Stomach Adenocarcinoma: Correlation between copy number variations of arm-level result and molecular subtypes
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and subtypes.

Summary

Testing the association between copy number variation 77 arm-level results and 6 molecular subtypes across 306 patients, 62 significant findings detected with Q value < 0.25.

- 1p gain cnv correlated to 'CN_CNMF'.

- 1q gain cnv correlated to 'CN_CNMF'.

- 2p gain cnv correlated to 'CN_CNMF'.

- 2q gain cnv correlated to 'CN_CNMF'.

- 5p gain cnv correlated to 'CN_CNMF'.

- 6p gain cnv correlated to 'CN_CNMF'.

- 6q gain cnv correlated to 'CN_CNMF'.

- 7p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 7q gain cnv correlated to 'CN_CNMF'.

- 8p gain cnv correlated to 'CN_CNMF'.

- 8q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 10p gain cnv correlated to 'CN_CNMF'.

- 10q gain cnv correlated to 'CN_CNMF'.

- 13q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 16p gain cnv correlated to 'CN_CNMF'.

- 20p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 20q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 1p loss cnv correlated to 'CN_CNMF'.

- 3p loss cnv correlated to 'CN_CNMF'.

- 3q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

- 4p loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

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

- 5p loss cnv correlated to 'CN_CNMF'.

- 5q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

- 7q loss cnv correlated to 'CN_CNMF'.

- 8p loss cnv correlated to 'CN_CNMF'.

- 9p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 9q loss cnv correlated to 'CN_CNMF'.

- 10p loss cnv correlated to 'CN_CNMF'.

- 10q loss cnv correlated to 'CN_CNMF'.

- 11p loss cnv correlated to 'CN_CNMF'.

- 11q loss cnv correlated to 'CN_CNMF'.

- 12p loss cnv correlated to 'CN_CNMF'.

- 13q loss cnv correlated to 'CN_CNMF'.

- 14q loss cnv correlated to 'CN_CNMF'.

- 15q loss cnv correlated to 'CN_CNMF'.

- 16p loss cnv correlated to 'CN_CNMF'.

- 16q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 17p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- 17q loss cnv correlated to 'CN_CNMF'.

- 18q loss cnv correlated to 'CN_CNMF'.

- 19p loss cnv correlated to 'CN_CNMF'.

- 19q loss cnv correlated to 'CN_CNMF'.

- 20p loss cnv correlated to 'CN_CNMF'.

- 21q loss cnv correlated to 'CN_CNMF'.

- 22q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 77 arm-level results and 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 62 significant findings detected.

