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

Bladder Urothelial Carcinoma (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/C1KD1WMP

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 70 focal events and 10 molecular subtypes across 264 patients, 70 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p34.2 cnv correlated to 'CN_CNMF'.
amp_1q21.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_1q23.3 cnv correlated to 'CN_CNMF'.
amp_3p25.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3q26.32 cnv correlated to 'CN_CNMF'.
amp_5p15.33 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
amp_6p22.3 cnv correlated to 'CN_CNMF'.
amp_7p21.1 cnv correlated to 'CN_CNMF'.
amp_7p11.2 cnv correlated to 'CN_CNMF'.
amp_8p11.23 cnv correlated to 'CN_CNMF'.
amp_8p11.21 cnv correlated to 'CN_CNMF'.
amp_8q22.3 cnv correlated to 'CN_CNMF'.
amp_9p24.1 cnv correlated to 'CN_CNMF'.
amp_10p14 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_11q13.3 cnv correlated to 'CN_CNMF'.
amp_14q11.2 cnv correlated to 'MIRSEQ_CHIERARCHICAL'.
amp_16p13.13 cnv correlated to 'CN_CNMF'.
amp_17q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
amp_17q12 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
amp_19q12 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_19q13.43 cnv correlated to 'CN_CNMF'.
amp_20q11.21 cnv correlated to 'CN_CNMF'.
del_2q37.1 cnv correlated to 'CN_CNMF'.
del_3p21.31 cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_3p14.2 cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_3p13 cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_5q11.2 cnv correlated to 'CN_CNMF'.
del_5q35.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_6q21 cnv correlated to 'CN_CNMF'.
del_6q27 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
del_8p23.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_8p12 cnv correlated to 'CN_CNMF'.
del_8p11.21 cnv correlated to 'CN_CNMF'.
del_9p23 cnv correlated to 'CN_CNMF'.
del_9p21.3 cnv correlated to 'CN_CNMF'.
del_9q33.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_11p15.5 cnv correlated to 'CN_CNMF'.
del_11q23.3 cnv correlated to 'CN_CNMF'.
del_14q12 cnv correlated to 'CN_CNMF'.
del_14q24.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_15q13.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
del_16q23.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
del_17p12 cnv correlated to 'CN_CNMF'.
del_18q21.2 cnv correlated to 'MIRSEQ_CHIERARCHICAL'.
del_22q13.31 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 70 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 70 significant findings detected.


