Correlation between copy number variation genes (focal events) and molecular subtypes
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
15 January 2014 | analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C19Z9396
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/C19Z9396
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 40 focal events and 8 molecular subtypes across 172 patients, 99 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

- 2p cnv correlated to 'CN_CNMF'.

- 2q cnv correlated to 'CN_CNMF'.

- 3p cnv correlated to 'CN_CNMF'.

- 3q cnv correlated to 'CN_CNMF'.

- 4p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 4q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

- 5p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 5q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 6p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

- 6q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

- 7p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 7q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 8q cnv correlated to 'METHLYATION_CNMF'.

- 9p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 9q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 10p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- 10q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 11p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 11q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 12p cnv correlated to 'CN_CNMF'.

- 12q cnv correlated to 'CN_CNMF'.

- 13q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 14q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

- 15q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 16p cnv correlated to 'CN_CNMF'.

- 16q cnv correlated to 'CN_CNMF'.

- 17p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 17q cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 18p cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

- 18q cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 19p cnv correlated to 'CN_CNMF'.

- 19q cnv correlated to 'CN_CNMF'.

- 22q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

- xq cnv correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 40 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, 99 significant findings detected.

|  | Clinical Features | CN CNMF | METHLYATION CNMF | MRNASEQ CNMF | MRNASEQ CHIERARCHICAL | MIRSEQ CNMF | MIRSEQ CHIERARCHICAL | MIRSEQ MATURE CNMF | MIRSEQ MATURE CHIERARCHICAL
| nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test
9q | 26 (15%) | 146 | 8.81e-07 (0.000249) | 1.32e-08 (4.02e-06) | 1.17e-08 (3.56e-06) | 1.09e-07 (3.24e-05) | 0.00475 (0.945) | 1.3e-05 (0.00346) | 0.0336 (1.00) | 1.83e-05 (0.00476)
10q | 17 (10%) | 155 | 6.87e-07 (0.000196) | 2.4e-07 (6.96e-05) | 0.000451 (0.106) | 0.0932 (1.00) | 0.605 (1.00) | 0.000372 (0.0889) | 0.507 (1.00) | 0.000635 (0.146)
14q | 37 (22%) | 135 | 2.82e-13 (8.87e-11) | 0.000432 (0.102) | 5.95e-05 (0.0151) | 4.08e-08 (1.22e-05) | 0.0941 (1.00) | 0.000843 (0.189) | 0.311 (1.00) | 0.0351 (1.00)
22q | 42 (24%) | 130 | 7.5e-07 (0.000214) | 1.18e-07 (3.48e-05) | 1.29e-07 (3.8e-05) | 0.000958 (0.213) | 0.0988 (1.00) | 1.61e-05 (0.00424) | 0.0294 (1.00) | 0.0182 (1.00)
1p | 26 (15%) | 146 | 1.74e-07 (5.11e-05) | 0.000735 (0.168) | 2.69e-05 (0.00697) | 0.000124 (0.0308) | 0.783 (1.00) | 0.677 (1.00) | 0.521 (1.00) | 0.87 (1.00)
4p | 24 (14%) | 148 | 2.9e-06 (8e-04) | 9.7e-09 (2.97e-06) | 3.28e-06 (0.000898) | 0.000532 (0.124) | 0.562 (1.00) | 0.0494 (1.00) | 0.456 (1.00) | 0.00325 (0.666)
7p | 101 (59%) | 71 | 1.14e-18 (3.66e-16) | 2.12e-07 (6.16e-05) | 1.43e-12 (4.48e-10) | 2.01e-07 (5.88e-05) | 0.0969 (1.00) | 0.00126 (0.277) | 0.17 (1.00) | 0.0408 (1.00)
7q | 102 (59%) | 70 | 4e-18 (1.28e-15) | 5.75e-07 (0.000166) | 2.02e-12 (6.29e-10) | 3.02e-07 (8.73e-05) | 0.149 (1.00) | 0.0054 (1.00) | 0.234 (1.00) | 0.126 (1.00)
9p | 25 (15%) | 147 | 7.59e-07 (0.000216) | 3.38e-08 (1.02e-05) | 3.66e-08 (1.1e-05) | 1.79e-05 (0.00469) | 0.00986 (1.00) | 0.00162 (0.35) | 0.045 (1.00) | 0.00197 (0.419)
10p | 17 (10%) | 155 | 1.51e-08 (4.56e-06) | 1.14e-06 (0.000318) | 0.000451 (0.106) | 0.26 (1.00) | 0.876 (1.00) | 0.00078 (0.176) | 0.842 (1.00) | 0.00123 (0.27)
17p | 110 (64%) | 62 | 1.05e-14 (3.32e-12) | 1.76e-05 (0.00462) | 9.26e-07 (0.000261) | 5.28e-06 (0.00142) | 0.0489 (1.00) | 0.00373 (0.754) | 0.101 (1.00) | 0.0854 (1.00)
