Correlation between copy number variations of arm-level result and molecular subtypes
Kidney Chromophobe (Primary solid tumor)
15 January 2014 | analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C12R3Q3F
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/C12R3Q3F
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, 54 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', and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

- 6q loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_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_MATURE_CHIERARCHICAL'.

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

- 13q loss cnv correlated to 'METHLYATION_CNMF'.

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

- 17q loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_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, 54 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 | Chi-square test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test
2p loss | 46 (70%) | 20 | 0.0875 (1.00) | 3.7e-07 (0.000178) | 8.54e-08 (4.16e-05) | 2.91e-07 (0.000141) | 0.0891 (1.00) | 0.000161 (0.072) | 0.0277 (1.00) | 2.02e-05 (0.00934)
2q loss | 46 (70%) | 20 | 0.0875 (1.00) | 3.7e-07 (0.000178) | 8.54e-08 (4.16e-05) | 2.91e-07 (0.000141) | 0.0891 (1.00) | 0.000161 (0.072) | 0.0277 (1.00) | 2.02e-05 (0.00934)
17p loss | 50 (76%) | 16 | 0.299 (1.00) | 4.75e-07 (0.000228) | 5.74e-07 (0.000273) | 5.55e-07 (0.000266) | 0.0506 (1.00) | 0.000396 (0.173) | 0.05 (1.00) | 0.000108 (0.0486)
17q loss | 50 (76%) | 16 | 0.299 (1.00) | 4.75e-07 (0.000228) | 5.74e-07 (0.000273) | 5.55e-07 (0.000266) | 0.0506 (1.00) | 0.000396 (0.173) | 0.05 (1.00) | 0.000108 (0.0486)
10p loss | 48 (73%) | 18 | 0.342 (1.00) | 0.00038 (0.166) | 8.47e-05 (0.0383) | 5.23e-06 (0.00245) | 0.287 (1.00) | 0.0097 (1.00) | 0.0145 (1.00) | 0.000336 (0.148)
1p loss | 53 (80%) | 13 | 0.671 (1.00) | 2.22e-05 (0.0102) | 0.000362 (0.159) | 5.73e-05 (0.0259) | 0.16 (1.00) | 0.00115 (0.49) | 0.166 (1.00) | 0.00118 (0.5)
1q loss | 52 (79%) | 14 | 0.475 (1.00) | 2.29e-06 (0.00108) | 5.05e-05 (0.0229) | 4.21e-06 (0.00198) | 0.24 (1.00) | 0.00192 (0.801) | 0.133 (1.00) | 0.00184 (0.768)
6p loss | 51 (77%) | 15 | 0.33 (1.00) | 0.000107 (0.0482) | 4.76e-05 (0.0217) | 0.00033 (0.146) | 0.355 (1.00) | 0.00305 (1.00) | 0.306 (1.00) | 0.00201 (0.837)
6q loss | 51 (77%) | 15 | 0.33 (1.00) | 0.000107 (0.0482) | 4.76e-05 (0.0217) | 0.00033 (0.146) | 0.355 (1.00) | 0.00305 (1.00) | 0.306 (1.00) | 0.00201 (0.837)
