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

Bladder Urothelial Carcinoma (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/C15T3J9P

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 408 patients, 125 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'.
amp_1q23.3 cnv correlated to 'CN_CNMF'.
amp_2p25.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3p25.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3q26.33 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_4p16.3 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
amp_4q13.3 cnv correlated to 'CN_CNMF'.
amp_5p15.33 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
amp_6p22.3 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7p21.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7p11.2 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8p11.23 cnv correlated to 'CN_CNMF'.
amp_8q22.3 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_9p24.1 cnv correlated to 'CN_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_10p14 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_11p13 cnv correlated to 'CN_CNMF'.
amp_11q13.3 cnv correlated to 'CN_CNMF'.
amp_11q22.2 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
amp_12p12.1 cnv correlated to 'CN_CNMF'.
amp_12q15 cnv correlated to 'CN_CNMF'.
amp_13q22.1 cnv correlated to 'CN_CNMF'.
amp_16p13.2 cnv correlated to 'CN_CNMF'.
amp_16p11.2 cnv correlated to 'CN_CNMF'.
amp_17q11.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q12 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q23.3 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19q12 cnv correlated to 'CN_CNMF'.
amp_19q13.43 cnv correlated to 'CN_CNMF'.
amp_20q11.21 cnv correlated to 'CN_CNMF'.
amp_22q12.2 cnv correlated to 'CN_CNMF'.
del_1q32.1 cnv correlated to 'CN_CNMF'.
del_2q22.1 cnv correlated to 'CN_CNMF'.
del_2q34 cnv correlated to 'CN_CNMF'.
del_2q37.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_3p14.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q22.1 cnv correlated to 'CN_CNMF'.
del_4q34.2 cnv correlated to 'CN_CNMF'.
del_5q12.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
del_6p25.3 cnv correlated to 'CN_CNMF'.
del_6q21 cnv correlated to 'CN_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q27 cnv correlated to 'CN_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_7q36.3 cnv correlated to 'CN_CNMF'.
del_8p23.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_9p23 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
del_9p21.3 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9q33.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'CN_CNMF'.
del_11p15.5 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_11q23.3 cnv correlated to 'CN_CNMF'.
del_11q25 cnv correlated to 'CN_CNMF'.
del_12p13.1 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
del_12q24.33 cnv correlated to 'CN_CNMF'.
del_13q14.2 cnv correlated to 'CN_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q24.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q13.1 cnv correlated to 'CN_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16p13.3 cnv correlated to 'CN_CNMF'.
del_16q23.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p12 cnv correlated to 'CN_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q23 cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_22q13.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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, 125 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
del 9q33 2	168 (41%)	240	1e-05 (0.007)	1e-05 (0.007)	0.0672 (1.00)	0.00298 (1.00)	1e-05 (0.007)	1e-05 (0.007)	0.0004 (0.232)	0.00032 (0.186)	1e-05 (0.007)	1e-05 (0.007)
amp 3p25 2	190 (47%)	218	1e-05 (0.007)	0.0531 (1.00)	0.079 (1.00)	0.0109 (1.00)	1e-05 (0.007)	1e-05 (0.007)	0.00019 (0.114)	1e-05 (0.007)	1e-05 (0.007)	1e-05 (0.007)
del 3p14 2	117 (29%)	291	0.00011 (0.0665)	0.108 (1.00)	0.0343 (1.00)	0.0175 (1.00)	1e-05 (0.007)	1e-05 (0.007)	0.881 (1.00)	4e-05 (0.0246)	6e-05 (0.0368)	1e-05 (0.007)
amp 4p16 3	74 (18%)	334	0.213 (1.00)	0.00027 (0.158)	0.0338 (1.00)	0.0266 (1.00)	0.00043 (0.248)	2e-05 (0.0125)	1e-05 (0.007)	0.0258 (1.00)	0.0581 (1.00)	0.022 (1.00)
amp 2p25 1	152 (37%)	256	1e-05 (0.007)	0.00024 (0.142)	0.801 (1.00)	0.613 (1.00)	0.0365 (1.00)	0.00139 (0.785)	0.0238 (1.00)	0.0163 (1.00)	0.0163 (1.00)	3e-05 (0.0187)
amp 9p24 1	88 (22%)	320	1e-05 (0.007)	0.0254 (1.00)	0.674 (1.00)	0.326 (1.00)	0.112 (1.00)	0.0381 (1.00)	0.693 (1.00)	0.0442 (1.00)	0.00012 (0.0725)	7e-05 (0.0427)
amp 10p14	182 (45%)	226	1e-05 (0.007)	0.294 (1.00)	0.355 (1.00)	0.422 (1.00)	0.168 (1.00)	0.00029 (0.17)	0.103 (1.00)	0.154 (1.00)	0.453 (1.00)	1e-05 (0.007)
amp 17q11 2	174 (43%)	234	1e-05 (0.007)	0.00096 (0.544)	0.0321 (1.00)	0.088 (1.00)	9e-05 (0.0548)	0.00234 (1.00)	0.0457 (1.00)	0.0119 (1.00)	0.00368 (1.00)	1e-05 (0.007)
del 6q21	190 (47%)	218	1e-05 (0.007)	0.049 (1.00)	0.883 (1.00)	0.47 (1.00)	0.491 (1.00)	0.0766 (1.00)	0.0152 (1.00)	0.00022 (0.131)	0.238 (1.00)	1e-05 (0.007)
