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

Lung Adenocarcinoma (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/C1HX1BFC

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 82 focal events and 12 molecular subtypes across 493 patients, 352 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p34.3 cnv correlated to 'CN_CNMF'.
amp_1p22.3 cnv correlated to 'CN_CNMF'.
amp_1q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_3q26.2 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_4q12 cnv correlated to 'CN_CNMF'.
amp_5p15.33 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5p13.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5q35.1 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6p21.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_7p21.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7p11.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7q31.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_8p11.23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_8p11.21 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q11.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_10p15.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_11q13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12p12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12q14.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12q15 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_13q33.3 cnv correlated to 'METHLYATION_CNMF'.
amp_14q13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_16p11.2 cnv correlated to 'CN_CNMF'.
amp_17q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_18q11.2 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19q12 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20p11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20q13.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_22q11.22 cnv correlated to 'CN_CNMF'.
amp_xq28 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_1p36.13 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_1p13.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_2q37.3 cnv correlated to 'CN_CNMF'.
del_3p26.3 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_3p21.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3q29 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_4p16.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q22.1 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q35.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q31.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q22.31 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_8p23.2 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_8p12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_8p11.21 cnv correlated to 'CN_CNMF'.
del_9p23 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
del_9p21.3 cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_9q21.11 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_10p15.3 cnv correlated to 'CN_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q26.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p15.5 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q23.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
del_11q25 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_12q12 cnv correlated to 'CN_CNMF'.
del_12q24.33 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_13q12.11 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_13q12.13 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_13q14.2 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q34 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_15q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_16q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_17p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_17p11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_18q21.32 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_18q23 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19q13.33 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_20p13 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_21q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_22q13.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp22.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 82 focal events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 352 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
amp 3q26 2	163 (33%)	330	0.00031 (0.199)	0.00178 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	0.01 (1.00)	0.00232 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	0.00036 (0.229)	1e-05 (0.00984)
del 4q35 1	182 (37%)	311	0.00205 (1.00)	0.00299 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	0.0398 (1.00)	2e-05 (0.0151)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)
amp 11q13 3	165 (33%)	328	0.00656 (1.00)	0.00246 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	0.0633 (1.00)	0.00394 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	2e-05 (0.0151)	3e-05 (0.0217)	1e-05 (0.00984)
amp 12p12 1	174 (35%)	319	0.197 (1.00)	0.0381 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	0.0419 (1.00)	0.0325 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)
amp 12q14 1	161 (33%)	332	0.404 (1.00)	0.286 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	0.0283 (1.00)	0.00477 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)
amp 12q15	162 (33%)	331	0.22 (1.00)	0.136 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	0.0393 (1.00)	0.00408 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)
amp 14q13 3	222 (45%)	271	0.798 (1.00)	0.538 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	0.0324 (1.00)	0.0245 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	0.00011 (0.075)	2e-05 (0.0151)
amp 17q23 1	241 (49%)	252	0.0795 (1.00)	0.3 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	0.0945 (1.00)	7e-05 (0.0487)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	4e-05 (0.0285)	0.0128 (1.00)	5e-05 (0.0352)
