Correlation between copy number variation genes (focal events) and molecular subtypes
Mesothelioma (Primary solid tumor)
28 January 2016 | analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C10P0ZFC
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C10P0ZFC
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 21 focal events and 10 molecular subtypes across 87 patients, 61 significant findings detected with P value < 0.05 and Q value < 0.25.

- del_1p36.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_1p21.3 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- del_2q35 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- del_3p21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_4q26 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- del_4q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_5q23.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- del_6q22.1 cnv correlated to 'CN_CNMF'.

- del_6q26 cnv correlated to 'CN_CNMF'.

- del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_10p15.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

- del_10q25.2 cnv correlated to 'MIRSEQ_CNMF'.

- del_11q23.2 cnv correlated to 'CN_CNMF'.

- del_12p13.31 cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CNMF'.

- del_13q14.11 cnv correlated to 'CN_CNMF'.

- del_14q32.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

- del_15q15.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_16q24.1 cnv correlated to 'CN_CNMF'.

- del_22q12.2 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 21 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, 61 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 3p21 1 | 48 (55%) | 39 | 0.00034 (0.0042) | 8e-05 (0.00153) | 0.517 (0.696) | 0.597 (0.751) | 0.00023 (0.00345) | 2e-05 (7e-04) | 0.0352 (0.142) | 0.0152 (0.0888) | 0.961 (0.989) | 0.00284 (0.0259)
del 9p21 3 | 51 (59%) | 36 | 1e-05 (0.00042) | 0.00588 (0.0457) | 0.0248 (0.116) | 0.0605 (0.188) | 0.025 (0.116) | 0.00011 (0.00192) | 0.0562 (0.183) | 0.13 (0.296) | 0.375 (0.55) | 0.0063 (0.0472)
del 1p36 31 | 33 (38%) | 54 | 3e-05 (0.000787) | 0.0101 (0.0683) | 0.0882 (0.235) | 0.236 (0.403) | 0.319 (0.5) | 0.0305 (0.128) | 0.18 (0.34) | 0.00881 (0.0631) | 0.882 (0.941) | 0.0462 (0.167)
del 4q26 | 38 (44%) | 49 | 1e-05 (0.00042) | 0.11 (0.271) | 0.2 (0.36) | 0.0946 (0.242) | 0.00234 (0.0234) | 0.0003 (0.0042) | 0.0141 (0.0872) | 0.05 (0.172) | 0.61 (0.758) | 0.0883 (0.235)
del 4q34 3 | 41 (47%) | 46 | 1e-05 (0.00042) | 0.00284 (0.0259) | 0.159 (0.328) | 0.576 (0.735) | 0.0426 (0.157) | 0.00067 (0.00703) | 0.0696 (0.208) | 0.239 (0.405) | 0.961 (0.989) | 0.0267 (0.117)
del 10p15 3 | 28 (32%) | 59 | 0.00021 (0.00339) | 0.0299 (0.128) | 0.165 (0.328) | 0.697 (0.822) | 0.0344 (0.142) | 0.0389 (0.149) | 0.0369 (0.146) | 0.443 (0.634) | 0.335 (0.503) | 0.111 (0.271)
