Correlation between copy number variation genes (focal events) and molecular subtypes
Pheochromocytoma and Paraganglioma (Primary solid tumor)
15 July 2014 | analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1SF2TZX
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1SF2TZX
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 30 focal events and 8 molecular subtypes across 160 patients, 35 significant findings detected with P value < 0.05 and Q value < 0.25.

- amp_1q21.3 cnv correlated to 'CN_CNMF'.

- amp_14q24.3 cnv correlated to 'CN_CNMF'.

- del_1p12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_3p24.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_3q26.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- del_11p15.4 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_11q22.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

- del_17p13.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- del_17q11.2 cnv correlated to 'CN_CNMF'.

- del_22q13.31 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_xp21.1 cnv correlated to 'MIRSEQ_CNMF'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 30 focal events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 35 significant findings detected.

|  | Clinical Features | 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 | 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 11p15 4 | 57 (36%) | 103 | 1e-05 (0.0024) | 3e-05 (0.00669) | 0.00024 (0.0516) | 1e-05 (0.0024) | 0.00012 (0.0263) | 1e-05 (0.0024) | 1e-05 (0.0024) | 4e-05 (0.00888)
del 1p12 | 111 (69%) | 49 | 1e-05 (0.0024) | 1e-05 (0.0024) | 1e-05 (0.0024) | 1e-05 (0.0024) | 0.00057 (0.121) | 0.0182 (1.00) | 0.00036 (0.077) | 0.00058 (0.122)
del 3p24 1 | 60 (38%) | 100 | 1e-05 (0.0024) | 0.00323 (0.623) | 0.00015 (0.0327) | 2e-05 (0.0045) | 2e-05 (0.0045) | 0.00022 (0.0475) | 8e-05 (0.0176) | 0.00086 (0.178)
del 22q13 31 | 64 (40%) | 96 | 1e-05 (0.0024) | 0.00962 (1.00) | 0.00312 (0.608) | 0.00018 (0.0391) | 0.00155 (0.316) | 0.0073 (1.00) | 0.00467 (0.873) | 0.0007 (0.146)
del 3q26 1 | 93 (58%) | 67 | 1e-05 (0.0024) | 0.573 (1.00) | 0.0199 (1.00) | 1e-05 (0.0024) | 0.0133 (1.00) | 0.006 (1.00) | 0.0957 (1.00) | 0.00362 (0.688)
del 11q22 1 | 44 (28%) | 116 | 1e-05 (0.0024) | 0.207 (1.00) | 0.00294 (0.576) | 0.00421 (0.791) | 0.00467 (0.873) | 0.00103 (0.212) | 0.00133 (0.273) | 0.00411 (0.777)
del 17p13 2 | 64 (40%) | 96 | 7e-05 (0.0155) | 0.00045 (0.0958) | 0.0128 (1.00) | 0.0053 (0.975) | 0.0241 (1.00) | 0.00707 (1.00) | 0.00213 (0.43) | 0.0194 (1.00)
amp 1q21 3 | 30 (19%) | 130 | 1e-05 (0.0024) | 0.608 (1.00) | 0.643 (1.00) | 0.958 (1.00) | 0.903 (1.00) | 0.442 (1.00) | 0.254 (1.00) | 0.842 (1.00)
amp 14q24 3 | 10 (6%) | 150 | 0.00076 (0.158) | 0.199 (1.00) | 0.853 (1.00) | 0.169 (1.00) | 0.457 (1.00) | 0.713 (1.00) | 0.0604 (1.00) | 0.598 (1.00)
del 17q11 2 | 42 (26%) | 118 | 1e-05 (0.0024) | 0.00335 (0.64) | 0.0222 (1.00) | 0.00254 (0.505) | 0.0924 (1.00) | 0.0682 (1.00) | 0.00251 (0.502) | 0.0321 (1.00)