del 4q22 1	154 (31%)	339	0.00023 (0.149)	0.00046 (0.288)	1e-05 (0.00984)	1e-05 (0.00984)	0.322 (1.00)	0.00584 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	0.00096 (0.573)	1e-05 (0.00984)
del 5q11 2	172 (35%)	321	0.258 (1.00)	0.163 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	0.00478 (1.00)	0.00508 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)
del 5q31 1	199 (40%)	294	0.0927 (1.00)	0.242 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	0.00842 (1.00)	0.00048 (0.3)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	3e-05 (0.0217)	1e-05 (0.00984)
del 19p13 3	265 (54%)	228	0.57 (1.00)	0.812 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	0.194 (1.00)	0.0633 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	0.00011 (0.075)	1e-05 (0.00984)
del 19p13 2	260 (53%)	233	0.694 (1.00)	1 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	0.242 (1.00)	0.0359 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	2e-05 (0.0151)	0.00011 (0.075)	1e-05 (0.00984)
del 22q13 32	240 (49%)	253	0.025 (1.00)	0.0783 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	0.135 (1.00)	0.00077 (0.47)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	2e-05 (0.0151)	1e-05 (0.00984)
amp 7p11 2	260 (53%)	233	0.959 (1.00)	0.902 (1.00)	1e-05 (0.00984)	0.00298 (1.00)	0.00104 (0.616)	0.0032 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)
amp 8q11 1	224 (45%)	269	0.0048 (1.00)	0.0383 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	0.027 (1.00)	0.00487 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	0.00146 (0.848)	1e-05 (0.00984)	2e-05 (0.0151)
amp 17q12	219 (44%)	274	0.089 (1.00)	0.0336 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	0.423 (1.00)	0.00084 (0.504)	2e-05 (0.0151)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	0.00184 (1.00)	1e-05 (0.00984)
amp 19q12	133 (27%)	360	0.0508 (1.00)	0.0106 (1.00)	0.00081 (0.49)	1e-05 (0.00984)	0.257 (1.00)	0.11 (1.00)	0.00021 (0.138)	3e-05 (0.0217)	2e-05 (0.0151)	2e-05 (0.0151)	4e-05 (0.0285)	2e-05 (0.0151)
amp 20p11 21	188 (38%)	305	0.0618 (1.00)	0.0992 (1.00)	2e-05 (0.0151)	1e-05 (0.00984)	0.351 (1.00)	0.0287 (1.00)	8e-05 (0.0553)	1e-05 (0.00984)	0.00015 (0.1)	0.00028 (0.18)	0.00051 (0.318)	4e-05 (0.0285)
amp 20q13 33	237 (48%)	256	0.00546 (1.00)	0.044 (1.00)	1e-05 (0.00984)	8e-05 (0.0553)	0.0102 (1.00)	0.0036 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	2e-05 (0.0151)	0.00042 (0.265)	5e-05 (0.0352)	1e-05 (0.00984)
del 3p21 31	237 (48%)	256	0.133 (1.00)	0.347 (1.00)	1e-05 (0.00984)	0.00011 (0.075)	0.0117 (1.00)	0.00023 (0.149)	0.0174 (1.00)	1e-05 (0.00984)	2e-05 (0.0151)	0.0001 (0.0686)	0.00221 (1.00)	0.0001 (0.0686)
del 4p16 3	126 (26%)	367	0.594 (1.00)	0.307 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	0.377 (1.00)	0.014 (1.00)	2e-05 (0.0151)	1e-05 (0.00984)	1e-05 (0.00984)	2e-05 (0.0151)	0.0052 (1.00)	0.00022 (0.143)
