Correlation between copy number variation genes and molecular subtypes
Adrenocortical Carcinoma (Primary solid tumor)
23 September 2013 | analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C18G8J01
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/C18G8J01
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 38 peak regions and 8 molecular subtypes across 77 patients, 27 significant findings detected with Q value < 0.25.

- Amp Peak 1(1q22) cnvs correlated to 'MRNASEQ_CHIERARCHICAL'.

- Amp Peak 3(4q35.1) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

- Amp Peak 4(5p15.33) cnvs correlated to 'CN_CNMF'.

- Amp Peak 5(5q35.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- Amp Peak 7(9q34.3) cnvs correlated to 'CN_CNMF'.

- Amp Peak 8(12q14.1) cnvs correlated to 'CN_CNMF'.

- Amp Peak 9(14q11.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- Amp Peak 10(16q22.1) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- Amp Peak 12(19p13.12) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

- Amp Peak 13(19q12) cnvs correlated to 'CN_CNMF'.

- Amp Peak 14(19q13.33) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

- Amp Peak 15(Xq28) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

- Del Peak 11(9p23) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 38 regions and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 27 significant findings detected.

|  | Molecular subtypes | CN CNMF | METHLYATION CNMF | MRNASEQ CNMF | MRNASEQ CHIERARCHICAL | MIRSEQ CNMF | MIRSEQ CHIERARCHICAL | MIRSEQ MATURE CNMF | MIRSEQ MATURE CHIERARCHICAL
| nCNV (%) | nWild-Type | 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 | Fisher's exact test
Amp Peak 5(5q35 3) | 0 (0%) | 23 | 3.98e-07 (0.000119) | 0.000585 (0.163) | 2.02e-07 (6.04e-05) | 2.36e-06 (0.000693) | 0.33 (1.00) | 0.754 (1.00) | 0.746 (1.00) | 0.615 (1.00)
Amp Peak 9(14q11 2) | 0 (0%) | 55 | 1.46e-05 (0.00425) | 0.0283 (1.00) | 2.89e-06 (0.000848) | 5.93e-07 (0.000176) | 0.0204 (1.00) | 0.0116 (1.00) | 0.0204 (1.00) | 0.0217 (1.00)
Del Peak 11(9p23) | 0 (0%) | 57 | 0.000178 (0.0499) | 0.00298 (0.794) | 1.55e-05 (0.00449) | 0.000785 (0.217) | 0.505 (1.00) | 0.513 (1.00) | 1 (1.00) | 0.172 (1.00)
Amp Peak 3(4q35 1) | 0 (0%) | 52 | 4.74e-05 (0.0135) | 0.209 (1.00) | 0.000777 (0.215) | 0.00911 (1.00) | 0.13 (1.00) | 0.179 (1.00) | 0.366 (1.00) | 0.366 (1.00)
Amp Peak 10(16q22 1) | 0 (0%) | 31 | 8.76e-09 (2.63e-06) | 0.173 (1.00) | 0.00446 (1.00) | 0.000815 (0.224) | 0.767 (1.00) | 0.735 (1.00) | 1 (1.00) | 0.57 (1.00)