1q | 27 (16%) | 145 | 1.38e-06 (0.000384) | 0.00394 (0.792) | 0.000341 (0.0822) | 0.000526 (0.123) | 0.603 (1.00) | 0.177 (1.00) | 0.523 (1.00) | 0.602 (1.00)
4q | 24 (14%) | 148 | 2.9e-06 (8e-04) | 2.21e-09 (6.79e-07) | 3.28e-06 (0.000898) | 0.00156 (0.338) | 0.843 (1.00) | 0.128 (1.00) | 0.355 (1.00) | 0.0125 (1.00)
5p | 33 (19%) | 139 | 7.13e-05 (0.018) | 3.5e-06 (0.000952) | 0.00594 (1.00) | 0.000122 (0.0306) | 0.0217 (1.00) | 0.122 (1.00) | 0.192 (1.00) | 0.163 (1.00)
5q | 33 (19%) | 139 | 0.000191 (0.0472) | 4.46e-05 (0.0114) | 0.00996 (1.00) | 0.000122 (0.0306) | 0.0217 (1.00) | 0.353 (1.00) | 0.192 (1.00) | 0.287 (1.00)
6p | 20 (12%) | 152 | 0.000544 (0.126) | 0.000899 (0.201) | 0.000357 (0.0858) | 0.0275 (1.00) | 0.0407 (1.00) | 0.123 (1.00) | 0.0911 (1.00) | 0.106 (1.00)
6q | 21 (12%) | 151 | 4.01e-06 (0.00109) | 3.3e-05 (0.00848) | 0.000423 (0.101) | 0.0121 (1.00) | 0.283 (1.00) | 0.173 (1.00) | 0.159 (1.00) | 0.152 (1.00)
11p | 18 (10%) | 154 | 2.72e-06 (0.000752) | 8.58e-06 (0.0023) | 0.0305 (1.00) | 0.000324 (0.0783) | 0.0229 (1.00) | 0.165 (1.00) | 0.518 (1.00) | 0.00927 (1.00)
11q | 21 (12%) | 151 | 3.45e-08 (1.04e-05) | 4.06e-08 (1.21e-05) | 0.011 (1.00) | 0.000532 (0.124) | 0.00966 (1.00) | 0.128 (1.00) | 0.417 (1.00) | 0.0334 (1.00)
13q | 36 (21%) | 136 | 5.57e-05 (0.0142) | 0.000199 (0.049) | 0.044 (1.00) | 0.000755 (0.171) | 0.0677 (1.00) | 0.0557 (1.00) | 0.123 (1.00) | 0.0675 (1.00)
15q | 24 (14%) | 148 | 5.82e-07 (0.000167) | 0.000618 (0.142) | 0.00291 (0.602) | 1.31e-06 (0.000366) | 0.302 (1.00) | 0.533 (1.00) | 0.354 (1.00) | 0.308 (1.00)
17q | 117 (68%) | 55 | 5.2e-12 (1.62e-09) | 0.00117 (0.259) | 9.37e-07 (0.000263) | 1.09e-05 (0.00291) | 0.293 (1.00) | 0.0743 (1.00) | 0.49 (1.00) | 0.122 (1.00)
18q | 35 (20%) | 137 | 0.00181 (0.386) | 7.14e-06 (0.00192) | 1.97e-05 (0.00513) | 0.000811 (0.182) | 0.0308 (1.00) | 0.0329 (1.00) | 0.186 (1.00) | 0.342 (1.00)
18p | 37 (22%) | 135 | 0.00142 (0.31) | 1.54e-05 (0.00409) | 3.04e-05 (0.00785) | 0.00212 (0.45) | 0.00974 (1.00) | 0.0299 (1.00) | 0.171 (1.00) | 0.189 (1.00)
2p | 34 (20%) | 138 | 1.27e-07 (3.76e-05) | 0.00446 (0.893) | 0.195 (1.00) | 0.665 (1.00) | 0.0771 (1.00) | 0.782 (1.00) | 0.0338 (1.00) | 0.857 (1.00)
2q | 36 (21%) | 136 | 7.07e-10 (2.18e-07) | 0.0187 (1.00) | 0.597 (1.00) | 0.455 (1.00) | 0.0859 (1.00) | 0.951 (1.00) | 0.0211 (1.00) | 0.863 (1.00)
3p | 60 (35%) | 112 | 7.81e-16 (2.48e-13) | 0.518 (1.00) | 0.352 (1.00) | 0.118 (1.00) | 0.839 (1.00) | 0.729 (1.00) | 0.809 (1.00) | 1 (1.00)
3q | 59 (34%) | 113 | 3.25e-17 (1.03e-14) | 0.223 (1.00) | 0.00179 (0.384) | 0.524 (1.00) | 0.348 (1.00) | 0.0266 (1.00) | 0.748 (1.00) | 0.124 (1.00)
8q | 19 (11%) | 153 | 0.00254 (0.533) | 0.000104 (0.026) | 0.0033 (0.672) | 0.0656 (1.00) | 0.00783 (1.00) | 0.0388 (1.00) | 0.0582 (1.00) | 0.0122 (1.00)
12p | 69 (40%) | 103 | 0.000301 (0.0731) | 0.605 (1.00) | 0.0287 (1.00) | 0.151 (1.00) | 0.389 (1.00) | 0.0801 (1.00) | 0.0806 (1.00) | 0.21 (1.00)
12q | 68 (40%) | 104 | 0.000236 (0.0575) | 0.461 (1.00) | 0.0156 (1.00) | 0.131 (1.00) | 0.288 (1.00) | 0.069 (1.00) | 0.0597 (1.00) | 0.209 (1.00)
16p | 93 (54%) | 79 | 1.68e-09 (5.17e-07) | 0.37 (1.00) | 0.00724 (1.00) | 0.00995 (1.00) | 0.0574 (1.00) | 0.0519 (1.00) | 0.0048 (0.951) | 0.0654 (1.00)
16q | 90 (52%) | 82 | 4.87e-10 (1.51e-07) | 0.349 (1.00) | 0.0024 (0.506) | 0.0227 (1.00) | 0.0274 (1.00) | 0.00617 (1.00) | 0.0058 (1.00) | 0.0346 (1.00)
19p | 15 (9%) | 157 | 0.000225 (0.0552) | 0.00306 (0.63) | 0.0297 (1.00) | 0.0114 (1.00) | 0.00737 (1.00) | 0.00343 (0.696) | 0.21 (1.00) | 0.00596 (1.00)
19q | 14 (8%) | 158 | 4.27e-05 (0.0109) | 0.00821 (1.00) | 0.029 (1.00) | 0.0491 (1.00) | 0.0127 (1.00) | 0.00811 (1.00) | 0.0737 (1.00) | 0.0178 (1.00)
xq | 74 (43%) | 98 | 1.18e-13 (3.72e-11) | 0.0521 (1.00) | 0.0611 (1.00) | 0.0732 (1.00) | 0.159 (1.00) | 0.222 (1.00) | 0.204 (1.00) | 0.668 (1.00)
8p | 18 (10%) | 154 | 0.138 (1.00) | 0.0188 (1.00) | 0.0903 (1.00) | 0.441 (1.00) | 0.0426 (1.00) | 0.0661 (1.00) | 0.107 (1.00) | 0.0215 (1.00)
20p | 59 (34%) | 113 | 0.00274 (0.572) | 0.109 (1.00) | 0.107 (1.00) | 0.42 (1.00) | 0.301 (1.00) | 0.69 (1.00) | 0.862 (1.00) | 0.778 (1.00)
20q | 60 (35%) | 112 | 0.00551 (1.00) | 0.109 (1.00) | 0.142 (1.00) | 0.452 (1.00) | 0.276 (1.00) | 0.729 (1.00) | 0.8 (1.00) | 0.747 (1.00)
21q | 42 (24%) | 130 | 0.00284 (0.591) | 0.0771 (1.00) | 0.0995 (1.00) | 0.0596 (1.00) | 0.312 (1.00) | 0.216 (1.00) | 0.0575 (1.00) | 0.823 (1.00)

