Correlation between copy number variations of arm-level result and molecular subtypes
Kidney Chromophobe (Primary solid tumor)
17 October 2014 | analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1M61J4H
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 variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1M61J4H
Overview
Introduction

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

Summary

Testing the association between copy number variation 61 arm-level events and 8 molecular subtypes across 66 patients, 55 significant findings detected with P value < 0.05 and Q value < 0.25.

- 4p gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- 4q gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- 11p gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- 11q gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- 16p gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- 16q gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

- 1q loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

- 2p loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

- 2q loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

- 6p loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 6q loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 8p loss cnv correlated to 'CN_CNMF'.

- 8q loss cnv correlated to 'CN_CNMF'.

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

- 10q loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

- 13q loss cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

- 17q loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 61 arm-level 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, 55 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
1q loss | 52 (79%) | 14 | 0.474 (1.00) | 1e-05 (0.00488) | 7e-05 (0.0317) | 5e-05 (0.0228) | 0.231 (1.00) | 0.00051 (0.221) | 0.176 (1.00) | 0.00402 (1.00)
2p loss | 46 (70%) | 20 | 0.0888 (1.00) | 1e-05 (0.00488) | 1e-05 (0.00488) | 1e-05 (0.00488) | 0.0815 (1.00) | 1e-05 (0.00488) | 0.0306 (1.00) | 0.00073 (0.314)
2q loss | 46 (70%) | 20 | 0.0888 (1.00) | 1e-05 (0.00488) | 1e-05 (0.00488) | 1e-05 (0.00488) | 0.0814 (1.00) | 1e-05 (0.00488) | 0.0306 (1.00) | 0.00062 (0.268)
6p loss | 51 (77%) | 15 | 0.332 (1.00) | 0.00014 (0.0626) | 3e-05 (0.0138) | 1e-05 (0.00488) | 0.352 (1.00) | 0.00118 (0.5) | 0.176 (1.00) | 0.0004 (0.175)
6q loss | 51 (77%) | 15 | 0.331 (1.00) | 0.00016 (0.071) | 3e-05 (0.0138) | 1e-05 (0.00488) | 0.351 (1.00) | 0.00104 (0.444) | 0.176 (1.00) | 0.00032 (0.14)
10p loss | 48 (73%) | 18 | 0.343 (1.00) | 0.00029 (0.128) | 7e-05 (0.0317) | 1e-05 (0.00488) | 0.276 (1.00) | 0.00014 (0.0626) | 0.759 (1.00) | 0.0101 (1.00)
