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

Head and Neck Squamous Cell Carcinoma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1222SHC

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 73 focal events and 10 molecular subtypes across 511 patients, 197 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_2q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_2q31.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3q26.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5p15.33 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_5p12 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', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8p11.23 cnv correlated to 'CN_CNMF'.
amp_8q11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_9p24.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_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_11p13 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'.
amp_13q22.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_13q34 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_17q12 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_18p11.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_18q11.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q21.2 cnv correlated to 'MIRSEQ_CNMF'.
del_2q22.1 cnv correlated to 'METHLYATION_CNMF'.
del_2q36.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_3p24.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4p15.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q35.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_5q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q15 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q35.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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_CHIERARCHICAL'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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' and 'METHLYATION_CNMF'.
del_10p11.21 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_11p15.5 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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_14q32.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_15q15.1 cnv correlated to 'CN_CNMF'.
del_16q23.3 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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_CHIERARCHICAL'.
del_18q23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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_CHIERARCHICAL'.
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 73 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, 197 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
amp 3q26 33	372 (73%)	139	1e-05 (0.0073)	1e-05 (0.0073)	0.13 (1.00)	0.311 (1.00)	1e-05 (0.0073)	7e-05 (0.0392)	0.00018 (0.0986)	0.216 (1.00)	0.0441 (1.00)	4e-05 (0.0228)
amp 8q24 21	379 (74%)	132	1e-05 (0.0073)	1e-05 (0.0073)	0.317 (1.00)	0.447 (1.00)	0.0131 (1.00)	2e-05 (0.0118)	0.064 (1.00)	0.00025 (0.135)	0.00203 (1.00)	8e-05 (0.0447)
del 1p36 21	94 (18%)	417	1e-05 (0.0073)	1e-05 (0.0073)	0.00082 (0.428)	0.00572 (1.00)	1e-05 (0.0073)	6e-05 (0.0338)	0.00093 (0.482)	0.0675 (1.00)	0.0421 (1.00)	1e-05 (0.0073)
del 3p24 1	357 (70%)	154	1e-05 (0.0073)	1e-05 (0.0073)	0.417 (1.00)	0.115 (1.00)	0.0016 (0.805)	2e-05 (0.0118)	0.00771 (1.00)	1e-05 (0.0073)	0.112 (1.00)	1e-05 (0.0073)
del 3p12 1	332 (65%)	179	1e-05 (0.0073)	1e-05 (0.0073)	0.83 (1.00)	0.901 (1.00)	0.0199 (1.00)	5e-05 (0.0283)	0.0752 (1.00)	0.00011 (0.0607)	0.34 (1.00)	1e-05 (0.0073)
del 5q11 2	209 (41%)	302	1e-05 (0.0073)	1e-05 (0.0073)	0.132 (1.00)	0.486 (1.00)	0.0985 (1.00)	1e-05 (0.0073)	0.187 (1.00)	1e-05 (0.0073)	0.383 (1.00)	1e-05 (0.0073)
del 5q15	219 (43%)	292	1e-05 (0.0073)	1e-05 (0.0073)	0.144 (1.00)	0.434 (1.00)	0.107 (1.00)	1e-05 (0.0073)	0.235 (1.00)	2e-05 (0.0118)	0.622 (1.00)	1e-05 (0.0073)
del 5q35 3	195 (38%)	316	1e-05 (0.0073)	1e-05 (0.0073)	0.24 (1.00)	0.72 (1.00)	0.0193 (1.00)	1e-05 (0.0073)	0.343 (1.00)	1e-05 (0.0073)	0.454 (1.00)	1e-05 (0.0073)
del 8p23 2	294 (58%)	217	1e-05 (0.0073)	1e-05 (0.0073)	0.279 (1.00)	0.325 (1.00)	0.00121 (0.615)	5e-05 (0.0283)	0.00218 (1.00)	0.00068 (0.356)	0.00022 (0.119)	1e-05 (0.0073)
del 9p23	233 (46%)	278	1e-05 (0.0073)	1e-05 (0.0073)	0.281 (1.00)	0.113 (1.00)	0.821 (1.00)	0.00024 (0.13)	0.77 (1.00)	0.00029 (0.156)	0.252 (1.00)	1e-05 (0.0073)
del 9p21 3	292 (57%)	219	1e-05 (0.0073)	1e-05 (0.0073)	0.671 (1.00)	0.361 (1.00)	0.147 (1.00)	1e-05 (0.0073)	1 (1.00)	1e-05 (0.0073)	0.108 (1.00)	1e-05 (0.0073)
del 11p15 5	156 (31%)	355	1e-05 (0.0073)	1e-05 (0.0073)	0.866 (1.00)	0.281 (1.00)	8e-05 (0.0447)	0.00267 (1.00)	1e-05 (0.0073)	0.0179 (1.00)	0.159 (1.00)	3e-05 (0.0172)
del 18q21 2	259 (51%)	252	1e-05 (0.0073)	1e-05 (0.0073)	0.899 (1.00)	0.379 (1.00)	0.00695 (1.00)	1e-05 (0.0073)	0.0181 (1.00)	1e-05 (0.0073)	0.193 (1.00)	1e-05 (0.0073)
del 18q23	278 (54%)	233	1e-05 (0.0073)	1e-05 (0.0073)	0.256 (1.00)	0.245 (1.00)	0.00565 (1.00)	1e-05 (0.0073)	0.0237 (1.00)	1e-05 (0.0073)	0.075 (1.00)	1e-05 (0.0073)
amp 2q11 2	104 (20%)	407	1e-05 (0.0073)	1e-05 (0.0073)	0.505 (1.00)	0.542 (1.00)	0.051 (1.00)	0.00034 (0.182)	0.0666 (1.00)	0.00105 (0.538)	0.145 (1.00)	1e-05 (0.0073)
amp 7p11 2	215 (42%)	296	1e-05 (0.0073)	1e-05 (0.0073)	0.997 (1.00)	0.671 (1.00)	0.0481 (1.00)	0.0105 (1.00)	0.717 (1.00)	1e-05 (0.0073)	0.266 (1.00)	0.0001 (0.0554)
amp 7q21 3	164 (32%)	347	1e-05 (0.0073)	1e-05 (0.0073)	0.332 (1.00)	0.441 (1.00)	0.307 (1.00)	0.282 (1.00)	0.0861 (1.00)	0.00027 (0.146)	0.288 (1.00)	0.00021 (0.114)
amp 8q11 21	305 (60%)	206	1e-05 (0.0073)	1e-05 (0.0073)	0.0977 (1.00)	0.634 (1.00)	0.00184 (0.922)	0.00011 (0.0607)	0.0326 (1.00)	0.00028 (0.151)	0.0479 (1.00)	0.00103 (0.529)
amp 18p11 31	152 (30%)	359	1e-05 (0.0073)	1e-05 (0.0073)	0.523 (1.00)	0.516 (1.00)	0.0833 (1.00)	1e-05 (0.0073)	0.77 (1.00)	0.0005 (0.266)	0.572 (1.00)	1e-05 (0.0073)
del 4p15 2	201 (39%)	310	1e-05 (0.0073)	1e-05 (0.0073)	0.0112 (1.00)	0.337 (1.00)	9e-05 (0.05)	0.00055 (0.291)	0.052 (1.00)	0.00627 (1.00)	0.00376 (1.00)	1e-05 (0.0073)
del 10q23 31	134 (26%)	377	2e-05 (0.0118)	1e-05 (0.0073)	0.133 (1.00)	0.978 (1.00)	9e-05 (0.05)	1e-05 (0.0073)	0.00734 (1.00)	0.337 (1.00)	0.0461 (1.00)	0.0558 (1.00)
del 11q23 1	239 (47%)	272	1e-05 (0.0073)	1e-05 (0.0073)	0.0877 (1.00)	0.165 (1.00)	1e-05 (0.0073)	1e-05 (0.0073)	0.00206 (1.00)	0.0329 (1.00)	0.0227 (1.00)	0.00906 (1.00)
del 13q14 2	209 (41%)	302	1e-05 (0.0073)	1e-05 (0.0073)	0.111 (1.00)	0.566 (1.00)	1e-05 (0.0073)	1e-05 (0.0073)	0.0037 (1.00)	0.422 (1.00)	0.199 (1.00)	0.00079 (0.413)
del 14q32 32	73 (14%)	438	0.00019 (0.104)	1e-05 (0.0073)	0.0177 (1.00)	0.467 (1.00)	2e-05 (0.0118)	1e-05 (0.0073)	0.003 (1.00)	0.0175 (1.00)	0.0193 (1.00)	0.00364 (1.00)
del 21q22 3	195 (38%)	316	1e-05 (0.0073)	1e-05 (0.0073)	0.612 (1.00)	0.935 (1.00)	0.0449 (1.00)	0.0653 (1.00)	0.609 (1.00)	3e-05 (0.0172)	0.914 (1.00)	0.00021 (0.114)
amp 2q31 2	108 (21%)	403	1e-05 (0.0073)	1e-05 (0.0073)	0.239 (1.00)	0.317 (1.00)	0.19 (1.00)	0.0127 (1.00)	0.198 (1.00)	0.00583 (1.00)	0.334 (1.00)	3e-05 (0.0172)
del 1p13 2	127 (25%)	384	1e-05 (0.0073)	1e-05 (0.0073)	0.0239 (1.00)	0.00747 (1.00)	0.0263 (1.00)	0.377 (1.00)	0.0182 (1.00)	0.00053 (0.281)	0.0982 (1.00)	2e-05 (0.0118)
del 4q22 1	164 (32%)	347	1e-05 (0.0073)	1e-05 (0.0073)	0.247 (1.00)	0.077 (1.00)	0.00967 (1.00)	0.00272 (1.00)	0.215 (1.00)	0.0171 (1.00)	0.486 (1.00)	1e-05 (0.0073)
