Correlation between copy number variation genes and molecular subtypes
Thyroid Adenocarcinoma (Primary solid tumor)
23 September 2013 | analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1MS3R4M
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/C1MS3R4M
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 29 peak regions and 10 molecular subtypes across 494 patients, 70 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', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

- Del Peak 9(8p23.2) cnvs correlated to 'CN_CNMF'.

- Del Peak 10(8p22) cnvs correlated to 'CN_CNMF'.

- Del Peak 11(8p12) cnvs correlated to 'CN_CNMF'.

- Del Peak 12(8q24.22) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

- Del Peak 14(10q21.2) cnvs correlated to 'CN_CNMF'.

- Del Peak 15(10q23.31) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

- Del Peak 16(11p15.1) cnvs correlated to 'CN_CNMF'.

- Del Peak 18(13q21.31) cnvs correlated to 'MRNASEQ_CHIERARCHICAL'.

- Del Peak 19(15q25.3) cnvs correlated to 'MIRSEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- Del Peak 23(18p11.21) cnvs correlated to 'CN_CNMF'.

- Del Peak 25(19p13.2) cnvs correlated to 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- Del Peak 28(21q21.1) cnvs correlated to 'CN_CNMF'.

- Del Peak 29(22q13.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- Del Peak 30(22q13.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

- Del Peak 32(22q13.32) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 29 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 70 significant findings detected.

