CNMF'.

- Del Peak 9(8p12) cnvs correlated to 'CN_CNMF'.

- Del Peak 10(8q24.22) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- Del Peak 11(9q21.13) cnvs correlated to 'CN_CNMF'.

- Del Peak 12(10q21.2) cnvs correlated to 'CN_CNMF'.

- Del Peak 13(10q23.31) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- Del Peak 14(11p15.1) cnvs correlated to 'CN_CNMF'.

- Del Peak 15(13q12.3) cnvs correlated to 'METHLYATION_CNMF'.

- Del Peak 17(15q25.3) cnvs correlated to 'CN_CNMF'.

- Del Peak 21(18p11.21) cnvs correlated to 'CN_CNMF'.

- Del Peak 22(18q22.2) cnvs correlated to 'CN_CNMF'.

- Del Peak 23(19p13.2) cnvs correlated to 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- Del Peak 26(21q21.1) cnvs correlated to 'CN_CNMF'.

- Del Peak 27(22q13.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

- Del Peak 28(22q13.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

- Del Peak 29(22q13.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

- Del Peak 30(22q13.32) 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 27 regions and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 52 significant findings detected.

|  | Molecular subtypes | CN CNMF | METHLYATION CNMF | RPPA CNMF | RPPA CHIERARCHICAL | 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
Del Peak 2(2p23 1) | 12 (3%) | 458 | 4.94e-10 (9.88e-08) | 2.89e-05 (0.00515) | 0.772 (1.00) | 0.0179 (1.00) | 1.83e-05 (0.00341) | 1.93e-05 (0.00356) | 1.19e-06 (0.000229) | 5.09e-07 (9.87e-05)
Del Peak 3(2q35) | 11 (2%) | 459 | 1.04e-11 (2.1e-09) | 2.47e-05 (0.00442) | 0.562 (1.00) | 0.00287 (0.425) | 1.83e-05 (0.00341) | 1.93e-05 (0.00356) | 1.19e-06 (0.000229) | 5.09e-07 (9.87e-05)
Del Peak 27(22q13 1) | 81 (17%) | 389 | 5.8e-86 (1.19e-83) | 0.000321 (0.0548) | 0.205 (1.00) | 0.0795 (1.00) | 3.11e-07 (6.12e-05) | 2e-05 (0.00365) | 0.00371 (0.545) | 0.00144 (0.228)
Del Peak 28(22q13 2) | 81 (17%) | 389 | 5.8e-86 (1.19e-83) | 0.000321 (0.0548) | 0.205 (1.00) | 0.0795 (1.00) | 3.11e-07 (6.12e-05) | 2e-05 (0.00365) | 0.00371 (0.545) | 0.00144 (0.228)
Del Peak 29(22q13 31) | 81 (17%) | 389 | 5.8e-86 (1.19e-83) | 0.000321 (0.0548) | 0.205 (1.00) | 0.0795 (1.00) | 3.11e-07 (6.12e-05) | 2e-05 (0.00365) | 0.00371 (0.545) | 0.00144 (0.228)
Del Peak 30(22q13 32) | 82 (17%) | 388 | 4.47e-84 (9.08e-82) | 0.000162 (0.0282) | 0.205 (1.00) | 0.0795 (1.00) | 1.64e-07 (3.25e-05) | 1.17e-05 (0.00222) | 0.00209 (0.322) | 0.000846 (0.139)
Del Peak 10(8q24 22) | 7 (1%) | 463 | 5.43e-05 (0.00962) | 0.00247 (0.373) | 0.837 (1.00) | 0.0549 (1.00) | 0.00213 (0.324) | 0.00122 (0.196) | 0.000185 (0.0319) | 0.000108 (0.019)
Del Peak 23(19p13 2) | 6 (1%) | 464 | 0.00498 (0.707) | 0.00102 (0.165) | 0.682 (1.00) | 0.256 (1.00) | 0.00664 (0.922) | 0.00259 (0.387) | 0.000641 (0.106) | 0.000407 (0.0684)