del 14q32 31 | 39 (45%) | 48 | 1e-05 (0.00042) | 0.00065 (0.00703) | 0.57 (0.734) | 0.326 (0.502) | 0.00048 (0.0056) | 4e-05 (0.000933) | 0.0751 (0.211) | 0.00901 (0.0631) | 0.0703 (0.208) | 0.0565 (0.183)
del 1p21 3 | 37 (43%) | 50 | 0.0422 (0.157) | 0.128 (0.296) | 0.0174 (0.0936) | 0.0926 (0.24) | 0.00032 (0.0042) | 0.00497 (0.0401) | 0.169 (0.329) | 0.31 (0.493) | 0.591 (0.748) | 0.224 (0.395)
del 22q12 2 | 68 (78%) | 19 | 0.0522 (0.177) | 0.0188 (0.0989) | 0.189 (0.352) | 0.816 (0.916) | 0.0391 (0.149) | 0.0151 (0.0888) | 0.0474 (0.169) | 0.628 (0.776) | 0.182 (0.341) | 0.322 (0.501)
del 15q15 1 | 28 (32%) | 59 | 0.00462 (0.0388) | 0.0742 (0.211) | 0.331 (0.502) | 0.454 (0.64) | 0.0207 (0.106) | 0.0713 (0.208) | 0.491 (0.675) | 0.526 (0.699) | 0.603 (0.753) | 0.022 (0.11)
del 2q35 | 17 (20%) | 70 | 0.00323 (0.0283) | 0.0758 (0.211) | 0.802 (0.905) | 0.201 (0.36) | 0.556 (0.725) | 0.0159 (0.0892) | 0.291 (0.477) | 0.0849 (0.232) | 1 (1.00) | 0.296 (0.479)
del 5q23 2 | 17 (20%) | 70 | 0.0104 (0.0683) | 0.786 (0.892) | 0.636 (0.776) | 0.255 (0.428) | 0.725 (0.85) | 0.0253 (0.116) | 0.23 (0.398) | 0.435 (0.626) | 1 (1.00) | 0.873 (0.935)
del 12p13 31 | 11 (13%) | 76 | 0.309 (0.493) | 0.059 (0.188) | 0.0628 (0.191) | 0.562 (0.729) | 0.0263 (0.117) | 0.152 (0.328) | 0.0161 (0.0892) | 0.105 (0.262) | 1 (1.00) | 0.194 (0.354)
del 6q22 1 | 41 (47%) | 46 | 8e-05 (0.00153) | 0.577 (0.735) | 0.831 (0.925) | 0.663 (0.795) | 0.162 (0.328) | 0.475 (0.665) | 0.175 (0.338) | 0.203 (0.361) | 0.289 (0.477) | 0.0542 (0.181)
del 6q26 | 36 (41%) | 51 | 1e-05 (0.00042) | 0.853 (0.928) | 0.328 (0.502) | 0.167 (0.328) | 0.744 (0.863) | 0.663 (0.795) | 0.0763 (0.211) | 0.497 (0.678) | 0.332 (0.502) | 0.114 (0.275)
del 10q25 2 | 31 (36%) | 56 | 0.316 (0.5) | 0.153 (0.328) | 0.164 (0.328) | 0.779 (0.889) | 0.355 (0.529) | 0.516 (0.696) | 0.0255 (0.116) | 0.193 (0.354) | 0.156 (0.328) | 0.226 (0.395)
del 11q23 2 | 18 (21%) | 69 | 0.0135 (0.086) | 0.861 (0.928) | 0.523 (0.699) | 0.41 (0.594) | 0.137 (0.31) | 0.258 (0.43) | 0.18 (0.34) | 0.13 (0.296) | 0.544 (0.719) | 0.061 (0.188)
del 13q14 11 | 44 (51%) | 43 | 3e-05 (0.000787) | 0.837 (0.925) | 0.403 (0.588) | 0.103 (0.26) | 0.485 (0.674) | 0.293 (0.477) | 0.923 (0.969) | 0.634 (0.776) | 0.116 (0.275) | 0.844 (0.928)
del 16q24 1 | 22 (25%) | 65 | 0.0491 (0.172) | 0.158 (0.328) | 0.853 (0.928) | 0.666 (0.795) | 0.231 (0.398) | 0.373 (0.55) | 0.946 (0.983) | 0.167 (0.328) | 1 (1.00) | 0.14 (0.312)
del 8p23 2 | 18 (21%) | 69 | 0.492 (0.675) | 0.161 (0.328) | 0.971 (0.994) | 0.899 (0.953) | 0.859 (0.928) | 0.915 (0.966) | 0.159 (0.328) | 0.834 (0.925) | 0.941 (0.983) | 0.73 (0.852)
del 16p13 3 | 6 (7%) | 81 | 0.448 (0.635) | 0.116 (0.275) | 0.55 (0.721) | 0.671 (0.796) | 0.166 (0.328) | 0.0897 (0.236) | 1 (1.00) | 0.662 (0.795) | 0.758 (0.87) | 0.748 (0.863)