		Clinical Features	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	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 3p25 2	127 (48%)	137	1e-05 (0.007)	4e-05 (0.0261)	0.0789 (1.00)	0.0103 (1.00)	1e-05 (0.007)	2e-05 (0.0132)	7e-05 (0.0454)	2e-05 (0.0132)	1e-05 (0.007)	8e-05 (0.0518)
amp 17q11 2	117 (44%)	147	1e-05 (0.007)	0.00022 (0.141)	0.0321 (1.00)	0.0885 (1.00)	0.00039 (0.246)	0.00305 (1.00)	0.0592 (1.00)	0.00071 (0.441)	0.00187 (1.00)	0.0101 (1.00)
del 14q24 1	86 (33%)	178	1e-05 (0.007)	1e-05 (0.007)	0.393 (1.00)	0.346 (1.00)	0.00283 (1.00)	1e-05 (0.007)	0.0464 (1.00)	0.00063 (0.393)	0.0846 (1.00)	0.0841 (1.00)
amp 1q21 3	128 (48%)	136	1e-05 (0.007)	2e-05 (0.0132)	0.391 (1.00)	0.722 (1.00)	0.0252 (1.00)	0.0383 (1.00)	0.0442 (1.00)	0.00376 (1.00)	0.335 (1.00)	0.125 (1.00)
amp 5p15 33	131 (50%)	133	1e-05 (0.007)	0.0406 (1.00)	0.0209 (1.00)	0.18 (1.00)	0.469 (1.00)	0.233 (1.00)	0.0091 (1.00)	0.00022 (0.141)	0.215 (1.00)	0.00429 (1.00)
amp 10p14	116 (44%)	148	1e-05 (0.007)	1e-05 (0.007)	0.357 (1.00)	0.426 (1.00)	0.515 (1.00)	0.11 (1.00)	0.433 (1.00)	0.162 (1.00)	0.388 (1.00)	0.23 (1.00)
amp 17q12	110 (42%)	154	1e-05 (0.007)	0.163 (1.00)	0.0779 (1.00)	0.0187 (1.00)	0.00511 (1.00)	0.0153 (1.00)	0.00363 (1.00)	0.00177 (1.00)	0.00017 (0.109)	0.00112 (0.689)
amp 19q12	109 (41%)	155	1e-05 (0.007)	0.00021 (0.135)	0.703 (1.00)	0.546 (1.00)	0.0582 (1.00)	0.159 (1.00)	0.356 (1.00)	0.00111 (0.684)	0.334 (1.00)	0.0454 (1.00)
del 3p21 31	77 (29%)	187	0.0358 (1.00)	0.383 (1.00)	0.0301 (1.00)	0.00733 (1.00)	1e-05 (0.007)	4e-05 (0.0261)	0.106 (1.00)	0.0195 (1.00)	0.134 (1.00)	0.0626 (1.00)
del 3p14 2	75 (28%)	189	0.0578 (1.00)	0.499 (1.00)	0.0337 (1.00)	0.0172 (1.00)	2e-05 (0.0132)	2e-05 (0.0132)	0.351 (1.00)	0.00261 (1.00)	0.0889 (1.00)	0.0405 (1.00)
del 3p13	71 (27%)	193	0.386 (1.00)	0.366 (1.00)	0.12 (1.00)	0.0023 (1.00)	2e-05 (0.0132)	0.00011 (0.0709)	0.536 (1.00)	0.041 (1.00)	0.172 (1.00)	0.0171 (1.00)
del 5q35 1	126 (48%)	138	3e-05 (0.0197)	0.00017 (0.109)	0.472 (1.00)	0.33 (1.00)	0.428 (1.00)	0.0591 (1.00)	0.393 (1.00)	0.00872 (1.00)	0.507 (1.00)	0.0481 (1.00)
del 6q27	119 (45%)	145	1e-05 (0.007)	0.0164 (1.00)	0.661 (1.00)	0.435 (1.00)	0.241 (1.00)	0.011 (1.00)	0.0805 (1.00)	3e-05 (0.0197)	0.166 (1.00)	0.0669 (1.00)
del 8p23 3	151 (57%)	113	1e-05 (0.007)	1e-05 (0.007)	0.553 (1.00)	0.194 (1.00)	0.182 (1.00)	0.857 (1.00)	0.00239 (1.00)	0.0125 (1.00)	0.0381 (1.00)	0.0333 (1.00)
del 9q33 2	104 (39%)	160	1e-05 (0.007)	0.0338 (1.00)	0.0667 (1.00)	0.00322 (1.00)	0.0129 (1.00)	0.00022 (0.141)	0.464 (1.00)	0.0994 (1.00)	0.129 (1.00)	0.0229 (1.00)
del 15q13 1	107 (41%)	157	0.00026 (0.166)	0.00127 (0.78)	0.319 (1.00)	0.572 (1.00)	0.947 (1.00)	0.567 (1.00)	0.162 (1.00)	6e-05 (0.0391)	0.282 (1.00)	0.165 (1.00)
del 16q23 1	73 (28%)	191	6e-05 (0.0391)	0.0342 (1.00)	0.503 (1.00)	0.0643 (1.00)	0.0884 (1.00)	0.182 (1.00)	0.0314 (1.00)	0.00031 (0.196)	0.154 (1.00)	0.014 (1.00)
amp 1p34 2	70 (27%)	194	1e-05 (0.007)	0.00164 (0.999)	0.178 (1.00)	0.381 (1.00)	0.792 (1.00)	0.433 (1.00)	0.148 (1.00)	0.302 (1.00)	0.822 (1.00)	0.929 (1.00)
amp 1q23 3	135 (51%)	129	1e-05 (0.007)	0.00162 (0.988)	0.551 (1.00)	0.886 (1.00)	0.123 (1.00)	0.309 (1.00)	0.00309 (1.00)	0.0144 (1.00)	0.0414 (1.00)	0.0495 (1.00)
amp 3q26 32	142 (54%)	122	1e-05 (0.007)	0.57 (1.00)	0.389 (1.00)	0.154 (1.00)	0.739 (1.00)	0.368 (1.00)	0.575 (1.00)	0.00653 (1.00)	0.417 (1.00)	0.0909 (1.00)
amp 6p22 3	111 (42%)	153	1e-05 (0.007)	0.0014 (0.857)	0.321 (1.00)	0.487 (1.00)	0.737 (1.00)	0.807 (1.00)	0.294 (1.00)	0.176 (1.00)	0.354 (1.00)	0.125 (1.00)
amp 7p21 1	134 (51%)	130	0.00014 (0.0902)	0.0131 (1.00)	0.133 (1.00)	0.32 (1.00)	0.888 (1.00)	0.88 (1.00)	0.193 (1.00)	0.0839 (1.00)	0.728 (1.00)	0.47 (1.00)