Del Peak 13(10q23 31) | 11 (2%) | 459 | 6.4e-05 (0.0113) | 0.0184 (1.00) | 0.0336 (1.00) | 0.0641 (1.00) | 0.00424 (0.611) | 0.00115 (0.187) | 0.0315 (1.00) | 0.0136 (1.00)
Amp Peak 1(Xq22 3) | 16 (3%) | 454 | 2.56e-06 (0.000486) | 0.461 (1.00) | 0.856 (1.00) | 0.129 (1.00) | 0.0422 (1.00) | 0.0361 (1.00) | 0.0704 (1.00) | 0.0468 (1.00)
Del Peak 6(6q22 31) | 6 (1%) | 464 | 0.000427 (0.0712) | 0.00547 (0.772) | 0.0379 (1.00) | 0.798 (1.00) | 0.0173 (1.00) | 0.00933 (1.00) | 0.00877 (1.00) | 0.00798 (1.00)
Del Peak 9(8p12) | 4 (1%) | 466 | 2.31e-05 (0.00416) | 0.0474 (1.00) |  |  | 0.0371 (1.00) | 0.0346 (1.00) | 0.00761 (1.00) | 0.00564 (0.789)
Del Peak 11(9q21 13) | 22 (5%) | 448 | 4.31e-14 (8.7e-12) | 0.155 (1.00) | 0.182 (1.00) | 0.0136 (1.00) | 0.245 (1.00) | 0.788 (1.00) | 0.0282 (1.00) | 0.0542 (1.00)
Del Peak 12(10q21 2) | 11 (2%) | 459 | 0.000788 (0.13) | 0.0668 (1.00) | 0.162 (1.00) | 1 (1.00) | 0.0513 (1.00) | 0.148 (1.00) | 0.373 (1.00) | 0.609 (1.00)
Del Peak 14(11p15 1) | 6 (1%) | 464 | 9.28e-08 (1.85e-05) | 0.0202 (1.00) | 0.499 (1.00) | 1 (1.00) | 0.0495 (1.00) | 0.166 (1.00) | 0.0256 (1.00) | 0.0361 (1.00)
Del Peak 15(13q12 3) | 15 (3%) | 455 | 0.0258 (1.00) | 0.00123 (0.197) | 0.388 (1.00) | 0.44 (1.00) | 0.00963 (1.00) | 0.0448 (1.00) | 0.0541 (1.00) | 0.0258 (1.00)
Del Peak 17(15q25 3) | 7 (1%) | 463 | 0.00134 (0.213) | 0.032 (1.00) | 0.444 (1.00) | 0.0817 (1.00) | 0.0841 (1.00) | 0.0672 (1.00) | 0.0046 (0.658) | 0.00247 (0.373)
Del Peak 21(18p11 21) | 4 (1%) | 466 | 0.000241 (0.0414) | 0.191 (1.00) | 1 (1.00) | 0.369 (1.00) | 0.242 (1.00) | 0.0893 (1.00) | 0.111 (1.00) | 0.0414 (1.00)
Del Peak 22(18q22 2) | 5 (1%) | 465 | 0.00151 (0.233) | 0.0616 (1.00) | 1 (1.00) | 0.256 (1.00) | 0.12 (1.00) | 0.0427 (1.00) | 0.0395 (1.00) | 0.0134 (1.00)
Del Peak 26(21q21 1) | 8 (2%) | 462 | 1.29e-05 (0.00242) | 0.172 (1.00) | 0.147 (1.00) | 0.206 (1.00) | 0.289 (1.00) | 0.459 (1.00) | 0.0516 (1.00) | 0.0866 (1.00)
Del Peak 4(5p15 2) | 3 (1%) | 467 | 0.261 (1.00) | 0.728 (1.00) |  |  |  |  |  |
Del Peak 8(7q34) | 4 (1%) | 466 | 0.646 (1.00) | 0.635 (1.00) |  |  | 0.747 (1.00) | 0.589 (1.00) | 1 (1.00) | 1 (1.00)
Del Peak 16(13q14 3) | 18 (4%) | 452 | 0.00717 (0.989) | 0.0318 (1.00) | 0.0908 (1.00) | 1 (1.00) | 0.0103 (1.00) | 0.0249 (1.00) | 0.0279 (1.00) | 0.021 (1.00)
Del Peak 19(16q23 3) | 6 (1%) | 464 | 0.0518 (1.00) | 0.126 (1.00) | 0.444 (1.00) | 0.103 (1.00) | 0.127 (1.00) | 0.111 (1.00) | 0.194 (1.00) | 0.292 (1.00)
Del Peak 20(17p13 1) | 8 (2%) | 462 | 0.0021 (0.322) | 0.884 (1.00) | 1 (1.00) | 1 (1.00) | 0.71 (1.00) | 0.642 (1.00) | 0.294 (1.00) | 0.308 (1.00)
Del Peak 31(Xq22 1) | 6 (1%) | 464 | 0.0793 (1.00) | 0.437 (1.00) | 0.0993 (1.00) | 0.12 (1.00) | 0.671 (1.00) | 0.861 (1.00) | 0.522 (1.00) | 0.386 (1.00)
Del Peak 32(Xq22 3) | 4 (1%) | 466 | 0.0568 (1.00) | 0.0474 (1.00) | 0.281 (1.00) | 0.369 (1.00) | 0.129 (1.00) | 0.4 (1.00) | 0.111 (1.00) | 0.0414 (1.00)

