Correlation between copy number variation genes (focal events) and molecular subtypes

Ovarian Serous Cystadenocarcinoma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

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 (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1ZG6R1D

Overview

Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 68 focal events and 13 molecular subtypes across 569 patients, 56 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p34.3 cnv correlated to 'CN_CNMF'.
amp_1q21.3 cnv correlated to 'CN_CNMF'.
amp_1q42.2 cnv correlated to 'CN_CNMF'.
amp_2p23.2 cnv correlated to 'CN_CNMF'.
amp_2q31.2 cnv correlated to 'CN_CNMF'.
amp_3q26.2 cnv correlated to 'CN_CNMF'.
amp_4p16.3 cnv correlated to 'CN_CNMF'.
amp_5p15.33 cnv correlated to 'CN_CNMF'.
amp_6p22.3 cnv correlated to 'CN_CNMF'.
amp_7q36.3 cnv correlated to 'CN_CNMF'.
amp_8p11.21 cnv correlated to 'CN_CNMF'.
amp_8q24.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'MRNASEQ_CNMF'.
amp_10p15.3 cnv correlated to 'CN_CNMF'.
amp_11q14.1 cnv correlated to 'CN_CNMF'.
amp_12p13.33 cnv correlated to 'CN_CNMF'.
amp_12p12.1 cnv correlated to 'CN_CNMF'.
amp_14q32.33 cnv correlated to 'CN_CNMF'.
amp_15q26.3 cnv correlated to 'CN_CNMF'.
amp_18q11.2 cnv correlated to 'CN_CNMF'.
amp_19p13.12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CNMF', and 'RPPA_CHIERARCHICAL'.
amp_19q12 cnv correlated to 'CN_CNMF'.
amp_19q13.2 cnv correlated to 'CN_CNMF'.
amp_20p13 cnv correlated to 'CN_CNMF'.
amp_20q11.21 cnv correlated to 'CN_CNMF'.
amp_20q13.33 cnv correlated to 'CN_CNMF'.
amp_xp11.23 cnv correlated to 'CN_CNMF'.
del_1p36.11 cnv correlated to 'CN_CNMF'.
del_1q41 cnv correlated to 'CN_CNMF'.
del_2q37.3 cnv correlated to 'CN_CNMF'.
del_3p26.2 cnv correlated to 'CN_CNMF'.
del_5q11.2 cnv correlated to 'CN_CNMF'.
del_5q13.2 cnv correlated to 'CN_CNMF'.
del_6q27 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_7p22.1 cnv correlated to 'CN_CNMF'.
del_8p23.3 cnv correlated to 'CN_CNMF'.
del_8p21.2 cnv correlated to 'CN_CNMF'.
del_9p24.3 cnv correlated to 'MRNA_CNMF' and 'MRNA_CHIERARCHICAL'.
del_9q34.13 cnv correlated to 'CN_CNMF'.
del_10q24.2 cnv correlated to 'CN_CNMF'.
del_11p15.5 cnv correlated to 'CN_CNMF'.
del_12q24.33 cnv correlated to 'CN_CNMF'.
del_13q14.2 cnv correlated to 'CN_CNMF'.
del_14q23.3 cnv correlated to 'CN_CNMF'.
del_15q15.1 cnv correlated to 'CN_CNMF'.
del_16q22.1 cnv correlated to 'CN_CNMF'.
del_16q23.1 cnv correlated to 'CN_CNMF'.
del_19q13.33 cnv correlated to 'MRNA_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 68 focal events and 13 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 56 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	MIR CNMF	MIR CHIERARCHICAL	CN 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	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	Fisher's exact test	Fisher's exact test
amp 19p13 12	308 (54%)	261	0.00027 (0.225)	0.00024 (0.2)	0.0375 (1.00)	0.251 (1.00)	1e-05 (0.00884)	0.00028 (0.233)	0.00011 (0.0922)	0.24 (1.00)	0.461 (1.00)	0.585 (1.00)	0.0952 (1.00)	0.985 (1.00)	0.287 (1.00)
amp 8q24 21	451 (79%)	118	1e-05 (0.00884)	1e-05 (0.00884)	0.25 (1.00)	0.00232 (1.00)	1e-05 (0.00884)	0.986 (1.00)	0.327 (1.00)	1e-05 (0.00884)	0.00031 (0.257)	0.162 (1.00)	0.0998 (1.00)	0.0634 (1.00)	0.0667 (1.00)