|  | Molecular subtypes | CN CNMF | METHLYATION CNMF | MRNASEQ CNMF | MRNASEQ CHIERARCHICAL | MIRSEQ CNMF | MIRSEQ 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
4q loss | 47 (15%) | 259 | 1.17e-14 (4.94e-12) | 0.000173 (0.0653) | 0.664 (1.00) | 0.55 (1.00) | 0.00291 (0.991) | 1.56e-07 (6.32e-05)
17p loss | 58 (19%) | 248 | 3.45e-18 (1.47e-15) | 0.000157 (0.0597) | 0.281 (1.00) | 0.0973 (1.00) | 0.00285 (0.975) | 0.00067 (0.247)
22q loss | 39 (13%) | 267 | 9.26e-17 (3.93e-14) | 8.17e-06 (0.00327) | 0.664 (1.00) | 1 (1.00) | 0.000238 (0.0894) | 0.000908 (0.33)
7p gain | 89 (29%) | 217 | 1.21e-18 (5.19e-16) | 0.000148 (0.0564) | 1 (1.00) | 0.523 (1.00) | 0.00664 (1.00) | 0.0132 (1.00)
8q gain | 108 (35%) | 198 | 4.09e-05 (0.0158) | 1.52e-05 (0.00598) | 0.364 (1.00) | 0.779 (1.00) | 0.00768 (1.00) | 0.116 (1.00)
13q gain | 62 (20%) | 244 | 2.58e-08 (1.07e-05) | 0.000677 (0.249) | 0.721 (1.00) | 0.885 (1.00) | 0.399 (1.00) | 0.135 (1.00)
20p gain | 122 (40%) | 184 | 2.71e-19 (1.16e-16) | 7.9e-05 (0.0302) | 0.129 (1.00) | 0.0165 (1.00) | 0.17 (1.00) | 0.0174 (1.00)
20q gain | 149 (49%) | 157 | 2.59e-29 (1.11e-26) | 4.18e-08 (1.71e-05) | 0.227 (1.00) | 0.0227 (1.00) | 0.00809 (1.00) | 0.00118 (0.429)
3q loss | 15 (5%) | 291 | 9.73e-06 (0.00384) | 0.0174 (1.00) | 0.233 (1.00) |  | 0.000629 (0.234) | 0.0137 (1.00)
4p loss | 49 (16%) | 257 | 7.25e-11 (3.02e-08) | 0.000706 (0.259) | 0.457 (1.00) | 0.674 (1.00) | 0.00646 (1.00) | 2.88e-07 (0.000116)
5q loss | 34 (11%) | 272 | 2.59e-12 (1.09e-09) | 0.00166 (0.593) | 1 (1.00) | 1 (1.00) | 0.0289 (1.00) | 0.000219 (0.0822)
9p loss | 47 (15%) | 259 | 4.54e-17 (1.93e-14) | 0.000291 (0.109) | 0.698 (1.00) | 0.863 (1.00) | 0.00646 (1.00) | 0.00453 (1.00)
16q loss | 26 (8%) | 280 | 7.49e-10 (3.1e-07) | 0.000502 (0.187) | 1 (1.00) | 0.349 (1.00) | 0.0386 (1.00) | 0.215 (1.00)
1p gain | 15 (5%) | 291 | 3.44e-05 (0.0134) | 0.924 (1.00) | 1 (1.00) | 0.643 (1.00) | 0.627 (1.00) | 0.926 (1.00)
1q gain | 41 (13%) | 265 | 2.96e-11 (1.24e-08) | 0.00499 (1.00) | 1 (1.00) | 0.73 (1.00) | 0.00209 (0.732) | 0.0318 (1.00)
2p gain | 21 (7%) | 285 | 4.42e-06 (0.00177) | 0.00225 (0.782) | 0.488 (1.00) |  | 0.23 (1.00) | 0.00766 (1.00)
2q gain | 22 (7%) | 284 | 6.4e-05 (0.0246) | 0.00225 (0.782) | 0.233 (1.00) | 0.268 (1.00) | 0.436 (1.00) | 0.067 (1.00)
5p gain | 36 (12%) | 270 | 8.5e-08 (3.47e-05) | 0.0208 (1.00) | 0.281 (1.00) | 0.464 (1.00) | 0.106 (1.00) | 0.117 (1.00)
6p gain | 23 (8%) | 283 | 1.57e-05 (0.00619) | 0.0041 (1.00) | 1 (1.00) | 1 (1.00) | 0.00644 (1.00) | 0.257 (1.00)
6q gain | 20 (7%) | 286 | 5.05e-05 (0.0194) | 0.00235 (0.813) | 1 (1.00) | 1 (1.00) | 0.0159 (1.00) | 0.139 (1.00)
7q gain | 72 (24%) | 234 | 1.59e-16 (6.72e-14) | 0.00384 (1.00) | 1 (1.00) | 1 (1.00) | 0.0156 (1.00) | 0.226 (1.00)
8p gain | 81 (26%) | 225 | 4.12e-05 (0.0159) | 0.00238 (0.821) | 0.543 (1.00) | 0.84 (1.00) | 0.0121 (1.00) | 0.657 (1.00)
10p gain | 42 (14%) | 264 | 3.14e-10 (1.3e-07) | 0.0017 (0.604) | 0.412 (1.00) | 0.557 (1.00) | 0.723 (1.00) | 0.0594 (1.00)
10q gain | 25 (8%) | 281 | 8.66e-06 (0.00344) | 0.0622 (1.00) | 0.607 (1.00) | 0.643 (1.00) | 0.316 (1.00) | 0.692 (1.00)
16p gain | 14 (5%) | 292 | 0.000637 (0.236) | 0.0569 (1.00) | 0.607 (1.00) | 0.643 (1.00) | 0.618 (1.00) | 0.251 (1.00)
1p loss | 14 (5%) | 292 | 4.12e-06 (0.00166) | 0.543 (1.00) | 0.488 (1.00) |  | 0.131 (1.00) | 1 (1.00)
3p loss | 26 (8%) | 280 | 4.42e-08 (1.81e-05) | 0.00759 (1.00) | 0.233 (1.00) |  | 0.00362 (1.00) | 0.0155 (1.00)
5p loss | 15 (5%) | 291 | 1.67e-05 (0.00654) | 0.0979 (1.00) | 0.488 (1.00) |  | 0.848 (1.00) | 0.199 (1.00)
7q loss | 12 (4%) | 294 | 2.9e-05 (0.0113) | 0.0674 (1.00) | 0.233 (1.00) |  | 0.0179 (1.00) | 0.0179 (1.00)
8p loss | 27 (9%) | 279 | 1.19e-06 (0.000481) | 0.121 (1.00) | 0.664 (1.00) | 0.73 (1.00) | 0.0142 (1.00) | 0.0301 (1.00)
9q loss | 25 (8%) | 281 | 3.15e-08 (1.3e-05) | 0.00141 (0.506) | 1 (1.00) |  | 0.163 (1.00) | 0.0301 (1.00)
10p loss | 17 (6%) | 289 | 0.000108 (0.0412) | 0.0103 (1.00) | 1 (1.00) | 0.203 (1.00) | 0.343 (1.00) | 0.337 (1.00)
10q loss | 17 (6%) | 289 | 8.39e-06 (0.00335) | 0.00576 (1.00) | 0.345 (1.00) | 0.481 (1.00) | 0.24 (1.00) | 0.209 (1.00)
11p loss | 19 (6%) | 287 | 1.63e-05 (0.00638) | 0.00172 (0.611) | 1 (1.00) | 0.0974 (1.00) | 0.059 (1.00) | 0.106 (1.00)
11q loss | 17 (6%) | 289 | 9.49e-06 (0.00376) | 0.00503 (1.00) | 1 (1.00) | 0.387 (1.00) | 0.0689 (1.00) | 0.32 (1.00)
12p loss | 19 (6%) | 287 | 0.00014 (0.0534) | 0.00784 (1.00) | 0.108 (1.00) | 0.0284 (1.00) | 0.24 (1.00) | 0.0907 (1.00)
