Correlation between copy number variation genes (focal events) and molecular subtypes
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
16 April 2014 | analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1ZW1JKB
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1ZW1JKB
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 8 molecular subtypes across 197 patients, 61 significant findings detected with P value < 0.05 and Q value < 0.25.

- amp_2p23.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- amp_2q32.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- amp_3q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- amp_7q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- amp_17q25.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- amp_19p13.2 cnv correlated to 'CN_CNMF'.

- del_1p36.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

- del_3p22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

- del_5p14.2 cnv correlated to 'METHLYATION_CNMF'.

- del_5q15 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- del_5q35.2 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

- del_10p11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

- del_11q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

- del_11q24.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- del_14q11.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- del_14q32.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

- del_15q15.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

- del_16q24.1 cnv correlated to 'METHLYATION_CNMF'.

- del_21q22.3 cnv correlated to 'CN_CNMF'.

- del_xp11.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

- del_xq28 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 28 focal events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 61 significant findings detected.

|  | Clinical Features | CN CNMF | METHLYATION CNMF | MRNASEQ CNMF | MRNASEQ CHIERARCHICAL | MIRSEQ CNMF | MIRSEQ CHIERARCHICAL | MIRSEQ MATURE CNMF | MIRSEQ MATURE CHIERARCHICAL
| nCNV (%) | nWild-Type | Chi-square test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test
del 3p22 1 | 15 (8%) | 182 | 1.54e-05 (0.00289) | 1.44e-07 (2.96e-05) | 1.73e-05 (0.00324) | 0.000192 (0.0341) | 0.186 (1.00) | 0.00139 (0.23) | 0.0193 (1.00) | 7.47e-07 (0.000151)
amp 3q22 3 | 68 (35%) | 129 | 2.54e-15 (5.61e-13) | 1.05e-05 (0.002) | 5.27e-07 (0.000107) | 0.000303 (0.0531) | 0.0532 (1.00) | 0.153 (1.00) | 0.163 (1.00) | 0.002 (0.324)
amp 7q22 1 | 119 (60%) | 78 | 1.51e-15 (3.34e-13) | 5.14e-06 (0.001) | 5.55e-13 (1.2e-10) | 1.18e-12 (2.54e-10) | 0.161 (1.00) | 0.534 (1.00) | 0.0975 (1.00) | 0.00352 (0.553)
del 9p21 3 | 27 (14%) | 170 | 3.56e-06 (0.000701) | 5.89e-11 (1.27e-08) | 4e-08 (8.37e-06) | 0.000148 (0.0266) | 0.039 (1.00) | 0.0218 (1.00) | 0.0923 (1.00) | 0.0037 (0.573)
amp 17q25 2 | 143 (73%) | 54 | 1.02e-09 (2.17e-07) | 0.00381 (0.587) | 3.42e-06 (0.000678) | 1.25e-07 (2.59e-05) | 0.504 (1.00) | 1 (1.00) | 0.605 (1.00) | 0.617 (1.00)
del 1p36 31 | 37 (19%) | 160 | 3.85e-13 (8.4e-11) | 8.32e-07 (0.000167) | 4.03e-07 (8.23e-05) | 0.053 (1.00) | 1 (1.00) | 0.945 (1.00) | 0.918 (1.00) | 0.1 (1.00)
del 4q34 3 | 21 (11%) | 176 | 1.2e-07 (2.49e-05) | 5.95e-10 (1.27e-07) | 3.79e-08 (7.96e-06) | 0.00241 (0.386) | 0.625 (1.00) | 0.411 (1.00) | 0.734 (1.00) | 0.0763 (1.00)
