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

Head and Neck Squamous Cell 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/C14B3054

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 77 focal events and 10 molecular subtypes across 522 patients, 217 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_2q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_2q31.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_3q26.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_5p15.33 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_6p12.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_6q12 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_7p11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_7q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_8p11.23 cnv correlated to 'CN_CNMF'.
amp_8q11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_9p24.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_9p23 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_9p13.3 cnv correlated to 'CN_CNMF'.
amp_9q34.3 cnv correlated to 'CN_CNMF'.
amp_11q13.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_12p13.33 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_12q15 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_13q22.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_13q34 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_15q26.3 cnv correlated to 'CN_CNMF'.
amp_17q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_18p11.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_18q11.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_19p13.2 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
amp_20p12.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_20q11.22 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_xq28 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_1p36.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_1p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_1q44 cnv correlated to 'CN_CNMF'.
del_2q22.1 cnv correlated to 'METHLYATION_CNMF'.
del_2q36.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_3p26.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_3p24.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_3p14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_3p12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_4p15.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_4q21.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_4q22.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_4q35.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_5q12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_5q15 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_5q35.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_6p25.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_7q36.1 cnv correlated to 'CN_CNMF'.
del_8p23.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_9q21.11 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_9q34.3 cnv correlated to 'CN_CNMF'.
del_10p15.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_10p11.21 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_11p15.5 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_11q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_12q24.33 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_13q12.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_13q14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_14q11.2 cnv correlated to 'CN_CNMF'.
del_14q32.32 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_15q15.1 cnv correlated to 'CN_CNMF'.
del_16q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_16q23.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_17p11.2 cnv correlated to 'CN_CNMF'.
del_17q25.3 cnv correlated to 'METHLYATION_CNMF'.
del_18q21.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_18q23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_19p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_19q13.43 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_21q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_xp22.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_xp21.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_xq21.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 77 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, 217 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 3p26 2	348 (67%)	174	1e-05 (0.0077)	1e-05 (0.0077)	0.525 (1.00)	0.21 (1.00)	8e-05 (0.047)	1e-05 (0.0077)	0.0182 (1.00)	1e-05 (0.0077)	4e-05 (0.0241)	0.00675 (1.00)
amp 3q26 33	380 (73%)	142	1e-05 (0.0077)	1e-05 (0.0077)	0.13 (1.00)	0.31 (1.00)	1e-05 (0.0077)	4e-05 (0.0241)	0.0005 (0.276)	0.591 (1.00)	0.00019 (0.109)	0.165 (1.00)
amp 18p11 31	156 (30%)	366	1e-05 (0.0077)	1e-05 (0.0077)	0.523 (1.00)	0.513 (1.00)	0.083 (1.00)	1e-05 (0.0077)	0.323 (1.00)	0.00017 (0.0976)	1e-05 (0.0077)	0.032 (1.00)
del 3p24 1	368 (70%)	154	1e-05 (0.0077)	1e-05 (0.0077)	0.418 (1.00)	0.117 (1.00)	0.00169 (0.882)	3e-05 (0.0183)	0.00264 (1.00)	5e-05 (0.0297)	2e-05 (0.0125)	0.0295 (1.00)
del 3p14 2	372 (71%)	150	1e-05 (0.0077)	1e-05 (0.0077)	0.612 (1.00)	0.174 (1.00)	0.0105 (1.00)	2e-05 (0.0125)	0.0898 (1.00)	0.00036 (0.201)	3e-05 (0.0183)	0.316 (1.00)
del 5q12 1	215 (41%)	307	1e-05 (0.0077)	1e-05 (0.0077)	0.0884 (1.00)	0.359 (1.00)	0.0626 (1.00)	1e-05 (0.0077)	0.0864 (1.00)	3e-05 (0.0183)	0.0004 (0.223)	0.0479 (1.00)
del 5q15	226 (43%)	296	1e-05 (0.0077)	1e-05 (0.0077)	0.145 (1.00)	0.43 (1.00)	0.108 (1.00)	1e-05 (0.0077)	0.108 (1.00)	1e-05 (0.0077)	0.00013 (0.075)	0.342 (1.00)
del 5q35 3	199 (38%)	323	1e-05 (0.0077)	1e-05 (0.0077)	0.239 (1.00)	0.722 (1.00)	0.0196 (1.00)	1e-05 (0.0077)	0.24 (1.00)	2e-05 (0.0125)	0.00019 (0.109)	0.117 (1.00)
del 8p23 2	304 (58%)	218	1e-05 (0.0077)	1e-05 (0.0077)	0.281 (1.00)	0.324 (1.00)	0.00124 (0.662)	6e-05 (0.0356)	0.0177 (1.00)	0.00419 (1.00)	1e-05 (0.0077)	3e-05 (0.0183)
del 9p23	239 (46%)	283	1e-05 (0.0077)	1e-05 (0.0077)	0.283 (1.00)	0.114 (1.00)	0.823 (1.00)	0.00022 (0.125)	0.407 (1.00)	7e-05 (0.0414)	1e-05 (0.0077)	0.311 (1.00)
del 9p21 3	302 (58%)	220	1e-05 (0.0077)	1e-05 (0.0077)	0.673 (1.00)	0.363 (1.00)	0.145 (1.00)	1e-05 (0.0077)	0.442 (1.00)	1e-05 (0.0077)	1e-05 (0.0077)	0.142 (1.00)
del 10q23 31	138 (26%)	384	1e-05 (0.0077)	1e-05 (0.0077)	0.135 (1.00)	0.98 (1.00)	0.0001 (0.058)	2e-05 (0.0125)	0.0227 (1.00)	0.464 (1.00)	0.00023 (0.13)	0.0324 (1.00)
del 11p15 5	163 (31%)	359	1e-05 (0.0077)	1e-05 (0.0077)	0.868 (1.00)	0.282 (1.00)	2e-05 (0.0125)	0.00261 (1.00)	1e-05 (0.0077)	0.00344 (1.00)	7e-05 (0.0414)	0.0077 (1.00)
del 16q23 1	98 (19%)	424	5e-05 (0.0297)	1e-05 (0.0077)	0.468 (1.00)	0.459 (1.00)	1e-05 (0.0077)	1e-05 (0.0077)	0.00826 (1.00)	0.0403 (1.00)	3e-05 (0.0183)	0.0013 (0.693)
del 16q23 3	105 (20%)	417	4e-05 (0.0241)	1e-05 (0.0077)	0.162 (1.00)	0.231 (1.00)	1e-05 (0.0077)	1e-05 (0.0077)	0.0219 (1.00)	0.163 (1.00)	8e-05 (0.047)	0.00345 (1.00)
del 18q21 2	268 (51%)	254	1e-05 (0.0077)	1e-05 (0.0077)	0.901 (1.00)	0.377 (1.00)	0.00685 (1.00)	1e-05 (0.0077)	0.0336 (1.00)	4e-05 (0.0241)	9e-05 (0.0526)	0.08 (1.00)
del 18q23	288 (55%)	234	1e-05 (0.0077)	1e-05 (0.0077)	0.258 (1.00)	0.249 (1.00)	0.00529 (1.00)	1e-05 (0.0077)	0.0612 (1.00)	2e-05 (0.0125)	1e-05 (0.0077)	0.0212 (1.00)
amp 8q24 21	386 (74%)	136	1e-05 (0.0077)	1e-05 (0.0077)	0.315 (1.00)	0.445 (1.00)	0.013 (1.00)	4e-05 (0.0241)	0.068 (1.00)	0.00101 (0.544)	0.00021 (0.12)	0.00831 (1.00)
del 1p36 21	95 (18%)	427	1e-05 (0.0077)	1e-05 (0.0077)	0.00073 (0.399)	0.00562 (1.00)	1e-05 (0.0077)	7e-05 (0.0414)	0.00147 (0.778)	0.0401 (1.00)	0.00114 (0.613)	0.0115 (1.00)
del 1p13 2	133 (25%)	389	1e-05 (0.0077)	1e-05 (0.0077)	0.0245 (1.00)	0.00684 (1.00)	0.025 (1.00)	0.379 (1.00)	0.00175 (0.912)	0.00021 (0.12)	0.00041 (0.228)	0.184 (1.00)
del 3p12 1	343 (66%)	179	1e-05 (0.0077)	1e-05 (0.0077)	0.831 (1.00)	0.901 (1.00)	0.0207 (1.00)	3e-05 (0.0183)	0.0601 (1.00)	0.00053 (0.293)	1e-05 (0.0077)	0.516 (1.00)
del 4p15 2	208 (40%)	314	1e-05 (0.0077)	1e-05 (0.0077)	0.0117 (1.00)	0.331 (1.00)	0.00011 (0.0637)	0.00061 (0.335)	0.00741 (1.00)	0.0299 (1.00)	0.00024 (0.136)	0.0168 (1.00)
del 11q23 1	246 (47%)	276	1e-05 (0.0077)	1e-05 (0.0077)	0.087 (1.00)	0.163 (1.00)	2e-05 (0.0125)	1e-05 (0.0077)	0.00826 (1.00)	0.0141 (1.00)	0.0732 (1.00)	0.246 (1.00)
del 13q14 2	217 (42%)	305	1e-05 (0.0077)	1e-05 (0.0077)	0.11 (1.00)	0.567 (1.00)	2e-05 (0.0125)	1e-05 (0.0077)	0.00137 (0.729)	0.214 (1.00)	0.00166 (0.868)	0.128 (1.00)
del 14q32 32	75 (14%)	447	0.0103 (1.00)	1e-05 (0.0077)	0.018 (1.00)	0.468 (1.00)	1e-05 (0.0077)	1e-05 (0.0077)	0.00115 (0.618)	0.0286 (1.00)	1e-05 (0.0077)	0.00077 (0.419)