|  | Molecular subtypes | CN CNMF | METHLYATION CNMF | RPPA CNMF | RPPA CHIERARCHICAL | MRNASEQ CNMF | MRNASEQ CHIERARCHICAL | MIRSEQ CNMF | MIRSEQ CHIERARCHICAL | MIRSEQ MATURE CNMF | MIRSEQ MATURE CHIERARCHICAL
| nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test
Del Peak 2(2p23 1) | 0 (0%) | 482 | 3.58e-10 (9.8e-08) | 1.21e-05 (0.00297) | 0.773 (1.00) | 0.0122 (1.00) | 7.58e-06 (0.00189) | 6.32e-06 (0.00158) | 4.59e-07 (0.000121) | 7.66e-08 (2.05e-05) | 2.4e-06 (0.000616) | 6.31e-08 (1.7e-05)
Del Peak 3(2q35) | 0 (0%) | 483 | 6.33e-12 (1.74e-09) | 4.68e-06 (0.00119) | 0.562 (1.00) | 0.00257 (0.493) | 2.32e-05 (0.00555) | 4.9e-06 (0.00124) | 1.59e-06 (0.000412) | 3.1e-07 (8.23e-05) | 7.65e-06 (0.0019) | 2.6e-07 (6.91e-05)
Del Peak 32(22q13 32) | 0 (0%) | 408 | 9.68e-89 (2.68e-86) | 1.11e-05 (0.00274) | 0.124 (1.00) | 0.209 (1.00) | 6.47e-09 (1.77e-06) | 7.15e-07 (0.000188) | 0.000943 (0.2) | 0.000337 (0.0769) | 2.95e-06 (0.000756) | 0.000212 (0.0492)
Del Peak 12(8q24 22) | 0 (0%) | 487 | 4.62e-05 (0.0109) | 0.000343 (0.0778) | 0.839 (1.00) | 0.0521 (1.00) | 0.00153 (0.315) | 0.000675 (0.146) | 0.000219 (0.0505) | 7.85e-05 (0.0184) | 0.000758 (0.162) | 7.02e-05 (0.0165)
Del Peak 29(22q13 1) | 0 (0%) | 409 | 1.19e-90 (3.34e-88) | 2.18e-05 (0.00528) | 0.124 (1.00) | 0.209 (1.00) | 1.22e-08 (3.31e-06) | 1.44e-06 (0.000378) | 0.00166 (0.34) | 0.000658 (0.144) | 6.1e-06 (0.00154) | 0.000387 (0.0871)
Del Peak 30(22q13 2) | 0 (0%) | 409 | 1.19e-90 (3.34e-88) | 2.18e-05 (0.00528) | 0.124 (1.00) | 0.209 (1.00) | 1.22e-08 (3.31e-06) | 1.44e-06 (0.000378) | 0.00166 (0.34) | 0.000658 (0.144) | 6.1e-06 (0.00154) | 0.000387 (0.0871)
Del Peak 31(22q13 31) | 0 (0%) | 409 | 1.19e-90 (3.34e-88) | 2.18e-05 (0.00528) | 0.124 (1.00) | 0.209 (1.00) | 1.22e-08 (3.31e-06) | 1.44e-06 (0.000378) | 0.00166 (0.34) | 0.000658 (0.144) | 6.1e-06 (0.00154) | 0.000387 (0.0871)
Del Peak 25(19p13 2) | 0 (0%) | 488 | 0.00452 (0.831) | 0.00139 (0.289) | 0.681 (1.00) | 0.25 (1.00) | 0.00446 (0.826) | 0.00178 (0.355) | 0.000739 (0.159) | 0.000308 (0.0706) | 0.00237 (0.456) | 0.00028 (0.0645)
Del Peak 15(10q23 31) | 0 (0%) | 483 | 3.37e-05 (0.00802) | 0.0112 (1.00) | 0.0328 (1.00) | 0.0483 (1.00) | 0.00183 (0.362) | 0.00144 (0.297) | 0.0117 (1.00) | 0.00532 (0.942) | 0.00105 (0.221) | 0.00358 (0.68)
Del Peak 19(15q25 3) | 0 (0%) | 486 | 0.00133 (0.278) | 0.00369 (0.697) | 0.444 (1.00) | 0.079 (1.00) | 0.0113 (1.00) | 0.00614 (1.00) | 0.00168 (0.34) | 0.000573 (0.127) | 0.00454 (0.831) | 0.000587 (0.129)
Amp Peak 1(Xq22 3) | 0 (0%) | 478 | 1.64e-06 (0.000422) | 0.514 (1.00) | 1 (1.00) | 0.126 (1.00) | 0.623 (1.00) | 0.598 (1.00) | 0.855 (1.00) | 0.651 (1.00) | 0.855 (1.00) | 0.555 (1.00)
Del Peak 6(6q22 31) | 0 (0%) | 488 | 0.000364 (0.0823) | 0.00505 (0.903) | 0.0381 (1.00) | 0.794 (1.00) | 0.0161 (1.00) | 0.0069 (1.00) | 0.00929 (1.00) | 0.00658 (1.00) | 0.0259 (1.00) | 0.00664 (1.00)
Del Peak 9(8p23 2) | 0 (0%) | 490 | 1.89e-05 (0.00464) | 0.0149 (1.00) |  |  | 0.0444 (1.00) | 0.0219 (1.00) | 0.00833 (1.00) | 0.00467 (0.85) | 0.0227 (1.00) | 0.00439 (0.825)
Del Peak 10(8p22) | 0 (0%) | 490 | 1.89e-05 (0.00464) | 0.0149 (1.00) |  |  | 0.0444 (1.00) | 0.0219 (1.00) | 0.00833 (1.00) | 0.00467 (0.85) | 0.0227 (1.00) | 0.00439 (0.825)
Del Peak 11(8p12) | 0 (0%) | 490 | 1.89e-05 (0.00464) | 0.0149 (1.00) |  |  | 0.0444 (1.00) | 0.0219 (1.00) | 0.00833 (1.00) | 0.00467 (0.85) | 0.0227 (1.00) | 0.00439 (0.825)
Del Peak 13(9q21 13) | 0 (0%) | 471 | 1.17e-13 (3.23e-11) | 0.0686 (1.00) | 0.211 (1.00) | 0.0102 (1.00) | 0.0961 (1.00) | 0.0978 (1.00) | 0.014 (1.00) | 0.0131 (1.00) | 0.015 (1.00) | 0.00808 (1.00)
Del Peak 14(10q21 2) | 0 (0%) | 483 | 0.000557 (0.124) | 0.163 (1.00) | 0.133 (1.00) | 1 (1.00) | 0.0336 (1.00) | 0.242 (1.00) | 0.235 (1.00) | 0.0872 (1.00) | 0.0632 (1.00) | 0.126 (1.00)
Del Peak 16(11p15 1) | 0 (0%) | 487 | 7.98e-08 (2.13e-05) | 0.00956 (1.00) | 0.495 (1.00) | 1 (1.00) | 0.00712 (1.00) | 0.0174 (1.00) | 0.00316 (0.604) | 0.00196 (0.385) | 0.00954 (1.00) | 0.00199 (0.388)
Del Peak 18(13q21 31) | 0 (0%) | 477 | 0.027 (1.00) | 0.0424 (1.00) | 0.12 (1.00) | 1 (1.00) | 0.0023 (0.447) | 0.000772 (0.164) | 0.00813 (1.00) | 0.00539 (0.948) | 0.00786 (1.00) | 0.00522 (0.929)
Del Peak 23(18p11 21) | 0 (0%) | 490 | 0.000207 (0.0482) | 0.22 (1.00) | 1 (1.00) | 0.284 (1.00) | 0.242 (1.00) | 0.121 (1.00) | 0.115 (1.00) | 0.037 (1.00) | 0.0227 (1.00) | 0.0402 (1.00)
Del Peak 28(21q21 1) | 0 (0%) | 485 | 5.66e-05 (0.0134) | 0.486 (1.00) | 0.148 (1.00) | 0.204 (1.00) | 0.406 (1.00) | 0.578 (1.00) | 0.0526 (1.00) | 0.266 (1.00) | 0.0537 (1.00) | 0.0436 (1.00)
Del Peak 4(5p15 2) | 0 (0%) | 490 | 0.348 (1.00) | 0.394 (1.00) |  |  | 0.424 (1.00) | 0.48 (1.00) | 0.555 (1.00) | 0.578 (1.00) | 0.476 (1.00) | 0.684 (1.00)
Del Peak 8(7q34) | 0 (0%) | 490 | 0.64 (1.00) | 0.649 (1.00) |  |  | 0.744 (1.00) | 0.395 (1.00) | 0.691 (1.00) | 0.822 (1.00) | 1 (1.00) | 0.828 (1.00)
Del Peak 17(13q12 3) | 0 (0%) | 479 | 0.0228 (1.00) | 0.00192 (0.378) | 0.39 (1.00) | 0.432 (1.00) | 0.00174 (0.35) | 0.0181 (1.00) | 0.0658 (1.00) | 0.0181 (1.00) | 0.0243 (1.00) | 0.0136 (1.00)
Del Peak 21(16q23 3) | 0 (0%) | 488 | 0.0483 (1.00) | 0.0744 (1.00) | 0.444 (1.00) | 0.102 (1.00) | 0.103 (1.00) | 0.386 (1.00) | 0.197 (1.00) | 0.387 (1.00) | 0.294 (1.00) | 0.293 (1.00)
Del Peak 22(17p13 1) | 0 (0%) | 486 | 0.00182 (0.362) | 0.335 (1.00) | 1 (1.00) | 0.284 (1.00) | 0.631 (1.00) | 0.626 (1.00) | 0.33 (1.00) | 0.307 (1.00) | 0.672 (1.00) | 0.282 (1.00)
Del Peak 24(18q22 2) | 0 (0%) | 489 | 0.00134 (0.28) | 0.0757 (1.00) | 1 (1.00) | 0.25 (1.00) | 0.119 (1.00) | 0.0361 (1.00) | 0.0415 (1.00) | 0.0115 (1.00) | 0.00735 (1.00) | 0.0127 (1.00)
Del Peak 33(Xq22 1) | 0 (0%) | 488 | 0.0736 (1.00) | 0.551 (1.00) | 0.0977 (1.00) | 0.118 (1.00) | 0.593 (1.00) | 0.705 (1.00) | 0.526 (1.00) | 0.294 (1.00) | 0.703 (1.00) | 0.341 (1.00)
Del Peak 34(Xq22 3) | 0 (0%) | 490 | 0.0538 (1.00) | 0.0594 (1.00) | 0.278 (1.00) | 0.364 (1.00) | 0.0947 (1.00) | 0.258 (1.00) | 0.115 (1.00) | 0.037 (1.00) | 0.226 (1.00) | 0.0402 (1.00)