'Amp Peak 1(Xq22.3) mutation analysis' versus 'CN_CNMF'

P value = 2.56e-06 (Fisher's exact test), Q value = 0.00049

Table S1. Gene #1: 'Amp Peak 1(Xq22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
AMP PEAK 1(XQ22.3) MUTATED | 8 | 8 | 0
AMP PEAK 1(XQ22.3) WILD-TYPE | 26 | 355 | 73

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(Xq22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 2(2p23.1) mutation analysis' versus 'CN_CNMF'

P value = 4.94e-10 (Fisher's exact test), Q value = 9.9e-08

Table S2. Gene #2: 'Del Peak 2(2p23.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
DEL PEAK 2(2P23.1) MUTATED | 9 | 1 | 2
DEL PEAK 2(2P23.1) WILD-TYPE | 25 | 362 | 71

Figure S2. Get High-res Image Gene #2: 'Del Peak 2(2p23.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 2(2p23.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.89e-05 (Fisher's exact test), Q value = 0.0052

Table S3. Gene #2: 'Del Peak 2(2p23.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 140 | 71 | 259
DEL PEAK 2(2P23.1) MUTATED | 10 | 2 | 0
DEL PEAK 2(2P23.1) WILD-TYPE | 130 | 69 | 259

Figure S3. Get High-res Image Gene #2: 'Del Peak 2(2p23.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 2(2p23.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.83e-05 (Fisher's exact test), Q value = 0.0034

Table S4. Gene #2: 'Del Peak 2(2p23.1) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 130 | 50 | 89 | 138
DEL PEAK 2(2P23.1) MUTATED | 11 | 0 | 0 | 0
DEL PEAK 2(2P23.1) WILD-TYPE | 119 | 50 | 89 | 138

Figure S4. Get High-res Image Gene #2: 'Del Peak 2(2p23.1) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 2(2p23.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.93e-05 (Fisher's exact test), Q value = 0.0036

Table S5. Gene #2: 'Del Peak 2(2p23.1) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 142 | 191 | 74
DEL PEAK 2(2P23.1) MUTATED | 11 | 0 | 0
DEL PEAK 2(2P23.1) WILD-TYPE | 131 | 191 | 74

Figure S5. Get High-res Image Gene #2: 'Del Peak 2(2p23.1) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 2(2p23.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.19e-06 (Fisher's exact test), Q value = 0.00023

Table S6. Gene #2: 'Del Peak 2(2p23.1) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 126 | 153 | 144
DEL PEAK 2(2P23.1) MUTATED | 11 | 0 | 0
DEL PEAK 2(2P23.1) WILD-TYPE | 115 | 153 | 144

Figure S6. Get High-res Image Gene #2: 'Del Peak 2(2p23.1) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'Del Peak 2(2p23.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.09e-07 (Fisher's exact test), Q value = 9.9e-05