del 19p13 3	175 (34%)	347	1e-05 (0.0077)	2e-05 (0.0125)	0.303 (1.00)	0.365 (1.00)	0.0168 (1.00)	0.0184 (1.00)	0.117 (1.00)	0.00021 (0.12)	1e-05 (0.0077)	0.09 (1.00)
del 21q22 3	208 (40%)	314	1e-05 (0.0077)	1e-05 (0.0077)	0.553 (1.00)	0.725 (1.00)	0.0168 (1.00)	0.0181 (1.00)	0.339 (1.00)	9e-05 (0.0526)	0.00012 (0.0694)	0.133 (1.00)
amp 2q11 2	107 (20%)	415	1e-05 (0.0077)	1e-05 (0.0077)	0.506 (1.00)	0.54 (1.00)	0.0511 (1.00)	0.0004 (0.223)	0.0241 (1.00)	0.00087 (0.472)	0.00244 (1.00)	0.0784 (1.00)
amp 7p11 2	222 (43%)	300	1e-05 (0.0077)	1e-05 (0.0077)	0.997 (1.00)	0.672 (1.00)	0.0482 (1.00)	0.0103 (1.00)	0.488 (1.00)	1e-05 (0.0077)	0.0015 (0.792)	0.123 (1.00)
amp 7q21 3	169 (32%)	353	1e-05 (0.0077)	1e-05 (0.0077)	0.333 (1.00)	0.441 (1.00)	0.306 (1.00)	0.281 (1.00)	0.043 (1.00)	0.00024 (0.136)	0.0613 (1.00)	0.875 (1.00)
amp 8q11 21	310 (59%)	212	1e-05 (0.0077)	1e-05 (0.0077)	0.0959 (1.00)	0.63 (1.00)	0.00164 (0.859)	0.00016 (0.092)	0.0338 (1.00)	0.00517 (1.00)	0.00094 (0.508)	0.00206 (1.00)
amp 9p24 1	126 (24%)	396	1e-05 (0.0077)	1e-05 (0.0077)	0.136 (1.00)	0.249 (1.00)	0.0029 (1.00)	0.0009 (0.487)	0.0772 (1.00)	0.00115 (0.618)	0.00031 (0.174)	0.0408 (1.00)
amp 17q12	91 (17%)	431	1e-05 (0.0077)	2e-05 (0.0125)	0.185 (1.00)	0.722 (1.00)	0.0111 (1.00)	0.0194 (1.00)	0.00303 (1.00)	7e-05 (0.0414)	0.00801 (1.00)	0.648 (1.00)
del 10p15 3	170 (33%)	352	1e-05 (0.0077)	1e-05 (0.0077)	0.474 (1.00)	0.707 (1.00)	0.121 (1.00)	0.0963 (1.00)	0.0147 (1.00)	0.0816 (1.00)	0.00024 (0.136)	0.343 (1.00)
del 13q12 11	233 (45%)	289	1e-05 (0.0077)	1e-05 (0.0077)	0.157 (1.00)	0.241 (1.00)	0.022 (1.00)	1e-05 (0.0077)	0.473 (1.00)	0.0303 (1.00)	0.0105 (1.00)	0.888 (1.00)
del xq21 33	80 (15%)	442	1e-05 (0.0077)	1e-05 (0.0077)	0.343 (1.00)	0.128 (1.00)	0.00179 (0.931)	0.022 (1.00)	0.00017 (0.0976)	0.0132 (1.00)	0.0418 (1.00)	0.174 (1.00)
amp 2q31 2	112 (21%)	410	1e-05 (0.0077)	1e-05 (0.0077)	0.242 (1.00)	0.31 (1.00)	0.191 (1.00)	0.0128 (1.00)	0.0778 (1.00)	0.00655 (1.00)	0.00065 (0.356)	0.00938 (1.00)
amp 5p15 33	240 (46%)	282	1e-05 (0.0077)	1e-05 (0.0077)	0.856 (1.00)	0.83 (1.00)	0.159 (1.00)	0.177 (1.00)	0.496 (1.00)	0.0332 (1.00)	0.48 (1.00)	0.984 (1.00)
amp 6p12 1	110 (21%)	412	1e-05 (0.0077)	3e-05 (0.0183)	0.456 (1.00)	0.952 (1.00)	0.855 (1.00)	0.0151 (1.00)	0.432 (1.00)	0.00252 (1.00)	0.0711 (1.00)	0.173 (1.00)
amp 6q12	96 (18%)	426	1e-05 (0.0077)	0.00015 (0.0864)	0.276 (1.00)	0.899 (1.00)	0.868 (1.00)	0.16 (1.00)	0.306 (1.00)	0.235 (1.00)	0.163 (1.00)	0.416 (1.00)
amp 9p23	124 (24%)	398	1e-05 (0.0077)	1e-05 (0.0077)	0.387 (1.00)	0.425 (1.00)	0.00317 (1.00)	0.00383 (1.00)	0.0776 (1.00)	0.00228 (1.00)	0.00123 (0.658)	0.214 (1.00)
amp 11q13 3	229 (44%)	293	1e-05 (0.0077)	1e-05 (0.0077)	0.833 (1.00)	0.728 (1.00)	0.171 (1.00)	0.134 (1.00)	0.782 (1.00)	0.00426 (1.00)	0.00142 (0.754)	0.0619 (1.00)
amp 12p13 33	167 (32%)	355	1e-05 (0.0077)	1e-05 (0.0077)	0.0423 (1.00)	0.521 (1.00)	0.00954 (1.00)	0.00198 (1.00)	0.00159 (0.835)	0.0861 (1.00)	0.00185 (0.958)	0.382 (1.00)
amp 12q15	103 (20%)	419	2e-05 (0.0125)	0.00035 (0.196)	0.0664 (1.00)	0.205 (1.00)	0.128 (1.00)	0.0681 (1.00)	0.743 (1.00)	0.321 (1.00)	0.958 (1.00)	0.374 (1.00)
amp 13q22 1	105 (20%)	417	1e-05 (0.0077)	1e-05 (0.0077)	0.148 (1.00)	0.156 (1.00)	0.329 (1.00)	0.289 (1.00)	0.215 (1.00)	0.16 (1.00)	0.014 (1.00)	0.269 (1.00)
amp 13q34	106 (20%)	416	1e-05 (0.0077)	4e-05 (0.0241)	0.226 (1.00)	0.492 (1.00)	0.156 (1.00)	0.121 (1.00)	0.097 (1.00)	0.133 (1.00)	0.0161 (1.00)	0.127 (1.00)
amp 18q11 2	106 (20%)	416	1e-05 (0.0077)	8e-05 (0.047)	0.521 (1.00)	0.204 (1.00)	0.365 (1.00)	0.014 (1.00)	0.0129 (1.00)	0.0282 (1.00)	0.0162 (1.00)	0.202 (1.00)
amp 19p13 2	60 (11%)	462	0.162 (1.00)	1e-05 (0.0077)	0.0395 (1.00)	1 (1.00)	0.00056 (0.309)	9e-05 (0.0526)	0.0208 (1.00)	0.23 (1.00)	0.254 (1.00)	0.18 (1.00)
amp 20p12 2	191 (37%)	331	3e-05 (0.0183)	4e-05 (0.0241)	0.872 (1.00)	0.934 (1.00)	0.0899 (1.00)	0.00952 (1.00)	0.109 (1.00)	0.0225 (1.00)	0.664 (1.00)	0.0431 (1.00)
amp 20q11 22	227 (43%)	295	1e-05 (0.0077)	2e-05 (0.0125)	0.505 (1.00)	0.832 (1.00)	0.108 (1.00)	0.0103 (1.00)	0.295 (1.00)	0.0237 (1.00)	0.834 (1.00)	0.0733 (1.00)
amp xq28	150 (29%)	372	1e-05 (0.0077)	2e-05 (0.0125)	0.641 (1.00)	0.197 (1.00)	0.305 (1.00)	0.145 (1.00)	0.255 (1.00)	0.093 (1.00)	0.26 (1.00)	0.0632 (1.00)
del 2q36 2	157 (30%)	365	1e-05 (0.0077)	1e-05 (0.0077)	0.0931 (1.00)	0.857 (1.00)	0.0109 (1.00)	0.0136 (1.00)	0.0598 (1.00)	0.0243 (1.00)	0.298 (1.00)	0.0493 (1.00)
del 4q21 3	156 (30%)	366	1e-05 (0.0077)	1e-05 (0.0077)	0.283 (1.00)	0.0469 (1.00)	0.0104 (1.00)	0.00152 (0.801)	0.401 (1.00)	0.0312 (1.00)	0.198 (1.00)	0.936 (1.00)
del 4q22 1	169 (32%)	353	1e-05 (0.0077)	1e-05 (0.0077)	0.25 (1.00)	0.0755 (1.00)	0.00841 (1.00)	0.00277 (1.00)	0.264 (1.00)	0.0382 (1.00)	0.0912 (1.00)	0.394 (1.00)
del 4q35 2	213 (41%)	309	1e-05 (0.0077)	1e-05 (0.0077)	0.845 (1.00)	0.183 (1.00)	0.0118 (1.00)	0.119 (1.00)	0.15 (1.00)	0.00583 (1.00)	0.119 (1.00)	0.241 (1.00)
del 6p25 3	96 (18%)	426	9e-05 (0.0526)	1e-05 (0.0077)	0.0416 (1.00)	0.0104 (1.00)	0.002 (1.00)	0.0974 (1.00)	0.176 (1.00)	0.727 (1.00)	0.23 (1.00)	0.66 (1.00)
del 9q21 11	108 (21%)	414	1e-05 (0.0077)	1e-05 (0.0077)	0.983 (1.00)	0.24 (1.00)	0.854 (1.00)	0.0269 (1.00)	0.796 (1.00)	0.00064 (0.351)	0.00364 (1.00)	0.92 (1.00)
del 10p11 21	162 (31%)	360	1e-05 (0.0077)	1e-05 (0.0077)	0.45 (1.00)	0.173 (1.00)	0.154 (1.00)	0.571 (1.00)	0.0416 (1.00)	0.0151 (1.00)	0.0248 (1.00)	0.707 (1.00)
del 12q24 33	63 (12%)	459	1e-05 (0.0077)	2e-05 (0.0125)	0.615 (1.00)	0.459 (1.00)	0.863 (1.00)	0.563 (1.00)	0.48 (1.00)	0.12 (1.00)	0.129 (1.00)	0.555 (1.00)
del 19q13 43	97 (19%)	425	1e-05 (0.0077)	2e-05 (0.0125)	0.33 (1.00)	0.587 (1.00)	0.882 (1.00)	0.344 (1.00)	0.437 (1.00)	0.0658 (1.00)	0.24 (1.00)	0.65 (1.00)
del xp22 2	157 (30%)	365	1e-05 (0.0077)	1e-05 (0.0077)	0.317 (1.00)	0.0026 (1.00)	0.0876 (1.00)	0.00566 (1.00)	0.00534 (1.00)	0.158 (1.00)	0.00471 (1.00)	0.337 (1.00)
del xp21 3	159 (30%)	363	1e-05 (0.0077)	1e-05 (0.0077)	0.56 (1.00)	0.0576 (1.00)	0.468 (1.00)	0.014 (1.00)	0.107 (1.00)	0.0869 (1.00)	0.0138 (1.00)	0.251 (1.00)
amp 8p11 23	161 (31%)	361	1e-05 (0.0077)	0.00489 (1.00)	0.807 (1.00)	0.873 (1.00)	0.124 (1.00)	0.0105 (1.00)	0.00212 (1.00)	0.0107 (1.00)	0.221 (1.00)	0.131 (1.00)
amp 9p13 3	139 (27%)	383	1e-05 (0.0077)	0.00231 (1.00)	0.485 (1.00)	0.122 (1.00)	0.00075 (0.409)	0.0154 (1.00)	0.0137 (1.00)	0.0593 (1.00)	0.042 (1.00)	0.42 (1.00)
amp 9q34 3	177 (34%)	345	1e-05 (0.0077)	0.0146 (1.00)	0.238 (1.00)	0.0229 (1.00)	0.957 (1.00)	0.384 (1.00)	0.58 (1.00)	0.0858 (1.00)	0.625 (1.00)	0.318 (1.00)
amp 15q26 3	105 (20%)	417	1e-05 (0.0077)	0.00666 (1.00)	0.454 (1.00)	0.33 (1.00)	0.604 (1.00)	0.983 (1.00)	0.162 (1.00)	0.0513 (1.00)	0.0485 (1.00)	0.541 (1.00)
del 1q44	48 (9%)	474	0.00044 (0.244)	0.017 (1.00)	0.73 (1.00)	0.909 (1.00)	0.0146 (1.00)	0.00428 (1.00)	0.0018 (0.934)	0.0454 (1.00)	0.0183 (1.00)	0.436 (1.00)
del 2q22 1	121 (23%)	401	0.0193 (1.00)	2e-05 (0.0125)	0.349 (1.00)	0.838 (1.00)	0.276 (1.00)	0.253 (1.00)	0.164 (1.00)	0.00144 (0.763)	0.031 (1.00)	0.0412 (1.00)
del 7q36 1	132 (25%)	390	0.00029 (0.163)	0.393 (1.00)	0.0446 (1.00)	0.679 (1.00)	0.769 (1.00)	0.706 (1.00)	0.791 (1.00)	0.33 (1.00)	0.993 (1.00)	0.979 (1.00)
del 9q34 3	79 (15%)	443	6e-05 (0.0356)	0.00069 (0.377)	0.612 (1.00)	0.371 (1.00)	0.437 (1.00)	0.0478 (1.00)	0.496 (1.00)	0.00901 (1.00)	0.00355 (1.00)	0.957 (1.00)
del 14q11 2	75 (14%)	447	0.00028 (0.157)	0.0159 (1.00)	0.319 (1.00)	0.9 (1.00)	0.118 (1.00)	0.28 (1.00)	0.00758 (1.00)	0.0315 (1.00)	0.00155 (0.815)	0.126 (1.00)
del 15q15 1	124 (24%)	398	1e-05 (0.0077)	0.119 (1.00)	0.668 (1.00)	0.413 (1.00)	0.0696 (1.00)	0.0833 (1.00)	0.706 (1.00)	0.637 (1.00)	0.0592 (1.00)	0.63 (1.00)
del 17p11 2	99 (19%)	423	1e-05 (0.0077)	0.00185 (0.958)	0.891 (1.00)	0.973 (1.00)	0.259 (1.00)	0.274 (1.00)	0.475 (1.00)	0.126 (1.00)	0.0248 (1.00)	0.927 (1.00)
del 17q25 3	71 (14%)	451	0.242 (1.00)	2e-05 (0.0125)	0.432 (1.00)	0.693 (1.00)	0.0122 (1.00)	0.00312 (1.00)	0.00905 (1.00)	0.0504 (1.00)	0.07 (1.00)	0.00343 (1.00)
amp 11p13	102 (20%)	420	0.00277 (1.00)	0.00086 (0.467)	0.46 (1.00)	0.181 (1.00)	0.959 (1.00)	0.22 (1.00)	0.753 (1.00)	0.492 (1.00)	0.00554 (1.00)	0.15 (1.00)
del 2q21 2	78 (15%)	444	0.913 (1.00)	0.0213 (1.00)	0.702 (1.00)	0.211 (1.00)	0.027 (1.00)	0.00654 (1.00)	0.00239 (1.00)	0.26 (1.00)	0.0393 (1.00)	0.0354 (1.00)
del 7q31 1	77 (15%)	445	0.00221 (1.00)	0.281 (1.00)	0.57 (1.00)	0.378 (1.00)	0.51 (1.00)	0.215 (1.00)	0.724 (1.00)	0.174 (1.00)	0.481 (1.00)	0.693 (1.00)