13q loss | 9 (3%) | 297 | 0.000419 (0.156) | 0.225 (1.00) | 0.488 (1.00) |  | 0.389 (1.00) | 0.486 (1.00)
14q loss | 25 (8%) | 281 | 8.66e-06 (0.00344) | 0.0622 (1.00) | 0.345 (1.00) | 0.481 (1.00) | 0.0535 (1.00) | 0.0677 (1.00)
15q loss | 22 (7%) | 284 | 1.09e-07 (4.42e-05) | 0.00666 (1.00) | 0.607 (1.00) | 0.745 (1.00) | 0.571 (1.00) | 0.114 (1.00)
16p loss | 24 (8%) | 282 | 1.01e-10 (4.18e-08) | 0.00734 (1.00) | 1 (1.00) | 1 (1.00) | 0.115 (1.00) | 0.32 (1.00)
17q loss | 19 (6%) | 287 | 2.17e-05 (0.00845) | 0.323 (1.00) | 0.664 (1.00) | 1 (1.00) | 0.0491 (1.00) | 0.00713 (1.00)
18q loss | 51 (17%) | 255 | 1.13e-07 (4.6e-05) | 0.0306 (1.00) | 0.736 (1.00) | 1 (1.00) | 0.127 (1.00) | 0.187 (1.00)
19p loss | 30 (10%) | 276 | 1.87e-12 (7.88e-10) | 0.0122 (1.00) | 0.0089 (1.00) | 0.0106 (1.00) | 0.219 (1.00) | 0.00203 (0.711)
19q loss | 21 (7%) | 285 | 3.32e-08 (1.37e-05) | 0.00548 (1.00) | 0.0211 (1.00) | 0.0358 (1.00) | 0.101 (1.00) | 0.00326 (1.00)
20p loss | 10 (3%) | 296 | 0.000171 (0.0645) | 0.00222 (0.776) | 0.488 (1.00) |  | 0.374 (1.00) | 1 (1.00)
21q loss | 53 (17%) | 253 | 1.73e-11 (7.25e-09) | 0.0209 (1.00) | 0.281 (1.00) | 0.0973 (1.00) | 0.00354 (1.00) | 0.452 (1.00)
3p gain | 9 (3%) | 297 | 0.433 (1.00) | 0.225 (1.00) | 0.488 (1.00) |  | 0.365 (1.00) | 0.577 (1.00)
3q gain | 26 (8%) | 280 | 0.00134 (0.482) | 0.256 (1.00) | 0.0211 (1.00) | 0.117 (1.00) | 0.453 (1.00) | 0.149 (1.00)
4p gain | 5 (2%) | 301 | 0.0396 (1.00) | 0.286 (1.00) | 1 (1.00) |  | 0.837 (1.00) | 0.689 (1.00)
5q gain | 9 (3%) | 297 | 0.00202 (0.71) | 1 (1.00) | 0.108 (1.00) | 0.101 (1.00) | 0.2 (1.00) | 0.535 (1.00)
9p gain | 20 (7%) | 286 | 0.14 (1.00) | 0.493 (1.00) | 0.345 (1.00) | 0.481 (1.00) | 0.94 (1.00) | 0.359 (1.00)
9q gain | 25 (8%) | 281 | 0.0146 (1.00) | 0.471 (1.00) | 0.185 (1.00) | 0.219 (1.00) | 0.74 (1.00) | 0.638 (1.00)
11p gain | 11 (4%) | 295 | 0.511 (1.00) | 0.112 (1.00) | 1 (1.00) |  | 0.7 (1.00) | 0.548 (1.00)
11q gain | 18 (6%) | 288 | 0.101 (1.00) | 0.03 (1.00) | 0.488 (1.00) |  | 0.266 (1.00) | 0.822 (1.00)
12p gain | 30 (10%) | 276 | 0.00259 (0.891) | 0.0664 (1.00) | 0.233 (1.00) | 0.268 (1.00) | 0.108 (1.00) | 0.759 (1.00)
12q gain | 23 (8%) | 283 | 0.296 (1.00) | 0.279 (1.00) | 0.108 (1.00) | 0.279 (1.00) | 0.24 (1.00) | 0.359 (1.00)
14q gain | 4 (1%) | 302 | 0.0834 (1.00) | 0.776 (1.00) | 1 (1.00) |  |  |
15q gain | 10 (3%) | 296 | 0.0159 (1.00) | 0.274 (1.00) |  |  | 0.7 (1.00) | 0.0527 (1.00)
16q gain | 11 (4%) | 295 | 0.00147 (0.526) | 0.87 (1.00) | 0.607 (1.00) | 0.643 (1.00) | 0.848 (1.00) | 0.123 (1.00)
17p gain | 7 (2%) | 299 | 0.0109 (1.00) | 0.803 (1.00) | 1 (1.00) |  | 0.346 (1.00) | 1 (1.00)
17q gain | 13 (4%) | 293 | 0.00272 (0.934) | 0.976 (1.00) | 1 (1.00) |  | 0.0906 (1.00) | 0.792 (1.00)
18p gain | 21 (7%) | 285 | 0.00376 (1.00) | 0.000849 (0.31) | 0.664 (1.00) | 0.84 (1.00) | 0.0303 (1.00) | 0.777 (1.00)
18q gain | 13 (4%) | 293 | 0.0558 (1.00) | 0.0934 (1.00) | 0.607 (1.00) | 1 (1.00) | 0.0701 (1.00) | 0.132 (1.00)
19p gain | 12 (4%) | 294 | 0.362 (1.00) | 0.0797 (1.00) | 0.345 (1.00) | 0.356 (1.00) | 0.066 (1.00) | 0.264 (1.00)
19q gain | 28 (9%) | 278 | 0.0159 (1.00) | 0.1 (1.00) | 0.412 (1.00) | 0.23 (1.00) | 0.592 (1.00) | 0.453 (1.00)
22q gain | 6 (2%) | 300 | 0.0199 (1.00) | 0.19 (1.00) |  |  | 0.453 (1.00) | 0.369 (1.00)
Xq gain | 4 (1%) | 302 | 0.0834 (1.00) | 0.123 (1.00) | 1 (1.00) |  |  |
1q loss | 4 (1%) | 302 | 0.0573 (1.00) | 0.75 (1.00) |  |  | 0.227 (1.00) | 0.689 (1.00)
2p loss | 4 (1%) | 302 | 0.0573 (1.00) | 0.542 (1.00) | 1 (1.00) |  | 1 (1.00) | 0.173 (1.00)
2q loss | 5 (2%) | 301 | 0.0272 (1.00) | 0.223 (1.00) | 1 (1.00) |  | 1 (1.00) | 0.087 (1.00)
6p loss | 14 (5%) | 292 | 0.00607 (1.00) | 0.552 (1.00) | 0.488 (1.00) |  | 0.191 (1.00) | 0.254 (1.00)
6q loss | 18 (6%) | 288 | 0.00198 (0.699) | 0.272 (1.00) | 0.607 (1.00) | 0.0105 (1.00) | 0.431 (1.00) | 0.405 (1.00)
7p loss | 5 (2%) | 301 | 0.0272 (1.00) | 0.861 (1.00) | 0.233 (1.00) |  | 0.453 (1.00) | 0.283 (1.00)
8q loss | 8 (3%) | 298 | 0.0013 (0.469) | 0.337 (1.00) | 1 (1.00) |  | 0.513 (1.00) | 0.0559 (1.00)
12q loss | 11 (4%) | 295 | 0.00593 (1.00) | 0.00147 (0.525) | 0.233 (1.00) |  | 0.374 (1.00) | 0.0561 (1.00)
18p loss | 36 (12%) | 270 | 0.000781 (0.286) | 0.102 (1.00) | 0.698 (1.00) | 0.863 (1.00) | 0.219 (1.00) | 0.126 (1.00)
Xq loss | 13 (4%) | 293 | 0.00107 (0.388) | 0.0516 (1.00) | 0.607 (1.00) | 0.745 (1.00) | 0.257 (1.00) | 0.383 (1.00)