del 6q27	190 (47%)	218	1e-05 (0.007)	0.0269 (1.00)	0.658 (1.00)	0.434 (1.00)	0.417 (1.00)	0.02 (1.00)	0.0222 (1.00)	2e-05 (0.0125)	0.376 (1.00)	1e-05 (0.007)
del 11p15 5	211 (52%)	197	1e-05 (0.007)	0.0003 (0.175)	0.365 (1.00)	0.242 (1.00)	0.00222 (1.00)	0.00026 (0.153)	0.0215 (1.00)	0.299 (1.00)	0.0127 (1.00)	0.0121 (1.00)
del 13q14 2	156 (38%)	252	1e-05 (0.007)	0.254 (1.00)	0.00783 (1.00)	0.00359 (1.00)	0.0128 (1.00)	0.0332 (1.00)	0.536 (1.00)	0.0003 (0.175)	0.00562 (1.00)	1e-05 (0.007)
del 14q24 1	137 (34%)	271	1e-05 (0.007)	0.124 (1.00)	0.392 (1.00)	0.346 (1.00)	0.00365 (1.00)	1e-05 (0.007)	0.00708 (1.00)	0.00102 (0.577)	0.00333 (1.00)	3e-05 (0.0187)
del 15q13 1	159 (39%)	249	1e-05 (0.007)	0.00654 (1.00)	0.317 (1.00)	0.569 (1.00)	0.701 (1.00)	0.0946 (1.00)	0.0262 (1.00)	6e-05 (0.0368)	0.0254 (1.00)	1e-05 (0.007)
del 17p12	209 (51%)	199	1e-05 (0.007)	0.0343 (1.00)	0.201 (1.00)	0.609 (1.00)	0.289 (1.00)	0.00351 (1.00)	0.605 (1.00)	0.00019 (0.114)	0.359 (1.00)	0.00019 (0.114)
del 18q23	178 (44%)	230	0.00041 (0.237)	0.105 (1.00)	0.632 (1.00)	0.785 (1.00)	0.214 (1.00)	0.616 (1.00)	1e-05 (0.007)	1e-05 (0.007)	0.033 (1.00)	0.00672 (1.00)
del 22q13 32	187 (46%)	221	1e-05 (0.007)	0.00023 (0.136)	0.549 (1.00)	0.0162 (1.00)	0.0141 (1.00)	0.0301 (1.00)	0.287 (1.00)	0.00159 (0.894)	0.00905 (1.00)	1e-05 (0.007)
amp 3q26 33	218 (53%)	190	1e-05 (0.007)	0.522 (1.00)	0.353 (1.00)	0.0927 (1.00)	0.315 (1.00)	0.132 (1.00)	0.54 (1.00)	0.00564 (1.00)	0.181 (1.00)	1e-05 (0.007)
amp 5p15 33	206 (50%)	202	1e-05 (0.007)	0.165 (1.00)	0.0216 (1.00)	0.178 (1.00)	0.616 (1.00)	0.0765 (1.00)	0.391 (1.00)	3e-05 (0.0187)	0.329 (1.00)	0.00086 (0.489)
amp 6p22 3	171 (42%)	237	1e-05 (0.007)	0.103 (1.00)	0.336 (1.00)	0.433 (1.00)	0.428 (1.00)	0.234 (1.00)	0.0708 (1.00)	0.262 (1.00)	0.26 (1.00)	1e-05 (0.007)
amp 7p21 1	201 (49%)	207	1e-05 (0.007)	0.0232 (1.00)	0.133 (1.00)	0.317 (1.00)	0.673 (1.00)	0.044 (1.00)	0.171 (1.00)	0.00697 (1.00)	0.401 (1.00)	1e-05 (0.007)
amp 7p11 2	190 (47%)	218	1e-05 (0.007)	0.0279 (1.00)	0.0898 (1.00)	0.599 (1.00)	0.723 (1.00)	0.166 (1.00)	0.514 (1.00)	0.0364 (1.00)	0.17 (1.00)	5e-05 (0.0307)
amp 8q22 3	264 (65%)	144	1e-05 (0.007)	0.00208 (1.00)	0.0243 (1.00)	0.19 (1.00)	0.231 (1.00)	0.259 (1.00)	0.0192 (1.00)	0.00597 (1.00)	0.072 (1.00)	9e-05 (0.0548)
amp 11q22 2	71 (17%)	337	0.00012 (0.0725)	0.275 (1.00)	0.734 (1.00)	0.412 (1.00)	0.847 (1.00)	0.0318 (1.00)	0.0423 (1.00)	0.0227 (1.00)	0.00038 (0.221)	0.0208 (1.00)
amp 17q12	165 (40%)	243	1e-05 (0.007)	0.0271 (1.00)	0.132 (1.00)	0.0369 (1.00)	0.00296 (1.00)	0.0688 (1.00)	0.00461 (1.00)	0.0353 (1.00)	0.0186 (1.00)	1e-05 (0.007)
amp 17q23 3	194 (48%)	214	1e-05 (0.007)	0.076 (1.00)	0.108 (1.00)	0.14 (1.00)	0.297 (1.00)	0.693 (1.00)	0.184 (1.00)	0.469 (1.00)	0.145 (1.00)	0.00015 (0.09)
del 2q37 1	207 (51%)	201	1e-05 (0.007)	0.00023 (0.136)	0.593 (1.00)	0.442 (1.00)	0.1 (1.00)	0.0898 (1.00)	0.022 (1.00)	0.0606 (1.00)	0.184 (1.00)	0.00549 (1.00)
del 5q12 1	202 (50%)	206	1e-05 (0.007)	0.015 (1.00)	0.935 (1.00)	0.573 (1.00)	0.255 (1.00)	0.0088 (1.00)	0.0223 (1.00)	0.00013 (0.0783)	0.0603 (1.00)	0.00093 (0.528)
del 8p23 1	245 (60%)	163	1e-05 (0.007)	0.0003 (0.175)	0.59 (1.00)	0.177 (1.00)	0.269 (1.00)	0.0385 (1.00)	0.0734 (1.00)	0.0265 (1.00)	0.161 (1.00)	0.0724 (1.00)
del 9p23	177 (43%)	231	1e-05 (0.007)	0.0268 (1.00)	0.219 (1.00)	0.205 (1.00)	0.268 (1.00)	0.0359 (1.00)	0.0653 (1.00)	0.0167 (1.00)	3e-05 (0.0187)	0.00079 (0.452)
del 9p21 3	239 (59%)	169	1e-05 (0.007)	0.266 (1.00)	0.451 (1.00)	0.00965 (1.00)	0.232 (1.00)	0.12 (1.00)	0.153 (1.00)	0.0944 (1.00)	0.0369 (1.00)	0.0001 (0.0607)
del 16q23 1	119 (29%)	289	1e-05 (0.007)	0.0151 (1.00)	0.502 (1.00)	0.0637 (1.00)	0.0572 (1.00)	0.275 (1.00)	0.131 (1.00)	0.0251 (1.00)	0.0852 (1.00)	5e-05 (0.0307)
del 19p13 3	145 (36%)	263	1e-05 (0.007)	0.822 (1.00)	0.938 (1.00)	0.563 (1.00)	0.0272 (1.00)	0.00531 (1.00)	0.334 (1.00)	0.00918 (1.00)	0.211 (1.00)	0.0002 (0.119)
amp 1p34 2	101 (25%)	307	1e-05 (0.007)	0.1 (1.00)	0.182 (1.00)	0.508 (1.00)	0.938 (1.00)	0.29 (1.00)	0.0351 (1.00)	0.0192 (1.00)	0.242 (1.00)	0.0115 (1.00)
amp 1q21 3	202 (50%)	206	1e-05 (0.007)	0.053 (1.00)	0.392 (1.00)	0.722 (1.00)	0.048 (1.00)	0.00724 (1.00)	0.14 (1.00)	0.0431 (1.00)	0.621 (1.00)	0.00373 (1.00)
amp 1q23 3	216 (53%)	192	1e-05 (0.007)	0.00383 (1.00)	0.552 (1.00)	0.886 (1.00)	0.106 (1.00)	0.00961 (1.00)	0.00203 (1.00)	0.00319 (1.00)	0.0413 (1.00)	0.00149 (0.84)
amp 4q13 3	62 (15%)	346	6e-05 (0.0368)	0.0269 (1.00)	0.582 (1.00)	0.702 (1.00)	0.265 (1.00)	0.502 (1.00)	0.00945 (1.00)	0.0668 (1.00)	0.0655 (1.00)	0.0435 (1.00)
amp 8p11 23	124 (30%)	284	1e-05 (0.007)	0.0949 (1.00)	0.749 (1.00)	0.791 (1.00)	0.658 (1.00)	0.323 (1.00)	0.0286 (1.00)	0.513 (1.00)	0.681 (1.00)	0.953 (1.00)
amp 11p13	51 (12%)	357	1e-05 (0.007)	0.00502 (1.00)	0.0331 (1.00)	0.00338 (1.00)	0.185 (1.00)	0.0136 (1.00)	0.253 (1.00)	0.118 (1.00)	0.0523 (1.00)	0.00295 (1.00)
amp 11q13 3	135 (33%)	273	1e-05 (0.007)	0.309 (1.00)	0.232 (1.00)	0.0779 (1.00)	0.071 (1.00)	0.0305 (1.00)	0.375 (1.00)	0.174 (1.00)	0.33 (1.00)	0.711 (1.00)