'del_1p36.31' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00079

Table S1. Gene #1: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 27 | 21 | 16 | 23
DEL PEAK 1(1P36.31) MUTATED | 1 | 14 | 10 | 8
DEL PEAK 1(1P36.31) WILD-TYPE | 26 | 7 | 6 | 15

Figure S1. Get High-res Image Gene #1: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.31' versus 'METHLYATION_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.068

Table S2. Gene #1: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 19 | 18 | 25 | 9
DEL PEAK 1(1P36.31) MUTATED | 1 | 9 | 11 | 8 | 4
DEL PEAK 1(1P36.31) WILD-TYPE | 15 | 10 | 7 | 17 | 5

Figure S2. Get High-res Image Gene #1: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0305 (Fisher's exact test), Q value = 0.13

Table S3. Gene #1: 'del_1p36.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 12 | 21 | 15 | 16
DEL PEAK 1(1P36.31) MUTATED | 4 | 8 | 11 | 5 | 5
DEL PEAK 1(1P36.31) WILD-TYPE | 19 | 4 | 10 | 10 | 11

Figure S3. Get High-res Image Gene #1: 'del_1p36.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00881 (Fisher's exact test), Q value = 0.063

Table S4. Gene #1: 'del_1p36.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 29 | 25 | 6 | 13 | 14
DEL PEAK 1(1P36.31) MUTATED | 9 | 12 | 5 | 6 | 1
DEL PEAK 1(1P36.31) WILD-TYPE | 20 | 13 | 1 | 7 | 13

Figure S4. Get High-res Image Gene #1: 'del_1p36.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0462 (Fisher's exact test), Q value = 0.17

Table S5. Gene #1: 'del_1p36.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 17 | 18 | 16 | 34
DEL PEAK 1(1P36.31) MUTATED | 2 | 10 | 7 | 14
DEL PEAK 1(1P36.31) WILD-TYPE | 15 | 8 | 9 | 20

Figure S5. Get High-res Image Gene #1: 'del_1p36.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p21.3' versus 'CN_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.16

Table S6. Gene #2: 'del_1p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 27 | 21 | 16 | 23
DEL PEAK 2(1P21.3) MUTATED | 6 | 11 | 10 | 10
DEL PEAK 2(1P21.3) WILD-TYPE | 21 | 10 | 6 | 13

Figure S6. Get High-res Image Gene #2: 'del_1p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p21.3' versus 'RPPA_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.094

Table S7. Gene #2: 'del_1p21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 8 | 24 | 24 | 7
DEL PEAK 2(1P21.3) MUTATED | 1 | 14 | 15 | 1
DEL PEAK 2(1P21.3) WILD-TYPE | 7 | 10 | 9 | 6

Figure S7. Get High-res Image Gene #2: 'del_1p21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_1p21.3' versus 'MRNASEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0042

Table S8. Gene #2: 'del_1p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 26 | 21 | 19 | 21
DEL PEAK 2(1P21.3) MUTATED | 5 | 11 | 5 | 16
DEL PEAK 2(1P21.3) WILD-TYPE | 21 | 10 | 14 | 5

Figure S8. Get High-res Image Gene #2: 'del_1p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00497 (Fisher's exact test), Q value = 0.04

Table S9. Gene #2: 'del_1p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 12 | 21 | 15 | 16
DEL PEAK 2(1P21.3) MUTATED | 5 | 8 | 10 | 3 | 11
DEL PEAK 2(1P21.3) WILD-TYPE | 18 | 4 | 11 | 12 | 5

Figure S9. Get High-res Image Gene #2: 'del_1p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q35' versus 'CN_CNMF'

P value = 0.00323 (Fisher's exact test), Q value = 0.028

Table S10. Gene #3: 'del_2q35' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 27 | 21 | 16 | 23
DEL PEAK 3(2Q35) MUTATED | 0 | 7 | 5 | 5
DEL PEAK 3(2Q35) WILD-TYPE | 27 | 14 | 11 | 18

Figure S10. Get High-res Image Gene #3: 'del_2q35' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q35' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0159 (Fisher's exact test), Q value = 0.089