'1p' versus 'CN_CNMF'

P value = 1.74e-07 (Fisher's exact test), Q value = 5.1e-05

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
1P MUTATED | 1 | 9 | 0 | 16
1P WILD-TYPE | 32 | 59 | 37 | 18

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

'1p' versus 'METHLYATION_CNMF'

P value = 0.000735 (Fisher's exact test), Q value = 0.17

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
1P MUTATED | 5 | 15 | 5
1P WILD-TYPE | 38 | 28 | 65

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

'1p' versus 'MRNASEQ_CNMF'

P value = 2.69e-05 (Fisher's exact test), Q value = 0.007

Table S3. Gene #1: '1p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
1P MUTATED | 19 | 3 | 1 | 0
1P WILD-TYPE | 39 | 46 | 30 | 23

Figure S3. Get High-res Image Gene #1: '1p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'1p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000124 (Fisher's exact test), Q value = 0.031

Table S4. Gene #1: '1p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
1P MUTATED | 12 | 8 | 3
1P WILD-TYPE | 19 | 58 | 61

Figure S4. Get High-res Image Gene #1: '1p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1q' versus 'CN_CNMF'

P value = 1.38e-06 (Fisher's exact test), Q value = 0.00038

Table S5. Gene #2: '1q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
1Q MUTATED | 1 | 9 | 1 | 16
1Q WILD-TYPE | 32 | 59 | 36 | 18

Figure S5. Get High-res Image Gene #2: '1q' versus Molecular Subtype #1: 'CN_CNMF'

'1q' versus 'MRNASEQ_CNMF'

P value = 0.000341 (Fisher's exact test), Q value = 0.082

Table S6. Gene #2: '1q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
1Q MUTATED | 18 | 3 | 3 | 0
1Q WILD-TYPE | 40 | 46 | 28 | 23

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

'1q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000526 (Fisher's exact test), Q value = 0.12

Table S7. Gene #2: '1q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
1Q MUTATED | 11 | 10 | 3
1Q WILD-TYPE | 20 | 56 | 61

Figure S7. Get High-res Image Gene #2: '1q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'2p' versus 'CN_CNMF'

P value = 1.27e-07 (Fisher's exact test), Q value = 3.8e-05

Table S8. Gene #3: '2p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
2P MUTATED | 12 | 3 | 3 | 16
2P WILD-TYPE | 21 | 65 | 34 | 18

Figure S8. Get High-res Image Gene #3: '2p' versus Molecular Subtype #1: 'CN_CNMF'

'2q' versus 'CN_CNMF'

P value = 7.07e-10 (Fisher's exact test), Q value = 2.2e-07

Table S9. Gene #4: '2q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
2Q MUTATED | 13 | 2 | 3 | 18
2Q WILD-TYPE | 20 | 66 | 34 | 16

Figure S9. Get High-res Image Gene #4: '2q' versus Molecular Subtype #1: 'CN_CNMF'

'3p' versus 'CN_CNMF'

P value = 7.81e-16 (Fisher's exact test), Q value = 2.5e-13

Table S10. Gene #5: '3p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
3P MUTATED | 31 | 10 | 5 | 14
3P WILD-TYPE | 2 | 58 | 32 | 20

Figure S10. Get High-res Image Gene #5: '3p' versus Molecular Subtype #1: 'CN_CNMF'

'3q' versus 'CN_CNMF'

P value = 3.25e-17 (Fisher's exact test), Q value = 1e-14

Table S11. Gene #6: '3q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
3Q MUTATED | 32 | 9 | 6 | 12
3Q WILD-TYPE | 1 | 59 | 31 | 22

Figure S11. Get High-res Image Gene #6: '3q' versus Molecular Subtype #1: 'CN_CNMF'

'4p' versus 'CN_CNMF'

P value = 2.9e-06 (Fisher's exact test), Q value = 8e-04

Table S12. Gene #7: '4p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
4P MUTATED | 1 | 7 | 1 | 15
4P WILD-TYPE | 32 | 61 | 36 | 19

Figure S12. Get High-res Image Gene #7: '4p' versus Molecular Subtype #1: 'CN_CNMF'

'4p' versus 'METHLYATION_CNMF'

P value = 9.7e-09 (Fisher's exact test), Q value = 3e-06

Table S13. Gene #7: '4p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
4P MUTATED | 1 | 18 | 2
4P WILD-TYPE | 42 | 25 | 68

Figure S13. Get High-res Image Gene #7: '4p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p' versus 'MRNASEQ_CNMF'