amp 12p12 1	132 (32%)	276	2e-05 (0.0125)	0.0459 (1.00)	0.692 (1.00)	0.469 (1.00)	0.533 (1.00)	0.376 (1.00)	0.822 (1.00)	0.0277 (1.00)	0.0749 (1.00)	0.0385 (1.00)
amp 12q15	118 (29%)	290	0.00013 (0.0783)	0.41 (1.00)	0.0379 (1.00)	0.0196 (1.00)	0.00217 (1.00)	0.00296 (1.00)	0.215 (1.00)	0.0211 (1.00)	0.00755 (1.00)	0.00044 (0.253)
amp 13q22 1	128 (31%)	280	0.0001 (0.0607)	0.352 (1.00)	0.962 (1.00)	0.849 (1.00)	0.978 (1.00)	0.611 (1.00)	0.877 (1.00)	0.556 (1.00)	0.732 (1.00)	0.224 (1.00)
amp 16p13 2	87 (21%)	321	1e-05 (0.007)	0.122 (1.00)	0.793 (1.00)	0.899 (1.00)	0.514 (1.00)	0.181 (1.00)	0.18 (1.00)	0.0717 (1.00)	0.229 (1.00)	0.0225 (1.00)
amp 16p11 2	97 (24%)	311	3e-05 (0.0187)	0.149 (1.00)	0.466 (1.00)	0.369 (1.00)	0.934 (1.00)	0.443 (1.00)	0.248 (1.00)	0.311 (1.00)	0.957 (1.00)	0.0719 (1.00)
amp 19q12	165 (40%)	243	1e-05 (0.007)	0.556 (1.00)	0.753 (1.00)	0.781 (1.00)	0.299 (1.00)	0.106 (1.00)	0.222 (1.00)	0.0106 (1.00)	0.158 (1.00)	0.0263 (1.00)
amp 19q13 43	155 (38%)	253	1e-05 (0.007)	0.0988 (1.00)	0.168 (1.00)	0.304 (1.00)	0.676 (1.00)	0.898 (1.00)	0.418 (1.00)	0.00263 (1.00)	0.0167 (1.00)	0.00281 (1.00)
amp 20q11 21	263 (64%)	145	1e-05 (0.007)	0.129 (1.00)	0.712 (1.00)	0.0545 (1.00)	0.682 (1.00)	0.0354 (1.00)	0.344 (1.00)	0.0308 (1.00)	0.195 (1.00)	0.00082 (0.467)
amp 22q12 2	87 (21%)	321	1e-05 (0.007)	0.00339 (1.00)	0.416 (1.00)	0.762 (1.00)	0.0397 (1.00)	0.216 (1.00)	0.129 (1.00)	0.256 (1.00)	0.478 (1.00)	0.0484 (1.00)
del 1q32 1	71 (17%)	337	0.00024 (0.142)	0.409 (1.00)	0.353 (1.00)	0.605 (1.00)	0.171 (1.00)	0.0671 (1.00)	0.55 (1.00)	0.277 (1.00)	0.402 (1.00)	0.131 (1.00)
del 2q22 1	134 (33%)	274	0.00042 (0.242)	0.007 (1.00)	0.274 (1.00)	0.943 (1.00)	0.0986 (1.00)	0.216 (1.00)	0.06 (1.00)	0.25 (1.00)	0.187 (1.00)	0.00885 (1.00)
del 2q34	174 (43%)	234	1e-05 (0.007)	0.015 (1.00)	0.751 (1.00)	0.582 (1.00)	0.461 (1.00)	0.453 (1.00)	0.11 (1.00)	0.533 (1.00)	0.487 (1.00)	0.00067 (0.384)
del 4q22 1	162 (40%)	246	1e-05 (0.007)	0.00838 (1.00)	0.509 (1.00)	0.505 (1.00)	0.0679 (1.00)	0.0192 (1.00)	0.897 (1.00)	0.00745 (1.00)	0.0242 (1.00)	0.0139 (1.00)
del 4q34 2	177 (43%)	231	1e-05 (0.007)	0.0399 (1.00)	0.487 (1.00)	0.772 (1.00)	0.368 (1.00)	0.201 (1.00)	0.292 (1.00)	0.0637 (1.00)	0.488 (1.00)	0.0008 (0.457)
del 6p25 3	106 (26%)	302	1e-05 (0.007)	0.0482 (1.00)	0.912 (1.00)	0.947 (1.00)	0.543 (1.00)	0.0527 (1.00)	0.253 (1.00)	0.0312 (1.00)	0.0519 (1.00)	0.00765 (1.00)
del 7q36 3	59 (14%)	349	0.0004 (0.232)	0.617 (1.00)	0.137 (1.00)	0.132 (1.00)	0.437 (1.00)	0.296 (1.00)	0.466 (1.00)	0.00157 (0.884)	0.0546 (1.00)	0.00335 (1.00)
del 10q23 31	167 (41%)	241	1e-05 (0.007)	0.0536 (1.00)	0.627 (1.00)	0.594 (1.00)	0.128 (1.00)	0.895 (1.00)	0.325 (1.00)	0.093 (1.00)	0.61 (1.00)	0.0646 (1.00)
del 11q23 3	156 (38%)	252	0.0002 (0.119)	0.00312 (1.00)	0.656 (1.00)	0.704 (1.00)	0.0694 (1.00)	0.257 (1.00)	0.236 (1.00)	0.173 (1.00)	0.584 (1.00)	0.519 (1.00)
del 11q25	144 (35%)	264	3e-05 (0.0187)	0.00776 (1.00)	0.773 (1.00)	0.621 (1.00)	0.0513 (1.00)	0.257 (1.00)	0.381 (1.00)	0.197 (1.00)	0.474 (1.00)	0.292 (1.00)
del 12p13 1	68 (17%)	340	0.00343 (1.00)	0.0728 (1.00)	0.78 (1.00)	0.662 (1.00)	0.00731 (1.00)	0.00025 (0.147)	0.571 (1.00)	0.619 (1.00)	0.0165 (1.00)	0.212 (1.00)
del 12q24 33	88 (22%)	320	2e-05 (0.0125)	0.929 (1.00)	0.915 (1.00)	0.32 (1.00)	0.604 (1.00)	0.651 (1.00)	1 (1.00)	0.627 (1.00)	0.982 (1.00)	0.242 (1.00)
del 16p13 3	173 (42%)	235	1e-05 (0.007)	0.00795 (1.00)	0.212 (1.00)	0.468 (1.00)	0.644 (1.00)	0.855 (1.00)	0.703 (1.00)	0.0432 (1.00)	0.522 (1.00)	0.0121 (1.00)
amp 6q21	34 (8%)	374	0.00233 (1.00)	0.824 (1.00)	0.514 (1.00)	0.0792 (1.00)	0.394 (1.00)	0.255 (1.00)	0.821 (1.00)	0.875 (1.00)	0.382 (1.00)	0.185 (1.00)
amp 6q23 3	46 (11%)	362	0.00046 (0.264)	0.811 (1.00)	0.945 (1.00)	0.0696 (1.00)	0.304 (1.00)	0.671 (1.00)	0.14 (1.00)	0.0998 (1.00)	0.148 (1.00)	0.126 (1.00)
amp 16q22 1	108 (26%)	300	0.00371 (1.00)	0.276 (1.00)	0.0429 (1.00)	0.0235 (1.00)	0.0317 (1.00)	0.0375 (1.00)	0.0431 (1.00)	0.00845 (1.00)	0.153 (1.00)	0.00712 (1.00)
amp 17p11 2	87 (21%)	321	0.00354 (1.00)	0.129 (1.00)	0.682 (1.00)	0.946 (1.00)	0.0749 (1.00)	0.42 (1.00)	0.637 (1.00)	0.844 (1.00)	0.531 (1.00)	0.342 (1.00)
del 1p36 11	91 (22%)	317	0.349 (1.00)	0.0443 (1.00)	0.165 (1.00)	0.024 (1.00)	0.832 (1.00)	0.888 (1.00)	0.705 (1.00)	0.0473 (1.00)	0.133 (1.00)	0.253 (1.00)
del 10p11 21	74 (18%)	334	0.082 (1.00)	0.395 (1.00)	0.535 (1.00)	0.244 (1.00)	0.00322 (1.00)	0.00311 (1.00)	0.782 (1.00)	0.0573 (1.00)	0.373 (1.00)	0.502 (1.00)
del xp11 3	92 (23%)	316	0.0932 (1.00)	0.396 (1.00)	0.735 (1.00)	0.618 (1.00)	0.282 (1.00)	0.948 (1.00)	0.106 (1.00)	0.29 (1.00)	0.518 (1.00)	0.0329 (1.00)
del xq21 33	84 (21%)	324	0.0167 (1.00)	0.0551 (1.00)	0.98 (1.00)	0.436 (1.00)	0.0547 (1.00)	0.199 (1.00)	0.0882 (1.00)	0.0509 (1.00)	0.0113 (1.00)	0.0177 (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	CLUS_4
ALL	87	103	156	62
AMP PEAK 1(1P34.2) MUTATED	27	45	16	13
AMP PEAK 1(1P34.2) WILD-TYPE	60	58	140	49