10q loss | 49 (74%) | 17 | 0.247 (1.00) | 0.00031 (0.136) | 2e-05 (0.00934) | 1e-05 (0.00488) | 0.225 (1.00) | 0.0002 (0.0886) | 0.538 (1.00) | 0.00338 (1.00)
17p loss | 50 (76%) | 16 | 0.298 (1.00) | 1e-05 (0.00488) | 1e-05 (0.00488) | 1e-05 (0.00488) | 0.0518 (1.00) | 9e-05 (0.0405) | 0.0491 (1.00) | 0.00211 (0.88)
17q loss | 50 (76%) | 16 | 0.298 (1.00) | 1e-05 (0.00488) | 1e-05 (0.00488) | 1e-05 (0.00488) | 0.0514 (1.00) | 0.0001 (0.0448) | 0.0491 (1.00) | 0.00212 (0.882)
1p loss | 53 (80%) | 13 | 0.672 (1.00) | 2e-05 (0.00934) | 0.00048 (0.209) | 0.00033 (0.145) | 0.162 (1.00) | 0.0013 (0.55) | 0.176 (1.00) | 0.00411 (1.00)
4p gain | 24 (36%) | 42 | 0.0554 (1.00) | 1 (1.00) | 2e-05 (0.00934) | 6e-05 (0.0272) | 0.769 (1.00) | 0.00903 (1.00) | 0.0349 (1.00) | 0.0173 (1.00)
4q gain | 24 (36%) | 42 | 0.0556 (1.00) | 1 (1.00) | 2e-05 (0.00934) | 5e-05 (0.0228) | 0.772 (1.00) | 0.00908 (1.00) | 0.0349 (1.00) | 0.0173 (1.00)
11p gain | 15 (23%) | 51 | 0.28 (1.00) | 0.676 (1.00) | 3e-05 (0.0138) | 0.00023 (0.102) | 0.871 (1.00) | 0.0279 (1.00) | 0.197 (1.00) | 0.0789 (1.00)
11q gain | 15 (23%) | 51 | 0.281 (1.00) | 0.679 (1.00) | 1e-05 (0.00488) | 5e-05 (0.0228) | 0.618 (1.00) | 0.0193 (1.00) | 0.197 (1.00) | 0.104 (1.00)
16p gain | 21 (32%) | 45 | 0.107 (1.00) | 1 (1.00) | 2e-05 (0.00934) | 8e-05 (0.0361) | 0.159 (1.00) | 0.00541 (1.00) | 0.0312 (1.00) | 0.0074 (1.00)
16q gain | 21 (32%) | 45 | 0.106 (1.00) | 1 (1.00) | 2e-05 (0.00934) | 9e-05 (0.0405) | 0.162 (1.00) | 0.00531 (1.00) | 0.0312 (1.00) | 0.00714 (1.00)
13q loss | 43 (65%) | 23 | 0.261 (1.00) | 0.00049 (0.213) | 0.00331 (1.00) | 0.00015 (0.0667) | 0.85 (1.00) | 0.196 (1.00) | 0.541 (1.00) | 0.00599 (1.00)
8p loss | 9 (14%) | 57 | 1e-05 (0.00488) | 0.0838 (1.00) | 0.0547 (1.00) | 0.0387 (1.00) | 0.15 (1.00) | 0.467 (1.00) | 0.142 (1.00) | 0.32 (1.00)
8q loss | 8 (12%) | 58 | 2e-05 (0.00934) | 0.0446 (1.00) | 0.134 (1.00) | 0.0718 (1.00) | 0.29 (1.00) | 0.529 (1.00) | 0.142 (1.00) | 0.32 (1.00)
3p gain | 8 (12%) | 58 | 0.272 (1.00) | 0.53 (1.00) | 0.951 (1.00) | 0.647 (1.00) | 0.516 (1.00) | 0.691 (1.00) | 0.669 (1.00) | 0.6 (1.00)
3q gain | 8 (12%) | 58 | 0.27 (1.00) | 0.53 (1.00) | 0.952 (1.00) | 0.648 (1.00) | 0.515 (1.00) | 0.69 (1.00) | 0.669 (1.00) | 0.602 (1.00)
5p gain | 8 (12%) | 58 | 0.424 (1.00) | 0.681 (1.00) | 0.448 (1.00) | 0.443 (1.00) | 0.367 (1.00) | 0.0584 (1.00) | 1 (1.00) | 0.126 (1.00)
5q gain | 8 (12%) | 58 | 0.424 (1.00) | 0.683 (1.00) | 0.449 (1.00) | 0.445 (1.00) | 0.362 (1.00) | 0.0602 (1.00) | 1 (1.00) | 0.127 (1.00)
7p gain | 24 (36%) | 42 | 0.15 (1.00) | 1 (1.00) | 0.0159 (1.00) | 0.0609 (1.00) | 0.899 (1.00) | 0.117 (1.00) | 0.766 (1.00) | 0.0991 (1.00)