P value = 3.28e-06 (Fisher's exact test), Q value = 9e-04

Table S14. Gene #7: '4p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
4P MUTATED | 20 | 2 | 1 | 0
4P WILD-TYPE | 38 | 47 | 30 | 23

Figure S14. Get High-res Image Gene #7: '4p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000532 (Fisher's exact test), Q value = 0.12

Table S15. Gene #7: '4p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
4P MUTATED | 11 | 9 | 3
4P WILD-TYPE | 20 | 57 | 61

Figure S15. Get High-res Image Gene #7: '4p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'4q' versus 'CN_CNMF'

P value = 2.9e-06 (Fisher's exact test), Q value = 8e-04

Table S16. Gene #8: '4q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
4Q MUTATED | 1 | 7 | 1 | 15
4Q WILD-TYPE | 32 | 61 | 36 | 19

Figure S16. Get High-res Image Gene #8: '4q' versus Molecular Subtype #1: 'CN_CNMF'

'4q' versus 'METHLYATION_CNMF'

P value = 2.21e-09 (Fisher's exact test), Q value = 6.8e-07

Table S17. Gene #8: '4q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
4Q MUTATED | 1 | 19 | 2
4Q WILD-TYPE | 42 | 24 | 68

Figure S17. Get High-res Image Gene #8: '4q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q' versus 'MRNASEQ_CNMF'

P value = 3.28e-06 (Fisher's exact test), Q value = 9e-04

Table S18. Gene #8: '4q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
4Q MUTATED | 20 | 2 | 1 | 0
4Q WILD-TYPE | 38 | 47 | 30 | 23

Figure S18. Get High-res Image Gene #8: '4q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'5p' versus 'CN_CNMF'

P value = 7.13e-05 (Fisher's exact test), Q value = 0.018

Table S19. Gene #9: '5p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
5P MUTATED | 3 | 14 | 1 | 15
5P WILD-TYPE | 30 | 54 | 36 | 19

Figure S19. Get High-res Image Gene #9: '5p' versus Molecular Subtype #1: 'CN_CNMF'

'5p' versus 'METHLYATION_CNMF'

P value = 3.5e-06 (Fisher's exact test), Q value = 0.00095

Table S20. Gene #9: '5p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
5P MUTATED | 9 | 18 | 3
5P WILD-TYPE | 34 | 25 | 67

Figure S20. Get High-res Image Gene #9: '5p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000122 (Fisher's exact test), Q value = 0.031

Table S21. Gene #9: '5p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
5P MUTATED | 10 | 19 | 3
5P WILD-TYPE | 21 | 47 | 61

Figure S21. Get High-res Image Gene #9: '5p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5q' versus 'CN_CNMF'

P value = 0.000191 (Fisher's exact test), Q value = 0.047

Table S22. Gene #10: '5q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
5Q MUTATED | 3 | 15 | 1 | 14
5Q WILD-TYPE | 30 | 53 | 36 | 20

Figure S22. Get High-res Image Gene #10: '5q' versus Molecular Subtype #1: 'CN_CNMF'

'5q' versus 'METHLYATION_CNMF'

P value = 4.46e-05 (Fisher's exact test), Q value = 0.011

Table S23. Gene #10: '5q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
5Q MUTATED | 9 | 17 | 4
5Q WILD-TYPE | 34 | 26 | 66

Figure S23. Get High-res Image Gene #10: '5q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000122 (Fisher's exact test), Q value = 0.031

Table S24. Gene #10: '5q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
5Q MUTATED | 10 | 19 | 3
5Q WILD-TYPE | 21 | 47 | 61

Figure S24. Get High-res Image Gene #10: '5q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6p' versus 'CN_CNMF'

P value = 0.000544 (Fisher's exact test), Q value = 0.13

Table S25. Gene #11: '6p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
6P MUTATED | 1 | 7 | 1 | 11
6P WILD-TYPE | 32 | 61 | 36 | 23

Figure S25. Get High-res Image Gene #11: '6p' versus Molecular Subtype #1: 'CN_CNMF'

'6p' versus 'METHLYATION_CNMF'

P value = 0.000899 (Fisher's exact test), Q value = 0.2

Table S26. Gene #11: '6p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
6P MUTATED | 2 | 12 | 4
6P WILD-TYPE | 41 | 31 | 66

Figure S26. Get High-res Image Gene #11: '6p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p' versus 'MRNASEQ_CNMF'

P value = 0.000357 (Fisher's exact test), Q value = 0.086

Table S27. Gene #11: '6p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
6P MUTATED | 15 | 4 | 0 | 0
6P WILD-TYPE | 43 | 45 | 31 | 23

Figure S27. Get High-res Image Gene #11: '6p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6q' versus 'CN_CNMF'

P value = 4.01e-06 (Fisher's exact test), Q value = 0.0011

Table S28. Gene #12: '6q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
6Q MUTATED | 1 | 5 | 1 | 14
6Q WILD-TYPE | 32 | 63 | 36 | 20

Figure S28. Get High-res Image Gene #12: '6q' versus Molecular Subtype #1: 'CN_CNMF'

'6q' versus 'METHLYATION_CNMF'

P value = 3.3e-05 (Fisher's exact test), Q value = 0.0085

Table S29. Gene #12: '6q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
6Q MUTATED | 2 | 14 | 3
6Q WILD-TYPE | 41 | 29 | 67

Figure S29. Get High-res Image Gene #12: '6q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q' versus 'MRNASEQ_CNMF'

P value = 0.000423 (Fisher's exact test), Q value = 0.1

Table S30. Gene #12: '6q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
6Q MUTATED | 16 | 3 | 1 | 0
6Q WILD-TYPE | 42 | 46 | 30 | 23

Figure S30. Get High-res Image Gene #12: '6q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7p' versus 'CN_CNMF'

P value = 1.14e-18 (Fisher's exact test), Q value = 3.7e-16

Table S31. Gene #13: '7p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
7P MUTATED | 31 | 19 | 37 | 14
7P WILD-TYPE | 2 | 49 | 0 | 20