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

P value = 1.64e-06 (Fisher's exact test), Q value = 0.00042

Table S1. Gene #1: 'Amp Peak 1(Xq22.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
AMP PEAK 1(XQ22.3) CNV | 8 | 8 | 0
AMP PEAK 1(XQ22.3) WILD-TYPE | 26 | 375 | 77

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(Xq22.3)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 3.58e-10 (Fisher's exact test), Q value = 9.8e-08

Table S2. Gene #2: 'Del Peak 2(2p23.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 2(2P23.1) CNV | 9 | 1 | 2
DEL PEAK 2(2P23.1) WILD-TYPE | 25 | 382 | 75

Figure S2. Get High-res Image Gene #2: 'Del Peak 2(2p23.1)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 1.21e-05 (Fisher's exact test), Q value = 0.003

Table S3. Gene #2: 'Del Peak 2(2p23.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
DEL PEAK 2(2P23.1) CNV | 11 | 1 | 0
DEL PEAK 2(2P23.1) WILD-TYPE | 140 | 82 | 260

Figure S3. Get High-res Image Gene #2: 'Del Peak 2(2p23.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 7.58e-06 (Fisher's exact test), Q value = 0.0019

Table S4. Gene #2: 'Del Peak 2(2p23.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 150 | 55 | 114 | 161
DEL PEAK 2(2P23.1) CNV | 12 | 0 | 0 | 0
DEL PEAK 2(2P23.1) WILD-TYPE | 138 | 55 | 114 | 161

Figure S4. Get High-res Image Gene #2: 'Del Peak 2(2p23.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

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

P value = 6.32e-06 (Fisher's exact test), Q value = 0.0016

Table S5. Gene #2: 'Del Peak 2(2p23.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 132 | 212 | 94 | 42
DEL PEAK 2(2P23.1) CNV | 11 | 0 | 0 | 1
DEL PEAK 2(2P23.1) WILD-TYPE | 121 | 212 | 94 | 41

Figure S5. Get High-res Image Gene #2: 'Del Peak 2(2p23.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

P value = 4.59e-07 (Fisher's exact test), Q value = 0.00012

Table S6. Gene #2: 'Del Peak 2(2p23.1)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
DEL PEAK 2(2P23.1) CNV | 12 | 0 | 0
DEL PEAK 2(2P23.1) WILD-TYPE | 138 | 173 | 170

Figure S6. Get High-res Image Gene #2: 'Del Peak 2(2p23.1)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

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

P value = 7.66e-08 (Fisher's exact test), Q value = 2.1e-05

Table S7. Gene #2: 'Del Peak 2(2p23.1)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
DEL PEAK 2(2P23.1) CNV | 0 | 12 | 0
DEL PEAK 2(2P23.1) WILD-TYPE | 155 | 118 | 208

Figure S7. Get High-res Image Gene #2: 'Del Peak 2(2p23.1)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 2(2p23.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.4e-06 (Fisher's exact test), Q value = 0.00062

Table S8. Gene #2: 'Del Peak 2(2p23.1)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
DEL PEAK 2(2P23.1) CNV | 12 | 0 | 0
DEL PEAK 2(2P23.1) WILD-TYPE | 151 | 169 | 161

Figure S8. Get High-res Image Gene #2: 'Del Peak 2(2p23.1)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Del Peak 2(2p23.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.31e-08 (Fisher's exact test), Q value = 1.7e-05

Table S9. Gene #2: 'Del Peak 2(2p23.1)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
DEL PEAK 2(2P23.1) CNV | 0 | 12 | 0
DEL PEAK 2(2P23.1) WILD-TYPE | 199 | 116 | 166