Table S11. Gene #3: 'del_2q35' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 12 | 21 | 15 | 16
DEL PEAK 3(2Q35) MUTATED | 1 | 6 | 6 | 2 | 2
DEL PEAK 3(2Q35) WILD-TYPE | 22 | 6 | 15 | 13 | 14

Figure S11. Get High-res Image Gene #3: 'del_2q35' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.1' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0042

Table S12. Gene #4: 'del_3p21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 27 | 21 | 16 | 23
DEL PEAK 4(3P21.1) MUTATED | 19 | 15 | 10 | 4
DEL PEAK 4(3P21.1) WILD-TYPE | 8 | 6 | 6 | 19

Figure S12. Get High-res Image Gene #4: 'del_3p21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p21.1' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0015

Table S13. Gene #4: 'del_3p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 19 | 18 | 25 | 9
DEL PEAK 4(3P21.1) MUTATED | 13 | 5 | 16 | 12 | 2
DEL PEAK 4(3P21.1) WILD-TYPE | 3 | 14 | 2 | 13 | 7

Figure S13. Get High-res Image Gene #4: 'del_3p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p21.1' versus 'MRNASEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0034

Table S14. Gene #4: 'del_3p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 26 | 21 | 19 | 21
DEL PEAK 4(3P21.1) MUTATED | 21 | 4 | 10 | 13
DEL PEAK 4(3P21.1) WILD-TYPE | 5 | 17 | 9 | 8

Figure S14. Get High-res Image Gene #4: 'del_3p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7e-04

Table S15. Gene #4: 'del_3p21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 12 | 21 | 15 | 16
DEL PEAK 4(3P21.1) MUTATED | 17 | 12 | 3 | 8 | 8
DEL PEAK 4(3P21.1) WILD-TYPE | 6 | 0 | 18 | 7 | 8

Figure S15. Get High-res Image Gene #4: 'del_3p21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.1' versus 'MIRSEQ_CNMF'

P value = 0.0352 (Fisher's exact test), Q value = 0.14

Table S16. Gene #4: 'del_3p21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 25 | 16 | 25
DEL PEAK 4(3P21.1) MUTATED | 10 | 19 | 5 | 14
DEL PEAK 4(3P21.1) WILD-TYPE | 11 | 6 | 11 | 11

Figure S16. Get High-res Image Gene #4: 'del_3p21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0152 (Fisher's exact test), Q value = 0.089

Table S17. Gene #4: 'del_3p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 29 | 25 | 6 | 13 | 14
DEL PEAK 4(3P21.1) MUTATED | 16 | 8 | 3 | 9 | 12
DEL PEAK 4(3P21.1) WILD-TYPE | 13 | 17 | 3 | 4 | 2

Figure S17. Get High-res Image Gene #4: 'del_3p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00284 (Fisher's exact test), Q value = 0.026

Table S18. Gene #4: 'del_3p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 17 | 18 | 16 | 34
DEL PEAK 4(3P21.1) MUTATED | 14 | 4 | 8 | 21
DEL PEAK 4(3P21.1) WILD-TYPE | 3 | 14 | 8 | 13

Figure S18. Get High-res Image Gene #4: 'del_3p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00042

Table S19. Gene #5: 'del_4q26' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 27 | 21 | 16 | 23
DEL PEAK 5(4Q26) MUTATED | 1 | 19 | 8 | 10
DEL PEAK 5(4Q26) WILD-TYPE | 26 | 2 | 8 | 13

Figure S19. Get High-res Image Gene #5: 'del_4q26' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q26' versus 'MRNASEQ_CNMF'

P value = 0.00234 (Fisher's exact test), Q value = 0.023

Table S20. Gene #5: 'del_4q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 26 | 21 | 19 | 21
DEL PEAK 5(4Q26) MUTATED | 4 | 11 | 9 | 14
DEL PEAK 5(4Q26) WILD-TYPE | 22 | 10 | 10 | 7

Figure S20. Get High-res Image Gene #5: 'del_4q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0042

