Correlation between copy number variation genes (focal events) and molecular subtypes
Pheochromocytoma and Paraganglioma (Primary solid tumor)
02 April 2015 | analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1F76BM0
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1F76BM0
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 28 focal events and 10 molecular subtypes across 162 patients, 94 significant findings detected with P value < 0.05 and Q value < 0.25.

- amp_1q21.3 cnv correlated to 'CN_CNMF'.

- amp_4q31.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- amp_12q13.3 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

- amp_14q24.3 cnv correlated to 'CN_CNMF'.

- amp_17q21.31 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

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

- del_1q42.13 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

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

- del_3q26.1 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_4q28.3 cnv correlated to 'MRNASEQ_CNMF'.

- del_6p12.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

- del_6q16.1 cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- del_8p22 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

- del_8q23.3 cnv correlated to 'CN_CNMF'.

- del_9q21.12 cnv correlated to 'CN_CNMF'.

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

- del_11q22.1 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_16q21 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

- del_17p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_17q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- del_22q13.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_xp21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 28 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 94 significant findings detected.

|  | Clinical Features | 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 1p12 | 113 (70%) | 49 | 1e-05 (0.000215) | 2e-05 (0.00035) | 0.033 (0.104) | 0.00131 (0.0108) | 2e-05 (0.00035) | 4e-05 (0.000589) | 0.00046 (0.00477) | 0.0167 (0.07) | 0.00763 (0.0427) | 0.015 (0.0665)
del 3p24 1 | 64 (40%) | 98 | 0.00151 (0.0121) | 0.00763 (0.0427) | 0.0338 (0.104) | 0.0862 (0.203) | 4e-05 (0.000589) | 3e-05 (0.000494) | 1e-05 (0.000215) | 0.00032 (0.0039) | 1e-05 (0.000215) | 1e-05 (0.000215)
del 3q26 1 | 93 (57%) | 69 | 2e-05 (0.00035) | 0.516 (0.681) | 0.0216 (0.0804) | 0.0141 (0.0639) | 0.0245 (0.0872) | 1e-05 (0.000215) | 0.0183 (0.0743) | 0.00941 (0.0488) | 0.0114 (0.0532) | 0.0105 (0.0523)
del 11p15 4 | 58 (36%) | 104 | 1e-05 (0.000215) | 1e-05 (0.000215) | 0.00167 (0.0126) | 0.112 (0.247) | 0.00044 (0.00477) | 1e-05 (0.000215) | 8e-05 (0.00112) | 1e-05 (0.000215) | 1e-05 (0.000215) | 0.00031 (0.0039)
del 11q22 1 | 48 (30%) | 114 | 1e-05 (0.000215) | 0.21 (0.377) | 0.0135 (0.0619) | 0.0614 (0.17) | 0.00076 (0.00665) | 0.00977 (0.0497) | 0.00333 (0.0239) | 0.00075 (0.00665) | 0.00034 (0.00397) | 0.0323 (0.104)
del 22q13 31 | 65 (40%) | 97 | 1e-05 (0.000215) | 0.0211 (0.0803) | 0.432 (0.611) | 0.0579 (0.167) | 0.0194 (0.0766) | 0.00056 (0.00541) | 0.0114 (0.0532) | 0.0266 (0.0913) | 0.0165 (0.0698) | 0.0212 (0.0803)
del 17p13 2 | 64 (40%) | 98 | 0.00014 (0.00187) | 0.00048 (0.0048) | 0.45 (0.621) | 0.0659 (0.177) | 0.0154 (0.0665) | 0.00619 (0.0377) | 0.0271 (0.0913) | 0.00778 (0.0427) | 0.17 (0.326) | 0.0175 (0.0721)
del xp21 1 | 46 (28%) | 116 | 0.00084 (0.00713) | 0.00605 (0.0377) | 0.077 (0.189) | 0.243 (0.415) | 0.0339 (0.104) | 0.00388 (0.0265) | 0.00069 (0.00644) | 0.0452 (0.136) | 0.183 (0.342) | 0.0327 (0.104)
del 6q16 1 | 24 (15%) | 138 | 0.135 (0.282) | 0.0744 (0.186) | 0.0536 (0.156) | 0.218 (0.39) | 0.0265 (0.0913) | 0.00702 (0.0409) | 0.0153 (0.0665) | 0.0062 (0.0377) | 0.0826 (0.198) | 0.0937 (0.213)