Figure S9. Get High-res Image Gene #2: 'Del Peak 2(2p23.1)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 6.33e-12 (Fisher's exact test), Q value = 1.7e-09

Table S10. Gene #3: 'Del Peak 3(2q35)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 3(2Q35) CNV | 10 | 1 | 0
DEL PEAK 3(2Q35) WILD-TYPE | 24 | 382 | 77

Figure S10. Get High-res Image Gene #3: 'Del Peak 3(2q35)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 4.68e-06 (Fisher's exact test), Q value = 0.0012

Table S11. Gene #3: 'Del Peak 3(2q35)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
DEL PEAK 3(2Q35) CNV | 11 | 0 | 0
DEL PEAK 3(2Q35) WILD-TYPE | 140 | 83 | 260

Figure S11. Get High-res Image Gene #3: 'Del Peak 3(2q35)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 2.32e-05 (Fisher's exact test), Q value = 0.0056

Table S12. Gene #3: 'Del Peak 3(2q35)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 150 | 55 | 114 | 161
DEL PEAK 3(2Q35) CNV | 11 | 0 | 0 | 0
DEL PEAK 3(2Q35) WILD-TYPE | 139 | 55 | 114 | 161

Figure S12. Get High-res Image Gene #3: 'Del Peak 3(2q35)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

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

P value = 4.9e-06 (Fisher's exact test), Q value = 0.0012

Table S13. Gene #3: 'Del Peak 3(2q35)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 132 | 212 | 94 | 42
DEL PEAK 3(2Q35) CNV | 11 | 0 | 0 | 0
DEL PEAK 3(2Q35) WILD-TYPE | 121 | 212 | 94 | 42

Figure S13. Get High-res Image Gene #3: 'Del Peak 3(2q35)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

P value = 1.59e-06 (Fisher's exact test), Q value = 0.00041

Table S14. Gene #3: 'Del Peak 3(2q35)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
DEL PEAK 3(2Q35) CNV | 11 | 0 | 0
DEL PEAK 3(2Q35) WILD-TYPE | 139 | 173 | 170

Figure S14. Get High-res Image Gene #3: 'Del Peak 3(2q35)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

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

P value = 3.1e-07 (Fisher's exact test), Q value = 8.2e-05

Table S15. Gene #3: 'Del Peak 3(2q35)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
DEL PEAK 3(2Q35) CNV | 0 | 11 | 0
DEL PEAK 3(2Q35) WILD-TYPE | 155 | 119 | 208

Figure S15. Get High-res Image Gene #3: 'Del Peak 3(2q35)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 3(2q35)' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.65e-06 (Fisher's exact test), Q value = 0.0019

Table S16. Gene #3: 'Del Peak 3(2q35)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
DEL PEAK 3(2Q35) CNV | 11 | 0 | 0
DEL PEAK 3(2Q35) WILD-TYPE | 152 | 169 | 161

Figure S16. Get High-res Image Gene #3: 'Del Peak 3(2q35)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Del Peak 3(2q35)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.6e-07 (Fisher's exact test), Q value = 6.9e-05

Table S17. Gene #3: 'Del Peak 3(2q35)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
DEL PEAK 3(2Q35) CNV | 0 | 11 | 0
DEL PEAK 3(2Q35) WILD-TYPE | 199 | 117 | 166

Figure S17. Get High-res Image Gene #3: 'Del Peak 3(2q35)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 0.000364 (Fisher's exact test), Q value = 0.082

Table S18. Gene #5: 'Del Peak 6(6q22.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 6(6Q22.31) CNV | 4 | 2 | 0
DEL PEAK 6(6Q22.31) WILD-TYPE | 30 | 381 | 77

Figure S18. Get High-res Image Gene #5: 'Del Peak 6(6q22.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 9(8p23.2)' versus 'CN_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0046

Table S19. Gene #7: 'Del Peak 9(8p23.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 9(8P23.2) CNV | 4 | 0 | 0
DEL PEAK 9(8P23.2) WILD-TYPE | 30 | 383 | 77

Figure S19. Get High-res Image Gene #7: 'Del Peak 9(8p23.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 10(8p22)' versus 'CN_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0046

Table S20. Gene #8: 'Del Peak 10(8p22)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 10(8P22) CNV | 4 | 0 | 0
DEL PEAK 10(8P22) WILD-TYPE | 30 | 383 | 77

Figure S20. Get High-res Image Gene #8: 'Del Peak 10(8p22)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 11(8p12)' versus 'CN_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0046

Table S21. Gene #9: 'Del Peak 11(8p12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 11(8P12) CNV | 4 | 0 | 0
DEL PEAK 11(8P12) WILD-TYPE | 30 | 383 | 77

Figure S21. Get High-res Image Gene #9: 'Del Peak 11(8p12)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 12(8q24.22)' versus 'CN_CNMF'

P value = 4.62e-05 (Fisher's exact test), Q value = 0.011

Table S22. Gene #10: 'Del Peak 12(8q24.22)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 12(8Q24.22) CNV | 5 | 2 | 0
DEL PEAK 12(8Q24.22) WILD-TYPE | 29 | 381 | 77

Figure S22. Get High-res Image Gene #10: 'Del Peak 12(8q24.22)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 12(8q24.22)' versus 'METHLYATION_CNMF'