del 11p15 5	135 (27%)	358	0.268 (1.00)	0.0317 (1.00)	1e-05 (0.00984)	0.00197 (1.00)	0.011 (1.00)	0.002 (1.00)	0.00037 (0.235)	1e-05 (0.00984)	0.00015 (0.1)	1e-05 (0.00984)	2e-05 (0.0151)	1e-05 (0.00984)
del 21q11 2	167 (34%)	326	0.0622 (1.00)	0.0471 (1.00)	1e-05 (0.00984)	0.00027 (0.174)	0.0557 (1.00)	0.0019 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	4e-05 (0.0285)	1e-05 (0.00984)	0.00123 (0.722)	0.00032 (0.205)
amp 8q24 21	310 (63%)	183	0.0349 (1.00)	0.0905 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	0.378 (1.00)	0.00934 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	0.00251 (1.00)	0.00108 (0.636)	1e-05 (0.00984)
amp 10p15 1	136 (28%)	357	0.0227 (1.00)	0.0168 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	0.00231 (1.00)	0.00043 (0.27)	2e-05 (0.0151)	1e-05 (0.00984)	0.00042 (0.265)	4e-05 (0.0285)	0.00912 (1.00)	9e-05 (0.0619)
amp 18q11 2	99 (20%)	394	0.197 (1.00)	0.0191 (1.00)	0.00052 (0.323)	1e-05 (0.00984)	0.13 (1.00)	0.00596 (1.00)	7e-05 (0.0487)	0.00014 (0.0941)	0.00023 (0.149)	1e-05 (0.00984)	0.0049 (1.00)	0.00017 (0.113)
del 10q26 3	142 (29%)	351	0.62 (1.00)	0.334 (1.00)	1e-05 (0.00984)	0.017 (1.00)	0.00526 (1.00)	0.00125 (0.732)	3e-05 (0.0217)	1e-05 (0.00984)	0.0044 (1.00)	1e-05 (0.00984)	7e-05 (0.0487)	0.00018 (0.119)
del 13q14 2	271 (55%)	222	0.00901 (1.00)	0.0659 (1.00)	1e-05 (0.00984)	0.00296 (1.00)	0.00036 (0.229)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	0.00205 (1.00)	0.00082 (0.494)	0.00082 (0.494)	0.00014 (0.0941)
amp 7p21 1	270 (55%)	223	0.848 (1.00)	0.901 (1.00)	1e-05 (0.00984)	0.00188 (1.00)	0.00502 (1.00)	0.00644 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	3e-05 (0.0217)	0.00359 (1.00)	0.00084 (0.504)	1e-05 (0.00984)
amp 8p11 21	170 (34%)	323	0.253 (1.00)	0.441 (1.00)	1e-05 (0.00984)	0.00048 (0.3)	0.0141 (1.00)	0.0032 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	0.00076 (0.464)	0.00177 (1.00)	0.00035 (0.223)	3e-05 (0.0217)
del 8p23 2	241 (49%)	252	0.00555 (1.00)	0.00982 (1.00)	1e-05 (0.00984)	0.00083 (0.499)	0.00808 (1.00)	0.0002 (0.132)	1e-05 (0.00984)	1e-05 (0.00984)	5e-05 (0.0352)	0.00462 (1.00)	0.00106 (0.625)	0.00059 (0.365)
del 8p12	215 (44%)	278	0.106 (1.00)	0.252 (1.00)	1e-05 (0.00984)	0.00018 (0.119)	0.0306 (1.00)	0.00417 (1.00)	1e-05 (0.00984)	0.00014 (0.0941)	0.00024 (0.155)	0.00807 (1.00)	0.00099 (0.59)	0.00243 (1.00)
del 15q11 2	253 (51%)	240	0.168 (1.00)	0.3 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	0.0448 (1.00)	0.00234 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	4e-05 (0.0285)	0.0938 (1.00)	0.115 (1.00)	0.00358 (1.00)
del 19q13 33	187 (38%)	306	0.271 (1.00)	0.251 (1.00)	1e-05 (0.00984)	0.00212 (1.00)	0.0995 (1.00)	0.414 (1.00)	0.00162 (0.936)	2e-05 (0.0151)	0.00017 (0.113)	5e-05 (0.0352)	0.0846 (1.00)	0.0002 (0.132)
amp 1q21 3	359 (73%)	134	0.358 (1.00)	0.519 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	0.361 (1.00)	0.961 (1.00)	0.00448 (1.00)	1e-05 (0.00984)	0.00768 (1.00)	5e-05 (0.0352)	0.0176 (1.00)	0.00507 (1.00)