del 5q35 2 | 11 (6%) | 186 | 0.0862 (1.00) | 2.03e-08 (4.3e-06) | 0.000682 (0.115) | 0.00116 (0.193) | 0.337 (1.00) | 0.0731 (1.00) | 0.217 (1.00) | 0.00466 (0.712)
del 10p11 21 | 12 (6%) | 185 | 0.000379 (0.0651) | 7.12e-06 (0.00137) | 0.000342 (0.0594) | 0.0509 (1.00) | 0.566 (1.00) | 0.0171 (1.00) | 0.235 (1.00) | 0.00328 (0.518)
del 11q22 3 | 18 (9%) | 179 | 0.000257 (0.0453) | 9.21e-05 (0.0167) | 0.00128 (0.213) | 0.053 (1.00) | 0.594 (1.00) | 0.0886 (1.00) | 0.137 (1.00) | 0.0712 (1.00)
del 14q32 2 | 39 (20%) | 158 | 1.78e-14 (3.91e-12) | 0.000432 (0.0734) | 0.000256 (0.0453) | 0.00159 (0.26) | 0.665 (1.00) | 0.55 (1.00) | 0.572 (1.00) | 0.224 (1.00)
del 15q15 2 | 22 (11%) | 175 | 5.4e-06 (0.00105) | 1.94e-05 (0.00361) | 0.00041 (0.07) | 0.0248 (1.00) | 0.0794 (1.00) | 0.158 (1.00) | 0.0562 (1.00) | 0.0479 (1.00)
del xp11 22 | 18 (9%) | 179 | 2.42e-06 (0.000481) | 3.02e-08 (6.37e-06) | 6.48e-06 (0.00125) | 0.00997 (1.00) | 0.17 (1.00) | 0.0549 (1.00) | 0.203 (1.00) | 0.0117 (1.00)
amp 2p23 2 | 37 (19%) | 160 | 1.12e-27 (2.51e-25) | 5.61e-05 (0.0103) | 0.0312 (1.00) | 0.104 (1.00) | 0.0519 (1.00) | 0.757 (1.00) | 0.00731 (1.00) | 0.68 (1.00)
amp 2q32 1 | 45 (23%) | 152 | 4.21e-24 (9.39e-22) | 0.000342 (0.0594) | 0.0428 (1.00) | 0.0295 (1.00) | 0.138 (1.00) | 0.831 (1.00) | 0.0286 (1.00) | 0.418 (1.00)
del 5q15 | 11 (6%) | 186 | 0.35 (1.00) | 3.35e-05 (0.00617) | 0.00493 (0.749) | 0.000185 (0.0331) | 0.287 (1.00) | 0.0731 (1.00) | 0.398 (1.00) | 0.0441 (1.00)
del 11q24 2 | 19 (10%) | 178 | 0.000848 (0.143) | 1.1e-05 (0.0021) | 0.00239 (0.384) | 0.134 (1.00) | 0.823 (1.00) | 0.177 (1.00) | 0.255 (1.00) | 0.0527 (1.00)
del 14q11 2 | 39 (20%) | 158 | 2.99e-14 (6.55e-12) | 0.00152 (0.249) | 0.00359 (0.56) | 0.00545 (0.823) | 0.665 (1.00) | 0.55 (1.00) | 0.572 (1.00) | 0.381 (1.00)
del xq28 | 17 (9%) | 180 | 1.38e-05 (0.0026) | 1.54e-06 (0.000308) | 0.00266 (0.423) | 0.265 (1.00) | 0.217 (1.00) | 0.417 (1.00) | 0.335 (1.00) | 0.065 (1.00)
amp 19p13 2 | 21 (11%) | 176 | 3.09e-07 (6.33e-05) | 0.185 (1.00) | 0.0358 (1.00) | 0.0688 (1.00) | 0.668 (1.00) | 0.798 (1.00) | 0.533 (1.00) | 0.834 (1.00)
del 5p14 2 | 10 (5%) | 187 | 0.506 (1.00) | 3.64e-06 (0.000713) | 0.144 (1.00) | 0.0599 (1.00) | 0.108 (1.00) | 0.337 (1.00) | 0.173 (1.00) | 0.327 (1.00)
del 16q24 1 | 7 (4%) | 190 | 0.0899 (1.00) | 8e-05 (0.0146) | 0.0309 (1.00) | 0.0778 (1.00) | 0.703 (1.00) | 0.589 (1.00) | 1 (1.00) | 0.0944 (1.00)
del 21q22 3 | 33 (17%) | 164 | 3.02e-05 (0.00559) | 0.166 (1.00) | 0.676 (1.00) | 1 (1.00) | 0.514 (1.00) | 0.6 (1.00) | 0.22 (1.00) | 0.808 (1.00)
del 2q37 3 | 9 (5%) | 188 | 0.1 (1.00) | 0.0283 (1.00) | 0.151 (1.00) | 0.0124 (1.00) | 0.25 (1.00) | 1 (1.00) | 0.0643 (1.00) | 0.496 (1.00)
del 6q21 | 17 (9%) | 180 | 0.00736 (1.00) | 0.00699 (1.00) | 0.012 (1.00) | 0.265 (1.00) | 1 (1.00) | 0.422 (1.00) | 0.503 (1.00) | 0.0983 (1.00)
del 6q22 31 | 18 (9%) | 179 | 0.0113 (1.00) | 0.0126 (1.00) | 0.00582 (0.872) | 0.183 (1.00) | 0.846 (1.00) | 0.321 (1.00) | 0.376 (1.00) | 0.0712 (1.00)
del 19p13 3 | 16 (8%) | 181 | 0.0192 (1.00) | 0.0331 (1.00) | 0.0321 (1.00) | 0.0361 (1.00) | 0.385 (1.00) | 0.182 (1.00) | 0.114 (1.00) | 0.0547 (1.00)
del 19q13 42 | 15 (8%) | 182 | 0.0394 (1.00) | 0.0767 (1.00) | 0.0108 (1.00) | 0.173 (1.00) | 0.5 (1.00) | 0.831 (1.00) | 0.0193 (1.00) | 0.914 (1.00)