P value = 0.000343 (Fisher's exact test), Q value = 0.078

Table S23. Gene #10: 'Del Peak 12(8q24.22)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
DEL PEAK 12(8Q24.22) CNV | 7 | 0 | 0
DEL PEAK 12(8Q24.22) WILD-TYPE | 144 | 83 | 260

Figure S23. Get High-res Image Gene #10: 'Del Peak 12(8q24.22)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 12(8q24.22)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000675 (Fisher's exact test), Q value = 0.15

Table S24. Gene #10: 'Del Peak 12(8q24.22)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 132 | 212 | 94 | 42
DEL PEAK 12(8Q24.22) CNV | 7 | 0 | 0 | 0
DEL PEAK 12(8Q24.22) WILD-TYPE | 125 | 212 | 94 | 42

Figure S24. Get High-res Image Gene #10: 'Del Peak 12(8q24.22)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 12(8q24.22)' versus 'MIRSEQ_CNMF'

P value = 0.000219 (Fisher's exact test), Q value = 0.05

Table S25. Gene #10: 'Del Peak 12(8q24.22)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
DEL PEAK 12(8Q24.22) CNV | 7 | 0 | 0
DEL PEAK 12(8Q24.22) WILD-TYPE | 143 | 173 | 170

Figure S25. Get High-res Image Gene #10: 'Del Peak 12(8q24.22)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 12(8q24.22)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.85e-05 (Fisher's exact test), Q value = 0.018

Table S26. Gene #10: 'Del Peak 12(8q24.22)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
DEL PEAK 12(8Q24.22) CNV | 0 | 7 | 0
DEL PEAK 12(8Q24.22) WILD-TYPE | 155 | 123 | 208

Figure S26. Get High-res Image Gene #10: 'Del Peak 12(8q24.22)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 12(8q24.22)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000758 (Fisher's exact test), Q value = 0.16

Table S27. Gene #10: 'Del Peak 12(8q24.22)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
DEL PEAK 12(8Q24.22) CNV | 7 | 0 | 0
DEL PEAK 12(8Q24.22) WILD-TYPE | 156 | 169 | 161

Figure S27. Get High-res Image Gene #10: 'Del Peak 12(8q24.22)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Del Peak 12(8q24.22)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.02e-05 (Fisher's exact test), Q value = 0.017

Table S28. Gene #10: 'Del Peak 12(8q24.22)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
DEL PEAK 12(8Q24.22) CNV | 0 | 7 | 0
DEL PEAK 12(8Q24.22) WILD-TYPE | 199 | 121 | 166

Figure S28. Get High-res Image Gene #10: 'Del Peak 12(8q24.22)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 13(9q21.13)' versus 'CN_CNMF'

P value = 1.17e-13 (Fisher's exact test), Q value = 3.2e-11

Table S29. Gene #11: 'Del Peak 13(9q21.13)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 13(9Q21.13) CNV | 15 | 7 | 1
DEL PEAK 13(9Q21.13) WILD-TYPE | 19 | 376 | 76

Figure S29. Get High-res Image Gene #11: 'Del Peak 13(9q21.13)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 14(10q21.2)' versus 'CN_CNMF'

P value = 0.000557 (Fisher's exact test), Q value = 0.12

Table S30. Gene #12: 'Del Peak 14(10q21.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 14(10Q21.2) CNV | 5 | 6 | 0
DEL PEAK 14(10Q21.2) WILD-TYPE | 29 | 377 | 77

Figure S30. Get High-res Image Gene #12: 'Del Peak 14(10q21.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 15(10q23.31)' versus 'CN_CNMF'

P value = 3.37e-05 (Fisher's exact test), Q value = 0.008

Table S31. Gene #13: 'Del Peak 15(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 15(10Q23.31) CNV | 6 | 5 | 0
DEL PEAK 15(10Q23.31) WILD-TYPE | 28 | 378 | 77

Figure S31. Get High-res Image Gene #13: 'Del Peak 15(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 15(10q23.31)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.22

Table S32. Gene #13: 'Del Peak 15(10q23.31)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
DEL PEAK 15(10Q23.31) CNV | 9 | 0 | 2
DEL PEAK 15(10Q23.31) WILD-TYPE | 154 | 169 | 159

Figure S32. Get High-res Image Gene #13: 'Del Peak 15(10q23.31)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Del Peak 16(11p15.1)' versus 'CN_CNMF'

P value = 7.98e-08 (Fisher's exact test), Q value = 2.1e-05

Table S33. Gene #14: 'Del Peak 16(11p15.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 16(11P15.1) CNV | 6 | 0 | 1
DEL PEAK 16(11P15.1) WILD-TYPE | 28 | 383 | 76

Figure S33. Get High-res Image Gene #14: 'Del Peak 16(11p15.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 18(13q21.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000772 (Fisher's exact test), Q value = 0.16

Table S34. Gene #16: 'Del Peak 18(13q21.31)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 132 | 212 | 94 | 42
DEL PEAK 18(13Q21.31) CNV | 10 | 1 | 5 | 0
DEL PEAK 18(13Q21.31) WILD-TYPE | 122 | 211 | 89 | 42

Figure S34. Get High-res Image Gene #16: 'Del Peak 18(13q21.31)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 19(15q25.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000573 (Fisher's exact test), Q value = 0.13

Table S35. Gene #17: 'Del Peak 19(15q25.3)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
DEL PEAK 19(15Q25.3) CNV | 0 | 7 | 1
DEL PEAK 19(15Q25.3) WILD-TYPE | 155 | 123 | 207