'1p gain mutation analysis' versus 'CN_CNMF'

P value = 3.44e-05 (Fisher's exact test), Q value = 0.013

Table S1. Gene #1: '1p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
1P GAIN MUTATED | 0 | 11 | 4
1P GAIN WILD-TYPE | 153 | 107 | 31

Figure S1. Get High-res Image Gene #1: '1p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'1q gain mutation analysis' versus 'CN_CNMF'

P value = 2.96e-11 (Fisher's exact test), Q value = 1.2e-08

Table S2. Gene #2: '1q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
1Q GAIN MUTATED | 2 | 27 | 12
1Q GAIN WILD-TYPE | 151 | 91 | 23

Figure S2. Get High-res Image Gene #2: '1q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'2p gain mutation analysis' versus 'CN_CNMF'

P value = 4.42e-06 (Fisher's exact test), Q value = 0.0018

Table S3. Gene #3: '2p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
2P GAIN MUTATED | 1 | 13 | 7
2P GAIN WILD-TYPE | 152 | 105 | 28

Figure S3. Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'2q gain mutation analysis' versus 'CN_CNMF'

P value = 6.4e-05 (Fisher's exact test), Q value = 0.025

Table S4. Gene #4: '2q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
2Q GAIN MUTATED | 2 | 14 | 6
2Q GAIN WILD-TYPE | 151 | 104 | 29

Figure S4. Get High-res Image Gene #4: '2q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'5p gain mutation analysis' versus 'CN_CNMF'

P value = 8.5e-08 (Fisher's exact test), Q value = 3.5e-05

Table S5. Gene #8: '5p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
5P GAIN MUTATED | 4 | 29 | 3
5P GAIN WILD-TYPE | 149 | 89 | 32

