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

Ovarian Serous Cystadenocarcinoma (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

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/C11J98PK

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 71 focal events and 14 molecular subtypes across 579 patients, 76 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' and 'METHLYATION_CNMF'.
amp_1q42.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_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_4q13.3 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' and 'METHLYATION_CNMF'.
amp_12p12.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_12q15 cnv correlated to 'CN_CNMF' and 'METHLYATION_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', 'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.
amp_19q12 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_19q13.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_20p13 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_20q11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
amp_20q13.33 cnv correlated to 'CN_CNMF' and 'METHLYATION_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_5q12.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_5q13.2 cnv correlated to 'CN_CNMF'.
del_6q27 cnv correlated to 'CN_CNMF', 'METHLYATION_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', 'MRNA_CHIERARCHICAL', and 'METHLYATION_CNMF'.
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' and 'METHLYATION_CNMF'.
del_14q23.3 cnv correlated to 'CN_CNMF'.
del_15q11.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_15q15.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_16q23.1 cnv correlated to 'CN_CNMF'.
del_19q13.33 cnv correlated to 'MRNA_CNMF'.
del_19q13.43 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 71 focal events and 14 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 76 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	MIR CNMF	MIR CHIERARCHICAL	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	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
amp 19p13 12	315 (54%)	264	0.00019 (0.175)	0.00025 (0.228)	0.0371 (1.00)	0.251 (1.00)	1e-05 (0.00986)	1e-05 (0.00986)	0.00035 (0.318)	0.0001 (0.0924)	0.24 (1.00)	0.465 (1.00)	0.586 (1.00)	0.0985 (1.00)	1 (1.00)	0.481 (1.00)
amp 8q24 21	461 (80%)	118	1e-05 (0.00986)	1e-05 (0.00986)	0.247 (1.00)	0.00262 (1.00)	1e-05 (0.00986)	0.00443 (1.00)	0.987 (1.00)	0.325 (1.00)	1e-05 (0.00986)	0.00029 (0.264)	0.161 (1.00)	0.0976 (1.00)	0.571 (1.00)	0.571 (1.00)
amp 20q11 21	348 (60%)	231	0.00271 (1.00)	0.00303 (1.00)	0.112 (1.00)	0.00296 (1.00)	1e-05 (0.00986)	1e-05 (0.00986)	0.13 (1.00)	0.0193 (1.00)	0.00019 (0.175)	0.0474 (1.00)	0.292 (1.00)	0.00054 (0.488)	1 (1.00)	0.335 (1.00)
del 6q27	380 (66%)	199	0.323 (1.00)	0.0612 (1.00)	0.271 (1.00)	0.103 (1.00)	1e-05 (0.00986)	4e-05 (0.0373)	0.62 (1.00)	0.56 (1.00)	2e-05 (0.0188)	0.0016 (1.00)	0.561 (1.00)	0.026 (1.00)	0.691 (1.00)	0.436 (1.00)
del 9p24 3	261 (45%)	318	0.00026 (0.237)	1e-05 (0.00986)	0.623 (1.00)	0.0132 (1.00)	0.0615 (1.00)	7e-05 (0.065)	0.321 (1.00)	0.955 (1.00)	0.0726 (1.00)	0.0516 (1.00)	0.0886 (1.00)	0.126 (1.00)	1 (1.00)	0.514 (1.00)
amp 1q21 3	367 (63%)	212	0.269 (1.00)	0.163 (1.00)	0.64 (1.00)	0.399 (1.00)	1e-05 (0.00986)	0.00022 (0.202)	0.0767 (1.00)	0.0711 (1.00)	0.657 (1.00)	0.371 (1.00)	0.841 (1.00)	0.00628 (1.00)	0.652 (1.00)	0.695 (1.00)