del xp21 1 | 46 (29%) | 114 | 0.00263 (0.521) | 0.00569 (1.00) | 0.0323 (1.00) | 0.00313 (0.608) | 0.00062 (0.13) | 0.0417 (1.00) | 0.0495 (1.00) | 0.0133 (1.00)
amp 4q25 | 6 (4%) | 154 | 0.697 (1.00) | 0.762 (1.00) | 0.133 (1.00) | 0.382 (1.00) | 0.765 (1.00) | 0.63 (1.00) | 0.377 (1.00) | 0.762 (1.00)
amp 4q31 1 | 12 (8%) | 148 | 0.0809 (1.00) | 0.086 (1.00) | 0.749 (1.00) | 0.0189 (1.00) | 0.199 (1.00) | 0.185 (1.00) | 0.128 (1.00) | 0.747 (1.00)
amp 11p15 2 | 7 (4%) | 153 | 0.405 (1.00) | 0.141 (1.00) | 0.0909 (1.00) | 0.0924 (1.00) | 0.165 (1.00) | 0.178 (1.00) | 0.0483 (1.00) | 0.107 (1.00)
amp 12q13 3 | 16 (10%) | 144 | 0.079 (1.00) | 0.14 (1.00) | 0.615 (1.00) | 0.621 (1.00) | 0.047 (1.00) | 0.261 (1.00) | 0.00821 (1.00) | 0.101 (1.00)
amp 17q21 31 | 15 (9%) | 145 | 0.122 (1.00) | 0.83 (1.00) | 0.702 (1.00) | 0.00158 (0.321) | 0.888 (1.00) | 0.2 (1.00) | 0.194 (1.00) | 0.396 (1.00)
del 1q44 | 21 (13%) | 139 | 0.0554 (1.00) | 0.35 (1.00) | 0.0809 (1.00) | 0.27 (1.00) | 0.381 (1.00) | 0.716 (1.00) | 0.023 (1.00) | 0.185 (1.00)
del 2q34 | 13 (8%) | 147 | 0.0594 (1.00) | 0.447 (1.00) | 0.418 (1.00) | 0.143 (1.00) | 0.532 (1.00) | 0.0946 (1.00) | 0.617 (1.00) | 0.305 (1.00)
del 4q22 1 | 15 (9%) | 145 | 0.018 (1.00) | 0.225 (1.00) | 0.00778 (1.00) | 0.0793 (1.00) | 0.127 (1.00) | 0.29 (1.00) | 0.122 (1.00) | 0.2 (1.00)
del 4q35 2 | 16 (10%) | 144 | 0.00276 (0.544) | 0.521 (1.00) | 0.233 (1.00) | 0.369 (1.00) | 0.752 (1.00) | 0.641 (1.00) | 0.528 (1.00) | 0.53 (1.00)
del 5q15 | 12 (8%) | 148 | 0.277 (1.00) | 1 (1.00) | 0.973 (1.00) | 1 (1.00) | 0.928 (1.00) | 0.187 (1.00) | 0.866 (1.00) | 0.75 (1.00)
del 6p12 3 | 10 (6%) | 150 | 0.185 (1.00) | 0.265 (1.00) | 0.0205 (1.00) | 0.0926 (1.00) | 0.199 (1.00) | 0.169 (1.00) | 0.767 (1.00) | 0.199 (1.00)
del 6q16 1 | 24 (15%) | 136 | 0.357 (1.00) | 0.0742 (1.00) | 0.0255 (1.00) | 0.00736 (1.00) | 0.0167 (1.00) | 0.00523 (0.968) | 0.00624 (1.00) | 0.00329 (0.632)
del 7q33 | 8 (5%) | 152 | 0.031 (1.00) | 0.257 (1.00) | 0.00662 (1.00) | 0.0505 (1.00) | 0.0167 (1.00) | 0.00612 (1.00) | 0.525 (1.00) | 0.00927 (1.00)
del 8p22 | 24 (15%) | 136 | 0.0605 (1.00) | 0.124 (1.00) | 0.00247 (0.496) | 0.00657 (1.00) | 0.152 (1.00) | 0.155 (1.00) | 0.0251 (1.00) | 0.187 (1.00)
del 9p24 2 | 15 (9%) | 145 | 0.476 (1.00) | 0.339 (1.00) | 0.0839 (1.00) | 0.167 (1.00) | 0.514 (1.00) | 0.0729 (1.00) | 0.351 (1.00) | 0.542 (1.00)
del 9q21 12 | 14 (9%) | 146 | 0.562 (1.00) | 0.553 (1.00) | 0.362 (1.00) | 0.358 (1.00) | 0.723 (1.00) | 0.116 (1.00) | 0.826 (1.00) | 1 (1.00)
del 12q21 33 | 8 (5%) | 152 | 0.323 (1.00) | 0.893 (1.00) | 0.912 (1.00) | 0.876 (1.00) | 0.594 (1.00) | 0.702 (1.00) | 0.409 (1.00) | 0.527 (1.00)
del 13q22 3 | 7 (4%) | 153 | 0.726 (1.00) | 0.889 (1.00) | 0.368 (1.00) | 0.676 (1.00) | 0.794 (1.00) | 0.451 (1.00) | 0.541 (1.00) | 0.484 (1.00)
del 16q21 | 5 (3%) | 155 | 0.0144 (1.00) | 0.114 (1.00) | 0.554 (1.00) | 0.0146 (1.00) | 0.212 (1.00) | 0.592 (1.00) | 0.452 (1.00) | 0.851 (1.00)