Figure S5. Get High-res Image Gene #8: '5p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'6p gain mutation analysis' versus 'CN_CNMF'

P value = 1.57e-05 (Fisher's exact test), Q value = 0.0062

Table S6. Gene #10: '6p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
6P GAIN MUTATED | 2 | 19 | 2
6P GAIN WILD-TYPE | 151 | 99 | 33

Figure S6. Get High-res Image Gene #10: '6p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'6q gain mutation analysis' versus 'CN_CNMF'

P value = 5.05e-05 (Fisher's exact test), Q value = 0.019

Table S7. Gene #11: '6q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
6Q GAIN MUTATED | 2 | 17 | 1
6Q GAIN WILD-TYPE | 151 | 101 | 34

Figure S7. Get High-res Image Gene #11: '6q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'7p gain mutation analysis' versus 'CN_CNMF'

P value = 1.21e-18 (Fisher's exact test), Q value = 5.2e-16

Table S8. Gene #12: '7p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
7P GAIN MUTATED | 13 | 49 | 27
7P GAIN WILD-TYPE | 140 | 69 | 8

Figure S8. Get High-res Image Gene #12: '7p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'7p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000148 (Fisher's exact test), Q value = 0.056

Table S9. Gene #12: '7p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
7P GAIN MUTATED | 8 | 24 | 7 | 34
7P GAIN WILD-TYPE | 29 | 55 | 57 | 44

Figure S9. Get High-res Image Gene #12: '7p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'7q gain mutation analysis' versus 'CN_CNMF'

P value = 1.59e-16 (Fisher's exact test), Q value = 6.7e-14

Table S10. Gene #13: '7q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
7Q GAIN MUTATED | 12 | 33 | 27
7Q GAIN WILD-TYPE | 141 | 85 | 8

Figure S10. Get High-res Image Gene #13: '7q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'8p gain mutation analysis' versus 'CN_CNMF'

P value = 4.12e-05 (Fisher's exact test), Q value = 0.016

Table S11. Gene #14: '8p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
8P GAIN MUTATED | 33 | 27 | 21
8P GAIN WILD-TYPE | 120 | 91 | 14

Figure S11. Get High-res Image Gene #14: '8p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'8q gain mutation analysis' versus 'CN_CNMF'

P value = 4.09e-05 (Fisher's exact test), Q value = 0.016

Table S12. Gene #15: '8q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
8Q GAIN MUTATED | 37 | 50 | 21
8Q GAIN WILD-TYPE | 116 | 68 | 14

Figure S12. Get High-res Image Gene #15: '8q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'8q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.52e-05 (Fisher's exact test), Q value = 0.006

Table S13. Gene #15: '8q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
8Q GAIN MUTATED | 12 | 30 | 6 | 35
8Q GAIN WILD-TYPE | 25 | 49 | 58 | 43

Figure S13. Get High-res Image Gene #15: '8q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'10p gain mutation analysis' versus 'CN_CNMF'

P value = 3.14e-10 (Fisher's exact test), Q value = 1.3e-07

Table S14. Gene #18: '10p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
10P GAIN MUTATED | 3 | 33 | 6
10P GAIN WILD-TYPE | 150 | 85 | 29

Figure S14. Get High-res Image Gene #18: '10p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'10q gain mutation analysis' versus 'CN_CNMF'

P value = 8.66e-06 (Fisher's exact test), Q value = 0.0034

Table S15. Gene #19: '10q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
10Q GAIN MUTATED | 3 | 21 | 1
10Q GAIN WILD-TYPE | 150 | 97 | 34

Figure S15. Get High-res Image Gene #19: '10q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'13q gain mutation analysis' versus 'CN_CNMF'

P value = 2.58e-08 (Fisher's exact test), Q value = 1.1e-05

Table S16. Gene #24: '13q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
13Q GAIN MUTATED | 12 | 34 | 16
13Q GAIN WILD-TYPE | 141 | 84 | 19

Figure S16. Get High-res Image Gene #24: '13q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'13q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000677 (Fisher's exact test), Q value = 0.25

Table S17. Gene #24: '13q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
13Q GAIN MUTATED | 5 | 15 | 5 | 27
13Q GAIN WILD-TYPE | 32 | 64 | 59 | 51

Figure S17. Get High-res Image Gene #24: '13q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'16p gain mutation analysis' versus 'CN_CNMF'

P value = 0.000637 (Fisher's exact test), Q value = 0.24

Table S18. Gene #27: '16p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
16P GAIN MUTATED | 1 | 12 | 1
16P GAIN WILD-TYPE | 152 | 106 | 34

Figure S18. Get High-res Image Gene #27: '16p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'20p gain mutation analysis' versus 'CN_CNMF'

P value = 2.71e-19 (Fisher's exact test), Q value = 1.2e-16

Table S19. Gene #35: '20p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
20P GAIN MUTATED | 25 | 67 | 30
20P GAIN WILD-TYPE | 128 | 51 | 5

Figure S19. Get High-res Image Gene #35: '20p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'20p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.9e-05 (Fisher's exact test), Q value = 0.03