'amp_2p23.2' versus 'CN_CNMF'

P value = 1.12e-27 (Chi-square test), Q value = 2.5e-25

Table S1. Gene #1: 'amp_2p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
AMP PEAK 1(2P23.2) MUTATED | 2 | 2 | 6 | 0 | 27
AMP PEAK 1(2P23.2) WILD-TYPE | 69 | 38 | 31 | 21 | 1

Figure S1. Get High-res Image Gene #1: 'amp_2p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2p23.2' versus 'METHLYATION_CNMF'

P value = 5.61e-05 (Chi-square test), Q value = 0.01

Table S2. Gene #1: 'amp_2p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
AMP PEAK 1(2P23.2) MUTATED | 3 | 8 | 4 | 18 | 1
AMP PEAK 1(2P23.2) WILD-TYPE | 35 | 16 | 29 | 30 | 37

Figure S2. Get High-res Image Gene #1: 'amp_2p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_2q32.1' versus 'CN_CNMF'

P value = 4.21e-24 (Chi-square test), Q value = 9.4e-22

Table S3. Gene #2: 'amp_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
AMP PEAK 2(2Q32.1) MUTATED | 5 | 2 | 9 | 1 | 28
AMP PEAK 2(2Q32.1) WILD-TYPE | 66 | 38 | 28 | 20 | 0

Figure S3. Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2q32.1' versus 'METHLYATION_CNMF'

P value = 0.000342 (Chi-square test), Q value = 0.059

Table S4. Gene #2: 'amp_2q32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
AMP PEAK 2(2Q32.1) MUTATED | 6 | 8 | 7 | 20 | 1
AMP PEAK 2(2Q32.1) WILD-TYPE | 32 | 16 | 26 | 28 | 37

Figure S4. Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q22.3' versus 'CN_CNMF'

P value = 2.54e-15 (Chi-square test), Q value = 5.6e-13

Table S5. Gene #3: 'amp_3q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
AMP PEAK 3(3Q22.3) MUTATED | 12 | 9 | 6 | 21 | 20
AMP PEAK 3(3Q22.3) WILD-TYPE | 59 | 31 | 31 | 0 | 8

Figure S5. Get High-res Image Gene #3: 'amp_3q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q22.3' versus 'METHLYATION_CNMF'

P value = 1.05e-05 (Chi-square test), Q value = 0.002

Table S6. Gene #3: 'amp_3q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
AMP PEAK 3(3Q22.3) MUTATED | 12 | 5 | 6 | 31 | 8
AMP PEAK 3(3Q22.3) WILD-TYPE | 26 | 19 | 27 | 17 | 30

Figure S6. Get High-res Image Gene #3: 'amp_3q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q22.3' versus 'MRNASEQ_CNMF'

P value = 5.27e-07 (Fisher's exact test), Q value = 0.00011

Table S7. Gene #3: 'amp_3q22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
AMP PEAK 3(3Q22.3) MUTATED | 22 | 7 | 23 | 16
AMP PEAK 3(3Q22.3) WILD-TYPE | 17 | 60 | 36 | 16

Figure S7. Get High-res Image Gene #3: 'amp_3q22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_3q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000303 (Fisher's exact test), Q value = 0.053

Table S8. Gene #3: 'amp_3q22.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 71 | 56
AMP PEAK 3(3Q22.3) MUTATED | 37 | 19 | 12
AMP PEAK 3(3Q22.3) WILD-TYPE | 33 | 52 | 44

Figure S8. Get High-res Image Gene #3: 'amp_3q22.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_7q22.1' versus 'CN_CNMF'

P value = 1.51e-15 (Chi-square test), Q value = 3.3e-13

Table S9. Gene #4: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
AMP PEAK 4(7Q22.1) MUTATED | 23 | 40 | 13 | 20 | 23
AMP PEAK 4(7Q22.1) WILD-TYPE | 48 | 0 | 24 | 1 | 5