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0024

Table S1. Gene #1: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 15 | 24 | 55 | 43 | 23
AMP PEAK 1(1Q21.3) MUTATED | 15 | 3 | 5 | 2 | 5
AMP PEAK 1(1Q21.3) WILD-TYPE | 0 | 21 | 50 | 41 | 18

Figure S1. Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_14q24.3' versus 'CN_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.16

Table S2. Gene #6: 'amp_14q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 15 | 24 | 55 | 43 | 23
AMP PEAK 6(14Q24.3) MUTATED | 0 | 0 | 1 | 9 | 0
AMP PEAK 6(14Q24.3) WILD-TYPE | 15 | 24 | 54 | 34 | 23

Figure S2. Get High-res Image Gene #6: 'amp_14q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0024

Table S3. Gene #8: 'del_1p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 15 | 24 | 55 | 43 | 23
DEL PEAK 1(1P12) MUTATED | 14 | 0 | 48 | 27 | 22
DEL PEAK 1(1P12) WILD-TYPE | 1 | 24 | 7 | 16 | 1

Figure S3. Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0024

Table S4. Gene #8: 'del_1p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 77 | 43
DEL PEAK 1(1P12) MUTATED | 24 | 67 | 20
DEL PEAK 1(1P12) WILD-TYPE | 16 | 10 | 23

Figure S4. Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0024

Table S5. Gene #8: 'del_1p12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 43 | 21
DEL PEAK 1(1P12) MUTATED | 24 | 57 | 20 | 10
DEL PEAK 1(1P12) WILD-TYPE | 9 | 6 | 23 | 11

Figure S5. Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_1p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0024

Table S6. Gene #8: 'del_1p12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 43 | 21
DEL PEAK 1(1P12) MUTATED | 18 | 57 | 27 | 9
DEL PEAK 1(1P12) WILD-TYPE | 15 | 6 | 16 | 12

Figure S6. Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_1p12' versus 'MIRSEQ_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.12

Table S7. Gene #8: 'del_1p12' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 64 | 57 | 39
DEL PEAK 1(1P12) MUTATED | 38 | 50 | 23
DEL PEAK 1(1P12) WILD-TYPE | 26 | 7 | 16

Figure S7. Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_1p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.077

Table S8. Gene #8: 'del_1p12' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 37 | 66 | 57
DEL PEAK 1(1P12) MUTATED | 21 | 57 | 33
DEL PEAK 1(1P12) WILD-TYPE | 16 | 9 | 24

Figure S8. Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_1p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.12

Table S9. Gene #8: 'del_1p12' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 68 | 53 | 39
DEL PEAK 1(1P12) MUTATED | 41 | 47 | 23
DEL PEAK 1(1P12) WILD-TYPE | 27 | 6 | 16

Figure S9. Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0024

Table S10. Gene #11: 'del_3p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 15 | 24 | 55 | 43 | 23
DEL PEAK 4(3P24.1) MUTATED | 9 | 1 | 12 | 32 | 6
DEL PEAK 4(3P24.1) WILD-TYPE | 6 | 23 | 43 | 11 | 17

Figure S10. Get High-res Image Gene #11: 'del_3p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p24.1' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.033

Table S11. Gene #11: 'del_3p24.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 43 | 21
DEL PEAK 4(3P24.1) MUTATED | 17 | 15 | 25 | 3
DEL PEAK 4(3P24.1) WILD-TYPE | 16 | 48 | 18 | 18

Figure S11. Get High-res Image Gene #11: 'del_3p24.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0045

Table S12. Gene #11: 'del_3p24.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 43 | 21
DEL PEAK 4(3P24.1) MUTATED | 11 | 16 | 30 | 3
DEL PEAK 4(3P24.1) WILD-TYPE | 22 | 47 | 13 | 18