amp 5p15 33	319 (65%)	174	0.879 (1.00)	0.806 (1.00)	1e-05 (0.00984)	0.169 (1.00)	0.101 (1.00)	0.0535 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	0.00329 (1.00)	0.0069 (1.00)	0.0197 (1.00)	7e-05 (0.0487)
amp 5p13 1	291 (59%)	202	0.264 (1.00)	1 (1.00)	1e-05 (0.00984)	0.0175 (1.00)	0.56 (1.00)	0.224 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	0.00041 (0.259)	0.00409 (1.00)	0.00656 (1.00)	6e-05 (0.042)
amp 5q35 1	123 (25%)	370	0.087 (1.00)	0.287 (1.00)	0.0345 (1.00)	0.00013 (0.0876)	0.0162 (1.00)	0.0452 (1.00)	0.00033 (0.211)	0.00214 (1.00)	0.00125 (0.732)	1e-05 (0.00984)	0.00249 (1.00)	0.00021 (0.138)
amp 8p11 23	134 (27%)	359	0.294 (1.00)	0.101 (1.00)	1e-05 (0.00984)	0.0001 (0.0686)	0.0613 (1.00)	0.0131 (1.00)	2e-05 (0.0151)	0.0002 (0.132)	0.0373 (1.00)	0.0173 (1.00)	0.11 (1.00)	0.0104 (1.00)
del 1p13 1	144 (29%)	349	0.619 (1.00)	0.451 (1.00)	1e-05 (0.00984)	0.00242 (1.00)	0.721 (1.00)	0.1 (1.00)	0.00015 (0.1)	0.00011 (0.075)	0.263 (1.00)	0.00012 (0.081)	0.248 (1.00)	0.00478 (1.00)
del 3p26 3	223 (45%)	270	0.0934 (1.00)	0.243 (1.00)	1e-05 (0.00984)	0.00225 (1.00)	0.0735 (1.00)	0.00017 (0.113)	0.0652 (1.00)	1e-05 (0.00984)	6e-05 (0.042)	0.00077 (0.47)	0.00435 (1.00)	0.00062 (0.381)
del 9q21 11	246 (50%)	247	0.0341 (1.00)	0.481 (1.00)	1e-05 (0.00984)	0.00046 (0.288)	0.277 (1.00)	0.00236 (1.00)	0.00273 (1.00)	2e-05 (0.0151)	0.0001 (0.0686)	3e-05 (0.0217)	0.0153 (1.00)	0.0006 (0.37)
del 10p15 3	122 (25%)	371	1 (1.00)	0.845 (1.00)	7e-05 (0.0487)	0.0349 (1.00)	0.518 (1.00)	0.2 (1.00)	0.00522 (1.00)	0.00089 (0.532)	0.00228 (1.00)	6e-05 (0.042)	0.00033 (0.211)	0.00021 (0.138)
del 13q12 11	282 (57%)	211	0.00125 (0.732)	0.0377 (1.00)	1e-05 (0.00984)	0.00201 (1.00)	0.00057 (0.353)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	0.00224 (1.00)	0.00366 (1.00)	0.00317 (1.00)	0.00051 (0.318)
del 13q12 13	282 (57%)	211	0.00867 (1.00)	0.0635 (1.00)	1e-05 (0.00984)	0.00102 (0.606)	0.00073 (0.447)	1e-05 (0.00984)	1e-05 (0.00984)	1e-05 (0.00984)	0.00448 (1.00)	0.00422 (1.00)	0.0047 (1.00)	0.00068 (0.418)
del 13q34	232 (47%)	261	0.0356 (1.00)	0.115 (1.00)	1e-05 (0.00984)	0.0298 (1.00)	0.00059 (0.365)	2e-05 (0.0151)	2e-05 (0.0151)	1e-05 (0.00984)	0.0228 (1.00)	0.031 (1.00)	0.0481 (1.00)	0.0932 (1.00)
del 16q23 1	167 (34%)	326	0.0582 (1.00)	0.877 (1.00)	2e-05 (0.0151)	1e-05 (0.00984)	0.0169 (1.00)	0.00341 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	0.0383 (1.00)	0.0128 (1.00)	0.0284 (1.00)	0.00078 (0.474)
del 17p13 3	265 (54%)	228	0.387 (1.00)	0.787 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	0.0628 (1.00)	0.00377 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	0.00636 (1.00)	0.207 (1.00)	0.0768 (1.00)	0.00165 (0.952)
del 17p11 2	216 (44%)	277	0.263 (1.00)	0.381 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	0.0107 (1.00)	0.00207 (1.00)	3e-05 (0.0217)	1e-05 (0.00984)	0.0218 (1.00)	0.0375 (1.00)	0.15 (1.00)	0.00455 (1.00)
amp 7q31 2	206 (42%)	287	0.483 (1.00)	0.31 (1.00)	1e-05 (0.00984)	0.00505 (1.00)	0.356 (1.00)	0.0992 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	0.0008 (0.486)	0.00241 (1.00)	0.00729 (1.00)	0.00148 (0.858)