amp 1q42 2	322 (56%)	257	0.0234 (1.00)	0.0274 (1.00)	0.884 (1.00)	0.00779 (1.00)	1e-05 (0.00986)	9e-05 (0.0834)	0.257 (1.00)	0.124 (1.00)	0.506 (1.00)	0.319 (1.00)	0.265 (1.00)	0.00297 (1.00)	1 (1.00)	0.51 (1.00)
amp 12p13 33	330 (57%)	249	0.0229 (1.00)	0.00345 (1.00)	0.263 (1.00)	0.0548 (1.00)	1e-05 (0.00986)	0.00014 (0.129)	0.196 (1.00)	0.151 (1.00)	0.0146 (1.00)	0.0311 (1.00)	0.535 (1.00)	0.00771 (1.00)	0.378 (1.00)	0.529 (1.00)
amp 12p12 1	313 (54%)	266	0.127 (1.00)	0.306 (1.00)	0.9 (1.00)	0.0412 (1.00)	1e-05 (0.00986)	3e-05 (0.0281)	0.615 (1.00)	0.0905 (1.00)	0.0117 (1.00)	0.301 (1.00)	0.442 (1.00)	0.00492 (1.00)	0.391 (1.00)	0.0414 (1.00)
amp 12q15	222 (38%)	357	0.0028 (1.00)	0.242 (1.00)	0.574 (1.00)	0.0023 (1.00)	1e-05 (0.00986)	1e-05 (0.00986)	0.0731 (1.00)	0.249 (1.00)	0.00141 (1.00)	0.0714 (1.00)	0.968 (1.00)	0.101 (1.00)	0.231 (1.00)	0.269 (1.00)
amp 19q12	322 (56%)	257	0.125 (1.00)	0.00619 (1.00)	0.0295 (1.00)	0.513 (1.00)	1e-05 (0.00986)	1e-05 (0.00986)	0.0471 (1.00)	0.213 (1.00)	0.552 (1.00)	0.375 (1.00)	0.346 (1.00)	0.06 (1.00)	1 (1.00)	0.782 (1.00)
amp 19q13 2	245 (42%)	334	0.945 (1.00)	0.537 (1.00)	0.665 (1.00)	0.39 (1.00)	1e-05 (0.00986)	0.00011 (0.102)	0.447 (1.00)	0.146 (1.00)	0.382 (1.00)	0.0869 (1.00)	0.977 (1.00)	0.552 (1.00)	0.675 (1.00)	0.612 (1.00)
amp 20p13	317 (55%)	262	0.188 (1.00)	0.00571 (1.00)	0.207 (1.00)	0.0332 (1.00)	1e-05 (0.00986)	1e-05 (0.00986)	0.321 (1.00)	0.573 (1.00)	0.0165 (1.00)	0.348 (1.00)	0.248 (1.00)	0.00082 (0.736)	1 (1.00)	0.936 (1.00)
amp 20q13 33	402 (69%)	177	0.0107 (1.00)	0.00088 (0.789)	0.683 (1.00)	0.00125 (1.00)	1e-05 (0.00986)	1e-05 (0.00986)	0.851 (1.00)	0.279 (1.00)	0.00841 (1.00)	0.00475 (1.00)	0.477 (1.00)	0.0491 (1.00)	0.624 (1.00)	0.0139 (1.00)
del 5q12 1	355 (61%)	224	0.883 (1.00)	0.874 (1.00)	0.577 (1.00)	0.0558 (1.00)	1e-05 (0.00986)	0.0002 (0.183)	0.685 (1.00)	0.863 (1.00)	0.295 (1.00)	0.0541 (1.00)	0.162 (1.00)	0.253 (1.00)	1 (1.00)	0.263 (1.00)
del 13q14 2	364 (63%)	215	0.0105 (1.00)	0.0155 (1.00)	0.613 (1.00)	0.0429 (1.00)	0.00024 (0.219)	1e-05 (0.00986)	0.00219 (1.00)	0.052 (1.00)	0.0991 (1.00)	0.677 (1.00)	0.377 (1.00)	0.367 (1.00)	0.675 (1.00)	0.249 (1.00)
del 15q11 2	299 (52%)	280	0.00546 (1.00)	0.0354 (1.00)	0.0106 (1.00)	0.0062 (1.00)	1e-05 (0.00986)	3e-05 (0.0281)	0.468 (1.00)	0.766 (1.00)	0.00509 (1.00)	0.159 (1.00)	0.0258 (1.00)	0.00973 (1.00)	1 (1.00)	0.372 (1.00)
del 15q15 1	363 (63%)	216	0.0259 (1.00)	0.0596 (1.00)	0.0211 (1.00)	0.00285 (1.00)	1e-05 (0.00986)	1e-05 (0.00986)	0.156 (1.00)	0.152 (1.00)	0.0115 (1.00)	0.5 (1.00)	0.395 (1.00)	0.00184 (1.00)	0.204 (1.00)	0.144 (1.00)
del 19q13 43	285 (49%)	294	0.0167 (1.00)	0.0817 (1.00)	0.0799 (1.00)	0.386 (1.00)	0.00011 (0.102)	5e-05 (0.0466)	0.161 (1.00)	0.488 (1.00)	0.564 (1.00)	0.985 (1.00)	0.518 (1.00)	0.121 (1.00)	0.0427 (1.00)	0.0214 (1.00)
amp 1p34 3	292 (50%)	287	0.431 (1.00)	0.0813 (1.00)	0.125 (1.00)	0.0851 (1.00)	1e-05 (0.00986)	0.195 (1.00)	0.112 (1.00)	0.388 (1.00)	0.555 (1.00)	0.184 (1.00)	0.0882 (1.00)	0.163 (1.00)	0.0743 (1.00)	0.927 (1.00)
amp 2p23 2	252 (44%)	327	0.326 (1.00)	0.0135 (1.00)	0.759 (1.00)	0.171 (1.00)	1e-05 (0.00986)	0.00441 (1.00)	0.145 (1.00)	0.213 (1.00)	0.0317 (1.00)	0.0202 (1.00)	0.92 (1.00)	0.202 (1.00)	1 (1.00)	0.671 (1.00)
amp 2q31 2	262 (45%)	317	0.114 (1.00)	0.173 (1.00)	0.0341 (1.00)	0.0298 (1.00)	1e-05 (0.00986)	0.00754 (1.00)	0.0491 (1.00)	0.321 (1.00)	0.151 (1.00)	0.271 (1.00)	0.286 (1.00)	0.0869 (1.00)	0.67 (1.00)	0.888 (1.00)