Table S7. Gene #2: 'Del Peak 2(2p23.1) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 173 | 133 | 117
DEL PEAK 2(2P23.1) MUTATED | 0 | 0 | 11
DEL PEAK 2(2P23.1) WILD-TYPE | 173 | 133 | 106

Figure S7. Get High-res Image Gene #2: 'Del Peak 2(2p23.1) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 3(2q35) mutation analysis' versus 'CN_CNMF'

P value = 1.04e-11 (Fisher's exact test), Q value = 2.1e-09

Table S8. Gene #3: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
DEL PEAK 3(2Q35) MUTATED | 10 | 1 | 0
DEL PEAK 3(2Q35) WILD-TYPE | 24 | 362 | 73

Figure S8. Get High-res Image Gene #3: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 3(2q35) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.47e-05 (Fisher's exact test), Q value = 0.0044

Table S9. Gene #3: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 140 | 71 | 259
DEL PEAK 3(2Q35) MUTATED | 10 | 1 | 0
DEL PEAK 3(2Q35) WILD-TYPE | 130 | 70 | 259

Figure S9. Get High-res Image Gene #3: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 3(2q35) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.83e-05 (Fisher's exact test), Q value = 0.0034

Table S10. Gene #3: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 130 | 50 | 89 | 138
DEL PEAK 3(2Q35) MUTATED | 11 | 0 | 0 | 0
DEL PEAK 3(2Q35) WILD-TYPE | 119 | 50 | 89 | 138

Figure S10. Get High-res Image Gene #3: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 3(2q35) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.93e-05 (Fisher's exact test), Q value = 0.0036

Table S11. Gene #3: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 142 | 191 | 74
DEL PEAK 3(2Q35) MUTATED | 11 | 0 | 0
DEL PEAK 3(2Q35) WILD-TYPE | 131 | 191 | 74

Figure S11. Get High-res Image Gene #3: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 3(2q35) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.19e-06 (Fisher's exact test), Q value = 0.00023

Table S12. Gene #3: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 126 | 153 | 144
DEL PEAK 3(2Q35) MUTATED | 11 | 0 | 0
DEL PEAK 3(2Q35) WILD-TYPE | 115 | 153 | 144

Figure S12. Get High-res Image Gene #3: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'Del Peak 3(2q35) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.09e-07 (Fisher's exact test), Q value = 9.9e-05

Table S13. Gene #3: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 173 | 133 | 117
DEL PEAK 3(2Q35) MUTATED | 0 | 0 | 11
DEL PEAK 3(2Q35) WILD-TYPE | 173 | 133 | 106

Figure S13. Get High-res Image Gene #3: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 6(6q22.31) mutation analysis' versus 'CN_CNMF'

P value = 0.000427 (Fisher's exact test), Q value = 0.071

Table S14. Gene #5: 'Del Peak 6(6q22.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
DEL PEAK 6(6Q22.31) MUTATED | 4 | 2 | 0
DEL PEAK 6(6Q22.31) WILD-TYPE | 30 | 361 | 73

Figure S14. Get High-res Image Gene #5: 'Del Peak 6(6q22.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 9(8p12) mutation analysis' versus 'CN_CNMF'

P value = 2.31e-05 (Fisher's exact test), Q value = 0.0042

Table S15. Gene #7: 'Del Peak 9(8p12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
DEL PEAK 9(8P12) MUTATED | 4 | 0 | 0
DEL PEAK 9(8P12) WILD-TYPE | 30 | 363 | 73

Figure S15. Get High-res Image Gene #7: 'Del Peak 9(8p12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 10(8q24.22) mutation analysis' versus 'CN_CNMF'

P value = 5.43e-05 (Fisher's exact test), Q value = 0.0096

Table S16. Gene #8: 'Del Peak 10(8q24.22) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
DEL PEAK 10(8Q24.22) MUTATED | 5 | 2 | 0
DEL PEAK 10(8Q24.22) WILD-TYPE | 29 | 361 | 73

Figure S16. Get High-res Image Gene #8: 'Del Peak 10(8q24.22) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 10(8q24.22) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00122 (Fisher's exact test), Q value = 0.2