del 8p22 | 25 (15%) | 137 | 0.00159 (0.0124) | 0.0825 (0.198) | 0.258 (0.433) | 0.646 (0.773) | 0.00668 (0.0398) | 0.00818 (0.0432) | 0.207 (0.377) | 0.238 (0.415) | 0.027 (0.0913) | 0.241 (0.415)
del 17q11 2 | 42 (26%) | 120 | 1e-05 (0.000215) | 0.00344 (0.0241) | 0.0678 (0.179) | 0.131 (0.276) | 0.0246 (0.0872) | 0.00284 (0.0209) | 0.103 (0.231) | 0.0705 (0.183) | 0.369 (0.543) | 0.14 (0.285)
amp 4q31 1 | 13 (8%) | 149 | 0.00569 (0.0371) | 0.0683 (0.179) | 0.568 (0.73) | 0.0641 (0.176) | 0.614 (0.751) | 0.00806 (0.0432) | 0.408 (0.586) | 0.228 (0.401) | 0.11 (0.245) | 0.322 (0.497)
amp 12q13 3 | 16 (10%) | 146 | 0.0442 (0.134) | 0.138 (0.283) | 0.777 (0.885) | 0.322 (0.497) | 0.613 (0.751) | 0.623 (0.756) | 0.0481 (0.143) | 0.273 (0.447) | 0.131 (0.276) | 0.323 (0.497)
del 1q42 13 | 18 (11%) | 144 | 0.0218 (0.0804) | 0.136 (0.282) | 0.276 (0.447) | 0.0597 (0.167) | 0.0244 (0.0872) | 0.178 (0.335) | 0.33 (0.501) | 0.532 (0.692) | 0.0722 (0.184) | 0.245 (0.416)
del 6p12 3 | 10 (6%) | 152 | 0.0108 (0.0523) | 0.269 (0.447) |  |  | 0.0206 (0.0803) | 0.0864 (0.203) | 0.199 (0.365) | 0.162 (0.318) | 0.927 (0.967) | 0.052 (0.153)
amp 1q21 3 | 30 (19%) | 132 | 0.0047 (0.0313) | 0.607 (0.751) | 0.979 (1.00) | 0.795 (0.894) | 0.638 (0.767) | 0.942 (0.977) | 0.904 (0.956) | 0.445 (0.621) | 0.69 (0.819) | 0.822 (0.914)
amp 14q24 3 | 10 (6%) | 152 | 0.029 (0.0956) | 0.198 (0.364) | 0.85 (0.932) | 0.163 (0.318) | 0.852 (0.932) | 0.177 (0.335) | 0.457 (0.621) | 0.714 (0.837) | 0.438 (0.617) | 0.859 (0.932)
amp 17q21 31 | 16 (10%) | 146 | 0.631 (0.761) | 0.888 (0.948) | 0.596 (0.745) | 0.351 (0.52) | 0.53 (0.692) | 0.00046 (0.00477) | 0.755 (0.87) | 0.145 (0.295) | 0.0672 (0.179) | 0.456 (0.621)
del 4q28 3 | 10 (6%) | 152 | 0.0734 (0.185) | 0.241 (0.415) | 0.501 (0.667) | 0.163 (0.318) | 0.019 (0.076) | 0.339 (0.508) | 0.456 (0.621) | 0.713 (0.837) | 0.328 (0.501) | 0.323 (0.497)
del 8q23 3 | 13 (8%) | 149 | 0.0327 (0.104) | 0.866 (0.937) | 0.149 (0.301) | 1 (1.00) | 0.274 (0.447) | 0.523 (0.687) | 0.0711 (0.183) | 0.466 (0.631) | 0.928 (0.967) | 0.302 (0.475)
del 9q21 12 | 14 (9%) | 148 | 0.0108 (0.0523) | 0.546 (0.707) | 0.154 (0.307) | 0.0593 (0.167) | 0.373 (0.547) | 0.39 (0.565) | 0.722 (0.839) | 0.114 (0.247) | 0.581 (0.74) | 0.345 (0.514)
del 16q21 | 5 (3%) | 157 | 0.065 (0.177) | 0.114 (0.247) | 0.746 (0.863) | 0.788 (0.89) | 0.553 (0.714) | 0.0279 (0.0931) | 0.209 (0.377) | 0.592 (0.745) | 0.0915 (0.212) | 0.83 (0.918)
amp 4q25 | 6 (4%) | 156 | 0.882 (0.946) | 0.759 (0.871) | 1 (1.00) | 0.451 (0.621) | 0.13 (0.276) | 0.385 (0.561) | 0.764 (0.873) | 0.624 (0.756) | 0.292 (0.467) | 0.503 (0.667)
amp 11p15 2 | 8 (5%) | 154 | 0.0937 (0.213) | 0.0791 (0.193) | 0.572 (0.732) | 0.223 (0.395) | 0.332 (0.502) | 0.103 (0.231) | 0.411 (0.587) | 0.396 (0.571) | 0.457 (0.621) | 0.811 (0.905)
del 5q15 | 12 (7%) | 150 | 0.595 (0.745) | 1 (1.00) | 0.165 (0.318) | 0.805 (0.902) | 0.974 (1.00) | 1 (1.00) | 0.929 (0.967) | 0.188 (0.348) | 0.242 (0.415) | 0.296 (0.471)
del 9p24 2 | 15 (9%) | 147 | 0.291 (0.467) | 0.339 (0.508) | 0.276 (0.447) | 0.164 (0.318) | 0.0911 (0.212) | 0.173 (0.33) | 0.481 (0.647) | 0.0762 (0.189) | 0.484 (0.649) | 0.302 (0.475)
del 12q21 33 | 8 (5%) | 154 | 0.0594 (0.167) | 0.892 (0.948) | 0.668 (0.796) | 0.608 (0.751) | 0.914 (0.963) | 0.875 (0.942) | 0.593 (0.745) | 0.697 (0.824) | 0.835 (0.92) | 1 (1.00)
del 13q22 3 | 8 (5%) | 154 | 0.247 (0.417) | 0.894 (0.948) | 0.128 (0.275) | 0.786 (0.89) | 0.271 (0.447) | 0.429 (0.609) | 1 (1.00) | 0.613 (0.751) | 0.72 (0.839) | 0.857 (0.932)

'amp_1q21.3' versus 'CN_CNMF'

P value = 0.0047 (Fisher's exact test), Q value = 0.031

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
AMP PEAK 1(1Q21.3) MUTATED | 10 | 6 | 14
AMP PEAK 1(1Q21.3) WILD-TYPE | 50 | 57 | 25

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

'amp_4q31.1' versus 'CN_CNMF'