Figure S31. Get High-res Image Gene #13: '7p' versus Molecular Subtype #1: 'CN_CNMF'

'7p' versus 'METHLYATION_CNMF'

P value = 2.12e-07 (Fisher's exact test), Q value = 6.2e-05

Table S32. Gene #13: '7p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
7P MUTATED | 20 | 14 | 57
7P WILD-TYPE | 23 | 29 | 13

Figure S32. Get High-res Image Gene #13: '7p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p' versus 'MRNASEQ_CNMF'

P value = 1.43e-12 (Fisher's exact test), Q value = 4.5e-10

Table S33. Gene #13: '7p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
7P MUTATED | 15 | 44 | 15 | 20
7P WILD-TYPE | 43 | 5 | 16 | 3

Figure S33. Get High-res Image Gene #13: '7p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.01e-07 (Fisher's exact test), Q value = 5.9e-05

Table S34. Gene #13: '7p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
7P MUTATED | 9 | 32 | 53
7P WILD-TYPE | 22 | 34 | 11

Figure S34. Get High-res Image Gene #13: '7p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7q' versus 'CN_CNMF'

P value = 4e-18 (Fisher's exact test), Q value = 1.3e-15

Table S35. Gene #14: '7q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
7Q MUTATED | 31 | 20 | 37 | 14
7Q WILD-TYPE | 2 | 48 | 0 | 20

Figure S35. Get High-res Image Gene #14: '7q' versus Molecular Subtype #1: 'CN_CNMF'

'7q' versus 'METHLYATION_CNMF'

P value = 5.75e-07 (Fisher's exact test), Q value = 0.00017

Table S36. Gene #14: '7q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
7Q MUTATED | 20 | 15 | 57
7Q WILD-TYPE | 23 | 28 | 13

Figure S36. Get High-res Image Gene #14: '7q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q' versus 'MRNASEQ_CNMF'

P value = 2.02e-12 (Fisher's exact test), Q value = 6.3e-10

Table S37. Gene #14: '7q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
7Q MUTATED | 15 | 44 | 16 | 20
7Q WILD-TYPE | 43 | 5 | 15 | 3

Figure S37. Get High-res Image Gene #14: '7q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.02e-07 (Fisher's exact test), Q value = 8.7e-05

Table S38. Gene #14: '7q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
7Q MUTATED | 9 | 33 | 53
7Q WILD-TYPE | 22 | 33 | 11

Figure S38. Get High-res Image Gene #14: '7q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8q' versus 'METHLYATION_CNMF'

P value = 0.000104 (Fisher's exact test), Q value = 0.026

Table S39. Gene #16: '8q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
8Q MUTATED | 2 | 12 | 2
8Q WILD-TYPE | 41 | 31 | 68

Figure S39. Get High-res Image Gene #16: '8q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p' versus 'CN_CNMF'

P value = 7.59e-07 (Fisher's exact test), Q value = 0.00022

Table S40. Gene #17: '9p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
9P MUTATED | 1 | 9 | 0 | 15
9P WILD-TYPE | 32 | 59 | 37 | 19

Figure S40. Get High-res Image Gene #17: '9p' versus Molecular Subtype #1: 'CN_CNMF'

'9p' versus 'METHLYATION_CNMF'

P value = 3.38e-08 (Fisher's exact test), Q value = 1e-05

Table S41. Gene #17: '9p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
9P MUTATED | 5 | 16 | 0
9P WILD-TYPE | 38 | 27 | 70

Figure S41. Get High-res Image Gene #17: '9p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p' versus 'MRNASEQ_CNMF'

P value = 3.66e-08 (Fisher's exact test), Q value = 1.1e-05

Table S42. Gene #17: '9p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
9P MUTATED | 22 | 0 | 1 | 1
9P WILD-TYPE | 36 | 49 | 30 | 22

Figure S42. Get High-res Image Gene #17: '9p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.79e-05 (Fisher's exact test), Q value = 0.0047

Table S43. Gene #17: '9p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
9P MUTATED | 11 | 12 | 1
9P WILD-TYPE | 20 | 54 | 63

Figure S43. Get High-res Image Gene #17: '9p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9q' versus 'CN_CNMF'

P value = 8.81e-07 (Fisher's exact test), Q value = 0.00025

Table S44. Gene #18: '9q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
9Q MUTATED | 1 | 10 | 0 | 15
9Q WILD-TYPE | 32 | 58 | 37 | 19

Figure S44. Get High-res Image Gene #18: '9q' versus Molecular Subtype #1: 'CN_CNMF'

'9q' versus 'METHLYATION_CNMF'

P value = 1.32e-08 (Fisher's exact test), Q value = 4e-06

Table S45. Gene #18: '9q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
9Q MUTATED | 6 | 17 | 0
9Q WILD-TYPE | 37 | 26 | 70

Figure S45. Get High-res Image Gene #18: '9q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q' versus 'MRNASEQ_CNMF'

P value = 1.17e-08 (Fisher's exact test), Q value = 3.6e-06

Table S46. Gene #18: '9q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
9Q MUTATED | 23 | 0 | 1 | 1
9Q WILD-TYPE | 35 | 49 | 30 | 22

Figure S46. Get High-res Image Gene #18: '9q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.09e-07 (Fisher's exact test), Q value = 3.2e-05

Table S47. Gene #18: '9q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
9Q MUTATED | 13 | 12 | 0
9Q WILD-TYPE | 18 | 54 | 64

Figure S47. Get High-res Image Gene #18: '9q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.3e-05 (Fisher's exact test), Q value = 0.0035

Table S48. Gene #18: '9q' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 80 | 74
9Q MUTATED | 6 | 2 | 18
9Q WILD-TYPE | 12 | 78 | 56

Figure S48. Get High-res Image Gene #18: '9q' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'9q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.83e-05 (Fisher's exact test), Q value = 0.0048