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	CLUS_4
ALL	87	103	156	62
AMP PEAK 2(1Q21.3) MUTATED	38	85	43	36
AMP PEAK 2(1Q21.3) WILD-TYPE	49	18	113	26

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

'amp_1q23.3' versus 'CN_CNMF'

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

Table S3. Gene #3: 'amp_1q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
AMP PEAK 3(1Q23.3) MUTATED	41	91	53	31
AMP PEAK 3(1Q23.3) WILD-TYPE	46	12	103	31

Figure S3. Get High-res Image Gene #3: 'amp_1q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2p25.1' versus 'CN_CNMF'

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

Table S4. Gene #4: 'amp_2p25.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
AMP PEAK 4(2P25.1) MUTATED	47	61	27	17
AMP PEAK 4(2P25.1) WILD-TYPE	40	42	129	45

Figure S4. Get High-res Image Gene #4: 'amp_2p25.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2p25.1' versus 'METHLYATION_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.14

Table S5. Gene #4: 'amp_2p25.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	137	68
AMP PEAK 4(2P25.1) MUTATED	57	66	13
AMP PEAK 4(2P25.1) WILD-TYPE	101	71	55

Figure S5. Get High-res Image Gene #4: 'amp_2p25.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_2p25.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.019

Table S6. Gene #4: 'amp_2p25.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
AMP PEAK 4(2P25.1) MUTATED	26	26	46	25	3	22
AMP PEAK 4(2P25.1) WILD-TYPE	48	20	47	41	28	62

Figure S6. Get High-res Image Gene #4: 'amp_2p25.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3p25.2' versus 'CN_CNMF'

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

Table S7. Gene #5: 'amp_3p25.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
AMP PEAK 5(3P25.2) MUTATED	49	80	37	24
AMP PEAK 5(3P25.2) WILD-TYPE	38	23	119	38

Figure S7. Get High-res Image Gene #5: 'amp_3p25.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3p25.2' versus 'MRNASEQ_CNMF'

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

Table S8. Gene #5: 'amp_3p25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	159	96
AMP PEAK 5(3P25.2) MUTATED	54	92	22
AMP PEAK 5(3P25.2) WILD-TYPE	44	67	74

Figure S8. Get High-res Image Gene #5: 'amp_3p25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3p25.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S9. Gene #5: 'amp_3p25.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	114	78	60
AMP PEAK 5(3P25.2) MUTATED	66	59	16	27
AMP PEAK 5(3P25.2) WILD-TYPE	35	55	62	33

Figure S9. Get High-res Image Gene #5: 'amp_3p25.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3p25.2' versus 'MIRSEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.11

Table S10. Gene #5: 'amp_3p25.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	96	189
AMP PEAK 5(3P25.2) MUTATED	44	62	83
AMP PEAK 5(3P25.2) WILD-TYPE	76	34	106

Figure S10. Get High-res Image Gene #5: 'amp_3p25.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_3p25.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S11. Gene #5: 'amp_3p25.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
AMP PEAK 5(3P25.2) MUTATED	27	59	33	42	28
AMP PEAK 5(3P25.2) WILD-TYPE	62	40	60	28	26

Figure S11. Get High-res Image Gene #5: '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 S12. Gene #5: 'amp_3p25.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
AMP PEAK 5(3P25.2) MUTATED	30	36	66	53
AMP PEAK 5(3P25.2) WILD-TYPE	68	7	68	66

Figure S12. Get High-res Image Gene #5: 'amp_3p25.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_3p25.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S13. Gene #5: 'amp_3p25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
AMP PEAK 5(3P25.2) MUTATED	36	34	63	23	2	27
AMP PEAK 5(3P25.2) WILD-TYPE	38	12	30	43	29	57

Figure S13. Get High-res Image Gene #5: 'amp_3p25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.33' versus 'CN_CNMF'

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

Table S14. Gene #6: 'amp_3q26.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
AMP PEAK 6(3Q26.33) MUTATED	54	74	57	33
AMP PEAK 6(3Q26.33) WILD-TYPE	33	29	99	29

Figure S14. Get High-res Image Gene #6: 'amp_3q26.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S15. Gene #6: 'amp_3q26.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
AMP PEAK 6(3Q26.33) MUTATED	36	30	58	42	4	40
AMP PEAK 6(3Q26.33) WILD-TYPE	38	16	35	24	27	44

Figure S15. Get High-res Image Gene #6: 'amp_3q26.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4p16.3' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.16

Table S16. Gene #7: 'amp_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	137	68
AMP PEAK 7(4P16.3) MUTATED	16	40	13
AMP PEAK 7(4P16.3) WILD-TYPE	142	97	55

Figure S16. Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_4p16.3' versus 'MRNASEQ_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.25

Table S17. Gene #7: 'amp_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	159	96
AMP PEAK 7(4P16.3) MUTATED	9	44	14
AMP PEAK 7(4P16.3) WILD-TYPE	89	115	82

Figure S17. Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S18. Gene #7: 'amp_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	114	78	60
AMP PEAK 7(4P16.3) MUTATED	17	37	11	2
AMP PEAK 7(4P16.3) WILD-TYPE	84	77	67	58

Figure S18. Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_4p16.3' versus 'MIRSEQ_CNMF'

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

Table S19. Gene #7: 'amp_4p16.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	96	189
AMP PEAK 7(4P16.3) MUTATED	6	28	40
AMP PEAK 7(4P16.3) WILD-TYPE	114	68	149

Figure S19. Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_4q13.3' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.037

Table S20. Gene #8: 'amp_4q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
AMP PEAK 8(4Q13.3) MUTATED	19	27	10	6
AMP PEAK 8(4Q13.3) WILD-TYPE	68	76	146	56

Figure S20. Get High-res Image Gene #8: 'amp_4q13.3' 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 S21. Gene #9: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
AMP PEAK 9(5P15.33) MUTATED	51	71	38	46
AMP PEAK 9(5P15.33) WILD-TYPE	36	32	118	16