Figure S35. Get High-res Image Gene #17: 'Del Peak 19(15q25.3)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 19(15q25.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000587 (Fisher's exact test), Q value = 0.13

Table S36. Gene #17: 'Del Peak 19(15q25.3)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
DEL PEAK 19(15Q25.3) CNV | 1 | 7 | 0
DEL PEAK 19(15Q25.3) WILD-TYPE | 198 | 121 | 166

Figure S36. Get High-res Image Gene #17: 'Del Peak 19(15q25.3)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 23(18p11.21)' versus 'CN_CNMF'

P value = 0.000207 (Fisher's exact test), Q value = 0.048

Table S37. Gene #20: 'Del Peak 23(18p11.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 23(18P11.21) CNV | 3 | 0 | 1
DEL PEAK 23(18P11.21) WILD-TYPE | 31 | 383 | 76

Figure S37. Get High-res Image Gene #20: 'Del Peak 23(18p11.21)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 25(19p13.2)' versus 'MIRSEQ_CNMF'

P value = 0.000739 (Fisher's exact test), Q value = 0.16

Table S38. Gene #22: 'Del Peak 25(19p13.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
DEL PEAK 25(19P13.2) CNV | 6 | 0 | 0
DEL PEAK 25(19P13.2) WILD-TYPE | 144 | 173 | 170

Figure S38. Get High-res Image Gene #22: 'Del Peak 25(19p13.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 25(19p13.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000308 (Fisher's exact test), Q value = 0.071

Table S39. Gene #22: 'Del Peak 25(19p13.2)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
DEL PEAK 25(19P13.2) CNV | 0 | 6 | 0
DEL PEAK 25(19P13.2) WILD-TYPE | 155 | 124 | 208

Figure S39. Get High-res Image Gene #22: 'Del Peak 25(19p13.2)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 25(19p13.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.064

Table S40. Gene #22: 'Del Peak 25(19p13.2)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
DEL PEAK 25(19P13.2) CNV | 0 | 6 | 0
DEL PEAK 25(19P13.2) WILD-TYPE | 199 | 122 | 166

Figure S40. Get High-res Image Gene #22: 'Del Peak 25(19p13.2)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 28(21q21.1)' versus 'CN_CNMF'

P value = 5.66e-05 (Fisher's exact test), Q value = 0.013

Table S41. Gene #23: 'Del Peak 28(21q21.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 28(21Q21.1) CNV | 5 | 2 | 2
DEL PEAK 28(21Q21.1) WILD-TYPE | 29 | 381 | 75

Figure S41. Get High-res Image Gene #23: 'Del Peak 28(21q21.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 29(22q13.1)' versus 'CN_CNMF'

P value = 1.19e-90 (Fisher's exact test), Q value = 3.3e-88

Table S42. Gene #24: 'Del Peak 29(22q13.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 29(22Q13.1) CNV | 8 | 0 | 77
DEL PEAK 29(22Q13.1) WILD-TYPE | 26 | 383 | 0

Figure S42. Get High-res Image Gene #24: 'Del Peak 29(22q13.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 29(22q13.1)' versus 'METHLYATION_CNMF'

P value = 2.18e-05 (Fisher's exact test), Q value = 0.0053

Table S43. Gene #24: 'Del Peak 29(22q13.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
DEL PEAK 29(22Q13.1) CNV | 44 | 7 | 34
DEL PEAK 29(22Q13.1) WILD-TYPE | 107 | 76 | 226

Figure S43. Get High-res Image Gene #24: 'Del Peak 29(22q13.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 29(22q13.1)' versus 'MRNASEQ_CNMF'

P value = 1.22e-08 (Fisher's exact test), Q value = 3.3e-06

Table S44. Gene #24: 'Del Peak 29(22q13.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 150 | 55 | 114 | 161
DEL PEAK 29(22Q13.1) CNV | 42 | 6 | 26 | 7
DEL PEAK 29(22Q13.1) WILD-TYPE | 108 | 49 | 88 | 154

Figure S44. Get High-res Image Gene #24: 'Del Peak 29(22q13.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 29(22q13.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.44e-06 (Fisher's exact test), Q value = 0.00038

Table S45. Gene #24: 'Del Peak 29(22q13.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 132 | 212 | 94 | 42
DEL PEAK 29(22Q13.1) CNV | 38 | 16 | 21 | 6
DEL PEAK 29(22Q13.1) WILD-TYPE | 94 | 196 | 73 | 36

Figure S45. Get High-res Image Gene #24: 'Del Peak 29(22q13.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 29(22q13.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000658 (Fisher's exact test), Q value = 0.14

Table S46. Gene #24: 'Del Peak 29(22q13.1)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
DEL PEAK 29(22Q13.1) CNV | 22 | 37 | 26
DEL PEAK 29(22Q13.1) WILD-TYPE | 133 | 93 | 182

Figure S46. Get High-res Image Gene #24: 'Del Peak 29(22q13.1)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 29(22q13.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.1e-06 (Fisher's exact test), Q value = 0.0015

Table S47. Gene #24: 'Del Peak 29(22q13.1)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
DEL PEAK 29(22Q13.1) CNV | 48 | 18 | 19
DEL PEAK 29(22Q13.1) WILD-TYPE | 115 | 151 | 142