Figure S12. Get High-res Image Gene #11: 'del_3p24.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p24.1' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0045

Table S13. Gene #11: 'del_3p24.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 64 | 57 | 39
DEL PEAK 4(3P24.1) MUTATED | 37 | 17 | 6
DEL PEAK 4(3P24.1) WILD-TYPE | 27 | 40 | 33

Figure S13. Get High-res Image Gene #11: 'del_3p24.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.048

Table S14. Gene #11: 'del_3p24.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 65 | 53 | 18 | 24
DEL PEAK 4(3P24.1) MUTATED | 37 | 14 | 6 | 3
DEL PEAK 4(3P24.1) WILD-TYPE | 28 | 39 | 12 | 21

Figure S14. Get High-res Image Gene #11: 'del_3p24.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.018

Table S15. Gene #11: 'del_3p24.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 37 | 66 | 57
DEL PEAK 4(3P24.1) MUTATED | 25 | 16 | 19
DEL PEAK 4(3P24.1) WILD-TYPE | 12 | 50 | 38

Figure S15. Get High-res Image Gene #11: 'del_3p24.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3p24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00086 (Fisher's exact test), Q value = 0.18

Table S16. Gene #11: 'del_3p24.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 68 | 53 | 39
DEL PEAK 4(3P24.1) MUTATED | 37 | 14 | 9
DEL PEAK 4(3P24.1) WILD-TYPE | 31 | 39 | 30

Figure S16. Get High-res Image Gene #11: 'del_3p24.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q26.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0024

Table S17. Gene #12: 'del_3q26.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 15 | 24 | 55 | 43 | 23
DEL PEAK 5(3Q26.1) MUTATED | 8 | 0 | 38 | 33 | 14
DEL PEAK 5(3Q26.1) WILD-TYPE | 7 | 24 | 17 | 10 | 9

Figure S17. Get High-res Image Gene #12: 'del_3q26.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q26.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0024

Table S18. Gene #12: 'del_3q26.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 43 | 21
DEL PEAK 5(3Q26.1) MUTATED | 6 | 47 | 33 | 7
DEL PEAK 5(3Q26.1) WILD-TYPE | 27 | 16 | 10 | 14

Figure S18. Get High-res Image Gene #12: 'del_3q26.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.4' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0024

Table S19. Gene #22: 'del_11p15.4' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 15 | 24 | 55 | 43 | 23
DEL PEAK 15(11P15.4) MUTATED | 5 | 5 | 0 | 36 | 11
DEL PEAK 15(11P15.4) WILD-TYPE | 10 | 19 | 55 | 7 | 12

Figure S19. Get High-res Image Gene #22: 'del_11p15.4' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.4' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0067

Table S20. Gene #22: 'del_11p15.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 77 | 43
DEL PEAK 15(11P15.4) MUTATED | 23 | 14 | 20
DEL PEAK 15(11P15.4) WILD-TYPE | 17 | 63 | 23

Figure S20. Get High-res Image Gene #22: 'del_11p15.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.4' versus 'MRNASEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.052

Table S21. Gene #22: 'del_11p15.4' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 43 | 21
DEL PEAK 15(11P15.4) MUTATED | 13 | 12 | 26 | 6
DEL PEAK 15(11P15.4) WILD-TYPE | 20 | 51 | 17 | 15

Figure S21. Get High-res Image Gene #22: 'del_11p15.4' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_11p15.4' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0024

Table S22. Gene #22: 'del_11p15.4' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 43 | 21
DEL PEAK 15(11P15.4) MUTATED | 11 | 9 | 31 | 6
DEL PEAK 15(11P15.4) WILD-TYPE | 22 | 54 | 12 | 15

Figure S22. Get High-res Image Gene #22: 'del_11p15.4' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.4' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.026

Table S23. Gene #22: 'del_11p15.4' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 64 | 57 | 39
DEL PEAK 15(11P15.4) MUTATED | 36 | 11 | 10
DEL PEAK 15(11P15.4) WILD-TYPE | 28 | 46 | 29

Figure S23. Get High-res Image Gene #22: 'del_11p15.4' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_11p15.4' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0024

Table S24. Gene #22: 'del_11p15.4' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 65 | 53 | 18 | 24
DEL PEAK 15(11P15.4) MUTATED | 39 | 7 | 5 | 6
DEL PEAK 15(11P15.4) WILD-TYPE | 26 | 46 | 13 | 18