10q loss | 49 (74%) | 17 | 0.248 (1.00) | 0.000262 (0.116) | 2.53e-05 (0.0116) | 2.88e-06 (0.00136) | 0.243 (1.00) | 0.00681 (1.00) | 0.0296 (1.00) | 0.00108 (0.458)
4p gain | 24 (36%) | 42 | 0.0552 (1.00) | 1 (1.00) | 2.78e-05 (0.0127) | 0.000215 (0.0956) | 0.788 (1.00) | 0.139 (1.00) | 0.734 (1.00) | 0.0309 (1.00)
4q gain | 24 (36%) | 42 | 0.0552 (1.00) | 1 (1.00) | 2.78e-05 (0.0127) | 0.000215 (0.0956) | 0.788 (1.00) | 0.139 (1.00) | 0.734 (1.00) | 0.0309 (1.00)
11p gain | 15 (23%) | 51 | 0.282 (1.00) | 0.679 (1.00) | 2e-05 (0.00928) | 4.44e-06 (0.00208) | 0.835 (1.00) | 0.106 (1.00) | 0.741 (1.00) | 0.071 (1.00)
11q gain | 15 (23%) | 51 | 0.282 (1.00) | 0.679 (1.00) | 6.69e-07 (0.000316) | 1.11e-07 (5.41e-05) | 0.63 (1.00) | 0.106 (1.00) | 0.441 (1.00) | 0.0453 (1.00)
16p gain | 21 (32%) | 45 | 0.106 (1.00) | 1 (1.00) | 6.22e-06 (0.00291) | 9.49e-06 (0.00441) | 0.158 (1.00) | 0.0481 (1.00) | 0.776 (1.00) | 0.0499 (1.00)
16q gain | 21 (32%) | 45 | 0.106 (1.00) | 1 (1.00) | 6.22e-06 (0.00291) | 9.49e-06 (0.00441) | 0.158 (1.00) | 0.0481 (1.00) | 0.776 (1.00) | 0.0499 (1.00)
8p loss | 9 (14%) | 57 | 8.11e-08 (3.96e-05) | 0.0857 (1.00) | 0.0531 (1.00) | 0.0036 (1.00) | 0.148 (1.00) | 0.341 (1.00) | 0.0757 (1.00) | 0.12 (1.00)
8q loss | 8 (12%) | 58 | 5.86e-07 (0.000278) | 0.0437 (1.00) | 0.134 (1.00) | 0.00434 (1.00) | 0.291 (1.00) | 0.586 (1.00) | 0.165 (1.00) | 0.224 (1.00)
13q loss | 43 (65%) | 23 | 0.27 (1.00) | 0.000529 (0.23) | 0.00364 (1.00) | 0.00343 (1.00) | 0.853 (1.00) | 0.0555 (1.00) | 0.93 (1.00) | 0.158 (1.00)
3p gain | 8 (12%) | 58 | 0.27 (1.00) | 0.53 (1.00) | 0.952 (1.00) | 0.614 (1.00) | 0.515 (1.00) | 0.298 (1.00) | 0.0206 (1.00) | 0.823 (1.00)
3q gain | 8 (12%) | 58 | 0.27 (1.00) | 0.53 (1.00) | 0.952 (1.00) | 0.614 (1.00) | 0.515 (1.00) | 0.298 (1.00) | 0.0206 (1.00) | 0.823 (1.00)
5p gain | 8 (12%) | 58 | 0.424 (1.00) | 0.682 (1.00) | 0.448 (1.00) | 0.629 (1.00) | 0.363 (1.00) | 0.0706 (1.00) | 0.633 (1.00) | 0.166 (1.00)
5q gain | 8 (12%) | 58 | 0.424 (1.00) | 0.682 (1.00) | 0.448 (1.00) | 0.629 (1.00) | 0.363 (1.00) | 0.0706 (1.00) | 0.633 (1.00) | 0.166 (1.00)
7p gain | 24 (36%) | 42 | 0.151 (1.00) | 1 (1.00) | 0.0169 (1.00) | 0.0167 (1.00) | 0.844 (1.00) | 1 (1.00) | 0.741 (1.00) | 0.423 (1.00)
7q gain | 24 (36%) | 42 | 0.151 (1.00) | 1 (1.00) | 0.0169 (1.00) | 0.0167 (1.00) | 0.844 (1.00) | 1 (1.00) | 0.741 (1.00) | 0.423 (1.00)
8p gain | 17 (26%) | 49 | 0.411 (1.00) | 0.411 (1.00) | 0.00393 (1.00) | 0.00701 (1.00) | 0.442 (1.00) | 1 (1.00) | 0.712 (1.00) | 0.155 (1.00)