P value = 0.00569 (Fisher's exact test), Q value = 0.037

Table S2. Gene #3: 'amp_4q31.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
AMP PEAK 3(4Q31.1) MUTATED | 10 | 3 | 0
AMP PEAK 3(4Q31.1) WILD-TYPE | 50 | 60 | 39

Figure S2. Get High-res Image Gene #3: 'amp_4q31.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00806 (Fisher's exact test), Q value = 0.043

Table S3. Gene #3: 'amp_4q31.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 64 | 43 | 21
AMP PEAK 3(4Q31.1) MUTATED | 7 | 5 | 0 | 1
AMP PEAK 3(4Q31.1) WILD-TYPE | 27 | 59 | 43 | 20

Figure S3. Get High-res Image Gene #3: 'amp_4q31.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_12q13.3' versus 'CN_CNMF'

P value = 0.0442 (Fisher's exact test), Q value = 0.13

Table S4. Gene #5: 'amp_12q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
AMP PEAK 5(12Q13.3) MUTATED | 3 | 5 | 8
AMP PEAK 5(12Q13.3) WILD-TYPE | 57 | 58 | 31

Figure S4. Get High-res Image Gene #5: 'amp_12q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q13.3' versus 'MIRSEQ_CNMF'

P value = 0.0481 (Fisher's exact test), Q value = 0.14

Table S5. Gene #5: 'amp_12q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 58 | 39
AMP PEAK 5(12Q13.3) MUTATED | 11 | 4 | 1
AMP PEAK 5(12Q13.3) WILD-TYPE | 54 | 54 | 38

Figure S5. Get High-res Image Gene #5: 'amp_12q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_14q24.3' versus 'CN_CNMF'

P value = 0.029 (Fisher's exact test), Q value = 0.096

Table S6. Gene #6: 'amp_14q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
AMP PEAK 6(14Q24.3) MUTATED | 1 | 3 | 6
AMP PEAK 6(14Q24.3) WILD-TYPE | 59 | 60 | 33

Figure S6. Get High-res Image Gene #6: 'amp_14q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.0048

Table S7. Gene #7: 'amp_17q21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 64 | 43 | 21
AMP PEAK 7(17Q21.31) MUTATED | 10 | 5 | 1 | 0
AMP PEAK 7(17Q21.31) WILD-TYPE | 24 | 59 | 42 | 21

Figure S7. Get High-res Image Gene #7: 'amp_17q21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S8. Gene #8: 'del_1p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
DEL PEAK 1(1P12) MUTATED | 54 | 27 | 32
DEL PEAK 1(1P12) WILD-TYPE | 6 | 36 | 7

Figure S8. Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p12' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00035

Table S9. Gene #8: 'del_1p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 78 | 44
DEL PEAK 1(1P12) MUTATED | 24 | 68 | 21
DEL PEAK 1(1P12) WILD-TYPE | 16 | 10 | 23

Figure S9. Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p12' versus 'RPPA_CNMF'

P value = 0.033 (Fisher's exact test), Q value = 0.1

Table S10. Gene #8: 'del_1p12' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 13 | 9 | 20 | 5 | 17 | 13
DEL PEAK 1(1P12) MUTATED | 11 | 7 | 18 | 3 | 9 | 6
DEL PEAK 1(1P12) WILD-TYPE | 2 | 2 | 2 | 2 | 8 | 7

Figure S10. Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_1p12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00131 (Fisher's exact test), Q value = 0.011

Table S11. Gene #8: 'del_1p12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 18 | 28
DEL PEAK 1(1P12) MUTATED | 15 | 17 | 22
DEL PEAK 1(1P12) WILD-TYPE | 16 | 1 | 6

Figure S11. Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_1p12' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00035

Table S12. Gene #8: 'del_1p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
DEL PEAK 1(1P12) MUTATED | 24 | 58 | 21 | 10
DEL PEAK 1(1P12) WILD-TYPE | 9 | 6 | 23 | 11

Figure S12. Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00059

Table S13. Gene #8: 'del_1p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 64 | 43 | 21
DEL PEAK 1(1P12) MUTATED | 19 | 58 | 27 | 9
DEL PEAK 1(1P12) WILD-TYPE | 15 | 6 | 16 | 12

Figure S13. Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p12' versus 'MIRSEQ_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0048

Table S14. Gene #8: 'del_1p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 58 | 39
DEL PEAK 1(1P12) MUTATED | 39 | 51 | 23
DEL PEAK 1(1P12) WILD-TYPE | 26 | 7 | 16

Figure S14. Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0167 (Fisher's exact test), Q value = 0.07

Table S15. Gene #8: 'del_1p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 66 | 54 | 18 | 24
DEL PEAK 1(1P12) MUTATED | 41 | 46 | 12 | 14
DEL PEAK 1(1P12) WILD-TYPE | 25 | 8 | 6 | 10

Figure S15. Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00763 (Fisher's exact test), Q value = 0.043

Table S16. Gene #8: 'del_1p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 34 | 58 | 11 | 35 | 23
DEL PEAK 1(1P12) MUTATED | 22 | 50 | 8 | 21 | 12
DEL PEAK 1(1P12) WILD-TYPE | 12 | 8 | 3 | 14 | 11

Figure S16. Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.015 (Fisher's exact test), Q value = 0.066

Table S17. Gene #8: 'del_1p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 71 | 53 | 18 | 19
DEL PEAK 1(1P12) MUTATED | 58 | 34 | 12 | 9
DEL PEAK 1(1P12) WILD-TYPE | 13 | 19 | 6 | 10

Figure S17. Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1q42.13' versus 'CN_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.08

Table S18. Gene #9: 'del_1q42.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
DEL PEAK 2(1Q42.13) MUTATED | 2 | 8 | 8
DEL PEAK 2(1Q42.13) WILD-TYPE | 58 | 55 | 31