Figure S47. Get High-res Image Gene #24: 'Del Peak 29(22q13.1)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Del Peak 29(22q13.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000387 (Fisher's exact test), Q value = 0.087

Table S48. Gene #24: 'Del Peak 29(22q13.1)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
DEL PEAK 29(22Q13.1) CNV | 24 | 37 | 24
DEL PEAK 29(22Q13.1) WILD-TYPE | 175 | 91 | 142

Figure S48. Get High-res Image Gene #24: 'Del Peak 29(22q13.1)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 30(22q13.2)' versus 'CN_CNMF'

P value = 1.19e-90 (Fisher's exact test), Q value = 3.3e-88

Table S49. Gene #25: 'Del Peak 30(22q13.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 30(22Q13.2) CNV | 8 | 0 | 77
DEL PEAK 30(22Q13.2) WILD-TYPE | 26 | 383 | 0

Figure S49. Get High-res Image Gene #25: 'Del Peak 30(22q13.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 30(22q13.2)' versus 'METHLYATION_CNMF'

P value = 2.18e-05 (Fisher's exact test), Q value = 0.0053

Table S50. Gene #25: 'Del Peak 30(22q13.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
DEL PEAK 30(22Q13.2) CNV | 44 | 7 | 34
DEL PEAK 30(22Q13.2) WILD-TYPE | 107 | 76 | 226

Figure S50. Get High-res Image Gene #25: 'Del Peak 30(22q13.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 30(22q13.2)' versus 'MRNASEQ_CNMF'

P value = 1.22e-08 (Fisher's exact test), Q value = 3.3e-06

Table S51. Gene #25: 'Del Peak 30(22q13.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 150 | 55 | 114 | 161
DEL PEAK 30(22Q13.2) CNV | 42 | 6 | 26 | 7
DEL PEAK 30(22Q13.2) WILD-TYPE | 108 | 49 | 88 | 154

Figure S51. Get High-res Image Gene #25: 'Del Peak 30(22q13.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 30(22q13.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.44e-06 (Fisher's exact test), Q value = 0.00038

Table S52. Gene #25: 'Del Peak 30(22q13.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 132 | 212 | 94 | 42
DEL PEAK 30(22Q13.2) CNV | 38 | 16 | 21 | 6
DEL PEAK 30(22Q13.2) WILD-TYPE | 94 | 196 | 73 | 36

Figure S52. Get High-res Image Gene #25: 'Del Peak 30(22q13.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 30(22q13.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000658 (Fisher's exact test), Q value = 0.14

Table S53. Gene #25: 'Del Peak 30(22q13.2)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
DEL PEAK 30(22Q13.2) CNV | 22 | 37 | 26
DEL PEAK 30(22Q13.2) WILD-TYPE | 133 | 93 | 182

Figure S53. Get High-res Image Gene #25: 'Del Peak 30(22q13.2)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 30(22q13.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.1e-06 (Fisher's exact test), Q value = 0.0015

Table S54. Gene #25: 'Del Peak 30(22q13.2)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
DEL PEAK 30(22Q13.2) CNV | 48 | 18 | 19
DEL PEAK 30(22Q13.2) WILD-TYPE | 115 | 151 | 142

Figure S54. Get High-res Image Gene #25: 'Del Peak 30(22q13.2)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Del Peak 30(22q13.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000387 (Fisher's exact test), Q value = 0.087

Table S55. Gene #25: 'Del Peak 30(22q13.2)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
DEL PEAK 30(22Q13.2) CNV | 24 | 37 | 24
DEL PEAK 30(22Q13.2) WILD-TYPE | 175 | 91 | 142

Figure S55. Get High-res Image Gene #25: 'Del Peak 30(22q13.2)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 31(22q13.31)' versus 'CN_CNMF'

P value = 1.19e-90 (Fisher's exact test), Q value = 3.3e-88

Table S56. Gene #26: 'Del Peak 31(22q13.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 31(22Q13.31) CNV | 8 | 0 | 77
DEL PEAK 31(22Q13.31) WILD-TYPE | 26 | 383 | 0

Figure S56. Get High-res Image Gene #26: 'Del Peak 31(22q13.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 31(22q13.31)' versus 'METHLYATION_CNMF'

P value = 2.18e-05 (Fisher's exact test), Q value = 0.0053

Table S57. Gene #26: 'Del Peak 31(22q13.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
DEL PEAK 31(22Q13.31) CNV | 44 | 7 | 34
DEL PEAK 31(22Q13.31) WILD-TYPE | 107 | 76 | 226

Figure S57. Get High-res Image Gene #26: 'Del Peak 31(22q13.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 31(22q13.31)' versus 'MRNASEQ_CNMF'

P value = 1.22e-08 (Fisher's exact test), Q value = 3.3e-06

Table S58. Gene #26: 'Del Peak 31(22q13.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 150 | 55 | 114 | 161
DEL PEAK 31(22Q13.31) CNV | 42 | 6 | 26 | 7
DEL PEAK 31(22Q13.31) WILD-TYPE | 108 | 49 | 88 | 154

Figure S58. Get High-res Image Gene #26: 'Del Peak 31(22q13.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 31(22q13.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.44e-06 (Fisher's exact test), Q value = 0.00038