Table S49. Gene #18: '9q' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 14 | 87 | 71
9Q MUTATED | 5 | 3 | 18
9Q WILD-TYPE | 9 | 84 | 53

Figure S49. Get High-res Image Gene #18: '9q' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p' versus 'CN_CNMF'

P value = 1.51e-08 (Fisher's exact test), Q value = 4.6e-06

Table S50. Gene #19: '10p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
10P MUTATED | 1 | 1 | 1 | 14
10P WILD-TYPE | 32 | 67 | 36 | 20

Figure S50. Get High-res Image Gene #19: '10p' versus Molecular Subtype #1: 'CN_CNMF'

'10p' versus 'METHLYATION_CNMF'

P value = 1.14e-06 (Fisher's exact test), Q value = 0.00032

Table S51. Gene #19: '10p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
10P MUTATED | 0 | 12 | 1
10P WILD-TYPE | 43 | 31 | 69

Figure S51. Get High-res Image Gene #19: '10p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p' versus 'MRNASEQ_CNMF'

P value = 0.000451 (Fisher's exact test), Q value = 0.11

Table S52. Gene #19: '10p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
10P MUTATED | 14 | 3 | 0 | 0
10P WILD-TYPE | 44 | 46 | 31 | 23

Figure S52. Get High-res Image Gene #19: '10p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.18

Table S53. Gene #19: '10p' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 80 | 74
10P MUTATED | 7 | 4 | 6
10P WILD-TYPE | 11 | 76 | 68

Figure S53. Get High-res Image Gene #19: '10p' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10q' versus 'CN_CNMF'

P value = 6.87e-07 (Fisher's exact test), Q value = 2e-04

Table S54. Gene #20: '10q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
10Q MUTATED | 1 | 2 | 1 | 13
10Q WILD-TYPE | 32 | 66 | 36 | 21

Figure S54. Get High-res Image Gene #20: '10q' versus Molecular Subtype #1: 'CN_CNMF'

'10q' versus 'METHLYATION_CNMF'

P value = 2.4e-07 (Fisher's exact test), Q value = 7e-05

Table S55. Gene #20: '10q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
10Q MUTATED | 0 | 13 | 1
10Q WILD-TYPE | 43 | 30 | 69

Figure S55. Get High-res Image Gene #20: '10q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q' versus 'MRNASEQ_CNMF'

P value = 0.000451 (Fisher's exact test), Q value = 0.11

Table S56. Gene #20: '10q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
10Q MUTATED | 14 | 3 | 0 | 0
10Q WILD-TYPE | 44 | 46 | 31 | 23

Figure S56. Get High-res Image Gene #20: '10q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000372 (Fisher's exact test), Q value = 0.089

Table S57. Gene #20: '10q' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 80 | 74
10Q MUTATED | 7 | 3 | 7
10Q WILD-TYPE | 11 | 77 | 67

Figure S57. Get High-res Image Gene #20: '10q' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000635 (Fisher's exact test), Q value = 0.15

Table S58. Gene #20: '10q' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 14 | 87 | 71
10Q MUTATED | 6 | 4 | 7
10Q WILD-TYPE | 8 | 83 | 64

Figure S58. Get High-res Image Gene #20: '10q' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p' versus 'CN_CNMF'

P value = 2.72e-06 (Fisher's exact test), Q value = 0.00075

Table S59. Gene #21: '11p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
11P MUTATED | 0 | 6 | 0 | 12
11P WILD-TYPE | 33 | 62 | 37 | 22

Figure S59. Get High-res Image Gene #21: '11p' versus Molecular Subtype #1: 'CN_CNMF'

'11p' versus 'METHLYATION_CNMF'

P value = 8.58e-06 (Fisher's exact test), Q value = 0.0023

Table S60. Gene #21: '11p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
11P MUTATED | 1 | 13 | 2
11P WILD-TYPE | 42 | 30 | 68

Figure S60. Get High-res Image Gene #21: '11p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000324 (Fisher's exact test), Q value = 0.078

Table S61. Gene #21: '11p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
11P MUTATED | 9 | 7 | 1
11P WILD-TYPE | 22 | 59 | 63

Figure S61. Get High-res Image Gene #21: '11p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'11q' versus 'CN_CNMF'

P value = 3.45e-08 (Fisher's exact test), Q value = 1e-05

Table S62. Gene #22: '11q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
11Q MUTATED | 0 | 6 | 0 | 15
11Q WILD-TYPE | 33 | 62 | 37 | 19

Figure S62. Get High-res Image Gene #22: '11q' versus Molecular Subtype #1: 'CN_CNMF'

'11q' versus 'METHLYATION_CNMF'

P value = 4.06e-08 (Fisher's exact test), Q value = 1.2e-05

Table S63. Gene #22: '11q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
11Q MUTATED | 1 | 17 | 2
11Q WILD-TYPE | 42 | 26 | 68

Figure S63. Get High-res Image Gene #22: '11q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000532 (Fisher's exact test), Q value = 0.12

Table S64. Gene #22: '11q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
11Q MUTATED | 8 | 11 | 1
11Q WILD-TYPE | 23 | 55 | 63

Figure S64. Get High-res Image Gene #22: '11q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'12p' versus 'CN_CNMF'

P value = 0.000301 (Fisher's exact test), Q value = 0.073

Table S65. Gene #23: '12p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
12P MUTATED | 21 | 16 | 20 | 12
12P WILD-TYPE | 12 | 52 | 17 | 22

Figure S65. Get High-res Image Gene #23: '12p' versus Molecular Subtype #1: 'CN_CNMF'

'12q' versus 'CN_CNMF'

P value = 0.000236 (Fisher's exact test), Q value = 0.058

Table S66. Gene #24: '12q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
12Q MUTATED | 21 | 16 | 20 | 11
12Q WILD-TYPE | 12 | 52 | 17 | 23