Figure S18. Get High-res Image Gene #9: 'del_1q42.13' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q42.13' versus 'MRNASEQ_CNMF'

P value = 0.0244 (Fisher's exact test), Q value = 0.087

Table S19. Gene #9: 'del_1q42.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
DEL PEAK 2(1Q42.13) MUTATED | 8 | 3 | 6 | 1
DEL PEAK 2(1Q42.13) WILD-TYPE | 25 | 61 | 38 | 20

Figure S19. Get High-res Image Gene #9: 'del_1q42.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p24.1' versus 'CN_CNMF'

P value = 0.00151 (Fisher's exact test), Q value = 0.012

Table S20. Gene #10: 'del_3p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
DEL PEAK 3(3P24.1) MUTATED | 15 | 25 | 24
DEL PEAK 3(3P24.1) WILD-TYPE | 45 | 38 | 15

Figure S20. Get High-res Image Gene #10: 'del_3p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p24.1' versus 'METHLYATION_CNMF'

P value = 0.00763 (Fisher's exact test), Q value = 0.043

Table S21. Gene #10: 'del_3p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 78 | 44
DEL PEAK 3(3P24.1) MUTATED | 23 | 22 | 19
DEL PEAK 3(3P24.1) WILD-TYPE | 17 | 56 | 25

Figure S21. Get High-res Image Gene #10: 'del_3p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p24.1' versus 'RPPA_CNMF'

P value = 0.0338 (Fisher's exact test), Q value = 0.1

Table S22. Gene #10: 'del_3p24.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 13 | 9 | 20 | 5 | 17 | 13
DEL PEAK 3(3P24.1) MUTATED | 2 | 2 | 9 | 3 | 4 | 9
DEL PEAK 3(3P24.1) WILD-TYPE | 11 | 7 | 11 | 2 | 13 | 4

Figure S22. Get High-res Image Gene #10: 'del_3p24.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_3p24.1' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00059

Table S23. Gene #10: 'del_3p24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
DEL PEAK 3(3P24.1) MUTATED | 18 | 15 | 27 | 4
DEL PEAK 3(3P24.1) WILD-TYPE | 15 | 49 | 17 | 17

Figure S23. Get High-res Image Gene #10: 'del_3p24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00049

Table S24. Gene #10: 'del_3p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 64 | 43 | 21
DEL PEAK 3(3P24.1) MUTATED | 12 | 17 | 31 | 4
DEL PEAK 3(3P24.1) WILD-TYPE | 22 | 47 | 12 | 17

Figure S24. Get High-res Image Gene #10: 'del_3p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p24.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S25. Gene #10: 'del_3p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 58 | 39
DEL PEAK 3(3P24.1) MUTATED | 39 | 19 | 6
DEL PEAK 3(3P24.1) WILD-TYPE | 26 | 39 | 33

Figure S25. Get High-res Image Gene #10: 'del_3p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.0039

Table S26. Gene #10: 'del_3p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 66 | 54 | 18 | 24
DEL PEAK 3(3P24.1) MUTATED | 39 | 15 | 6 | 4
DEL PEAK 3(3P24.1) WILD-TYPE | 27 | 39 | 12 | 20

Figure S26. Get High-res Image Gene #10: 'del_3p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S27. Gene #10: 'del_3p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 34 | 58 | 11 | 35 | 23
DEL PEAK 3(3P24.1) MUTATED | 12 | 15 | 2 | 29 | 6
DEL PEAK 3(3P24.1) WILD-TYPE | 22 | 43 | 9 | 6 | 17

Figure S27. Get High-res Image Gene #10: 'del_3p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S28. Gene #10: 'del_3p24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 71 | 53 | 18 | 19
DEL PEAK 3(3P24.1) MUTATED | 18 | 36 | 6 | 4
DEL PEAK 3(3P24.1) WILD-TYPE | 53 | 17 | 12 | 15

Figure S28. Get High-res Image Gene #10: 'del_3p24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q26.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00035

Table S29. Gene #11: 'del_3q26.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
DEL PEAK 4(3Q26.1) MUTATED | 40 | 22 | 31
DEL PEAK 4(3Q26.1) WILD-TYPE | 20 | 41 | 8

Figure S29. Get High-res Image Gene #11: 'del_3q26.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q26.1' versus 'RPPA_CNMF'

P value = 0.0216 (Fisher's exact test), Q value = 0.08

Table S30. Gene #11: 'del_3q26.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 13 | 9 | 20 | 5 | 17 | 13
DEL PEAK 4(3Q26.1) MUTATED | 8 | 7 | 15 | 4 | 4 | 8
DEL PEAK 4(3Q26.1) WILD-TYPE | 5 | 2 | 5 | 1 | 13 | 5

Figure S30. Get High-res Image Gene #11: 'del_3q26.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_3q26.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0141 (Fisher's exact test), Q value = 0.064

Table S31. Gene #11: 'del_3q26.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 18 | 28
DEL PEAK 4(3Q26.1) MUTATED | 13 | 15 | 18
DEL PEAK 4(3Q26.1) WILD-TYPE | 18 | 3 | 10

Figure S31. Get High-res Image Gene #11: 'del_3q26.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_3q26.1' versus 'MRNASEQ_CNMF'

P value = 0.0245 (Fisher's exact test), Q value = 0.087

Table S32. Gene #11: 'del_3q26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
DEL PEAK 4(3Q26.1) MUTATED | 20 | 44 | 22 | 7
DEL PEAK 4(3Q26.1) WILD-TYPE | 13 | 20 | 22 | 14