Figure S9. Get High-res Image Gene #4: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q22.1' versus 'METHLYATION_CNMF'

P value = 5.14e-06 (Chi-square test), Q value = 0.001

Table S10. Gene #4: 'amp_7q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
AMP PEAK 4(7Q22.1) MUTATED | 18 | 9 | 12 | 39 | 30
AMP PEAK 4(7Q22.1) WILD-TYPE | 20 | 15 | 21 | 9 | 8

Figure S10. Get High-res Image Gene #4: 'amp_7q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q22.1' versus 'MRNASEQ_CNMF'

P value = 5.55e-13 (Fisher's exact test), Q value = 1.2e-10

Table S11. Gene #4: 'amp_7q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
AMP PEAK 4(7Q22.1) MUTATED | 21 | 19 | 53 | 26
AMP PEAK 4(7Q22.1) WILD-TYPE | 18 | 48 | 6 | 6

Figure S11. Get High-res Image Gene #4: 'amp_7q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_7q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.18e-12 (Fisher's exact test), Q value = 2.5e-10

Table S12. Gene #4: 'amp_7q22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 71 | 56
AMP PEAK 4(7Q22.1) MUTATED | 65 | 28 | 26
AMP PEAK 4(7Q22.1) WILD-TYPE | 5 | 43 | 30

Figure S12. Get High-res Image Gene #4: 'amp_7q22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_17q25.2' versus 'CN_CNMF'

P value = 1.02e-09 (Chi-square test), Q value = 2.2e-07

Table S13. Gene #5: 'amp_17q25.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
AMP PEAK 5(17Q25.2) MUTATED | 38 | 40 | 19 | 19 | 27
AMP PEAK 5(17Q25.2) WILD-TYPE | 33 | 0 | 18 | 2 | 1

Figure S13. Get High-res Image Gene #5: 'amp_17q25.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q25.2' versus 'MRNASEQ_CNMF'

P value = 3.42e-06 (Fisher's exact test), Q value = 0.00068

Table S14. Gene #5: 'amp_17q25.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
AMP PEAK 5(17Q25.2) MUTATED | 31 | 34 | 54 | 24
AMP PEAK 5(17Q25.2) WILD-TYPE | 8 | 33 | 5 | 8

Figure S14. Get High-res Image Gene #5: 'amp_17q25.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_17q25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.25e-07 (Fisher's exact test), Q value = 2.6e-05

Table S15. Gene #5: 'amp_17q25.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 71 | 56
AMP PEAK 5(17Q25.2) MUTATED | 66 | 47 | 30
AMP PEAK 5(17Q25.2) WILD-TYPE | 4 | 24 | 26

Figure S15. Get High-res Image Gene #5: 'amp_17q25.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

P value = 3.09e-07 (Chi-square test), Q value = 6.3e-05

Table S16. Gene #6: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
AMP PEAK 6(19P13.2) MUTATED | 0 | 14 | 4 | 0 | 3
AMP PEAK 6(19P13.2) WILD-TYPE | 71 | 26 | 33 | 21 | 25

Figure S16. Get High-res Image Gene #6: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.31' versus 'CN_CNMF'

P value = 3.85e-13 (Chi-square test), Q value = 8.4e-11

Table S17. Gene #7: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
DEL PEAK 1(1P36.31) MUTATED | 7 | 0 | 23 | 0 | 7
DEL PEAK 1(1P36.31) WILD-TYPE | 64 | 40 | 14 | 21 | 21

Figure S17. Get High-res Image Gene #7: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.31' versus 'METHLYATION_CNMF'

P value = 8.32e-07 (Chi-square test), Q value = 0.00017

Table S18. Gene #7: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
DEL PEAK 1(1P36.31) MUTATED | 6 | 14 | 6 | 8 | 0
DEL PEAK 1(1P36.31) WILD-TYPE | 32 | 10 | 27 | 40 | 38

Figure S18. Get High-res Image Gene #7: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.31' versus 'MRNASEQ_CNMF'

P value = 4.03e-07 (Fisher's exact test), Q value = 8.2e-05

Table S19. Gene #7: 'del_1p36.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
DEL PEAK 1(1P36.31) MUTATED | 5 | 27 | 5 | 0
DEL PEAK 1(1P36.31) WILD-TYPE | 34 | 40 | 54 | 32

Figure S19. Get High-res Image Gene #7: 'del_1p36.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p22.1' versus 'CN_CNMF'