7q gain | 24 (36%) | 42 | 0.152 (1.00) | 1 (1.00) | 0.0166 (1.00) | 0.0618 (1.00) | 0.901 (1.00) | 0.119 (1.00) | 0.766 (1.00) | 0.0995 (1.00)
8p gain | 17 (26%) | 49 | 0.413 (1.00) | 0.417 (1.00) | 0.0036 (1.00) | 0.0317 (1.00) | 0.464 (1.00) | 0.101 (1.00) | 1 (1.00) | 0.0292 (1.00)
8q gain | 18 (27%) | 48 | 0.343 (1.00) | 0.377 (1.00) | 0.00108 (0.459) | 0.00964 (1.00) | 0.696 (1.00) | 0.0878 (1.00) | 0.751 (1.00) | 0.0424 (1.00)
9p gain | 10 (15%) | 56 | 1 (1.00) | 1 (1.00) | 0.723 (1.00) | 0.813 (1.00) | 0.833 (1.00) | 0.602 (1.00) | 1 (1.00) | 0.265 (1.00)
9q gain | 10 (15%) | 56 | 1 (1.00) | 1 (1.00) | 0.723 (1.00) | 0.813 (1.00) | 0.831 (1.00) | 0.599 (1.00) | 1 (1.00) | 0.262 (1.00)
10p gain | 4 (6%) | 62 | 0.441 (1.00) | 0.162 (1.00) | 0.517 (1.00) | 0.204 (1.00) | 1 (1.00) | 0.167 (1.00) | 1 (1.00) | 0.458 (1.00)
12p gain | 19 (29%) | 47 | 0.481 (1.00) | 0.767 (1.00) | 0.0797 (1.00) | 0.158 (1.00) | 1 (1.00) | 0.0667 (1.00) | 0.213 (1.00) | 0.156 (1.00)
12q gain | 20 (30%) | 46 | 0.444 (1.00) | 0.595 (1.00) | 0.145 (1.00) | 0.0824 (1.00) | 0.943 (1.00) | 0.0323 (1.00) | 0.235 (1.00) | 0.132 (1.00)
14q gain | 21 (32%) | 45 | 0.106 (1.00) | 0.829 (1.00) | 0.00087 (0.373) | 0.00514 (1.00) | 0.427 (1.00) | 0.0566 (1.00) | 0.0312 (1.00) | 0.0773 (1.00)
15q gain | 21 (32%) | 45 | 0.106 (1.00) | 0.83 (1.00) | 0.00171 (0.718) | 0.0621 (1.00) | 0.757 (1.00) | 0.215 (1.00) | 0.762 (1.00) | 0.473 (1.00)
18p gain | 17 (26%) | 49 | 0.518 (1.00) | 0.805 (1.00) | 0.00194 (0.811) | 0.013 (1.00) | 0.937 (1.00) | 0.0495 (1.00) | 0.341 (1.00) | 0.0472 (1.00)
18q gain | 16 (24%) | 50 | 0.64 (1.00) | 0.926 (1.00) | 0.001 (0.428) | 0.0189 (1.00) | 0.821 (1.00) | 0.0519 (1.00) | 0.119 (1.00) | 0.0623 (1.00)
19p gain | 19 (29%) | 47 | 0.483 (1.00) | 0.273 (1.00) | 0.0215 (1.00) | 0.00799 (1.00) | 0.66 (1.00) | 0.039 (1.00) | 1 (1.00) | 0.708 (1.00)
19q gain | 17 (26%) | 49 | 0.518 (1.00) | 0.31 (1.00) | 0.00137 (0.578) | 0.00166 (0.699) | 0.411 (1.00) | 0.0475 (1.00) | 1 (1.00) | 0.655 (1.00)
20p gain | 20 (30%) | 46 | 0.216 (1.00) | 0.595 (1.00) | 0.0296 (1.00) | 0.0317 (1.00) | 0.708 (1.00) | 0.0305 (1.00) | 0.535 (1.00) | 0.182 (1.00)
20q gain | 21 (32%) | 45 | 0.227 (1.00) | 0.386 (1.00) | 0.0675 (1.00) | 0.0168 (1.00) | 0.677 (1.00) | 0.0369 (1.00) | 0.762 (1.00) | 0.0991 (1.00)
21q gain | 4 (6%) | 62 | 0.438 (1.00) | 0.163 (1.00) | 0.513 (1.00) | 0.106 (1.00) | 0.674 (1.00) | 0.165 (1.00) | 1 (1.00) | 0.41 (1.00)
22q gain | 19 (29%) | 47 | 0.901 (1.00) | 0.712 (1.00) | 0.07 (1.00) | 0.361 (1.00) | 0.552 (1.00) | 0.0233 (1.00) | 1 (1.00) | 0.00935 (1.00)