8q gain | 18 (27%) | 48 | 0.342 (1.00) | 0.399 (1.00) | 0.00128 (0.54) | 0.00181 (0.76) | 0.679 (1.00) | 1 (1.00) | 0.926 (1.00) | 0.0785 (1.00)
9p gain | 10 (15%) | 56 | 1 (1.00) | 1 (1.00) | 0.722 (1.00) | 0.644 (1.00) | 0.832 (1.00) | 0.616 (1.00) | 0.188 (1.00) | 0.47 (1.00)
9q gain | 10 (15%) | 56 | 1 (1.00) | 1 (1.00) | 0.722 (1.00) | 0.644 (1.00) | 0.832 (1.00) | 0.616 (1.00) | 0.188 (1.00) | 0.47 (1.00)
10p gain | 4 (6%) | 62 | 0.438 (1.00) | 0.162 (1.00) | 0.515 (1.00) | 0.336 (1.00) | 1 (1.00) | 0.452 (1.00) | 0.534 (1.00) | 0.0739 (1.00)
12p gain | 19 (29%) | 47 | 0.482 (1.00) | 0.766 (1.00) | 0.0793 (1.00) | 0.13 (1.00) | 1 (1.00) | 0.709 (1.00) | 0.845 (1.00) | 0.0871 (1.00)
12q gain | 20 (30%) | 46 | 0.445 (1.00) | 0.591 (1.00) | 0.14 (1.00) | 0.052 (1.00) | 0.917 (1.00) | 1 (1.00) | 0.921 (1.00) | 0.169 (1.00)
14q gain | 21 (32%) | 45 | 0.106 (1.00) | 0.796 (1.00) | 0.000833 (0.36) | 0.00261 (1.00) | 0.423 (1.00) | 0.252 (1.00) | 0.878 (1.00) | 0.0499 (1.00)
15q gain | 21 (32%) | 45 | 0.106 (1.00) | 0.796 (1.00) | 0.00209 (0.866) | 0.00789 (1.00) | 0.761 (1.00) | 0.252 (1.00) | 0.998 (1.00) | 0.312 (1.00)
18p gain | 17 (26%) | 49 | 0.518 (1.00) | 0.806 (1.00) | 0.00215 (0.887) | 0.00497 (1.00) | 0.905 (1.00) | 0.684 (1.00) | 0.315 (1.00) | 0.033 (1.00)
18q gain | 16 (24%) | 50 | 0.638 (1.00) | 0.928 (1.00) | 0.00105 (0.448) | 0.00379 (1.00) | 0.785 (1.00) | 1 (1.00) | 0.385 (1.00) | 0.0366 (1.00)
19p gain | 19 (29%) | 47 | 0.482 (1.00) | 0.268 (1.00) | 0.0218 (1.00) | 0.0111 (1.00) | 0.642 (1.00) | 1 (1.00) | 0.929 (1.00) | 0.0518 (1.00)
19q gain | 17 (26%) | 49 | 0.518 (1.00) | 0.305 (1.00) | 0.00143 (0.602) | 0.00123 (0.52) | 0.4 (1.00) | 0.427 (1.00) | 0.912 (1.00) | 0.00957 (1.00)
20p gain | 20 (30%) | 46 | 0.216 (1.00) | 0.591 (1.00) | 0.0316 (1.00) | 0.00987 (1.00) | 0.681 (1.00) | 0.712 (1.00) | 0.637 (1.00) | 0.349 (1.00)
20q gain | 21 (32%) | 45 | 0.227 (1.00) | 0.394 (1.00) | 0.067 (1.00) | 0.0217 (1.00) | 0.667 (1.00) | 1 (1.00) | 0.519 (1.00) | 0.368 (1.00)
21q gain | 4 (6%) | 62 | 0.438 (1.00) | 0.162 (1.00) | 0.515 (1.00) | 0.336 (1.00) | 0.678 (1.00) | 0.452 (1.00) | 0.461 (1.00) | 0.361 (1.00)
22q gain | 19 (29%) | 47 | 0.901 (1.00) | 0.698 (1.00) | 0.0721 (1.00) | 0.16 (1.00) | 0.505 (1.00) | 1 (1.00) | 0.996 (1.00) | 0.169 (1.00)
xq gain | 6 (9%) | 60 | 1 (1.00) | 0.722 (1.00) | 0.00689 (1.00) | 0.163 (1.00) | 0.264 (1.00) | 0.585 (1.00) | 0.52 (1.00) | 0.00993 (1.00)