amp 3q26 2	485 (84%)	94	0.00906 (1.00)	0.0255 (1.00)	0.818 (1.00)	0.28 (1.00)	1e-05 (0.00986)	0.0356 (1.00)	0.405 (1.00)	0.28 (1.00)	0.00703 (1.00)	0.0114 (1.00)	0.125 (1.00)	0.0679 (1.00)	1 (1.00)	0.578 (1.00)
amp 4q13 3	113 (20%)	466	0.905 (1.00)	0.465 (1.00)	0.387 (1.00)	0.986 (1.00)	0.00025 (0.228)	0.522 (1.00)	0.617 (1.00)	0.539 (1.00)	0.182 (1.00)	0.484 (1.00)	0.966 (1.00)	0.693 (1.00)	0.323 (1.00)	0.696 (1.00)
amp 5p15 33	309 (53%)	270	1 (1.00)	0.0553 (1.00)	0.626 (1.00)	0.25 (1.00)	1e-05 (0.00986)	0.0972 (1.00)	0.981 (1.00)	0.237 (1.00)	0.243 (1.00)	0.391 (1.00)	0.0245 (1.00)	0.148 (1.00)	0.231 (1.00)	0.268 (1.00)
amp 6p22 3	306 (53%)	273	0.176 (1.00)	0.0301 (1.00)	0.275 (1.00)	0.0728 (1.00)	1e-05 (0.00986)	0.012 (1.00)	0.0736 (1.00)	0.0566 (1.00)	0.867 (1.00)	0.213 (1.00)	0.378 (1.00)	0.614 (1.00)	1 (1.00)	0.254 (1.00)
amp 7q36 3	320 (55%)	259	0.106 (1.00)	0.178 (1.00)	0.36 (1.00)	0.989 (1.00)	3e-05 (0.0281)	0.455 (1.00)	0.0319 (1.00)	0.201 (1.00)	0.845 (1.00)	0.97 (1.00)	0.211 (1.00)	0.502 (1.00)	0.198 (1.00)	0.263 (1.00)
amp 8p11 21	211 (36%)	368	0.11 (1.00)	0.352 (1.00)	0.102 (1.00)	0.533 (1.00)	1e-05 (0.00986)	0.0161 (1.00)	0.011 (1.00)	0.42 (1.00)	0.279 (1.00)	0.172 (1.00)	0.769 (1.00)	0.326 (1.00)	0.231 (1.00)	0.858 (1.00)
amp 10p15 3	252 (44%)	327	0.823 (1.00)	0.102 (1.00)	0.0536 (1.00)	0.165 (1.00)	1e-05 (0.00986)	0.00043 (0.39)	0.488 (1.00)	0.501 (1.00)	0.242 (1.00)	0.121 (1.00)	0.378 (1.00)	0.0675 (1.00)	1 (1.00)	0.608 (1.00)
amp 11q14 1	257 (44%)	322	0.00528 (1.00)	0.00385 (1.00)	0.773 (1.00)	0.31 (1.00)	1e-05 (0.00986)	0.00263 (1.00)	0.38 (1.00)	0.228 (1.00)	0.00457 (1.00)	0.0268 (1.00)	0.131 (1.00)	0.923 (1.00)	0.0427 (1.00)	0.435 (1.00)
amp 14q32 33	156 (27%)	423	0.437 (1.00)	0.653 (1.00)	0.198 (1.00)	0.0172 (1.00)	5e-05 (0.0466)	0.289 (1.00)	1 (1.00)	0.203 (1.00)	0.166 (1.00)	0.241 (1.00)	0.373 (1.00)	0.423 (1.00)	0.0964 (1.00)	0.139 (1.00)
amp 15q26 3	163 (28%)	416	0.084 (1.00)	0.426 (1.00)	0.507 (1.00)	0.426 (1.00)	1e-05 (0.00986)	0.805 (1.00)	0.978 (1.00)	0.18 (1.00)	0.203 (1.00)	0.548 (1.00)	0.155 (1.00)	0.0648 (1.00)	0.675 (1.00)	0.785 (1.00)
amp 18q11 2	143 (25%)	436	0.823 (1.00)	0.782 (1.00)	0.953 (1.00)	0.222 (1.00)	1e-05 (0.00986)	0.00386 (1.00)	0.156 (1.00)	0.42 (1.00)	0.0422 (1.00)	0.0761 (1.00)	0.148 (1.00)	0.511 (1.00)	0.381 (1.00)	0.093 (1.00)
amp xp11 23	159 (27%)	420	0.664 (1.00)	0.867 (1.00)	0.418 (1.00)	0.632 (1.00)	1e-05 (0.00986)	0.00169 (1.00)	0.718 (1.00)	0.902 (1.00)	0.448 (1.00)	0.929 (1.00)	0.277 (1.00)	0.0318 (1.00)	0.675 (1.00)	0.634 (1.00)
del 1p36 11	269 (46%)	310	0.738 (1.00)	0.0687 (1.00)	0.0294 (1.00)	0.117 (1.00)	6e-05 (0.0558)	0.0889 (1.00)	0.125 (1.00)	0.392 (1.00)	0.852 (1.00)	0.42 (1.00)	0.22 (1.00)	0.171 (1.00)	0.675 (1.00)	0.978 (1.00)
del 1q41	97 (17%)	482	0.0884 (1.00)	0.625 (1.00)	0.299 (1.00)	0.837 (1.00)	1e-05 (0.00986)	0.135 (1.00)	0.487 (1.00)	0.0179 (1.00)	0.282 (1.00)	0.246 (1.00)	0.921 (1.00)	0.97 (1.00)	0.455 (1.00)
del 2q37 3	175 (30%)	404	0.0159 (1.00)	0.464 (1.00)	0.635 (1.00)	0.0269 (1.00)	2e-05 (0.0188)	0.0882 (1.00)	0.748 (1.00)	0.588 (1.00)	0.014 (1.00)	0.00236 (1.00)	0.0229 (1.00)	0.0192 (1.00)	0.323 (1.00)	0.966 (1.00)
del 3p26 2	209 (36%)	370	0.156 (1.00)	0.00057 (0.515)	0.00582 (1.00)	0.00437 (1.00)	9e-05 (0.0834)	0.00057 (0.515)	0.97 (1.00)	0.24 (1.00)	0.00293 (1.00)	0.00982 (1.00)	0.63 (1.00)	0.123 (1.00)	0.415 (1.00)	0.94 (1.00)
del 5q13 2	419 (72%)	160	0.747 (1.00)	0.623 (1.00)	0.9 (1.00)	0.257 (1.00)	1e-05 (0.00986)	0.104 (1.00)	0.791 (1.00)	0.831 (1.00)	0.517 (1.00)	0.0924 (1.00)	0.155 (1.00)	0.107 (1.00)	1 (1.00)	0.723 (1.00)
del 7p22 1	253 (44%)	326	0.394 (1.00)	0.514 (1.00)	0.771 (1.00)	0.0614 (1.00)	1e-05 (0.00986)	0.626 (1.00)	0.818 (1.00)	0.602 (1.00)	0.347 (1.00)	0.127 (1.00)	0.349 (1.00)	0.905 (1.00)	0.231 (1.00)	0.784 (1.00)
del 8p23 3	388 (67%)	191	0.0448 (1.00)	0.152 (1.00)	0.572 (1.00)	0.0115 (1.00)	1e-05 (0.00986)	0.0515 (1.00)	0.892 (1.00)	0.449 (1.00)	0.895 (1.00)	0.912 (1.00)	0.247 (1.00)	0.249 (1.00)	1 (1.00)
del 8p21 2	406 (70%)	173	0.0425 (1.00)	0.0919 (1.00)	0.183 (1.00)	0.00522 (1.00)	1e-05 (0.00986)	0.147 (1.00)	0.875 (1.00)	0.994 (1.00)	0.458 (1.00)	0.701 (1.00)	0.58 (1.00)	0.518 (1.00)	1 (1.00)
del 9q34 13	342 (59%)	237	0.017 (1.00)	0.00089 (0.797)	0.698 (1.00)	0.41 (1.00)	1e-05 (0.00986)	0.0183 (1.00)	0.675 (1.00)	0.163 (1.00)	0.0774 (1.00)	0.0806 (1.00)	0.0503 (1.00)	0.1 (1.00)	1 (1.00)	0.793 (1.00)
del 10q24 2	251 (43%)	328	0.00318 (1.00)	0.00276 (1.00)	0.0073 (1.00)	0.236 (1.00)	9e-05 (0.0834)	0.00196 (1.00)	0.0162 (1.00)	0.00243 (1.00)	0.532 (1.00)	0.365 (1.00)	0.00187 (1.00)	0.368 (1.00)	1 (1.00)	0.784 (1.00)
del 11p15 5	346 (60%)	233	0.111 (1.00)	0.971 (1.00)	0.619 (1.00)	0.0855 (1.00)	1e-05 (0.00986)	0.00758 (1.00)	0.946 (1.00)	0.711 (1.00)	0.7 (1.00)	0.506 (1.00)	0.106 (1.00)	0.00864 (1.00)	0.204 (1.00)	0.927 (1.00)
del 12q24 33	220 (38%)	359	0.00112 (1.00)	0.0992 (1.00)	0.163 (1.00)	0.0146 (1.00)	1e-05 (0.00986)	0.0198 (1.00)	0.292 (1.00)	0.224 (1.00)	0.0503 (1.00)	0.0321 (1.00)	0.0155 (1.00)	0.00464 (1.00)	0.646 (1.00)	1 (1.00)
del 14q23 3	305 (53%)	274	0.0656 (1.00)	0.506 (1.00)	0.651 (1.00)	0.609 (1.00)	6e-05 (0.0558)	0.737 (1.00)	0.23 (1.00)	0.508 (1.00)	0.856 (1.00)	0.282 (1.00)	0.9 (1.00)	0.595 (1.00)	0.666 (1.00)	0.14 (1.00)
del 16q23 1	452 (78%)	127	0.108 (1.00)	0.243 (1.00)	0.103 (1.00)	0.0606 (1.00)	0.00015 (0.138)	0.538 (1.00)	0.812 (1.00)	0.227 (1.00)	0.274 (1.00)	0.169 (1.00)	0.0568 (1.00)	0.0484 (1.00)	1 (1.00)	0.902 (1.00)
del 19q13 33	299 (52%)	280	0.00023 (0.21)	0.00229 (1.00)	0.0457 (1.00)	0.0199 (1.00)	0.0143 (1.00)	0.00278 (1.00)	0.0289 (1.00)	0.301 (1.00)	0.00628 (1.00)	0.123 (1.00)	0.321 (1.00)	0.13 (1.00)	0.391 (1.00)	0.112 (1.00)
amp 4p16 3	160 (28%)	419	1 (1.00)	0.32 (1.00)	0.0293 (1.00)	0.479 (1.00)	0.00042 (0.381)	0.0277 (1.00)	0.27 (1.00)	0.688 (1.00)	0.687 (1.00)	0.983 (1.00)	0.629 (1.00)	0.0187 (1.00)	0.652 (1.00)	0.579 (1.00)
amp 10q22 3	184 (32%)	395	0.371 (1.00)	0.265 (1.00)	0.608 (1.00)	0.949 (1.00)	0.0788 (1.00)	0.843 (1.00)	0.772 (1.00)	0.82 (1.00)	0.342 (1.00)	0.898 (1.00)	0.228 (1.00)	0.648 (1.00)	0.67 (1.00)	0.303 (1.00)
amp 14q11 2	148 (26%)	431	0.0168 (1.00)	0.0592 (1.00)	0.29 (1.00)	0.00669 (1.00)	0.0687 (1.00)	0.193 (1.00)	0.532 (1.00)	0.47 (1.00)	0.34 (1.00)	0.411 (1.00)	0.3 (1.00)	0.822 (1.00)	0.323 (1.00)	0.277 (1.00)
amp 17q25 3	215 (37%)	364	0.468 (1.00)	0.0561 (1.00)	0.982 (1.00)	0.665 (1.00)	0.00382 (1.00)	0.774 (1.00)	0.0727 (1.00)	0.128 (1.00)	0.0119 (1.00)	0.0259 (1.00)	0.326 (1.00)	0.129 (1.00)	1 (1.00)	0.709 (1.00)
amp 22q12 2	91 (16%)	488	0.623 (1.00)	0.157 (1.00)	0.0698 (1.00)	0.0359 (1.00)	0.00762 (1.00)	0.00061 (0.55)	0.983 (1.00)	0.0911 (1.00)	0.0591 (1.00)	0.0595 (1.00)	0.108 (1.00)	0.0144 (1.00)	1 (1.00)	0.0865 (1.00)