Amp Peak 12(19p13 12) | 0 (0%) | 28 | 0.000101 (0.0286) | 0.12 (1.00) | 0.00084 (0.23) | 0.00443 (1.00) | 0.768 (1.00) | 0.854 (1.00) | 0.768 (1.00) | 1 (1.00)
Amp Peak 14(19q13 33) | 0 (0%) | 29 | 1.23e-05 (0.00358) | 0.207 (1.00) | 0.000408 (0.114) | 0.00396 (1.00) | 1 (1.00) | 0.623 (1.00) | 1 (1.00) | 0.845 (1.00)
Amp Peak 15(Xq28) | 0 (0%) | 32 | 3.92e-05 (0.0113) | 0.366 (1.00) | 9.64e-05 (0.0273) | 0.00684 (1.00) | 1 (1.00) | 0.858 (1.00) | 0.566 (1.00) | 0.923 (1.00)
Del Peak 12(9p21 3) | 0 (0%) | 55 | 0.00198 (0.535) | 0.00111 (0.301) | 1.43e-06 (0.000423) | 4.45e-05 (0.0127) | 0.205 (1.00) | 0.839 (1.00) | 0.528 (1.00) | 0.142 (1.00)
Amp Peak 1(1q22) | 0 (0%) | 63 | 0.00193 (0.524) | 0.00429 (1.00) | 0.00971 (1.00) | 0.000415 (0.116) | 0.486 (1.00) | 0.141 (1.00) | 0.486 (1.00) | 0.128 (1.00)
Amp Peak 4(5p15 33) | 0 (0%) | 19 | 1.95e-06 (0.000574) | 0.657 (1.00) | 0.00482 (1.00) | 0.0534 (1.00) | 1 (1.00) | 0.817 (1.00) | 1 (1.00) | 0.811 (1.00)
Amp Peak 7(9q34 3) | 0 (0%) | 52 | 4.43e-05 (0.0127) | 0.00439 (1.00) | 0.00453 (1.00) | 0.00253 (0.681) | 0.3 (1.00) | 0.32 (1.00) | 0.731 (1.00) | 0.729 (1.00)
Amp Peak 8(12q14 1) | 0 (0%) | 18 | 2.21e-05 (0.0064) | 0.275 (1.00) | 0.0111 (1.00) | 0.0416 (1.00) | 1 (1.00) | 0.826 (1.00) | 1 (1.00) | 0.811 (1.00)
Amp Peak 13(19q12) | 0 (0%) | 30 | 8.46e-05 (0.024) | 0.0767 (1.00) | 0.00102 (0.278) | 0.00808 (1.00) | 1 (1.00) | 0.623 (1.00) | 1 (1.00) | 0.845 (1.00)
Amp Peak 2(4p16 3) | 0 (0%) | 44 | 0.00666 (1.00) | 0.463 (1.00) | 0.00523 (1.00) | 0.00951 (1.00) | 0.561 (1.00) | 0.8 (1.00) | 1 (1.00) | 0.855 (1.00)
Amp Peak 6(6q24 3) | 0 (0%) | 61 | 0.123 (1.00) | 0.852 (1.00) | 0.0609 (1.00) | 0.88 (1.00) | 0.269 (1.00) | 0.457 (1.00) | 0.715 (1.00) | 1 (1.00)
Amp Peak 11(17q25 3) | 0 (0%) | 64 | 0.193 (1.00) | 0.0638 (1.00) | 0.00681 (1.00) | 0.0413 (1.00) | 0.715 (1.00) | 1 (1.00) | 1 (1.00) | 0.877 (1.00)
Del Peak 1(1p36 23) | 0 (0%) | 47 | 0.0572 (1.00) | 0.0423 (1.00) | 0.239 (1.00) | 0.0335 (1.00) | 0.566 (1.00) | 0.154 (1.00) | 0.566 (1.00) | 0.526 (1.00)
Del Peak 2(1q24 1) | 0 (0%) | 67 | 0.0874 (1.00) | 0.0334 (1.00) | 0.711 (1.00) | 0.631 (1.00) | 0.158 (1.00) | 0.0824 (1.00) | 0.158 (1.00) | 0.042 (1.00)
Del Peak 3(2q37 3) | 0 (0%) | 61 | 0.017 (1.00) | 0.0282 (1.00) | 0.734 (1.00) | 0.469 (1.00) | 0.734 (1.00) | 0.325 (1.00) | 0.734 (1.00) | 0.49 (1.00)
Del Peak 4(3q13 31) | 0 (0%) | 56 | 0.213 (1.00) | 0.292 (1.00) | 0.00665 (1.00) | 0.123 (1.00) | 0.15 (1.00) | 0.457 (1.00) | 0.475 (1.00) | 0.279 (1.00)