Figure S32. Get High-res Image Gene #11: 'del_3q26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3q26.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S33. Gene #11: 'del_3q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 64 | 43 | 21
DEL PEAK 4(3Q26.1) MUTATED | 6 | 47 | 33 | 7
DEL PEAK 4(3Q26.1) WILD-TYPE | 28 | 17 | 10 | 14

Figure S33. Get High-res Image Gene #11: 'del_3q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3q26.1' versus 'MIRSEQ_CNMF'

P value = 0.0183 (Fisher's exact test), Q value = 0.074

Table S34. Gene #11: 'del_3q26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 58 | 39
DEL PEAK 4(3Q26.1) MUTATED | 39 | 39 | 15
DEL PEAK 4(3Q26.1) WILD-TYPE | 26 | 19 | 24

Figure S34. Get High-res Image Gene #11: 'del_3q26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3q26.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00941 (Fisher's exact test), Q value = 0.049

Table S35. Gene #11: 'del_3q26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 66 | 54 | 18 | 24
DEL PEAK 4(3Q26.1) MUTATED | 39 | 38 | 5 | 11
DEL PEAK 4(3Q26.1) WILD-TYPE | 27 | 16 | 13 | 13

Figure S35. Get High-res Image Gene #11: 'del_3q26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3q26.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.053

Table S36. Gene #11: 'del_3q26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 34 | 58 | 11 | 35 | 23
DEL PEAK 4(3Q26.1) MUTATED | 12 | 41 | 5 | 23 | 12
DEL PEAK 4(3Q26.1) WILD-TYPE | 22 | 17 | 6 | 12 | 11

Figure S36. Get High-res Image Gene #11: 'del_3q26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3q26.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.052

Table S37. Gene #11: 'del_3q26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 71 | 53 | 18 | 19
DEL PEAK 4(3Q26.1) MUTATED | 44 | 36 | 5 | 8
DEL PEAK 4(3Q26.1) WILD-TYPE | 27 | 17 | 13 | 11

Figure S37. Get High-res Image Gene #11: 'del_3q26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q28.3' versus 'MRNASEQ_CNMF'

P value = 0.019 (Fisher's exact test), Q value = 0.076

Table S38. Gene #12: 'del_4q28.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
DEL PEAK 5(4Q28.3) MUTATED | 0 | 2 | 7 | 1
DEL PEAK 5(4Q28.3) WILD-TYPE | 33 | 62 | 37 | 20

Figure S38. Get High-res Image Gene #12: 'del_4q28.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6p12.3' versus 'CN_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.052

Table S39. Gene #14: 'del_6p12.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
DEL PEAK 7(6P12.3) MUTATED | 0 | 5 | 5
DEL PEAK 7(6P12.3) WILD-TYPE | 60 | 58 | 34

Figure S39. Get High-res Image Gene #14: 'del_6p12.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p12.3' versus 'MRNASEQ_CNMF'

P value = 0.0206 (Fisher's exact test), Q value = 0.08

Table S40. Gene #14: 'del_6p12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
DEL PEAK 7(6P12.3) MUTATED | 1 | 1 | 4 | 4
DEL PEAK 7(6P12.3) WILD-TYPE | 32 | 63 | 40 | 17

Figure S40. Get High-res Image Gene #14: 'del_6p12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q16.1' versus 'MRNASEQ_CNMF'

P value = 0.0265 (Fisher's exact test), Q value = 0.091

Table S41. Gene #15: 'del_6q16.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
DEL PEAK 8(6Q16.1) MUTATED | 1 | 15 | 4 | 4
DEL PEAK 8(6Q16.1) WILD-TYPE | 32 | 49 | 40 | 17

Figure S41. Get High-res Image Gene #15: 'del_6q16.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q16.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00702 (Fisher's exact test), Q value = 0.041

Table S42. Gene #15: 'del_6q16.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 64 | 43 | 21
DEL PEAK 8(6Q16.1) MUTATED | 1 | 16 | 3 | 4
DEL PEAK 8(6Q16.1) WILD-TYPE | 33 | 48 | 40 | 17

Figure S42. Get High-res Image Gene #15: 'del_6q16.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q16.1' versus 'MIRSEQ_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.066

Table S43. Gene #15: 'del_6q16.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 58 | 39
DEL PEAK 8(6Q16.1) MUTATED | 4 | 14 | 6
DEL PEAK 8(6Q16.1) WILD-TYPE | 61 | 44 | 33

Figure S43. Get High-res Image Gene #15: 'del_6q16.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6q16.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0062 (Fisher's exact test), Q value = 0.038

Table S44. Gene #15: 'del_6q16.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 66 | 54 | 18 | 24
DEL PEAK 8(6Q16.1) MUTATED | 4 | 15 | 1 | 4
DEL PEAK 8(6Q16.1) WILD-TYPE | 62 | 39 | 17 | 20

Figure S44. Get High-res Image Gene #15: 'del_6q16.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p22' versus 'CN_CNMF'

P value = 0.00159 (Fisher's exact test), Q value = 0.012

Table S45. Gene #16: 'del_8p22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
DEL PEAK 9(8P22) MUTATED | 10 | 3 | 12
DEL PEAK 9(8P22) WILD-TYPE | 50 | 60 | 27

Figure S45. Get High-res Image Gene #16: 'del_8p22' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p22' versus 'MRNASEQ_CNMF'

P value = 0.00668 (Fisher's exact test), Q value = 0.04

Table S46. Gene #16: 'del_8p22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
DEL PEAK 9(8P22) MUTATED | 3 | 18 | 3 | 1
DEL PEAK 9(8P22) WILD-TYPE | 30 | 46 | 41 | 20