Figure S21. Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.019

Table S22. Gene #9: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
AMP PEAK 9(5P15.33) MUTATED	43	63	27	41	31
AMP PEAK 9(5P15.33) WILD-TYPE	46	36	66	29	23

Figure S22. 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 S23. Gene #10: 'amp_6p22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
AMP PEAK 10(6P22.3) MUTATED	32	79	25	35
AMP PEAK 10(6P22.3) WILD-TYPE	55	24	131	27

Figure S23. Get High-res Image Gene #10: 'amp_6p22.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S24. Gene #10: 'amp_6p22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
AMP PEAK 10(6P22.3) MUTATED	28	19	58	20	4	40
AMP PEAK 10(6P22.3) WILD-TYPE	46	27	35	46	27	44

Figure S24. Get High-res Image Gene #10: 'amp_6p22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p21.1' versus 'CN_CNMF'

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

Table S25. Gene #13: 'amp_7p21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
AMP PEAK 13(7P21.1) MUTATED	54	74	35	38
AMP PEAK 13(7P21.1) WILD-TYPE	33	29	121	24

Figure S25. Get High-res Image Gene #13: 'amp_7p21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S26. Gene #13: 'amp_7p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
AMP PEAK 13(7P21.1) MUTATED	29	21	55	38	2	49
AMP PEAK 13(7P21.1) WILD-TYPE	45	25	38	28	29	35

Figure S26. Get High-res Image Gene #13: 'amp_7p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

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

Table S27. Gene #14: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
AMP PEAK 14(7P11.2) MUTATED	59	61	30	40
AMP PEAK 14(7P11.2) WILD-TYPE	28	42	126	22

Figure S27. Get High-res Image Gene #14: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.031

Table S28. Gene #14: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
AMP PEAK 14(7P11.2) MUTATED	27	21	51	35	3	47
AMP PEAK 14(7P11.2) WILD-TYPE	47	25	42	31	28	37

Figure S28. Get High-res Image Gene #14: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p11.23' versus 'CN_CNMF'

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

Table S29. Gene #15: 'amp_8p11.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
AMP PEAK 15(8P11.23) MUTATED	49	25	35	15
AMP PEAK 15(8P11.23) WILD-TYPE	38	78	121	47

Figure S29. Get High-res Image Gene #15: 'amp_8p11.23' 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 S30. Gene #16: 'amp_8q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
AMP PEAK 16(8Q22.3) MUTATED	74	78	75	37
AMP PEAK 16(8Q22.3) WILD-TYPE	13	25	81	25

Figure S30. Get High-res Image Gene #16: 'amp_8q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.055

Table S31. Gene #16: 'amp_8q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
AMP PEAK 16(8Q22.3) MUTATED	42	36	71	43	10	55
AMP PEAK 16(8Q22.3) WILD-TYPE	32	10	22	23	21	29

Figure S31. Get High-res Image Gene #16: 'amp_8q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9p24.1' versus 'CN_CNMF'

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

Table S32. Gene #17: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
AMP PEAK 17(9P24.1) MUTATED	14	27	17	30
AMP PEAK 17(9P24.1) WILD-TYPE	73	76	139	32

Figure S32. Get High-res Image Gene #17: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.072

Table S33. Gene #17: 'amp_9p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
AMP PEAK 17(9P24.1) MUTATED	38	7	18	22
AMP PEAK 17(9P24.1) WILD-TYPE	60	36	116	97

Figure S33. Get High-res Image Gene #17: 'amp_9p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_9p24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.043

Table S34. Gene #17: 'amp_9p24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
AMP PEAK 17(9P24.1) MUTATED	18	8	19	6	2	32
AMP PEAK 17(9P24.1) WILD-TYPE	56	38	74	60	29	52

Figure S34. Get High-res Image Gene #17: 'amp_9p24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10p14' versus 'CN_CNMF'

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

Table S35. Gene #18: 'amp_10p14' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
AMP PEAK 18(10P14) MUTATED	55	69	24	34
AMP PEAK 18(10P14) WILD-TYPE	32	34	132	28

Figure S35. Get High-res Image Gene #18: 'amp_10p14' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10p14' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.17

Table S36. Gene #18: 'amp_10p14' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	114	78	60
AMP PEAK 18(10P14) MUTATED	62	39	28	28
AMP PEAK 18(10P14) WILD-TYPE	39	75	50	32

Figure S36. Get High-res Image Gene #18: 'amp_10p14' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_10p14' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S37. Gene #18: 'amp_10p14' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
AMP PEAK 18(10P14) MUTATED	35	24	52	32	2	31
AMP PEAK 18(10P14) WILD-TYPE	39	22	41	34	29	53

Figure S37. Get High-res Image Gene #18: 'amp_10p14' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11p13' versus 'CN_CNMF'

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

Table S38. Gene #19: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
AMP PEAK 19(11P13) MUTATED	9	13	7	22
AMP PEAK 19(11P13) WILD-TYPE	78	90	149	40

Figure S38. Get High-res Image Gene #19: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'CN_CNMF'

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

Table S39. Gene #20: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
AMP PEAK 20(11Q13.3) MUTATED	51	35	36	13
AMP PEAK 20(11Q13.3) WILD-TYPE	36	68	120	49

Figure S39. Get High-res Image Gene #20: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q22.2' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.072

Table S40. Gene #21: 'amp_11q22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
AMP PEAK 21(11Q22.2) MUTATED	27	21	13	10
AMP PEAK 21(11Q22.2) WILD-TYPE	60	82	143	52

Figure S40. Get High-res Image Gene #21: 'amp_11q22.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.22

Table S41. Gene #21: 'amp_11q22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
AMP PEAK 21(11Q22.2) MUTATED	29	12	15	15
AMP PEAK 21(11Q22.2) WILD-TYPE	69	31	119	104

Figure S41. Get High-res Image Gene #21: 'amp_11q22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_12p12.1' versus 'CN_CNMF'

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

Table S42. Gene #22: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
AMP PEAK 22(12P12.1) MUTATED	42	38	28	24
AMP PEAK 22(12P12.1) WILD-TYPE	45	65	128	38

Figure S42. Get High-res Image Gene #22: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q15' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.078

Table S43. Gene #23: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
AMP PEAK 23(12Q15) MUTATED	36	39	34	9
AMP PEAK 23(12Q15) WILD-TYPE	51	64	122	53

Figure S43. Get High-res Image Gene #23: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q22.1' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.061

Table S44. Gene #24: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
AMP PEAK 24(13Q22.1) MUTATED	36	34	30	28
AMP PEAK 24(13Q22.1) WILD-TYPE	51	69	126	34

Figure S44. Get High-res Image Gene #24: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_16p13.2' versus 'CN_CNMF'

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

Table S45. Gene #25: 'amp_16p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
AMP PEAK 25(16P13.2) MUTATED	15	43	21	8
AMP PEAK 25(16P13.2) WILD-TYPE	72	60	135	54

Figure S45. Get High-res Image Gene #25: 'amp_16p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_16p11.2' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.019

Table S46. Gene #26: 'amp_16p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
AMP PEAK 26(16P11.2) MUTATED	21	42	24	10
AMP PEAK 26(16P11.2) WILD-TYPE	66	61	132	52

Figure S46. Get High-res Image Gene #26: 'amp_16p11.2' 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 S47. Gene #29: 'amp_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
AMP PEAK 29(17Q11.2) MUTATED	54	65	34	21
AMP PEAK 29(17Q11.2) WILD-TYPE	33	38	122	41