Table S20. Gene #35: '20p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
20P GAIN MUTATED | 18 | 29 | 11 | 41
20P GAIN WILD-TYPE | 19 | 50 | 53 | 37

Figure S20. Get High-res Image Gene #35: '20p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'20q gain mutation analysis' versus 'CN_CNMF'

P value = 2.59e-29 (Fisher's exact test), Q value = 1.1e-26

Table S21. Gene #36: '20q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
20Q GAIN MUTATED | 27 | 90 | 32
20Q GAIN WILD-TYPE | 126 | 28 | 3

Figure S21. Get High-res Image Gene #36: '20q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'20q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.18e-08 (Fisher's exact test), Q value = 1.7e-05

Table S22. Gene #36: '20q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
20Q GAIN MUTATED | 19 | 38 | 13 | 55
20Q GAIN WILD-TYPE | 18 | 41 | 51 | 23

Figure S22. Get High-res Image Gene #36: '20q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'1p loss mutation analysis' versus 'CN_CNMF'

P value = 4.12e-06 (Fisher's exact test), Q value = 0.0017

Table S23. Gene #39: '1p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
1P LOSS MUTATED | 0 | 14 | 0
1P LOSS WILD-TYPE | 153 | 104 | 35

Figure S23. Get High-res Image Gene #39: '1p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'3p loss mutation analysis' versus 'CN_CNMF'

P value = 4.42e-08 (Fisher's exact test), Q value = 1.8e-05

Table S24. Gene #43: '3p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
3P LOSS MUTATED | 1 | 23 | 2
3P LOSS WILD-TYPE | 152 | 95 | 33

Figure S24. Get High-res Image Gene #43: '3p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'3q loss mutation analysis' versus 'CN_CNMF'

P value = 9.73e-06 (Fisher's exact test), Q value = 0.0038

Table S25. Gene #44: '3q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
3Q LOSS MUTATED | 0 | 14 | 1
3Q LOSS WILD-TYPE | 153 | 104 | 34

Figure S25. Get High-res Image Gene #44: '3q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'3q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000629 (Fisher's exact test), Q value = 0.23

Table S26. Gene #44: '3q loss mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 89 | 55 | 92
3Q LOSS MUTATED | 0 | 0 | 9
3Q LOSS WILD-TYPE | 89 | 55 | 83

Figure S26. Get High-res Image Gene #44: '3q loss mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

'4p loss mutation analysis' versus 'CN_CNMF'

P value = 7.25e-11 (Fisher's exact test), Q value = 3e-08

Table S27. Gene #45: '4p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
4P LOSS MUTATED | 5 | 39 | 5
4P LOSS WILD-TYPE | 148 | 79 | 30

Figure S27. Get High-res Image Gene #45: '4p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'4p loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.88e-07 (Fisher's exact test), Q value = 0.00012

Table S28. Gene #45: '4p loss mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 59 | 104 | 73
4P LOSS MUTATED | 23 | 8 | 5
4P LOSS WILD-TYPE | 36 | 96 | 68

Figure S28. Get High-res Image Gene #45: '4p loss mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'4q loss mutation analysis' versus 'CN_CNMF'

P value = 1.17e-14 (Fisher's exact test), Q value = 4.9e-12

Table S29. Gene #46: '4q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
4Q LOSS MUTATED | 2 | 41 | 4
4Q LOSS WILD-TYPE | 151 | 77 | 31

Figure S29. Get High-res Image Gene #46: '4q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'4q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000173 (Fisher's exact test), Q value = 0.065

Table S30. Gene #46: '4q loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
4Q LOSS MUTATED | 0 | 14 | 6 | 22
4Q LOSS WILD-TYPE | 37 | 65 | 58 | 56

Figure S30. Get High-res Image Gene #46: '4q loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'4q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.56e-07 (Fisher's exact test), Q value = 6.3e-05

Table S31. Gene #46: '4q loss mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 59 | 104 | 73
4Q LOSS MUTATED | 22 | 7 | 4
4Q LOSS WILD-TYPE | 37 | 97 | 69

Figure S31. Get High-res Image Gene #46: '4q loss mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'5p loss mutation analysis' versus 'CN_CNMF'

P value = 1.67e-05 (Fisher's exact test), Q value = 0.0065

Table S32. Gene #47: '5p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
5P LOSS MUTATED | 0 | 13 | 2
5P LOSS WILD-TYPE | 153 | 105 | 33

Figure S32. Get High-res Image Gene #47: '5p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'5q loss mutation analysis' versus 'CN_CNMF'

P value = 2.59e-12 (Fisher's exact test), Q value = 1.1e-09

Table S33. Gene #48: '5q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
5Q LOSS MUTATED | 0 | 30 | 4
5Q LOSS WILD-TYPE | 153 | 88 | 31

Figure S33. Get High-res Image Gene #48: '5q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'5q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000219 (Fisher's exact test), Q value = 0.082

Table S34. Gene #48: '5q loss mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 59 | 104 | 73
5Q LOSS MUTATED | 14 | 7 | 2
5Q LOSS WILD-TYPE | 45 | 97 | 71