del 13q12 11	224 (44%)	287	1e-05 (0.0073)	1e-05 (0.0073)	0.148 (1.00)	0.315 (1.00)	0.0246 (1.00)	4e-05 (0.0228)	0.832 (1.00)	0.0184 (1.00)	0.589 (1.00)	0.00126 (0.636)
del 16q23 3	102 (20%)	409	0.00124 (0.629)	1e-05 (0.0073)	0.16 (1.00)	0.232 (1.00)	1e-05 (0.0073)	1e-05 (0.0073)	0.00432 (1.00)	0.143 (1.00)	0.00623 (1.00)	0.0518 (1.00)
del 19p13 3	165 (32%)	346	1e-05 (0.0073)	1e-05 (0.0073)	0.448 (1.00)	0.462 (1.00)	0.0189 (1.00)	0.0161 (1.00)	0.223 (1.00)	6e-05 (0.0338)	0.538 (1.00)	0.00088 (0.458)
del xq21 33	74 (14%)	437	2e-05 (0.0118)	1e-05 (0.0073)	0.491 (1.00)	0.171 (1.00)	0.00087 (0.453)	0.0143 (1.00)	0.00011 (0.0607)	0.0712 (1.00)	0.217 (1.00)	0.00064 (0.336)
amp 5p15 33	231 (45%)	280	1e-05 (0.0073)	1e-05 (0.0073)	0.855 (1.00)	0.828 (1.00)	0.157 (1.00)	0.177 (1.00)	0.7 (1.00)	0.0799 (1.00)	0.965 (1.00)	0.804 (1.00)
amp 5p12	203 (40%)	308	1e-05 (0.0073)	4e-05 (0.0228)	0.582 (1.00)	0.189 (1.00)	0.306 (1.00)	0.11 (1.00)	0.583 (1.00)	0.0346 (1.00)	0.993 (1.00)	0.739 (1.00)
amp 6p12 1	107 (21%)	404	1e-05 (0.0073)	2e-05 (0.0118)	0.459 (1.00)	0.952 (1.00)	0.857 (1.00)	0.0143 (1.00)	0.454 (1.00)	0.00124 (0.629)	0.929 (1.00)	0.0571 (1.00)
amp 6q12	92 (18%)	419	1e-05 (0.0073)	0.00029 (0.156)	0.275 (1.00)	0.901 (1.00)	0.868 (1.00)	0.161 (1.00)	0.301 (1.00)	0.221 (1.00)	0.809 (1.00)	0.588 (1.00)
amp 9p24 1	122 (24%)	389	1e-05 (0.0073)	2e-05 (0.0118)	0.137 (1.00)	0.25 (1.00)	0.00266 (1.00)	0.00103 (0.529)	0.0347 (1.00)	0.0039 (1.00)	0.163 (1.00)	0.00432 (1.00)
amp 9p23	121 (24%)	390	1e-05 (0.0073)	2e-05 (0.0118)	0.386 (1.00)	0.424 (1.00)	0.00361 (1.00)	0.00379 (1.00)	0.0601 (1.00)	0.00688 (1.00)	0.274 (1.00)	0.0483 (1.00)
amp 11q13 3	223 (44%)	288	1e-05 (0.0073)	1e-05 (0.0073)	0.834 (1.00)	0.728 (1.00)	0.169 (1.00)	0.13 (1.00)	0.413 (1.00)	0.0076 (1.00)	0.257 (1.00)	0.22 (1.00)
amp 12p13 33	162 (32%)	349	1e-05 (0.0073)	1e-05 (0.0073)	0.0418 (1.00)	0.521 (1.00)	0.00919 (1.00)	0.00218 (1.00)	0.0224 (1.00)	0.0202 (1.00)	0.167 (1.00)	0.00259 (1.00)
amp 13q22 1	104 (20%)	407	1e-05 (0.0073)	2e-05 (0.0118)	0.148 (1.00)	0.156 (1.00)	0.325 (1.00)	0.288 (1.00)	0.44 (1.00)	0.0272 (1.00)	0.84 (1.00)	0.0264 (1.00)
amp 13q34	106 (21%)	405	1e-05 (0.0073)	6e-05 (0.0338)	0.253 (1.00)	0.289 (1.00)	0.202 (1.00)	0.281 (1.00)	0.352 (1.00)	0.012 (1.00)	0.338 (1.00)	0.0356 (1.00)
amp 17q12	88 (17%)	423	1e-05 (0.0073)	1e-05 (0.0073)	0.186 (1.00)	0.719 (1.00)	0.0107 (1.00)	0.0189 (1.00)	0.00965 (1.00)	0.00052 (0.277)	1 (1.00)	0.00745 (1.00)
amp 18q11 2	101 (20%)	410	1e-05 (0.0073)	8e-05 (0.0447)	0.518 (1.00)	0.205 (1.00)	0.368 (1.00)	0.014 (1.00)	0.0373 (1.00)	0.0537 (1.00)	0.823 (1.00)	0.02 (1.00)
amp 20p12 2	189 (37%)	322	4e-05 (0.0228)	5e-05 (0.0283)	0.873 (1.00)	0.934 (1.00)	0.0891 (1.00)	0.00938 (1.00)	0.151 (1.00)	0.00896 (1.00)	0.0228 (1.00)	0.0411 (1.00)
amp 20q11 22	224 (44%)	287	1e-05 (0.0073)	2e-05 (0.0118)	0.503 (1.00)	0.833 (1.00)	0.105 (1.00)	0.0106 (1.00)	0.471 (1.00)	0.0189 (1.00)	0.234 (1.00)	0.064 (1.00)
amp xq28	145 (28%)	366	1e-05 (0.0073)	2e-05 (0.0118)	0.639 (1.00)	0.199 (1.00)	0.304 (1.00)	0.147 (1.00)	0.156 (1.00)	0.0295 (1.00)	0.949 (1.00)	0.0242 (1.00)
del 2q36 2	152 (30%)	359	1e-05 (0.0073)	1e-05 (0.0073)	0.0929 (1.00)	0.856 (1.00)	0.0107 (1.00)	0.0138 (1.00)	0.0901 (1.00)	0.033 (1.00)	0.129 (1.00)	0.00981 (1.00)
del 4q35 2	206 (40%)	305	1e-05 (0.0073)	4e-05 (0.0228)	0.842 (1.00)	0.187 (1.00)	0.012 (1.00)	0.118 (1.00)	0.323 (1.00)	0.00102 (0.526)	0.414 (1.00)	0.00055 (0.291)
del 6p25 3	93 (18%)	418	0.00034 (0.182)	1e-05 (0.0073)	0.0431 (1.00)	0.0106 (1.00)	0.00226 (1.00)	0.0967 (1.00)	0.193 (1.00)	0.396 (1.00)	0.683 (1.00)	0.065 (1.00)
del 9q21 11	103 (20%)	408	1e-05 (0.0073)	1e-05 (0.0073)	0.983 (1.00)	0.237 (1.00)	0.854 (1.00)	0.026 (1.00)	0.732 (1.00)	0.00054 (0.286)	0.48 (1.00)	0.00267 (1.00)
del 10p15 3	165 (32%)	346	1e-05 (0.0073)	1e-05 (0.0073)	0.608 (1.00)	0.575 (1.00)	0.127 (1.00)	0.153 (1.00)	0.144 (1.00)	0.0272 (1.00)	0.0986 (1.00)	0.00102 (0.526)
del 10p11 21	152 (30%)	359	1e-05 (0.0073)	1e-05 (0.0073)	0.448 (1.00)	0.173 (1.00)	0.277 (1.00)	0.746 (1.00)	0.0166 (1.00)	0.0457 (1.00)	0.133 (1.00)	0.00118 (0.601)
del 12q24 33	60 (12%)	451	2e-05 (0.0118)	2e-05 (0.0118)	0.616 (1.00)	0.457 (1.00)	0.867 (1.00)	0.562 (1.00)	0.489 (1.00)	0.399 (1.00)	0.0626 (1.00)	0.433 (1.00)
del 19q13 43	94 (18%)	417	1e-05 (0.0073)	1e-05 (0.0073)	0.331 (1.00)	0.589 (1.00)	0.882 (1.00)	0.344 (1.00)	0.624 (1.00)	0.0121 (1.00)	0.609 (1.00)	0.0592 (1.00)
del xp22 2	152 (30%)	359	1e-05 (0.0073)	1e-05 (0.0073)	0.318 (1.00)	0.00223 (1.00)	0.0859 (1.00)	0.00573 (1.00)	0.0171 (1.00)	0.0988 (1.00)	0.392 (1.00)	0.0135 (1.00)
del xp21 3	154 (30%)	357	1e-05 (0.0073)	1e-05 (0.0073)	0.56 (1.00)	0.0549 (1.00)	0.468 (1.00)	0.0135 (1.00)	0.208 (1.00)	0.0772 (1.00)	0.742 (1.00)	0.00884 (1.00)
amp 8p11 23	156 (31%)	355	1e-05 (0.0073)	0.00646 (1.00)	0.81 (1.00)	0.873 (1.00)	0.125 (1.00)	0.0115 (1.00)	0.00314 (1.00)	0.0508 (1.00)	0.294 (1.00)	0.0376 (1.00)
amp 9p13 3	135 (26%)	376	1e-05 (0.0073)	0.0029 (1.00)	0.485 (1.00)	0.122 (1.00)	0.00089 (0.462)	0.0159 (1.00)	0.00326 (1.00)	0.0373 (1.00)	0.839 (1.00)	0.212 (1.00)
amp 9q34 3	174 (34%)	337	1e-05 (0.0073)	0.0172 (1.00)	0.238 (1.00)	0.0242 (1.00)	0.956 (1.00)	0.383 (1.00)	0.71 (1.00)	0.158 (1.00)	0.931 (1.00)	0.685 (1.00)
amp 11p13	101 (20%)	410	0.0002 (0.109)	0.00142 (0.716)	0.461 (1.00)	0.179 (1.00)	0.958 (1.00)	0.223 (1.00)	0.817 (1.00)	0.536 (1.00)	0.313 (1.00)	0.057 (1.00)
amp 12q15	101 (20%)	410	1e-05 (0.0073)	0.00058 (0.306)	0.0674 (1.00)	0.204 (1.00)	0.127 (1.00)	0.0677 (1.00)	0.92 (1.00)	0.153 (1.00)	1 (1.00)	0.393 (1.00)
del 2q21 2	73 (14%)	438	0.828 (1.00)	0.0108 (1.00)	0.703 (1.00)	0.21 (1.00)	0.0262 (1.00)	0.00671 (1.00)	0.00029 (0.156)	0.184 (1.00)	0.0657 (1.00)	0.0708 (1.00)
del 2q22 1	114 (22%)	397	0.0682 (1.00)	0.0001 (0.0554)	0.348 (1.00)	0.838 (1.00)	0.279 (1.00)	0.254 (1.00)	0.181 (1.00)	0.00865 (1.00)	0.896 (1.00)	0.134 (1.00)
del 7q36 1	127 (25%)	384	0.00014 (0.0769)	0.369 (1.00)	0.0445 (1.00)	0.676 (1.00)	0.771 (1.00)	0.706 (1.00)	0.624 (1.00)	0.312 (1.00)	0.743 (1.00)	0.761 (1.00)
del 9q34 3	76 (15%)	435	1e-05 (0.0073)	0.00109 (0.557)	0.612 (1.00)	0.368 (1.00)	0.44 (1.00)	0.0476 (1.00)	0.729 (1.00)	0.0217 (1.00)	0.202 (1.00)	0.0198 (1.00)
del 15q15 1	119 (23%)	392	1e-05 (0.0073)	0.202 (1.00)	0.671 (1.00)	0.411 (1.00)	0.0712 (1.00)	0.0823 (1.00)	0.801 (1.00)	0.511 (1.00)	0.69 (1.00)	0.17 (1.00)
del 17q25 3	68 (13%)	443	0.038 (1.00)	1e-05 (0.0073)	0.434 (1.00)	0.694 (1.00)	0.0127 (1.00)	0.00339 (1.00)	0.00367 (1.00)	0.0304 (1.00)	0.00489 (1.00)	0.103 (1.00)
amp 15q26 3	102 (20%)	409	0.00169 (0.848)	0.00874 (1.00)	0.456 (1.00)	0.328 (1.00)	0.604 (1.00)	0.982 (1.00)	0.339 (1.00)	0.0122 (1.00)	0.69 (1.00)	0.146 (1.00)
del 1q44	47 (9%)	464	0.00094 (0.486)	0.0168 (1.00)	0.731 (1.00)	0.908 (1.00)	0.0139 (1.00)	0.0042 (1.00)	0.0006 (0.316)	0.0478 (1.00)	0.023 (1.00)	0.277 (1.00)
del 7q31 1	74 (14%)	437	0.00621 (1.00)	0.175 (1.00)	0.572 (1.00)	0.381 (1.00)	0.514 (1.00)	0.217 (1.00)	0.874 (1.00)	0.332 (1.00)	0.568 (1.00)	0.846 (1.00)
del 14q11 2	72 (14%)	439	0.00342 (1.00)	0.0116 (1.00)	0.324 (1.00)	0.898 (1.00)	0.117 (1.00)	0.277 (1.00)	0.0347 (1.00)	0.0216 (1.00)	0.161 (1.00)	0.00929 (1.00)
del 22q13 31	84 (16%)	427	0.00113 (0.576)	0.0277 (1.00)	0.688 (1.00)	0.892 (1.00)	0.02 (1.00)	0.524 (1.00)	0.011 (1.00)	0.21 (1.00)	0.126 (1.00)	0.00188 (0.94)