Figure S47. Get High-res Image Gene #29: 'amp_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q11.2' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.055

Table S48. Gene #29: 'amp_17q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	159	96
AMP PEAK 29(17Q11.2) MUTATED	40	85	26
AMP PEAK 29(17Q11.2) WILD-TYPE	58	74	70

Figure S48. Get High-res Image Gene #29: 'amp_17q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S49. Gene #29: 'amp_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
AMP PEAK 29(17Q11.2) MUTATED	27	26	61	27	5	24
AMP PEAK 29(17Q11.2) WILD-TYPE	47	20	32	39	26	60

Figure S49. Get High-res Image Gene #29: 'amp_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

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

Table S50. Gene #30: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
AMP PEAK 30(17Q12) MUTATED	51	55	38	21
AMP PEAK 30(17Q12) WILD-TYPE	36	48	118	41

Figure S50. Get High-res Image Gene #30: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S51. Gene #30: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
AMP PEAK 30(17Q12) MUTATED	23	25	57	25	5	26
AMP PEAK 30(17Q12) WILD-TYPE	51	21	36	41	26	58

Figure S51. Get High-res Image Gene #30: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q23.3' versus 'CN_CNMF'

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

Table S52. Gene #31: 'amp_17q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
AMP PEAK 31(17Q23.3) MUTATED	56	65	47	26
AMP PEAK 31(17Q23.3) WILD-TYPE	31	38	109	36

Figure S52. Get High-res Image Gene #31: 'amp_17q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.09

Table S53. Gene #31: 'amp_17q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
AMP PEAK 31(17Q23.3) MUTATED	28	27	55	38	6	36
AMP PEAK 31(17Q23.3) WILD-TYPE	46	19	38	28	25	48

Figure S53. Get High-res Image Gene #31: 'amp_17q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

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

Table S54. Gene #32: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
AMP PEAK 32(19Q12) MUTATED	44	67	33	21
AMP PEAK 32(19Q12) WILD-TYPE	43	36	123	41

Figure S54. Get High-res Image Gene #32: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q13.43' versus 'CN_CNMF'

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

Table S55. Gene #33: 'amp_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
AMP PEAK 33(19Q13.43) MUTATED	44	56	33	22
AMP PEAK 33(19Q13.43) WILD-TYPE	43	47	123	40

Figure S55. Get High-res Image Gene #33: 'amp_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q11.21' versus 'CN_CNMF'

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

Table S56. Gene #34: 'amp_20q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
AMP PEAK 34(20Q11.21) MUTATED	70	78	65	50
AMP PEAK 34(20Q11.21) WILD-TYPE	17	25	91	12

Figure S56. Get High-res Image Gene #34: 'amp_20q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_22q12.2' versus 'CN_CNMF'

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

Table S57. Gene #35: 'amp_22q12.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
AMP PEAK 35(22Q12.2) MUTATED	27	38	14	8
AMP PEAK 35(22Q12.2) WILD-TYPE	60	65	142	54

Figure S57. Get High-res Image Gene #35: 'amp_22q12.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q32.1' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.14

Table S58. Gene #37: 'del_1q32.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
DEL PEAK 2(1Q32.1) MUTATED	15	29	13	14
DEL PEAK 2(1Q32.1) WILD-TYPE	72	74	143	48

Figure S58. Get High-res Image Gene #37: 'del_1q32.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'CN_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.24

Table S59. Gene #38: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
DEL PEAK 3(2Q22.1) MUTATED	34	43	32	25
DEL PEAK 3(2Q22.1) WILD-TYPE	53	60	124	37

Figure S59. Get High-res Image Gene #38: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q34' versus 'CN_CNMF'

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

Table S60. Gene #39: 'del_2q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
DEL PEAK 4(2Q34) MUTATED	36	65	35	38
DEL PEAK 4(2Q34) WILD-TYPE	51	38	121	24

Figure S60. Get High-res Image Gene #39: 'del_2q34' 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 S61. Gene #40: 'del_2q37.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
DEL PEAK 5(2Q37.1) MUTATED	48	75	45	39
DEL PEAK 5(2Q37.1) WILD-TYPE	39	28	111	23

Figure S61. Get High-res Image Gene #40: 'del_2q37.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.1' versus 'METHLYATION_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.14

Table S62. Gene #40: 'del_2q37.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	137	68
DEL PEAK 5(2Q37.1) MUTATED	66	89	31
DEL PEAK 5(2Q37.1) WILD-TYPE	92	48	37

Figure S62. Get High-res Image Gene #40: 'del_2q37.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p14.2' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.067

Table S63. Gene #41: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
DEL PEAK 6(3P14.2) MUTATED	39	35	29	14
DEL PEAK 6(3P14.2) WILD-TYPE	48	68	127	48

Figure S63. Get High-res Image Gene #41: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.2' versus 'MRNASEQ_CNMF'

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

Table S64. Gene #41: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	159	96
DEL PEAK 6(3P14.2) MUTATED	20	30	50
DEL PEAK 6(3P14.2) WILD-TYPE	78	129	46

Figure S64. Get High-res Image Gene #41: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S65. Gene #41: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	114	78	60
DEL PEAK 6(3P14.2) MUTATED	23	18	44	15
DEL PEAK 6(3P14.2) WILD-TYPE	78	96	34	45

Figure S65. Get High-res Image Gene #41: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.025

Table S66. Gene #41: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
DEL PEAK 6(3P14.2) MUTATED	42	25	14	25	11
DEL PEAK 6(3P14.2) WILD-TYPE	47	74	79	45	43

Figure S66. Get High-res Image Gene #41: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.037

Table S67. Gene #41: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
DEL PEAK 6(3P14.2) MUTATED	47	10	31	27
DEL PEAK 6(3P14.2) WILD-TYPE	51	33	103	92

Figure S67. Get High-res Image Gene #41: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S68. Gene #41: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
DEL PEAK 6(3P14.2) MUTATED	11	12	29	26	1	36
DEL PEAK 6(3P14.2) WILD-TYPE	63	34	64	40	30	48

Figure S68. Get High-res Image Gene #41: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

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

Table S69. Gene #42: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
DEL PEAK 7(4Q22.1) MUTATED	41	49	35	37
DEL PEAK 7(4Q22.1) WILD-TYPE	46	54	121	25

Figure S69. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.2' versus 'CN_CNMF'

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

Table S70. Gene #43: 'del_4q34.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
DEL PEAK 8(4Q34.2) MUTATED	42	57	34	44
DEL PEAK 8(4Q34.2) WILD-TYPE	45	46	122	18

Figure S70. Get High-res Image Gene #43: 'del_4q34.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q12.1' versus 'CN_CNMF'

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

Table S71. Gene #44: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
DEL PEAK 9(5Q12.1) MUTATED	56	71	39	36
DEL PEAK 9(5Q12.1) WILD-TYPE	31	32	117	26

Figure S71. Get High-res Image Gene #44: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.078

Table S72. Gene #44: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
DEL PEAK 9(5Q12.1) MUTATED	42	60	28	43	29
DEL PEAK 9(5Q12.1) WILD-TYPE	47	39	65	27	25

Figure S72. Get High-res Image Gene #44: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

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

Table S73. Gene #45: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
DEL PEAK 10(6P25.3) MUTATED	39	34	13	20
DEL PEAK 10(6P25.3) WILD-TYPE	48	69	143	42

Figure S73. Get High-res Image Gene #45: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q21' versus 'CN_CNMF'