Del Peak 5(3q13 31) | 0 (0%) | 56 | 0.53 (1.00) | 0.291 (1.00) | 0.0361 (1.00) | 0.286 (1.00) | 0.505 (1.00) | 0.912 (1.00) | 1 (1.00) | 0.811 (1.00)
Del Peak 6(4q34 3) | 0 (0%) | 58 | 0.00293 (0.783) | 0.0704 (1.00) | 0.0138 (1.00) | 0.0284 (1.00) | 0.475 (1.00) | 1 (1.00) | 0.475 (1.00) | 0.279 (1.00)
Del Peak 7(4q35 1) | 0 (0%) | 57 | 0.0311 (1.00) | 0.0447 (1.00) | 0.0754 (1.00) | 0.0324 (1.00) | 1 (1.00) | 0.624 (1.00) | 1 (1.00) | 0.886 (1.00)
Del Peak 8(6p25 2) | 0 (0%) | 66 | 0.415 (1.00) | 0.625 (1.00) | 0.434 (1.00) | 0.5 (1.00) | 1 (1.00) | 0.688 (1.00) | 1 (1.00) | 1 (1.00)
Del Peak 9(6q26) | 0 (0%) | 61 | 0.0909 (1.00) | 0.248 (1.00) | 0.0638 (1.00) | 0.167 (1.00) | 1 (1.00) | 0.679 (1.00) | 1 (1.00) | 0.877 (1.00)
Del Peak 10(7q32 3) | 0 (0%) | 71 | 0.158 (1.00) | 0.00702 (1.00) | 0.00938 (1.00) | 0.00292 (0.783) | 1 (1.00) | 0.779 (1.00) | 1 (1.00) | 1 (1.00)
Del Peak 13(10q26 3) | 0 (0%) | 68 | 0.749 (1.00) | 0.163 (1.00) | 0.371 (1.00) | 0.227 (1.00) | 0.242 (1.00) | 0.416 (1.00) | 0.242 (1.00) | 0.42 (1.00)
Del Peak 14(11p15 5) | 0 (0%) | 58 | 0.145 (1.00) | 0.0144 (1.00) | 0.169 (1.00) | 0.28 (1.00) | 1 (1.00) | 0.017 (1.00) | 1 (1.00) | 0.0803 (1.00)
Del Peak 15(11q24 3) | 0 (0%) | 56 | 0.133 (1.00) | 0.0594 (1.00) | 0.289 (1.00) | 0.442 (1.00) | 0.746 (1.00) | 0.433 (1.00) | 1 (1.00) | 0.685 (1.00)
Del Peak 16(12q14 2) | 0 (0%) | 73 | 0.561 (1.00) | 0.514 (1.00) | 0.434 (1.00) | 0.56 (1.00) | 1 (1.00) | 0.651 (1.00) | 1 (1.00) | 0.631 (1.00)
Del Peak 17(13q14 2) | 0 (0%) | 47 | 0.00645 (1.00) | 0.0771 (1.00) | 0.061 (1.00) | 0.262 (1.00) | 0.543 (1.00) | 0.617 (1.00) | 0.543 (1.00) | 0.783 (1.00)
Del Peak 18(16p13 3) | 0 (0%) | 71 | 0.158 (1.00) | 0.37 (1.00) | 0.38 (1.00) | 1 (1.00) | 0.194 (1.00) |  | 0.194 (1.00) |
Del Peak 19(16q23 1) | 0 (0%) | 71 | 0.158 (1.00) | 0.521 (1.00) | 0.017 (1.00) | 0.166 (1.00) | 1 (1.00) |  | 1 (1.00) |
Del Peak 20(17q11 2) | 0 (0%) | 58 | 0.0366 (1.00) | 0.00716 (1.00) | 0.0919 (1.00) | 0.0997 (1.00) | 0.269 (1.00) | 0.881 (1.00) | 0.269 (1.00) | 0.333 (1.00)
Del Peak 21(17q21 31) | 0 (0%) | 56 | 0.0149 (1.00) | 0.00939 (1.00) | 0.117 (1.00) | 0.0351 (1.00) | 0.0152 (1.00) | 0.125 (1.00) | 0.0152 (1.00) | 0.038 (1.00)
Del Peak 22(17q24 2) | 0 (0%) | 57 | 0.0138 (1.00) | 0.00944 (1.00) | 0.259 (1.00) | 0.0223 (1.00) | 0.0809 (1.00) | 0.666 (1.00) | 0.0809 (1.00) | 0.0783 (1.00)
Del Peak 23(22q12 1) | 0 (0%) | 36 | 0.0132 (1.00) | 0.231 (1.00) | 0.779 (1.00) | 0.588 (1.00) | 0.248 (1.00) | 0.438 (1.00) | 0.0823 (1.00) | 0.303 (1.00)