P value = 1.54e-05 (Chi-square test), Q value = 0.0029

Table S20. Gene #9: 'del_3p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
DEL PEAK 3(3P22.1) MUTATED | 2 | 0 | 10 | 0 | 3
DEL PEAK 3(3P22.1) WILD-TYPE | 69 | 40 | 27 | 21 | 25

Figure S20. Get High-res Image Gene #9: 'del_3p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p22.1' versus 'METHLYATION_CNMF'

P value = 1.44e-07 (Chi-square test), Q value = 3e-05

Table S21. Gene #9: 'del_3p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
DEL PEAK 3(3P22.1) MUTATED | 0 | 8 | 6 | 0 | 0
DEL PEAK 3(3P22.1) WILD-TYPE | 38 | 16 | 27 | 48 | 38

Figure S21. Get High-res Image Gene #9: 'del_3p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p22.1' versus 'MRNASEQ_CNMF'

P value = 1.73e-05 (Fisher's exact test), Q value = 0.0032

Table S22. Gene #9: 'del_3p22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
DEL PEAK 3(3P22.1) MUTATED | 1 | 14 | 0 | 0
DEL PEAK 3(3P22.1) WILD-TYPE | 38 | 53 | 59 | 32

Figure S22. Get High-res Image Gene #9: 'del_3p22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000192 (Fisher's exact test), Q value = 0.034

Table S23. Gene #9: 'del_3p22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 71 | 56
DEL PEAK 3(3P22.1) MUTATED | 0 | 12 | 3
DEL PEAK 3(3P22.1) WILD-TYPE | 70 | 59 | 53

Figure S23. Get High-res Image Gene #9: 'del_3p22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00139 (Fisher's exact test), Q value = 0.23

Table S24. Gene #9: 'del_3p22.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 78 | 90
DEL PEAK 3(3P22.1) MUTATED | 7 | 6 | 2
DEL PEAK 3(3P22.1) WILD-TYPE | 22 | 72 | 88

Figure S24. Get High-res Image Gene #9: 'del_3p22.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.47e-07 (Fisher's exact test), Q value = 0.00015

Table S25. Gene #9: 'del_3p22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 75 | 99 | 23
DEL PEAK 3(3P22.1) MUTATED | 5 | 1 | 9
DEL PEAK 3(3P22.1) WILD-TYPE | 70 | 98 | 14

Figure S25. Get High-res Image Gene #9: 'del_3p22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 1.2e-07 (Chi-square test), Q value = 2.5e-05

Table S26. Gene #10: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
DEL PEAK 4(4Q34.3) MUTATED | 4 | 0 | 14 | 0 | 3
DEL PEAK 4(4Q34.3) WILD-TYPE | 67 | 40 | 23 | 21 | 25

Figure S26. Get High-res Image Gene #10: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 5.95e-10 (Chi-square test), Q value = 1.3e-07

Table S27. Gene #10: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
DEL PEAK 4(4Q34.3) MUTATED | 1 | 12 | 4 | 2 | 0
DEL PEAK 4(4Q34.3) WILD-TYPE | 37 | 12 | 29 | 46 | 38

Figure S27. Get High-res Image Gene #10: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 3.79e-08 (Fisher's exact test), Q value = 8e-06

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
DEL PEAK 4(4Q34.3) MUTATED | 1 | 20 | 0 | 0
DEL PEAK 4(4Q34.3) WILD-TYPE | 38 | 47 | 59 | 32

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

'del_5p14.2' versus 'METHLYATION_CNMF'

P value = 3.64e-06 (Chi-square test), Q value = 0.00071

Table S29. Gene #11: 'del_5p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
DEL PEAK 5(5P14.2) MUTATED | 1 | 7 | 0 | 2 | 0
DEL PEAK 5(5P14.2) WILD-TYPE | 37 | 17 | 33 | 46 | 38

Figure S29. Get High-res Image Gene #11: 'del_5p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q15' versus 'METHLYATION_CNMF'

P value = 3.35e-05 (Chi-square test), Q value = 0.0062

Table S30. Gene #12: 'del_5q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
DEL PEAK 6(5Q15) MUTATED | 1 | 7 | 1 | 1 | 1
DEL PEAK 6(5Q15) WILD-TYPE | 37 | 17 | 32 | 47 | 37

Figure S30. Get High-res Image Gene #12: 'del_5q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000185 (Fisher's exact test), Q value = 0.033

Table S31. Gene #12: 'del_5q15' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 71 | 56
DEL PEAK 6(5Q15) MUTATED | 0 | 2 | 9
DEL PEAK 6(5Q15) WILD-TYPE | 70 | 69 | 47