'amp_2q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 1(2Q11.2) MUTATED	54	35	12	3
AMP PEAK 1(2Q11.2) WILD-TYPE	124	67	177	39

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 = 0.0073

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	82	76	96	87	78	74	18
AMP PEAK 1(2Q11.2) MUTATED	6	31	20	37	2	4	4
AMP PEAK 1(2Q11.2) WILD-TYPE	76	45	76	50	76	70	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 = 0.00034 (Fisher's exact test), Q value = 0.18

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_2q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S4. Gene #1: 'amp_2q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	99	128	79	108	57
AMP PEAK 1(2Q11.2) MUTATED	18	43	3	23	8
AMP PEAK 1(2Q11.2) WILD-TYPE	81	85	76	85	49

Figure S4. Get High-res Image Gene #1: 'amp_2q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_2q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S5. Gene #2: 'amp_2q31.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 2(2Q31.2) MUTATED	55	40	10	3
AMP PEAK 2(2Q31.2) WILD-TYPE	123	62	179	39

Figure S5. 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 = 0.0073

Table S6. 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	82	76	96	87	78	74	18
AMP PEAK 2(2Q31.2) MUTATED	8	25	18	46	5	3	3
AMP PEAK 2(2Q31.2) WILD-TYPE	74	51	78	41	73	71	15

Figure S6. Get High-res Image Gene #2: 'amp_2q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_2q31.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S7. Gene #2: 'amp_2q31.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	99	128	79	108	57
AMP PEAK 2(2Q31.2) MUTATED	21	42	3	27	9
AMP PEAK 2(2Q31.2) WILD-TYPE	78	86	76	81	48

Figure S7. Get High-res Image Gene #2: 'amp_2q31.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S8. Gene #3: 'amp_3q26.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 3(3Q26.33) MUTATED	149	97	96	30
AMP PEAK 3(3Q26.33) WILD-TYPE	29	5	93	12

Figure S8. 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 = 0.0073

Table S9. 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	82	76	96	87	78	74	18
AMP PEAK 3(3Q26.33) MUTATED	49	63	77	81	62	27	13
AMP PEAK 3(3Q26.33) WILD-TYPE	33	13	19	6	16	47	5

Figure S9. 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 = 0.0073

Table S10. 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 S10. Get High-res Image Gene #3: 'amp_3q26.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3q26.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.039

Table S11. 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 S11. Get High-res Image Gene #3: 'amp_3q26.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.099

Table S12. Gene #3: 'amp_3q26.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	216	146
AMP PEAK 3(3Q26.33) MUTATED	90	176	102
AMP PEAK 3(3Q26.33) WILD-TYPE	55	40	44

Figure S12. Get High-res Image Gene #3: 'amp_3q26.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_3q26.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.023

Table S13. Gene #3: 'amp_3q26.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	99	128	79	108	57
AMP PEAK 3(3Q26.33) MUTATED	58	109	48	82	39
AMP PEAK 3(3Q26.33) WILD-TYPE	41	19	31	26	18

Figure S13. Get High-res Image Gene #3: 'amp_3q26.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S14. Gene #4: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 4(5P15.33) MUTATED	111	66	39	15
AMP PEAK 4(5P15.33) WILD-TYPE	67	36	150	27

Figure S14. 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 = 0.0073

Table S15. 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	82	76	96	87	78	74	18
AMP PEAK 4(5P15.33) MUTATED	27	42	54	49	35	14	10
AMP PEAK 4(5P15.33) WILD-TYPE	55	34	42	38	43	60	8

Figure S15. Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S16. Gene #5: 'amp_5p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 5(5P12) MUTATED	97	58	33	15
AMP PEAK 5(5P12) WILD-TYPE	81	44	156	27

Figure S16. Get High-res Image Gene #5: 'amp_5p12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p12' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.023

Table S17. Gene #5: 'amp_5p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	82	76	96	87	78	74	18
AMP PEAK 5(5P12) MUTATED	21	38	48	43	28	15	10
AMP PEAK 5(5P12) WILD-TYPE	61	38	48	44	50	59	8

Figure S17. Get High-res Image Gene #5: 'amp_5p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S18. Gene #6: 'amp_6p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 6(6P12.1) MUTATED	52	29	14	12
AMP PEAK 6(6P12.1) WILD-TYPE	126	73	175	30

Figure S18. Get High-res Image Gene #6: 'amp_6p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p12.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S19. Gene #6: '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	82	76	96	87	78	74	18
AMP PEAK 6(6P12.1) MUTATED	10	25	32	22	7	7	4
AMP PEAK 6(6P12.1) WILD-TYPE	72	51	64	65	71	67	14

Figure S19. Get High-res Image Gene #6: 'amp_6p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S20. Gene #7: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 7(6Q12) MUTATED	47	23	10	12
AMP PEAK 7(6Q12) WILD-TYPE	131	79	179	30

Figure S20. Get High-res Image Gene #7: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q12' versus 'METHLYATION_CNMF'

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

Table S21. Gene #7: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	82	76	96	87	78	74	18
AMP PEAK 7(6Q12) MUTATED	10	18	26	22	4	8	4
AMP PEAK 7(6Q12) WILD-TYPE	72	58	70	65	74	66	14