Figure S66. Get High-res Image Gene #24: '12q' versus Molecular Subtype #1: 'CN_CNMF'

'13q' versus 'CN_CNMF'

P value = 5.57e-05 (Fisher's exact test), Q value = 0.014

Table S67. Gene #25: '13q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
13Q MUTATED | 7 | 10 | 2 | 17
13Q WILD-TYPE | 26 | 58 | 35 | 17

Figure S67. Get High-res Image Gene #25: '13q' versus Molecular Subtype #1: 'CN_CNMF'

'13q' versus 'METHLYATION_CNMF'

P value = 0.000199 (Fisher's exact test), Q value = 0.049

Table S68. Gene #25: '13q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
13Q MUTATED | 5 | 19 | 9
13Q WILD-TYPE | 38 | 24 | 61

Figure S68. Get High-res Image Gene #25: '13q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000755 (Fisher's exact test), Q value = 0.17

Table S69. Gene #25: '13q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
13Q MUTATED | 15 | 13 | 8
13Q WILD-TYPE | 16 | 53 | 56

Figure S69. Get High-res Image Gene #25: '13q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'14q' versus 'CN_CNMF'

P value = 2.82e-13 (Fisher's exact test), Q value = 8.9e-11

Table S70. Gene #26: '14q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
14Q MUTATED | 1 | 12 | 0 | 24
14Q WILD-TYPE | 32 | 56 | 37 | 10

Figure S70. Get High-res Image Gene #26: '14q' versus Molecular Subtype #1: 'CN_CNMF'

'14q' versus 'METHLYATION_CNMF'

P value = 0.000432 (Fisher's exact test), Q value = 0.1

Table S71. Gene #26: '14q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
14Q MUTATED | 10 | 17 | 6
14Q WILD-TYPE | 33 | 26 | 64

Figure S71. Get High-res Image Gene #26: '14q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q' versus 'MRNASEQ_CNMF'

P value = 5.95e-05 (Fisher's exact test), Q value = 0.015

Table S72. Gene #26: '14q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
14Q MUTATED | 23 | 2 | 6 | 3
14Q WILD-TYPE | 35 | 47 | 25 | 20

Figure S72. Get High-res Image Gene #26: '14q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'14q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.08e-08 (Fisher's exact test), Q value = 1.2e-05

Table S73. Gene #26: '14q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
14Q MUTATED | 18 | 13 | 3
14Q WILD-TYPE | 13 | 53 | 61

Figure S73. Get High-res Image Gene #26: '14q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'14q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000843 (Fisher's exact test), Q value = 0.19

Table S74. Gene #26: '14q' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 80 | 74
14Q MUTATED | 9 | 9 | 19
14Q WILD-TYPE | 9 | 71 | 55

Figure S74. Get High-res Image Gene #26: '14q' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'15q' versus 'CN_CNMF'

P value = 5.82e-07 (Fisher's exact test), Q value = 0.00017

Table S75. Gene #27: '15q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
15Q MUTATED | 1 | 8 | 0 | 15
15Q WILD-TYPE | 32 | 60 | 37 | 19

Figure S75. Get High-res Image Gene #27: '15q' versus Molecular Subtype #1: 'CN_CNMF'

'15q' versus 'METHLYATION_CNMF'

P value = 0.000618 (Fisher's exact test), Q value = 0.14

Table S76. Gene #27: '15q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
15Q MUTATED | 7 | 13 | 3
15Q WILD-TYPE | 36 | 30 | 67

Figure S76. Get High-res Image Gene #27: '15q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.31e-06 (Fisher's exact test), Q value = 0.00037

Table S77. Gene #27: '15q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
15Q MUTATED | 13 | 7 | 1
15Q WILD-TYPE | 18 | 59 | 63

Figure S77. Get High-res Image Gene #27: '15q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16p' versus 'CN_CNMF'

P value = 1.68e-09 (Fisher's exact test), Q value = 5.2e-07

Table S78. Gene #28: '16p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
16P MUTATED | 33 | 29 | 15 | 16
16P WILD-TYPE | 0 | 39 | 22 | 18

Figure S78. Get High-res Image Gene #28: '16p' versus Molecular Subtype #1: 'CN_CNMF'

'16q' versus 'CN_CNMF'

P value = 4.87e-10 (Fisher's exact test), Q value = 1.5e-07

Table S79. Gene #29: '16q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
16Q MUTATED | 33 | 29 | 14 | 14
16Q WILD-TYPE | 0 | 39 | 23 | 20

Figure S79. Get High-res Image Gene #29: '16q' versus Molecular Subtype #1: 'CN_CNMF'

'17p' versus 'CN_CNMF'

P value = 1.05e-14 (Fisher's exact test), Q value = 3.3e-12

Table S80. Gene #30: '17p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
17P MUTATED | 32 | 24 | 36 | 18
17P WILD-TYPE | 1 | 44 | 1 | 16

Figure S80. Get High-res Image Gene #30: '17p' versus Molecular Subtype #1: 'CN_CNMF'

'17p' versus 'METHLYATION_CNMF'

P value = 1.76e-05 (Fisher's exact test), Q value = 0.0046

Table S81. Gene #30: '17p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
17P MUTATED | 19 | 22 | 58
17P WILD-TYPE | 24 | 21 | 12

Figure S81. Get High-res Image Gene #30: '17p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p' versus 'MRNASEQ_CNMF'

P value = 9.26e-07 (Fisher's exact test), Q value = 0.00026

Table S82. Gene #30: '17p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
17P MUTATED | 23 | 44 | 19 | 15
17P WILD-TYPE | 35 | 5 | 12 | 8

Figure S82. Get High-res Image Gene #30: '17p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.28e-06 (Fisher's exact test), Q value = 0.0014

Table S83. Gene #30: '17p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
17P MUTATED | 12 | 35 | 54
17P WILD-TYPE | 19 | 31 | 10