3p loss | 9 (14%) | 57 | 0.0367 (1.00) | 0.895 (1.00) | 0.0643 (1.00) | 0.00352 (1.00) | 0.904 (1.00) | 0.341 (1.00) | 0.0267 (1.00) | 0.0345 (1.00)
3q loss | 8 (12%) | 58 | 0.0211 (1.00) | 0.367 (1.00) | 0.0251 (1.00) | 0.000866 (0.371) | 0.572 (1.00) | 0.586 (1.00) | 0.00763 (1.00) | 0.0089 (1.00)
5p loss | 10 (15%) | 56 | 0.0987 (1.00) | 0.253 (1.00) | 0.000748 (0.324) | 0.000841 (0.361) | 0.427 (1.00) | 0.334 (1.00) | 0.619 (1.00) | 0.154 (1.00)
5q loss | 10 (15%) | 56 | 0.0987 (1.00) | 0.253 (1.00) | 0.000748 (0.324) | 0.000841 (0.361) | 0.427 (1.00) | 0.334 (1.00) | 0.619 (1.00) | 0.154 (1.00)
9p loss | 10 (15%) | 56 | 1 (1.00) | 0.902 (1.00) | 0.0649 (1.00) | 0.714 (1.00) | 0.912 (1.00) | 0.616 (1.00) | 0.896 (1.00) | 0.371 (1.00)
9q loss | 10 (15%) | 56 | 1 (1.00) | 0.902 (1.00) | 0.0649 (1.00) | 0.714 (1.00) | 0.912 (1.00) | 0.616 (1.00) | 0.896 (1.00) | 0.371 (1.00)
11p loss | 7 (11%) | 59 | 0.628 (1.00) | 0.574 (1.00) | 0.11 (1.00) | 0.497 (1.00) | 0.203 (1.00) | 1 (1.00) | 0.269 (1.00) | 0.0436 (1.00)
11q loss | 7 (11%) | 59 | 0.628 (1.00) | 0.574 (1.00) | 0.11 (1.00) | 0.497 (1.00) | 0.203 (1.00) | 1 (1.00) | 0.269 (1.00) | 0.0436 (1.00)
16p loss | 4 (6%) | 62 | 0.685 (1.00) | 0.517 (1.00) | 0.0232 (1.00) | 0.00987 (1.00) | 0.678 (1.00) | 0.452 (1.00) | 0.461 (1.00) | 1 (1.00)
16q loss | 5 (8%) | 61 | 0.721 (1.00) | 0.385 (1.00) | 0.00592 (1.00) | 0.000834 (0.36) | 0.428 (1.00) | 0.134 (1.00) | 0.192 (1.00) | 0.616 (1.00)
18p loss | 8 (12%) | 58 | 0.677 (1.00) | 0.0965 (1.00) | 0.315 (1.00) | 0.0503 (1.00) | 0.72 (1.00) | 1 (1.00) | 0.877 (1.00) | 1 (1.00)
18q loss | 10 (15%) | 56 | 0.62 (1.00) | 0.0796 (1.00) | 0.443 (1.00) | 0.138 (1.00) | 0.575 (1.00) | 0.616 (1.00) | 0.49 (1.00) | 0.958 (1.00)
19q loss | 3 (5%) | 63 | 0.646 (1.00) | 0.766 (1.00) | 0.767 (1.00) | 0.823 (1.00) | 0.515 (1.00) | 0.361 (1.00) | 0.69 (1.00) | 0.439 (1.00)
20p loss | 4 (6%) | 62 | 0.301 (1.00) | 0.807 (1.00) | 0.209 (1.00) | 0.213 (1.00) | 0.45 (1.00) | 1 (1.00) | 0.37 (1.00) | 0.202 (1.00)
20q loss | 3 (5%) | 63 | 1 (1.00) | 0.418 (1.00) | 0.226 (1.00) | 0.132 (1.00) | 0.294 (1.00) | 1 (1.00) | 0.219 (1.00) | 0.439 (1.00)
21q loss | 35 (53%) | 31 | 0.742 (1.00) | 0.00886 (1.00) | 0.247 (1.00) | 0.0443 (1.00) | 1 (1.00) | 0.724 (1.00) | 0.754 (1.00) | 0.141 (1.00)
22q loss | 8 (12%) | 58 | 0.83 (1.00) | 0.134 (1.00) | 0.247 (1.00) | 0.0645 (1.00) | 0.897 (1.00) | 0.586 (1.00) | 0.731 (1.00) | 0.267 (1.00)
xq loss | 39 (59%) | 27 | 0.532 (1.00) | 0.0787 (1.00) | 0.00683 (1.00) | 0.00129 (0.545) | 0.293 (1.00) | 0.026 (1.00) | 0.0691 (1.00) | 0.0281 (1.00)