xq gain | 6 (9%) | 60 | 1 (1.00) | 0.722 (1.00) | 0.00676 (1.00) | 0.121 (1.00) | 0.264 (1.00) | 0.118 (1.00) | 0.142 (1.00) | 0.0714 (1.00)
3p loss | 9 (14%) | 57 | 0.0362 (1.00) | 0.895 (1.00) | 0.0645 (1.00) | 0.00299 (1.00) | 0.903 (1.00) | 0.2 (1.00) | 0.381 (1.00) | 0.845 (1.00)
3q loss | 8 (12%) | 58 | 0.0207 (1.00) | 0.367 (1.00) | 0.0243 (1.00) | 0.00187 (0.784) | 0.571 (1.00) | 0.182 (1.00) | 0.142 (1.00) | 0.689 (1.00)
5p loss | 10 (15%) | 56 | 0.0984 (1.00) | 0.253 (1.00) | 0.00066 (0.284) | 0.0193 (1.00) | 0.425 (1.00) | 0.0147 (1.00) | 0.451 (1.00) | 0.344 (1.00)
5q loss | 10 (15%) | 56 | 0.0991 (1.00) | 0.253 (1.00) | 0.00063 (0.272) | 0.0191 (1.00) | 0.425 (1.00) | 0.0144 (1.00) | 0.451 (1.00) | 0.345 (1.00)
9p loss | 10 (15%) | 56 | 1 (1.00) | 0.904 (1.00) | 0.0644 (1.00) | 0.0163 (1.00) | 0.909 (1.00) | 0.603 (1.00) | 0.695 (1.00) | 0.891 (1.00)
9q loss | 10 (15%) | 56 | 1 (1.00) | 0.903 (1.00) | 0.0637 (1.00) | 0.0168 (1.00) | 0.912 (1.00) | 0.601 (1.00) | 0.695 (1.00) | 0.89 (1.00)
11p loss | 7 (11%) | 59 | 0.631 (1.00) | 0.575 (1.00) | 0.109 (1.00) | 0.317 (1.00) | 0.205 (1.00) | 0.937 (1.00) | 0.381 (1.00) | 0.579 (1.00)
11q loss | 7 (11%) | 59 | 0.628 (1.00) | 0.573 (1.00) | 0.109 (1.00) | 0.317 (1.00) | 0.204 (1.00) | 0.937 (1.00) | 0.381 (1.00) | 0.575 (1.00)
16p loss | 4 (6%) | 62 | 0.683 (1.00) | 0.521 (1.00) | 0.023 (1.00) | 0.0366 (1.00) | 0.676 (1.00) | 0.0875 (1.00) | 0.286 (1.00) | 0.985 (1.00)
16q loss | 5 (8%) | 61 | 0.721 (1.00) | 0.387 (1.00) | 0.00596 (1.00) | 0.00666 (1.00) | 0.427 (1.00) | 0.0497 (1.00) | 0.0724 (1.00) | 0.688 (1.00)
18p loss | 8 (12%) | 58 | 0.677 (1.00) | 0.0964 (1.00) | 0.315 (1.00) | 0.212 (1.00) | 0.72 (1.00) | 0.949 (1.00) | 0.669 (1.00) | 0.771 (1.00)
18q loss | 10 (15%) | 56 | 0.622 (1.00) | 0.0799 (1.00) | 0.443 (1.00) | 0.281 (1.00) | 0.572 (1.00) | 0.864 (1.00) | 0.695 (1.00) | 0.512 (1.00)
19q loss | 3 (5%) | 63 | 0.644 (1.00) | 0.765 (1.00) | 0.767 (1.00) | 0.823 (1.00) | 0.516 (1.00) | 0.864 (1.00) | 1 (1.00) | 0.821 (1.00)
20p loss | 4 (6%) | 62 | 0.3 (1.00) | 0.807 (1.00) | 0.211 (1.00) | 0.215 (1.00) | 0.451 (1.00) | 0.659 (1.00) | 0.286 (1.00) | 0.551 (1.00)
20q loss | 3 (5%) | 63 | 1 (1.00) | 0.416 (1.00) | 0.226 (1.00) | 0.0581 (1.00) | 0.295 (1.00) | 0.826 (1.00) | 0.056 (1.00) | 0.717 (1.00)
21q loss | 35 (53%) | 31 | 0.774 (1.00) | 0.0105 (1.00) | 0.249 (1.00) | 0.195 (1.00) | 1 (1.00) | 0.128 (1.00) | 1 (1.00) | 0.0425 (1.00)
22q loss | 8 (12%) | 58 | 0.829 (1.00) | 0.133 (1.00) | 0.246 (1.00) | 0.234 (1.00) | 0.898 (1.00) | 0.214 (1.00) | 0.687 (1.00) | 0.357 (1.00)
xq loss | 39 (59%) | 27 | 0.599 (1.00) | 0.0735 (1.00) | 0.00689 (1.00) | 0.00361 (1.00) | 0.327 (1.00) | 0.00107 (0.456) | 0.77 (1.00) | 0.0372 (1.00)