Table S21. Gene #5: 'del_4q26' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 12 | 21 | 15 | 16
DEL PEAK 5(4Q26) MUTATED | 2 | 9 | 11 | 6 | 10
DEL PEAK 5(4Q26) WILD-TYPE | 21 | 3 | 10 | 9 | 6

Figure S21. Get High-res Image Gene #5: 'del_4q26' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q26' versus 'MIRSEQ_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.087

Table S22. Gene #5: 'del_4q26' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 25 | 16 | 25
DEL PEAK 5(4Q26) MUTATED | 14 | 12 | 7 | 5
DEL PEAK 5(4Q26) WILD-TYPE | 7 | 13 | 9 | 20

Figure S22. Get High-res Image Gene #5: 'del_4q26' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.05 (Fisher's exact test), Q value = 0.17

Table S23. Gene #5: 'del_4q26' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 29 | 25 | 6 | 13 | 14
DEL PEAK 5(4Q26) MUTATED | 14 | 12 | 5 | 5 | 2
DEL PEAK 5(4Q26) WILD-TYPE | 15 | 13 | 1 | 8 | 12

Figure S23. Get High-res Image Gene #5: 'del_4q26' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00042

Table S24. Gene #6: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 27 | 21 | 16 | 23
DEL PEAK 6(4Q34.3) MUTATED | 0 | 19 | 10 | 12
DEL PEAK 6(4Q34.3) WILD-TYPE | 27 | 2 | 6 | 11

Figure S24. Get High-res Image Gene #6: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 0.00284 (Fisher's exact test), Q value = 0.026

Table S25. Gene #6: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 19 | 18 | 25 | 9
DEL PEAK 6(4Q34.3) MUTATED | 3 | 14 | 12 | 8 | 4
DEL PEAK 6(4Q34.3) WILD-TYPE | 13 | 5 | 6 | 17 | 5

Figure S25. Get High-res Image Gene #6: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 0.0426 (Fisher's exact test), Q value = 0.16

Table S26. Gene #6: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 26 | 21 | 19 | 21
DEL PEAK 6(4Q34.3) MUTATED | 7 | 13 | 8 | 13
DEL PEAK 6(4Q34.3) WILD-TYPE | 19 | 8 | 11 | 8

Figure S26. Get High-res Image Gene #6: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00067 (Fisher's exact test), Q value = 0.007

Table S27. Gene #6: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 12 | 21 | 15 | 16
DEL PEAK 6(4Q34.3) MUTATED | 3 | 9 | 13 | 6 | 10
DEL PEAK 6(4Q34.3) WILD-TYPE | 20 | 3 | 8 | 9 | 6

Figure S27. Get High-res Image Gene #6: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0267 (Fisher's exact test), Q value = 0.12

Table S28. Gene #6: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 17 | 18 | 16 | 34
DEL PEAK 6(4Q34.3) MUTATED | 4 | 12 | 5 | 19
DEL PEAK 6(4Q34.3) WILD-TYPE | 13 | 6 | 11 | 15

Figure S28. Get High-res Image Gene #6: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q23.2' versus 'CN_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.068

Table S29. Gene #7: 'del_5q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 27 | 21 | 16 | 23
DEL PEAK 7(5Q23.2) MUTATED | 2 | 6 | 7 | 2
DEL PEAK 7(5Q23.2) WILD-TYPE | 25 | 15 | 9 | 21

Figure S29. Get High-res Image Gene #7: 'del_5q23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0253 (Fisher's exact test), Q value = 0.12

Table S30. Gene #7: 'del_5q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 12 | 21 | 15 | 16
DEL PEAK 7(5Q23.2) MUTATED | 3 | 7 | 3 | 2 | 2
DEL PEAK 7(5Q23.2) WILD-TYPE | 20 | 5 | 18 | 13 | 14

Figure S30. Get High-res Image Gene #7: 'del_5q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q22.1' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0015

Table S31. Gene #8: 'del_6q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 27 | 21 | 16 | 23
DEL PEAK 8(6Q22.1) MUTATED | 14 | 17 | 7 | 3
DEL PEAK 8(6Q22.1) WILD-TYPE | 13 | 4 | 9 | 20