amp 7p11 2	131 (50%)	133	1e-05 (0.007)	0.0148 (1.00)	0.0897 (1.00)	0.6 (1.00)	0.987 (1.00)	0.516 (1.00)	0.404 (1.00)	0.24 (1.00)	0.642 (1.00)	0.543 (1.00)
amp 8p11 23	84 (32%)	180	1e-05 (0.007)	0.097 (1.00)	0.746 (1.00)	0.791 (1.00)	1 (1.00)	0.75 (1.00)	0.244 (1.00)	0.544 (1.00)	0.0679 (1.00)	0.411 (1.00)
amp 8p11 21	86 (33%)	178	1e-05 (0.007)	0.0274 (1.00)	0.888 (1.00)	0.949 (1.00)	0.522 (1.00)	0.399 (1.00)	0.032 (1.00)	0.00147 (0.898)	0.0208 (1.00)	0.0189 (1.00)
amp 8q22 3	169 (64%)	95	1e-05 (0.007)	0.00075 (0.465)	0.0243 (1.00)	0.193 (1.00)	0.612 (1.00)	0.629 (1.00)	0.0802 (1.00)	0.00064 (0.399)	0.0179 (1.00)	0.114 (1.00)
amp 9p24 1	53 (20%)	211	1e-05 (0.007)	0.284 (1.00)	0.671 (1.00)	0.326 (1.00)	0.33 (1.00)	0.0795 (1.00)	0.942 (1.00)	0.0389 (1.00)	0.826 (1.00)	0.276 (1.00)
amp 11q13 3	101 (38%)	163	8e-05 (0.0518)	0.323 (1.00)	0.234 (1.00)	0.0794 (1.00)	0.183 (1.00)	0.153 (1.00)	0.17 (1.00)	0.00423 (1.00)	0.653 (1.00)	0.716 (1.00)
amp 14q11 2	63 (24%)	201	0.742 (1.00)	0.422 (1.00)	0.614 (1.00)	0.0903 (1.00)	0.355 (1.00)	0.317 (1.00)	0.49 (1.00)	0.00029 (0.184)	0.573 (1.00)	1 (1.00)
amp 16p13 13	56 (21%)	208	0.00039 (0.246)	0.253 (1.00)	0.52 (1.00)	0.673 (1.00)	0.35 (1.00)	0.782 (1.00)	0.617 (1.00)	0.286 (1.00)	0.504 (1.00)	0.414 (1.00)
amp 19q13 43	103 (39%)	161	1e-05 (0.007)	0.00908 (1.00)	0.167 (1.00)	0.302 (1.00)	0.305 (1.00)	0.945 (1.00)	0.672 (1.00)	0.0352 (1.00)	0.26 (1.00)	0.0367 (1.00)
amp 20q11 21	171 (65%)	93	0.0003 (0.19)	0.0459 (1.00)	0.713 (1.00)	0.0554 (1.00)	0.944 (1.00)	0.32 (1.00)	0.488 (1.00)	0.00195 (1.00)	0.33 (1.00)	0.575 (1.00)
del 2q37 1	130 (49%)	134	1e-05 (0.007)	0.0117 (1.00)	0.593 (1.00)	0.443 (1.00)	0.307 (1.00)	0.122 (1.00)	0.0685 (1.00)	0.0762 (1.00)	0.0841 (1.00)	0.0636 (1.00)
del 5q11 2	133 (50%)	131	1e-05 (0.007)	0.00092 (0.569)	0.958 (1.00)	0.625 (1.00)	0.578 (1.00)	0.0779 (1.00)	0.172 (1.00)	0.00279 (1.00)	0.609 (1.00)	0.142 (1.00)
del 6q21	117 (44%)	147	1e-05 (0.007)	0.0255 (1.00)	0.855 (1.00)	0.432 (1.00)	0.645 (1.00)	0.069 (1.00)	0.326 (1.00)	0.00472 (1.00)	0.415 (1.00)	0.101 (1.00)
del 8p12	129 (49%)	135	1e-05 (0.007)	0.00062 (0.388)	0.553 (1.00)	0.516 (1.00)	0.133 (1.00)	0.885 (1.00)	0.0383 (1.00)	0.219 (1.00)	0.126 (1.00)	0.0642 (1.00)
del 8p11 21	69 (26%)	195	8e-05 (0.0518)	0.449 (1.00)	0.213 (1.00)	0.248 (1.00)	0.228 (1.00)	0.277 (1.00)	0.0654 (1.00)	0.395 (1.00)	0.0546 (1.00)	0.0547 (1.00)
del 9p23	115 (44%)	149	1e-05 (0.007)	0.345 (1.00)	0.22 (1.00)	0.203 (1.00)	0.866 (1.00)	0.0481 (1.00)	0.402 (1.00)	0.668 (1.00)	0.694 (1.00)	0.691 (1.00)
del 9p21 3	157 (59%)	107	1e-05 (0.007)	0.863 (1.00)	0.452 (1.00)	0.0103 (1.00)	0.726 (1.00)	0.0742 (1.00)	0.884 (1.00)	0.933 (1.00)	0.593 (1.00)	0.833 (1.00)
del 11p15 5	129 (49%)	135	1e-05 (0.007)	0.00093 (0.574)	0.365 (1.00)	0.243 (1.00)	0.0252 (1.00)	0.00062 (0.388)	0.0299 (1.00)	0.102 (1.00)	0.0152 (1.00)	0.119 (1.00)
del 11q23 3	100 (38%)	164	1e-05 (0.007)	0.124 (1.00)	0.775 (1.00)	0.839 (1.00)	0.032 (1.00)	0.0841 (1.00)	0.242 (1.00)	0.804 (1.00)	0.316 (1.00)	0.625 (1.00)
del 14q12	80 (30%)	184	1e-05 (0.007)	0.00042 (0.264)	0.121 (1.00)	0.0709 (1.00)	0.144 (1.00)	0.0226 (1.00)	0.0399 (1.00)	0.0266 (1.00)	0.117 (1.00)	0.352 (1.00)
del 17p12	137 (52%)	127	1e-05 (0.007)	0.0225 (1.00)	0.201 (1.00)	0.609 (1.00)	0.376 (1.00)	0.0599 (1.00)	0.751 (1.00)	0.0103 (1.00)	0.869 (1.00)	0.864 (1.00)
del 18q21 2	115 (44%)	149	0.0571 (1.00)	0.876 (1.00)	0.872 (1.00)	0.745 (1.00)	0.877 (1.00)	0.672 (1.00)	0.00457 (1.00)	0.00028 (0.178)	0.0596 (1.00)	0.0345 (1.00)
del 22q13 31	118 (45%)	146	3e-05 (0.0197)	0.00178 (1.00)	0.451 (1.00)	0.00774 (1.00)	0.102 (1.00)	0.462 (1.00)	0.645 (1.00)	0.106 (1.00)	0.0981 (1.00)	0.499 (1.00)
amp 4p16 3	53 (20%)	211	0.00245 (1.00)	0.0489 (1.00)	0.0329 (1.00)	0.0267 (1.00)	0.00787 (1.00)	0.00068 (0.423)	0.0205 (1.00)	0.00504 (1.00)	0.00804 (1.00)	0.0174 (1.00)