'4p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0093

Table S1. Gene #3: '4p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
4P GAIN MUTATED | 4 | 17 | 2 | 1
4P GAIN WILD-TYPE | 15 | 5 | 13 | 9

Figure S1. Get High-res Image Gene #3: '4p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.027

Table S2. Gene #3: '4p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
4P GAIN MUTATED | 4 | 14 | 3 | 1 | 1 | 1 | 0
4P GAIN WILD-TYPE | 15 | 2 | 4 | 5 | 9 | 3 | 4

Figure S2. Get High-res Image Gene #3: '4p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0093

Table S3. Gene #4: '4q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
4Q GAIN MUTATED | 4 | 17 | 2 | 1
4Q GAIN WILD-TYPE | 15 | 5 | 13 | 9

Figure S3. Get High-res Image Gene #4: '4q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.023

Table S4. Gene #4: '4q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
4Q GAIN MUTATED | 4 | 14 | 3 | 1 | 1 | 1 | 0
4Q GAIN WILD-TYPE | 15 | 2 | 4 | 5 | 9 | 3 | 4

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

'11p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S5. Gene #14: '11p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
11P GAIN MUTATED | 1 | 13 | 1 | 0
11P GAIN WILD-TYPE | 18 | 9 | 14 | 10

Figure S5. Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.1

Table S6. Gene #14: '11p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
11P GAIN MUTATED | 1 | 11 | 1 | 1 | 1 | 0 | 0
11P GAIN WILD-TYPE | 18 | 5 | 6 | 5 | 9 | 4 | 4

Figure S6. Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S7. Gene #15: '11q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
11Q GAIN MUTATED | 1 | 14 | 0 | 0
11Q GAIN WILD-TYPE | 18 | 8 | 15 | 10

Figure S7. Get High-res Image Gene #15: '11q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.023

Table S8. Gene #15: '11q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
11Q GAIN MUTATED | 1 | 12 | 1 | 1 | 0 | 0 | 0
11Q GAIN WILD-TYPE | 18 | 4 | 6 | 5 | 10 | 4 | 4

Figure S8. Get High-res Image Gene #15: '11q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0093

Table S9. Gene #20: '16p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
16P GAIN MUTATED | 4 | 16 | 1 | 0
16P GAIN WILD-TYPE | 15 | 6 | 14 | 10