'Amp Peak 1(1q22)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000415 (Fisher's exact test), Q value = 0.12

Table S1. Gene #1: 'Amp Peak 1(1q22)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 23 | 32 | 21
AMP PEAK 1(1Q22) CNV | 10 | 4 | 0
AMP PEAK 1(1Q22) WILD-TYPE | 13 | 28 | 21

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1q22)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 3(4q35.1)' versus 'CN_CNMF'

P value = 4.74e-05 (Fisher's exact test), Q value = 0.014

Table S2. Gene #3: 'Amp Peak 3(4q35.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 19 | 19 | 10
AMP PEAK 3(4Q35.1) CNV | 2 | 6 | 9 | 8
AMP PEAK 3(4Q35.1) WILD-TYPE | 27 | 13 | 10 | 2

Figure S2. Get High-res Image Gene #3: 'Amp Peak 3(4q35.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 3(4q35.1)' versus 'MRNASEQ_CNMF'

P value = 0.000777 (Fisher's exact test), Q value = 0.22

Table S3. Gene #3: 'Amp Peak 3(4q35.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 12 | 17 | 23
AMP PEAK 3(4Q35.1) CNV | 1 | 4 | 9 | 11
AMP PEAK 3(4Q35.1) WILD-TYPE | 23 | 8 | 8 | 12

Figure S3. Get High-res Image Gene #3: 'Amp Peak 3(4q35.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Amp Peak 4(5p15.33)' versus 'CN_CNMF'

P value = 1.95e-06 (Fisher's exact test), Q value = 0.00057

Table S4. Gene #4: 'Amp Peak 4(5p15.33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 19 | 19 | 10
AMP PEAK 4(5P15.33) CNV | 12 | 18 | 18 | 10
AMP PEAK 4(5P15.33) WILD-TYPE | 17 | 1 | 1 | 0

Figure S4. Get High-res Image Gene #4: 'Amp Peak 4(5p15.33)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 5(5q35.3)' versus 'CN_CNMF'

P value = 3.98e-07 (Fisher's exact test), Q value = 0.00012

Table S5. Gene #5: 'Amp Peak 5(5q35.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 19 | 19 | 10
AMP PEAK 5(5Q35.3) CNV | 10 | 19 | 17 | 8
AMP PEAK 5(5Q35.3) WILD-TYPE | 19 | 0 | 2 | 2

Figure S5. Get High-res Image Gene #5: 'Amp Peak 5(5q35.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 5(5q35.3)' versus 'METHLYATION_CNMF'

P value = 0.000585 (Chi-square test), Q value = 0.16

Table S6. Gene #5: 'Amp Peak 5(5q35.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 19 | 18 | 11
AMP PEAK 5(5Q35.3) CNV | 6 | 7 | 18 | 13 | 10
AMP PEAK 5(5Q35.3) WILD-TYPE | 12 | 4 | 1 | 5 | 1

Figure S6. Get High-res Image Gene #5: 'Amp Peak 5(5q35.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 5(5q35.3)' versus 'MRNASEQ_CNMF'

P value = 2.02e-07 (Fisher's exact test), Q value = 6e-05

Table S7. Gene #5: 'Amp Peak 5(5q35.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 12 | 17 | 23
AMP PEAK 5(5Q35.3) CNV | 6 | 11 | 16 | 20
AMP PEAK 5(5Q35.3) WILD-TYPE | 18 | 1 | 1 | 3

Figure S7. Get High-res Image Gene #5: 'Amp Peak 5(5q35.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Amp Peak 5(5q35.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.36e-06 (Fisher's exact test), Q value = 0.00069

Table S8. Gene #5: 'Amp Peak 5(5q35.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 23 | 32 | 21
AMP PEAK 5(5Q35.3) CNV | 7 | 26 | 20
AMP PEAK 5(5Q35.3) WILD-TYPE | 16 | 6 | 1

Figure S8. Get High-res Image Gene #5: 'Amp Peak 5(5q35.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 7(9q34.3)' versus 'CN_CNMF'

P value = 4.43e-05 (Fisher's exact test), Q value = 0.013

Table S9. Gene #7: 'Amp Peak 7(9q34.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 19 | 19 | 10
AMP PEAK 7(9Q34.3) CNV | 8 | 1 | 14 | 2
AMP PEAK 7(9Q34.3) WILD-TYPE | 21 | 18 | 5 | 8

Figure S9. Get High-res Image Gene #7: 'Amp Peak 7(9q34.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 8(12q14.1)' versus 'CN_CNMF'

P value = 2.21e-05 (Fisher's exact test), Q value = 0.0064

Table S10. Gene #8: 'Amp Peak 8(12q14.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 19 | 19 | 10
AMP PEAK 8(12Q14.1) CNV | 14 | 19 | 18 | 8
AMP PEAK 8(12Q14.1) WILD-TYPE | 15 | 0 | 1 | 2