amp xq28	220 (38%)	359	0.245 (1.00)	0.848 (1.00)	0.555 (1.00)	0.123 (1.00)	0.00047 (0.425)	0.178 (1.00)	0.456 (1.00)	0.444 (1.00)	0.627 (1.00)	0.939 (1.00)	0.878 (1.00)	0.802 (1.00)	0.0427 (1.00)	0.624 (1.00)
del 2p25 3	120 (21%)	459	0.881 (1.00)	0.267 (1.00)	0.422 (1.00)	0.159 (1.00)	0.401 (1.00)	0.638 (1.00)	0.261 (1.00)	0.542 (1.00)	0.0632 (1.00)	0.239 (1.00)	0.876 (1.00)	0.95 (1.00)	0.381 (1.00)	0.426 (1.00)
del 2q22 1	137 (24%)	442	0.106 (1.00)	0.273 (1.00)	0.568 (1.00)	0.00388 (1.00)	0.0767 (1.00)	0.665 (1.00)	0.604 (1.00)	0.719 (1.00)	0.919 (1.00)	0.301 (1.00)	0.479 (1.00)	0.603 (1.00)	1 (1.00)	0.266 (1.00)
del 3q13 31	84 (15%)	495	0.328 (1.00)	0.227 (1.00)	0.568 (1.00)	0.626 (1.00)	0.11 (1.00)	0.0825 (1.00)	0.25 (1.00)	0.453 (1.00)	0.407 (1.00)	0.396 (1.00)	0.519 (1.00)	0.523 (1.00)	1 (1.00)
del 4q22 1	394 (68%)	185	0.0535 (1.00)	0.0237 (1.00)	1 (1.00)	0.166 (1.00)	0.0155 (1.00)	0.225 (1.00)	0.191 (1.00)	0.0615 (1.00)	0.071 (1.00)	0.388 (1.00)	0.303 (1.00)	0.255 (1.00)	0.675 (1.00)	0.413 (1.00)
del 4q34 3	421 (73%)	158	0.0533 (1.00)	0.00075 (0.674)	0.0626 (1.00)	0.0281 (1.00)	0.184 (1.00)	0.58 (1.00)	0.669 (1.00)	0.199 (1.00)	0.0839 (1.00)	0.0193 (1.00)	0.42 (1.00)	0.53 (1.00)	1 (1.00)	0.56 (1.00)
del 10p15 3	120 (21%)	459	0.179 (1.00)	0.709 (1.00)	0.087 (1.00)	0.319 (1.00)	0.0972 (1.00)	0.351 (1.00)	0.29 (1.00)	0.0409 (1.00)	0.0143 (1.00)	0.0889 (1.00)	0.253 (1.00)	0.266 (1.00)	0.594 (1.00)	0.105 (1.00)
del 11q25	201 (35%)	378	0.623 (1.00)	0.652 (1.00)	0.209 (1.00)	0.0532 (1.00)	0.273 (1.00)	0.417 (1.00)	0.322 (1.00)	0.267 (1.00)	0.931 (1.00)	0.454 (1.00)	0.708 (1.00)	0.274 (1.00)	1 (1.00)	0.768 (1.00)
del 16p13 3	313 (54%)	266	0.602 (1.00)	0.0718 (1.00)	0.274 (1.00)	0.0295 (1.00)	0.108 (1.00)	0.419 (1.00)	0.84 (1.00)	0.821 (1.00)	0.37 (1.00)	0.426 (1.00)	0.224 (1.00)	0.485 (1.00)	0.675 (1.00)	0.787 (1.00)
del 16q22 1	461 (80%)	118	0.499 (1.00)	0.706 (1.00)	0.0319 (1.00)	0.449 (1.00)	0.00089 (0.797)	0.64 (1.00)	0.694 (1.00)	0.143 (1.00)	0.221 (1.00)	0.285 (1.00)	0.313 (1.00)	0.0482 (1.00)	1 (1.00)	0.385 (1.00)
del 17p12	491 (85%)	88	0.143 (1.00)	0.336 (1.00)	0.595 (1.00)	0.69 (1.00)	0.709 (1.00)	0.322 (1.00)	0.907 (1.00)	0.371 (1.00)	0.154 (1.00)	0.194 (1.00)	0.504 (1.00)	0.21 (1.00)	1 (1.00)
del 17q11 2	472 (82%)	107	0.921 (1.00)	0.19 (1.00)	0.734 (1.00)	0.217 (1.00)	0.00072 (0.648)	0.00276 (1.00)	0.767 (1.00)	0.0359 (1.00)	0.373 (1.00)	0.439 (1.00)	0.151 (1.00)	0.164 (1.00)	1 (1.00)	0.339 (1.00)
del 18q23	381 (66%)	198	0.883 (1.00)	0.854 (1.00)	0.369 (1.00)	0.957 (1.00)	0.00275 (1.00)	0.587 (1.00)	0.48 (1.00)	0.185 (1.00)	0.152 (1.00)	0.362 (1.00)	0.66 (1.00)	0.492 (1.00)	0.646 (1.00)	0.794 (1.00)
del 19p13 3	512 (88%)	67	0.158 (1.00)	0.091 (1.00)	0.839 (1.00)	0.547 (1.00)	0.00034 (0.309)	0.0181 (1.00)	0.622 (1.00)	0.405 (1.00)	0.335 (1.00)	0.517 (1.00)	0.477 (1.00)	0.732 (1.00)	1 (1.00)
del 21q22 3	227 (39%)	352	0.371 (1.00)	0.0417 (1.00)	0.693 (1.00)	0.205 (1.00)	0.795 (1.00)	0.263 (1.00)	0.659 (1.00)	0.714 (1.00)	0.246 (1.00)	0.127 (1.00)	0.82 (1.00)	0.727 (1.00)	0.162 (1.00)	0.928 (1.00)
del 22q13 32	503 (87%)	76	0.209 (1.00)	0.123 (1.00)	0.0352 (1.00)	0.285 (1.00)	0.0175 (1.00)	0.159 (1.00)	0.122 (1.00)	0.0447 (1.00)	0.169 (1.00)	0.0136 (1.00)	0.0366 (1.00)	0.577 (1.00)
del xp21 1	355 (61%)	224	0.405 (1.00)	0.644 (1.00)	0.0998 (1.00)	0.8 (1.00)	0.167 (1.00)	0.0203 (1.00)	0.461 (1.00)	0.108 (1.00)	0.885 (1.00)	0.238 (1.00)	0.976 (1.00)	0.716 (1.00)	0.594 (1.00)	0.282 (1.00)