'amp_2q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S1. Gene #1: 'amp_2q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
AMP PEAK 1(2Q11.2) MUTATED	36	59	10	2
AMP PEAK 1(2Q11.2) WILD-TYPE	119	76	179	41

Figure S1. Get High-res Image Gene #1: 'amp_2q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S2. Gene #1: 'amp_2q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
AMP PEAK 1(2Q11.2) MUTATED	6	32	20	39	2	4	4
AMP PEAK 1(2Q11.2) WILD-TYPE	78	47	76	53	76	71	14

Figure S2. Get High-res Image Gene #1: 'amp_2q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_2q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.22

Table S3. Gene #1: 'amp_2q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	157	155	130
AMP PEAK 1(2Q11.2) MUTATED	23	29	24	26
AMP PEAK 1(2Q11.2) WILD-TYPE	28	128	131	104

Figure S3. Get High-res Image Gene #1: 'amp_2q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_2q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S4. Gene #2: 'amp_2q31.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
AMP PEAK 2(2Q31.2) MUTATED	37	63	10	2
AMP PEAK 2(2Q31.2) WILD-TYPE	118	72	179	41

Figure S4. Get High-res Image Gene #2: 'amp_2q31.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2q31.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
AMP PEAK 2(2Q31.2) MUTATED	8	25	18	49	5	4	3
AMP PEAK 2(2Q31.2) WILD-TYPE	76	54	78	43	73	71	15

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

'amp_3q26.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S6. Gene #3: 'amp_3q26.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
AMP PEAK 3(3Q26.33) MUTATED	130	125	94	31
AMP PEAK 3(3Q26.33) WILD-TYPE	25	10	95	12

Figure S6. Get High-res Image Gene #3: 'amp_3q26.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S7. Gene #3: 'amp_3q26.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
AMP PEAK 3(3Q26.33) MUTATED	49	66	77	85	62	28	13
AMP PEAK 3(3Q26.33) WILD-TYPE	35	13	19	7	16	47	5

Figure S7. Get High-res Image Gene #3: 'amp_3q26.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q26.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S8. Gene #3: 'amp_3q26.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	207	134	152
AMP PEAK 3(3Q26.33) MUTATED	174	101	88
AMP PEAK 3(3Q26.33) WILD-TYPE	33	33	64

Figure S8. Get High-res Image Gene #3: 'amp_3q26.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3q26.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.024

Table S9. Gene #3: 'amp_3q26.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	157	155	130
AMP PEAK 3(3Q26.33) MUTATED	41	118	94	110
AMP PEAK 3(3Q26.33) WILD-TYPE	10	39	61	20

Figure S9. Get High-res Image Gene #3: 'amp_3q26.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'MIRSEQ_MATURE_CNMF'

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

Table S10. Gene #3: 'amp_3q26.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	72	140	98	116	47
AMP PEAK 3(3Q26.33) MUTATED	57	84	84	80	32
AMP PEAK 3(3Q26.33) WILD-TYPE	15	56	14	36	15

Figure S10. Get High-res Image Gene #3: 'amp_3q26.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S11. Gene #4: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
AMP PEAK 4(5P15.33) MUTATED	93	88	44	15
AMP PEAK 4(5P15.33) WILD-TYPE	62	47	145	28

Figure S11. Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S12. Gene #4: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
AMP PEAK 4(5P15.33) MUTATED	29	45	54	52	35	15	10
AMP PEAK 4(5P15.33) WILD-TYPE	55	34	42	40	43	60	8

Figure S12. Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S13. Gene #5: 'amp_6p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
AMP PEAK 5(6P12.1) MUTATED	46	37	16	11
AMP PEAK 5(6P12.1) WILD-TYPE	109	98	173	32

Figure S13. Get High-res Image Gene #5: 'amp_6p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p12.1' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S14. Gene #5: 'amp_6p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
AMP PEAK 5(6P12.1) MUTATED	10	26	32	23	7	8	4
AMP PEAK 5(6P12.1) WILD-TYPE	74	53	64	69	71	67	14

Figure S14. Get High-res Image Gene #5: 'amp_6p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S15. Gene #6: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
AMP PEAK 6(6Q12) MUTATED	44	30	12	10
AMP PEAK 6(6Q12) WILD-TYPE	111	105	177	33

Figure S15. Get High-res Image Gene #6: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q12' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.086

Table S16. Gene #6: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
AMP PEAK 6(6Q12) MUTATED	10	18	26	25	4	9	4
AMP PEAK 6(6Q12) WILD-TYPE	74	61	70	67	74	66	14

Figure S16. Get High-res Image Gene #6: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S17. Gene #7: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
AMP PEAK 7(7P11.2) MUTATED	90	72	41	19
AMP PEAK 7(7P11.2) WILD-TYPE	65	63	148	24

Figure S17. Get High-res Image Gene #7: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S18. Gene #7: 'amp_7p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
AMP PEAK 7(7P11.2) MUTATED	30	43	52	56	6	24	11
AMP PEAK 7(7P11.2) WILD-TYPE	54	36	44	36	72	51	7

Figure S18. Get High-res Image Gene #7: 'amp_7p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S19. Gene #7: 'amp_7p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
AMP PEAK 7(7P11.2) MUTATED	84	83	52
AMP PEAK 7(7P11.2) WILD-TYPE	106	59	134