Figure S10. Get High-res Image Gene #8: 'Amp Peak 8(12q14.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 9(14q11.2)' versus 'CN_CNMF'

P value = 1.46e-05 (Fisher's exact test), Q value = 0.0043

Table S11. Gene #9: 'Amp Peak 9(14q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 19 | 19 | 10
AMP PEAK 9(14Q11.2) CNV | 3 | 4 | 14 | 1
AMP PEAK 9(14Q11.2) WILD-TYPE | 26 | 15 | 5 | 9

Figure S11. Get High-res Image Gene #9: 'Amp Peak 9(14q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 9(14q11.2)' versus 'MRNASEQ_CNMF'

P value = 2.89e-06 (Fisher's exact test), Q value = 0.00085

Table S12. Gene #9: 'Amp Peak 9(14q11.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 12 | 17 | 23
AMP PEAK 9(14Q11.2) CNV | 4 | 6 | 11 | 0
AMP PEAK 9(14Q11.2) WILD-TYPE | 20 | 6 | 6 | 23

Figure S12. Get High-res Image Gene #9: 'Amp Peak 9(14q11.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Amp Peak 9(14q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.93e-07 (Fisher's exact test), Q value = 0.00018

Table S13. Gene #9: 'Amp Peak 9(14q11.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 23 | 32 | 21
AMP PEAK 9(14Q11.2) CNV | 4 | 2 | 15
AMP PEAK 9(14Q11.2) WILD-TYPE | 19 | 30 | 6

Figure S13. Get High-res Image Gene #9: 'Amp Peak 9(14q11.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 10(16q22.1)' versus 'CN_CNMF'

P value = 8.76e-09 (Fisher's exact test), Q value = 2.6e-06

Table S14. Gene #10: 'Amp Peak 10(16q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 19 | 19 | 10
AMP PEAK 10(16Q22.1) CNV | 7 | 19 | 16 | 4
AMP PEAK 10(16Q22.1) WILD-TYPE | 22 | 0 | 3 | 6

Figure S14. Get High-res Image Gene #10: 'Amp Peak 10(16q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 10(16q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000815 (Fisher's exact test), Q value = 0.22

Table S15. Gene #10: 'Amp Peak 10(16q22.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 23 | 32 | 21
AMP PEAK 10(16Q22.1) CNV | 7 | 20 | 18
AMP PEAK 10(16Q22.1) WILD-TYPE | 16 | 12 | 3

Figure S15. Get High-res Image Gene #10: 'Amp Peak 10(16q22.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 12(19p13.12)' versus 'CN_CNMF'

P value = 0.000101 (Fisher's exact test), Q value = 0.029

Table S16. Gene #12: 'Amp Peak 12(19p13.12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 19 | 19 | 10
AMP PEAK 12(19P13.12) CNV | 12 | 11 | 19 | 7
AMP PEAK 12(19P13.12) WILD-TYPE | 17 | 8 | 0 | 3

Figure S16. Get High-res Image Gene #12: 'Amp Peak 12(19p13.12)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 12(19p13.12)' versus 'MRNASEQ_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.23

Table S17. Gene #12: 'Amp Peak 12(19p13.12)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 12 | 17 | 23
AMP PEAK 12(19P13.12) CNV | 11 | 12 | 14 | 11
AMP PEAK 12(19P13.12) WILD-TYPE | 13 | 0 | 3 | 12

Figure S17. Get High-res Image Gene #12: 'Amp Peak 12(19p13.12)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Amp Peak 13(19q12)' versus 'CN_CNMF'

P value = 8.46e-05 (Fisher's exact test), Q value = 0.024

Table S18. Gene #13: 'Amp Peak 13(19q12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 19 | 19 | 10
AMP PEAK 13(19Q12) CNV | 12 | 10 | 19 | 6
AMP PEAK 13(19Q12) WILD-TYPE | 17 | 9 | 0 | 4

Figure S18. Get High-res Image Gene #13: 'Amp Peak 13(19q12)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 14(19q13.33)' versus 'CN_CNMF'

P value = 1.23e-05 (Fisher's exact test), Q value = 0.0036

Table S19. Gene #14: 'Amp Peak 14(19q13.33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 19 | 19 | 10
AMP PEAK 14(19Q13.33) CNV | 10 | 13 | 19 | 6
AMP PEAK 14(19Q13.33) WILD-TYPE | 19 | 6 | 0 | 4

Figure S19. Get High-res Image Gene #14: 'Amp Peak 14(19q13.33)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 14(19q13.33)' versus 'MRNASEQ_CNMF'

P value = 0.000408 (Fisher's exact test), Q value = 0.11

Table S20. Gene #14: 'Amp Peak 14(19q13.33)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 12 | 17 | 23
AMP PEAK 14(19Q13.33) CNV | 10 | 12 | 14 | 11
AMP PEAK 14(19Q13.33) WILD-TYPE | 14 | 0 | 3 | 12

Figure S20. Get High-res Image Gene #14: 'Amp Peak 14(19q13.33)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Amp Peak 15(Xq28)' versus 'CN_CNMF'

P value = 3.92e-05 (Fisher's exact test), Q value = 0.011

Table S21. Gene #15: 'Amp Peak 15(Xq28)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 19 | 19 | 10
AMP PEAK 15(XQ28) CNV | 8 | 16 | 16 | 5
AMP PEAK 15(XQ28) WILD-TYPE | 21 | 3 | 3 | 5

Figure S21. Get High-res Image Gene #15: 'Amp Peak 15(Xq28)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 15(Xq28)' versus 'MRNASEQ_CNMF'

P value = 9.64e-05 (Fisher's exact test), Q value = 0.027

Table S22. Gene #15: 'Amp Peak 15(Xq28)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 12 | 17 | 23
AMP PEAK 15(XQ28) CNV | 6 | 11 | 14 | 14
AMP PEAK 15(XQ28) WILD-TYPE | 18 | 1 | 3 | 9

Figure S22. Get High-res Image Gene #15: 'Amp Peak 15(Xq28)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 11(9p23)' versus 'CN_CNMF'

P value = 0.000178 (Fisher's exact test), Q value = 0.05

Table S23. Gene #26: 'Del Peak 11(9p23)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 19 | 19 | 10
DEL PEAK 11(9P23) CNV | 15 | 0 | 4 | 1
DEL PEAK 11(9P23) WILD-TYPE | 14 | 19 | 15 | 9

Figure S23. Get High-res Image Gene #26: 'Del Peak 11(9p23)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 11(9p23)' versus 'MRNASEQ_CNMF'

P value = 1.55e-05 (Fisher's exact test), Q value = 0.0045

Table S24. Gene #26: 'Del Peak 11(9p23)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 12 | 17 | 23
DEL PEAK 11(9P23) CNV | 15 | 1 | 3 | 1
DEL PEAK 11(9P23) WILD-TYPE | 9 | 11 | 14 | 22

Figure S24. Get High-res Image Gene #26: 'Del Peak 11(9p23)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 11(9p23)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000785 (Fisher's exact test), Q value = 0.22

Table S25. Gene #26: 'Del Peak 11(9p23)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 23 | 32 | 21
DEL PEAK 11(9P23) CNV | 13 | 4 | 3
DEL PEAK 11(9P23) WILD-TYPE | 10 | 28 | 18

Figure S25. Get High-res Image Gene #26: 'Del Peak 11(9p23)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

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

P value = 1.43e-06 (Fisher's exact test), Q value = 0.00042

Table S26. Gene #27: 'Del Peak 12(9p21.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 12 | 17 | 23
DEL PEAK 12(9P21.3) CNV | 17 | 1 | 2 | 2
DEL PEAK 12(9P21.3) WILD-TYPE | 7 | 11 | 15 | 21

Figure S26. Get High-res Image Gene #27: 'Del Peak 12(9p21.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 12(9p21.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.45e-05 (Fisher's exact test), Q value = 0.013

Table S27. Gene #27: 'Del Peak 12(9p21.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 23 | 32 | 21
DEL PEAK 12(9P21.3) CNV | 15 | 4 | 3
DEL PEAK 12(9P21.3) WILD-TYPE | 8 | 28 | 18

Figure S27. Get High-res Image Gene #27: 'Del Peak 12(9p21.3)' versus Molecular Subtype #4: 'MRNASEQ_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 = ACC-TP.transferedmergedcluster.txt

- Number of patients = 77

- Number of copy number variation regions = 38

- 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

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] 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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