'amp_1p34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 1(1P34.3) MUTATED	58	114	120
AMP PEAK 1(1P34.3) WILD-TYPE	113	92	82

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 = 0.0099

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 2(1Q21.3) MUTATED	86	114	167
AMP PEAK 2(1Q21.3) WILD-TYPE	85	92	35

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

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.2

Table S3. Gene #2: 'amp_1q21.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 2(1Q21.3) MUTATED	128	92	141
AMP PEAK 2(1Q21.3) WILD-TYPE	44	83	80

Figure S3. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_1q42.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S4. Gene #3: 'amp_1q42.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 3(1Q42.2) MUTATED	88	87	147
AMP PEAK 3(1Q42.2) WILD-TYPE	83	119	55

Figure S4. Get High-res Image Gene #3: 'amp_1q42.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_1q42.2' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.083

Table S5. Gene #3: 'amp_1q42.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 3(1Q42.2) MUTATED	119	87	108
AMP PEAK 3(1Q42.2) WILD-TYPE	53	88	113

Figure S5. Get High-res Image Gene #3: 'amp_1q42.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_2p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S6. Gene #4: 'amp_2p23.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 4(2P23.2) MUTATED	47	87	118
AMP PEAK 4(2P23.2) WILD-TYPE	124	119	84

Figure S6. 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 = 0.0099

Table S7. Gene #5: 'amp_2q31.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 5(2Q31.2) MUTATED	46	102	114
AMP PEAK 5(2Q31.2) WILD-TYPE	125	104	88

Figure S7. 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 = 0.0099

Table S8. Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 6(3Q26.2) MUTATED	113	181	191
AMP PEAK 6(3Q26.2) WILD-TYPE	58	25	11

Figure S8. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_4q13.3' versus 'CN_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.23

Table S9. Gene #8: 'amp_4q13.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 8(4Q13.3) MUTATED	17	54	42
AMP PEAK 8(4Q13.3) WILD-TYPE	154	152	160

Figure S9. Get High-res Image Gene #8: 'amp_4q13.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S10. Gene #9: 'amp_5p15.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 9(5P15.33) MUTATED	60	123	126
AMP PEAK 9(5P15.33) WILD-TYPE	111	83	76

Figure S10. 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 = 0.0099

Table S11. Gene #10: 'amp_6p22.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 10(6P22.3) MUTATED	59	124	123
AMP PEAK 10(6P22.3) WILD-TYPE	112	82	79

Figure S11. 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 = 0.028

Table S12. Gene #11: 'amp_7q36.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 11(7Q36.3) MUTATED	69	124	127
AMP PEAK 11(7Q36.3) WILD-TYPE	102	82	75

Figure S12. Get High-res Image Gene #11: 'amp_7q36.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S13. Gene #12: 'amp_8p11.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 12(8P11.21) MUTATED	42	70	99
AMP PEAK 12(8P11.21) WILD-TYPE	129	136	103

Figure S13. 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 = 0.0099

Table S14. 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 S14. 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 = 0.0099

Table S15. 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 S15. 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 = 0.0099

Table S16. Gene #13: 'amp_8q24.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 13(8Q24.21) MUTATED	113	200	148
AMP PEAK 13(8Q24.21) WILD-TYPE	58	6	54

Figure S16. 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 = 0.0099

Table S17. Gene #13: 'amp_8q24.21' versus Molecular Subtype #9: '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 S17. Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S18. Gene #14: 'amp_10p15.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 14(10P15.3) MUTATED	45	81	126
AMP PEAK 14(10P15.3) WILD-TYPE	126	125	76

Figure S18. 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 = 0.0099

Table S19. Gene #16: 'amp_11q14.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 16(11Q14.1) MUTATED	54	117	86
AMP PEAK 16(11Q14.1) WILD-TYPE	117	89	116

Figure S19. 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 = 0.0099

Table S20. Gene #17: 'amp_12p13.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 17(12P13.33) MUTATED	71	111	148
AMP PEAK 17(12P13.33) WILD-TYPE	100	95	54

Figure S20. Get High-res Image Gene #17: 'amp_12p13.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_12p13.33' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.13

Table S21. Gene #17: 'amp_12p13.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 17(12P13.33) MUTATED	119	96	108
AMP PEAK 17(12P13.33) WILD-TYPE	53	79	113

Figure S21. Get High-res Image Gene #17: 'amp_12p13.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_12p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S22. Gene #18: 'amp_12p12.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 18(12P12.1) MUTATED	66	98	149
AMP PEAK 18(12P12.1) WILD-TYPE	105	108	53

Figure S22. Get High-res Image Gene #18: 'amp_12p12.1' versus Molecular Subtype #5: 'CN_CNMF'

'amp_12p12.1' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.028

Table S23. Gene #18: 'amp_12p12.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 18(12P12.1) MUTATED	117	87	102
AMP PEAK 18(12P12.1) WILD-TYPE	55	88	119

Figure S23. Get High-res Image Gene #18: 'amp_12p12.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_12q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S24. Gene #19: 'amp_12q15' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 19(12Q15) MUTATED	52	58	112
AMP PEAK 19(12Q15) WILD-TYPE	119	148	90

Figure S24. Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #5: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S25. Gene #19: 'amp_12q15' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 19(12Q15) MUTATED	90	62	65
AMP PEAK 19(12Q15) WILD-TYPE	82	113	156

Figure S25. Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_14q32.33' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.047

Table S26. Gene #21: 'amp_14q32.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 21(14Q32.33) MUTATED	41	77	38
AMP PEAK 21(14Q32.33) WILD-TYPE	130	129	164

Figure S26. Get High-res Image Gene #21: '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 = 0.0099

Table S27. Gene #22: 'amp_15q26.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 22(15Q26.3) MUTATED	34	90	39
AMP PEAK 22(15Q26.3) WILD-TYPE	137	116	163

Figure S27. Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_18q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S28. Gene #24: 'amp_18q11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 24(18Q11.2) MUTATED	25	44	74
AMP PEAK 24(18Q11.2) WILD-TYPE	146	162	128

Figure S28. Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19p13.12' versus 'MRNA_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.17

Table S29. Gene #25: 'amp_19p13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	216	126
AMP PEAK 25(19P13.12) MUTATED	136	115	51
AMP PEAK 25(19P13.12) WILD-TYPE	79	101	75

Figure S29. Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19p13.12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.23

Table S30. Gene #25: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	310	158	89
AMP PEAK 25(19P13.12) MUTATED	186	64	52
AMP PEAK 25(19P13.12) WILD-TYPE	124	94	37

Figure S30. Get High-res Image Gene #25: '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 = 0.0099

Table S31. Gene #25: 'amp_19p13.12' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 25(19P13.12) MUTATED	72	92	151
AMP PEAK 25(19P13.12) WILD-TYPE	99	114	51

Figure S31. Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19p13.12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S32. Gene #25: 'amp_19p13.12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 25(19P13.12) MUTATED	118	73	116
AMP PEAK 25(19P13.12) WILD-TYPE	54	102	105