Figure S19. Get High-res Image Gene #7: 'amp_7p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S20. Gene #8: 'amp_7q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
AMP PEAK 8(7Q21.3) MUTATED	52	78	25	14
AMP PEAK 8(7Q21.3) WILD-TYPE	103	57	164	29

Figure S20. Get High-res Image Gene #8: 'amp_7q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S21. Gene #8: 'amp_7q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
AMP PEAK 8(7Q21.3) MUTATED	14	35	29	62	9	13	7
AMP PEAK 8(7Q21.3) WILD-TYPE	70	44	67	30	69	62	11

Figure S21. Get High-res Image Gene #8: 'amp_7q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q21.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S22. Gene #8: 'amp_7q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
AMP PEAK 8(7Q21.3) MUTATED	56	65	45
AMP PEAK 8(7Q21.3) WILD-TYPE	134	77	141

Figure S22. Get High-res Image Gene #8: 'amp_7q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S23. Gene #9: 'amp_8p11.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
AMP PEAK 9(8P11.23) MUTATED	34	70	47	10
AMP PEAK 9(8P11.23) WILD-TYPE	121	65	142	33

Figure S23. Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S24. Gene #10: 'amp_8q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
AMP PEAK 10(8Q11.21) MUTATED	117	79	80	34
AMP PEAK 10(8Q11.21) WILD-TYPE	38	56	109	9

Figure S24. Get High-res Image Gene #10: 'amp_8q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S25. Gene #10: 'amp_8q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
AMP PEAK 10(8Q11.21) MUTATED	54	43	80	51	29	40	13
AMP PEAK 10(8Q11.21) WILD-TYPE	30	36	16	41	49	35	5

Figure S25. Get High-res Image Gene #10: 'amp_8q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.092

Table S26. Gene #10: 'amp_8q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	157	155	130
AMP PEAK 10(8Q11.21) MUTATED	28	112	95	59
AMP PEAK 10(8Q11.21) WILD-TYPE	23	45	60	71

Figure S26. Get High-res Image Gene #10: 'amp_8q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S27. Gene #11: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
AMP PEAK 11(8Q24.21) MUTATED	139	105	105	37
AMP PEAK 11(8Q24.21) WILD-TYPE	16	30	84	6

Figure S27. Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S28. Gene #11: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
AMP PEAK 11(8Q24.21) MUTATED	65	58	87	73	35	51	17
AMP PEAK 11(8Q24.21) WILD-TYPE	19	21	9	19	43	24	1

Figure S28. Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.024

Table S29. Gene #11: 'amp_8q24.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	157	155	130
AMP PEAK 11(8Q24.21) MUTATED	37	130	122	77
AMP PEAK 11(8Q24.21) WILD-TYPE	14	27	33	53

Figure S29. Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.12

Table S30. Gene #11: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	72	140	98	116	47
AMP PEAK 11(8Q24.21) MUTATED	54	114	68	91	22
AMP PEAK 11(8Q24.21) WILD-TYPE	18	26	30	25	25

Figure S30. Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_9p24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S31. Gene #12: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
AMP PEAK 12(9P24.1) MUTATED	26	21	41	38
AMP PEAK 12(9P24.1) WILD-TYPE	129	114	148	5

Figure S31. Get High-res Image Gene #12: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p24.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S32. Gene #12: 'amp_9p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
AMP PEAK 12(9P24.1) MUTATED	16	8	21	19	20	39	3
AMP PEAK 12(9P24.1) WILD-TYPE	68	71	75	73	58	36	15

Figure S32. Get High-res Image Gene #12: 'amp_9p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9p24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.17

Table S33. Gene #12: 'amp_9p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	72	140	98	116	47
AMP PEAK 12(9P24.1) MUTATED	11	47	12	36	14
AMP PEAK 12(9P24.1) WILD-TYPE	61	93	86	80	33

Figure S33. Get High-res Image Gene #12: 'amp_9p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S34. Gene #13: 'amp_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
AMP PEAK 13(9P23) MUTATED	23	23	40	38
AMP PEAK 13(9P23) WILD-TYPE	132	112	149	5

Figure S34. Get High-res Image Gene #13: 'amp_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S35. Gene #13: 'amp_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
AMP PEAK 13(9P23) MUTATED	17	7	20	20	19	38	3
AMP PEAK 13(9P23) WILD-TYPE	67	72	76	72	59	37	15

Figure S35. Get High-res Image Gene #13: 'amp_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S36. Gene #14: 'amp_9p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
AMP PEAK 14(9P13.3) MUTATED	37	31	36	35
AMP PEAK 14(9P13.3) WILD-TYPE	118	104	153	8

Figure S36. Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S37. Gene #15: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
AMP PEAK 15(9Q34.3) MUTATED	42	57	43	35
AMP PEAK 15(9Q34.3) WILD-TYPE	113	78	146	8

Figure S37. Get High-res Image Gene #15: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S38. Gene #17: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
AMP PEAK 17(11Q13.3) MUTATED	90	85	37	17
AMP PEAK 17(11Q13.3) WILD-TYPE	65	50	152	26

Figure S38. Get High-res Image Gene #17: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S39. Gene #17: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
AMP PEAK 17(11Q13.3) MUTATED	31	31	62	55	15	21	14
AMP PEAK 17(11Q13.3) WILD-TYPE	53	48	34	37	63	54	4

Figure S39. Get High-res Image Gene #17: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12p13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S40. Gene #18: 'amp_12p13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
AMP PEAK 18(12P13.33) MUTATED	60	70	22	15
AMP PEAK 18(12P13.33) WILD-TYPE	95	65	167	28

Figure S40. Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p13.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S41. Gene #18: 'amp_12p13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
AMP PEAK 18(12P13.33) MUTATED	14	36	33	46	23	11	4
AMP PEAK 18(12P13.33) WILD-TYPE	70	43	63	46	55	64	14

Figure S41. Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12q15' versus 'CN_CNMF'

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

Table S42. Gene #19: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
AMP PEAK 19(12Q15) MUTATED	34	40	17	12
AMP PEAK 19(12Q15) WILD-TYPE	121	95	172	31

Figure S42. Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.2

Table S43. Gene #19: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
AMP PEAK 19(12Q15) MUTATED	8	21	22	30	13	7	2
AMP PEAK 19(12Q15) WILD-TYPE	76	58	74	62	65	68	16

Figure S43. Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S44. Gene #20: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
AMP PEAK 20(13Q22.1) MUTATED	61	27	14	3
AMP PEAK 20(13Q22.1) WILD-TYPE	94	108	175	40

Figure S44. Get High-res Image Gene #20: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S45. Gene #20: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
AMP PEAK 20(13Q22.1) MUTATED	8	20	35	18	12	5	7
AMP PEAK 20(13Q22.1) WILD-TYPE	76	59	61	74	66	70	11

Figure S45. Get High-res Image Gene #20: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S46. Gene #21: 'amp_13q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
AMP PEAK 21(13Q34) MUTATED	59	22	18	7
AMP PEAK 21(13Q34) WILD-TYPE	96	113	171	36

Figure S46. Get High-res Image Gene #21: 'amp_13q34' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q34' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.024

Table S47. Gene #21: 'amp_13q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
AMP PEAK 21(13Q34) MUTATED	11	18	34	20	10	6	7
AMP PEAK 21(13Q34) WILD-TYPE	73	61	62	72	68	69	11

Figure S47. Get High-res Image Gene #21: 'amp_13q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_15q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S48. Gene #22: 'amp_15q26.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
AMP PEAK 22(15Q26.3) MUTATED	39	42	17	7
AMP PEAK 22(15Q26.3) WILD-TYPE	116	93	172	36

Figure S48. Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S49. Gene #23: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
AMP PEAK 23(17Q12) MUTATED	26	48	9	8
AMP PEAK 23(17Q12) WILD-TYPE	129	87	180	35

Figure S49. Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

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

Table S50. Gene #23: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
AMP PEAK 23(17Q12) MUTATED	7	21	21	29	6	6	1
AMP PEAK 23(17Q12) WILD-TYPE	77	58	75	63	72	69	17

Figure S50. Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.041

Table S51. Gene #23: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
AMP PEAK 23(17Q12) MUTATED	31	41	18
AMP PEAK 23(17Q12) WILD-TYPE	159	101	168

Figure S51. Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_18p11.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S52. Gene #24: 'amp_18p11.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
AMP PEAK 24(18P11.31) MUTATED	61	63	23	9
AMP PEAK 24(18P11.31) WILD-TYPE	94	72	166	34

Figure S52. Get High-res Image Gene #24: 'amp_18p11.31' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18p11.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S53. Gene #24: 'amp_18p11.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
AMP PEAK 24(18P11.31) MUTATED	9	45	33	34	21	10	4
AMP PEAK 24(18P11.31) WILD-TYPE	75	34	63	58	57	65	14

Figure S53. Get High-res Image Gene #24: 'amp_18p11.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_18p11.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S54. Gene #24: 'amp_18p11.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	157	155	130
AMP PEAK 24(18P11.31) MUTATED	35	45	30	39
AMP PEAK 24(18P11.31) WILD-TYPE	16	112	125	91

Figure S54. Get High-res Image Gene #24: 'amp_18p11.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_18p11.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.098

Table S55. Gene #24: 'amp_18p11.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
AMP PEAK 24(18P11.31) MUTATED	49	62	44
AMP PEAK 24(18P11.31) WILD-TYPE	141	80	142

Figure S55. Get High-res Image Gene #24: 'amp_18p11.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_18p11.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S56. Gene #24: 'amp_18p11.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	72	140	98	116	47
AMP PEAK 24(18P11.31) MUTATED	25	28	47	30	7
AMP PEAK 24(18P11.31) WILD-TYPE	47	112	51	86	40

Figure S56. Get High-res Image Gene #24: 'amp_18p11.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_18q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S57. Gene #25: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
AMP PEAK 25(18Q11.2) MUTATED	42	40	19	5
AMP PEAK 25(18Q11.2) WILD-TYPE	113	95	170	38

Figure S57. Get High-res Image Gene #25: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.047

Table S58. Gene #25: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
AMP PEAK 25(18Q11.2) MUTATED	6	24	24	26	17	6	3
AMP PEAK 25(18Q11.2) WILD-TYPE	78	55	72	66	61	69	15