Figure S21. Get High-res Image Gene #7: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S22. Gene #8: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 8(7P11.2) MUTATED	106	50	41	18
AMP PEAK 8(7P11.2) WILD-TYPE	72	52	148	24

Figure S22. Get High-res Image Gene #8: '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 = 0.0073

Table S23. Gene #8: '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	82	76	96	87	78	74	18
AMP PEAK 8(7P11.2) MUTATED	29	41	52	53	6	23	11
AMP PEAK 8(7P11.2) WILD-TYPE	53	35	44	34	72	51	7

Figure S23. Get High-res Image Gene #8: '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 = 0.0073

Table S24. Gene #8: 'amp_7p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	198	124	185
AMP PEAK 8(7P11.2) MUTATED	94	71	47
AMP PEAK 8(7P11.2) WILD-TYPE	104	53	138

Figure S24. Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.055

Table S25. Gene #8: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	99	128	79	108	57
AMP PEAK 8(7P11.2) MUTATED	45	62	15	48	27
AMP PEAK 8(7P11.2) WILD-TYPE	54	66	64	60	30

Figure S25. Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S26. Gene #9: 'amp_7q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 9(7Q21.3) MUTATED	84	46	22	12
AMP PEAK 9(7Q21.3) WILD-TYPE	94	56	167	30

Figure S26. Get High-res Image Gene #9: '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 = 0.0073

Table S27. Gene #9: '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	82	76	96	87	78	74	18
AMP PEAK 9(7Q21.3) MUTATED	14	34	29	58	9	13	7
AMP PEAK 9(7Q21.3) WILD-TYPE	68	42	67	29	69	61	11

Figure S27. Get High-res Image Gene #9: 'amp_7q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.15

Table S28. Gene #9: 'amp_7q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	198	124	185
AMP PEAK 9(7Q21.3) MUTATED	63	56	42
AMP PEAK 9(7Q21.3) WILD-TYPE	135	68	143

Figure S28. Get High-res Image Gene #9: 'amp_7q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.11

Table S29. Gene #9: 'amp_7q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	99	128	79	108	57
AMP PEAK 9(7Q21.3) MUTATED	29	59	13	35	14
AMP PEAK 9(7Q21.3) WILD-TYPE	70	69	66	73	43

Figure S29. Get High-res Image Gene #9: 'amp_7q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S30. Gene #10: 'amp_8p11.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 10(8P11.23) MUTATED	45	54	45	12
AMP PEAK 10(8P11.23) WILD-TYPE	133	48	144	30

Figure S30. Get High-res Image Gene #10: '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 = 0.0073

Table S31. Gene #11: 'amp_8q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 11(8Q11.21) MUTATED	135	55	81	34
AMP PEAK 11(8Q11.21) WILD-TYPE	43	47	108	8

Figure S31. Get High-res Image Gene #11: '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 = 0.0073

Table S32. Gene #11: '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	82	76	96	87	78	74	18
AMP PEAK 11(8Q11.21) MUTATED	52	43	80	48	29	40	13
AMP PEAK 11(8Q11.21) WILD-TYPE	30	33	16	39	49	34	5

Figure S32. Get High-res Image Gene #11: 'amp_8q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.061

Table S33. Gene #11: '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 11(8Q11.21) MUTATED	28	112	95	59
AMP PEAK 11(8Q11.21) WILD-TYPE	23	45	60	71

Figure S33. Get High-res Image Gene #11: 'amp_8q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.15

Table S34. Gene #11: 'amp_8q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	198	124	185
AMP PEAK 11(8Q11.21) MUTATED	139	71	93
AMP PEAK 11(8Q11.21) WILD-TYPE	59	53	92

Figure S34. Get High-res Image Gene #11: 'amp_8q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S35. Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 12(8Q24.21) MUTATED	167	72	105	35
AMP PEAK 12(8Q24.21) WILD-TYPE	11	30	84	7

Figure S35. Get High-res Image Gene #12: '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 = 0.0073

Table S36. Gene #12: '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	82	76	96	87	78	74	18
AMP PEAK 12(8Q24.21) MUTATED	63	58	87	69	35	50	17
AMP PEAK 12(8Q24.21) WILD-TYPE	19	18	9	18	43	24	1

Figure S36. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S37. Gene #12: '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 12(8Q24.21) MUTATED	37	130	122	77
AMP PEAK 12(8Q24.21) WILD-TYPE	14	27	33	53

Figure S37. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.14

Table S38. Gene #12: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	198	124	185
AMP PEAK 12(8Q24.21) MUTATED	162	96	118
AMP PEAK 12(8Q24.21) WILD-TYPE	36	28	67

Figure S38. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.045

Table S39. Gene #12: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	99	128	79	108	57
AMP PEAK 12(8Q24.21) MUTATED	81	92	42	88	47
AMP PEAK 12(8Q24.21) WILD-TYPE	18	36	37	20	10

Figure S39. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9p24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S40. Gene #13: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 13(9P24.1) MUTATED	29	13	42	38
AMP PEAK 13(9P24.1) WILD-TYPE	149	89	147	4

Figure S40. Get High-res Image Gene #13: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p24.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S41. Gene #13: '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	82	76	96	87	78	74	18
AMP PEAK 13(9P24.1) MUTATED	15	8	21	17	20	38	3
AMP PEAK 13(9P24.1) WILD-TYPE	67	68	75	70	58	36	15

Figure S41. Get High-res Image Gene #13: 'amp_9p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S42. Gene #14: 'amp_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 14(9P23) MUTATED	30	14	40	37
AMP PEAK 14(9P23) WILD-TYPE	148	88	149	5

Figure S42. Get High-res Image Gene #14: 'amp_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p23' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S43. Gene #14: 'amp_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	82	76	96	87	78	74	18
AMP PEAK 14(9P23) MUTATED	16	7	20	19	19	37	3
AMP PEAK 14(9P23) WILD-TYPE	66	69	76	68	59	37	15

Figure S43. Get High-res Image Gene #14: 'amp_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S44. Gene #15: 'amp_9p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 15(9P13.3) MUTATED	39	24	37	35
AMP PEAK 15(9P13.3) WILD-TYPE	139	78	152	7

Figure S44. Get High-res Image Gene #15: '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 = 0.0073

Table S45. Gene #16: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 16(9Q34.3) MUTATED	55	47	38	34
AMP PEAK 16(9Q34.3) WILD-TYPE	123	55	151	8

Figure S45. Get High-res Image Gene #16: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11p13' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.11

Table S46. Gene #17: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 17(11P13) MUTATED	50	13	25	13
AMP PEAK 17(11P13) WILD-TYPE	128	89	164	29

Figure S46. Get High-res Image Gene #17: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S47. Gene #18: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 18(11Q13.3) MUTATED	133	39	37	14
AMP PEAK 18(11Q13.3) WILD-TYPE	45	63	152	28

Figure S47. Get High-res Image Gene #18: '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 = 0.0073

Table S48. Gene #18: '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	82	76	96	87	78	74	18
AMP PEAK 18(11Q13.3) MUTATED	30	30	62	52	15	20	14
AMP PEAK 18(11Q13.3) WILD-TYPE	52	46	34	35	63	54	4

Figure S48. Get High-res Image Gene #18: '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 = 0.0073

Table S49. Gene #19: 'amp_12p13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 19(12P13.33) MUTATED	73	56	19	14
AMP PEAK 19(12P13.33) WILD-TYPE	105	46	170	28

Figure S49. Get High-res Image Gene #19: '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 = 0.0073

Table S50. Gene #19: '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	82	76	96	87	78	74	18
AMP PEAK 19(12P13.33) MUTATED	13	36	33	43	23	10	4
AMP PEAK 19(12P13.33) WILD-TYPE	69	40	63	44	55	64	14

Figure S50. Get High-res Image Gene #19: 'amp_12p13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S51. Gene #20: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 20(12Q15) MUTATED	47	28	14	12
AMP PEAK 20(12Q15) WILD-TYPE	131	74	175	30

Figure S51. Get High-res Image Gene #20: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S52. Gene #21: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 21(13Q22.1) MUTATED	71	13	17	3
AMP PEAK 21(13Q22.1) WILD-TYPE	107	89	172	39

Figure S52. Get High-res Image Gene #21: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q22.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S53. Gene #21: '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	82	76	96	87	78	74	18
AMP PEAK 21(13Q22.1) MUTATED	8	19	35	18	12	5	7
AMP PEAK 21(13Q22.1) WILD-TYPE	74	57	61	69	66	69	11

Figure S53. Get High-res Image Gene #21: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S54. Gene #22: 'amp_13q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 22(13Q34) MUTATED	66	11	21	8
AMP PEAK 22(13Q34) WILD-TYPE	112	91	168	34

Figure S54. Get High-res Image Gene #22: 'amp_13q34' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q34' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.034

Table S55. Gene #22: 'amp_13q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	82	76	96	87	78	74	18
AMP PEAK 22(13Q34) MUTATED	11	18	33	20	11	6	7
AMP PEAK 22(13Q34) WILD-TYPE	71	58	63	67	67	68	11

Figure S55. Get High-res Image Gene #22: 'amp_13q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S56. Gene #24: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 24(17Q12) MUTATED	42	27	9	10
AMP PEAK 24(17Q12) WILD-TYPE	136	75	180	32

Figure S56. Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S57. Gene #24: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	82	76	96	87	78	74	18
AMP PEAK 24(17Q12) MUTATED	6	19	21	29	6	6	1
AMP PEAK 24(17Q12) WILD-TYPE	76	57	75	58	72	68	17