Table S17. Gene #8: 'Del Peak 10(8q24.22) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 142 | 191 | 74
DEL PEAK 10(8Q24.22) MUTATED | 7 | 0 | 0
DEL PEAK 10(8Q24.22) WILD-TYPE | 135 | 191 | 74

Figure S17. Get High-res Image Gene #8: 'Del Peak 10(8q24.22) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 10(8q24.22) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000185 (Fisher's exact test), Q value = 0.032

Table S18. Gene #8: 'Del Peak 10(8q24.22) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 126 | 153 | 144
DEL PEAK 10(8Q24.22) MUTATED | 7 | 0 | 0
DEL PEAK 10(8Q24.22) WILD-TYPE | 119 | 153 | 144

Figure S18. Get High-res Image Gene #8: 'Del Peak 10(8q24.22) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'Del Peak 10(8q24.22) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000108 (Fisher's exact test), Q value = 0.019

Table S19. Gene #8: 'Del Peak 10(8q24.22) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 173 | 133 | 117
DEL PEAK 10(8Q24.22) MUTATED | 0 | 0 | 7
DEL PEAK 10(8Q24.22) WILD-TYPE | 173 | 133 | 110

Figure S19. Get High-res Image Gene #8: 'Del Peak 10(8q24.22) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 11(9q21.13) mutation analysis' versus 'CN_CNMF'

P value = 4.31e-14 (Fisher's exact test), Q value = 8.7e-12

Table S20. Gene #9: 'Del Peak 11(9q21.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
DEL PEAK 11(9Q21.13) MUTATED | 15 | 7 | 0
DEL PEAK 11(9Q21.13) WILD-TYPE | 19 | 356 | 73

Figure S20. Get High-res Image Gene #9: 'Del Peak 11(9q21.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 12(10q21.2) mutation analysis' versus 'CN_CNMF'

P value = 0.000788 (Fisher's exact test), Q value = 0.13

Table S21. Gene #10: 'Del Peak 12(10q21.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
DEL PEAK 12(10Q21.2) MUTATED | 5 | 6 | 0
DEL PEAK 12(10Q21.2) WILD-TYPE | 29 | 357 | 73

Figure S21. Get High-res Image Gene #10: 'Del Peak 12(10q21.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 13(10q23.31) mutation analysis' versus 'CN_CNMF'

P value = 6.4e-05 (Fisher's exact test), Q value = 0.011

Table S22. Gene #11: 'Del Peak 13(10q23.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
DEL PEAK 13(10Q23.31) MUTATED | 6 | 5 | 0
DEL PEAK 13(10Q23.31) WILD-TYPE | 28 | 358 | 73

Figure S22. Get High-res Image Gene #11: 'Del Peak 13(10q23.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 13(10q23.31) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00115 (Fisher's exact test), Q value = 0.19

Table S23. Gene #11: 'Del Peak 13(10q23.31) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 142 | 191 | 74
DEL PEAK 13(10Q23.31) MUTATED | 8 | 0 | 2
DEL PEAK 13(10Q23.31) WILD-TYPE | 134 | 191 | 72

Figure S23. Get High-res Image Gene #11: 'Del Peak 13(10q23.31) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 14(11p15.1) mutation analysis' versus 'CN_CNMF'

P value = 9.28e-08 (Fisher's exact test), Q value = 1.8e-05

Table S24. Gene #12: 'Del Peak 14(11p15.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
DEL PEAK 14(11P15.1) MUTATED | 6 | 0 | 0
DEL PEAK 14(11P15.1) WILD-TYPE | 28 | 363 | 73

Figure S24. Get High-res Image Gene #12: 'Del Peak 14(11p15.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 15(13q12.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.00123 (Fisher's exact test), Q value = 0.2

Table S25. Gene #13: 'Del Peak 15(13q12.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 140 | 71 | 259
DEL PEAK 15(13Q12.3) MUTATED | 10 | 3 | 2
DEL PEAK 15(13Q12.3) WILD-TYPE | 130 | 68 | 257

Figure S25. Get High-res Image Gene #13: 'Del Peak 15(13q12.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 17(15q25.3) mutation analysis' versus 'CN_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.21