amp 4q13 3	49 (19%)	215	0.00049 (0.308)	0.00807 (1.00)	0.581 (1.00)	0.705 (1.00)	0.371 (1.00)	0.317 (1.00)	0.428 (1.00)	0.0779 (1.00)	0.0735 (1.00)	0.0713 (1.00)
amp 4q31 21	29 (11%)	235	0.182 (1.00)	0.201 (1.00)	0.123 (1.00)	0.263 (1.00)	0.293 (1.00)	0.18 (1.00)	0.236 (1.00)	0.0653 (1.00)	0.842 (1.00)	0.332 (1.00)
amp 6q21	23 (9%)	241	0.0418 (1.00)	0.0918 (1.00)	0.515 (1.00)	0.0789 (1.00)	0.484 (1.00)	0.605 (1.00)	0.789 (1.00)	0.229 (1.00)	0.74 (1.00)	0.836 (1.00)
amp 11q22 2	49 (19%)	215	0.151 (1.00)	0.129 (1.00)	0.731 (1.00)	0.413 (1.00)	0.0676 (1.00)	0.0145 (1.00)	0.096 (1.00)	0.00133 (0.815)	0.16 (1.00)	0.161 (1.00)
amp 12q15	77 (29%)	187	0.00703 (1.00)	0.132 (1.00)	0.0385 (1.00)	0.0198 (1.00)	0.022 (1.00)	0.0215 (1.00)	0.188 (1.00)	0.0174 (1.00)	0.0357 (1.00)	0.00833 (1.00)
amp 13q22 1	84 (32%)	180	0.291 (1.00)	0.75 (1.00)	0.962 (1.00)	0.85 (1.00)	0.886 (1.00)	0.954 (1.00)	0.752 (1.00)	0.683 (1.00)	0.575 (1.00)	0.335 (1.00)
amp 16p11 2	64 (24%)	200	0.0101 (1.00)	0.251 (1.00)	0.469 (1.00)	0.368 (1.00)	0.782 (1.00)	0.712 (1.00)	0.867 (1.00)	0.656 (1.00)	0.755 (1.00)	0.962 (1.00)
amp 16q22 1	75 (28%)	189	0.0651 (1.00)	0.859 (1.00)	0.0843 (1.00)	0.0861 (1.00)	0.0695 (1.00)	0.0555 (1.00)	0.413 (1.00)	0.191 (1.00)	0.289 (1.00)	0.5 (1.00)
amp 22q11 23	55 (21%)	209	0.00058 (0.364)	0.0363 (1.00)	0.592 (1.00)	0.61 (1.00)	0.0279 (1.00)	0.103 (1.00)	0.162 (1.00)	0.235 (1.00)	0.433 (1.00)	0.519 (1.00)
del 1p36 11	52 (20%)	212	0.46 (1.00)	0.177 (1.00)	0.251 (1.00)	0.0303 (1.00)	0.189 (1.00)	0.603 (1.00)	0.814 (1.00)	0.329 (1.00)	0.52 (1.00)	0.344 (1.00)
del 1q32 1	47 (18%)	217	0.0973 (1.00)	0.142 (1.00)	0.353 (1.00)	0.601 (1.00)	0.43 (1.00)	0.107 (1.00)	0.157 (1.00)	0.0102 (1.00)	0.0973 (1.00)	0.339 (1.00)
del 2q22 1	80 (30%)	184	0.00331 (1.00)	0.0896 (1.00)	0.271 (1.00)	0.943 (1.00)	0.137 (1.00)	0.152 (1.00)	0.309 (1.00)	0.254 (1.00)	0.138 (1.00)	0.388 (1.00)
del 4q22 1	109 (41%)	155	0.273 (1.00)	0.258 (1.00)	0.507 (1.00)	0.502 (1.00)	0.0919 (1.00)	0.0685 (1.00)	0.304 (1.00)	0.14 (1.00)	0.0855 (1.00)	0.0344 (1.00)
del 4q34 2	119 (45%)	145	0.0127 (1.00)	0.338 (1.00)	0.458 (1.00)	0.795 (1.00)	0.732 (1.00)	0.488 (1.00)	0.0532 (1.00)	0.146 (1.00)	0.186 (1.00)	0.079 (1.00)
del 6p25 3	69 (26%)	195	0.0165 (1.00)	0.034 (1.00)	0.839 (1.00)	0.872 (1.00)	0.425 (1.00)	0.0744 (1.00)	0.604 (1.00)	0.274 (1.00)	0.948 (1.00)	0.544 (1.00)
del 7q36 3	39 (15%)	225	0.449 (1.00)	0.0545 (1.00)	0.206 (1.00)	0.238 (1.00)	0.291 (1.00)	0.404 (1.00)	0.717 (1.00)	0.0156 (1.00)	1 (1.00)	0.894 (1.00)
del 10p12 1	43 (16%)	221	0.954 (1.00)	0.155 (1.00)	0.891 (1.00)	0.43 (1.00)	0.0157 (1.00)	0.0367 (1.00)	0.362 (1.00)	0.264 (1.00)	0.363 (1.00)	0.418 (1.00)
del 10q23 31	106 (40%)	158	0.00251 (1.00)	0.0159 (1.00)	0.628 (1.00)	0.594 (1.00)	0.0882 (1.00)	0.635 (1.00)	0.713 (1.00)	0.105 (1.00)	0.67 (1.00)	0.385 (1.00)
del 13q14 2	103 (39%)	161	0.0004 (0.252)	0.575 (1.00)	0.00803 (1.00)	0.00318 (1.00)	0.0237 (1.00)	0.471 (1.00)	0.782 (1.00)	0.0252 (1.00)	0.366 (1.00)	0.693 (1.00)
del 16p13 3	104 (39%)	160	0.00087 (0.539)	0.0138 (1.00)	0.213 (1.00)	0.466 (1.00)	0.694 (1.00)	0.918 (1.00)	0.947 (1.00)	0.0361 (1.00)	0.759 (1.00)	0.832 (1.00)
del 19p13 3	96 (36%)	168	0.00222 (1.00)	0.281 (1.00)	0.855 (1.00)	0.608 (1.00)	0.0415 (1.00)	0.0743 (1.00)	0.452 (1.00)	0.0585 (1.00)	0.178 (1.00)	0.36 (1.00)
del xp11 3	62 (23%)	202	0.0317 (1.00)	0.029 (1.00)	0.735 (1.00)	0.617 (1.00)	0.207 (1.00)	0.962 (1.00)	0.0941 (1.00)	0.838 (1.00)	0.291 (1.00)	0.785 (1.00)
del xq21 33	53 (20%)	211	0.00276 (1.00)	0.0198 (1.00)	0.98 (1.00)	0.439 (1.00)	0.0341 (1.00)	0.239 (1.00)	0.0493 (1.00)	0.375 (1.00)	0.225 (1.00)	0.056 (1.00)
del xq23	49 (19%)	215	0.0654 (1.00)	0.0305 (1.00)	0.995 (1.00)	0.623 (1.00)	0.338 (1.00)	0.655 (1.00)	0.224 (1.00)	0.424 (1.00)	0.18 (1.00)	0.196 (1.00)