Figure S57. Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_18p11.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S58. Gene #25: 'amp_18p11.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 25(18P11.31) MUTATED	73	53	19	7
AMP PEAK 25(18P11.31) WILD-TYPE	105	49	170	35

Figure S58. Get High-res Image Gene #25: '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 = 0.0073

Table S59. Gene #25: '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	82	76	96	87	78	74	18
AMP PEAK 25(18P11.31) MUTATED	9	43	33	32	21	10	4
AMP PEAK 25(18P11.31) WILD-TYPE	73	33	63	55	57	64	14

Figure S59. Get High-res Image Gene #25: '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 = 0.0073

Table S60. Gene #25: '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 25(18P11.31) MUTATED	35	45	30	39
AMP PEAK 25(18P11.31) WILD-TYPE	16	112	125	91

Figure S60. Get High-res Image Gene #25: 'amp_18p11.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_18p11.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S61. Gene #25: 'amp_18p11.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	99	128	79	108	57
AMP PEAK 25(18P11.31) MUTATED	25	58	11	31	10
AMP PEAK 25(18P11.31) WILD-TYPE	74	70	68	77	47

Figure S61. Get High-res Image Gene #25: 'amp_18p11.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S62. Gene #26: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 26(18Q11.2) MUTATED	45	34	17	5
AMP PEAK 26(18Q11.2) WILD-TYPE	133	68	172	37

Figure S62. Get High-res Image Gene #26: '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 = 0.045

Table S63. Gene #26: '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	82	76	96	87	78	74	18
AMP PEAK 26(18Q11.2) MUTATED	5	22	24	24	17	6	3
AMP PEAK 26(18Q11.2) WILD-TYPE	77	54	72	63	61	68	15

Figure S63. Get High-res Image Gene #26: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20p12.2' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.023

Table S64. Gene #27: 'amp_20p12.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 27(20P12.2) MUTATED	83	39	46	21
AMP PEAK 27(20P12.2) WILD-TYPE	95	63	143	21

Figure S64. Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20p12.2' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.028

Table S65. 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	82	76	96	87	78	74	18
AMP PEAK 27(20P12.2) MUTATED	28	24	54	38	21	16	8
AMP PEAK 27(20P12.2) WILD-TYPE	54	52	42	49	57	58	10

Figure S65. 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 = 0.0073

Table S66. Gene #28: 'amp_20q11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 28(20Q11.22) MUTATED	99	50	51	24
AMP PEAK 28(20Q11.22) WILD-TYPE	79	52	138	18

Figure S66. 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 = 0.012

Table S67. 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	82	76	96	87	78	74	18
AMP PEAK 28(20Q11.22) MUTATED	31	37	59	44	27	17	9
AMP PEAK 28(20Q11.22) WILD-TYPE	51	39	37	43	51	57	9

Figure S67. 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 = 0.0073

Table S68. Gene #29: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 29(XQ28) MUTATED	83	23	28	11
AMP PEAK 29(XQ28) WILD-TYPE	95	79	161	31

Figure S68. 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 = 0.012

Table S69. 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	82	76	96	87	78	74	18
AMP PEAK 29(XQ28) MUTATED	11	19	42	34	20	12	7
AMP PEAK 29(XQ28) WILD-TYPE	71	57	54	53	58	62	11

Figure S69. 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 = 0.0073

Table S70. Gene #30: 'del_1p36.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 1(1P36.21) MUTATED	33	41	13	7
DEL PEAK 1(1P36.21) WILD-TYPE	145	61	176	35

Figure S70. 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 = 0.0073

Table S71. 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	82	76	96	87	78	74	18
DEL PEAK 1(1P36.21) MUTATED	4	16	8	48	8	8	2
DEL PEAK 1(1P36.21) WILD-TYPE	78	60	88	39	70	66	16

Figure S71. 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 = 0.0073

Table S72. 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 S72. Get High-res Image Gene #30: 'del_1p36.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p36.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.034

Table S73. 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 S73. Get High-res Image Gene #30: 'del_1p36.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S74. Gene #30: 'del_1p36.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	99	128	79	108	57
DEL PEAK 1(1P36.21) MUTATED	10	44	7	19	5
DEL PEAK 1(1P36.21) WILD-TYPE	89	84	72	89	52

Figure S74. Get High-res Image Gene #30: 'del_1p36.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S75. Gene #31: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 2(1P13.2) MUTATED	55	49	12	11
DEL PEAK 2(1P13.2) WILD-TYPE	123	53	177	31

Figure S75. 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 = 0.0073

Table S76. 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	82	76	96	87	78	74	18
DEL PEAK 2(1P13.2) MUTATED	12	24	20	52	6	7	6
DEL PEAK 2(1P13.2) WILD-TYPE	70	52	76	35	72	67	12

Figure S76. Get High-res Image Gene #31: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S77. Gene #31: 'del_1p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	99	128	79	108	57
DEL PEAK 2(1P13.2) MUTATED	16	52	9	30	10
DEL PEAK 2(1P13.2) WILD-TYPE	83	76	70	78	47

Figure S77. Get High-res Image Gene #31: 'del_1p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q21.2' versus 'MIRSEQ_CNMF'

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

Table S78. Gene #33: 'del_2q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	216	146
DEL PEAK 4(2Q21.2) MUTATED	34	28	10
DEL PEAK 4(2Q21.2) WILD-TYPE	111	188	136

Figure S78. Get High-res Image Gene #33: 'del_2q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.055

Table S79. 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	82	76	96	87	78	74	18
DEL PEAK 5(2Q22.1) MUTATED	9	14	23	34	11	22	1
DEL PEAK 5(2Q22.1) WILD-TYPE	73	62	73	53	67	52	17

Figure S79. 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 = 0.0073

Table S80. Gene #35: 'del_2q36.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 6(2Q36.2) MUTATED	58	51	31	12
DEL PEAK 6(2Q36.2) WILD-TYPE	120	51	158	30

Figure S80. 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 = 0.0073

Table S81. 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	82	76	96	87	78	74	18
DEL PEAK 6(2Q36.2) MUTATED	6	24	26	46	24	21	5
DEL PEAK 6(2Q36.2) WILD-TYPE	76	52	70	41	54	53	13

Figure S81. Get High-res Image Gene #35: 'del_2q36.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S82. Gene #36: 'del_3p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 7(3P24.1) MUTATED	164	89	74	30
DEL PEAK 7(3P24.1) WILD-TYPE	14	13	115	12

Figure S82. Get High-res Image Gene #36: '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 = 0.0073

Table S83. Gene #36: '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	82	76	96	87	78	74	18
DEL PEAK 7(3P24.1) MUTATED	49	68	87	77	29	30	17
DEL PEAK 7(3P24.1) WILD-TYPE	33	8	9	10	49	44	1

Figure S83. Get High-res Image Gene #36: 'del_3p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S84. Gene #36: '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 7(3P24.1) MUTATED	46	124	100	77
DEL PEAK 7(3P24.1) WILD-TYPE	5	33	55	53

Figure S84. Get High-res Image Gene #36: 'del_3p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S85. Gene #36: 'del_3p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	198	124	185
DEL PEAK 7(3P24.1) MUTATED	154	96	104
DEL PEAK 7(3P24.1) WILD-TYPE	44	28	81

Figure S85. Get High-res Image Gene #36: 'del_3p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S86. Gene #36: 'del_3p24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	99	128	79	108	57
DEL PEAK 7(3P24.1) MUTATED	64	101	35	85	42
DEL PEAK 7(3P24.1) WILD-TYPE	35	27	44	23	15

Figure S86. Get High-res Image Gene #36: 'del_3p24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S87. Gene #37: 'del_3p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 8(3P12.1) MUTATED	157	86	60	29
DEL PEAK 8(3P12.1) WILD-TYPE	21	16	129	13

Figure S87. Get High-res Image Gene #37: '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 = 0.0073

Table S88. Gene #37: '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	82	76	96	87	78	74	18
DEL PEAK 8(3P12.1) MUTATED	45	66	77	78	24	26	16
DEL PEAK 8(3P12.1) WILD-TYPE	37	10	19	9	54	48	2

Figure S88. Get High-res Image Gene #37: 'del_3p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.028

Table S89. Gene #37: '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 8(3P12.1) MUTATED	45	114	92	73
DEL PEAK 8(3P12.1) WILD-TYPE	6	43	63	57

Figure S89. Get High-res Image Gene #37: 'del_3p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.061

Table S90. Gene #37: 'del_3p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	198	124	185
DEL PEAK 8(3P12.1) MUTATED	139	92	98
DEL PEAK 8(3P12.1) WILD-TYPE	59	32	87

Figure S90. Get High-res Image Gene #37: 'del_3p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S91. Gene #37: 'del_3p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	99	128	79	108	57
DEL PEAK 8(3P12.1) MUTATED	62	101	29	75	35
DEL PEAK 8(3P12.1) WILD-TYPE	37	27	50	33	22

Figure S91. Get High-res Image Gene #37: 'del_3p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4p15.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S92. Gene #38: 'del_4p15.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 9(4P15.2) MUTATED	88	67	32	14
DEL PEAK 9(4P15.2) WILD-TYPE	90	35	157	28

Figure S92. Get High-res Image Gene #38: '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 = 0.0073

Table S93. Gene #38: '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	82	76	96	87	78	74	18
DEL PEAK 9(4P15.2) MUTATED	20	44	29	63	21	14	10
DEL PEAK 9(4P15.2) WILD-TYPE	62	32	67	24	57	60	8