Figure S9. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.036

Table S10. Gene #20: '16p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
16P GAIN MUTATED | 4 | 13 | 2 | 1 | 0 | 1 | 0
16P GAIN WILD-TYPE | 15 | 3 | 5 | 5 | 10 | 3 | 4

Figure S10. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0093

Table S11. Gene #21: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
16Q GAIN MUTATED | 4 | 16 | 1 | 0
16Q GAIN WILD-TYPE | 15 | 6 | 14 | 10

Figure S11. Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.04

Table S12. Gene #21: '16q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
16Q GAIN MUTATED | 4 | 13 | 2 | 1 | 0 | 1 | 0
16Q GAIN WILD-TYPE | 15 | 3 | 5 | 5 | 10 | 3 | 4

Figure S12. Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0093

Table S13. Gene #31: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
1P LOSS MUTATED | 17 | 32 | 4
1P LOSS WILD-TYPE | 1 | 3 | 9

Figure S13. Get High-res Image Gene #31: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.21

Table S14. Gene #31: '1p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
1P LOSS MUTATED | 19 | 16 | 14 | 4
1P LOSS WILD-TYPE | 0 | 6 | 1 | 6

Figure S14. Get High-res Image Gene #31: '1p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.14

Table S15. Gene #31: '1p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
1P LOSS MUTATED | 19 | 11 | 6 | 4 | 9 | 4 | 0
1P LOSS WILD-TYPE | 0 | 5 | 1 | 2 | 1 | 0 | 4

Figure S15. Get High-res Image Gene #31: '1p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S16. Gene #32: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
1Q LOSS MUTATED | 17 | 32 | 3
1Q LOSS WILD-TYPE | 1 | 3 | 10

Figure S16. Get High-res Image Gene #32: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.032

Table S17. Gene #32: '1q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
1Q LOSS MUTATED | 19 | 16 | 14 | 3
1Q LOSS WILD-TYPE | 0 | 6 | 1 | 7

Figure S17. Get High-res Image Gene #32: '1q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.023

Table S18. Gene #32: '1q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
1Q LOSS MUTATED | 19 | 11 | 5 | 3 | 10 | 4 | 0
1Q LOSS WILD-TYPE | 0 | 5 | 2 | 3 | 0 | 0 | 4

Figure S18. Get High-res Image Gene #32: '1q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.22

Table S19. Gene #32: '1q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9
1Q LOSS MUTATED | 18 | 8 | 11 | 3 | 4 | 5 | 3
1Q LOSS WILD-TYPE | 0 | 3 | 1 | 3 | 1 | 0 | 6

Figure S19. Get High-res Image Gene #32: '1q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S20. Gene #33: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
2P LOSS MUTATED | 17 | 28 | 1
2P LOSS WILD-TYPE | 1 | 7 | 12

Figure S20. Get High-res Image Gene #33: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S21. Gene #33: '2p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
2P LOSS MUTATED | 19 | 14 | 13 | 0
2P LOSS WILD-TYPE | 0 | 8 | 2 | 10

Figure S21. Get High-res Image Gene #33: '2p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S22. Gene #33: '2p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
2P LOSS MUTATED | 19 | 10 | 4 | 0 | 10 | 3 | 0
2P LOSS WILD-TYPE | 0 | 6 | 3 | 6 | 0 | 1 | 4

Figure S22. Get High-res Image Gene #33: '2p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S23. Gene #33: '2p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9
2P LOSS MUTATED | 18 | 7 | 10 | 2 | 3 | 5 | 1
2P LOSS WILD-TYPE | 0 | 4 | 2 | 4 | 2 | 0 | 8

Figure S23. Get High-res Image Gene #33: '2p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S24. Gene #34: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
2Q LOSS MUTATED | 17 | 28 | 1
2Q LOSS WILD-TYPE | 1 | 7 | 12

Figure S24. Get High-res Image Gene #34: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S25. Gene #34: '2q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
2Q LOSS MUTATED | 19 | 14 | 13 | 0
2Q LOSS WILD-TYPE | 0 | 8 | 2 | 10