'amp_1p34.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S1. Gene #1: 'amp_1p34.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
AMP PEAK 1(1P34.2) MUTATED	33	17	20
AMP PEAK 1(1P34.2) WILD-TYPE	34	79	81

Figure S1. Get High-res Image Gene #1: 'amp_1p34.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S2. Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
AMP PEAK 2(1Q21.3) MUTATED	55	35	38
AMP PEAK 2(1Q21.3) WILD-TYPE	12	61	63

Figure S2. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S3. Gene #2: 'amp_1q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	60	54	47
AMP PEAK 2(1Q21.3) MUTATED	34	46	23	20
AMP PEAK 2(1Q21.3) WILD-TYPE	55	14	31	27

Figure S3. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S4. Gene #3: 'amp_1q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
AMP PEAK 3(1Q23.3) MUTATED	57	37	41
AMP PEAK 3(1Q23.3) WILD-TYPE	10	59	60

Figure S4. Get High-res Image Gene #3: 'amp_1q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3p25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S5. Gene #4: 'amp_3p25.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
AMP PEAK 4(3P25.2) MUTATED	53	28	46
AMP PEAK 4(3P25.2) WILD-TYPE	14	68	55

Figure S5. Get High-res Image Gene #4: 'amp_3p25.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3p25.2' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.026

Table S6. Gene #4: 'amp_3p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	60	54	47
AMP PEAK 4(3P25.2) MUTATED	29	43	25	25
AMP PEAK 4(3P25.2) WILD-TYPE	60	17	29	22

Figure S6. Get High-res Image Gene #4: 'amp_3p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3p25.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S7. Gene #4: 'amp_3p25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	72	73
AMP PEAK 4(3P25.2) MUTATED	72	37	18
AMP PEAK 4(3P25.2) WILD-TYPE	46	35	55

Figure S7. Get High-res Image Gene #4: 'amp_3p25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3p25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S8. Gene #4: 'amp_3p25.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	44	64	59
AMP PEAK 4(3P25.2) MUTATED	57	20	38	12
AMP PEAK 4(3P25.2) WILD-TYPE	39	24	26	47

Figure S8. Get High-res Image Gene #4: 'amp_3p25.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3p25.2' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.045

Table S9. Gene #4: 'amp_3p25.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	115	85
AMP PEAK 4(3P25.2) MUTATED	45	50	31
AMP PEAK 4(3P25.2) WILD-TYPE	18	65	54

Figure S9. Get High-res Image Gene #4: 'amp_3p25.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_3p25.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S10. Gene #4: 'amp_3p25.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	44	24	31	34	47	36	47
AMP PEAK 4(3P25.2) MUTATED	34	11	23	13	22	10	13
AMP PEAK 4(3P25.2) WILD-TYPE	10	13	8	21	25	26	34

Figure S10. Get High-res Image Gene #4: 'amp_3p25.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3p25.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S11. Gene #4: 'amp_3p25.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	112	104
AMP PEAK 4(3P25.2) MUTATED	36	41	49
AMP PEAK 4(3P25.2) WILD-TYPE	11	71	55

Figure S11. Get High-res Image Gene #4: 'amp_3p25.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_3p25.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.052