Table S26. Gene #15: 'Del Peak 17(15q25.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
DEL PEAK 17(15Q25.3) MUTATED | 4 | 3 | 0
DEL PEAK 17(15Q25.3) WILD-TYPE | 30 | 360 | 73

Figure S26. Get High-res Image Gene #15: 'Del Peak 17(15q25.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 21(18p11.21) mutation analysis' versus 'CN_CNMF'

P value = 0.000241 (Fisher's exact test), Q value = 0.041

Table S27. Gene #18: 'Del Peak 21(18p11.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
DEL PEAK 21(18P11.21) MUTATED | 3 | 0 | 1
DEL PEAK 21(18P11.21) WILD-TYPE | 31 | 363 | 72

Figure S27. Get High-res Image Gene #18: 'Del Peak 21(18p11.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 22(18q22.2) mutation analysis' versus 'CN_CNMF'

P value = 0.00151 (Fisher's exact test), Q value = 0.23

Table S28. Gene #19: 'Del Peak 22(18q22.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
DEL PEAK 22(18Q22.2) MUTATED | 3 | 1 | 1
DEL PEAK 22(18Q22.2) WILD-TYPE | 31 | 362 | 72

Figure S28. Get High-res Image Gene #19: 'Del Peak 22(18q22.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 23(19p13.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.17

Table S29. Gene #20: 'Del Peak 23(19p13.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 140 | 71 | 259
DEL PEAK 23(19P13.2) MUTATED | 6 | 0 | 0
DEL PEAK 23(19P13.2) WILD-TYPE | 134 | 71 | 259

Figure S29. Get High-res Image Gene #20: 'Del Peak 23(19p13.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 23(19p13.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000641 (Fisher's exact test), Q value = 0.11

Table S30. Gene #20: 'Del Peak 23(19p13.2) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 126 | 153 | 144
DEL PEAK 23(19P13.2) MUTATED | 6 | 0 | 0
DEL PEAK 23(19P13.2) WILD-TYPE | 120 | 153 | 144

Figure S30. Get High-res Image Gene #20: 'Del Peak 23(19p13.2) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'Del Peak 23(19p13.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000407 (Fisher's exact test), Q value = 0.068

Table S31. Gene #20: 'Del Peak 23(19p13.2) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 173 | 133 | 117
DEL PEAK 23(19P13.2) MUTATED | 0 | 0 | 6
DEL PEAK 23(19P13.2) WILD-TYPE | 173 | 133 | 111

Figure S31. Get High-res Image Gene #20: 'Del Peak 23(19p13.2) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 26(21q21.1) mutation analysis' versus 'CN_CNMF'

P value = 1.29e-05 (Fisher's exact test), Q value = 0.0024

Table S32. Gene #21: 'Del Peak 26(21q21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
DEL PEAK 26(21Q21.1) MUTATED | 5 | 1 | 2
DEL PEAK 26(21Q21.1) WILD-TYPE | 29 | 362 | 71

Figure S32. Get High-res Image Gene #21: 'Del Peak 26(21q21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 27(22q13.1) mutation analysis' versus 'CN_CNMF'

P value = 5.8e-86 (Fisher's exact test), Q value = 1.2e-83

Table S33. Gene #22: 'Del Peak 27(22q13.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
DEL PEAK 27(22Q13.1) MUTATED | 8 | 0 | 73
DEL PEAK 27(22Q13.1) WILD-TYPE | 26 | 363 | 0

Figure S33. Get High-res Image Gene #22: 'Del Peak 27(22q13.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 27(22q13.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000321 (Fisher's exact test), Q value = 0.055

Table S34. Gene #22: 'Del Peak 27(22q13.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 140 | 71 | 259
DEL PEAK 27(22Q13.1) MUTATED | 39 | 6 | 36
DEL PEAK 27(22Q13.1) WILD-TYPE | 101 | 65 | 223

Figure S34. Get High-res Image Gene #22: 'Del Peak 27(22q13.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 27(22q13.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.11e-07 (Fisher's exact test), Q value = 6.1e-05