amp xq28	149 (30%)	344	0.301 (1.00)	0.242 (1.00)	1e-05 (0.00984)	0.00101 (0.601)	0.198 (1.00)	0.0541 (1.00)	3e-05 (0.0217)	2e-05 (0.0151)	0.0133 (1.00)	0.414 (1.00)	0.00629 (1.00)	0.0633 (1.00)
del 1p36 13	116 (24%)	377	0.792 (1.00)	0.381 (1.00)	0.00011 (0.075)	0.0008 (0.486)	0.764 (1.00)	0.551 (1.00)	9e-05 (0.0619)	1e-05 (0.00984)	0.0349 (1.00)	0.00054 (0.335)	0.0396 (1.00)	0.00642 (1.00)
del 3q29	133 (27%)	360	0.713 (1.00)	0.615 (1.00)	0.0551 (1.00)	0.00021 (0.138)	0.214 (1.00)	0.0811 (1.00)	0.00013 (0.0876)	1e-05 (0.00984)	0.87 (1.00)	0.0011 (0.647)	0.61 (1.00)	0.862 (1.00)
del 11q23 2	116 (24%)	377	0.434 (1.00)	0.845 (1.00)	2e-05 (0.0151)	0.0002 (0.132)	0.116 (1.00)	0.242 (1.00)	0.00011 (0.075)	0.0017 (0.979)	0.002 (1.00)	0.0488 (1.00)	0.0289 (1.00)	0.0849 (1.00)
del 12q24 33	123 (25%)	370	0.0625 (1.00)	0.0694 (1.00)	3e-05 (0.0217)	0.0408 (1.00)	0.0258 (1.00)	0.00226 (1.00)	2e-05 (0.0151)	1e-05 (0.00984)	0.302 (1.00)	0.035 (1.00)	0.189 (1.00)	0.277 (1.00)
del 18q21 32	241 (49%)	252	0.114 (1.00)	0.0801 (1.00)	1e-05 (0.00984)	0.715 (1.00)	0.0153 (1.00)	0.00311 (1.00)	1e-05 (0.00984)	2e-05 (0.0151)	0.00678 (1.00)	0.0808 (1.00)	0.265 (1.00)	0.115 (1.00)
del 18q23	238 (48%)	255	0.0288 (1.00)	0.0253 (1.00)	1e-05 (0.00984)	0.564 (1.00)	0.00461 (1.00)	0.00595 (1.00)	2e-05 (0.0151)	4e-05 (0.0285)	0.00309 (1.00)	0.117 (1.00)	0.106 (1.00)	0.0722 (1.00)
del 20p13	126 (26%)	367	0.104 (1.00)	0.223 (1.00)	1e-05 (0.00984)	0.00042 (0.265)	0.00281 (1.00)	0.00249 (1.00)	6e-05 (0.042)	1e-05 (0.00984)	0.98 (1.00)	0.69 (1.00)	0.274 (1.00)	0.75 (1.00)
del xp22 2	135 (27%)	358	0.691 (1.00)	0.892 (1.00)	1e-05 (0.00984)	0.00818 (1.00)	0.0162 (1.00)	0.0396 (1.00)	0.00028 (0.18)	0.00038 (0.241)	0.294 (1.00)	0.646 (1.00)	0.7 (1.00)	0.696 (1.00)
amp 6p21 1	186 (38%)	307	0.677 (1.00)	0.255 (1.00)	1e-05 (0.00984)	1e-05 (0.00984)	0.078 (1.00)	1 (1.00)	0.00386 (1.00)	0.00073 (0.447)	0.0168 (1.00)	0.153 (1.00)	0.0728 (1.00)	0.041 (1.00)
del 6q22 31	246 (50%)	247	0.536 (1.00)	0.143 (1.00)	0.0207 (1.00)	1e-05 (0.00984)	0.498 (1.00)	0.0931 (1.00)	0.0272 (1.00)	8e-05 (0.0553)	0.79 (1.00)	0.0223 (1.00)	0.538 (1.00)	0.241 (1.00)
del 9p21 3	278 (56%)	215	0.523 (1.00)	0.806 (1.00)	0.0035 (1.00)	0.361 (1.00)	0.209 (1.00)	0.0729 (1.00)	1e-05 (0.00984)	3e-05 (0.0217)	0.197 (1.00)	0.0212 (1.00)	0.566 (1.00)	0.745 (1.00)
del 11q25	112 (23%)	381	0.108 (1.00)	0.484 (1.00)	0.00022 (0.143)	0.00102 (0.606)	0.0132 (1.00)	0.113 (1.00)	0.00038 (0.241)	0.01 (1.00)	0.152 (1.00)	0.447 (1.00)	0.261 (1.00)	0.169 (1.00)
amp 1p34 3	132 (27%)	361	0.555 (1.00)	0.581 (1.00)	1e-05 (0.00984)	0.414 (1.00)	0.251 (1.00)	0.067 (1.00)	0.0536 (1.00)	0.00179 (1.00)	0.175 (1.00)	0.0288 (1.00)	0.282 (1.00)	0.0423 (1.00)
amp 1p22 3	133 (27%)	360	0.875 (1.00)	1 (1.00)	1e-05 (0.00984)	0.377 (1.00)	0.549 (1.00)	0.147 (1.00)	0.043 (1.00)	0.0154 (1.00)	0.0819 (1.00)	0.0326 (1.00)	0.462 (1.00)	0.334 (1.00)