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

Table S74. Gene #46: 'del_6q21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
DEL PEAK 11(6Q21) MUTATED	71	58	32	29
DEL PEAK 11(6Q21) WILD-TYPE	16	45	124	33

Figure S74. Get High-res Image Gene #46: 'del_6q21' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.13

Table S75. Gene #46: 'del_6q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
DEL PEAK 11(6Q21) MUTATED	36	60	27	39	27
DEL PEAK 11(6Q21) WILD-TYPE	53	39	66	31	27

Figure S75. Get High-res Image Gene #46: 'del_6q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S76. Gene #46: 'del_6q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
DEL PEAK 11(6Q21) MUTATED	30	30	54	37	4	32
DEL PEAK 11(6Q21) WILD-TYPE	44	16	39	29	27	52

Figure S76. Get High-res Image Gene #46: 'del_6q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q27' versus 'CN_CNMF'

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

Table S77. Gene #47: 'del_6q27' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
DEL PEAK 12(6Q27) MUTATED	67	61	32	30
DEL PEAK 12(6Q27) WILD-TYPE	20	42	124	32

Figure S77. Get High-res Image Gene #47: 'del_6q27' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q27' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S78. Gene #47: 'del_6q27' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
DEL PEAK 12(6Q27) MUTATED	33	57	28	44	27
DEL PEAK 12(6Q27) WILD-TYPE	56	42	65	26	27

Figure S78. Get High-res Image Gene #47: 'del_6q27' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q27' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S79. Gene #47: 'del_6q27' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
DEL PEAK 12(6Q27) MUTATED	33	28	55	38	3	30
DEL PEAK 12(6Q27) WILD-TYPE	41	18	38	28	28	54

Figure S79. Get High-res Image Gene #47: 'del_6q27' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q36.3' versus 'CN_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.23

Table S80. Gene #48: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
DEL PEAK 13(7Q36.3) MUTATED	10	26	11	12
DEL PEAK 13(7Q36.3) WILD-TYPE	77	77	145	50

Figure S80. Get High-res Image Gene #48: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.1' versus 'CN_CNMF'

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

Table S81. Gene #49: 'del_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
DEL PEAK 14(8P23.1) MUTATED	47	86	66	46
DEL PEAK 14(8P23.1) WILD-TYPE	40	17	90	16

Figure S81. Get High-res Image Gene #49: 'del_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.1' versus 'METHLYATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.18

Table S82. Gene #49: 'del_8p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	137	68
DEL PEAK 14(8P23.1) MUTATED	104	89	26
DEL PEAK 14(8P23.1) WILD-TYPE	54	48	42

Figure S82. Get High-res Image Gene #49: 'del_8p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p23' versus 'CN_CNMF'

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

Table S83. Gene #50: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
DEL PEAK 15(9P23) MUTATED	47	50	76	4
DEL PEAK 15(9P23) WILD-TYPE	40	53	80	58

Figure S83. Get High-res Image Gene #50: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.019

Table S84. Gene #50: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
DEL PEAK 15(9P23) MUTATED	22	25	69	56
DEL PEAK 15(9P23) WILD-TYPE	76	18	65	63

Figure S84. Get High-res Image Gene #50: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'CN_CNMF'

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

Table S85. Gene #51: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
DEL PEAK 16(9P21.3) MUTATED	67	57	107	8
DEL PEAK 16(9P21.3) WILD-TYPE	20	46	49	54

Figure S85. Get High-res Image Gene #51: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.061

Table S86. Gene #51: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
DEL PEAK 16(9P21.3) MUTATED	34	33	52	49	25	39
DEL PEAK 16(9P21.3) WILD-TYPE	40	13	41	17	6	45

Figure S86. Get High-res Image Gene #51: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q33.2' versus 'CN_CNMF'

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

Table S87. Gene #52: 'del_9q33.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
DEL PEAK 17(9Q33.2) MUTATED	46	45	72	5
DEL PEAK 17(9Q33.2) WILD-TYPE	41	58	84	57

Figure S87. Get High-res Image Gene #52: 'del_9q33.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q33.2' versus 'METHLYATION_CNMF'

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

Table S88. Gene #52: 'del_9q33.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	137	68
DEL PEAK 17(9Q33.2) MUTATED	44	77	33
DEL PEAK 17(9Q33.2) WILD-TYPE	114	60	35

Figure S88. Get High-res Image Gene #52: 'del_9q33.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9q33.2' versus 'MRNASEQ_CNMF'

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

Table S89. Gene #52: 'del_9q33.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	159	96
DEL PEAK 17(9Q33.2) MUTATED	35	89	25
DEL PEAK 17(9Q33.2) WILD-TYPE	63	70	71

Figure S89. Get High-res Image Gene #52: 'del_9q33.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9q33.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S90. Gene #52: 'del_9q33.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	114	78	60
DEL PEAK 17(9Q33.2) MUTATED	56	62	16	15
DEL PEAK 17(9Q33.2) WILD-TYPE	45	52	62	45

Figure S90. Get High-res Image Gene #52: 'del_9q33.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9q33.2' versus 'MIRSEQ_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.23

Table S91. Gene #52: 'del_9q33.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	96	189
DEL PEAK 17(9Q33.2) MUTATED	35	53	80
DEL PEAK 17(9Q33.2) WILD-TYPE	85	43	109

Figure S91. Get High-res Image Gene #52: 'del_9q33.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9q33.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.19

Table S92. Gene #52: 'del_9q33.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
DEL PEAK 17(9Q33.2) MUTATED	20	46	40	39	23
DEL PEAK 17(9Q33.2) WILD-TYPE	69	53	53	31	31

Figure S92. Get High-res Image Gene #52: 'del_9q33.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9q33.2' versus 'MIRSEQ_MATURE_CNMF'

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

Table S93. Gene #52: 'del_9q33.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
DEL PEAK 17(9Q33.2) MUTATED	15	27	75	47
DEL PEAK 17(9Q33.2) WILD-TYPE	83	16	59	72

Figure S93. Get High-res Image Gene #52: 'del_9q33.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9q33.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S94. Gene #52: 'del_9q33.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
DEL PEAK 17(9Q33.2) MUTATED	28	27	44	32	24	9
DEL PEAK 17(9Q33.2) WILD-TYPE	46	19	49	34	7	75

Figure S94. Get High-res Image Gene #52: 'del_9q33.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

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

Table S95. Gene #54: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
DEL PEAK 19(10Q23.31) MUTATED	40	61	32	34
DEL PEAK 19(10Q23.31) WILD-TYPE	47	42	124	28

Figure S95. Get High-res Image Gene #54: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.5' versus 'CN_CNMF'

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

Table S96. Gene #55: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
DEL PEAK 20(11P15.5) MUTATED	56	74	62	19
DEL PEAK 20(11P15.5) WILD-TYPE	31	29	94	43

Figure S96. Get High-res Image Gene #55: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.18

Table S97. Gene #55: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	137	68
DEL PEAK 20(11P15.5) MUTATED	62	85	39
DEL PEAK 20(11P15.5) WILD-TYPE	96	52	29

Figure S97. Get High-res Image Gene #55: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.15

Table S98. Gene #55: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	114	78	60
DEL PEAK 20(11P15.5) MUTATED	65	63	28	23
DEL PEAK 20(11P15.5) WILD-TYPE	36	51	50	37

Figure S98. Get High-res Image Gene #55: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.3' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.12

Table S99. Gene #56: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
DEL PEAK 21(11Q23.3) MUTATED	45	49	42	20
DEL PEAK 21(11Q23.3) WILD-TYPE	42	54	114	42