Figure S34. Get High-res Image Gene #48: '5q loss mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'7q loss mutation analysis' versus 'CN_CNMF'

P value = 2.9e-05 (Fisher's exact test), Q value = 0.011

Table S35. Gene #52: '7q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
7Q LOSS MUTATED | 0 | 12 | 0
7Q LOSS WILD-TYPE | 153 | 106 | 35

Figure S35. Get High-res Image Gene #52: '7q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'8p loss mutation analysis' versus 'CN_CNMF'

P value = 1.19e-06 (Fisher's exact test), Q value = 0.00048

Table S36. Gene #53: '8p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
8P LOSS MUTATED | 3 | 23 | 1
8P LOSS WILD-TYPE | 150 | 95 | 34

Figure S36. Get High-res Image Gene #53: '8p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'9p loss mutation analysis' versus 'CN_CNMF'

P value = 4.54e-17 (Fisher's exact test), Q value = 1.9e-14

Table S37. Gene #55: '9p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
9P LOSS MUTATED | 2 | 44 | 1
9P LOSS WILD-TYPE | 151 | 74 | 34

Figure S37. Get High-res Image Gene #55: '9p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'9p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000291 (Fisher's exact test), Q value = 0.11

Table S38. Gene #55: '9p loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
9P LOSS MUTATED | 1 | 11 | 5 | 23
9P LOSS WILD-TYPE | 36 | 68 | 59 | 55

Figure S38. Get High-res Image Gene #55: '9p loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'9q loss mutation analysis' versus 'CN_CNMF'

P value = 3.15e-08 (Fisher's exact test), Q value = 1.3e-05

Table S39. Gene #56: '9q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
9Q LOSS MUTATED | 1 | 23 | 1
9Q LOSS WILD-TYPE | 152 | 95 | 34

Figure S39. Get High-res Image Gene #56: '9q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'10p loss mutation analysis' versus 'CN_CNMF'

P value = 0.000108 (Fisher's exact test), Q value = 0.041

Table S40. Gene #57: '10p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
10P LOSS MUTATED | 1 | 14 | 2
10P LOSS WILD-TYPE | 152 | 104 | 33

Figure S40. Get High-res Image Gene #57: '10p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'10q loss mutation analysis' versus 'CN_CNMF'

P value = 8.39e-06 (Fisher's exact test), Q value = 0.0033

Table S41. Gene #58: '10q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
10Q LOSS MUTATED | 0 | 14 | 3
10Q LOSS WILD-TYPE | 153 | 104 | 32

Figure S41. Get High-res Image Gene #58: '10q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'11p loss mutation analysis' versus 'CN_CNMF'

P value = 1.63e-05 (Fisher's exact test), Q value = 0.0064

Table S42. Gene #59: '11p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
11P LOSS MUTATED | 2 | 17 | 0
11P LOSS WILD-TYPE | 151 | 101 | 35

Figure S42. Get High-res Image Gene #59: '11p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'11q loss mutation analysis' versus 'CN_CNMF'

P value = 9.49e-06 (Fisher's exact test), Q value = 0.0038

Table S43. Gene #60: '11q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
11Q LOSS MUTATED | 1 | 16 | 0
11Q LOSS WILD-TYPE | 152 | 102 | 35

Figure S43. Get High-res Image Gene #60: '11q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'12p loss mutation analysis' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.053

Table S44. Gene #61: '12p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
12P LOSS MUTATED | 2 | 16 | 1
12P LOSS WILD-TYPE | 151 | 102 | 34

Figure S44. Get High-res Image Gene #61: '12p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'13q loss mutation analysis' versus 'CN_CNMF'

P value = 0.000419 (Fisher's exact test), Q value = 0.16

Table S45. Gene #63: '13q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
13Q LOSS MUTATED | 0 | 9 | 0
13Q LOSS WILD-TYPE | 153 | 109 | 35

Figure S45. Get High-res Image Gene #63: '13q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'14q loss mutation analysis' versus 'CN_CNMF'

P value = 8.66e-06 (Fisher's exact test), Q value = 0.0034

Table S46. Gene #64: '14q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
14Q LOSS MUTATED | 3 | 21 | 1
14Q LOSS WILD-TYPE | 150 | 97 | 34

Figure S46. Get High-res Image Gene #64: '14q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'15q loss mutation analysis' versus 'CN_CNMF'

P value = 1.09e-07 (Fisher's exact test), Q value = 4.4e-05

Table S47. Gene #65: '15q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
15Q LOSS MUTATED | 0 | 19 | 3
15Q LOSS WILD-TYPE | 153 | 99 | 32

Figure S47. Get High-res Image Gene #65: '15q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'16p loss mutation analysis' versus 'CN_CNMF'

P value = 1.01e-10 (Fisher's exact test), Q value = 4.2e-08

Table S48. Gene #66: '16p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
16P LOSS MUTATED | 0 | 24 | 0
16P LOSS WILD-TYPE | 153 | 94 | 35

Figure S48. Get High-res Image Gene #66: '16p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'16q loss mutation analysis' versus 'CN_CNMF'