amp 4q12	93 (19%)	400	0.702 (1.00)	0.255 (1.00)	1e-05 (0.00984)	0.139 (1.00)	0.121 (1.00)	0.00927 (1.00)	0.00442 (1.00)	0.00718 (1.00)	0.00526 (1.00)	0.0142 (1.00)	0.0864 (1.00)	0.00141 (0.821)
amp 13q33 3	77 (16%)	416	0.463 (1.00)	0.521 (1.00)	0.0821 (1.00)	0.00023 (0.149)	0.768 (1.00)	0.427 (1.00)	0.474 (1.00)	0.0208 (1.00)	0.141 (1.00)	0.24 (1.00)	0.278 (1.00)	0.0476 (1.00)
amp 16p11 2	159 (32%)	334	0.799 (1.00)	0.393 (1.00)	1e-05 (0.00984)	0.0334 (1.00)	0.23 (1.00)	0.0314 (1.00)	0.327 (1.00)	0.0565 (1.00)	0.0194 (1.00)	0.103 (1.00)	0.486 (1.00)	0.0371 (1.00)
amp 22q11 22	87 (18%)	406	0.266 (1.00)	0.125 (1.00)	1e-05 (0.00984)	0.478 (1.00)	0.0393 (1.00)	0.0234 (1.00)	0.561 (1.00)	0.0622 (1.00)	0.0803 (1.00)	0.356 (1.00)	0.0477 (1.00)	0.0414 (1.00)
del 2q37 3	63 (13%)	430	0.704 (1.00)	0.254 (1.00)	2e-05 (0.0151)	0.0119 (1.00)	0.0772 (1.00)	0.0496 (1.00)	0.0459 (1.00)	0.0709 (1.00)	0.00318 (1.00)	0.00824 (1.00)	0.0106 (1.00)	0.00081 (0.49)
del 8p11 21	113 (23%)	380	0.796 (1.00)	0.506 (1.00)	1e-05 (0.00984)	0.231 (1.00)	0.395 (1.00)	0.289 (1.00)	0.0311 (1.00)	0.0982 (1.00)	0.3 (1.00)	0.547 (1.00)	0.263 (1.00)	0.287 (1.00)
del 9p23	271 (55%)	222	0.52 (1.00)	0.807 (1.00)	0.0119 (1.00)	0.578 (1.00)	0.551 (1.00)	0.243 (1.00)	0.00335 (1.00)	3e-05 (0.0217)	0.325 (1.00)	0.166 (1.00)	0.493 (1.00)	0.748 (1.00)
del 12q12	94 (19%)	399	0.598 (1.00)	0.754 (1.00)	0.00015 (0.1)	0.151 (1.00)	0.0264 (1.00)	0.0193 (1.00)	0.00704 (1.00)	0.0225 (1.00)	0.0693 (1.00)	0.00815 (1.00)	0.618 (1.00)	0.362 (1.00)
del 2q22 1	44 (9%)	449	0.87 (1.00)	0.78 (1.00)	0.00268 (1.00)	0.027 (1.00)	0.0295 (1.00)	0.588 (1.00)	0.0247 (1.00)	0.00466 (1.00)	0.0267 (1.00)	0.00628 (1.00)	0.195 (1.00)	0.00796 (1.00)
del 3q11 1	136 (28%)	357	0.612 (1.00)	0.683 (1.00)	0.177 (1.00)	0.0291 (1.00)	0.773 (1.00)	0.579 (1.00)	0.0857 (1.00)	0.0016 (0.926)	0.793 (1.00)	0.016 (1.00)	0.867 (1.00)	0.406 (1.00)
del 6q12	174 (35%)	319	0.486 (1.00)	0.518 (1.00)	0.0951 (1.00)	0.0748 (1.00)	0.348 (1.00)	0.363 (1.00)	0.899 (1.00)	0.175 (1.00)	0.028 (1.00)	0.0234 (1.00)	0.709 (1.00)	0.225 (1.00)
del 6q26	249 (51%)	244	0.369 (1.00)	0.331 (1.00)	0.00392 (1.00)	0.00105 (0.621)	0.429 (1.00)	0.105 (1.00)	0.101 (1.00)	0.00523 (1.00)	0.83 (1.00)	0.0277 (1.00)	0.3 (1.00)	0.222 (1.00)
del 8q11 21	63 (13%)	430	1 (1.00)	1 (1.00)	0.0124 (1.00)	0.622 (1.00)	0.411 (1.00)	0.354 (1.00)	0.35 (1.00)	0.21 (1.00)	0.318 (1.00)	0.846 (1.00)	0.965 (1.00)	0.592 (1.00)
del 12p13 2	134 (27%)	359	0.254 (1.00)	0.899 (1.00)	0.00132 (0.77)	0.00649 (1.00)	0.0213 (1.00)	0.0538 (1.00)	0.00484 (1.00)	0.0123 (1.00)	0.795 (1.00)	0.982 (1.00)	0.442 (1.00)	0.911 (1.00)
del 14q32 33	144 (29%)	349	0.703 (1.00)	0.287 (1.00)	0.0577 (1.00)	0.478 (1.00)	0.0949 (1.00)	0.16 (1.00)	0.215 (1.00)	0.0973 (1.00)	0.134 (1.00)	0.038 (1.00)	0.125 (1.00)	0.0149 (1.00)
del 20q13 12	81 (16%)	412	0.167 (1.00)	0.581 (1.00)	0.6 (1.00)	0.102 (1.00)	0.13 (1.00)	0.162 (1.00)	0.184 (1.00)	0.0412 (1.00)	0.178 (1.00)	0.126 (1.00)	0.0341 (1.00)	0.243 (1.00)