Figure S58. Get High-res Image Gene #25: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S59. Gene #26: 'amp_19p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
AMP PEAK 26(19P13.2) MUTATED	4	9	4	20	20	2	1
AMP PEAK 26(19P13.2) WILD-TYPE	80	70	92	72	58	73	17

Figure S59. Get High-res Image Gene #26: 'amp_19p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.053

Table S60. Gene #26: 'amp_19p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	157	155	130
AMP PEAK 26(19P13.2) MUTATED	4	11	9	29
AMP PEAK 26(19P13.2) WILD-TYPE	47	146	146	101

Figure S60. Get High-res Image Gene #26: 'amp_19p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20p12.2' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S61. Gene #27: 'amp_20p12.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
AMP PEAK 27(20P12.2) MUTATED	80	46	48	17
AMP PEAK 27(20P12.2) WILD-TYPE	75	89	141	26

Figure S61. Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20p12.2' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.024

Table S62. Gene #27: 'amp_20p12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
AMP PEAK 27(20P12.2) MUTATED	28	25	54	39	21	16	8
AMP PEAK 27(20P12.2) WILD-TYPE	56	54	42	53	57	59	10

Figure S62. Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S63. Gene #28: 'amp_20q11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
AMP PEAK 28(20Q11.22) MUTATED	94	60	53	20
AMP PEAK 28(20Q11.22) WILD-TYPE	61	75	136	23

Figure S63. Get High-res Image Gene #28: 'amp_20q11.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q11.22' versus 'METHLYATION_CNMF'

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

Table S64. Gene #28: 'amp_20q11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
AMP PEAK 28(20Q11.22) MUTATED	31	38	59	45	27	18	9
AMP PEAK 28(20Q11.22) WILD-TYPE	53	41	37	47	51	57	9

Figure S64. Get High-res Image Gene #28: 'amp_20q11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xq28' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S65. Gene #29: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
AMP PEAK 29(XQ28) MUTATED	66	46	26	12
AMP PEAK 29(XQ28) WILD-TYPE	89	89	163	31

Figure S65. Get High-res Image Gene #29: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq28' versus 'METHLYATION_CNMF'

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

Table S66. Gene #29: 'amp_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
AMP PEAK 29(XQ28) MUTATED	11	20	42	37	20	13	7
AMP PEAK 29(XQ28) WILD-TYPE	73	59	54	55	58	62	11

Figure S66. Get High-res Image Gene #29: 'amp_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S67. Gene #30: 'del_1p36.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 1(1P36.21) MUTATED	26	50	15	4
DEL PEAK 1(1P36.21) WILD-TYPE	129	85	174	39

Figure S67. Get High-res Image Gene #30: 'del_1p36.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S68. Gene #30: 'del_1p36.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 1(1P36.21) MUTATED	4	17	8	48	8	8	2
DEL PEAK 1(1P36.21) WILD-TYPE	80	62	88	44	70	67	16

Figure S68. Get High-res Image Gene #30: 'del_1p36.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S69. Gene #30: 'del_1p36.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	207	134	152
DEL PEAK 1(1P36.21) MUTATED	60	21	11
DEL PEAK 1(1P36.21) WILD-TYPE	147	113	141

Figure S69. Get High-res Image Gene #30: 'del_1p36.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p36.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.041

Table S70. Gene #30: 'del_1p36.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	157	155	130
DEL PEAK 1(1P36.21) MUTATED	11	26	15	40
DEL PEAK 1(1P36.21) WILD-TYPE	40	131	140	90

Figure S70. Get High-res Image Gene #30: 'del_1p36.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S71. Gene #31: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 2(1P13.2) MUTATED	51	61	11	10
DEL PEAK 2(1P13.2) WILD-TYPE	104	74	178	33

Figure S71. Get High-res Image Gene #31: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S72. Gene #31: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 2(1P13.2) MUTATED	13	25	20	55	6	8	6
DEL PEAK 2(1P13.2) WILD-TYPE	71	54	76	37	72	67	12

Figure S72. Get High-res Image Gene #31: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.12

Table S73. Gene #31: 'del_1p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 2(1P13.2) MUTATED	47	53	31
DEL PEAK 2(1P13.2) WILD-TYPE	143	89	155

Figure S73. Get High-res Image Gene #31: 'del_1p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.23

Table S74. Gene #31: 'del_1p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	72	140	98	116	47
DEL PEAK 2(1P13.2) MUTATED	29	28	34	24	6
DEL PEAK 2(1P13.2) WILD-TYPE	43	112	64	92	41

Figure S74. Get High-res Image Gene #31: 'del_1p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1q44' versus 'CN_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.24

Table S75. Gene #32: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 3(1Q44) MUTATED	25	10	7	6
DEL PEAK 3(1Q44) WILD-TYPE	130	125	182	37

Figure S75. Get High-res Image Gene #32: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

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

Table S76. Gene #34: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 5(2Q22.1) MUTATED	10	16	23	38	11	22	1
DEL PEAK 5(2Q22.1) WILD-TYPE	74	63	73	54	67	53	17

Figure S76. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q36.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S77. Gene #35: 'del_2q36.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 6(2Q36.2) MUTATED	48	64	32	13
DEL PEAK 6(2Q36.2) WILD-TYPE	107	71	157	30

Figure S77. Get High-res Image Gene #35: 'del_2q36.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q36.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S78. Gene #35: 'del_2q36.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 6(2Q36.2) MUTATED	7	25	26	49	24	21	5
DEL PEAK 6(2Q36.2) WILD-TYPE	77	54	70	43	54	54	13

Figure S78. Get High-res Image Gene #35: 'del_2q36.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S79. Gene #36: 'del_3p26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 7(3P26.2) MUTATED	144	115	60	29
DEL PEAK 7(3P26.2) WILD-TYPE	11	20	129	14

Figure S79. Get High-res Image Gene #36: 'del_3p26.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p26.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S80. Gene #36: 'del_3p26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 7(3P26.2) MUTATED	50	67	87	77	19	31	17
DEL PEAK 7(3P26.2) WILD-TYPE	34	12	9	15	59	44	1

Figure S80. Get High-res Image Gene #36: 'del_3p26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p26.2' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.047

Table S81. Gene #36: 'del_3p26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	207	134	152
DEL PEAK 7(3P26.2) MUTATED	122	108	98
DEL PEAK 7(3P26.2) WILD-TYPE	85	26	54

Figure S81. Get High-res Image Gene #36: 'del_3p26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S82. Gene #36: 'del_3p26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	157	155	130
DEL PEAK 7(3P26.2) MUTATED	44	122	99	63
DEL PEAK 7(3P26.2) WILD-TYPE	7	35	56	67

Figure S82. Get High-res Image Gene #36: 'del_3p26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S83. Gene #36: 'del_3p26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 7(3P26.2) MUTATED	144	106	96
DEL PEAK 7(3P26.2) WILD-TYPE	46	36	90

Figure S83. Get High-res Image Gene #36: 'del_3p26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.024

Table S84. Gene #36: 'del_3p26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	72	140	98	116	47
DEL PEAK 7(3P26.2) MUTATED	57	91	64	86	17
DEL PEAK 7(3P26.2) WILD-TYPE	15	49	34	30	30

Figure S84. Get High-res Image Gene #36: 'del_3p26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S85. Gene #37: 'del_3p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 8(3P24.1) MUTATED	145	124	69	30
DEL PEAK 8(3P24.1) WILD-TYPE	10	11	120	13

Figure S85. Get High-res Image Gene #37: 'del_3p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p24.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S86. Gene #37: 'del_3p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 8(3P24.1) MUTATED	51	71	87	82	29	31	17
DEL PEAK 8(3P24.1) WILD-TYPE	33	8	9	10	49	44	1

Figure S86. Get High-res Image Gene #37: 'del_3p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S87. Gene #37: 'del_3p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	157	155	130
DEL PEAK 8(3P24.1) MUTATED	46	124	100	77
DEL PEAK 8(3P24.1) WILD-TYPE	5	33	55	53

Figure S87. Get High-res Image Gene #37: 'del_3p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.03

Table S88. Gene #37: 'del_3p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 8(3P24.1) MUTATED	147	110	108
DEL PEAK 8(3P24.1) WILD-TYPE	43	32	78

Figure S88. Get High-res Image Gene #37: 'del_3p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p24.1' versus 'MIRSEQ_MATURE_CNMF'

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

Table S89. Gene #37: 'del_3p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	72	140	98	116	47
DEL PEAK 8(3P24.1) MUTATED	60	91	72	89	20
DEL PEAK 8(3P24.1) WILD-TYPE	12	49	26	27	27

Figure S89. Get High-res Image Gene #37: 'del_3p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S90. Gene #38: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 9(3P14.2) MUTATED	146	128	67	31
DEL PEAK 9(3P14.2) WILD-TYPE	9	7	122	12

Figure S90. Get High-res Image Gene #38: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S91. Gene #38: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 9(3P14.2) MUTATED	51	72	85	84	34	29	17
DEL PEAK 9(3P14.2) WILD-TYPE	33	7	11	8	44	46	1

Figure S91. Get High-res Image Gene #38: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S92. Gene #38: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	157	155	130
DEL PEAK 9(3P14.2) MUTATED	47	124	97	83
DEL PEAK 9(3P14.2) WILD-TYPE	4	33	58	47

Figure S92. Get High-res Image Gene #38: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.2

Table S93. Gene #38: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 9(3P14.2) MUTATED	145	111	113
DEL PEAK 9(3P14.2) WILD-TYPE	45	31	73

Figure S93. Get High-res Image Gene #38: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S94. Gene #38: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	72	140	98	116	47
DEL PEAK 9(3P14.2) MUTATED	58	91	77	90	19
DEL PEAK 9(3P14.2) WILD-TYPE	14	49	21	26	28

Figure S94. Get High-res Image Gene #38: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S95. Gene #39: 'del_3p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 10(3P12.1) MUTATED	139	124	52	28
DEL PEAK 10(3P12.1) WILD-TYPE	16	11	137	15

Figure S95. Get High-res Image Gene #39: 'del_3p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S96. Gene #39: 'del_3p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 10(3P12.1) MUTATED	47	69	77	83	24	27	16
DEL PEAK 10(3P12.1) WILD-TYPE	37	10	19	9	54	48	2