Figure S93. Get High-res Image Gene #38: 'del_4p15.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4p15.2' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.05

Table S94. Gene #38: 'del_4p15.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	207	134	152
DEL PEAK 9(4P15.2) MUTATED	97	59	39
DEL PEAK 9(4P15.2) WILD-TYPE	110	75	113

Figure S94. Get High-res Image Gene #38: 'del_4p15.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4p15.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S95. Gene #38: 'del_4p15.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	99	128	79	108	57
DEL PEAK 9(4P15.2) MUTATED	26	74	15	49	17
DEL PEAK 9(4P15.2) WILD-TYPE	73	54	64	59	40

Figure S95. Get High-res Image Gene #38: 'del_4p15.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S96. Gene #39: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 10(4Q22.1) MUTATED	70	57	23	14
DEL PEAK 10(4Q22.1) WILD-TYPE	108	45	166	28

Figure S96. Get High-res Image Gene #39: '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 = 0.0073

Table S97. Gene #39: '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	82	76	96	87	78	74	18
DEL PEAK 10(4Q22.1) MUTATED	12	31	29	55	18	14	5
DEL PEAK 10(4Q22.1) WILD-TYPE	70	45	67	32	60	60	13

Figure S97. Get High-res Image Gene #39: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S98. Gene #39: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	99	128	79	108	57
DEL PEAK 10(4Q22.1) MUTATED	18	62	16	36	22
DEL PEAK 10(4Q22.1) WILD-TYPE	81	66	63	72	35

Figure S98. Get High-res Image Gene #39: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q35.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S99. Gene #40: 'del_4q35.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 11(4Q35.2) MUTATED	90	56	38	22
DEL PEAK 11(4Q35.2) WILD-TYPE	88	46	151	20

Figure S99. Get High-res Image Gene #40: 'del_4q35.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q35.2' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.023

Table S100. Gene #40: '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	82	76	96	87	78	74	18
DEL PEAK 11(4Q35.2) MUTATED	23	37	44	51	20	23	8
DEL PEAK 11(4Q35.2) WILD-TYPE	59	39	52	36	58	51	10

Figure S100. Get High-res Image Gene #40: 'del_4q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S101. Gene #41: 'del_5q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 12(5Q11.2) MUTATED	112	65	21	11
DEL PEAK 12(5Q11.2) WILD-TYPE	66	37	168	31

Figure S101. Get High-res Image Gene #41: 'del_5q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S102. Gene #41: 'del_5q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	82	76	96	87	78	74	18
DEL PEAK 12(5Q11.2) MUTATED	18	51	53	59	10	8	10
DEL PEAK 12(5Q11.2) WILD-TYPE	64	25	43	28	68	66	8

Figure S102. Get High-res Image Gene #41: 'del_5q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S103. Gene #41: 'del_5q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	157	155	130
DEL PEAK 12(5Q11.2) MUTATED	34	74	39	56
DEL PEAK 12(5Q11.2) WILD-TYPE	17	83	116	74

Figure S103. Get High-res Image Gene #41: 'del_5q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S104. Gene #41: 'del_5q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	198	124	185
DEL PEAK 12(5Q11.2) MUTATED	88	67	51
DEL PEAK 12(5Q11.2) WILD-TYPE	110	57	134

Figure S104. Get High-res Image Gene #41: 'del_5q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S105. Gene #41: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	99	128	79	108	57
DEL PEAK 12(5Q11.2) MUTATED	34	70	14	53	21
DEL PEAK 12(5Q11.2) WILD-TYPE	65	58	65	55	36

Figure S105. Get High-res Image Gene #41: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S106. Gene #42: 'del_5q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 13(5Q15) MUTATED	114	68	26	11
DEL PEAK 13(5Q15) WILD-TYPE	64	34	163	31

Figure S106. Get High-res Image Gene #42: 'del_5q15' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q15' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S107. Gene #42: 'del_5q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	82	76	96	87	78	74	18
DEL PEAK 13(5Q15) MUTATED	19	52	52	62	12	11	11
DEL PEAK 13(5Q15) WILD-TYPE	63	24	44	25	66	63	7

Figure S107. Get High-res Image Gene #42: 'del_5q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S108. Gene #42: 'del_5q15' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	157	155	130
DEL PEAK 13(5Q15) MUTATED	34	76	44	58
DEL PEAK 13(5Q15) WILD-TYPE	17	81	111	72

Figure S108. Get High-res Image Gene #42: 'del_5q15' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q15' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S109. Gene #42: 'del_5q15' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	198	124	185
DEL PEAK 13(5Q15) MUTATED	90	70	56
DEL PEAK 13(5Q15) WILD-TYPE	108	54	129

Figure S109. Get High-res Image Gene #42: 'del_5q15' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q15' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S110. Gene #42: 'del_5q15' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	99	128	79	108	57
DEL PEAK 13(5Q15) MUTATED	41	74	13	52	22
DEL PEAK 13(5Q15) WILD-TYPE	58	54	66	56	35

Figure S110. Get High-res Image Gene #42: 'del_5q15' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q35.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S111. Gene #43: 'del_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 14(5Q35.3) MUTATED	92	68	22	13
DEL PEAK 14(5Q35.3) WILD-TYPE	86	34	167	29

Figure S111. Get High-res Image Gene #43: '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 = 0.0073

Table S112. Gene #43: '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	82	76	96	87	78	74	18
DEL PEAK 14(5Q35.3) MUTATED	19	55	45	50	11	5	10
DEL PEAK 14(5Q35.3) WILD-TYPE	63	21	51	37	67	69	8

Figure S112. Get High-res Image Gene #43: '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 = 0.0073

Table S113. Gene #43: '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 14(5Q35.3) MUTATED	37	68	35	51
DEL PEAK 14(5Q35.3) WILD-TYPE	14	89	120	79

Figure S113. Get High-res Image Gene #43: 'del_5q35.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q35.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S114. Gene #43: 'del_5q35.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	198	124	185
DEL PEAK 14(5Q35.3) MUTATED	83	64	45
DEL PEAK 14(5Q35.3) WILD-TYPE	115	60	140

Figure S114. Get High-res Image Gene #43: 'del_5q35.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q35.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S115. Gene #43: 'del_5q35.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	99	128	79	108	57
DEL PEAK 14(5Q35.3) MUTATED	33	66	10	47	22
DEL PEAK 14(5Q35.3) WILD-TYPE	66	62	69	61	35

Figure S115. Get High-res Image Gene #43: 'del_5q35.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.18

Table S116. Gene #44: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 15(6P25.3) MUTATED	38	30	19	6
DEL PEAK 15(6P25.3) WILD-TYPE	140	72	170	36

Figure S116. Get High-res Image Gene #44: '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 = 0.0073

Table S117. Gene #44: '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	82	76	96	87	78	74	18
DEL PEAK 15(6P25.3) MUTATED	10	12	17	35	11	5	3
DEL PEAK 15(6P25.3) WILD-TYPE	72	64	79	52	67	69	15

Figure S117. Get High-res Image Gene #44: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q36.1' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.077

Table S118. Gene #46: 'del_7q36.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 17(7Q36.1) MUTATED	60	24	28	15
DEL PEAK 17(7Q36.1) WILD-TYPE	118	78	161	27

Figure S118. Get High-res Image Gene #46: '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 = 0.0073

Table S119. Gene #47: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 18(8P23.2) MUTATED	152	43	74	25
DEL PEAK 18(8P23.2) WILD-TYPE	26	59	115	17

Figure S119. Get High-res Image Gene #47: '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 = 0.0073

Table S120. Gene #47: '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	82	76	96	87	78	74	18
DEL PEAK 18(8P23.2) MUTATED	48	38	71	58	16	50	13
DEL PEAK 18(8P23.2) WILD-TYPE	34	38	25	29	62	24	5

Figure S120. Get High-res Image Gene #47: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.028

Table S121. Gene #47: '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 18(8P23.2) MUTATED	25	106	99	55
DEL PEAK 18(8P23.2) WILD-TYPE	26	51	56	75

Figure S121. Get High-res Image Gene #47: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

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

Table S122. Gene #47: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	159	138
DEL PEAK 18(8P23.2) MUTATED	108	71	92
DEL PEAK 18(8P23.2) WILD-TYPE	66	88	46

Figure S122. Get High-res Image Gene #47: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S123. Gene #47: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	99	128	79	108	57
DEL PEAK 18(8P23.2) MUTATED	71	66	25	72	37
DEL PEAK 18(8P23.2) WILD-TYPE	28	62	54	36	20

Figure S123. Get High-res Image Gene #47: '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 = 0.0073

Table S124. Gene #48: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 19(9P23) MUTATED	125	63	43	2
DEL PEAK 19(9P23) WILD-TYPE	53	39	146	40

Figure S124. Get High-res Image Gene #48: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S125. Gene #48: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	82	76	96	87	78	74	18
DEL PEAK 19(9P23) MUTATED	27	54	52	62	9	18	11
DEL PEAK 19(9P23) WILD-TYPE	55	22	44	25	69	56	7

Figure S125. Get High-res Image Gene #48: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.13

Table S126. Gene #48: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	157	155	130
DEL PEAK 19(9P23) MUTATED	37	73	69	47
DEL PEAK 19(9P23) WILD-TYPE	14	84	86	83

Figure S126. Get High-res Image Gene #48: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S127. Gene #48: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	198	124	185
DEL PEAK 19(9P23) MUTATED	91	73	66
DEL PEAK 19(9P23) WILD-TYPE	107	51	119