Figure S46. Get High-res Image Gene #16: 'del_8p22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00818 (Fisher's exact test), Q value = 0.043

Table S47. Gene #16: 'del_8p22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 64 | 43 | 21
DEL PEAK 9(8P22) MUTATED | 5 | 17 | 2 | 1
DEL PEAK 9(8P22) WILD-TYPE | 29 | 47 | 41 | 20

Figure S47. Get High-res Image Gene #16: 'del_8p22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.027 (Fisher's exact test), Q value = 0.091

Table S48. Gene #16: 'del_8p22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 34 | 58 | 11 | 35 | 23
DEL PEAK 9(8P22) MUTATED | 5 | 16 | 0 | 3 | 1
DEL PEAK 9(8P22) WILD-TYPE | 29 | 42 | 11 | 32 | 22

Figure S48. Get High-res Image Gene #16: 'del_8p22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8q23.3' versus 'CN_CNMF'

P value = 0.0327 (Fisher's exact test), Q value = 0.1

Table S49. Gene #17: 'del_8q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
DEL PEAK 10(8Q23.3) MUTATED | 7 | 1 | 5
DEL PEAK 10(8Q23.3) WILD-TYPE | 53 | 62 | 34

Figure S49. Get High-res Image Gene #17: 'del_8q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q21.12' versus 'CN_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.052

Table S50. Gene #19: 'del_9q21.12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
DEL PEAK 12(9Q21.12) MUTATED | 4 | 2 | 8
DEL PEAK 12(9Q21.12) WILD-TYPE | 56 | 61 | 31

Figure S50. Get High-res Image Gene #19: 'del_9q21.12' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.4' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S51. Gene #20: 'del_11p15.4' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
DEL PEAK 13(11P15.4) MUTATED | 2 | 39 | 17
DEL PEAK 13(11P15.4) WILD-TYPE | 58 | 24 | 22

Figure S51. Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.4' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S52. Gene #20: 'del_11p15.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 78 | 44
DEL PEAK 13(11P15.4) MUTATED | 23 | 14 | 21
DEL PEAK 13(11P15.4) WILD-TYPE | 17 | 64 | 23

Figure S52. Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.4' versus 'RPPA_CNMF'

P value = 0.00167 (Fisher's exact test), Q value = 0.013

Table S53. Gene #20: 'del_11p15.4' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 13 | 9 | 20 | 5 | 17 | 13
DEL PEAK 13(11P15.4) MUTATED | 3 | 1 | 3 | 3 | 8 | 10
DEL PEAK 13(11P15.4) WILD-TYPE | 10 | 8 | 17 | 2 | 9 | 3

Figure S53. Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_11p15.4' versus 'MRNASEQ_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0048

Table S54. Gene #20: 'del_11p15.4' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
DEL PEAK 13(11P15.4) MUTATED | 13 | 13 | 26 | 6
DEL PEAK 13(11P15.4) WILD-TYPE | 20 | 51 | 18 | 15

Figure S54. Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11p15.4' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S55. Gene #20: 'del_11p15.4' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 64 | 43 | 21
DEL PEAK 13(11P15.4) MUTATED | 11 | 10 | 31 | 6
DEL PEAK 13(11P15.4) WILD-TYPE | 23 | 54 | 12 | 15

Figure S55. Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.4' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0011

Table S56. Gene #20: 'del_11p15.4' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 58 | 39
DEL PEAK 13(11P15.4) MUTATED | 36 | 12 | 10
DEL PEAK 13(11P15.4) WILD-TYPE | 29 | 46 | 29

Figure S56. Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11p15.4' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S57. Gene #20: 'del_11p15.4' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 66 | 54 | 18 | 24
DEL PEAK 13(11P15.4) MUTATED | 39 | 8 | 5 | 6
DEL PEAK 13(11P15.4) WILD-TYPE | 27 | 46 | 13 | 18

Figure S57. Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.4' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S58. Gene #20: 'del_11p15.4' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 34 | 58 | 11 | 35 | 23
DEL PEAK 13(11P15.4) MUTATED | 12 | 8 | 2 | 24 | 11
DEL PEAK 13(11P15.4) WILD-TYPE | 22 | 50 | 9 | 11 | 12

Figure S58. Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11p15.4' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.0039

Table S59. Gene #20: 'del_11p15.4' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 71 | 53 | 18 | 19
DEL PEAK 13(11P15.4) MUTATED | 16 | 31 | 5 | 5
DEL PEAK 13(11P15.4) WILD-TYPE | 55 | 22 | 13 | 14

Figure S59. Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S60. Gene #21: 'del_11q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
DEL PEAK 14(11Q22.1) MUTATED | 4 | 26 | 18
DEL PEAK 14(11Q22.1) WILD-TYPE | 56 | 37 | 21

Figure S60. Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q22.1' versus 'RPPA_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.062

Table S61. Gene #21: 'del_11q22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 13 | 9 | 20 | 5 | 17 | 13
DEL PEAK 14(11Q22.1) MUTATED | 4 | 1 | 5 | 2 | 9 | 10
DEL PEAK 14(11Q22.1) WILD-TYPE | 9 | 8 | 15 | 3 | 8 | 3

Figure S61. Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_11q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0066

Table S62. Gene #21: 'del_11q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
DEL PEAK 14(11Q22.1) MUTATED | 9 | 10 | 23 | 6
DEL PEAK 14(11Q22.1) WILD-TYPE | 24 | 54 | 21 | 15

Figure S62. Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00977 (Fisher's exact test), Q value = 0.05