Table S12. Gene #4: 'amp_3p25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	132	88
AMP PEAK 4(3P25.2) MUTATED	33	51	42
AMP PEAK 4(3P25.2) WILD-TYPE	10	81	46

Figure S12. Get High-res Image Gene #4: 'amp_3p25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S13. Gene #5: 'amp_3q26.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
AMP PEAK 5(3Q26.32) MUTATED	51	36	55
AMP PEAK 5(3Q26.32) WILD-TYPE	16	60	46

Figure S13. Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S14. Gene #9: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
AMP PEAK 9(5P15.33) MUTATED	51	36	44
AMP PEAK 9(5P15.33) WILD-TYPE	16	60	57

Figure S14. Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.14

Table S15. Gene #9: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	44	24	31	34	47	36	47
AMP PEAK 9(5P15.33) MUTATED	28	14	19	17	27	16	9
AMP PEAK 9(5P15.33) WILD-TYPE	16	10	12	17	20	20	38

Figure S15. Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6p22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S16. Gene #10: 'amp_6p22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
AMP PEAK 10(6P22.3) MUTATED	52	32	27
AMP PEAK 10(6P22.3) WILD-TYPE	15	64	74

Figure S16. Get High-res Image Gene #10: 'amp_6p22.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p21.1' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.09

Table S17. Gene #12: 'amp_7p21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
AMP PEAK 12(7P21.1) MUTATED	46	34	54
AMP PEAK 12(7P21.1) WILD-TYPE	21	62	47

Figure S17. Get High-res Image Gene #12: 'amp_7p21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S18. Gene #13: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
AMP PEAK 13(7P11.2) MUTATED	48	28	55
AMP PEAK 13(7P11.2) WILD-TYPE	19	68	46

Figure S18. Get High-res Image Gene #13: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S19. Gene #14: 'amp_8p11.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
AMP PEAK 14(8P11.23) MUTATED	27	7	50
AMP PEAK 14(8P11.23) WILD-TYPE	40	89	51

Figure S19. Get High-res Image Gene #14: 'amp_8p11.23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S20. Gene #15: 'amp_8p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
AMP PEAK 15(8P11.21) MUTATED	29	8	49
AMP PEAK 15(8P11.21) WILD-TYPE	38	88	52

Figure S20. Get High-res Image Gene #15: 'amp_8p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S21. Gene #16: 'amp_8q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
AMP PEAK 16(8Q22.3) MUTATED	54	41	74
AMP PEAK 16(8Q22.3) WILD-TYPE	13	55	27

Figure S21. Get High-res Image Gene #16: 'amp_8q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S22. Gene #17: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
AMP PEAK 17(9P24.1) MUTATED	21	26	6
AMP PEAK 17(9P24.1) WILD-TYPE	46	70	95

Figure S22. Get High-res Image Gene #17: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10p14' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S23. Gene #18: 'amp_10p14' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
AMP PEAK 18(10P14) MUTATED	50	28	38
AMP PEAK 18(10P14) WILD-TYPE	17	68	63

Figure S23. Get High-res Image Gene #18: 'amp_10p14' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10p14' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S24. Gene #18: 'amp_10p14' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	60	54	47
AMP PEAK 18(10P14) MUTATED	32	45	17	18
AMP PEAK 18(10P14) WILD-TYPE	57	15	37	29

Figure S24. Get High-res Image Gene #18: 'amp_10p14' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.052

Table S25. Gene #19: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
AMP PEAK 19(11Q13.3) MUTATED	31	20	50
AMP PEAK 19(11Q13.3) WILD-TYPE	36	76	51

Figure S25. Get High-res Image Gene #19: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_14q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.18

Table S26. Gene #23: 'amp_14q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	44	24	31	34	47	36	47
AMP PEAK 23(14Q11.2) MUTATED	12	8	12	11	2	12	5
AMP PEAK 23(14Q11.2) WILD-TYPE	32	16	19	23	45	24	42

Figure S26. Get High-res Image Gene #23: 'amp_14q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_16p13.13' versus 'CN_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.25

Table S27. Gene #24: 'amp_16p13.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
AMP PEAK 24(16P13.13) MUTATED	25	11	20
AMP PEAK 24(16P13.13) WILD-TYPE	42	85	81

Figure S27. Get High-res Image Gene #24: 'amp_16p13.13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S28. Gene #27: 'amp_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
AMP PEAK 27(17Q11.2) MUTATED	45	17	55
AMP PEAK 27(17Q11.2) WILD-TYPE	22	79	46

Figure S28. Get High-res Image Gene #27: 'amp_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q11.2' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.14

Table S29. Gene #27: 'amp_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	60	54	47
AMP PEAK 27(17Q11.2) MUTATED	24	36	30	21
AMP PEAK 27(17Q11.2) WILD-TYPE	65	24	24	26

Figure S29. Get High-res Image Gene #27: 'amp_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.25

Table S30. Gene #27: 'amp_17q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	72	73
AMP PEAK 27(17Q11.2) MUTATED	68	27	22
AMP PEAK 27(17Q11.2) WILD-TYPE	50	45	51

Figure S30. Get High-res Image Gene #27: 'amp_17q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S31. Gene #28: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
AMP PEAK 28(17Q12) MUTATED	40	19	51
AMP PEAK 28(17Q12) WILD-TYPE	27	77	50