Figure S96. Get High-res Image Gene #39: 'del_3p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S97. Gene #39: 'del_3p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	157	155	130
DEL PEAK 10(3P12.1) MUTATED	45	114	92	73
DEL PEAK 10(3P12.1) WILD-TYPE	6	43	63	57

Figure S97. Get High-res Image Gene #39: 'del_3p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S98. Gene #39: 'del_3p12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	72	140	98	116	47
DEL PEAK 10(3P12.1) MUTATED	56	84	69	83	15
DEL PEAK 10(3P12.1) WILD-TYPE	16	56	29	33	32

Figure S98. Get High-res Image Gene #39: 'del_3p12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4p15.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S99. Gene #40: 'del_4p15.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 11(4P15.2) MUTATED	71	94	29	14
DEL PEAK 11(4P15.2) WILD-TYPE	84	41	160	29

Figure S99. Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_4p15.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S100. Gene #40: 'del_4p15.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 11(4P15.2) MUTATED	21	46	29	66	21	15	10
DEL PEAK 11(4P15.2) WILD-TYPE	63	33	67	26	57	60	8

Figure S100. Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4p15.2' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.064

Table S101. Gene #40: 'del_4p15.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	207	134	152
DEL PEAK 11(4P15.2) MUTATED	97	59	39
DEL PEAK 11(4P15.2) WILD-TYPE	110	75	113

Figure S101. Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4p15.2' versus 'MIRSEQ_MATURE_CNMF'

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

Table S102. Gene #40: 'del_4p15.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	72	140	98	116	47
DEL PEAK 11(4P15.2) MUTATED	38	40	48	48	11
DEL PEAK 11(4P15.2) WILD-TYPE	34	100	50	68	36

Figure S102. Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S103. Gene #41: 'del_4q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 12(4Q21.3) MUTATED	54	68	21	13
DEL PEAK 12(4Q21.3) WILD-TYPE	101	67	168	30

Figure S103. Get High-res Image Gene #41: 'del_4q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S104. Gene #41: 'del_4q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 12(4Q21.3) MUTATED	15	29	29	49	17	14	3
DEL PEAK 12(4Q21.3) WILD-TYPE	69	50	67	43	61	61	15

Figure S104. Get High-res Image Gene #41: 'del_4q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S105. Gene #42: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 13(4Q22.1) MUTATED	62	73	21	13
DEL PEAK 13(4Q22.1) WILD-TYPE	93	62	168	30

Figure S105. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S106. Gene #42: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 13(4Q22.1) MUTATED	12	31	29	59	18	15	5
DEL PEAK 13(4Q22.1) WILD-TYPE	72	48	67	33	60	60	13

Figure S106. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q35.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S107. Gene #43: 'del_4q35.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 14(4Q35.2) MUTATED	90	73	31	19
DEL PEAK 14(4Q35.2) WILD-TYPE	65	62	158	24

Figure S107. Get High-res Image Gene #43: 'del_4q35.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q35.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S108. Gene #43: 'del_4q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 14(4Q35.2) MUTATED	23	39	44	56	20	23	8
DEL PEAK 14(4Q35.2) WILD-TYPE	61	40	52	36	58	52	10

Figure S108. Get High-res Image Gene #43: 'del_4q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S109. Gene #44: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 15(5Q12.1) MUTATED	86	96	22	11
DEL PEAK 15(5Q12.1) WILD-TYPE	69	39	167	32

Figure S109. Get High-res Image Gene #44: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S110. Gene #44: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 15(5Q12.1) MUTATED	17	52	53	63	10	10	10
DEL PEAK 15(5Q12.1) WILD-TYPE	67	27	43	29	68	65	8

Figure S110. Get High-res Image Gene #44: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S111. Gene #44: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	157	155	130
DEL PEAK 15(5Q12.1) MUTATED	34	75	39	55
DEL PEAK 15(5Q12.1) WILD-TYPE	17	82	116	75

Figure S111. Get High-res Image Gene #44: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S112. Gene #44: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 15(5Q12.1) MUTATED	84	75	53
DEL PEAK 15(5Q12.1) WILD-TYPE	106	67	133

Figure S112. Get High-res Image Gene #44: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.22

Table S113. Gene #44: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	72	140	98	116	47
DEL PEAK 15(5Q12.1) MUTATED	31	55	54	48	8
DEL PEAK 15(5Q12.1) WILD-TYPE	41	85	44	68	39

Figure S113. Get High-res Image Gene #44: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S114. Gene #45: 'del_5q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 16(5Q15) MUTATED	88	98	28	12
DEL PEAK 16(5Q15) WILD-TYPE	67	37	161	31

Figure S114. Get High-res Image Gene #45: 'del_5q15' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q15' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S115. Gene #45: 'del_5q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 16(5Q15) MUTATED	19	54	52	66	12	12	11
DEL PEAK 16(5Q15) WILD-TYPE	65	25	44	26	66	63	7

Figure S115. Get High-res Image Gene #45: 'del_5q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S116. Gene #45: 'del_5q15' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	157	155	130
DEL PEAK 16(5Q15) MUTATED	34	76	44	58
DEL PEAK 16(5Q15) WILD-TYPE	17	81	111	72

Figure S116. Get High-res Image Gene #45: 'del_5q15' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q15' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S117. Gene #45: 'del_5q15' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 16(5Q15) MUTATED	86	80	57
DEL PEAK 16(5Q15) WILD-TYPE	104	62	129

Figure S117. Get High-res Image Gene #45: 'del_5q15' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q15' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.075

Table S118. Gene #45: 'del_5q15' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	72	140	98	116	47
DEL PEAK 16(5Q15) MUTATED	31	58	57	51	8
DEL PEAK 16(5Q15) WILD-TYPE	41	82	41	65	39

Figure S118. Get High-res Image Gene #45: 'del_5q15' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5q35.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S119. Gene #46: 'del_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 17(5Q35.3) MUTATED	68	93	25	13
DEL PEAK 17(5Q35.3) WILD-TYPE	87	42	164	30

Figure S119. Get High-res Image Gene #46: 'del_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q35.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S120. Gene #46: 'del_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 17(5Q35.3) MUTATED	19	57	45	51	11	6	10
DEL PEAK 17(5Q35.3) WILD-TYPE	65	22	51	41	67	69	8

Figure S120. Get High-res Image Gene #46: 'del_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q35.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S121. Gene #46: 'del_5q35.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	157	155	130
DEL PEAK 17(5Q35.3) MUTATED	37	68	35	51
DEL PEAK 17(5Q35.3) WILD-TYPE	14	89	120	79

Figure S121. Get High-res Image Gene #46: 'del_5q35.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q35.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S122. Gene #46: 'del_5q35.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 17(5Q35.3) MUTATED	79	70	47
DEL PEAK 17(5Q35.3) WILD-TYPE	111	72	139

Figure S122. Get High-res Image Gene #46: 'del_5q35.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q35.3' versus 'MIRSEQ_MATURE_CNMF'

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

Table S123. Gene #46: 'del_5q35.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	72	140	98	116	47
DEL PEAK 17(5Q35.3) MUTATED	28	51	52	41	7
DEL PEAK 17(5Q35.3) WILD-TYPE	44	89	46	75	40

Figure S123. Get High-res Image Gene #46: 'del_5q35.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6p25.3' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.053

Table S124. Gene #47: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 18(6P25.3) MUTATED	30	41	19	6
DEL PEAK 18(6P25.3) WILD-TYPE	125	94	170	37

Figure S124. Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S125. Gene #47: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 18(6P25.3) MUTATED	11	12	17	37	11	5	3
DEL PEAK 18(6P25.3) WILD-TYPE	73	67	79	55	67	70	15

Figure S125. Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q36.1' versus 'CN_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.16

Table S126. Gene #49: 'del_7q36.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 20(7Q36.1) MUTATED	50	39	28	15
DEL PEAK 20(7Q36.1) WILD-TYPE	105	96	161	28

Figure S126. Get High-res Image Gene #49: 'del_7q36.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S127. Gene #50: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 21(8P23.2) MUTATED	125	78	74	27
DEL PEAK 21(8P23.2) WILD-TYPE	30	57	115	16

Figure S127. Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S128. Gene #50: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 21(8P23.2) MUTATED	50	40	71	63	16	51	13
DEL PEAK 21(8P23.2) WILD-TYPE	34	39	25	29	62	24	5

Figure S128. Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.036

Table S129. Gene #50: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	157	155	130
DEL PEAK 21(8P23.2) MUTATED	25	106	99	55
DEL PEAK 21(8P23.2) WILD-TYPE	26	51	56	75

Figure S129. Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S130. Gene #50: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	72	140	98	116	47
DEL PEAK 21(8P23.2) MUTATED	47	95	44	75	14
DEL PEAK 21(8P23.2) WILD-TYPE	25	45	54	41	33

Figure S130. Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S131. Gene #50: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	244	89
DEL PEAK 21(8P23.2) MUTATED	96	117	62
DEL PEAK 21(8P23.2) WILD-TYPE	44	127	27

Figure S131. Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S132. Gene #51: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 22(9P23) MUTATED	103	94	41	1
DEL PEAK 22(9P23) WILD-TYPE	52	41	148	42

Figure S132. Get High-res Image Gene #51: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S133. Gene #51: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 22(9P23) MUTATED	27	57	52	65	9	18	11
DEL PEAK 22(9P23) WILD-TYPE	57	22	44	27	69	57	7

Figure S133. Get High-res Image Gene #51: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.12

Table S134. Gene #51: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	157	155	130
DEL PEAK 22(9P23) MUTATED	37	73	69	47
DEL PEAK 22(9P23) WILD-TYPE	14	84	86	83

Figure S134. Get High-res Image Gene #51: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.041

Table S135. Gene #51: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 22(9P23) MUTATED	85	85	66
DEL PEAK 22(9P23) WILD-TYPE	105	57	120

Figure S135. Get High-res Image Gene #51: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S136. Gene #51: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	72	140	98	116	47
DEL PEAK 22(9P23) MUTATED	44	56	58	51	6
DEL PEAK 22(9P23) WILD-TYPE	28	84	40	65	41

Figure S136. Get High-res Image Gene #51: '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 = 0.0077

Table S137. Gene #52: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 23(9P21.3) MUTATED	110	109	69	14
DEL PEAK 23(9P21.3) WILD-TYPE	45	26	120	29