Table S35. Gene #22: 'Del Peak 27(22q13.1) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 130 | 50 | 89 | 138
DEL PEAK 27(22Q13.1) MUTATED | 36 | 4 | 21 | 7
DEL PEAK 27(22Q13.1) WILD-TYPE | 94 | 46 | 68 | 131

Figure S35. Get High-res Image Gene #22: 'Del Peak 27(22q13.1) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 27(22q13.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0037

Table S36. Gene #22: 'Del Peak 27(22q13.1) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 142 | 191 | 74
DEL PEAK 27(22Q13.1) MUTATED | 36 | 15 | 17
DEL PEAK 27(22Q13.1) WILD-TYPE | 106 | 176 | 57

Figure S36. Get High-res Image Gene #22: 'Del Peak 27(22q13.1) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 27(22q13.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00144 (Fisher's exact test), Q value = 0.23

Table S37. Gene #22: 'Del Peak 27(22q13.1) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 173 | 133 | 117
DEL PEAK 27(22Q13.1) MUTATED | 21 | 19 | 33
DEL PEAK 27(22Q13.1) WILD-TYPE | 152 | 114 | 84

Figure S37. Get High-res Image Gene #22: 'Del Peak 27(22q13.1) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 28(22q13.2) mutation analysis' versus 'CN_CNMF'

P value = 5.8e-86 (Fisher's exact test), Q value = 1.2e-83

Table S38. Gene #23: 'Del Peak 28(22q13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
DEL PEAK 28(22Q13.2) MUTATED | 8 | 0 | 73
DEL PEAK 28(22Q13.2) WILD-TYPE | 26 | 363 | 0

Figure S38. Get High-res Image Gene #23: 'Del Peak 28(22q13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 28(22q13.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000321 (Fisher's exact test), Q value = 0.055

Table S39. Gene #23: 'Del Peak 28(22q13.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 140 | 71 | 259
DEL PEAK 28(22Q13.2) MUTATED | 39 | 6 | 36
DEL PEAK 28(22Q13.2) WILD-TYPE | 101 | 65 | 223

Figure S39. Get High-res Image Gene #23: 'Del Peak 28(22q13.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 28(22q13.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.11e-07 (Fisher's exact test), Q value = 6.1e-05

Table S40. Gene #23: 'Del Peak 28(22q13.2) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 130 | 50 | 89 | 138
DEL PEAK 28(22Q13.2) MUTATED | 36 | 4 | 21 | 7
DEL PEAK 28(22Q13.2) WILD-TYPE | 94 | 46 | 68 | 131

Figure S40. Get High-res Image Gene #23: 'Del Peak 28(22q13.2) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 28(22q13.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0037

Table S41. Gene #23: 'Del Peak 28(22q13.2) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 142 | 191 | 74
DEL PEAK 28(22Q13.2) MUTATED | 36 | 15 | 17
DEL PEAK 28(22Q13.2) WILD-TYPE | 106 | 176 | 57

Figure S41. Get High-res Image Gene #23: 'Del Peak 28(22q13.2) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 28(22q13.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00144 (Fisher's exact test), Q value = 0.23

Table S42. Gene #23: 'Del Peak 28(22q13.2) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 173 | 133 | 117
DEL PEAK 28(22Q13.2) MUTATED | 21 | 19 | 33
DEL PEAK 28(22Q13.2) WILD-TYPE | 152 | 114 | 84

Figure S42. Get High-res Image Gene #23: 'Del Peak 28(22q13.2) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 29(22q13.31) mutation analysis' versus 'CN_CNMF'

P value = 5.8e-86 (Fisher's exact test), Q value = 1.2e-83

Table S43. Gene #24: 'Del Peak 29(22q13.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
DEL PEAK 29(22Q13.31) MUTATED | 8 | 0 | 73
DEL PEAK 29(22Q13.31) WILD-TYPE | 26 | 363 | 0

Figure S43. Get High-res Image Gene #24: 'Del Peak 29(22q13.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 29(22q13.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000321 (Fisher's exact test), Q value = 0.055