Figure S32. Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_19p13.12' versus 'RPPA_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.092

Table S33. Gene #25: 'amp_19p13.12' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	96	128	58
AMP PEAK 25(19P13.12) MUTATED	44	55	86	31
AMP PEAK 25(19P13.12) WILD-TYPE	72	41	42	27

Figure S33. Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S34. Gene #26: 'amp_19q12' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 26(19Q12) MUTATED	67	83	172
AMP PEAK 26(19Q12) WILD-TYPE	104	123	30

Figure S34. Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S35. Gene #26: 'amp_19q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 26(19Q12) MUTATED	128	70	121
AMP PEAK 26(19Q12) WILD-TYPE	44	105	100

Figure S35. Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_19q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S36. Gene #27: 'amp_19q13.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 27(19Q13.2) MUTATED	51	71	123
AMP PEAK 27(19Q13.2) WILD-TYPE	120	135	79

Figure S36. Get High-res Image Gene #27: 'amp_19q13.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19q13.2' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.1

Table S37. Gene #27: 'amp_19q13.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 27(19Q13.2) MUTATED	94	56	91
AMP PEAK 27(19Q13.2) WILD-TYPE	78	119	130

Figure S37. Get High-res Image Gene #27: 'amp_19q13.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_20p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S38. Gene #28: 'amp_20p13' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 28(20P13) MUTATED	69	97	151
AMP PEAK 28(20P13) WILD-TYPE	102	109	51

Figure S38. Get High-res Image Gene #28: 'amp_20p13' versus Molecular Subtype #5: 'CN_CNMF'

'amp_20p13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S39. Gene #28: 'amp_20p13' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 28(20P13) MUTATED	123	81	103
AMP PEAK 28(20P13) WILD-TYPE	49	94	118

Figure S39. Get High-res Image Gene #28: 'amp_20p13' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S40. Gene #29: 'amp_20q11.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 29(20Q11.21) MUTATED	79	95	174
AMP PEAK 29(20Q11.21) WILD-TYPE	92	111	28

Figure S40. Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_20q11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S41. Gene #29: 'amp_20q11.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 29(20Q11.21) MUTATED	140	91	109
AMP PEAK 29(20Q11.21) WILD-TYPE	32	84	112

Figure S41. Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.17

Table S42. Gene #29: 'amp_20q11.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	67	91
AMP PEAK 29(20Q11.21) MUTATED	63	28	67
AMP PEAK 29(20Q11.21) WILD-TYPE	37	39	24

Figure S42. Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_20q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S43. Gene #30: 'amp_20q13.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 30(20Q13.33) MUTATED	87	132	183
AMP PEAK 30(20Q13.33) WILD-TYPE	84	74	19

Figure S43. Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_20q13.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S44. Gene #30: 'amp_20q13.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 30(20Q13.33) MUTATED	144	109	140
AMP PEAK 30(20Q13.33) WILD-TYPE	28	66	81

Figure S44. Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_xp11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S45. Gene #32: 'amp_xp11.23' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 32(XP11.23) MUTATED	25	55	79
AMP PEAK 32(XP11.23) WILD-TYPE	146	151	123

Figure S45. Get High-res Image Gene #32: 'amp_xp11.23' versus Molecular Subtype #5: 'CN_CNMF'

'del_1p36.11' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.056

Table S46. Gene #34: 'del_1p36.11' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 1(1P36.11) MUTATED	87	113	69
DEL PEAK 1(1P36.11) WILD-TYPE	84	93	133

Figure S46. Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #5: 'CN_CNMF'

'del_1q41' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S47. Gene #35: 'del_1q41' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 2(1Q41) MUTATED	14	60	23
DEL PEAK 2(1Q41) WILD-TYPE	157	146	179

Figure S47. Get High-res Image Gene #35: 'del_1q41' versus Molecular Subtype #5: 'CN_CNMF'

'del_2q37.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.019

Table S48. Gene #38: 'del_2q37.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 5(2Q37.3) MUTATED	35	86	54
DEL PEAK 5(2Q37.3) WILD-TYPE	136	120	148

Figure S48. Get High-res Image Gene #38: 'del_2q37.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_3p26.2' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.083

Table S49. Gene #39: 'del_3p26.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 6(3P26.2) MUTATED	47	66	96
DEL PEAK 6(3P26.2) WILD-TYPE	124	140	106

Figure S49. Get High-res Image Gene #39: 'del_3p26.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S50. Gene #43: 'del_5q12.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 10(5Q12.1) MUTATED	73	145	137
DEL PEAK 10(5Q12.1) WILD-TYPE	98	61	65

Figure S50. Get High-res Image Gene #43: 'del_5q12.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.18

Table S51. Gene #43: 'del_5q12.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
DEL PEAK 10(5Q12.1) MUTATED	117	85	146
DEL PEAK 10(5Q12.1) WILD-TYPE	55	90	75

Figure S51. Get High-res Image Gene #43: 'del_5q12.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_5q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S52. Gene #44: 'del_5q13.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 11(5Q13.2) MUTATED	92	180	147
DEL PEAK 11(5Q13.2) WILD-TYPE	79	26	55

Figure S52. Get High-res Image Gene #44: 'del_5q13.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_6q27' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S53. Gene #45: 'del_6q27' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 12(6Q27) MUTATED	121	162	97
DEL PEAK 12(6Q27) WILD-TYPE	50	44	105

Figure S53. Get High-res Image Gene #45: 'del_6q27' versus Molecular Subtype #5: 'CN_CNMF'

'del_6q27' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.037

Table S54. Gene #45: 'del_6q27' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
DEL PEAK 12(6Q27) MUTATED	91	132	152
DEL PEAK 12(6Q27) WILD-TYPE	81	43	69

Figure S54. Get High-res Image Gene #45: 'del_6q27' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_6q27' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.019

Table S55. Gene #45: 'del_6q27' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	67	91
DEL PEAK 12(6Q27) MUTATED	66	52	38
DEL PEAK 12(6Q27) WILD-TYPE	34	15	53