Table S63. Gene #21: 'del_11q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 64 | 43 | 21
DEL PEAK 14(11Q22.1) MUTATED | 10 | 12 | 21 | 5
DEL PEAK 14(11Q22.1) WILD-TYPE | 24 | 52 | 22 | 16

Figure S63. Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q22.1' versus 'MIRSEQ_CNMF'

P value = 0.00333 (Fisher's exact test), Q value = 0.024

Table S64. Gene #21: 'del_11q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 58 | 39
DEL PEAK 14(11Q22.1) MUTATED | 28 | 9 | 11
DEL PEAK 14(11Q22.1) WILD-TYPE | 37 | 49 | 28

Figure S64. Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00075 (Fisher's exact test), Q value = 0.0066

Table S65. Gene #21: 'del_11q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 66 | 54 | 18 | 24
DEL PEAK 14(11Q22.1) MUTATED | 30 | 8 | 2 | 8
DEL PEAK 14(11Q22.1) WILD-TYPE | 36 | 46 | 16 | 16

Figure S65. Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.004

Table S66. Gene #21: 'del_11q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 34 | 58 | 11 | 35 | 23
DEL PEAK 14(11Q22.1) MUTATED | 10 | 8 | 2 | 20 | 8
DEL PEAK 14(11Q22.1) WILD-TYPE | 24 | 50 | 9 | 15 | 15

Figure S66. Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0323 (Fisher's exact test), Q value = 0.1

Table S67. Gene #21: 'del_11q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 71 | 53 | 18 | 19
DEL PEAK 14(11Q22.1) MUTATED | 17 | 23 | 2 | 6
DEL PEAK 14(11Q22.1) WILD-TYPE | 54 | 30 | 16 | 13

Figure S67. Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0279 (Fisher's exact test), Q value = 0.093

Table S68. Gene #24: 'del_16q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 64 | 43 | 21
DEL PEAK 17(16Q21) MUTATED | 4 | 1 | 0 | 0
DEL PEAK 17(16Q21) WILD-TYPE | 30 | 63 | 43 | 21

Figure S68. Get High-res Image Gene #24: 'del_16q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.2' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0019

Table S69. Gene #25: 'del_17p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
DEL PEAK 18(17P13.2) MUTATED | 22 | 16 | 26
DEL PEAK 18(17P13.2) WILD-TYPE | 38 | 47 | 13

Figure S69. Get High-res Image Gene #25: 'del_17p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.2' versus 'METHLYATION_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.0048

Table S70. Gene #25: 'del_17p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 78 | 44
DEL PEAK 18(17P13.2) MUTATED | 9 | 43 | 12
DEL PEAK 18(17P13.2) WILD-TYPE | 31 | 35 | 32

Figure S70. Get High-res Image Gene #25: 'del_17p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p13.2' versus 'MRNASEQ_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.066

Table S71. Gene #25: 'del_17p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
DEL PEAK 18(17P13.2) MUTATED | 10 | 35 | 14 | 5
DEL PEAK 18(17P13.2) WILD-TYPE | 23 | 29 | 30 | 16

Figure S71. Get High-res Image Gene #25: 'del_17p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00619 (Fisher's exact test), Q value = 0.038

Table S72. Gene #25: 'del_17p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 64 | 43 | 21
DEL PEAK 18(17P13.2) MUTATED | 10 | 36 | 13 | 5
DEL PEAK 18(17P13.2) WILD-TYPE | 24 | 28 | 30 | 16

Figure S72. Get High-res Image Gene #25: 'del_17p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.2' versus 'MIRSEQ_CNMF'

P value = 0.0271 (Fisher's exact test), Q value = 0.091

Table S73. Gene #25: 'del_17p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 58 | 39
DEL PEAK 18(17P13.2) MUTATED | 21 | 31 | 12
DEL PEAK 18(17P13.2) WILD-TYPE | 44 | 27 | 27

Figure S73. Get High-res Image Gene #25: 'del_17p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00778 (Fisher's exact test), Q value = 0.043

Table S74. Gene #25: 'del_17p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 66 | 54 | 18 | 24
DEL PEAK 18(17P13.2) MUTATED | 18 | 30 | 9 | 7
DEL PEAK 18(17P13.2) WILD-TYPE | 48 | 24 | 9 | 17

Figure S74. Get High-res Image Gene #25: 'del_17p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0175 (Fisher's exact test), Q value = 0.072

Table S75. Gene #25: 'del_17p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 71 | 53 | 18 | 19
DEL PEAK 18(17P13.2) MUTATED | 36 | 13 | 9 | 6
DEL PEAK 18(17P13.2) WILD-TYPE | 35 | 40 | 9 | 13

Figure S75. Get High-res Image Gene #25: 'del_17p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S76. Gene #26: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
DEL PEAK 19(17Q11.2) MUTATED | 13 | 4 | 25
DEL PEAK 19(17Q11.2) WILD-TYPE | 47 | 59 | 14

Figure S76. Get High-res Image Gene #26: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q11.2' versus 'METHLYATION_CNMF'

P value = 0.00344 (Fisher's exact test), Q value = 0.024

Table S77. Gene #26: 'del_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 78 | 44
DEL PEAK 19(17Q11.2) MUTATED | 4 | 29 | 9
DEL PEAK 19(17Q11.2) WILD-TYPE | 36 | 49 | 35

Figure S77. Get High-res Image Gene #26: 'del_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q11.2' versus 'MRNASEQ_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 0.087

Table S78. Gene #26: 'del_17q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
DEL PEAK 19(17Q11.2) MUTATED | 5 | 25 | 9 | 3
DEL PEAK 19(17Q11.2) WILD-TYPE | 28 | 39 | 35 | 18