Table S59. Gene #26: 'Del Peak 31(22q13.31)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 132 | 212 | 94 | 42
DEL PEAK 31(22Q13.31) CNV | 38 | 16 | 21 | 6
DEL PEAK 31(22Q13.31) WILD-TYPE | 94 | 196 | 73 | 36

Figure S59. Get High-res Image Gene #26: 'Del Peak 31(22q13.31)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 31(22q13.31)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000658 (Fisher's exact test), Q value = 0.14

Table S60. Gene #26: 'Del Peak 31(22q13.31)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
DEL PEAK 31(22Q13.31) CNV | 22 | 37 | 26
DEL PEAK 31(22Q13.31) WILD-TYPE | 133 | 93 | 182

Figure S60. Get High-res Image Gene #26: 'Del Peak 31(22q13.31)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 31(22q13.31)' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.1e-06 (Fisher's exact test), Q value = 0.0015

Table S61. Gene #26: 'Del Peak 31(22q13.31)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
DEL PEAK 31(22Q13.31) CNV | 48 | 18 | 19
DEL PEAK 31(22Q13.31) WILD-TYPE | 115 | 151 | 142

Figure S61. Get High-res Image Gene #26: 'Del Peak 31(22q13.31)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Del Peak 31(22q13.31)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000387 (Fisher's exact test), Q value = 0.087

Table S62. Gene #26: 'Del Peak 31(22q13.31)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
DEL PEAK 31(22Q13.31) CNV | 24 | 37 | 24
DEL PEAK 31(22Q13.31) WILD-TYPE | 175 | 91 | 142

Figure S62. Get High-res Image Gene #26: 'Del Peak 31(22q13.31)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 32(22q13.32)' versus 'CN_CNMF'

P value = 9.68e-89 (Fisher's exact test), Q value = 2.7e-86

Table S63. Gene #27: 'Del Peak 32(22q13.32)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 32(22Q13.32) CNV | 8 | 1 | 77
DEL PEAK 32(22Q13.32) WILD-TYPE | 26 | 382 | 0

Figure S63. Get High-res Image Gene #27: 'Del Peak 32(22q13.32)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 32(22q13.32)' versus 'METHLYATION_CNMF'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.0027

Table S64. Gene #27: 'Del Peak 32(22q13.32)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
DEL PEAK 32(22Q13.32) CNV | 45 | 7 | 34
DEL PEAK 32(22Q13.32) WILD-TYPE | 106 | 76 | 226

Figure S64. Get High-res Image Gene #27: 'Del Peak 32(22q13.32)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 32(22q13.32)' versus 'MRNASEQ_CNMF'

P value = 6.47e-09 (Fisher's exact test), Q value = 1.8e-06

Table S65. Gene #27: 'Del Peak 32(22q13.32)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 150 | 55 | 114 | 161
DEL PEAK 32(22Q13.32) CNV | 43 | 6 | 26 | 7
DEL PEAK 32(22Q13.32) WILD-TYPE | 107 | 49 | 88 | 154

Figure S65. Get High-res Image Gene #27: 'Del Peak 32(22q13.32)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 32(22q13.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.15e-07 (Fisher's exact test), Q value = 0.00019

Table S66. Gene #27: 'Del Peak 32(22q13.32)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 132 | 212 | 94 | 42
DEL PEAK 32(22Q13.32) CNV | 39 | 16 | 21 | 6
DEL PEAK 32(22Q13.32) WILD-TYPE | 93 | 196 | 73 | 36

Figure S66. Get High-res Image Gene #27: 'Del Peak 32(22q13.32)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 32(22q13.32)' versus 'MIRSEQ_CNMF'

P value = 0.000943 (Fisher's exact test), Q value = 0.2

Table S67. Gene #27: 'Del Peak 32(22q13.32)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
DEL PEAK 32(22Q13.32) CNV | 41 | 24 | 21
DEL PEAK 32(22Q13.32) WILD-TYPE | 109 | 149 | 149

Figure S67. Get High-res Image Gene #27: 'Del Peak 32(22q13.32)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 32(22q13.32)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000337 (Fisher's exact test), Q value = 0.077

Table S68. Gene #27: 'Del Peak 32(22q13.32)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
DEL PEAK 32(22Q13.32) CNV | 22 | 38 | 26
DEL PEAK 32(22Q13.32) WILD-TYPE | 133 | 92 | 182

Figure S68. Get High-res Image Gene #27: 'Del Peak 32(22q13.32)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 32(22q13.32)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.95e-06 (Fisher's exact test), Q value = 0.00076

Table S69. Gene #27: 'Del Peak 32(22q13.32)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
DEL PEAK 32(22Q13.32) CNV | 49 | 18 | 19
DEL PEAK 32(22Q13.32) WILD-TYPE | 114 | 151 | 142

Figure S69. Get High-res Image Gene #27: 'Del Peak 32(22q13.32)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Del Peak 32(22q13.32)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000212 (Fisher's exact test), Q value = 0.049

Table S70. Gene #27: 'Del Peak 32(22q13.32)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
DEL PEAK 32(22Q13.32) CNV | 24 | 38 | 24
DEL PEAK 32(22Q13.32) WILD-TYPE | 175 | 90 | 142

Figure S70. Get High-res Image Gene #27: 'Del Peak 32(22q13.32)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_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 = 494

- Number of copy number variation regions = 29

- Number of molecular subtypes = 10

- 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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] 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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