Figure S31. Get High-res Image Gene #8: 'del_6q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00042

Table S32. Gene #9: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 27 | 21 | 16 | 23
DEL PEAK 9(6Q26) MUTATED | 10 | 19 | 5 | 2
DEL PEAK 9(6Q26) WILD-TYPE | 17 | 2 | 11 | 21

Figure S32. Get High-res Image Gene #9: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00042

Table S33. Gene #11: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 27 | 21 | 16 | 23
DEL PEAK 11(9P21.3) MUTATED | 5 | 20 | 15 | 11
DEL PEAK 11(9P21.3) WILD-TYPE | 22 | 1 | 1 | 12

Figure S33. Get High-res Image Gene #11: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 0.00588 (Fisher's exact test), Q value = 0.046

Table S34. Gene #11: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 19 | 18 | 25 | 9
DEL PEAK 11(9P21.3) MUTATED | 5 | 13 | 16 | 13 | 4
DEL PEAK 11(9P21.3) WILD-TYPE | 11 | 6 | 2 | 12 | 5

Figure S34. Get High-res Image Gene #11: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

P value = 0.0248 (Fisher's exact test), Q value = 0.12

Table S35. Gene #11: 'del_9p21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 8 | 24 | 24 | 7
DEL PEAK 11(9P21.3) MUTATED | 3 | 19 | 11 | 6
DEL PEAK 11(9P21.3) WILD-TYPE | 5 | 5 | 13 | 1

Figure S35. Get High-res Image Gene #11: 'del_9p21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 0.12

Table S36. Gene #11: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 26 | 21 | 19 | 21
DEL PEAK 11(9P21.3) MUTATED | 9 | 14 | 12 | 16
DEL PEAK 11(9P21.3) WILD-TYPE | 17 | 7 | 7 | 5

Figure S36. Get High-res Image Gene #11: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.0019

Table S37. Gene #11: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 12 | 21 | 15 | 16
DEL PEAK 11(9P21.3) MUTATED | 5 | 12 | 14 | 9 | 11
DEL PEAK 11(9P21.3) WILD-TYPE | 18 | 0 | 7 | 6 | 5

Figure S37. Get High-res Image Gene #11: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0063 (Fisher's exact test), Q value = 0.047

Table S38. Gene #11: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 17 | 18 | 16 | 34
DEL PEAK 11(9P21.3) MUTATED | 4 | 12 | 9 | 25
DEL PEAK 11(9P21.3) WILD-TYPE | 13 | 6 | 7 | 9

Figure S38. Get High-res Image Gene #11: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0034

Table S39. Gene #12: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 27 | 21 | 16 | 23
DEL PEAK 12(10P15.3) MUTATED | 2 | 12 | 9 | 5
DEL PEAK 12(10P15.3) WILD-TYPE | 25 | 9 | 7 | 18

Figure S39. Get High-res Image Gene #12: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 0.0299 (Fisher's exact test), Q value = 0.13

Table S40. Gene #12: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 19 | 18 | 25 | 9
DEL PEAK 12(10P15.3) MUTATED | 1 | 9 | 9 | 7 | 2
DEL PEAK 12(10P15.3) WILD-TYPE | 15 | 10 | 9 | 18 | 7

Figure S40. Get High-res Image Gene #12: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 0.0344 (Fisher's exact test), Q value = 0.14

Table S41. Gene #12: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 26 | 21 | 19 | 21
DEL PEAK 12(10P15.3) MUTATED | 3 | 8 | 7 | 10
DEL PEAK 12(10P15.3) WILD-TYPE | 23 | 13 | 12 | 11

Figure S41. Get High-res Image Gene #12: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0389 (Fisher's exact test), Q value = 0.15

Table S42. Gene #12: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 12 | 21 | 15 | 16
DEL PEAK 12(10P15.3) MUTATED | 2 | 6 | 7 | 6 | 7
DEL PEAK 12(10P15.3) WILD-TYPE | 21 | 6 | 14 | 9 | 9

Figure S42. Get High-res Image Gene #12: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_CNMF'