Figure S83. Get High-res Image Gene #30: '17p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17q' versus 'CN_CNMF'

P value = 5.2e-12 (Fisher's exact test), Q value = 1.6e-09

Table S84. Gene #31: '17q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
17Q MUTATED | 32 | 29 | 36 | 20
17Q WILD-TYPE | 1 | 39 | 1 | 14

Figure S84. Get High-res Image Gene #31: '17q' versus Molecular Subtype #1: 'CN_CNMF'

'17q' versus 'MRNASEQ_CNMF'

P value = 9.37e-07 (Fisher's exact test), Q value = 0.00026

Table S85. Gene #31: '17q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
17Q MUTATED | 25 | 45 | 22 | 16
17Q WILD-TYPE | 33 | 4 | 9 | 7

Figure S85. Get High-res Image Gene #31: '17q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.09e-05 (Fisher's exact test), Q value = 0.0029

Table S86. Gene #31: '17q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
17Q MUTATED | 12 | 41 | 55
17Q WILD-TYPE | 19 | 25 | 9

Figure S86. Get High-res Image Gene #31: '17q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'18p' versus 'METHLYATION_CNMF'

P value = 1.54e-05 (Fisher's exact test), Q value = 0.0041

Table S87. Gene #32: '18p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
18P MUTATED | 4 | 20 | 8
18P WILD-TYPE | 39 | 23 | 62

Figure S87. Get High-res Image Gene #32: '18p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p' versus 'MRNASEQ_CNMF'

P value = 3.04e-05 (Fisher's exact test), Q value = 0.0078

Table S88. Gene #32: '18p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
18P MUTATED | 24 | 3 | 4 | 2
18P WILD-TYPE | 34 | 46 | 27 | 21

Figure S88. Get High-res Image Gene #32: '18p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'18q' versus 'METHLYATION_CNMF'

P value = 7.14e-06 (Fisher's exact test), Q value = 0.0019

Table S89. Gene #33: '18q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
18Q MUTATED | 4 | 20 | 7
18Q WILD-TYPE | 39 | 23 | 63

Figure S89. Get High-res Image Gene #33: '18q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q' versus 'MRNASEQ_CNMF'

P value = 1.97e-05 (Fisher's exact test), Q value = 0.0051

Table S90. Gene #33: '18q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
18Q MUTATED | 23 | 2 | 4 | 2
18Q WILD-TYPE | 35 | 47 | 27 | 21

Figure S90. Get High-res Image Gene #33: '18q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'18q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000811 (Fisher's exact test), Q value = 0.18

Table S91. Gene #33: '18q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
18Q MUTATED | 11 | 16 | 4
18Q WILD-TYPE | 20 | 50 | 60

Figure S91. Get High-res Image Gene #33: '18q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19p' versus 'CN_CNMF'

P value = 0.000225 (Fisher's exact test), Q value = 0.055

Table S92. Gene #34: '19p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
19P MUTATED | 1 | 2 | 2 | 10
19P WILD-TYPE | 32 | 66 | 35 | 24

Figure S92. Get High-res Image Gene #34: '19p' versus Molecular Subtype #1: 'CN_CNMF'

'19q' versus 'CN_CNMF'

P value = 4.27e-05 (Fisher's exact test), Q value = 0.011

Table S93. Gene #35: '19q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
19Q MUTATED | 1 | 1 | 2 | 10
19Q WILD-TYPE | 32 | 67 | 35 | 24

Figure S93. Get High-res Image Gene #35: '19q' versus Molecular Subtype #1: 'CN_CNMF'

'22q' versus 'CN_CNMF'

P value = 7.5e-07 (Fisher's exact test), Q value = 0.00021

Table S94. Gene #39: '22q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
22Q MUTATED | 1 | 16 | 5 | 20
22Q WILD-TYPE | 32 | 52 | 32 | 14

Figure S94. Get High-res Image Gene #39: '22q' versus Molecular Subtype #1: 'CN_CNMF'

'22q' versus 'METHLYATION_CNMF'

P value = 1.18e-07 (Fisher's exact test), Q value = 3.5e-05

Table S95. Gene #39: '22q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 43 | 43 | 70
22Q MUTATED | 5 | 25 | 9
22Q WILD-TYPE | 38 | 18 | 61

Figure S95. Get High-res Image Gene #39: '22q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q' versus 'MRNASEQ_CNMF'

P value = 1.29e-07 (Fisher's exact test), Q value = 3.8e-05

Table S96. Gene #39: '22q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 49 | 31 | 23
22Q MUTATED | 29 | 5 | 5 | 0
22Q WILD-TYPE | 29 | 44 | 26 | 23

Figure S96. Get High-res Image Gene #39: '22q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'22q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000958 (Fisher's exact test), Q value = 0.21

Table S97. Gene #39: '22q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 66 | 64
22Q MUTATED | 11 | 22 | 6
22Q WILD-TYPE | 20 | 44 | 58

Figure S97. Get High-res Image Gene #39: '22q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'22q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.61e-05 (Fisher's exact test), Q value = 0.0042

Table S98. Gene #39: '22q' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 80 | 74
22Q MUTATED | 13 | 13 | 16
22Q WILD-TYPE | 5 | 67 | 58

Figure S98. Get High-res Image Gene #39: '22q' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'xq' versus 'CN_CNMF'

P value = 1.18e-13 (Fisher's exact test), Q value = 3.7e-11

Table S99. Gene #40: 'xq' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 68 | 37 | 34
XQ MUTATED | 30 | 9 | 16 | 19
XQ WILD-TYPE | 3 | 59 | 21 | 15

Figure S99. Get High-res Image Gene #40: 'xq' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data
Input

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

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

- Number of patients = 172

- Number of significantly focal cnvs = 40

- Number of molecular subtypes = 8

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

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
Copyright © 2014 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle