Correlation between copy number variations of arm-level result and molecular subtypes

Skin Cutaneous Melanoma (Metastatic)

23 May 2013 | analyses__2013_05_23

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1HX19SF

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 78 arm-level results and 10 molecular subtypes across 260 patients, 40 significant findings detected with Q value < 0.25.

1q gain cnv correlated to 'CN_CNMF'.
5p gain cnv correlated to 'CN_CNMF'.
5q gain cnv correlated to 'CN_CNMF'.
6p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
7p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
7q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
8p gain cnv correlated to 'CN_CNMF'.
8q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
12p gain cnv correlated to 'CN_CNMF'.
13q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
14q gain cnv correlated to 'CN_CNMF'.
15q gain cnv correlated to 'CN_CNMF'.
16p gain cnv correlated to 'CN_CNMF'.
19q gain cnv correlated to 'MRNASEQ_CNMF'.
20p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
20q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
22q gain cnv correlated to 'CN_CNMF'.
5q loss cnv correlated to 'CN_CNMF'.
6q loss cnv correlated to 'CN_CNMF'.
9p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
9q loss cnv correlated to 'METHLYATION_CNMF'.
10p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
10q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
11p loss cnv correlated to 'CN_CNMF'.
11q loss cnv correlated to 'CN_CNMF'.
14q loss cnv correlated to 'CN_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 78 arm-level results and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 40 significant findings detected.


		Molecular subtypes	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	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	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
10q loss	0 (0%)	140	2.63e-06 (0.00201)	2.32e-05 (0.0175)	0.539 (1.00)	0.192 (1.00)	2.52e-07 (0.000193)	0.000187 (0.139)	0.516 (1.00)	0.659 (1.00)	0.655 (1.00)	0.94 (1.00)
20p gain	0 (0%)	184	4.29e-10 (3.34e-07)	0.000205 (0.153)	0.345 (1.00)	0.904 (1.00)	0.000225 (0.167)	0.00204 (1.00)	0.05 (1.00)	0.167 (1.00)	0.00648 (1.00)	0.101 (1.00)
10p loss	0 (0%)	154	2.74e-08 (2.12e-05)	3.74e-06 (0.00285)	0.66 (1.00)	0.0897 (1.00)	3.62e-07 (0.000277)	0.000648 (0.475)	0.299 (1.00)	0.391 (1.00)	0.669 (1.00)	0.793 (1.00)
6p gain	0 (0%)	178	4.95e-05 (0.0371)	2.28e-05 (0.0172)	0.0894 (1.00)	0.589 (1.00)	0.0848 (1.00)	0.0699 (1.00)	0.0188 (1.00)	0.000823 (0.598)	0.245 (1.00)	0.000755 (0.551)
7p gain	0 (0%)	153	2.35e-09 (1.82e-06)	0.0882 (1.00)	0.195 (1.00)	0.298 (1.00)	0.000225 (0.167)	0.0343 (1.00)	0.826 (1.00)	0.431 (1.00)	0.818 (1.00)	0.199 (1.00)
7q gain	0 (0%)	151	3.86e-08 (2.97e-05)	0.123 (1.00)	0.13 (1.00)	0.167 (1.00)	0.00014 (0.105)	0.0308 (1.00)	0.319 (1.00)	0.108 (1.00)	0.4 (1.00)	0.0863 (1.00)
8q gain	0 (0%)	172	1.44e-09 (1.12e-06)	6.53e-06 (0.00496)	0.603 (1.00)	0.924 (1.00)	0.000609 (0.448)	0.00968 (1.00)	0.424 (1.00)	0.62 (1.00)	0.049 (1.00)	0.754 (1.00)
13q gain	0 (0%)	219	1.29e-07 (9.9e-05)	1.95e-05 (0.0147)	0.399 (1.00)	0.174 (1.00)	0.0193 (1.00)	0.0545 (1.00)	0.394 (1.00)	0.477 (1.00)	0.949 (1.00)	0.891 (1.00)
20q gain	0 (0%)	165	3.28e-12 (2.55e-09)	0.000294 (0.217)	0.448 (1.00)	0.802 (1.00)	0.0026 (1.00)	0.0664 (1.00)	0.382 (1.00)	0.42 (1.00)	0.0772 (1.00)	0.135 (1.00)
9p loss	0 (0%)	118	3.14e-08 (2.43e-05)	5.8e-06 (0.00441)	0.188 (1.00)	0.131 (1.00)	0.000721 (0.527)	0.000627 (0.46)	0.74 (1.00)	0.532 (1.00)	0.389 (1.00)	0.749 (1.00)
1q gain	0 (0%)	177	0.000182 (0.136)	0.00253 (1.00)	0.366 (1.00)	0.103 (1.00)	0.0953 (1.00)	0.719 (1.00)	0.205 (1.00)	0.0163 (1.00)	0.166 (1.00)	0.0126 (1.00)
5p gain	0 (0%)	230	6.46e-05 (0.0484)	0.205 (1.00)	0.758 (1.00)	0.819 (1.00)	0.849 (1.00)	0.201 (1.00)	0.249 (1.00)	0.754 (1.00)	0.0322 (1.00)	0.145 (1.00)
5q gain	0 (0%)	243	6.69e-05 (0.0501)	0.194 (1.00)	0.853 (1.00)	0.433 (1.00)	0.709 (1.00)	0.202 (1.00)	0.227 (1.00)	0.145 (1.00)	0.447 (1.00)	0.248 (1.00)
8p gain	0 (0%)	205	2.95e-07 (0.000226)	0.00269 (1.00)	0.0562 (1.00)	0.364 (1.00)	0.0153 (1.00)	0.0398 (1.00)	0.733 (1.00)	0.438 (1.00)	0.182 (1.00)	0.854 (1.00)
12p gain	0 (0%)	235	1.91e-05 (0.0145)	0.133 (1.00)	1 (1.00)	0.994 (1.00)	0.00929 (1.00)	0.139 (1.00)	0.211 (1.00)	0.311 (1.00)	0.0689 (1.00)	0.134 (1.00)
14q gain	0 (0%)	243	3.16e-05 (0.0238)	0.052 (1.00)	0.0431 (1.00)	0.257 (1.00)	1 (1.00)	0.791 (1.00)	0.484 (1.00)	0.801 (1.00)	1 (1.00)	0.923 (1.00)
15q gain	0 (0%)	225	4.8e-05 (0.0361)	0.53 (1.00)	0.567 (1.00)	0.912 (1.00)	0.546 (1.00)	0.243 (1.00)	0.833 (1.00)	0.0954 (1.00)	0.602 (1.00)	0.31 (1.00)
16p gain	0 (0%)	240	4.8e-05 (0.0361)	0.00375 (1.00)	0.452 (1.00)	0.724 (1.00)	0.0378 (1.00)	0.125 (1.00)	0.674 (1.00)	0.512 (1.00)	0.129 (1.00)	0.404 (1.00)
19q gain	0 (0%)	239	0.00293 (1.00)	0.075 (1.00)	0.415 (1.00)	0.678 (1.00)	0.000299 (0.221)	0.0684 (1.00)	0.727 (1.00)	0.834 (1.00)	0.838 (1.00)	0.515 (1.00)
22q gain	0 (0%)	198	7.63e-08 (5.87e-05)	0.17 (1.00)	0.803 (1.00)	0.933 (1.00)	0.527 (1.00)	0.867 (1.00)	0.717 (1.00)	0.581 (1.00)	0.255 (1.00)	0.197 (1.00)
5q loss	0 (0%)	211	1.48e-05 (0.0112)	0.13 (1.00)	0.0689 (1.00)	0.553 (1.00)	0.47 (1.00)	0.536 (1.00)	0.578 (1.00)	0.86 (1.00)	0.373 (1.00)	0.745 (1.00)
6q loss	0 (0%)	169	2.21e-09 (1.72e-06)	0.00391 (1.00)	0.338 (1.00)	0.608 (1.00)	0.000819 (0.596)	0.0533 (1.00)	0.546 (1.00)	0.343 (1.00)	0.738 (1.00)	0.223 (1.00)
9q loss	0 (0%)	154	0.00627 (1.00)	0.000232 (0.172)	0.448 (1.00)	0.364 (1.00)	0.346 (1.00)	0.794 (1.00)	0.766 (1.00)	0.464 (1.00)	0.419 (1.00)	0.484 (1.00)
11p loss	0 (0%)	199	6.5e-07 (0.000496)	0.0011 (0.8)	0.459 (1.00)	0.204 (1.00)	0.0607 (1.00)	0.0146 (1.00)	0.179 (1.00)	0.37 (1.00)	0.151 (1.00)	0.221 (1.00)
11q loss	0 (0%)	189	3.47e-07 (0.000266)	0.0122 (1.00)	0.949 (1.00)	0.684 (1.00)	0.0695 (1.00)	0.0129 (1.00)	0.579 (1.00)	0.574 (1.00)	0.492 (1.00)	0.533 (1.00)
14q loss	0 (0%)	202	1.23e-07 (9.43e-05)	0.0719 (1.00)	0.411 (1.00)	0.276 (1.00)	0.00397 (1.00)	0.328 (1.00)	0.522 (1.00)	0.436 (1.00)	0.459 (1.00)	0.458 (1.00)
1p gain	0 (0%)	231	0.0397 (1.00)	0.292 (1.00)	0.0563 (1.00)	0.433 (1.00)	0.0894 (1.00)	0.187 (1.00)	0.756 (1.00)	0.542 (1.00)	0.535 (1.00)	0.374 (1.00)
2p gain	0 (0%)	229	0.00457 (1.00)	0.156 (1.00)	0.0617 (1.00)	0.455 (1.00)	0.00194 (1.00)	0.0173 (1.00)	0.0939 (1.00)	0.0117 (1.00)	0.198 (1.00)	0.034 (1.00)
2q gain	0 (0%)	230	0.000773 (0.563)	0.218 (1.00)	0.02 (1.00)	0.433 (1.00)	0.000522 (0.384)	0.00468 (1.00)	0.0106 (1.00)	0.000713 (0.522)	0.0185 (1.00)	0.00273 (1.00)
3p gain	0 (0%)	237	0.0237 (1.00)	0.103 (1.00)	1 (1.00)	0.771 (1.00)	0.174 (1.00)	0.271 (1.00)	0.577 (1.00)	0.758 (1.00)	0.96 (1.00)	0.48 (1.00)
3q gain	0 (0%)	230	0.011 (1.00)	0.218 (1.00)	0.565 (1.00)	0.594 (1.00)	0.366 (1.00)	0.497 (1.00)	0.848 (1.00)	0.67 (1.00)	0.724 (1.00)	0.307 (1.00)
4p gain	0 (0%)	234	0.00173 (1.00)	0.0364 (1.00)	0.979 (1.00)	0.469 (1.00)	0.733 (1.00)	0.526 (1.00)	0.697 (1.00)	0.586 (1.00)	1 (1.00)	0.434 (1.00)
4q gain	0 (0%)	239	0.0142 (1.00)	0.0274 (1.00)	0.923 (1.00)	0.945 (1.00)	0.514 (1.00)	0.535 (1.00)	0.458 (1.00)	0.614 (1.00)	0.877 (1.00)	0.234 (1.00)
6q gain	0 (0%)	238	0.217 (1.00)	0.0859 (1.00)	1 (1.00)	0.498 (1.00)	0.916 (1.00)	0.31 (1.00)	0.718 (1.00)	0.641 (1.00)	0.628 (1.00)	0.409 (1.00)
9p gain	0 (0%)	250	1 (1.00)	0.431 (1.00)	0.12 (1.00)	0.435 (1.00)	0.395 (1.00)	0.805 (1.00)	0.766 (1.00)	0.459 (1.00)	0.837 (1.00)	0.259 (1.00)
9q gain	0 (0%)	249	0.538 (1.00)	0.797 (1.00)	0.236 (1.00)	0.6 (1.00)	0.784 (1.00)	0.836 (1.00)	0.766 (1.00)	0.341 (1.00)	0.837 (1.00)	0.298 (1.00)
11p gain	0 (0%)	243	0.0128 (1.00)	0.902 (1.00)	0.147 (1.00)	0.474 (1.00)	0.0172 (1.00)	0.483 (1.00)	0.541 (1.00)	0.0761 (1.00)	0.391 (1.00)	0.173 (1.00)
11q gain	0 (0%)	245	0.00771 (1.00)	0.441 (1.00)	0.307 (1.00)	0.72 (1.00)	0.0213 (1.00)	0.298 (1.00)	0.776 (1.00)	0.0625 (1.00)	0.647 (1.00)	0.205 (1.00)
12q gain	0 (0%)	248	0.0116 (1.00)	0.658 (1.00)	0.847 (1.00)	0.807 (1.00)	0.046 (1.00)	0.0261 (1.00)	0.421 (1.00)	0.231 (1.00)	0.499 (1.00)	0.0487 (1.00)
16q gain	0 (0%)	243	0.00129 (0.932)	0.0339 (1.00)	0.192 (1.00)	0.527 (1.00)	0.0373 (1.00)	0.231 (1.00)	0.743 (1.00)	0.228 (1.00)	0.199 (1.00)	0.306 (1.00)
17p gain	0 (0%)	243	0.232 (1.00)	0.265 (1.00)	0.781 (1.00)	0.829 (1.00)	0.335 (1.00)	0.604 (1.00)	0.555 (1.00)	0.606 (1.00)	0.0776 (1.00)	0.359 (1.00)
17q gain	0 (0%)	231	0.0145 (1.00)	0.149 (1.00)	0.628 (1.00)	0.213 (1.00)	0.51 (1.00)	0.209 (1.00)	0.165 (1.00)	0.422 (1.00)	0.0503 (1.00)	0.271 (1.00)
18p gain	0 (0%)	231	0.0234 (1.00)	0.149 (1.00)	0.91 (1.00)	0.801 (1.00)	0.0754 (1.00)	0.0714 (1.00)	0.356 (1.00)	0.293 (1.00)	0.424 (1.00)	0.327 (1.00)
18q gain	0 (0%)	241	0.0292 (1.00)	0.113 (1.00)	0.536 (1.00)	0.308 (1.00)	0.236 (1.00)	0.0449 (1.00)	1 (1.00)	0.927 (1.00)	1 (1.00)	0.661 (1.00)
19p gain	0 (0%)	243	0.00843 (1.00)	0.0301 (1.00)	0.623 (1.00)	0.204 (1.00)	0.00382 (1.00)	0.00207 (1.00)	0.285 (1.00)	0.801 (1.00)	0.948 (1.00)	0.525 (1.00)
21q gain	0 (0%)	231	0.0286 (1.00)	0.000504 (0.372)	0.182 (1.00)	0.402 (1.00)	0.0461 (1.00)	0.00908 (1.00)	0.47 (1.00)	0.956 (1.00)	0.26 (1.00)	0.61 (1.00)
Xq gain	0 (0%)	256	1 (1.00)	1 (1.00)	1 (1.00)	0.507 (1.00)	0.038 (1.00)	0.118 (1.00)	0.566 (1.00)	0.422 (1.00)	0.31 (1.00)	0.392 (1.00)
1p loss	0 (0%)	243	0.0623 (1.00)	0.00497 (1.00)	0.666 (1.00)	0.73 (1.00)	0.0607 (1.00)	0.169 (1.00)	0.323 (1.00)	0.698 (1.00)	0.27 (1.00)	0.736 (1.00)
1q loss	0 (0%)	253	0.00249 (1.00)	0.391 (1.00)	0.545 (1.00)	0.563 (1.00)	0.179 (1.00)	0.525 (1.00)	0.7 (1.00)	0.734 (1.00)	0.805 (1.00)	1 (1.00)
2p loss	0 (0%)	241	0.309 (1.00)	0.113 (1.00)	0.306 (1.00)	0.0384 (1.00)	0.533 (1.00)	0.276 (1.00)	0.00126 (0.913)	0.0017 (1.00)	0.00376 (1.00)	0.0232 (1.00)
2q loss	0 (0%)	240	0.271 (1.00)	0.0185 (1.00)	0.208 (1.00)	0.15 (1.00)	0.376 (1.00)	0.237 (1.00)	0.0023 (1.00)	0.00987 (1.00)	0.00589 (1.00)	0.0546 (1.00)
3p loss	0 (0%)	237	0.0333 (1.00)	0.0873 (1.00)	0.382 (1.00)	0.364 (1.00)	0.0021 (1.00)	0.027 (1.00)	0.778 (1.00)	0.479 (1.00)	0.783 (1.00)	0.783 (1.00)
3q loss	0 (0%)	240	0.207 (1.00)	0.0744 (1.00)	0.421 (1.00)	0.209 (1.00)	0.0675 (1.00)	0.343 (1.00)	0.954 (1.00)	0.315 (1.00)	0.691 (1.00)	0.57 (1.00)
4p loss	0 (0%)	229	0.516 (1.00)	0.156 (1.00)	0.342 (1.00)	0.132 (1.00)	0.00477 (1.00)	0.221 (1.00)	0.403 (1.00)	0.482 (1.00)	0.0484 (1.00)	0.548 (1.00)
4q loss	0 (0%)	228	0.0712 (1.00)	0.0449 (1.00)	0.308 (1.00)	0.0206 (1.00)	0.00645 (1.00)	0.0285 (1.00)	0.291 (1.00)	0.143 (1.00)	0.00364 (1.00)	0.0977 (1.00)
5p loss	0 (0%)	226	0.00378 (1.00)	0.287 (1.00)	0.272 (1.00)	0.333 (1.00)	0.366 (1.00)	0.283 (1.00)	0.0912 (1.00)	0.166 (1.00)	0.0949 (1.00)	0.138 (1.00)
6p loss	0 (0%)	234	0.0186 (1.00)	0.382 (1.00)	0.672 (1.00)	0.472 (1.00)	0.257 (1.00)	0.312 (1.00)	0.226 (1.00)	0.322 (1.00)	0.72 (1.00)	0.517 (1.00)
7p loss	0 (0%)	253	0.24 (1.00)	0.0508 (1.00)	0.664 (1.00)	0.471 (1.00)	0.716 (1.00)	0.786 (1.00)	0.618 (1.00)	1 (1.00)	0.647 (1.00)	1 (1.00)
7q loss	0 (0%)	254	0.245 (1.00)	0.128 (1.00)	0.779 (1.00)	0.703 (1.00)	1 (1.00)	0.875 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.808 (1.00)
8p loss	0 (0%)	231	0.213 (1.00)	0.292 (1.00)	0.057 (1.00)	0.486 (1.00)	0.0594 (1.00)	0.349 (1.00)	0.202 (1.00)	0.133 (1.00)	0.342 (1.00)	0.179 (1.00)
8q loss	0 (0%)	255	1 (1.00)	0.122 (1.00)	0.139 (1.00)	0.515 (1.00)	0.327 (1.00)	0.285 (1.00)	0.853 (1.00)	1 (1.00)	0.277 (1.00)	1 (1.00)
12p loss	0 (0%)	243	0.0698 (1.00)	0.00675 (1.00)	0.424 (1.00)	0.787 (1.00)	0.2 (1.00)	0.387 (1.00)	0.837 (1.00)	0.726 (1.00)	0.71 (1.00)	0.916 (1.00)
12q loss	0 (0%)	236	0.0313 (1.00)	0.000381 (0.281)	0.345 (1.00)	0.727 (1.00)	0.291 (1.00)	0.26 (1.00)	0.959 (1.00)	0.64 (1.00)	0.848 (1.00)	0.835 (1.00)
13q loss	0 (0%)	223	0.00398 (1.00)	0.416 (1.00)	0.172 (1.00)	0.656 (1.00)	0.389 (1.00)	0.609 (1.00)	0.121 (1.00)	0.236 (1.00)	0.147 (1.00)	0.0975 (1.00)
15q loss	0 (0%)	245	0.0518 (1.00)	0.114 (1.00)	0.651 (1.00)	0.138 (1.00)	0.632 (1.00)	0.884 (1.00)	0.208 (1.00)	0.0568 (1.00)	0.313 (1.00)	0.136 (1.00)
16p loss	0 (0%)	237	0.0475 (1.00)	0.0333 (1.00)	0.956 (1.00)	0.204 (1.00)	0.313 (1.00)	0.39 (1.00)	0.109 (1.00)	0.321 (1.00)	0.0843 (1.00)	0.221 (1.00)
16q loss	0 (0%)	213	0.00122 (0.885)	0.089 (1.00)	0.571 (1.00)	0.373 (1.00)	0.0213 (1.00)	0.0791 (1.00)	0.134 (1.00)	0.146 (1.00)	0.117 (1.00)	0.0824 (1.00)
17p loss	0 (0%)	209	0.201 (1.00)	0.0824 (1.00)	0.398 (1.00)	0.654 (1.00)	0.0853 (1.00)	1 (1.00)	0.595 (1.00)	0.458 (1.00)	0.0257 (1.00)	0.656 (1.00)
17q loss	0 (0%)	238	0.016 (1.00)	0.299 (1.00)	0.387 (1.00)	0.47 (1.00)	0.0553 (1.00)	0.562 (1.00)	0.663 (1.00)	1 (1.00)	0.443 (1.00)	0.713 (1.00)
18p loss	0 (0%)	211	0.00761 (1.00)	0.00199 (1.00)	0.372 (1.00)	0.415 (1.00)	0.000886 (0.643)	0.0473 (1.00)	0.978 (1.00)	0.815 (1.00)	0.208 (1.00)	0.727 (1.00)
18q loss	0 (0%)	215	0.0121 (1.00)	0.0082 (1.00)	0.0502 (1.00)	0.188 (1.00)	0.0934 (1.00)	0.55 (1.00)	0.932 (1.00)	0.666 (1.00)	0.955 (1.00)	0.843 (1.00)
19p loss	0 (0%)	241	0.0628 (1.00)	0.574 (1.00)	0.00578 (1.00)	0.536 (1.00)	0.149 (1.00)	0.137 (1.00)	0.485 (1.00)	0.641 (1.00)	0.307 (1.00)	0.234 (1.00)
19q loss	0 (0%)	241	0.0804 (1.00)	0.37 (1.00)	0.654 (1.00)	0.347 (1.00)	0.376 (1.00)	0.544 (1.00)	0.685 (1.00)	0.641 (1.00)	0.829 (1.00)	0.234 (1.00)
20p loss	0 (0%)	247	0.0803 (1.00)	0.626 (1.00)	0.153 (1.00)	0.744 (1.00)	0.615 (1.00)	0.288 (1.00)	0.0858 (1.00)	0.459 (1.00)	0.392 (1.00)	0.659 (1.00)
20q loss	0 (0%)	257	0.497 (1.00)	0.261 (1.00)			0.636 (1.00)	0.303 (1.00)	0.793 (1.00)	1 (1.00)	0.633 (1.00)	1 (1.00)
21q loss	0 (0%)	229	0.0121 (1.00)	0.0732 (1.00)	0.823 (1.00)	0.634 (1.00)	0.436 (1.00)	0.751 (1.00)	0.903 (1.00)	0.552 (1.00)	0.105 (1.00)	0.58 (1.00)
22q loss	0 (0%)	240	0.0223 (1.00)	0.195 (1.00)	0.591 (1.00)	0.428 (1.00)	0.802 (1.00)	0.485 (1.00)	0.0758 (1.00)	0.521 (1.00)	0.542 (1.00)	0.256 (1.00)
Xq loss	0 (0%)	250	0.559 (1.00)	0.00446 (1.00)	0.283 (1.00)	0.188 (1.00)	0.335 (1.00)	0.0616 (1.00)	0.243 (1.00)	0.501 (1.00)	0.074 (1.00)	1 (1.00)

'1q gain' versus 'CN_CNMF'

P value = 0.000182 (Fisher's exact test), Q value = 0.14

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
1Q GAIN CNV	26	42	15
1Q GAIN WILD-TYPE	46	55	76

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

'5p gain' versus 'CN_CNMF'

P value = 6.46e-05 (Fisher's exact test), Q value = 0.048

Table S2. Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
5P GAIN CNV	13	16	1
5P GAIN WILD-TYPE	59	81	90

Figure S2. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 6.69e-05 (Fisher's exact test), Q value = 0.05

Table S3. Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
5Q GAIN CNV	3	14	0
5Q GAIN WILD-TYPE	69	83	91

Figure S3. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 4.95e-05 (Fisher's exact test), Q value = 0.037

Table S4. Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
6P GAIN CNV	22	45	15
6P GAIN WILD-TYPE	50	52	76

Figure S4. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 2.28e-05 (Fisher's exact test), Q value = 0.017

Table S5. Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	97	97
6P GAIN CNV	33	33	16
6P GAIN WILD-TYPE	33	64	81

Figure S5. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 2.35e-09 (Fisher's exact test), Q value = 1.8e-06

Table S6. Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
7P GAIN CNV	49	40	18
7P GAIN WILD-TYPE	23	57	73

Figure S6. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.000225 (Fisher's exact test), Q value = 0.17

Table S7. Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	70	92
7P GAIN CNV	47	19	35
7P GAIN WILD-TYPE	32	51	57

Figure S7. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 3.86e-08 (Fisher's exact test), Q value = 3e-05

Table S8. Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
7Q GAIN CNV	49	39	21
7Q GAIN WILD-TYPE	23	58	70

Figure S8. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.1

Table S9. Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	70	92
7Q GAIN CNV	49	21	34
7Q GAIN WILD-TYPE	30	49	58

Figure S9. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 2.95e-07 (Fisher's exact test), Q value = 0.00023

Table S10. Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
8P GAIN CNV	26	25	4
8P GAIN WILD-TYPE	46	72	87

Figure S10. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 1.44e-09 (Fisher's exact test), Q value = 1.1e-06

Table S11. Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
8Q GAIN CNV	36	43	9
8Q GAIN WILD-TYPE	36	54	82

Figure S11. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 6.53e-06 (Fisher's exact test), Q value = 0.005

Table S12. Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	97	97
8Q GAIN CNV	38	30	20
8Q GAIN WILD-TYPE	28	67	77

Figure S12. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1.91e-05 (Fisher's exact test), Q value = 0.014

Table S13. Gene #21: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
12P GAIN CNV	16	8	1
12P GAIN WILD-TYPE	56	89	90

Figure S13. Get High-res Image Gene #21: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 1.29e-07 (Fisher's exact test), Q value = 9.9e-05

Table S14. Gene #23: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
13Q GAIN CNV	13	27	1
13Q GAIN WILD-TYPE	59	70	90

Figure S14. Get High-res Image Gene #23: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 1.95e-05 (Fisher's exact test), Q value = 0.015

Table S15. Gene #23: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	97	97
13Q GAIN CNV	20	17	4
13Q GAIN WILD-TYPE	46	80	93

Figure S15. Get High-res Image Gene #23: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 3.16e-05 (Fisher's exact test), Q value = 0.024

Table S16. Gene #24: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
14Q GAIN CNV	13	3	1
14Q GAIN WILD-TYPE	59	94	90

Figure S16. Get High-res Image Gene #24: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'15q gain' versus 'CN_CNMF'

P value = 4.8e-05 (Fisher's exact test), Q value = 0.036

Table S17. Gene #25: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
15Q GAIN CNV	21	9	5
15Q GAIN WILD-TYPE	51	88	86

Figure S17. Get High-res Image Gene #25: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 4.8e-05 (Fisher's exact test), Q value = 0.036

Table S18. Gene #26: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
16P GAIN CNV	14	5	1
16P GAIN WILD-TYPE	58	92	90

Figure S18. Get High-res Image Gene #26: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.000299 (Fisher's exact test), Q value = 0.22

Table S19. Gene #33: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	70	92
19Q GAIN CNV	13	0	6
19Q GAIN WILD-TYPE	66	70	86

Figure S19. Get High-res Image Gene #33: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 4.29e-10 (Fisher's exact test), Q value = 3.3e-07

Table S20. Gene #34: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
20P GAIN CNV	38	31	7
20P GAIN WILD-TYPE	34	66	84

Figure S20. Get High-res Image Gene #34: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.000205 (Fisher's exact test), Q value = 0.15

Table S21. Gene #34: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	97	97
20P GAIN CNV	29	32	15
20P GAIN WILD-TYPE	37	65	82

Figure S21. Get High-res Image Gene #34: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.000225 (Fisher's exact test), Q value = 0.17

Table S22. Gene #34: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	70	92
20P GAIN CNV	36	11	23
20P GAIN WILD-TYPE	43	59	69

Figure S22. Get High-res Image Gene #34: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 3.28e-12 (Fisher's exact test), Q value = 2.6e-09

Table S23. Gene #35: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
20Q GAIN CNV	46	39	10
20Q GAIN WILD-TYPE	26	58	81

Figure S23. Get High-res Image Gene #35: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.000294 (Fisher's exact test), Q value = 0.22

Table S24. Gene #35: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	97	97
20Q GAIN CNV	33	41	21
20Q GAIN WILD-TYPE	33	56	76

Figure S24. Get High-res Image Gene #35: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 7.63e-08 (Fisher's exact test), Q value = 5.9e-05

Table S25. Gene #37: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
22Q GAIN CNV	35	17	10
22Q GAIN WILD-TYPE	37	80	81

Figure S25. Get High-res Image Gene #37: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 1.48e-05 (Fisher's exact test), Q value = 0.011

Table S26. Gene #48: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
5Q LOSS CNV	26	7	16
5Q LOSS WILD-TYPE	46	90	75

Figure S26. Get High-res Image Gene #48: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 2.21e-09 (Fisher's exact test), Q value = 1.7e-06

Table S27. Gene #50: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
6Q LOSS CNV	32	49	10
6Q LOSS WILD-TYPE	40	48	81

Figure S27. Get High-res Image Gene #50: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 3.14e-08 (Fisher's exact test), Q value = 2.4e-05

Table S28. Gene #55: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
9P LOSS CNV	53	61	28
9P LOSS WILD-TYPE	19	36	63

Figure S28. Get High-res Image Gene #55: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 5.8e-06 (Fisher's exact test), Q value = 0.0044

Table S29. Gene #55: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	97	97
9P LOSS CNV	42	66	34
9P LOSS WILD-TYPE	24	31	63

Figure S29. Get High-res Image Gene #55: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 0.000232 (Fisher's exact test), Q value = 0.17

Table S30. Gene #56: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	97	97
9Q LOSS CNV	26	54	26
9Q LOSS WILD-TYPE	40	43	71

Figure S30. Get High-res Image Gene #56: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 2.74e-08 (Fisher's exact test), Q value = 2.1e-05

Table S31. Gene #57: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
10P LOSS CNV	45	44	17
10P LOSS WILD-TYPE	27	53	74

Figure S31. Get High-res Image Gene #57: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 3.74e-06 (Fisher's exact test), Q value = 0.0028

Table S32. Gene #57: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	97	97
10P LOSS CNV	37	48	21
10P LOSS WILD-TYPE	29	49	76

Figure S32. Get High-res Image Gene #57: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 3.62e-07 (Fisher's exact test), Q value = 0.00028

Table S33. Gene #57: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	70	92
10P LOSS CNV	50	14	36
10P LOSS WILD-TYPE	29	56	56

Figure S33. Get High-res Image Gene #57: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 2.63e-06 (Fisher's exact test), Q value = 0.002

Table S34. Gene #58: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
10Q LOSS CNV	48	47	25
10Q LOSS WILD-TYPE	24	50	66

Figure S34. Get High-res Image Gene #58: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 2.32e-05 (Fisher's exact test), Q value = 0.018

Table S35. Gene #58: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	97	97
10Q LOSS CNV	38	55	27
10Q LOSS WILD-TYPE	28	42	70

Figure S35. Get High-res Image Gene #58: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 2.52e-07 (Fisher's exact test), Q value = 0.00019

Table S36. Gene #58: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	70	92
10Q LOSS CNV	55	18	39
10Q LOSS WILD-TYPE	24	52	53

Figure S36. Get High-res Image Gene #58: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000187 (Fisher's exact test), Q value = 0.14

Table S37. Gene #58: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	57	122
10Q LOSS CNV	26	40	46
10Q LOSS WILD-TYPE	36	17	76

Figure S37. Get High-res Image Gene #58: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 6.5e-07 (Fisher's exact test), Q value = 5e-04

Table S38. Gene #59: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
11P LOSS CNV	32	21	8
11P LOSS WILD-TYPE	40	76	83

Figure S38. Get High-res Image Gene #59: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 3.47e-07 (Fisher's exact test), Q value = 0.00027

Table S39. Gene #60: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
11Q LOSS CNV	34	28	9
11Q LOSS WILD-TYPE	38	69	82

Figure S39. Get High-res Image Gene #60: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 1.23e-07 (Fisher's exact test), Q value = 9.4e-05

Table S40. Gene #64: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
14Q LOSS CNV	26	28	4
14Q LOSS WILD-TYPE	46	69	87

Figure S40. Get High-res Image Gene #64: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data

Input

Mutation data file = broad_values_by_arm.mutsig.cluster.txt
Molecular subtypes file = SKCM-TM.transferedmergedcluster.txt
Number of patients = 260
Number of significantly arm-level cnvs = 78
Number of molecular subtypes = 10
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

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

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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