Figure S31. Get High-res Image Gene #12: 'del_5q15' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_5q35.2' versus 'METHLYATION_CNMF'

P value = 2.03e-08 (Chi-square test), Q value = 4.3e-06

Table S32. Gene #13: 'del_5q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
DEL PEAK 7(5Q35.2) MUTATED | 1 | 8 | 1 | 0 | 0
DEL PEAK 7(5Q35.2) WILD-TYPE | 37 | 16 | 32 | 48 | 38

Figure S32. Get High-res Image Gene #13: 'del_5q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q35.2' versus 'MRNASEQ_CNMF'

P value = 0.000682 (Fisher's exact test), Q value = 0.12

Table S33. Gene #13: 'del_5q35.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
DEL PEAK 7(5Q35.2) MUTATED | 1 | 10 | 0 | 0
DEL PEAK 7(5Q35.2) WILD-TYPE | 38 | 57 | 59 | 32

Figure S33. Get High-res Image Gene #13: 'del_5q35.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_5q35.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00116 (Fisher's exact test), Q value = 0.19

Table S34. Gene #13: 'del_5q35.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 71 | 56
DEL PEAK 7(5Q35.2) MUTATED | 0 | 3 | 8
DEL PEAK 7(5Q35.2) WILD-TYPE | 70 | 68 | 48

Figure S34. Get High-res Image Gene #13: 'del_5q35.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 3.56e-06 (Chi-square test), Q value = 7e-04

Table S35. Gene #16: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
DEL PEAK 10(9P21.3) MUTATED | 8 | 1 | 15 | 0 | 3
DEL PEAK 10(9P21.3) WILD-TYPE | 63 | 39 | 22 | 21 | 25

Figure S35. Get High-res Image Gene #16: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 5.89e-11 (Chi-square test), Q value = 1.3e-08

Table S36. Gene #16: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
DEL PEAK 10(9P21.3) MUTATED | 4 | 14 | 5 | 1 | 0
DEL PEAK 10(9P21.3) WILD-TYPE | 34 | 10 | 28 | 47 | 38

Figure S36. Get High-res Image Gene #16: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 4e-08 (Fisher's exact test), Q value = 8.4e-06

Table S37. Gene #16: 'del_9p21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
DEL PEAK 10(9P21.3) MUTATED | 3 | 23 | 0 | 1
DEL PEAK 10(9P21.3) WILD-TYPE | 36 | 44 | 59 | 31

Figure S37. Get High-res Image Gene #16: 'del_9p21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000148 (Fisher's exact test), Q value = 0.027

Table S38. Gene #16: 'del_9p21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 71 | 56
DEL PEAK 10(9P21.3) MUTATED | 1 | 13 | 13
DEL PEAK 10(9P21.3) WILD-TYPE | 69 | 58 | 43

Figure S38. Get High-res Image Gene #16: 'del_9p21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_10p11.21' versus 'CN_CNMF'

P value = 0.000379 (Chi-square test), Q value = 0.065

Table S39. Gene #17: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
DEL PEAK 11(10P11.21) MUTATED | 1 | 0 | 7 | 0 | 4
DEL PEAK 11(10P11.21) WILD-TYPE | 70 | 40 | 30 | 21 | 24

Figure S39. Get High-res Image Gene #17: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p11.21' versus 'METHLYATION_CNMF'

P value = 7.12e-06 (Chi-square test), Q value = 0.0014

Table S40. Gene #17: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
DEL PEAK 11(10P11.21) MUTATED | 0 | 7 | 3 | 1 | 0
DEL PEAK 11(10P11.21) WILD-TYPE | 38 | 17 | 30 | 47 | 38

Figure S40. Get High-res Image Gene #17: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p11.21' versus 'MRNASEQ_CNMF'

P value = 0.000342 (Fisher's exact test), Q value = 0.059

Table S41. Gene #17: 'del_10p11.21' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
DEL PEAK 11(10P11.21) MUTATED | 0 | 11 | 1 | 0
DEL PEAK 11(10P11.21) WILD-TYPE | 39 | 56 | 58 | 32

Figure S41. Get High-res Image Gene #17: 'del_10p11.21' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_11q22.3' versus 'CN_CNMF'

P value = 0.000257 (Chi-square test), Q value = 0.045

Table S42. Gene #18: 'del_11q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
DEL PEAK 12(11Q22.3) MUTATED | 3 | 1 | 10 | 0 | 4
DEL PEAK 12(11Q22.3) WILD-TYPE | 68 | 39 | 27 | 21 | 24