Figure S31. Get High-res Image Gene #28: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.11

Table S32. Gene #28: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	112	104
AMP PEAK 28(17Q12) MUTATED	30	33	46
AMP PEAK 28(17Q12) WILD-TYPE	17	79	58

Figure S32. Get High-res Image Gene #28: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S33. Gene #29: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
AMP PEAK 29(19Q12) MUTATED	46	22	41
AMP PEAK 29(19Q12) WILD-TYPE	21	74	60

Figure S33. Get High-res Image Gene #29: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.13

Table S34. Gene #29: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	60	54	47
AMP PEAK 29(19Q12) MUTATED	28	39	17	20
AMP PEAK 29(19Q12) WILD-TYPE	61	21	37	27

Figure S34. Get High-res Image Gene #29: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q13.43' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S35. Gene #30: 'amp_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
AMP PEAK 30(19Q13.43) MUTATED	38	21	44
AMP PEAK 30(19Q13.43) WILD-TYPE	29	75	57

Figure S35. Get High-res Image Gene #30: 'amp_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q11.21' versus 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.19

Table S36. Gene #31: 'amp_20q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
AMP PEAK 31(20Q11.21) MUTATED	55	50	66
AMP PEAK 31(20Q11.21) WILD-TYPE	12	46	35

Figure S36. Get High-res Image Gene #31: 'amp_20q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S37. Gene #36: 'del_2q37.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
DEL PEAK 4(2Q37.1) MUTATED	49	34	47
DEL PEAK 4(2Q37.1) WILD-TYPE	18	62	54

Figure S37. Get High-res Image Gene #36: 'del_2q37.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p21.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S38. Gene #37: 'del_3p21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	72	73
DEL PEAK 5(3P21.31) MUTATED	27	12	38
DEL PEAK 5(3P21.31) WILD-TYPE	91	60	35

Figure S38. Get High-res Image Gene #37: 'del_3p21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.026

Table S39. Gene #37: 'del_3p21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	44	64	59
DEL PEAK 5(3P21.31) MUTATED	21	9	14	33
DEL PEAK 5(3P21.31) WILD-TYPE	75	35	50	26

Figure S39. Get High-res Image Gene #37: 'del_3p21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S40. Gene #38: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	72	73
DEL PEAK 6(3P14.2) MUTATED	25	13	36
DEL PEAK 6(3P14.2) WILD-TYPE	93	59	37

Figure S40. Get High-res Image Gene #38: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S41. Gene #38: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	44	64	59
DEL PEAK 6(3P14.2) MUTATED	19	8	15	32
DEL PEAK 6(3P14.2) WILD-TYPE	77	36	49	27

Figure S41. Get High-res Image Gene #38: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p13' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S42. Gene #39: 'del_3p13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	72	73
DEL PEAK 7(3P13) MUTATED	23	12	35
DEL PEAK 7(3P13) WILD-TYPE	95	60	38

Figure S42. Get High-res Image Gene #39: 'del_3p13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.071

Table S43. Gene #39: 'del_3p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	44	64	59
DEL PEAK 7(3P13) MUTATED	18	8	14	30
DEL PEAK 7(3P13) WILD-TYPE	78	36	50	29

Figure S43. Get High-res Image Gene #39: 'del_3p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S44. Gene #42: 'del_5q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
DEL PEAK 10(5Q11.2) MUTATED	51	33	49
DEL PEAK 10(5Q11.2) WILD-TYPE	16	63	52

Figure S44. Get High-res Image Gene #42: 'del_5q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q35.1' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S45. Gene #43: 'del_5q35.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
DEL PEAK 11(5Q35.1) MUTATED	45	30	51
DEL PEAK 11(5Q35.1) WILD-TYPE	22	66	50

Figure S45. Get High-res Image Gene #43: 'del_5q35.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q35.1' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.11

Table S46. Gene #43: 'del_5q35.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	60	54	47
DEL PEAK 11(5Q35.1) MUTATED	38	42	27	13
DEL PEAK 11(5Q35.1) WILD-TYPE	51	18	27	34

Figure S46. Get High-res Image Gene #43: 'del_5q35.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S47. Gene #45: 'del_6q21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
DEL PEAK 13(6Q21) MUTATED	43	19	55
DEL PEAK 13(6Q21) WILD-TYPE	24	77	46

Figure S47. Get High-res Image Gene #45: 'del_6q21' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q27' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S48. Gene #46: 'del_6q27' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
DEL PEAK 14(6Q27) MUTATED	44	25	50
DEL PEAK 14(6Q27) WILD-TYPE	23	71	51

Figure S48. Get High-res Image Gene #46: 'del_6q27' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q27' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S49. Gene #46: 'del_6q27' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	44	24	31	34	47	36	47
DEL PEAK 14(6Q27) MUTATED	26	13	21	17	23	10	9
DEL PEAK 14(6Q27) WILD-TYPE	18	11	10	17	24	26	38

Figure S49. Get High-res Image Gene #46: 'del_6q27' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S50. Gene #48: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
DEL PEAK 16(8P23.3) MUTATED	56	54	41
DEL PEAK 16(8P23.3) WILD-TYPE	11	42	60

Figure S50. Get High-res Image Gene #48: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S51. Gene #48: 'del_8p23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	60	54	47
DEL PEAK 16(8P23.3) MUTATED	57	49	20	17
DEL PEAK 16(8P23.3) WILD-TYPE	32	11	34	30