del 6q27	381 (67%)	188	0.169 (1.00)	0.046 (1.00)	0.265 (1.00)	0.145 (1.00)	1e-05 (0.00884)	0.452 (1.00)	0.247 (1.00)	3e-05 (0.0254)	0.00094 (0.77)	0.371 (1.00)	0.0287 (1.00)	0.34 (1.00)	0.491 (1.00)
del 9p24 3	257 (45%)	312	0.00028 (0.233)	5e-05 (0.042)	0.62 (1.00)	0.0132 (1.00)	0.0395 (1.00)	0.325 (1.00)	0.955 (1.00)	0.073 (1.00)	0.0519 (1.00)	0.0878 (1.00)	0.125 (1.00)	0.0632 (1.00)	0.158 (1.00)
amp 1p34 3	287 (50%)	282	0.431 (1.00)	0.0815 (1.00)	0.125 (1.00)	0.0889 (1.00)	1e-05 (0.00884)	0.112 (1.00)	0.386 (1.00)	0.559 (1.00)	0.186 (1.00)	0.0869 (1.00)	0.166 (1.00)	0.0664 (1.00)	0.413 (1.00)
amp 1q21 3	361 (63%)	208	0.268 (1.00)	0.162 (1.00)	0.642 (1.00)	0.397 (1.00)	1e-05 (0.00884)	0.0766 (1.00)	0.0709 (1.00)	0.66 (1.00)	0.372 (1.00)	0.844 (1.00)	0.00584 (1.00)	0.744 (1.00)	0.35 (1.00)
amp 1q42 2	314 (55%)	255	0.0233 (1.00)	0.0269 (1.00)	0.885 (1.00)	0.00751 (1.00)	1e-05 (0.00884)	0.256 (1.00)	0.124 (1.00)	0.503 (1.00)	0.323 (1.00)	0.267 (1.00)	0.00291 (1.00)	0.364 (1.00)	0.327 (1.00)
amp 2p23 2	245 (43%)	324	0.33 (1.00)	0.0132 (1.00)	0.758 (1.00)	0.171 (1.00)	1e-05 (0.00884)	0.143 (1.00)	0.215 (1.00)	0.033 (1.00)	0.0203 (1.00)	0.919 (1.00)	0.2 (1.00)	0.939 (1.00)	0.628 (1.00)
amp 2q31 2	259 (46%)	310	0.112 (1.00)	0.173 (1.00)	0.0325 (1.00)	0.0302 (1.00)	1e-05 (0.00884)	0.0494 (1.00)	0.324 (1.00)	0.152 (1.00)	0.271 (1.00)	0.289 (1.00)	0.0848 (1.00)	0.082 (1.00)	0.449 (1.00)
amp 3q26 2	476 (84%)	93	0.00905 (1.00)	0.0268 (1.00)	0.817 (1.00)	0.279 (1.00)	1e-05 (0.00884)	0.407 (1.00)	0.278 (1.00)	0.00664 (1.00)	0.0115 (1.00)	0.126 (1.00)	0.068 (1.00)	0.478 (1.00)	0.764 (1.00)
amp 4p16 3	157 (28%)	412	1 (1.00)	0.321 (1.00)	0.0299 (1.00)	0.479 (1.00)	0.00028 (0.233)	0.273 (1.00)	0.691 (1.00)	0.691 (1.00)	0.983 (1.00)	0.627 (1.00)	0.0193 (1.00)	0.753 (1.00)	0.963 (1.00)
amp 5p15 33	304 (53%)	265	1 (1.00)	0.0543 (1.00)	0.627 (1.00)	0.249 (1.00)	1e-05 (0.00884)	0.982 (1.00)	0.238 (1.00)	0.244 (1.00)	0.389 (1.00)	0.0252 (1.00)	0.146 (1.00)	0.105 (1.00)	0.264 (1.00)
amp 6p22 3	300 (53%)	269	0.173 (1.00)	0.031 (1.00)	0.275 (1.00)	0.0745 (1.00)	1e-05 (0.00884)	0.0735 (1.00)	0.056 (1.00)	0.866 (1.00)	0.213 (1.00)	0.378 (1.00)	0.616 (1.00)	0.168 (1.00)	0.514 (1.00)
amp 7q36 3	311 (55%)	258	0.107 (1.00)	0.177 (1.00)	0.358 (1.00)	0.988 (1.00)	3e-05 (0.0254)	0.0318 (1.00)	0.204 (1.00)	0.845 (1.00)	0.971 (1.00)	0.21 (1.00)	0.501 (1.00)	0.0237 (1.00)	0.442 (1.00)
amp 8p11 21	207 (36%)	362	0.11 (1.00)	0.354 (1.00)	0.101 (1.00)	0.533 (1.00)	4e-05 (0.0337)	0.0109 (1.00)	0.425 (1.00)	0.276 (1.00)	0.173 (1.00)	0.769 (1.00)	0.325 (1.00)	0.673 (1.00)	0.975 (1.00)
amp 10p15 3	246 (43%)	323	0.824 (1.00)	0.1 (1.00)	0.0532 (1.00)	0.168 (1.00)	1e-05 (0.00884)	0.486 (1.00)	0.504 (1.00)	0.241 (1.00)	0.121 (1.00)	0.376 (1.00)	0.0665 (1.00)	0.601 (1.00)	0.581 (1.00)
amp 11q14 1	253 (44%)	316	0.0053 (1.00)	0.004 (1.00)	0.772 (1.00)	0.308 (1.00)	1e-05 (0.00884)	0.383 (1.00)	0.226 (1.00)	0.00434 (1.00)	0.0279 (1.00)	0.132 (1.00)	0.922 (1.00)	0.214 (1.00)	0.912 (1.00)
amp 12p13 33	323 (57%)	246	0.0236 (1.00)	0.00349 (1.00)	0.265 (1.00)	0.0546 (1.00)	1e-05 (0.00884)	0.193 (1.00)	0.157 (1.00)	0.0147 (1.00)	0.032 (1.00)	0.535 (1.00)	0.0078 (1.00)	0.833 (1.00)	0.817 (1.00)