Figure S42. Get High-res Image Gene #18: 'del_11q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q22.3' versus 'METHLYATION_CNMF'

P value = 9.21e-05 (Chi-square test), Q value = 0.017

Table S43. Gene #18: 'del_11q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
DEL PEAK 12(11Q22.3) MUTATED | 2 | 8 | 5 | 2 | 0
DEL PEAK 12(11Q22.3) WILD-TYPE | 36 | 16 | 28 | 46 | 38

Figure S43. Get High-res Image Gene #18: 'del_11q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q22.3' versus 'MRNASEQ_CNMF'

P value = 0.00128 (Fisher's exact test), Q value = 0.21

Table S44. Gene #18: 'del_11q22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
DEL PEAK 12(11Q22.3) MUTATED | 2 | 14 | 1 | 1
DEL PEAK 12(11Q22.3) WILD-TYPE | 37 | 53 | 58 | 31

Figure S44. Get High-res Image Gene #18: 'del_11q22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_11q24.2' versus 'CN_CNMF'

P value = 0.000848 (Chi-square test), Q value = 0.14

Table S45. Gene #19: 'del_11q24.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
DEL PEAK 13(11Q24.2) MUTATED | 3 | 1 | 10 | 1 | 4
DEL PEAK 13(11Q24.2) WILD-TYPE | 68 | 39 | 27 | 20 | 24

Figure S45. Get High-res Image Gene #19: 'del_11q24.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q24.2' versus 'METHLYATION_CNMF'

P value = 1.1e-05 (Chi-square test), Q value = 0.0021

Table S46. Gene #19: 'del_11q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
DEL PEAK 13(11Q24.2) MUTATED | 2 | 9 | 5 | 2 | 0
DEL PEAK 13(11Q24.2) WILD-TYPE | 36 | 15 | 28 | 46 | 38

Figure S46. Get High-res Image Gene #19: 'del_11q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q11.2' versus 'CN_CNMF'

P value = 2.99e-14 (Chi-square test), Q value = 6.5e-12

Table S47. Gene #20: 'del_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
DEL PEAK 14(14Q11.2) MUTATED | 5 | 1 | 25 | 2 | 6
DEL PEAK 14(14Q11.2) WILD-TYPE | 66 | 39 | 12 | 19 | 22

Figure S47. Get High-res Image Gene #20: 'del_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q11.2' versus 'METHLYATION_CNMF'

P value = 0.00152 (Chi-square test), Q value = 0.25

Table S48. Gene #20: 'del_14q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
DEL PEAK 14(14Q11.2) MUTATED | 11 | 10 | 3 | 8 | 2
DEL PEAK 14(14Q11.2) WILD-TYPE | 27 | 14 | 30 | 40 | 36

Figure S48. Get High-res Image Gene #20: 'del_14q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q32.2' versus 'CN_CNMF'

P value = 1.78e-14 (Chi-square test), Q value = 3.9e-12

Table S49. Gene #21: 'del_14q32.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
DEL PEAK 15(14Q32.2) MUTATED | 7 | 0 | 25 | 1 | 6
DEL PEAK 15(14Q32.2) WILD-TYPE | 64 | 40 | 12 | 20 | 22

Figure S49. Get High-res Image Gene #21: 'del_14q32.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.2' versus 'METHLYATION_CNMF'

P value = 0.000432 (Chi-square test), Q value = 0.073

Table S50. Gene #21: 'del_14q32.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
DEL PEAK 15(14Q32.2) MUTATED | 11 | 11 | 3 | 8 | 2
DEL PEAK 15(14Q32.2) WILD-TYPE | 27 | 13 | 30 | 40 | 36

Figure S50. Get High-res Image Gene #21: 'del_14q32.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q32.2' versus 'MRNASEQ_CNMF'

P value = 0.000256 (Fisher's exact test), Q value = 0.045

Table S51. Gene #21: 'del_14q32.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
DEL PEAK 15(14Q32.2) MUTATED | 8 | 24 | 4 | 3
DEL PEAK 15(14Q32.2) WILD-TYPE | 31 | 43 | 55 | 29

Figure S51. Get High-res Image Gene #21: 'del_14q32.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_15q15.2' versus 'CN_CNMF'

P value = 5.4e-06 (Chi-square test), Q value = 0.001

Table S52. Gene #22: 'del_15q15.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
DEL PEAK 16(15Q15.2) MUTATED | 4 | 0 | 13 | 1 | 4
DEL PEAK 16(15Q15.2) WILD-TYPE | 67 | 40 | 24 | 20 | 24