Figure S51. Get High-res Image Gene #48: 'del_8p23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S52. Gene #49: 'del_8p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
DEL PEAK 17(8P12) MUTATED	50	50	29
DEL PEAK 17(8P12) WILD-TYPE	17	46	72

Figure S52. Get High-res Image Gene #49: 'del_8p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p11.21' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.052

Table S53. Gene #50: 'del_8p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
DEL PEAK 18(8P11.21) MUTATED	23	34	12
DEL PEAK 18(8P11.21) WILD-TYPE	44	62	89

Figure S53. Get High-res Image Gene #50: 'del_8p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S54. Gene #51: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
DEL PEAK 19(9P23) MUTATED	24	19	72
DEL PEAK 19(9P23) WILD-TYPE	43	77	29

Figure S54. Get High-res Image Gene #51: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S55. Gene #52: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
DEL PEAK 20(9P21.3) MUTATED	32	37	88
DEL PEAK 20(9P21.3) WILD-TYPE	35	59	13

Figure S55. Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q33.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S56. Gene #53: 'del_9q33.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
DEL PEAK 21(9Q33.2) MUTATED	24	20	60
DEL PEAK 21(9Q33.2) WILD-TYPE	43	76	41

Figure S56. Get High-res Image Gene #53: 'del_9q33.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q33.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.14

Table S57. Gene #53: 'del_9q33.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	44	64	59
DEL PEAK 21(9Q33.2) MUTATED	43	12	36	13
DEL PEAK 21(9Q33.2) WILD-TYPE	53	32	28	46

Figure S57. Get High-res Image Gene #53: 'del_9q33.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S58. Gene #56: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
DEL PEAK 24(11P15.5) MUTATED	43	21	65
DEL PEAK 24(11P15.5) WILD-TYPE	24	75	36

Figure S58. Get High-res Image Gene #56: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S59. Gene #57: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
DEL PEAK 25(11Q23.3) MUTATED	33	17	50
DEL PEAK 25(11Q23.3) WILD-TYPE	34	79	51

Figure S59. Get High-res Image Gene #57: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S60. Gene #59: 'del_14q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
DEL PEAK 27(14Q12) MUTATED	33	12	35
DEL PEAK 27(14Q12) WILD-TYPE	34	84	66

Figure S60. Get High-res Image Gene #59: 'del_14q12' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S61. Gene #60: 'del_14q24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
DEL PEAK 28(14Q24.1) MUTATED	39	14	33
DEL PEAK 28(14Q24.1) WILD-TYPE	28	82	68

Figure S61. Get High-res Image Gene #60: 'del_14q24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q24.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S62. Gene #60: 'del_14q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	60	54	47
DEL PEAK 28(14Q24.1) MUTATED	21	36	10	16
DEL PEAK 28(14Q24.1) WILD-TYPE	68	24	44	31

Figure S62. Get High-res Image Gene #60: 'del_14q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S63. Gene #60: 'del_14q24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	44	64	59
DEL PEAK 28(14Q24.1) MUTATED	35	8	34	9
DEL PEAK 28(14Q24.1) WILD-TYPE	61	36	30	50

Figure S63. Get High-res Image Gene #60: 'del_14q24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q13.1' versus 'CN_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.17

Table S64. Gene #61: 'del_15q13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
DEL PEAK 29(15Q13.1) MUTATED	41	35	31
DEL PEAK 29(15Q13.1) WILD-TYPE	26	61	70

Figure S64. Get High-res Image Gene #61: 'del_15q13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.039

Table S65. Gene #61: 'del_15q13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	44	24	31	34	47	36	47
DEL PEAK 29(15Q13.1) MUTATED	23	13	19	18	15	12	7
DEL PEAK 29(15Q13.1) WILD-TYPE	21	11	12	16	32	24	40

Figure S65. Get High-res Image Gene #61: 'del_15q13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.039

Table S66. Gene #63: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
DEL PEAK 31(16Q23.1) MUTATED	33	22	18
DEL PEAK 31(16Q23.1) WILD-TYPE	34	74	83

Figure S66. Get High-res Image Gene #63: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.2

Table S67. Gene #63: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	44	24	31	34	47	36	47
DEL PEAK 31(16Q23.1) MUTATED	20	5	13	8	6	15	6
DEL PEAK 31(16Q23.1) WILD-TYPE	24	19	18	26	41	21	41

Figure S67. Get High-res Image Gene #63: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S68. Gene #64: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
DEL PEAK 32(17P12) MUTATED	48	25	64
DEL PEAK 32(17P12) WILD-TYPE	19	71	37

Figure S68. Get High-res Image Gene #64: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.18

Table S69. Gene #65: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	44	24	31	34	47	36	47
DEL PEAK 33(18Q21.2) MUTATED	25	17	16	18	19	9	11
DEL PEAK 33(18Q21.2) WILD-TYPE	19	7	15	16	28	27	36

Figure S69. Get High-res Image Gene #65: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S70. Gene #67: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	96	101
DEL PEAK 35(22Q13.31) MUTATED	46	42	30
DEL PEAK 35(22Q13.31) WILD-TYPE	21	54	71

Figure S70. Get High-res Image Gene #67: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = BLCA-TP.transferedmergedcluster.txt
Number of patients = 264
Number of significantly focal cnvs = 70
Number of molecular subtypes = 10
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)

Made with Nozzle