amp 12p12 1	306 (54%)	263	0.131 (1.00)	0.308 (1.00)	0.902 (1.00)	0.0415 (1.00)	1e-05 (0.00884)	0.616 (1.00)	0.0912 (1.00)	0.0126 (1.00)	0.303 (1.00)	0.442 (1.00)	0.00475 (1.00)	0.734 (1.00)	0.18 (1.00)
amp 14q32 33	153 (27%)	416	0.437 (1.00)	0.649 (1.00)	0.197 (1.00)	0.017 (1.00)	0.00028 (0.233)	1 (1.00)	0.203 (1.00)	0.166 (1.00)	0.242 (1.00)	0.373 (1.00)	0.421 (1.00)	0.476 (1.00)	0.561 (1.00)
amp 15q26 3	161 (28%)	408	0.0854 (1.00)	0.422 (1.00)	0.509 (1.00)	0.424 (1.00)	1e-05 (0.00884)	0.979 (1.00)	0.185 (1.00)	0.205 (1.00)	0.546 (1.00)	0.153 (1.00)	0.066 (1.00)	0.164 (1.00)	0.428 (1.00)
amp 18q11 2	142 (25%)	427	0.823 (1.00)	0.779 (1.00)	0.953 (1.00)	0.22 (1.00)	7e-05 (0.0587)	0.156 (1.00)	0.418 (1.00)	0.0422 (1.00)	0.0769 (1.00)	0.148 (1.00)	0.514 (1.00)	0.171 (1.00)	0.277 (1.00)
amp 19q12	319 (56%)	250	0.125 (1.00)	0.00654 (1.00)	0.0283 (1.00)	0.516 (1.00)	1e-05 (0.00884)	0.0476 (1.00)	0.213 (1.00)	0.553 (1.00)	0.376 (1.00)	0.349 (1.00)	0.06 (1.00)	0.83 (1.00)	0.106 (1.00)
amp 19q13 2	241 (42%)	328	0.946 (1.00)	0.54 (1.00)	0.661 (1.00)	0.39 (1.00)	1e-05 (0.00884)	0.445 (1.00)	0.148 (1.00)	0.381 (1.00)	0.0873 (1.00)	0.977 (1.00)	0.551 (1.00)	0.711 (1.00)	0.358 (1.00)
amp 20p13	313 (55%)	256	0.47 (1.00)	0.0166 (1.00)	0.142 (1.00)	0.04 (1.00)	1e-05 (0.00884)	0.198 (1.00)	0.419 (1.00)	0.0818 (1.00)	0.702 (1.00)	0.189 (1.00)	0.00852 (1.00)	0.663 (1.00)	0.94 (1.00)
amp 20q11 21	340 (60%)	229	0.00283 (1.00)	0.0035 (1.00)	0.112 (1.00)	0.00286 (1.00)	1e-05 (0.00884)	0.133 (1.00)	0.019 (1.00)	0.00037 (0.306)	0.048 (1.00)	0.289 (1.00)	0.00057 (0.469)	0.736 (1.00)	0.865 (1.00)
amp 20q13 33	393 (69%)	176	0.00996 (1.00)	0.00084 (0.689)	0.683 (1.00)	0.00142 (1.00)	1e-05 (0.00884)	0.851 (1.00)	0.282 (1.00)	0.00768 (1.00)	0.00468 (1.00)	0.477 (1.00)	0.0497 (1.00)	0.691 (1.00)	0.65 (1.00)
amp xp11 23	154 (27%)	415	0.665 (1.00)	0.865 (1.00)	0.419 (1.00)	0.634 (1.00)	5e-05 (0.042)	0.719 (1.00)	0.904 (1.00)	0.445 (1.00)	0.929 (1.00)	0.276 (1.00)	0.031 (1.00)	0.454 (1.00)	0.91 (1.00)
del 1p36 11	267 (47%)	302	0.739 (1.00)	0.0677 (1.00)	0.0288 (1.00)	0.117 (1.00)	2e-05 (0.017)	0.123 (1.00)	0.391 (1.00)	0.854 (1.00)	0.419 (1.00)	0.22 (1.00)	0.17 (1.00)	0.347 (1.00)	0.0585 (1.00)
del 1q41	95 (17%)	474	0.0882 (1.00)	0.624 (1.00)	0.297 (1.00)	0.836 (1.00)	1e-05 (0.00884)	0.486 (1.00)	0.0191 (1.00)	0.28 (1.00)	0.247 (1.00)	0.921 (1.00)	0.97 (1.00)	0.76 (1.00)	0.672 (1.00)
del 2q37 3	173 (30%)	396	0.0161 (1.00)	0.526 (1.00)	0.767 (1.00)	0.0172 (1.00)	3e-05 (0.0254)	0.815 (1.00)	0.69 (1.00)	0.0163 (1.00)	0.00424 (1.00)	0.0137 (1.00)	0.015 (1.00)	0.054 (1.00)	0.0259 (1.00)
del 3p26 2	209 (37%)	360	0.154 (1.00)	0.00052 (0.429)	0.00562 (1.00)	0.0045 (1.00)	2e-05 (0.017)	0.97 (1.00)	0.239 (1.00)	0.00326 (1.00)	0.00953 (1.00)	0.634 (1.00)	0.123 (1.00)	0.975 (1.00)	0.827 (1.00)
del 5q11 2	347 (61%)	222	0.923 (1.00)	0.828 (1.00)	0.638 (1.00)	0.0421 (1.00)	1e-05 (0.00884)	0.745 (1.00)	0.87 (1.00)	0.209 (1.00)	0.0407 (1.00)	0.0924 (1.00)	0.182 (1.00)	0.0659 (1.00)	0.0561 (1.00)
del 5q13 2	412 (72%)	157	0.747 (1.00)	0.623 (1.00)	0.898 (1.00)	0.259 (1.00)	1e-05 (0.00884)	0.791 (1.00)	0.831 (1.00)	0.517 (1.00)	0.0925 (1.00)	0.157 (1.00)	0.108 (1.00)	0.212 (1.00)	0.175 (1.00)
del 7p22 1	248 (44%)	321	0.397 (1.00)	0.517 (1.00)	0.772 (1.00)	0.0629 (1.00)	1e-05 (0.00884)	0.818 (1.00)	0.605 (1.00)	0.346 (1.00)	0.126 (1.00)	0.346 (1.00)	0.906 (1.00)	0.698 (1.00)	0.293 (1.00)
del 8p23 3	382 (67%)	187	0.0443 (1.00)	0.152 (1.00)	0.573 (1.00)	0.0114 (1.00)	1e-05 (0.00884)	0.893 (1.00)	0.451 (1.00)	0.893 (1.00)	0.912 (1.00)	0.244 (1.00)	0.246 (1.00)	0.171 (1.00)	0.332 (1.00)
del 8p21 2	400 (70%)	169	0.0434 (1.00)	0.0904 (1.00)	0.181 (1.00)	0.00554 (1.00)	1e-05 (0.00884)	0.876 (1.00)	0.994 (1.00)	0.457 (1.00)	0.701 (1.00)	0.581 (1.00)	0.513 (1.00)	0.919 (1.00)	0.0752 (1.00)
del 9q34 13	337 (59%)	232	0.0286 (1.00)	0.00122 (0.997)	0.963 (1.00)	0.454 (1.00)	2e-05 (0.017)	0.418 (1.00)	0.0881 (1.00)	0.207 (1.00)	0.144 (1.00)	0.0349 (1.00)	0.198 (1.00)	0.132 (1.00)	0.078 (1.00)
del 10q24 2	246 (43%)	323	0.00181 (1.00)	0.00279 (1.00)	0.00633 (1.00)	0.214 (1.00)	4e-05 (0.0337)	0.0108 (1.00)	0.00203 (1.00)	0.444 (1.00)	0.295 (1.00)	0.00187 (1.00)	0.453 (1.00)	0.0103 (1.00)	0.00578 (1.00)
del 11p15 5	338 (59%)	231	0.111 (1.00)	0.971 (1.00)	0.618 (1.00)	0.0848 (1.00)	1e-05 (0.00884)	0.945 (1.00)	0.712 (1.00)	0.698 (1.00)	0.504 (1.00)	0.105 (1.00)	0.00913 (1.00)	0.156 (1.00)	0.195 (1.00)
del 12q24 33	217 (38%)	352	0.00096 (0.785)	0.0998 (1.00)	0.164 (1.00)	0.0145 (1.00)	1e-05 (0.00884)	0.295 (1.00)	0.224 (1.00)	0.052 (1.00)	0.0318 (1.00)	0.0151 (1.00)	0.0046 (1.00)	0.0189 (1.00)	0.0267 (1.00)
del 13q14 2	358 (63%)	211	0.01 (1.00)	0.0158 (1.00)	0.613 (1.00)	0.0427 (1.00)	1e-05 (0.00884)	0.00174 (1.00)	0.0513 (1.00)	0.0988 (1.00)	0.681 (1.00)	0.377 (1.00)	0.367 (1.00)	0.452 (1.00)	0.387 (1.00)
del 14q23 3	299 (53%)	270	0.0656 (1.00)	0.505 (1.00)	0.655 (1.00)	0.612 (1.00)	0.00013 (0.109)	0.227 (1.00)	0.511 (1.00)	0.856 (1.00)	0.283 (1.00)	0.899 (1.00)	0.592 (1.00)	0.711 (1.00)	0.798 (1.00)
del 15q15 1	360 (63%)	209	0.0262 (1.00)	0.0601 (1.00)	0.0222 (1.00)	0.00285 (1.00)	1e-05 (0.00884)	0.157 (1.00)	0.151 (1.00)	0.0109 (1.00)	0.497 (1.00)	0.396 (1.00)	0.00206 (1.00)	0.204 (1.00)	0.0237 (1.00)
del 16q22 1	453 (80%)	116	0.497 (1.00)	0.704 (1.00)	0.0309 (1.00)	0.449 (1.00)	0.00017 (0.142)	0.697 (1.00)	0.143 (1.00)	0.223 (1.00)	0.291 (1.00)	0.313 (1.00)	0.0475 (1.00)	0.0601 (1.00)	0.0899 (1.00)
del 16q23 1	444 (78%)	125	0.108 (1.00)	0.245 (1.00)	0.101 (1.00)	0.0611 (1.00)	3e-05 (0.0254)	0.813 (1.00)	0.222 (1.00)	0.273 (1.00)	0.168 (1.00)	0.057 (1.00)	0.0482 (1.00)	0.0407 (1.00)	0.00628 (1.00)
del 19q13 33	295 (52%)	274	0.00026 (0.217)	0.00229 (1.00)	0.0458 (1.00)	0.021 (1.00)	0.0957 (1.00)	0.0293 (1.00)	0.301 (1.00)	0.00675 (1.00)	0.122 (1.00)	0.321 (1.00)	0.129 (1.00)	0.292 (1.00)	0.475 (1.00)
amp 4q13 3	110 (19%)	459	0.952 (1.00)	0.429 (1.00)	0.345 (1.00)	0.987 (1.00)	0.00038 (0.314)	0.554 (1.00)	0.423 (1.00)	0.125 (1.00)	0.478 (1.00)	1 (1.00)	0.723 (1.00)	0.876 (1.00)	0.835 (1.00)
amp 10q22 3	181 (32%)	388	0.471 (1.00)	0.298 (1.00)	0.542 (1.00)	0.964 (1.00)	0.219 (1.00)	0.656 (1.00)	0.845 (1.00)	0.194 (1.00)	0.765 (1.00)	0.268 (1.00)	0.517 (1.00)	0.907 (1.00)	0.412 (1.00)
amp 14q11 2	146 (26%)	423	0.0166 (1.00)	0.0589 (1.00)	0.293 (1.00)	0.00687 (1.00)	0.04 (1.00)	0.536 (1.00)	0.467 (1.00)	0.343 (1.00)	0.408 (1.00)	0.301 (1.00)	0.822 (1.00)	0.217 (1.00)	0.298 (1.00)
amp 17q25 3	212 (37%)	357	0.47 (1.00)	0.0577 (1.00)	0.981 (1.00)	0.666 (1.00)	0.00219 (1.00)	0.072 (1.00)	0.131 (1.00)	0.0116 (1.00)	0.0261 (1.00)	0.323 (1.00)	0.127 (1.00)	0.297 (1.00)	0.0506 (1.00)
amp 22q12 2	89 (16%)	480	0.624 (1.00)	0.155 (1.00)	0.0717 (1.00)	0.0342 (1.00)	0.00128 (1.00)	0.984 (1.00)	0.0878 (1.00)	0.0596 (1.00)	0.0597 (1.00)	0.109 (1.00)	0.0145 (1.00)	0.0374 (1.00)	0.0165 (1.00)
amp xq28	217 (38%)	352	0.242 (1.00)	0.846 (1.00)	0.558 (1.00)	0.123 (1.00)	0.00131 (1.00)	0.454 (1.00)	0.445 (1.00)	0.625 (1.00)	0.938 (1.00)	0.881 (1.00)	0.806 (1.00)	0.868 (1.00)	0.991 (1.00)
del 2p25 3	120 (21%)	449	0.88 (1.00)	0.269 (1.00)	0.421 (1.00)	0.157 (1.00)	0.244 (1.00)	0.26 (1.00)	0.541 (1.00)	0.0625 (1.00)	0.237 (1.00)	0.875 (1.00)	0.951 (1.00)	0.892 (1.00)	1 (1.00)
del 2q22 1	136 (24%)	433	0.107 (1.00)	0.272 (1.00)	0.566 (1.00)	0.00356 (1.00)	0.0851 (1.00)	0.602 (1.00)	0.721 (1.00)	0.921 (1.00)	0.301 (1.00)	0.481 (1.00)	0.599 (1.00)	0.418 (1.00)	0.414 (1.00)
del 4q22 1	388 (68%)	181	0.0522 (1.00)	0.0228 (1.00)	1 (1.00)	0.166 (1.00)	0.0203 (1.00)	0.19 (1.00)	0.0609 (1.00)	0.0703 (1.00)	0.389 (1.00)	0.306 (1.00)	0.253 (1.00)	0.0296 (1.00)	0.224 (1.00)
del 4q34 3	415 (73%)	154	0.0532 (1.00)	0.00062 (0.509)	0.0627 (1.00)	0.0277 (1.00)	0.151 (1.00)	0.669 (1.00)	0.199 (1.00)	0.0834 (1.00)	0.0179 (1.00)	0.423 (1.00)	0.529 (1.00)	0.161 (1.00)	0.279 (1.00)
del 10p15 3	120 (21%)	449	0.177 (1.00)	0.708 (1.00)	0.0887 (1.00)	0.322 (1.00)	0.148 (1.00)	0.289 (1.00)	0.0397 (1.00)	0.0144 (1.00)	0.0887 (1.00)	0.252 (1.00)	0.264 (1.00)	0.113 (1.00)	0.41 (1.00)
del 11q25	195 (34%)	374	0.714 (1.00)	0.636 (1.00)	0.173 (1.00)	0.0634 (1.00)	0.147 (1.00)	0.317 (1.00)	0.197 (1.00)	0.932 (1.00)	0.31 (1.00)	0.634 (1.00)	0.18 (1.00)	0.683 (1.00)	0.19 (1.00)
del 16p13 3	307 (54%)	262	0.608 (1.00)	0.0727 (1.00)	0.274 (1.00)	0.0292 (1.00)	0.0536 (1.00)	0.84 (1.00)	0.818 (1.00)	0.366 (1.00)	0.431 (1.00)	0.221 (1.00)	0.485 (1.00)	0.112 (1.00)	0.455 (1.00)
del 17p12	483 (85%)	86	0.142 (1.00)	0.333 (1.00)	0.594 (1.00)	0.691 (1.00)	0.737 (1.00)	0.907 (1.00)	0.369 (1.00)	0.153 (1.00)	0.194 (1.00)	0.508 (1.00)	0.21 (1.00)	0.467 (1.00)	0.415 (1.00)
del 17q11 2	466 (82%)	103	0.92 (1.00)	0.193 (1.00)	0.733 (1.00)	0.216 (1.00)	0.00057 (0.469)	0.765 (1.00)	0.036 (1.00)	0.373 (1.00)	0.441 (1.00)	0.15 (1.00)	0.164 (1.00)	0.0251 (1.00)	0.762 (1.00)
del 18q23	377 (66%)	192	0.986 (1.00)	0.992 (1.00)	0.147 (1.00)	0.807 (1.00)	0.0158 (1.00)	0.335 (1.00)	0.203 (1.00)	0.126 (1.00)	0.367 (1.00)	0.484 (1.00)	0.176 (1.00)	0.0745 (1.00)	0.743 (1.00)
del 19p13 3	502 (88%)	67	0.159 (1.00)	0.0896 (1.00)	0.84 (1.00)	0.546 (1.00)	0.00053 (0.437)	0.624 (1.00)	0.404 (1.00)	0.333 (1.00)	0.52 (1.00)	0.478 (1.00)	0.731 (1.00)	0.442 (1.00)	0.19 (1.00)
del 19q13 43	279 (49%)	290	0.0115 (1.00)	0.0642 (1.00)	0.0966 (1.00)	0.388 (1.00)	0.00281 (1.00)	0.18 (1.00)	0.416 (1.00)	0.475 (1.00)	0.941 (1.00)	0.523 (1.00)	0.139 (1.00)	0.369 (1.00)	0.654 (1.00)
del 21q22 3	224 (39%)	345	0.369 (1.00)	0.0418 (1.00)	0.692 (1.00)	0.204 (1.00)	0.815 (1.00)	0.661 (1.00)	0.717 (1.00)	0.244 (1.00)	0.127 (1.00)	0.821 (1.00)	0.732 (1.00)	0.198 (1.00)	0.453 (1.00)
del 22q13 32	495 (87%)	74	0.166 (1.00)	0.124 (1.00)	0.0221 (1.00)	0.31 (1.00)	0.00486 (1.00)	0.102 (1.00)	0.0446 (1.00)	0.106 (1.00)	0.0139 (1.00)	0.0308 (1.00)	0.6 (1.00)	0.027 (1.00)	0.11 (1.00)
del xp21 1	350 (62%)	219	0.405 (1.00)	0.646 (1.00)	0.0984 (1.00)	0.797 (1.00)	0.123 (1.00)	0.461 (1.00)	0.106 (1.00)	0.883 (1.00)	0.242 (1.00)	0.976 (1.00)	0.718 (1.00)	0.861 (1.00)	0.108 (1.00)

'amp_1p34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S1. Gene #1: 'amp_1p34.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
AMP PEAK 1(1P34.3) MUTATED	59	120	108
AMP PEAK 1(1P34.3) WILD-TYPE	115	86	81

Figure S1. Get High-res Image Gene #1: 'amp_1p34.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S2. Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
AMP PEAK 2(1Q21.3) MUTATED	90	115	156
AMP PEAK 2(1Q21.3) WILD-TYPE	84	91	33

Figure S2. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_1q42.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S3. Gene #3: 'amp_1q42.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
AMP PEAK 3(1Q42.2) MUTATED	90	86	138
AMP PEAK 3(1Q42.2) WILD-TYPE	84	120	51

Figure S3. Get High-res Image Gene #3: 'amp_1q42.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_2p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S4. Gene #4: 'amp_2p23.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
AMP PEAK 4(2P23.2) MUTATED	48	86	111
AMP PEAK 4(2P23.2) WILD-TYPE	126	120	78

Figure S4. Get High-res Image Gene #4: 'amp_2p23.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_2q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S5. Gene #5: 'amp_2q31.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
AMP PEAK 5(2Q31.2) MUTATED	47	102	110
AMP PEAK 5(2Q31.2) WILD-TYPE	127	104	79

Figure S5. Get High-res Image Gene #5: 'amp_2q31.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_3q26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S6. Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
AMP PEAK 6(3Q26.2) MUTATED	118	182	176
AMP PEAK 6(3Q26.2) WILD-TYPE	56	24	13

Figure S6. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_4p16.3' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.23

Table S7. Gene #7: 'amp_4p16.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
AMP PEAK 7(4P16.3) MUTATED	34	77	46
AMP PEAK 7(4P16.3) WILD-TYPE	140	129	143

Figure S7. Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S8. Gene #9: 'amp_5p15.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
AMP PEAK 9(5P15.33) MUTATED	64	125	115
AMP PEAK 9(5P15.33) WILD-TYPE	110	81	74

Figure S8. Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_6p22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S9. Gene #10: 'amp_6p22.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
AMP PEAK 10(6P22.3) MUTATED	63	124	113
AMP PEAK 10(6P22.3) WILD-TYPE	111	82	76

Figure S9. Get High-res Image Gene #10: 'amp_6p22.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_7q36.3' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S10. Gene #11: 'amp_7q36.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
AMP PEAK 11(7Q36.3) MUTATED	70	125	116
AMP PEAK 11(7Q36.3) WILD-TYPE	104	81	73

Figure S10. Get High-res Image Gene #11: 'amp_7q36.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_8p11.21' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.034

Table S11. Gene #12: 'amp_8p11.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
AMP PEAK 12(8P11.21) MUTATED	43	73	91
AMP PEAK 12(8P11.21) WILD-TYPE	131	133	98

Figure S11. Get High-res Image Gene #12: 'amp_8p11.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_8q24.21' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S12. Gene #13: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	216	126
AMP PEAK 13(8Q24.21) MUTATED	144	188	110
AMP PEAK 13(8Q24.21) WILD-TYPE	71	28	16

Figure S12. Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8q24.21' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S13. Gene #13: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	310	158	89
AMP PEAK 13(8Q24.21) MUTATED	245	144	53
AMP PEAK 13(8Q24.21) WILD-TYPE	65	14	36

Figure S13. Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S14. Gene #13: 'amp_8q24.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
AMP PEAK 13(8Q24.21) MUTATED	118	199	134
AMP PEAK 13(8Q24.21) WILD-TYPE	56	7	55

Figure S14. Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S15. Gene #13: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	67	91
AMP PEAK 13(8Q24.21) MUTATED	90	61	56
AMP PEAK 13(8Q24.21) WILD-TYPE	10	6	35

Figure S15. Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CNMF'

'amp_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S16. Gene #14: 'amp_10p15.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
AMP PEAK 14(10P15.3) MUTATED	46	80	120
AMP PEAK 14(10P15.3) WILD-TYPE	128	126	69

Figure S16. Get High-res Image Gene #14: 'amp_10p15.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_11q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S17. Gene #16: 'amp_11q14.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
AMP PEAK 16(11Q14.1) MUTATED	57	121	75
AMP PEAK 16(11Q14.1) WILD-TYPE	117	85	114

Figure S17. Get High-res Image Gene #16: 'amp_11q14.1' versus Molecular Subtype #5: 'CN_CNMF'

'amp_12p13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S18. Gene #17: 'amp_12p13.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
AMP PEAK 17(12P13.33) MUTATED	72	114	137
AMP PEAK 17(12P13.33) WILD-TYPE	102	92	52

Figure S18. Get High-res Image Gene #17: 'amp_12p13.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_12p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S19. Gene #18: 'amp_12p12.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
AMP PEAK 18(12P12.1) MUTATED	67	99	140
AMP PEAK 18(12P12.1) WILD-TYPE	107	107	49

Figure S19. Get High-res Image Gene #18: 'amp_12p12.1' versus Molecular Subtype #5: 'CN_CNMF'