P value = 0.0369 (Fisher's exact test), Q value = 0.15

Table S43. Gene #12: 'del_10p15.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 25 | 16 | 25
DEL PEAK 12(10P15.3) MUTATED | 9 | 12 | 2 | 5
DEL PEAK 12(10P15.3) WILD-TYPE | 12 | 13 | 14 | 20

Figure S43. Get High-res Image Gene #12: 'del_10p15.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q25.2' versus 'MIRSEQ_CNMF'

P value = 0.0255 (Fisher's exact test), Q value = 0.12

Table S44. Gene #13: 'del_10q25.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 25 | 16 | 25
DEL PEAK 13(10Q25.2) MUTATED | 13 | 9 | 3 | 6
DEL PEAK 13(10Q25.2) WILD-TYPE | 8 | 16 | 13 | 19

Figure S44. Get High-res Image Gene #13: 'del_10q25.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11q23.2' versus 'CN_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.086

Table S45. Gene #14: 'del_11q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 27 | 21 | 16 | 23
DEL PEAK 14(11Q23.2) MUTATED | 3 | 1 | 5 | 9
DEL PEAK 14(11Q23.2) WILD-TYPE | 24 | 20 | 11 | 14

Figure S45. Get High-res Image Gene #14: 'del_11q23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.31' versus 'MRNASEQ_CNMF'

P value = 0.0263 (Fisher's exact test), Q value = 0.12

Table S46. Gene #15: 'del_12p13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 26 | 21 | 19 | 21
DEL PEAK 15(12P13.31) MUTATED | 0 | 5 | 4 | 2
DEL PEAK 15(12P13.31) WILD-TYPE | 26 | 16 | 15 | 19

Figure S46. Get High-res Image Gene #15: 'del_12p13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_12p13.31' versus 'MIRSEQ_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.089

Table S47. Gene #15: 'del_12p13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 25 | 16 | 25
DEL PEAK 15(12P13.31) MUTATED | 6 | 4 | 1 | 0
DEL PEAK 15(12P13.31) WILD-TYPE | 15 | 21 | 15 | 25

Figure S47. Get High-res Image Gene #15: 'del_12p13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_13q14.11' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00079

Table S48. Gene #16: 'del_13q14.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 27 | 21 | 16 | 23
DEL PEAK 16(13Q14.11) MUTATED | 10 | 20 | 8 | 6
DEL PEAK 16(13Q14.11) WILD-TYPE | 17 | 1 | 8 | 17

Figure S48. Get High-res Image Gene #16: 'del_13q14.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00042

Table S49. Gene #17: 'del_14q32.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 27 | 21 | 16 | 23
DEL PEAK 17(14Q32.31) MUTATED | 1 | 16 | 9 | 13
DEL PEAK 17(14Q32.31) WILD-TYPE | 26 | 5 | 7 | 10

Figure S49. Get High-res Image Gene #17: 'del_14q32.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.31' versus 'METHLYATION_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.007

Table S50. Gene #17: 'del_14q32.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 19 | 18 | 25 | 9
DEL PEAK 17(14Q32.31) MUTATED | 3 | 16 | 7 | 8 | 5
DEL PEAK 17(14Q32.31) WILD-TYPE | 13 | 3 | 11 | 17 | 4

Figure S50. Get High-res Image Gene #17: 'del_14q32.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q32.31' versus 'MRNASEQ_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.0056

Table S51. Gene #17: 'del_14q32.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 26 | 21 | 19 | 21
DEL PEAK 17(14Q32.31) MUTATED | 7 | 17 | 5 | 10
DEL PEAK 17(14Q32.31) WILD-TYPE | 19 | 4 | 14 | 11

Figure S51. Get High-res Image Gene #17: 'del_14q32.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q32.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00093

Table S52. Gene #17: 'del_14q32.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 12 | 21 | 15 | 16
DEL PEAK 17(14Q32.31) MUTATED | 5 | 8 | 17 | 2 | 7
DEL PEAK 17(14Q32.31) WILD-TYPE | 18 | 4 | 4 | 13 | 9

Figure S52. Get High-res Image Gene #17: 'del_14q32.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00901 (Fisher's exact test), Q value = 0.063