Figure S137. Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S138. Gene #52: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 23(9P21.3) MUTATED	42	66	67	69	11	35	12
DEL PEAK 23(9P21.3) WILD-TYPE	42	13	29	23	67	40	6

Figure S138. Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S139. Gene #52: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	157	155	130
DEL PEAK 23(9P21.3) MUTATED	42	96	95	52
DEL PEAK 23(9P21.3) WILD-TYPE	9	61	60	78

Figure S139. Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S140. Gene #52: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 23(9P21.3) MUTATED	113	108	79
DEL PEAK 23(9P21.3) WILD-TYPE	77	34	107

Figure S140. Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S141. Gene #52: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	72	140	98	116	47
DEL PEAK 23(9P21.3) MUTATED	54	77	66	63	12
DEL PEAK 23(9P21.3) WILD-TYPE	18	63	32	53	35

Figure S141. Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9q21.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S142. Gene #53: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 24(9Q21.11) MUTATED	51	35	21	1
DEL PEAK 24(9Q21.11) WILD-TYPE	104	100	168	42

Figure S142. Get High-res Image Gene #53: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q21.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S143. Gene #53: 'del_9q21.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 24(9Q21.11) MUTATED	12	30	20	28	4	5	9
DEL PEAK 24(9Q21.11) WILD-TYPE	72	49	76	64	74	70	9

Figure S143. Get High-res Image Gene #53: 'del_9q21.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9q34.3' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.036

Table S144. Gene #54: 'del_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 25(9Q34.3) MUTATED	38	22	18	1
DEL PEAK 25(9Q34.3) WILD-TYPE	117	113	171	42

Figure S144. Get High-res Image Gene #54: 'del_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S145. Gene #55: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 26(10P15.3) MUTATED	77	48	29	16
DEL PEAK 26(10P15.3) WILD-TYPE	78	87	160	27

Figure S145. Get High-res Image Gene #55: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S146. Gene #55: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 26(10P15.3) MUTATED	18	23	43	43	10	22	11
DEL PEAK 26(10P15.3) WILD-TYPE	66	56	53	49	68	53	7

Figure S146. Get High-res Image Gene #55: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MIRSEQ_MATURE_CNMF'

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

Table S147. Gene #55: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	72	140	98	116	47
DEL PEAK 26(10P15.3) MUTATED	29	42	24	53	7
DEL PEAK 26(10P15.3) WILD-TYPE	43	98	74	63	40

Figure S147. Get High-res Image Gene #55: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S148. Gene #56: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 27(10P11.21) MUTATED	74	50	24	14
DEL PEAK 27(10P11.21) WILD-TYPE	81	85	165	29

Figure S148. Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S149. Gene #56: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 27(10P11.21) MUTATED	14	24	42	42	12	19	9
DEL PEAK 27(10P11.21) WILD-TYPE	70	55	54	50	66	56	9

Figure S149. Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S150. Gene #57: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 28(10Q23.31) MUTATED	46	58	27	7
DEL PEAK 28(10Q23.31) WILD-TYPE	109	77	162	36

Figure S150. Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S151. Gene #57: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 28(10Q23.31) MUTATED	8	25	30	38	24	8	5
DEL PEAK 28(10Q23.31) WILD-TYPE	76	54	66	54	54	67	13

Figure S151. Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.058

Table S152. Gene #57: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	207	134	152
DEL PEAK 28(10Q23.31) MUTATED	73	33	23
DEL PEAK 28(10Q23.31) WILD-TYPE	134	101	129

Figure S152. Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S153. Gene #57: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	157	155	130
DEL PEAK 28(10Q23.31) MUTATED	17	39	22	51
DEL PEAK 28(10Q23.31) WILD-TYPE	34	118	133	79

Figure S153. Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.13

Table S154. Gene #57: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	72	140	98	116	47
DEL PEAK 28(10Q23.31) MUTATED	21	24	42	24	14
DEL PEAK 28(10Q23.31) WILD-TYPE	51	116	56	92	33

Figure S154. Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S155. Gene #58: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 29(11P15.5) MUTATED	42	80	35	6
DEL PEAK 29(11P15.5) WILD-TYPE	113	55	154	37

Figure S155. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S156. Gene #58: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 29(11P15.5) MUTATED	20	30	24	53	26	6	4
DEL PEAK 29(11P15.5) WILD-TYPE	64	49	72	39	52	69	14

Figure S156. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.5' versus 'MRNASEQ_CNMF'

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

Table S157. Gene #58: 'del_11p15.5' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	207	134	152
DEL PEAK 29(11P15.5) MUTATED	85	35	30
DEL PEAK 29(11P15.5) WILD-TYPE	122	99	122

Figure S157. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S158. Gene #58: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	221	152	145
DEL PEAK 29(11P15.5) MUTATED	98	25	40
DEL PEAK 29(11P15.5) WILD-TYPE	123	127	105

Figure S158. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.041

Table S159. Gene #58: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	72	140	98	116	47
DEL PEAK 29(11P15.5) MUTATED	25	27	47	31	16
DEL PEAK 29(11P15.5) WILD-TYPE	47	113	51	85	31

Figure S159. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S160. Gene #59: 'del_11q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 30(11Q23.1) MUTATED	72	89	66	19
DEL PEAK 30(11Q23.1) WILD-TYPE	83	46	123	24

Figure S160. Get High-res Image Gene #59: 'del_11q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S161. Gene #59: 'del_11q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 30(11Q23.1) MUTATED	27	33	49	49	65	13	10
DEL PEAK 30(11Q23.1) WILD-TYPE	57	46	47	43	13	62	8

Figure S161. Get High-res Image Gene #59: 'del_11q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q23.1' versus 'MRNASEQ_CNMF'

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

Table S162. Gene #59: 'del_11q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	207	134	152
DEL PEAK 30(11Q23.1) MUTATED	120	58	52
DEL PEAK 30(11Q23.1) WILD-TYPE	87	76	100

Figure S162. Get High-res Image Gene #59: 'del_11q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S163. Gene #59: 'del_11q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	157	155	130
DEL PEAK 30(11Q23.1) MUTATED	18	64	56	92
DEL PEAK 30(11Q23.1) WILD-TYPE	33	93	99	38

Figure S163. Get High-res Image Gene #59: 'del_11q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12q24.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S164. Gene #60: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 31(12Q24.33) MUTATED	26	28	6	3
DEL PEAK 31(12Q24.33) WILD-TYPE	129	107	183	40

Figure S164. Get High-res Image Gene #60: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q24.33' versus 'METHLYATION_CNMF'

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

Table S165. Gene #60: 'del_12q24.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 31(12Q24.33) MUTATED	5	13	13	23	4	1	4
DEL PEAK 31(12Q24.33) WILD-TYPE	79	66	83	69	74	74	14

Figure S165. Get High-res Image Gene #60: 'del_12q24.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q12.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S166. Gene #61: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 32(13Q12.11) MUTATED	80	98	37	18
DEL PEAK 32(13Q12.11) WILD-TYPE	75	37	152	25

Figure S166. Get High-res Image Gene #61: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q12.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S167. Gene #61: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 32(13Q12.11) MUTATED	22	53	48	61	25	17	7
DEL PEAK 32(13Q12.11) WILD-TYPE	62	26	48	31	53	58	11

Figure S167. Get High-res Image Gene #61: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q12.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S168. Gene #61: 'del_13q12.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	157	155	130
DEL PEAK 32(13Q12.11) MUTATED	37	74	52	54
DEL PEAK 32(13Q12.11) WILD-TYPE	14	83	103	76

Figure S168. Get High-res Image Gene #61: 'del_13q12.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S169. Gene #62: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 33(13Q14.2) MUTATED	53	92	55	17
DEL PEAK 33(13Q14.2) WILD-TYPE	102	43	134	26

Figure S169. Get High-res Image Gene #62: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S170. Gene #62: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 33(13Q14.2) MUTATED	18	46	39	51	44	16	3
DEL PEAK 33(13Q14.2) WILD-TYPE	66	33	57	41	34	59	15

Figure S170. Get High-res Image Gene #62: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

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

Table S171. Gene #62: 'del_13q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	207	134	152
DEL PEAK 33(13Q14.2) MUTATED	110	52	42
DEL PEAK 33(13Q14.2) WILD-TYPE	97	82	110

Figure S171. Get High-res Image Gene #62: 'del_13q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S172. Gene #62: 'del_13q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	157	155	130
DEL PEAK 33(13Q14.2) MUTATED	32	61	42	69
DEL PEAK 33(13Q14.2) WILD-TYPE	19	96	113	61

Figure S172. Get High-res Image Gene #62: 'del_13q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q11.2' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.16

Table S173. Gene #63: 'del_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 34(14Q11.2) MUTATED	27	31	15	2
DEL PEAK 34(14Q11.2) WILD-TYPE	128	104	174	41

Figure S173. Get High-res Image Gene #63: 'del_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S174. Gene #64: 'del_14q32.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 35(14Q32.32) MUTATED	3	11	7	18	32	3	1
DEL PEAK 35(14Q32.32) WILD-TYPE	81	68	89	74	46	72	17

Figure S174. Get High-res Image Gene #64: 'del_14q32.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q32.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S175. Gene #64: 'del_14q32.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	207	134	152
DEL PEAK 35(14Q32.32) MUTATED	48	14	7
DEL PEAK 35(14Q32.32) WILD-TYPE	159	120	145

Figure S175. Get High-res Image Gene #64: 'del_14q32.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q32.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S176. Gene #64: 'del_14q32.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	157	155	130
DEL PEAK 35(14Q32.32) MUTATED	6	15	7	41
DEL PEAK 35(14Q32.32) WILD-TYPE	45	142	148	89

Figure S176. Get High-res Image Gene #64: 'del_14q32.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S177. Gene #64: 'del_14q32.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	72	140	98	116	47
DEL PEAK 35(14Q32.32) MUTATED	11	8	28	5	15
DEL PEAK 35(14Q32.32) WILD-TYPE	61	132	70	111	32

Figure S177. Get High-res Image Gene #64: 'del_14q32.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_15q15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S178. Gene #65: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 36(15Q15.1) MUTATED	49	35	21	19
DEL PEAK 36(15Q15.1) WILD-TYPE	106	100	168	24