'amp_14q32.33' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.23

Table S20. Gene #20: 'amp_14q32.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
AMP PEAK 20(14Q32.33) MUTATED	43	75	35
AMP PEAK 20(14Q32.33) WILD-TYPE	131	131	154

Figure S20. Get High-res Image Gene #20: 'amp_14q32.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_15q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S21. Gene #21: 'amp_15q26.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
AMP PEAK 21(15Q26.3) MUTATED	35	91	35
AMP PEAK 21(15Q26.3) WILD-TYPE	139	115	154

Figure S21. Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_18q11.2' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.059

Table S22. Gene #23: 'amp_18q11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
AMP PEAK 23(18Q11.2) MUTATED	26	48	68
AMP PEAK 23(18Q11.2) WILD-TYPE	148	158	121

Figure S22. Get High-res Image Gene #23: 'amp_18q11.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19p13.12' versus 'MRNA_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.22

Table S23. Gene #24: 'amp_19p13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	216	126
AMP PEAK 24(19P13.12) MUTATED	136	115	51
AMP PEAK 24(19P13.12) WILD-TYPE	79	101	75

Figure S23. Get High-res Image Gene #24: 'amp_19p13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19p13.12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.2

Table S24. Gene #24: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	310	158	89
AMP PEAK 24(19P13.12) MUTATED	186	64	52
AMP PEAK 24(19P13.12) WILD-TYPE	124	94	37

Figure S24. Get High-res Image Gene #24: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19p13.12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S25. Gene #24: 'amp_19p13.12' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
AMP PEAK 24(19P13.12) MUTATED	72	95	141
AMP PEAK 24(19P13.12) WILD-TYPE	102	111	48

Figure S25. Get High-res Image Gene #24: 'amp_19p13.12' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19p13.12' versus 'RPPA_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.23

Table S26. Gene #24: 'amp_19p13.12' versus Molecular Subtype #6: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	196	82
AMP PEAK 24(19P13.12) MUTATED	59	125	32
AMP PEAK 24(19P13.12) WILD-TYPE	61	71	50

Figure S26. Get High-res Image Gene #24: 'amp_19p13.12' versus Molecular Subtype #6: 'RPPA_CNMF'

'amp_19p13.12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.092

Table S27. Gene #24: 'amp_19p13.12' versus Molecular Subtype #7: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	96	128	58
AMP PEAK 24(19P13.12) MUTATED	44	55	86	31
AMP PEAK 24(19P13.12) WILD-TYPE	72	41	42	27

Figure S27. Get High-res Image Gene #24: 'amp_19p13.12' versus Molecular Subtype #7: 'RPPA_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S28. Gene #25: 'amp_19q12' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
AMP PEAK 25(19Q12) MUTATED	66	88	165
AMP PEAK 25(19Q12) WILD-TYPE	108	118	24

Figure S28. Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S29. Gene #26: 'amp_19q13.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
AMP PEAK 26(19Q13.2) MUTATED	51	71	119
AMP PEAK 26(19Q13.2) WILD-TYPE	123	135	70

Figure S29. Get High-res Image Gene #26: 'amp_19q13.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_20p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S30. Gene #27: 'amp_20p13' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
AMP PEAK 27(20P13) MUTATED	72	100	141
AMP PEAK 27(20P13) WILD-TYPE	102	106	48

Figure S30. Get High-res Image Gene #27: 'amp_20p13' versus Molecular Subtype #5: 'CN_CNMF'

'amp_20q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S31. Gene #28: 'amp_20q11.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
AMP PEAK 28(20Q11.21) MUTATED	78	97	165
AMP PEAK 28(20Q11.21) WILD-TYPE	96	109	24

Figure S31. Get High-res Image Gene #28: 'amp_20q11.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_20q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S32. Gene #29: 'amp_20q13.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
AMP PEAK 29(20Q13.33) MUTATED	88	136	169
AMP PEAK 29(20Q13.33) WILD-TYPE	86	70	20

Figure S32. Get High-res Image Gene #29: 'amp_20q13.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_xp11.23' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.042

Table S33. Gene #31: 'amp_xp11.23' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
AMP PEAK 31(XP11.23) MUTATED	28	55	71
AMP PEAK 31(XP11.23) WILD-TYPE	146	151	118

Figure S33. Get High-res Image Gene #31: 'amp_xp11.23' versus Molecular Subtype #5: 'CN_CNMF'

'del_1p36.11' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S34. Gene #33: 'del_1p36.11' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
DEL PEAK 1(1P36.11) MUTATED	92	113	62
DEL PEAK 1(1P36.11) WILD-TYPE	82	93	127

Figure S34. Get High-res Image Gene #33: 'del_1p36.11' versus Molecular Subtype #5: 'CN_CNMF'

'del_1q41' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S35. Gene #34: 'del_1q41' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
DEL PEAK 2(1Q41) MUTATED	15	58	22
DEL PEAK 2(1Q41) WILD-TYPE	159	148	167

Figure S35. Get High-res Image Gene #34: 'del_1q41' versus Molecular Subtype #5: 'CN_CNMF'

'del_2q37.3' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S36. Gene #37: 'del_2q37.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
DEL PEAK 5(2Q37.3) MUTATED	39	88	46
DEL PEAK 5(2Q37.3) WILD-TYPE	135	118	143

Figure S36. Get High-res Image Gene #37: 'del_2q37.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_3p26.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S37. Gene #38: 'del_3p26.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
DEL PEAK 6(3P26.2) MUTATED	45	71	93
DEL PEAK 6(3P26.2) WILD-TYPE	129	135	96

Figure S37. Get High-res Image Gene #38: 'del_3p26.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_5q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S38. Gene #41: 'del_5q11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
DEL PEAK 9(5Q11.2) MUTATED	74	146	127
DEL PEAK 9(5Q11.2) WILD-TYPE	100	60	62