'4p gain' versus 'MRNASEQ_CNMF'

P value = 2.78e-05 (Fisher's exact test), Q value = 0.013

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 = 0.000215 (Chi-square test), Q value = 0.096

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
4P GAIN MUTATED | 1 | 2 | 14 | 2 | 5
4P GAIN WILD-TYPE | 9 | 8 | 3 | 4 | 18

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

'4q gain' versus 'MRNASEQ_CNMF'

P value = 2.78e-05 (Fisher's exact test), Q value = 0.013

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 = 0.000215 (Chi-square test), Q value = 0.096

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
4Q GAIN MUTATED | 1 | 2 | 14 | 2 | 5
4Q GAIN WILD-TYPE | 9 | 8 | 3 | 4 | 18

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

'11p gain' versus 'MRNASEQ_CNMF'

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

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 = 4.44e-06 (Chi-square test), Q value = 0.0021

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
11P GAIN MUTATED | 1 | 1 | 12 | 0 | 1
11P GAIN WILD-TYPE | 9 | 9 | 5 | 6 | 22

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

'11q gain' versus 'MRNASEQ_CNMF'

P value = 6.69e-07 (Fisher's exact test), Q value = 0.00032

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 = 1.11e-07 (Chi-square test), Q value = 5.4e-05

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
11Q GAIN MUTATED | 0 | 1 | 13 | 0 | 1
11Q GAIN WILD-TYPE | 10 | 9 | 4 | 6 | 22

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

'16p gain' versus 'MRNASEQ_CNMF'

P value = 6.22e-06 (Fisher's exact test), Q value = 0.0029

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 = 9.49e-06 (Chi-square test), Q value = 0.0044

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
16P GAIN MUTATED | 0 | 1 | 14 | 1 | 5
16P GAIN WILD-TYPE | 10 | 9 | 3 | 5 | 18

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

'16q gain' versus 'MRNASEQ_CNMF'

P value = 6.22e-06 (Fisher's exact test), Q value = 0.0029

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 = 9.49e-06 (Chi-square test), Q value = 0.0044

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
16Q GAIN MUTATED | 0 | 1 | 14 | 1 | 5
16Q GAIN WILD-TYPE | 10 | 9 | 3 | 5 | 18

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

'1p loss' versus 'METHLYATION_CNMF'

P value = 2.22e-05 (Fisher's exact test), Q value = 0.01

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 = 0.000362 (Fisher's exact test), Q value = 0.16

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 = 5.73e-05 (Chi-square test), Q value = 0.026

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
1P LOSS MUTATED | 9 | 3 | 12 | 6 | 23
1P LOSS WILD-TYPE | 1 | 7 | 5 | 0 | 0

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

'1q loss' versus 'METHLYATION_CNMF'

P value = 2.29e-06 (Fisher's exact test), Q value = 0.0011

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 = 5.05e-05 (Fisher's exact test), Q value = 0.023

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 = 4.21e-06 (Chi-square test), Q value = 0.002

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
1Q LOSS MUTATED | 10 | 2 | 12 | 5 | 23
1Q LOSS WILD-TYPE | 0 | 8 | 5 | 1 | 0

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

'2p loss' versus 'METHLYATION_CNMF'

P value = 3.7e-07 (Fisher's exact test), Q value = 0.00018

Table S19. 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 S19. Get High-res Image Gene #33: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 8.54e-08 (Fisher's exact test), Q value = 4.2e-05

Table S20. 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 S20. Get High-res Image Gene #33: '2p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.91e-07 (Chi-square test), Q value = 0.00014

Table S21. Gene #33: '2p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
2P LOSS MUTATED | 10 | 0 | 11 | 3 | 22
2P LOSS WILD-TYPE | 0 | 10 | 6 | 3 | 1

Figure S21. Get High-res Image Gene #33: '2p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000161 (Fisher's exact test), Q value = 0.072

Table S22. Gene #33: '2p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 9 | 57
2P LOSS MUTATED | 1 | 45
2P LOSS WILD-TYPE | 8 | 12

Figure S22. Get High-res Image Gene #33: '2p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.02e-05 (Fisher's exact test), Q value = 0.0093

Table S23. Gene #33: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 12 | 8 | 25 | 21
2P LOSS MUTATED | 3 | 4 | 18 | 21
2P LOSS WILD-TYPE | 9 | 4 | 7 | 0

Figure S23. Get High-res Image Gene #33: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'METHLYATION_CNMF'

P value = 3.7e-07 (Fisher's exact test), Q value = 0.00018

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 = 8.54e-08 (Fisher's exact test), Q value = 4.2e-05

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 = 2.91e-07 (Chi-square test), Q value = 0.00014

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
2Q LOSS MUTATED | 10 | 0 | 11 | 3 | 22
2Q LOSS WILD-TYPE | 0 | 10 | 6 | 3 | 1

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

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000161 (Fisher's exact test), Q value = 0.072

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

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 9 | 57
2Q LOSS MUTATED | 1 | 45
2Q LOSS WILD-TYPE | 8 | 12

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

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.02e-05 (Fisher's exact test), Q value = 0.0093

Table S28. Gene #34: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 12 | 8 | 25 | 21
2Q LOSS MUTATED | 3 | 4 | 18 | 21
2Q LOSS WILD-TYPE | 9 | 4 | 7 | 0

Figure S28. Get High-res Image Gene #34: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.000107 (Fisher's exact test), Q value = 0.048

Table S29. 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 S29. Get High-res Image Gene #39: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 4.76e-05 (Fisher's exact test), Q value = 0.022

Table S30. 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 S30. Get High-res Image Gene #39: '6p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00033 (Chi-square test), Q value = 0.15

Table S31. Gene #39: '6p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
6P LOSS MUTATED | 10 | 3 | 12 | 4 | 22
6P LOSS WILD-TYPE | 0 | 7 | 5 | 2 | 1

Figure S31. Get High-res Image Gene #39: '6p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.000107 (Fisher's exact test), Q value = 0.048

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 = 4.76e-05 (Fisher's exact test), Q value = 0.022

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 = 0.00033 (Chi-square test), Q value = 0.15

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
6Q LOSS MUTATED | 10 | 3 | 12 | 4 | 22
6Q LOSS WILD-TYPE | 0 | 7 | 5 | 2 | 1

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

'8p loss' versus 'CN_CNMF'

P value = 8.11e-08 (Fisher's exact test), Q value = 4e-05

Table S35. 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 S35. Get High-res Image Gene #41: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'CN_CNMF'

P value = 5.86e-07 (Fisher's exact test), Q value = 0.00028

Table S36. 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 S36. Get High-res Image Gene #42: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.17

Table S37. 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 S37. Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 8.47e-05 (Fisher's exact test), Q value = 0.038

Table S38. 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 S38. Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.23e-06 (Chi-square test), Q value = 0.0024

Table S39. Gene #45: '10p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
10P LOSS MUTATED | 10 | 2 | 9 | 4 | 23
10P LOSS WILD-TYPE | 0 | 8 | 8 | 2 | 0

Figure S39. Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000336 (Fisher's exact test), Q value = 0.15

Table S40. Gene #45: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 12 | 8 | 25 | 21
10P LOSS MUTATED | 6 | 3 | 18 | 21
10P LOSS WILD-TYPE | 6 | 5 | 7 | 0

Figure S40. Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.000262 (Fisher's exact test), Q value = 0.12

Table S41. 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 S41. Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 2.53e-05 (Fisher's exact test), Q value = 0.012

Table S42. 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 S42. Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.88e-06 (Chi-square test), Q value = 0.0014

Table S43. Gene #46: '10q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
10Q LOSS MUTATED | 10 | 2 | 9 | 5 | 23
10Q LOSS WILD-TYPE | 0 | 8 | 8 | 1 | 0

Figure S43. Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.000529 (Fisher's exact test), Q value = 0.23

Table S44. 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 S44. Get High-res Image Gene #49: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 4.75e-07 (Fisher's exact test), Q value = 0.00023

Table S45. 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 S45. Get High-res Image Gene #52: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 5.74e-07 (Fisher's exact test), Q value = 0.00027

Table S46. 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 S46. Get High-res Image Gene #52: '17p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.55e-07 (Chi-square test), Q value = 0.00027

Table S47. Gene #52: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
17P LOSS MUTATED | 10 | 1 | 12 | 4 | 23
17P LOSS WILD-TYPE | 0 | 9 | 5 | 2 | 0

Figure S47. Get High-res Image Gene #52: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000396 (Fisher's exact test), Q value = 0.17

Table S48. Gene #52: '17p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 9 | 57
17P LOSS MUTATED | 2 | 48
17P LOSS WILD-TYPE | 7 | 9

Figure S48. Get High-res Image Gene #52: '17p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000108 (Fisher's exact test), Q value = 0.049

Table S49. Gene #52: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 12 | 8 | 25 | 21
17P LOSS MUTATED | 4 | 5 | 20 | 21
17P LOSS WILD-TYPE | 8 | 3 | 5 | 0

Figure S49. Get High-res Image Gene #52: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'METHLYATION_CNMF'

P value = 4.75e-07 (Fisher's exact test), Q value = 0.00023

Table S50. 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 S50. Get High-res Image Gene #53: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 5.74e-07 (Fisher's exact test), Q value = 0.00027

Table S51. 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 S51. Get High-res Image Gene #53: '17q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.55e-07 (Chi-square test), Q value = 0.00027

Table S52. Gene #53: '17q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
17Q LOSS MUTATED | 10 | 1 | 12 | 4 | 23
17Q LOSS WILD-TYPE | 0 | 9 | 5 | 2 | 0

Figure S52. Get High-res Image Gene #53: '17q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000396 (Fisher's exact test), Q value = 0.17

Table S53. Gene #53: '17q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 9 | 57
17Q LOSS MUTATED | 2 | 48
17Q LOSS WILD-TYPE | 7 | 9

Figure S53. Get High-res Image Gene #53: '17q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000108 (Fisher's exact test), Q value = 0.049

Table S54. Gene #53: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 12 | 8 | 25 | 21
17Q LOSS MUTATED | 4 | 5 | 20 | 21
17Q LOSS WILD-TYPE | 8 | 3 | 5 | 0

Figure S54. Get High-res Image Gene #53: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_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

Chi-square test

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

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