Figure S55. Get High-res Image Gene #45: 'del_6q27' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_7p22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S56. Gene #46: 'del_7p22.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 13(7P22.1) MUTATED	48	135	70
DEL PEAK 13(7P22.1) WILD-TYPE	123	71	132

Figure S56. Get High-res Image Gene #46: '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 = 0.0099

Table S57. Gene #47: 'del_8p23.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 14(8P23.3) MUTATED	78	162	148
DEL PEAK 14(8P23.3) WILD-TYPE	93	44	54

Figure S57. Get High-res Image Gene #47: '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 = 0.0099

Table S58. Gene #48: 'del_8p21.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 15(8P21.2) MUTATED	88	166	152
DEL PEAK 15(8P21.2) WILD-TYPE	83	40	50

Figure S58. Get High-res Image Gene #48: 'del_8p21.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_9p24.3' versus 'MRNA_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.24

Table S59. Gene #49: 'del_9p24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	216	126
DEL PEAK 16(9P24.3) MUTATED	109	73	66
DEL PEAK 16(9P24.3) WILD-TYPE	106	143	60

Figure S59. Get High-res Image Gene #49: 'del_9p24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p24.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S60. Gene #49: 'del_9p24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	310	158	89
DEL PEAK 16(9P24.3) MUTATED	120	69	59
DEL PEAK 16(9P24.3) WILD-TYPE	190	89	30

Figure S60. Get High-res Image Gene #49: 'del_9p24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p24.3' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.065

Table S61. Gene #49: 'del_9p24.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
DEL PEAK 16(9P24.3) MUTATED	92	90	75
DEL PEAK 16(9P24.3) WILD-TYPE	80	85	146

Figure S61. Get High-res Image Gene #49: 'del_9p24.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_9q34.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S62. Gene #50: 'del_9q34.13' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 17(9Q34.13) MUTATED	93	98	151
DEL PEAK 17(9Q34.13) WILD-TYPE	78	108	51

Figure S62. Get High-res Image Gene #50: 'del_9q34.13' versus Molecular Subtype #5: 'CN_CNMF'

'del_10q24.2' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.083

Table S63. Gene #52: 'del_10q24.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 19(10Q24.2) MUTATED	53	111	87
DEL PEAK 19(10Q24.2) WILD-TYPE	118	95	115

Figure S63. Get High-res Image Gene #52: '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 = 0.0099

Table S64. Gene #53: 'del_11p15.5' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 20(11P15.5) MUTATED	77	163	106
DEL PEAK 20(11P15.5) WILD-TYPE	94	43	96

Figure S64. Get High-res Image Gene #53: '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 = 0.0099

Table S65. Gene #55: 'del_12q24.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 22(12Q24.33) MUTATED	56	113	51
DEL PEAK 22(12Q24.33) WILD-TYPE	115	93	151

Figure S65. Get High-res Image Gene #55: 'del_12q24.33' versus Molecular Subtype #5: 'CN_CNMF'

'del_13q14.2' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.22

Table S66. Gene #56: 'del_13q14.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 23(13Q14.2) MUTATED	90	150	124
DEL PEAK 23(13Q14.2) WILD-TYPE	81	56	78

Figure S66. Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S67. Gene #56: 'del_13q14.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
DEL PEAK 23(13Q14.2) MUTATED	109	88	161
DEL PEAK 23(13Q14.2) WILD-TYPE	63	87	60

Figure S67. Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_14q23.3' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.056

Table S68. Gene #57: 'del_14q23.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 24(14Q23.3) MUTATED	70	104	131
DEL PEAK 24(14Q23.3) WILD-TYPE	101	102	71

Figure S68. Get High-res Image Gene #57: 'del_14q23.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_15q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S69. Gene #58: 'del_15q11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 25(15Q11.2) MUTATED	68	76	155
DEL PEAK 25(15Q11.2) WILD-TYPE	103	130	47

Figure S69. Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_15q11.2' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.028

Table S70. Gene #58: 'del_15q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
DEL PEAK 25(15Q11.2) MUTATED	114	82	100
DEL PEAK 25(15Q11.2) WILD-TYPE	58	93	121

Figure S70. Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_15q15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S71. Gene #59: 'del_15q15.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 26(15Q15.1) MUTATED	81	115	167
DEL PEAK 26(15Q15.1) WILD-TYPE	90	91	35

Figure S71. Get High-res Image Gene #59: 'del_15q15.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_15q15.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S72. Gene #59: 'del_15q15.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
DEL PEAK 26(15Q15.1) MUTATED	134	97	129
DEL PEAK 26(15Q15.1) WILD-TYPE	38	78	92

Figure S72. Get High-res Image Gene #59: 'del_15q15.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.14

Table S73. Gene #62: 'del_16q23.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 29(16Q23.1) MUTATED	114	168	170
DEL PEAK 29(16Q23.1) WILD-TYPE	57	38	32

Figure S73. Get High-res Image Gene #62: 'del_16q23.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_19q13.33' versus 'MRNA_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.21

Table S74. Gene #67: 'del_19q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	216	126
DEL PEAK 34(19Q13.33) MUTATED	127	117	46
DEL PEAK 34(19Q13.33) WILD-TYPE	88	99	80

Figure S74. Get High-res Image Gene #67: 'del_19q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19q13.43' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.1

Table S75. Gene #68: 'del_19q13.43' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 35(19Q13.43) MUTATED	84	80	121
DEL PEAK 35(19Q13.43) WILD-TYPE	87	126	81

Figure S75. Get High-res Image Gene #68: 'del_19q13.43' versus Molecular Subtype #5: 'CN_CNMF'

'del_19q13.43' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.047

Table S76. Gene #68: 'del_19q13.43' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
DEL PEAK 35(19Q13.43) MUTATED	105	64	111
DEL PEAK 35(19Q13.43) WILD-TYPE	67	111	110

Figure S76. Get High-res Image Gene #68: 'del_19q13.43' versus Molecular Subtype #6: 'METHLYATION_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = OV-TP.transferedmergedcluster.txt
Number of patients = 579
Number of significantly focal cnvs = 71
Number of molecular subtypes = 14
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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