Figure S25. Get High-res Image Gene #34: '2q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S26. Gene #34: '2q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
2Q LOSS MUTATED | 19 | 10 | 4 | 0 | 10 | 3 | 0
2Q LOSS WILD-TYPE | 0 | 6 | 3 | 6 | 0 | 1 | 4

Figure S26. Get High-res Image Gene #34: '2q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S27. Gene #34: '2q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9
2Q LOSS MUTATED | 18 | 7 | 10 | 2 | 3 | 5 | 1
2Q LOSS WILD-TYPE | 0 | 4 | 2 | 4 | 2 | 0 | 8

Figure S27. Get High-res Image Gene #34: '2q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.063

Table S28. Gene #39: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
6P LOSS MUTATED | 17 | 30 | 4
6P LOSS WILD-TYPE | 1 | 5 | 9

Figure S28. Get High-res Image Gene #39: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S29. Gene #39: '6p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
6P LOSS MUTATED | 19 | 15 | 14 | 3
6P LOSS WILD-TYPE | 0 | 7 | 1 | 7

Figure S29. Get High-res Image Gene #39: '6p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S30. Gene #39: '6p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
6P LOSS MUTATED | 19 | 11 | 6 | 1 | 10 | 4 | 0
6P LOSS WILD-TYPE | 0 | 5 | 1 | 5 | 0 | 0 | 4

Figure S30. Get High-res Image Gene #39: '6p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.17

Table S31. Gene #39: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 10 | 6 | 5 | 8 | 4 | 6 | 5 | 4
6P LOSS MUTATED | 8 | 3 | 5 | 8 | 4 | 6 | 2 | 0
6P LOSS WILD-TYPE | 2 | 3 | 0 | 0 | 0 | 0 | 3 | 4

Figure S31. Get High-res Image Gene #39: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.071

Table S32. Gene #40: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
6Q LOSS MUTATED | 17 | 30 | 4
6Q LOSS WILD-TYPE | 1 | 5 | 9

Figure S32. Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S33. Gene #40: '6q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
6Q LOSS MUTATED | 19 | 15 | 14 | 3
6Q LOSS WILD-TYPE | 0 | 7 | 1 | 7

Figure S33. Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S34. Gene #40: '6q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
6Q LOSS MUTATED | 19 | 11 | 6 | 1 | 10 | 4 | 0
6Q LOSS WILD-TYPE | 0 | 5 | 1 | 5 | 0 | 0 | 4

Figure S34. Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.14

Table S35. Gene #40: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 10 | 6 | 5 | 8 | 4 | 6 | 5 | 4
6Q LOSS MUTATED | 8 | 3 | 5 | 8 | 4 | 6 | 2 | 0
6Q LOSS WILD-TYPE | 2 | 3 | 0 | 0 | 0 | 0 | 3 | 4

Figure S35. Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S36. Gene #41: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 5 | 47 | 14
8P LOSS MUTATED | 0 | 0 | 9
8P LOSS WILD-TYPE | 5 | 47 | 5

Figure S36. Get High-res Image Gene #41: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0093

Table S37. Gene #42: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 5 | 47 | 14
8Q LOSS MUTATED | 0 | 0 | 8
8Q LOSS WILD-TYPE | 5 | 47 | 6

Figure S37. Get High-res Image Gene #42: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.13

Table S38. Gene #45: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
10P LOSS MUTATED | 17 | 27 | 4
10P LOSS WILD-TYPE | 1 | 8 | 9

Figure S38. Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.032

Table S39. Gene #45: '10p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
10P LOSS MUTATED | 19 | 13 | 13 | 3
10P LOSS WILD-TYPE | 0 | 9 | 2 | 7

Figure S39. Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S40. Gene #45: '10p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
10P LOSS MUTATED | 19 | 8 | 6 | 2 | 10 | 3 | 0
10P LOSS WILD-TYPE | 0 | 8 | 1 | 4 | 0 | 1 | 4