Figure S127. Get High-res Image Gene #48: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S128. Gene #48: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	99	128	79	108	57
DEL PEAK 19(9P23) MUTATED	46	77	14	53	23
DEL PEAK 19(9P23) WILD-TYPE	53	51	65	55	34

Figure S128. Get High-res Image Gene #48: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S129. Gene #49: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 20(9P21.3) MUTATED	137	72	73	10
DEL PEAK 20(9P21.3) WILD-TYPE	41	30	116	32

Figure S129. Get High-res Image Gene #49: '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 = 0.0073

Table S130. Gene #49: '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	82	76	96	87	78	74	18
DEL PEAK 20(9P21.3) MUTATED	41	63	67	64	11	34	12
DEL PEAK 20(9P21.3) WILD-TYPE	41	13	29	23	67	40	6

Figure S130. Get High-res Image Gene #49: '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 = 0.0073

Table S131. Gene #49: '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 20(9P21.3) MUTATED	42	96	95	52
DEL PEAK 20(9P21.3) WILD-TYPE	9	61	60	78

Figure S131. Get High-res Image Gene #49: '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 = 0.0073

Table S132. Gene #49: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	198	124	185
DEL PEAK 20(9P21.3) MUTATED	120	91	79
DEL PEAK 20(9P21.3) WILD-TYPE	78	33	106

Figure S132. Get High-res Image Gene #49: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S133. Gene #49: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	99	128	79	108	57
DEL PEAK 20(9P21.3) MUTATED	67	86	17	66	30
DEL PEAK 20(9P21.3) WILD-TYPE	32	42	62	42	27

Figure S133. Get High-res Image Gene #49: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q21.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S134. Gene #50: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 21(9Q21.11) MUTATED	68	19	15	1
DEL PEAK 21(9Q21.11) WILD-TYPE	110	83	174	41

Figure S134. Get High-res Image Gene #50: '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 = 0.0073

Table S135. Gene #50: '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	82	76	96	87	78	74	18
DEL PEAK 21(9Q21.11) MUTATED	12	29	20	25	4	4	9
DEL PEAK 21(9Q21.11) WILD-TYPE	70	47	76	62	74	70	9

Figure S135. Get High-res Image Gene #50: 'del_9q21.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S136. Gene #51: 'del_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 22(9Q34.3) MUTATED	46	14	16	0
DEL PEAK 22(9Q34.3) WILD-TYPE	132	88	173	42

Figure S136. Get High-res Image Gene #51: '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 = 0.0073

Table S137. Gene #52: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 23(10P15.3) MUTATED	83	31	37	14
DEL PEAK 23(10P15.3) WILD-TYPE	95	71	152	28

Figure S137. Get High-res Image Gene #52: '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 = 0.0073

Table S138. Gene #52: '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	82	76	96	87	78	74	18
DEL PEAK 23(10P15.3) MUTATED	17	24	42	39	11	21	11
DEL PEAK 23(10P15.3) WILD-TYPE	65	52	54	48	67	53	7

Figure S138. Get High-res Image Gene #52: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S139. Gene #53: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 24(10P11.21) MUTATED	79	32	29	12
DEL PEAK 24(10P11.21) WILD-TYPE	99	70	160	30

Figure S139. Get High-res Image Gene #53: '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 = 0.0073

Table S140. Gene #53: '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	82	76	96	87	78	74	18
DEL PEAK 24(10P11.21) MUTATED	11	24	41	37	12	18	9
DEL PEAK 24(10P11.21) WILD-TYPE	71	52	55	50	66	56	9

Figure S140. Get High-res Image Gene #53: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S141. Gene #54: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 25(10Q23.31) MUTATED	58	40	29	7
DEL PEAK 25(10Q23.31) WILD-TYPE	120	62	160	35

Figure S141. Get High-res Image Gene #54: '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 = 0.0073

Table S142. Gene #54: '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	82	76	96	87	78	74	18
DEL PEAK 25(10Q23.31) MUTATED	7	25	30	36	24	7	5
DEL PEAK 25(10Q23.31) WILD-TYPE	75	51	66	51	54	67	13

Figure S142. Get High-res Image Gene #54: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.05

Table S143. Gene #54: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	207	134	152
DEL PEAK 25(10Q23.31) MUTATED	73	33	23
DEL PEAK 25(10Q23.31) WILD-TYPE	134	101	129

Figure S143. Get High-res Image Gene #54: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S144. Gene #54: '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 25(10Q23.31) MUTATED	17	39	22	51
DEL PEAK 25(10Q23.31) WILD-TYPE	34	118	133	79

Figure S144. Get High-res Image Gene #54: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S145. Gene #55: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 26(11P15.5) MUTATED	64	54	34	4
DEL PEAK 26(11P15.5) WILD-TYPE	114	48	155	38

Figure S145. Get High-res Image Gene #55: '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 = 0.0073

Table S146. Gene #55: '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	82	76	96	87	78	74	18
DEL PEAK 26(11P15.5) MUTATED	19	28	24	50	26	5	4
DEL PEAK 26(11P15.5) WILD-TYPE	63	48	72	37	52	69	14

Figure S146. Get High-res Image Gene #55: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.045

Table S147. Gene #55: 'del_11p15.5' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	207	134	152
DEL PEAK 26(11P15.5) MUTATED	85	35	30
DEL PEAK 26(11P15.5) WILD-TYPE	122	99	122

Figure S147. Get High-res Image Gene #55: '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 = 0.0073

Table S148. Gene #55: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	216	146
DEL PEAK 26(11P15.5) MUTATED	24	93	39
DEL PEAK 26(11P15.5) WILD-TYPE	121	123	107

Figure S148. Get High-res Image Gene #55: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S149. Gene #55: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	99	128	79	108	57
DEL PEAK 26(11P15.5) MUTATED	23	61	21	29	9
DEL PEAK 26(11P15.5) WILD-TYPE	76	67	58	79	48

Figure S149. Get High-res Image Gene #55: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S150. Gene #56: 'del_11q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 27(11Q23.1) MUTATED	107	53	63	16
DEL PEAK 27(11Q23.1) WILD-TYPE	71	49	126	26

Figure S150. Get High-res Image Gene #56: '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 = 0.0073

Table S151. Gene #56: '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	82	76	96	87	78	74	18
DEL PEAK 27(11Q23.1) MUTATED	26	31	49	46	65	12	10
DEL PEAK 27(11Q23.1) WILD-TYPE	56	45	47	41	13	62	8

Figure S151. Get High-res Image Gene #56: 'del_11q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S152. Gene #56: 'del_11q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	207	134	152
DEL PEAK 27(11Q23.1) MUTATED	120	58	52
DEL PEAK 27(11Q23.1) WILD-TYPE	87	76	100

Figure S152. Get High-res Image Gene #56: '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 = 0.0073

Table S153. Gene #56: '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 27(11Q23.1) MUTATED	18	64	56	92
DEL PEAK 27(11Q23.1) WILD-TYPE	33	93	99	38

Figure S153. Get High-res Image Gene #56: 'del_11q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12q24.33' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S154. Gene #57: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 28(12Q24.33) MUTATED	37	13	7	3
DEL PEAK 28(12Q24.33) WILD-TYPE	141	89	182	39

Figure S154. Get High-res Image Gene #57: '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 = 0.012

Table S155. Gene #57: '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	82	76	96	87	78	74	18
DEL PEAK 28(12Q24.33) MUTATED	5	12	13	21	4	1	4
DEL PEAK 28(12Q24.33) WILD-TYPE	77	64	83	66	74	73	14

Figure S155. Get High-res Image Gene #57: '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 = 0.0073

Table S156. Gene #58: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 29(13Q12.11) MUTATED	99	73	35	17
DEL PEAK 29(13Q12.11) WILD-TYPE	79	29	154	25

Figure S156. Get High-res Image Gene #58: '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 = 0.0073

Table S157. Gene #58: '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	82	76	96	87	78	74	18
DEL PEAK 29(13Q12.11) MUTATED	21	51	48	57	25	16	6
DEL PEAK 29(13Q12.11) WILD-TYPE	61	25	48	30	53	58	12

Figure S157. Get High-res Image Gene #58: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q12.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.023

Table S158. Gene #58: '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 29(13Q12.11) MUTATED	37	73	52	54
DEL PEAK 29(13Q12.11) WILD-TYPE	14	84	103	76

Figure S158. Get High-res Image Gene #58: '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 = 0.0073

Table S159. Gene #59: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 30(13Q14.2) MUTATED	69	76	49	15
DEL PEAK 30(13Q14.2) WILD-TYPE	109	26	140	27

Figure S159. Get High-res Image Gene #59: '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 = 0.0073

Table S160. Gene #59: '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	82	76	96	87	78	74	18
DEL PEAK 30(13Q14.2) MUTATED	17	44	39	47	44	15	3
DEL PEAK 30(13Q14.2) WILD-TYPE	65	32	57	40	34	59	15

Figure S160. Get High-res Image Gene #59: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S161. Gene #59: 'del_13q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	207	134	152
DEL PEAK 30(13Q14.2) MUTATED	110	52	42
DEL PEAK 30(13Q14.2) WILD-TYPE	97	82	110

Figure S161. Get High-res Image Gene #59: '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 = 0.0073

Table S162. Gene #59: '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 30(13Q14.2) MUTATED	32	61	42	69
DEL PEAK 30(13Q14.2) WILD-TYPE	19	96	113	61

Figure S162. Get High-res Image Gene #59: 'del_13q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.32' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.1