Figure S38. Get High-res Image Gene #41: 'del_5q11.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_5q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S39. Gene #42: 'del_5q13.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
DEL PEAK 10(5Q13.2) MUTATED	95	178	139
DEL PEAK 10(5Q13.2) WILD-TYPE	79	28	50

Figure S39. Get High-res Image Gene #42: 'del_5q13.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_6q27' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S40. Gene #43: 'del_6q27' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
DEL PEAK 11(6Q27) MUTATED	127	162	92
DEL PEAK 11(6Q27) WILD-TYPE	47	44	97

Figure S40. Get High-res Image Gene #43: 'del_6q27' versus Molecular Subtype #5: 'CN_CNMF'

'del_6q27' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S41. Gene #43: 'del_6q27' versus Molecular Subtype #8: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	67	91
DEL PEAK 11(6Q27) MUTATED	67	52	39
DEL PEAK 11(6Q27) WILD-TYPE	33	15	52

Figure S41. Get High-res Image Gene #43: 'del_6q27' versus Molecular Subtype #8: 'MRNASEQ_CNMF'

'del_7p22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S42. Gene #44: 'del_7p22.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
DEL PEAK 12(7P22.1) MUTATED	51	133	64
DEL PEAK 12(7P22.1) WILD-TYPE	123	73	125

Figure S42. Get High-res Image Gene #44: 'del_7p22.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_8p23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S43. Gene #45: 'del_8p23.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
DEL PEAK 13(8P23.3) MUTATED	80	164	138
DEL PEAK 13(8P23.3) WILD-TYPE	94	42	51

Figure S43. Get High-res Image Gene #45: 'del_8p23.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_8p21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S44. Gene #46: 'del_8p21.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
DEL PEAK 14(8P21.2) MUTATED	91	166	143
DEL PEAK 14(8P21.2) WILD-TYPE	83	40	46

Figure S44. Get High-res Image Gene #46: 'del_8p21.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_9p24.3' versus 'MRNA_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.23

Table S45. Gene #47: 'del_9p24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	216	126
DEL PEAK 15(9P24.3) MUTATED	109	73	66
DEL PEAK 15(9P24.3) WILD-TYPE	106	143	60

Figure S45. Get High-res Image Gene #47: 'del_9p24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p24.3' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.042

Table S46. Gene #47: 'del_9p24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	310	158	89
DEL PEAK 15(9P24.3) MUTATED	120	69	59
DEL PEAK 15(9P24.3) WILD-TYPE	190	89	30

Figure S46. Get High-res Image Gene #47: 'del_9p24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9q34.13' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S47. Gene #48: 'del_9q34.13' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
DEL PEAK 16(9Q34.13) MUTATED	91	105	141
DEL PEAK 16(9Q34.13) WILD-TYPE	83	101	48

Figure S47. Get High-res Image Gene #48: 'del_9q34.13' versus Molecular Subtype #5: 'CN_CNMF'

'del_10q24.2' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.034

Table S48. Gene #50: 'del_10q24.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
DEL PEAK 18(10Q24.2) MUTATED	55	113	78
DEL PEAK 18(10Q24.2) WILD-TYPE	119	93	111

Figure S48. Get High-res Image Gene #50: 'del_10q24.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S49. Gene #51: 'del_11p15.5' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
DEL PEAK 19(11P15.5) MUTATED	81	158	99
DEL PEAK 19(11P15.5) WILD-TYPE	93	48	90

Figure S49. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #5: 'CN_CNMF'

'del_12q24.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S50. Gene #53: 'del_12q24.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
DEL PEAK 21(12Q24.33) MUTATED	58	112	47
DEL PEAK 21(12Q24.33) WILD-TYPE	116	94	142

Figure S50. Get High-res Image Gene #53: 'del_12q24.33' versus Molecular Subtype #5: 'CN_CNMF'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S51. Gene #54: 'del_13q14.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
DEL PEAK 22(13Q14.2) MUTATED	88	156	114
DEL PEAK 22(13Q14.2) WILD-TYPE	86	50	75

Figure S51. Get High-res Image Gene #54: 'del_13q14.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_14q23.3' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.11

Table S52. Gene #55: 'del_14q23.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
DEL PEAK 23(14Q23.3) MUTATED	75	102	122
DEL PEAK 23(14Q23.3) WILD-TYPE	99	104	67

Figure S52. Get High-res Image Gene #55: 'del_14q23.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_15q15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S53. Gene #56: 'del_15q15.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
DEL PEAK 24(15Q15.1) MUTATED	83	122	155
DEL PEAK 24(15Q15.1) WILD-TYPE	91	84	34

Figure S53. Get High-res Image Gene #56: 'del_15q15.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_16q22.1' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.14

Table S54. Gene #58: 'del_16q22.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
DEL PEAK 26(16Q22.1) MUTATED	120	171	162
DEL PEAK 26(16Q22.1) WILD-TYPE	54	35	27

Figure S54. Get High-res Image Gene #58: 'del_16q22.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S55. Gene #59: 'del_16q23.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	206	189
DEL PEAK 27(16Q23.1) MUTATED	114	168	162
DEL PEAK 27(16Q23.1) WILD-TYPE	60	38	27

Figure S55. Get High-res Image Gene #59: 'del_16q23.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_19q13.33' versus 'MRNA_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.22

Table S56. Gene #64: 'del_19q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	216	126
DEL PEAK 32(19Q13.33) MUTATED	127	117	46
DEL PEAK 32(19Q13.33) WILD-TYPE	88	99	80

Figure S56. Get High-res Image Gene #64: 'del_19q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = OV-TP.transferedmergedcluster.txt
Number of patients = 569
Number of significantly focal cnvs = 68
Number of molecular subtypes = 13
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

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

Q value calculation

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

Download Results

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

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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