Figure S40. Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.063

Table S41. Gene #45: '10p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9
10P LOSS MUTATED | 18 | 6 | 11 | 2 | 4 | 4 | 3
10P LOSS WILD-TYPE | 0 | 5 | 1 | 4 | 1 | 1 | 6

Figure S41. Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.14

Table S42. Gene #46: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
10Q LOSS MUTATED | 17 | 28 | 4
10Q LOSS WILD-TYPE | 1 | 7 | 9

Figure S42. Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0093

Table S43. Gene #46: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
10Q LOSS MUTATED | 19 | 13 | 14 | 3
10Q LOSS WILD-TYPE | 0 | 9 | 1 | 7

Figure S43. Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S44. Gene #46: '10q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
10Q LOSS MUTATED | 19 | 8 | 6 | 2 | 10 | 4 | 0
10Q LOSS WILD-TYPE | 0 | 8 | 1 | 4 | 0 | 0 | 4

Figure S44. Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.089

Table S45. Gene #46: '10q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9
10Q LOSS MUTATED | 18 | 7 | 11 | 2 | 4 | 4 | 3
10Q LOSS WILD-TYPE | 0 | 4 | 1 | 4 | 1 | 1 | 6

Figure S45. Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.21

Table S46. Gene #49: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
13Q LOSS MUTATED | 11 | 29 | 3
13Q LOSS WILD-TYPE | 7 | 6 | 10

Figure S46. Get High-res Image Gene #49: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.067

Table S47. Gene #49: '13q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
13Q LOSS MUTATED | 15 | 10 | 5 | 0 | 10 | 3 | 0
13Q LOSS WILD-TYPE | 4 | 6 | 2 | 6 | 0 | 1 | 4

Figure S47. Get High-res Image Gene #49: '13q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S48. Gene #52: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
17P LOSS MUTATED | 17 | 31 | 2
17P LOSS WILD-TYPE | 1 | 4 | 11

Figure S48. Get High-res Image Gene #52: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S49. Gene #52: '17p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
17P LOSS MUTATED | 19 | 16 | 14 | 1
17P LOSS WILD-TYPE | 0 | 6 | 1 | 9

Figure S49. Get High-res Image Gene #52: '17p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S50. Gene #52: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
17P LOSS MUTATED | 19 | 11 | 6 | 0 | 10 | 4 | 0
17P LOSS WILD-TYPE | 0 | 5 | 1 | 6 | 0 | 0 | 4

Figure S50. Get High-res Image Gene #52: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.04

Table S51. Gene #52: '17p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9
17P LOSS MUTATED | 18 | 8 | 11 | 3 | 3 | 5 | 2
17P LOSS WILD-TYPE | 0 | 3 | 1 | 3 | 2 | 0 | 7

Figure S51. Get High-res Image Gene #52: '17p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S52. Gene #53: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
17Q LOSS MUTATED | 17 | 31 | 2
17Q LOSS WILD-TYPE | 1 | 4 | 11

Figure S52. Get High-res Image Gene #53: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S53. Gene #53: '17q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
17Q LOSS MUTATED | 19 | 16 | 14 | 1
17Q LOSS WILD-TYPE | 0 | 6 | 1 | 9

Figure S53. Get High-res Image Gene #53: '17q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S54. Gene #53: '17q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
17Q LOSS MUTATED | 19 | 11 | 6 | 0 | 10 | 4 | 0
17Q LOSS WILD-TYPE | 0 | 5 | 1 | 6 | 0 | 0 | 4

Figure S54. Get High-res Image Gene #53: '17q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.045

Table S55. Gene #53: '17q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9
17Q LOSS MUTATED | 18 | 8 | 11 | 3 | 3 | 5 | 2
17Q LOSS WILD-TYPE | 0 | 3 | 1 | 3 | 2 | 0 | 7

Figure S55. Get High-res Image Gene #53: '17q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

Methods & Data
Input

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

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

- Number of patients = 66

- Number of significantly arm-level cnvs = 61

- Number of molecular subtypes = 8

- 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

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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