Table S53. Gene #17: 'del_14q32.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 29 | 25 | 6 | 13 | 14
DEL PEAK 17(14Q32.31) MUTATED | 8 | 15 | 4 | 9 | 3
DEL PEAK 17(14Q32.31) WILD-TYPE | 21 | 10 | 2 | 4 | 11

Figure S53. Get High-res Image Gene #17: 'del_14q32.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q15.1' versus 'CN_CNMF'

P value = 0.00462 (Fisher's exact test), Q value = 0.039

Table S54. Gene #18: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 27 | 21 | 16 | 23
DEL PEAK 18(15Q15.1) MUTATED | 4 | 6 | 11 | 7
DEL PEAK 18(15Q15.1) WILD-TYPE | 23 | 15 | 5 | 16

Figure S54. Get High-res Image Gene #18: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q15.1' versus 'MRNASEQ_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.11

Table S55. Gene #18: 'del_15q15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 26 | 21 | 19 | 21
DEL PEAK 18(15Q15.1) MUTATED | 3 | 11 | 6 | 8
DEL PEAK 18(15Q15.1) WILD-TYPE | 23 | 10 | 13 | 13

Figure S55. Get High-res Image Gene #18: 'del_15q15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.022 (Fisher's exact test), Q value = 0.11

Table S56. Gene #18: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 17 | 18 | 16 | 34
DEL PEAK 18(15Q15.1) MUTATED | 3 | 8 | 1 | 14
DEL PEAK 18(15Q15.1) WILD-TYPE | 14 | 10 | 15 | 20

Figure S56. Get High-res Image Gene #18: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q24.1' versus 'CN_CNMF'

P value = 0.0491 (Fisher's exact test), Q value = 0.17

Table S57. Gene #20: 'del_16q24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 27 | 21 | 16 | 23
DEL PEAK 20(16Q24.1) MUTATED | 2 | 8 | 5 | 7
DEL PEAK 20(16Q24.1) WILD-TYPE | 25 | 13 | 11 | 16

Figure S57. Get High-res Image Gene #20: 'del_16q24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q12.2' versus 'METHLYATION_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.099

Table S58. Gene #21: 'del_22q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 19 | 18 | 25 | 9
DEL PEAK 21(22Q12.2) MUTATED | 12 | 15 | 18 | 15 | 8
DEL PEAK 21(22Q12.2) WILD-TYPE | 4 | 4 | 0 | 10 | 1

Figure S58. Get High-res Image Gene #21: 'del_22q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q12.2' versus 'MRNASEQ_CNMF'

P value = 0.0391 (Fisher's exact test), Q value = 0.15

Table S59. Gene #21: 'del_22q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 26 | 21 | 19 | 21
DEL PEAK 21(22Q12.2) MUTATED | 20 | 17 | 11 | 20
DEL PEAK 21(22Q12.2) WILD-TYPE | 6 | 4 | 8 | 1

Figure S59. Get High-res Image Gene #21: 'del_22q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0151 (Fisher's exact test), Q value = 0.089

Table S60. Gene #21: 'del_22q12.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 12 | 21 | 15 | 16
DEL PEAK 21(22Q12.2) MUTATED | 16 | 12 | 17 | 8 | 15
DEL PEAK 21(22Q12.2) WILD-TYPE | 7 | 0 | 4 | 7 | 1

Figure S60. Get High-res Image Gene #21: 'del_22q12.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q12.2' versus 'MIRSEQ_CNMF'

P value = 0.0474 (Fisher's exact test), Q value = 0.17

Table S61. Gene #21: 'del_22q12.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 25 | 16 | 25
DEL PEAK 21(22Q12.2) MUTATED | 19 | 22 | 9 | 18
DEL PEAK 21(22Q12.2) WILD-TYPE | 2 | 3 | 7 | 7

Figure S61. Get High-res Image Gene #21: 'del_22q12.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

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/MESO-TP/22533663/transformed.cor.cli.txt

- Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/MESO-TP/22541489/MESO-TP.transferedmergedcluster.txt

- Number of patients = 87

- Number of significantly focal cnvs = 21

- 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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