Figure S52. Get High-res Image Gene #22: 'del_15q15.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q15.2' versus 'METHLYATION_CNMF'

P value = 1.94e-05 (Chi-square test), Q value = 0.0036

Table S53. Gene #22: 'del_15q15.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
DEL PEAK 16(15Q15.2) MUTATED | 7 | 9 | 2 | 2 | 0
DEL PEAK 16(15Q15.2) WILD-TYPE | 31 | 15 | 31 | 46 | 38

Figure S53. Get High-res Image Gene #22: 'del_15q15.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q15.2' versus 'MRNASEQ_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.07

Table S54. Gene #22: 'del_15q15.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
DEL PEAK 16(15Q15.2) MUTATED | 4 | 16 | 2 | 0
DEL PEAK 16(15Q15.2) WILD-TYPE | 35 | 51 | 57 | 32

Figure S54. Get High-res Image Gene #22: 'del_15q15.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_16q24.1' versus 'METHLYATION_CNMF'

P value = 8e-05 (Chi-square test), Q value = 0.015

Table S55. Gene #23: 'del_16q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
DEL PEAK 17(16Q24.1) MUTATED | 0 | 5 | 2 | 0 | 0
DEL PEAK 17(16Q24.1) WILD-TYPE | 38 | 19 | 31 | 48 | 38

Figure S55. Get High-res Image Gene #23: 'del_16q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q22.3' versus 'CN_CNMF'

P value = 3.02e-05 (Chi-square test), Q value = 0.0056

Table S56. Gene #26: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
DEL PEAK 20(21Q22.3) MUTATED | 5 | 4 | 9 | 2 | 13
DEL PEAK 20(21Q22.3) WILD-TYPE | 66 | 36 | 28 | 19 | 15

Figure S56. Get High-res Image Gene #26: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp11.22' versus 'CN_CNMF'

P value = 2.42e-06 (Chi-square test), Q value = 0.00048

Table S57. Gene #27: 'del_xp11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
DEL PEAK 21(XP11.22) MUTATED | 4 | 0 | 12 | 0 | 2
DEL PEAK 21(XP11.22) WILD-TYPE | 67 | 40 | 25 | 21 | 26

Figure S57. Get High-res Image Gene #27: 'del_xp11.22' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp11.22' versus 'METHLYATION_CNMF'

P value = 3.02e-08 (Chi-square test), Q value = 6.4e-06

Table S58. Gene #27: 'del_xp11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
DEL PEAK 21(XP11.22) MUTATED | 1 | 10 | 4 | 1 | 0
DEL PEAK 21(XP11.22) WILD-TYPE | 37 | 14 | 29 | 47 | 38

Figure S58. Get High-res Image Gene #27: 'del_xp11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp11.22' versus 'MRNASEQ_CNMF'

P value = 6.48e-06 (Fisher's exact test), Q value = 0.0012

Table S59. Gene #27: 'del_xp11.22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 67 | 59 | 32
DEL PEAK 21(XP11.22) MUTATED | 2 | 16 | 0 | 0
DEL PEAK 21(XP11.22) WILD-TYPE | 37 | 51 | 59 | 32

Figure S59. Get High-res Image Gene #27: 'del_xp11.22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_xq28' versus 'CN_CNMF'

P value = 1.38e-05 (Chi-square test), Q value = 0.0026

Table S60. Gene #28: 'del_xq28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 71 | 40 | 37 | 21 | 28
DEL PEAK 22(XQ28) MUTATED | 5 | 0 | 11 | 0 | 1
DEL PEAK 22(XQ28) WILD-TYPE | 66 | 40 | 26 | 21 | 27

Figure S60. Get High-res Image Gene #28: 'del_xq28' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq28' versus 'METHLYATION_CNMF'

P value = 1.54e-06 (Chi-square test), Q value = 0.00031

Table S61. Gene #28: 'del_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 38 | 24 | 33 | 48 | 38
DEL PEAK 22(XQ28) MUTATED | 1 | 9 | 2 | 3 | 0
DEL PEAK 22(XQ28) WILD-TYPE | 37 | 15 | 31 | 45 | 38

Figure S61. Get High-res Image Gene #28: 'del_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

Methods & Data
Input

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

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

- Number of patients = 197

- Number of significantly focal cnvs = 28

- Number of molecular subtypes = 8

- Exclude genes that fewer than K tumors have alterations, K = 3

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[2] 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)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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