P value = 7.49e-10 (Fisher's exact test), Q value = 3.1e-07

Table S49. Gene #67: '16q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
16Q LOSS MUTATED | 1 | 25 | 0
16Q LOSS WILD-TYPE | 152 | 93 | 35

Figure S49. Get High-res Image Gene #67: '16q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'16q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000502 (Fisher's exact test), Q value = 0.19

Table S50. Gene #67: '16q loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
16Q LOSS MUTATED | 0 | 5 | 1 | 14
16Q LOSS WILD-TYPE | 37 | 74 | 63 | 64

Figure S50. Get High-res Image Gene #67: '16q loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'17p loss mutation analysis' versus 'CN_CNMF'

P value = 3.45e-18 (Fisher's exact test), Q value = 1.5e-15

Table S51. Gene #68: '17p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
17P LOSS MUTATED | 2 | 49 | 7
17P LOSS WILD-TYPE | 151 | 69 | 28

Figure S51. Get High-res Image Gene #68: '17p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'17p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000157 (Fisher's exact test), Q value = 0.06

Table S52. Gene #68: '17p loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
17P LOSS MUTATED | 3 | 13 | 5 | 27
17P LOSS WILD-TYPE | 34 | 66 | 59 | 51

Figure S52. Get High-res Image Gene #68: '17p loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'17p loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00067 (Fisher's exact test), Q value = 0.25

Table S53. Gene #68: '17p loss mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 59 | 104 | 73
17P LOSS MUTATED | 21 | 16 | 7
17P LOSS WILD-TYPE | 38 | 88 | 66

Figure S53. Get High-res Image Gene #68: '17p loss mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'17q loss mutation analysis' versus 'CN_CNMF'

P value = 2.17e-05 (Fisher's exact test), Q value = 0.0084

Table S54. Gene #69: '17q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
17Q LOSS MUTATED | 1 | 16 | 2
17Q LOSS WILD-TYPE | 152 | 102 | 33

Figure S54. Get High-res Image Gene #69: '17q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'18q loss mutation analysis' versus 'CN_CNMF'

P value = 1.13e-07 (Fisher's exact test), Q value = 4.6e-05

Table S55. Gene #71: '18q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
18Q LOSS MUTATED | 9 | 37 | 5
18Q LOSS WILD-TYPE | 144 | 81 | 30

Figure S55. Get High-res Image Gene #71: '18q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'19p loss mutation analysis' versus 'CN_CNMF'

P value = 1.87e-12 (Fisher's exact test), Q value = 7.9e-10

Table S56. Gene #72: '19p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
19P LOSS MUTATED | 0 | 29 | 1
19P LOSS WILD-TYPE | 153 | 89 | 34

Figure S56. Get High-res Image Gene #72: '19p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'19q loss mutation analysis' versus 'CN_CNMF'

P value = 3.32e-08 (Fisher's exact test), Q value = 1.4e-05

Table S57. Gene #73: '19q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
19Q LOSS MUTATED | 0 | 20 | 1
19Q LOSS WILD-TYPE | 153 | 98 | 34

Figure S57. Get High-res Image Gene #73: '19q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'20p loss mutation analysis' versus 'CN_CNMF'

P value = 0.000171 (Fisher's exact test), Q value = 0.064

Table S58. Gene #74: '20p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
20P LOSS MUTATED | 0 | 10 | 0
20P LOSS WILD-TYPE | 153 | 108 | 35

Figure S58. Get High-res Image Gene #74: '20p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'21q loss mutation analysis' versus 'CN_CNMF'

P value = 1.73e-11 (Fisher's exact test), Q value = 7.2e-09

Table S59. Gene #75: '21q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
21Q LOSS MUTATED | 5 | 40 | 8
21Q LOSS WILD-TYPE | 148 | 78 | 27

Figure S59. Get High-res Image Gene #75: '21q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'22q loss mutation analysis' versus 'CN_CNMF'

P value = 9.26e-17 (Fisher's exact test), Q value = 3.9e-14

Table S60. Gene #76: '22q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
22Q LOSS MUTATED | 0 | 38 | 1
22Q LOSS WILD-TYPE | 153 | 80 | 34

Figure S60. Get High-res Image Gene #76: '22q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'22q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.17e-06 (Fisher's exact test), Q value = 0.0033

Table S61. Gene #76: '22q loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
22Q LOSS MUTATED | 0 | 9 | 2 | 21
22Q LOSS WILD-TYPE | 37 | 70 | 62 | 57

Figure S61. Get High-res Image Gene #76: '22q loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'22q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000238 (Fisher's exact test), Q value = 0.089

Table S62. Gene #76: '22q loss mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 89 | 55 | 92
22Q LOSS MUTATED | 11 | 0 | 19
22Q LOSS WILD-TYPE | 78 | 55 | 73

Figure S62. Get High-res Image Gene #76: '22q loss mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

Methods & Data
Input

- Mutation data file = broad_values_by_arm.mutsig.cluster.txt

- Molecular subtypes file = STAD-TP.transferedmergedcluster.txt

- Number of patients = 306

- Number of significantly arm-level cnvs = 77

- Number of molecular subtypes = 6

- Exclude genes that fewer than K tumors have mutations, 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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

- 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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