Figure S178. Get High-res Image Gene #65: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.03

Table S179. Gene #66: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 37(16Q23.1) MUTATED	16	40	28	14
DEL PEAK 37(16Q23.1) WILD-TYPE	139	95	161	29

Figure S179. Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S180. Gene #66: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 37(16Q23.1) MUTATED	5	17	10	30	27	6	3
DEL PEAK 37(16Q23.1) WILD-TYPE	79	62	86	62	51	69	15

Figure S180. Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S181. Gene #66: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	207	134	152
DEL PEAK 37(16Q23.1) MUTATED	63	19	12
DEL PEAK 37(16Q23.1) WILD-TYPE	144	115	140

Figure S181. Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S182. Gene #66: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	157	155	130
DEL PEAK 37(16Q23.1) MUTATED	13	21	13	47
DEL PEAK 37(16Q23.1) WILD-TYPE	38	136	142	83

Figure S182. Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S183. Gene #66: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	72	140	98	116	47
DEL PEAK 37(16Q23.1) MUTATED	12	16	36	15	9
DEL PEAK 37(16Q23.1) WILD-TYPE	60	124	62	101	38

Figure S183. Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q23.3' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.024

Table S184. Gene #67: 'del_16q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 38(16Q23.3) MUTATED	19	42	29	15
DEL PEAK 38(16Q23.3) WILD-TYPE	136	93	160	28

Figure S184. Get High-res Image Gene #67: 'del_16q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S185. Gene #67: 'del_16q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 38(16Q23.3) MUTATED	6	16	8	33	27	11	4
DEL PEAK 38(16Q23.3) WILD-TYPE	78	63	88	59	51	64	14

Figure S185. Get High-res Image Gene #67: 'del_16q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S186. Gene #67: 'del_16q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	207	134	152
DEL PEAK 38(16Q23.3) MUTATED	63	22	15
DEL PEAK 38(16Q23.3) WILD-TYPE	144	112	137

Figure S186. Get High-res Image Gene #67: 'del_16q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S187. Gene #67: 'del_16q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	157	155	130
DEL PEAK 38(16Q23.3) MUTATED	13	25	14	48
DEL PEAK 38(16Q23.3) WILD-TYPE	38	132	141	82

Figure S187. Get High-res Image Gene #67: 'del_16q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.047

Table S188. Gene #67: 'del_16q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	72	140	98	116	47
DEL PEAK 38(16Q23.3) MUTATED	14	17	37	17	9
DEL PEAK 38(16Q23.3) WILD-TYPE	58	123	61	99	38

Figure S188. Get High-res Image Gene #67: 'del_16q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S189. Gene #68: 'del_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 39(17P11.2) MUTATED	41	37	13	8
DEL PEAK 39(17P11.2) WILD-TYPE	114	98	176	35

Figure S189. Get High-res Image Gene #68: 'del_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q25.3' versus 'METHLYATION_CNMF'

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

Table S190. Gene #69: 'del_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 40(17Q25.3) MUTATED	3	8	10	22	19	4	5
DEL PEAK 40(17Q25.3) WILD-TYPE	81	71	86	70	59	71	13

Figure S190. Get High-res Image Gene #69: 'del_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S191. Gene #70: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 41(18Q21.2) MUTATED	122	80	44	22
DEL PEAK 41(18Q21.2) WILD-TYPE	33	55	145	21

Figure S191. Get High-res Image Gene #70: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S192. Gene #70: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 41(18Q21.2) MUTATED	43	56	65	63	5	26	10
DEL PEAK 41(18Q21.2) WILD-TYPE	41	23	31	29	73	49	8

Figure S192. Get High-res Image Gene #70: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S193. Gene #70: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	157	155	130
DEL PEAK 41(18Q21.2) MUTATED	38	97	78	39
DEL PEAK 41(18Q21.2) WILD-TYPE	13	60	77	91

Figure S193. Get High-res Image Gene #70: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.024

Table S194. Gene #70: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 41(18Q21.2) MUTATED	111	86	69
DEL PEAK 41(18Q21.2) WILD-TYPE	79	56	117

Figure S194. Get High-res Image Gene #70: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.053

Table S195. Gene #70: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	72	140	98	116	47
DEL PEAK 41(18Q21.2) MUTATED	39	76	53	69	9
DEL PEAK 41(18Q21.2) WILD-TYPE	33	64	45	47	38

Figure S195. Get High-res Image Gene #70: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_18q23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S196. Gene #71: 'del_18q23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 42(18Q23) MUTATED	128	89	48	23
DEL PEAK 42(18Q23) WILD-TYPE	27	46	141	20

Figure S196. Get High-res Image Gene #71: 'del_18q23' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S197. Gene #71: 'del_18q23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 42(18Q23) MUTATED	45	57	71	70	9	25	11
DEL PEAK 42(18Q23) WILD-TYPE	39	22	25	22	69	50	7

Figure S197. Get High-res Image Gene #71: 'del_18q23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S198. Gene #71: 'del_18q23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	157	155	130
DEL PEAK 42(18Q23) MUTATED	39	103	83	46
DEL PEAK 42(18Q23) WILD-TYPE	12	54	72	84

Figure S198. Get High-res Image Gene #71: 'del_18q23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S199. Gene #71: 'del_18q23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 42(18Q23) MUTATED	119	92	75
DEL PEAK 42(18Q23) WILD-TYPE	71	50	111

Figure S199. Get High-res Image Gene #71: 'del_18q23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S200. Gene #71: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	72	140	98	116	47
DEL PEAK 42(18Q23) MUTATED	45	84	57	68	9
DEL PEAK 42(18Q23) WILD-TYPE	27	56	41	48	38

Figure S200. Get High-res Image Gene #71: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S201. Gene #72: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 43(19P13.3) MUTATED	77	55	27	16
DEL PEAK 43(19P13.3) WILD-TYPE	78	80	162	27

Figure S201. Get High-res Image Gene #72: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

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

Table S202. Gene #72: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 43(19P13.3) MUTATED	17	28	49	41	14	21	5
DEL PEAK 43(19P13.3) WILD-TYPE	67	51	47	51	64	54	13

Figure S202. Get High-res Image Gene #72: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.12

Table S203. Gene #72: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 43(19P13.3) MUTATED	72	59	41
DEL PEAK 43(19P13.3) WILD-TYPE	118	83	145

Figure S203. Get High-res Image Gene #72: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S204. Gene #72: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	72	140	98	116	47
DEL PEAK 43(19P13.3) MUTATED	28	51	24	51	3
DEL PEAK 43(19P13.3) WILD-TYPE	44	89	74	65	44

Figure S204. Get High-res Image Gene #72: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19q13.43' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S205. Gene #73: 'del_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 44(19Q13.43) MUTATED	45	38	9	5
DEL PEAK 44(19Q13.43) WILD-TYPE	110	97	180	38

Figure S205. Get High-res Image Gene #73: 'del_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.43' versus 'METHLYATION_CNMF'

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

Table S206. Gene #73: 'del_19q13.43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 44(19Q13.43) MUTATED	7	18	27	30	5	6	4
DEL PEAK 44(19Q13.43) WILD-TYPE	77	61	69	62	73	69	14

Figure S206. Get High-res Image Gene #73: 'del_19q13.43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S207. Gene #74: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 45(21Q22.3) MUTATED	88	73	28	19
DEL PEAK 45(21Q22.3) WILD-TYPE	67	62	161	24

Figure S207. Get High-res Image Gene #74: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S208. Gene #74: 'del_21q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 45(21Q22.3) MUTATED	24	35	54	53	12	19	11
DEL PEAK 45(21Q22.3) WILD-TYPE	60	44	42	39	66	56	7

Figure S208. Get High-res Image Gene #74: 'del_21q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.053

Table S209. Gene #74: 'del_21q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 45(21Q22.3) MUTATED	88	68	51
DEL PEAK 45(21Q22.3) WILD-TYPE	102	74	135

Figure S209. Get High-res Image Gene #74: 'del_21q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_21q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.069

Table S210. Gene #74: 'del_21q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	72	140	98	116	47
DEL PEAK 45(21Q22.3) MUTATED	39	60	39	49	6
DEL PEAK 45(21Q22.3) WILD-TYPE	33	80	59	67	41

Figure S210. Get High-res Image Gene #74: 'del_21q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xp22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S211. Gene #75: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 46(XP22.2) MUTATED	60	62	26	9
DEL PEAK 46(XP22.2) WILD-TYPE	95	73	163	34

Figure S211. Get High-res Image Gene #75: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp22.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S212. Gene #75: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 46(XP22.2) MUTATED	14	25	35	50	17	9	7
DEL PEAK 46(XP22.2) WILD-TYPE	70	54	61	42	61	66	11

Figure S212. Get High-res Image Gene #75: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S213. Gene #76: 'del_xp21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 47(XP21.3) MUTATED	66	59	27	7
DEL PEAK 47(XP21.3) WILD-TYPE	89	76	162	36

Figure S213. Get High-res Image Gene #76: 'del_xp21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S214. Gene #76: 'del_xp21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 47(XP21.3) MUTATED	16	26	38	45	15	12	7
DEL PEAK 47(XP21.3) WILD-TYPE	68	53	58	47	63	63	11

Figure S214. Get High-res Image Gene #76: 'del_xp21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq21.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S215. Gene #77: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	135	189	43
DEL PEAK 48(XQ21.33) MUTATED	34	34	10	2
DEL PEAK 48(XQ21.33) WILD-TYPE	121	101	179	41

Figure S215. Get High-res Image Gene #77: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq21.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S216. Gene #77: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	79	96	92	78	75	18
DEL PEAK 48(XQ21.33) MUTATED	4	16	15	31	11	0	3
DEL PEAK 48(XQ21.33) WILD-TYPE	80	63	81	61	67	75	15

Figure S216. Get High-res Image Gene #77: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq21.33' versus 'MIRSEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.098

Table S217. Gene #77: 'del_xq21.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	221	152	145
DEL PEAK 48(XQ21.33) MUTATED	51	15	13
DEL PEAK 48(XQ21.33) WILD-TYPE	170	137	132

Figure S217. Get High-res Image Gene #77: 'del_xq21.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = HNSC-TP.transferedmergedcluster.txt
Number of patients = 522
Number of significantly focal cnvs = 77
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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