Figure S24. Get High-res Image Gene #22: 'del_11p15.4' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.4' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0024

Table S25. Gene #22: 'del_11p15.4' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 37 | 66 | 57
DEL PEAK 15(11P15.4) MUTATED | 26 | 13 | 18
DEL PEAK 15(11P15.4) WILD-TYPE | 11 | 53 | 39

Figure S25. Get High-res Image Gene #22: 'del_11p15.4' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_11p15.4' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.0089

Table S26. Gene #22: 'del_11p15.4' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 68 | 53 | 39
DEL PEAK 15(11P15.4) MUTATED | 38 | 9 | 10
DEL PEAK 15(11P15.4) WILD-TYPE | 30 | 44 | 29

Figure S26. Get High-res Image Gene #22: 'del_11p15.4' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0024

Table S27. Gene #23: 'del_11q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 15 | 24 | 55 | 43 | 23
DEL PEAK 16(11Q22.1) MUTATED | 3 | 3 | 3 | 33 | 2
DEL PEAK 16(11Q22.1) WILD-TYPE | 12 | 21 | 52 | 10 | 21

Figure S27. Get High-res Image Gene #23: 'del_11q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00103 (Fisher's exact test), Q value = 0.21

Table S28. Gene #23: 'del_11q22.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 65 | 53 | 18 | 24
DEL PEAK 16(11Q22.1) MUTATED | 28 | 7 | 2 | 7
DEL PEAK 16(11Q22.1) WILD-TYPE | 37 | 46 | 16 | 17

Figure S28. Get High-res Image Gene #23: 'del_11q22.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_17p13.2' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.015

Table S29. Gene #27: 'del_17p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 15 | 24 | 55 | 43 | 23
DEL PEAK 20(17P13.2) MUTATED | 5 | 4 | 31 | 22 | 2
DEL PEAK 20(17P13.2) WILD-TYPE | 10 | 20 | 24 | 21 | 21

Figure S29. Get High-res Image Gene #27: 'del_17p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.2' versus 'METHLYATION_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.096

Table S30. Gene #27: 'del_17p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 77 | 43
DEL PEAK 20(17P13.2) MUTATED | 9 | 43 | 12
DEL PEAK 20(17P13.2) WILD-TYPE | 31 | 34 | 31

Figure S30. Get High-res Image Gene #27: 'del_17p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0024

Table S31. Gene #28: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 15 | 24 | 55 | 43 | 23
DEL PEAK 21(17Q11.2) MUTATED | 1 | 0 | 25 | 16 | 0
DEL PEAK 21(17Q11.2) WILD-TYPE | 14 | 24 | 30 | 27 | 23

Figure S31. Get High-res Image Gene #28: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0024

Table S32. Gene #29: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 15 | 24 | 55 | 43 | 23
DEL PEAK 22(22Q13.31) MUTATED | 6 | 6 | 39 | 11 | 2
DEL PEAK 22(22Q13.31) WILD-TYPE | 9 | 18 | 16 | 32 | 21

Figure S32. Get High-res Image Gene #29: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.039

Table S33. Gene #29: 'del_22q13.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 43 | 21
DEL PEAK 22(22Q13.31) MUTATED | 13 | 37 | 7 | 7
DEL PEAK 22(22Q13.31) WILD-TYPE | 20 | 26 | 36 | 14

Figure S33. Get High-res Image Gene #29: 'del_22q13.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.15

Table S34. Gene #29: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 68 | 53 | 39
DEL PEAK 22(22Q13.31) MUTATED | 16 | 30 | 18
DEL PEAK 22(22Q13.31) WILD-TYPE | 52 | 23 | 21

Figure S34. Get High-res Image Gene #29: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.13

Table S35. Gene #30: 'del_xp21.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 64 | 57 | 39
DEL PEAK 23(XP21.1) MUTATED | 13 | 27 | 6
DEL PEAK 23(XP21.1) WILD-TYPE | 51 | 30 | 33

Figure S35. Get High-res Image Gene #30: 'del_xp21.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

Methods & Data
Input

- Copy number data file = transformed.cor.cli.txt

- Molecular subtype file = PCPG-TP.transferedmergedcluster.txt

- Number of patients = 160

- Number of significantly focal cnvs = 30

- Number of molecular subtypes = 8

- Exclude genes 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)
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