Figure S99. Get High-res Image Gene #56: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q25' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.019

Table S100. Gene #57: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
DEL PEAK 22(11Q25) MUTATED	43	47	36	18
DEL PEAK 22(11Q25) WILD-TYPE	44	56	120	44

Figure S100. Get High-res Image Gene #57: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.15

Table S101. Gene #58: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	114	78	60
DEL PEAK 23(12P13.1) MUTATED	28	18	5	4
DEL PEAK 23(12P13.1) WILD-TYPE	73	96	73	56

Figure S101. Get High-res Image Gene #58: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12q24.33' versus 'CN_CNMF'

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

Table S102. Gene #59: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
DEL PEAK 24(12Q24.33) MUTATED	20	28	15	25
DEL PEAK 24(12Q24.33) WILD-TYPE	67	75	141	37

Figure S102. Get High-res Image Gene #59: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'CN_CNMF'

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

Table S103. Gene #60: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
DEL PEAK 25(13Q14.2) MUTATED	29	56	24	47
DEL PEAK 25(13Q14.2) WILD-TYPE	58	47	132	15

Figure S103. Get High-res Image Gene #60: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.18

Table S104. Gene #60: 'del_13q14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
DEL PEAK 25(13Q14.2) MUTATED	47	42	21	30	16
DEL PEAK 25(13Q14.2) WILD-TYPE	42	57	72	40	38

Figure S104. Get High-res Image Gene #60: 'del_13q14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S105. Gene #60: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
DEL PEAK 25(13Q14.2) MUTATED	17	18	48	21	3	47
DEL PEAK 25(13Q14.2) WILD-TYPE	57	28	45	45	28	37

Figure S105. Get High-res Image Gene #60: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q24.1' versus 'CN_CNMF'

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

Table S106. Gene #61: 'del_14q24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
DEL PEAK 26(14Q24.1) MUTATED	35	63	27	12
DEL PEAK 26(14Q24.1) WILD-TYPE	52	40	129	50

Figure S106. Get High-res Image Gene #61: 'del_14q24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q24.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S107. Gene #61: 'del_14q24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	114	78	60
DEL PEAK 26(14Q24.1) MUTATED	55	34	15	12
DEL PEAK 26(14Q24.1) WILD-TYPE	46	80	63	48

Figure S107. Get High-res Image Gene #61: 'del_14q24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.019

Table S108. Gene #61: 'del_14q24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
DEL PEAK 26(14Q24.1) MUTATED	22	22	40	31	3	16
DEL PEAK 26(14Q24.1) WILD-TYPE	52	24	53	35	28	68

Figure S108. Get High-res Image Gene #61: 'del_14q24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q13.1' versus 'CN_CNMF'

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

Table S109. Gene #62: 'del_15q13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
DEL PEAK 27(15Q13.1) MUTATED	41	58	22	38
DEL PEAK 27(15Q13.1) WILD-TYPE	46	45	134	24

Figure S109. Get High-res Image Gene #62: '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 = 0.037

Table S110. Gene #62: 'del_15q13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
DEL PEAK 27(15Q13.1) MUTATED	30	51	21	37	20
DEL PEAK 27(15Q13.1) WILD-TYPE	59	48	72	33	34

Figure S110. Get High-res Image Gene #62: 'del_15q13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S111. Gene #62: 'del_15q13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
DEL PEAK 27(15Q13.1) MUTATED	24	25	45	24	1	37
DEL PEAK 27(15Q13.1) WILD-TYPE	50	21	48	42	30	47

Figure S111. Get High-res Image Gene #62: 'del_15q13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16p13.3' versus 'CN_CNMF'

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

Table S112. Gene #63: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
DEL PEAK 28(16P13.3) MUTATED	37	61	28	47
DEL PEAK 28(16P13.3) WILD-TYPE	50	42	128	15

Figure S112. Get High-res Image Gene #63: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'CN_CNMF'

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

Table S113. Gene #64: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
DEL PEAK 29(16Q23.1) MUTATED	29	40	15	35
DEL PEAK 29(16Q23.1) WILD-TYPE	58	63	141	27

Figure S113. Get High-res Image Gene #64: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.031

Table S114. Gene #64: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
DEL PEAK 29(16Q23.1) MUTATED	12	15	37	15	2	34
DEL PEAK 29(16Q23.1) WILD-TYPE	62	31	56	51	29	50

Figure S114. Get High-res Image Gene #64: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

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

Table S115. Gene #65: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
DEL PEAK 30(17P12) MUTATED	67	68	50	24
DEL PEAK 30(17P12) WILD-TYPE	20	35	106	38

Figure S115. Get High-res Image Gene #65: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.11

Table S116. Gene #65: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
DEL PEAK 30(17P12) MUTATED	43	51	34	51	28
DEL PEAK 30(17P12) WILD-TYPE	46	48	59	19	26

Figure S116. Get High-res Image Gene #65: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.11

Table S117. Gene #65: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
DEL PEAK 30(17P12) MUTATED	32	26	60	41	7	36
DEL PEAK 30(17P12) WILD-TYPE	42	20	33	25	24	48

Figure S117. Get High-res Image Gene #65: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q23' versus 'CN_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.24

Table S118. Gene #66: 'del_18q23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
DEL PEAK 31(18Q23) MUTATED	42	57	48	31
DEL PEAK 31(18Q23) WILD-TYPE	45	46	108	31

Figure S118. Get High-res Image Gene #66: 'del_18q23' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q23' versus 'MIRSEQ_CNMF'

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

Table S119. Gene #66: 'del_18q23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	96	189
DEL PEAK 31(18Q23) MUTATED	53	62	62
DEL PEAK 31(18Q23) WILD-TYPE	67	34	127

Figure S119. Get High-res Image Gene #66: 'del_18q23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q23' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S120. Gene #66: 'del_18q23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
DEL PEAK 31(18Q23) MUTATED	29	71	29	28	20
DEL PEAK 31(18Q23) WILD-TYPE	60	28	64	42	34

Figure S120. Get High-res Image Gene #66: 'del_18q23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

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

Table S121. Gene #67: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
DEL PEAK 32(19P13.3) MUTATED	38	53	33	21
DEL PEAK 32(19P13.3) WILD-TYPE	49	50	123	41

Figure S121. Get High-res Image Gene #67: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.12

Table S122. Gene #67: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
DEL PEAK 32(19P13.3) MUTATED	20	18	36	34	2	30
DEL PEAK 32(19P13.3) WILD-TYPE	54	28	57	32	29	54

Figure S122. Get High-res Image Gene #67: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

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

Table S123. Gene #68: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
DEL PEAK 33(22Q13.32) MUTATED	32	75	29	51
DEL PEAK 33(22Q13.32) WILD-TYPE	55	28	127	11

Figure S123. Get High-res Image Gene #68: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.32' versus 'METHLYATION_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.14

Table S124. Gene #68: 'del_22q13.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	137	68
DEL PEAK 33(22Q13.32) MUTATED	82	65	16
DEL PEAK 33(22Q13.32) WILD-TYPE	76	72	52

Figure S124. Get High-res Image Gene #68: 'del_22q13.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S125. Gene #68: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
DEL PEAK 33(22Q13.32) MUTATED	29	19	50	34	1	50
DEL PEAK 33(22Q13.32) WILD-TYPE	45	27	43	32	30	34

Figure S125. Get High-res Image Gene #68: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = BLCA-TP.transferedmergedcluster.txt
Number of patients = 408
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)

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