Table S163. Gene #61: 'del_14q32.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 32(14Q32.32) MUTATED	12	26	29	6
DEL PEAK 32(14Q32.32) WILD-TYPE	166	76	160	36

Figure S163. Get High-res Image Gene #61: 'del_14q32.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S164. Gene #61: '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	82	76	96	87	78	74	18
DEL PEAK 32(14Q32.32) MUTATED	2	11	7	17	32	3	1
DEL PEAK 32(14Q32.32) WILD-TYPE	80	65	89	70	46	71	17

Figure S164. Get High-res Image Gene #61: 'del_14q32.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q32.32' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S165. Gene #61: 'del_14q32.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

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

Figure S165. Get High-res Image Gene #61: '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 = 0.0073

Table S166. Gene #61: '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 32(14Q32.32) MUTATED	6	15	7	41
DEL PEAK 32(14Q32.32) WILD-TYPE	45	142	148	89

Figure S166. Get High-res Image Gene #61: 'del_14q32.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S167. Gene #62: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 33(15Q15.1) MUTATED	56	26	18	19
DEL PEAK 33(15Q15.1) WILD-TYPE	122	76	171	23

Figure S167. Get High-res Image Gene #62: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S168. Gene #63: '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	82	76	96	87	78	74	18
DEL PEAK 34(16Q23.3) MUTATED	6	16	8	31	27	10	4
DEL PEAK 34(16Q23.3) WILD-TYPE	76	60	88	56	51	64	14

Figure S168. Get High-res Image Gene #63: '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 = 0.0073

Table S169. Gene #63: 'del_16q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	207	134	152
DEL PEAK 34(16Q23.3) MUTATED	63	22	15
DEL PEAK 34(16Q23.3) WILD-TYPE	144	112	137

Figure S169. Get High-res Image Gene #63: '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 = 0.0073

Table S170. Gene #63: '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 34(16Q23.3) MUTATED	13	25	14	48
DEL PEAK 34(16Q23.3) WILD-TYPE	38	132	141	82

Figure S170. Get High-res Image Gene #63: 'del_16q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17q25.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S171. Gene #64: '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	82	76	96	87	78	74	18
DEL PEAK 35(17Q25.3) MUTATED	3	8	10	20	19	3	5
DEL PEAK 35(17Q25.3) WILD-TYPE	79	68	86	67	59	71	13

Figure S171. Get High-res Image Gene #64: '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 = 0.0073

Table S172. Gene #65: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 36(18Q21.2) MUTATED	133	56	48	22
DEL PEAK 36(18Q21.2) WILD-TYPE	45	46	141	20

Figure S172. Get High-res Image Gene #65: '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 = 0.0073

Table S173. Gene #65: '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	82	76	96	87	78	74	18
DEL PEAK 36(18Q21.2) MUTATED	41	54	65	59	5	25	10
DEL PEAK 36(18Q21.2) WILD-TYPE	41	22	31	28	73	49	8

Figure S173. Get High-res Image Gene #65: '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 = 0.0073

Table S174. Gene #65: '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 36(18Q21.2) MUTATED	38	97	78	39
DEL PEAK 36(18Q21.2) WILD-TYPE	13	60	77	91

Figure S174. Get High-res Image Gene #65: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S175. Gene #65: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	198	124	185
DEL PEAK 36(18Q21.2) MUTATED	117	75	65
DEL PEAK 36(18Q21.2) WILD-TYPE	81	49	120

Figure S175. Get High-res Image Gene #65: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S176. Gene #65: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	99	128	79	108	57
DEL PEAK 36(18Q21.2) MUTATED	51	78	18	59	33
DEL PEAK 36(18Q21.2) WILD-TYPE	48	50	61	49	24

Figure S176. Get High-res Image Gene #65: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S177. Gene #66: 'del_18q23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 37(18Q23) MUTATED	141	63	52	22
DEL PEAK 37(18Q23) WILD-TYPE	37	39	137	20

Figure S177. Get High-res Image Gene #66: 'del_18q23' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S178. Gene #66: 'del_18q23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	82	76	96	87	78	74	18
DEL PEAK 37(18Q23) MUTATED	43	55	71	65	9	24	11
DEL PEAK 37(18Q23) WILD-TYPE	39	21	25	22	69	50	7

Figure S178. Get High-res Image Gene #66: 'del_18q23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S179. Gene #66: 'del_18q23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	157	155	130
DEL PEAK 37(18Q23) MUTATED	39	103	83	46
DEL PEAK 37(18Q23) WILD-TYPE	12	54	72	84

Figure S179. Get High-res Image Gene #66: 'del_18q23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S180. Gene #66: 'del_18q23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	198	124	185
DEL PEAK 37(18Q23) MUTATED	123	81	72
DEL PEAK 37(18Q23) WILD-TYPE	75	43	113

Figure S180. Get High-res Image Gene #66: 'del_18q23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S181. Gene #66: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	99	128	79	108	57
DEL PEAK 37(18Q23) MUTATED	57	82	19	64	34
DEL PEAK 37(18Q23) WILD-TYPE	42	46	60	44	23

Figure S181. Get High-res Image Gene #66: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S182. Gene #67: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 38(19P13.3) MUTATED	79	37	32	17
DEL PEAK 38(19P13.3) WILD-TYPE	99	65	157	25

Figure S182. Get High-res Image Gene #67: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S183. Gene #67: '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	82	76	96	87	78	74	18
DEL PEAK 38(19P13.3) MUTATED	15	26	49	38	13	19	5
DEL PEAK 38(19P13.3) WILD-TYPE	67	50	47	49	65	55	13

Figure S183. Get High-res Image Gene #67: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.034

Table S184. Gene #67: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	198	124	185
DEL PEAK 38(19P13.3) MUTATED	75	50	37
DEL PEAK 38(19P13.3) WILD-TYPE	123	74	148

Figure S184. Get High-res Image Gene #67: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.43' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S185. Gene #68: 'del_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 39(19Q13.43) MUTATED	48	25	13	8
DEL PEAK 39(19Q13.43) WILD-TYPE	130	77	176	34

Figure S185. Get High-res Image Gene #68: 'del_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.43' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S186. Gene #68: '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	82	76	96	87	78	74	18
DEL PEAK 39(19Q13.43) MUTATED	7	17	27	29	5	5	4
DEL PEAK 39(19Q13.43) WILD-TYPE	75	59	69	58	73	69	14

Figure S186. Get High-res Image Gene #68: '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 = 0.0073

Table S187. Gene #69: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 40(21Q22.3) MUTATED	89	55	30	21
DEL PEAK 40(21Q22.3) WILD-TYPE	89	47	159	21

Figure S187. Get High-res Image Gene #69: '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 = 0.0073

Table S188. Gene #69: '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	82	76	96	87	78	74	18
DEL PEAK 40(21Q22.3) MUTATED	19	33	53	48	12	18	12
DEL PEAK 40(21Q22.3) WILD-TYPE	63	43	43	39	66	56	6

Figure S188. Get High-res Image Gene #69: 'del_21q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S189. Gene #69: 'del_21q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	198	124	185
DEL PEAK 40(21Q22.3) MUTATED	85	62	46
DEL PEAK 40(21Q22.3) WILD-TYPE	113	62	139

Figure S189. Get High-res Image Gene #69: 'del_21q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_21q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.11

Table S190. Gene #69: 'del_21q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	99	128	79	108	57
DEL PEAK 40(21Q22.3) MUTATED	36	59	14	45	27
DEL PEAK 40(21Q22.3) WILD-TYPE	63	69	65	63	30

Figure S190. Get High-res Image Gene #69: 'del_21q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S191. Gene #71: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 42(XP22.2) MUTATED	76	37	29	10
DEL PEAK 42(XP22.2) WILD-TYPE	102	65	160	32

Figure S191. Get High-res Image Gene #71: '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 = 0.0073

Table S192. Gene #71: '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	82	76	96	87	78	74	18
DEL PEAK 42(XP22.2) MUTATED	14	23	35	47	17	9	7
DEL PEAK 42(XP22.2) WILD-TYPE	68	53	61	40	61	65	11

Figure S192. Get High-res Image Gene #71: '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 = 0.0073

Table S193. Gene #72: 'del_xp21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 43(XP21.3) MUTATED	81	34	30	9
DEL PEAK 43(XP21.3) WILD-TYPE	97	68	159	33

Figure S193. Get High-res Image Gene #72: '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 = 0.0073

Table S194. Gene #72: '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	82	76	96	87	78	74	18
DEL PEAK 43(XP21.3) MUTATED	16	24	38	42	15	12	7
DEL PEAK 43(XP21.3) WILD-TYPE	66	52	58	45	63	62	11

Figure S194. Get High-res Image Gene #72: 'del_xp21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq21.33' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S195. Gene #73: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 44(XQ21.33) MUTATED	36	24	13	1
DEL PEAK 44(XQ21.33) WILD-TYPE	142	78	176	41

Figure S195. Get High-res Image Gene #73: '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 = 0.0073

Table S196. Gene #73: '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	82	76	96	87	78	74	18
DEL PEAK 44(XQ21.33) MUTATED	4	13	14	29	11	0	3
DEL PEAK 44(XQ21.33) WILD-TYPE	78	63	82	58	67	74	15

Figure S196. Get High-res Image Gene #73: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq21.33' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.061

Table S197. Gene #73: 'del_xq21.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	216	146
DEL PEAK 44(XQ21.33) MUTATED	14	48	11
DEL PEAK 44(XQ21.33) WILD-TYPE	131	168	135

Figure S197. Get High-res Image Gene #73: '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 = 511
Number of significantly focal cnvs = 73
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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