Figure S78. Get High-res Image Gene #26: 'del_17q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00284 (Fisher's exact test), Q value = 0.021

Table S79. Gene #26: 'del_17q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 64 | 43 | 21
DEL PEAK 19(17Q11.2) MUTATED | 6 | 27 | 6 | 3
DEL PEAK 19(17Q11.2) WILD-TYPE | 28 | 37 | 37 | 18

Figure S79. Get High-res Image Gene #26: 'del_17q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S80. Gene #27: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
DEL PEAK 20(22Q13.31) MUTATED | 40 | 9 | 16
DEL PEAK 20(22Q13.31) WILD-TYPE | 20 | 54 | 23

Figure S80. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.31' versus 'METHLYATION_CNMF'

P value = 0.0211 (Fisher's exact test), Q value = 0.08

Table S81. Gene #27: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 78 | 44
DEL PEAK 20(22Q13.31) MUTATED | 11 | 40 | 14
DEL PEAK 20(22Q13.31) WILD-TYPE | 29 | 38 | 30

Figure S81. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.31' versus 'MRNASEQ_CNMF'

P value = 0.0194 (Fisher's exact test), Q value = 0.077

Table S82. Gene #27: 'del_22q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
DEL PEAK 20(22Q13.31) MUTATED | 9 | 35 | 13 | 8
DEL PEAK 20(22Q13.31) WILD-TYPE | 24 | 29 | 31 | 13

Figure S82. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0054

Table S83. Gene #27: 'del_22q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 64 | 43 | 21
DEL PEAK 20(22Q13.31) MUTATED | 13 | 37 | 8 | 7
DEL PEAK 20(22Q13.31) WILD-TYPE | 21 | 27 | 35 | 14

Figure S83. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.053

Table S84. Gene #27: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 58 | 39
DEL PEAK 20(22Q13.31) MUTATED | 17 | 29 | 19
DEL PEAK 20(22Q13.31) WILD-TYPE | 48 | 29 | 20

Figure S84. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0266 (Fisher's exact test), Q value = 0.091

Table S85. Gene #27: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 66 | 54 | 18 | 24
DEL PEAK 20(22Q13.31) MUTATED | 18 | 29 | 7 | 11
DEL PEAK 20(22Q13.31) WILD-TYPE | 48 | 25 | 11 | 13

Figure S85. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.07

Table S86. Gene #27: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 34 | 58 | 11 | 35 | 23
DEL PEAK 20(22Q13.31) MUTATED | 13 | 33 | 4 | 8 | 7
DEL PEAK 20(22Q13.31) WILD-TYPE | 21 | 25 | 7 | 27 | 16

Figure S86. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0212 (Fisher's exact test), Q value = 0.08

Table S87. Gene #27: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 71 | 53 | 18 | 19
DEL PEAK 20(22Q13.31) MUTATED | 37 | 13 | 7 | 8
DEL PEAK 20(22Q13.31) WILD-TYPE | 34 | 40 | 11 | 11

Figure S87. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp21.1' versus 'CN_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.0071

Table S88. Gene #28: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 39
DEL PEAK 21(XP21.1) MUTATED | 21 | 8 | 17
DEL PEAK 21(XP21.1) WILD-TYPE | 39 | 55 | 22

Figure S88. Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 0.00605 (Fisher's exact test), Q value = 0.038

Table S89. Gene #28: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 78 | 44
DEL PEAK 21(XP21.1) MUTATED | 9 | 31 | 6
DEL PEAK 21(XP21.1) WILD-TYPE | 31 | 47 | 38

Figure S89. Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp21.1' versus 'MRNASEQ_CNMF'

P value = 0.0339 (Fisher's exact test), Q value = 0.1

Table S90. Gene #28: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 64 | 44 | 21
DEL PEAK 21(XP21.1) MUTATED | 10 | 25 | 9 | 2
DEL PEAK 21(XP21.1) WILD-TYPE | 23 | 39 | 35 | 19

Figure S90. Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00388 (Fisher's exact test), Q value = 0.026

Table S91. Gene #28: 'del_xp21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 64 | 43 | 21
DEL PEAK 21(XP21.1) MUTATED | 7 | 27 | 11 | 1
DEL PEAK 21(XP21.1) WILD-TYPE | 27 | 37 | 32 | 20

Figure S91. Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0064

Table S92. Gene #28: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 58 | 39
DEL PEAK 21(XP21.1) MUTATED | 13 | 27 | 6
DEL PEAK 21(XP21.1) WILD-TYPE | 52 | 31 | 33

Figure S92. Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xp21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0452 (Fisher's exact test), Q value = 0.14

Table S93. Gene #28: 'del_xp21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 66 | 54 | 18 | 24
DEL PEAK 21(XP21.1) MUTATED | 15 | 21 | 7 | 3
DEL PEAK 21(XP21.1) WILD-TYPE | 51 | 33 | 11 | 21

Figure S93. Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0327 (Fisher's exact test), Q value = 0.1

Table S94. Gene #28: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 71 | 53 | 18 | 19
DEL PEAK 21(XP21.1) MUTATED | 25 | 13 | 7 | 1
DEL PEAK 21(XP21.1) WILD-TYPE | 46 | 40 | 11 | 18

Figure S94. Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

- Copy number data file = all_lesions.txt from GISTIC pipeline

- Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PCPG-TP/15096462/transformed.cor.cli.txt

- Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PCPG-TP/15107813/PCPG-TP.transferedmergedcluster.txt

- Number of patients = 162

- Number of significantly focal cnvs = 28

- Number of molecular subtypes = 10

- 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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