Table S44. Gene #24: 'Del Peak 29(22q13.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 140 | 71 | 259
DEL PEAK 29(22Q13.31) MUTATED | 39 | 6 | 36
DEL PEAK 29(22Q13.31) WILD-TYPE | 101 | 65 | 223

Figure S44. Get High-res Image Gene #24: 'Del Peak 29(22q13.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 29(22q13.31) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.11e-07 (Fisher's exact test), Q value = 6.1e-05

Table S45. Gene #24: 'Del Peak 29(22q13.31) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 130 | 50 | 89 | 138
DEL PEAK 29(22Q13.31) MUTATED | 36 | 4 | 21 | 7
DEL PEAK 29(22Q13.31) WILD-TYPE | 94 | 46 | 68 | 131

Figure S45. Get High-res Image Gene #24: 'Del Peak 29(22q13.31) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 29(22q13.31) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0037

Table S46. Gene #24: 'Del Peak 29(22q13.31) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 142 | 191 | 74
DEL PEAK 29(22Q13.31) MUTATED | 36 | 15 | 17
DEL PEAK 29(22Q13.31) WILD-TYPE | 106 | 176 | 57

Figure S46. Get High-res Image Gene #24: 'Del Peak 29(22q13.31) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 29(22q13.31) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00144 (Fisher's exact test), Q value = 0.23

Table S47. Gene #24: 'Del Peak 29(22q13.31) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 173 | 133 | 117
DEL PEAK 29(22Q13.31) MUTATED | 21 | 19 | 33
DEL PEAK 29(22Q13.31) WILD-TYPE | 152 | 114 | 84

Figure S47. Get High-res Image Gene #24: 'Del Peak 29(22q13.31) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 30(22q13.32) mutation analysis' versus 'CN_CNMF'

P value = 4.47e-84 (Fisher's exact test), Q value = 9.1e-82

Table S48. Gene #25: 'Del Peak 30(22q13.32) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
DEL PEAK 30(22Q13.32) MUTATED | 8 | 1 | 73
DEL PEAK 30(22Q13.32) WILD-TYPE | 26 | 362 | 0

Figure S48. Get High-res Image Gene #25: 'Del Peak 30(22q13.32) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 30(22q13.32) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000162 (Fisher's exact test), Q value = 0.028

Table S49. Gene #25: 'Del Peak 30(22q13.32) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 140 | 71 | 259
DEL PEAK 30(22Q13.32) MUTATED | 40 | 6 | 36
DEL PEAK 30(22Q13.32) WILD-TYPE | 100 | 65 | 223

Figure S49. Get High-res Image Gene #25: 'Del Peak 30(22q13.32) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 30(22q13.32) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.64e-07 (Fisher's exact test), Q value = 3.3e-05

Table S50. Gene #25: 'Del Peak 30(22q13.32) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 130 | 50 | 89 | 138
DEL PEAK 30(22Q13.32) MUTATED | 37 | 4 | 21 | 7
DEL PEAK 30(22Q13.32) WILD-TYPE | 93 | 46 | 68 | 131

Figure S50. Get High-res Image Gene #25: 'Del Peak 30(22q13.32) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 30(22q13.32) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.17e-05 (Fisher's exact test), Q value = 0.0022

Table S51. Gene #25: 'Del Peak 30(22q13.32) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 142 | 191 | 74
DEL PEAK 30(22Q13.32) MUTATED | 37 | 15 | 17
DEL PEAK 30(22Q13.32) WILD-TYPE | 105 | 176 | 57

Figure S51. Get High-res Image Gene #25: 'Del Peak 30(22q13.32) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 30(22q13.32) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000846 (Fisher's exact test), Q value = 0.14

Table S52. Gene #25: 'Del Peak 30(22q13.32) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 173 | 133 | 117
DEL PEAK 30(22Q13.32) MUTATED | 21 | 19 | 34
DEL PEAK 30(22Q13.32) WILD-TYPE | 152 | 114 | 83

Figure S52. Get High-res Image Gene #25: 'Del Peak 30(22q13.32) mutation analysis' versus Clinical Feature #8: '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 = THCA-TP.transferedmergedcluster.txt

- Number of patients = 470

- Number of copy number variation regions = 27

- 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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