'amp_1p34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 1(1P34.3) MUTATED	80	34	18
AMP PEAK 1(1P34.3) WILD-TYPE	106	182	73

Figure S1. Get High-res Image Gene #1: 'amp_1p34.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1p22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S2. Gene #2: 'amp_1p22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 2(1P22.3) MUTATED	81	31	21
AMP PEAK 2(1P22.3) WILD-TYPE	105	185	70

Figure S2. Get High-res Image Gene #2: 'amp_1p22.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 3(1Q21.3) MUTATED	150	131	78
AMP PEAK 3(1Q21.3) WILD-TYPE	36	85	13

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

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S4. Gene #3: 'amp_1q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
AMP PEAK 3(1Q21.3) MUTATED	58	114	92	53
AMP PEAK 3(1Q21.3) WILD-TYPE	34	11	23	46

Figure S4. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S5. Gene #3: 'amp_1q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
AMP PEAK 3(1Q21.3) MUTATED	65	39	23	60	44	43	38	5	36
AMP PEAK 3(1Q21.3) WILD-TYPE	18	18	21	24	2	8	11	13	18

Figure S5. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.035

Table S6. Gene #3: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
AMP PEAK 3(1Q21.3) MUTATED	55	42	88	83	65	22
AMP PEAK 3(1Q21.3) WILD-TYPE	16	2	30	54	18	13

Figure S6. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MRNA_CNMF'

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

Table S7. Gene #4: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	5	9	12	6
AMP PEAK 4(3Q26.2) MUTATED	0	6	0	4
AMP PEAK 4(3Q26.2) WILD-TYPE	5	3	12	2

Figure S7. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S8. Gene #4: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 4(3Q26.2) MUTATED	74	47	42
AMP PEAK 4(3Q26.2) WILD-TYPE	112	169	49

Figure S8. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S9. Gene #4: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
AMP PEAK 4(3Q26.2) MUTATED	7	59	38	35
AMP PEAK 4(3Q26.2) WILD-TYPE	85	66	77	64

Figure S9. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S10. Gene #4: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 4(3Q26.2) MUTATED	56	7	32	50	17
AMP PEAK 4(3Q26.2) WILD-TYPE	82	105	44	56	37

Figure S10. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S11. Gene #4: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
AMP PEAK 4(3Q26.2) MUTATED	23	5	20	57	5	17	18	5	12
AMP PEAK 4(3Q26.2) WILD-TYPE	60	52	24	27	41	34	31	13	42

Figure S11. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S12. Gene #4: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 4(3Q26.2) MUTATED	38	102	21
AMP PEAK 4(3Q26.2) WILD-TYPE	141	129	57

Figure S12. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S13. Gene #4: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
AMP PEAK 4(3Q26.2) MUTATED	11	13	48	37	46	6
AMP PEAK 4(3Q26.2) WILD-TYPE	60	31	70	100	37	29

Figure S13. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.23

Table S14. Gene #4: 'amp_3q26.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 4(3Q26.2) MUTATED	34	80	23
AMP PEAK 4(3Q26.2) WILD-TYPE	121	112	55

Figure S14. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S15. Gene #4: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
AMP PEAK 4(3Q26.2) MUTATED	40	92	5
AMP PEAK 4(3Q26.2) WILD-TYPE	146	117	25

Figure S15. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S16. Gene #5: 'amp_4q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 5(4Q12) MUTATED	62	19	12
AMP PEAK 5(4Q12) WILD-TYPE	124	197	79

Figure S16. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S17. Gene #6: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 6(5P15.33) MUTATED	163	99	57
AMP PEAK 6(5P15.33) WILD-TYPE	23	117	34

Figure S17. Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S18. Gene #6: 'amp_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 6(5P15.33) MUTATED	111	63	33	73	33
AMP PEAK 6(5P15.33) WILD-TYPE	27	49	43	33	21

Figure S18. Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S19. Gene #6: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
AMP PEAK 6(5P15.33) MUTATED	65	33	28	70	20	34	30	0	33
AMP PEAK 6(5P15.33) WILD-TYPE	18	24	16	14	26	17	19	18	21

Figure S19. Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.049

Table S20. Gene #6: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
AMP PEAK 6(5P15.33) MUTATED	101	157	20
AMP PEAK 6(5P15.33) WILD-TYPE	85	52	10

Figure S20. Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S21. Gene #7: 'amp_5p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 7(5P13.1) MUTATED	148	87	56
AMP PEAK 7(5P13.1) WILD-TYPE	38	129	35

Figure S21. Get High-res Image Gene #7: 'amp_5p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S22. Gene #7: 'amp_5p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 7(5P13.1) MUTATED	94	55	29	76	31
AMP PEAK 7(5P13.1) WILD-TYPE	44	57	47	30	23

Figure S22. Get High-res Image Gene #7: 'amp_5p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S23. Gene #7: 'amp_5p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
AMP PEAK 7(5P13.1) MUTATED	59	29	22	67	18	36	24	0	30
AMP PEAK 7(5P13.1) WILD-TYPE	24	28	22	17	28	15	25	18	24

Figure S23. Get High-res Image Gene #7: 'amp_5p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.042

Table S24. Gene #7: 'amp_5p13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
AMP PEAK 7(5P13.1) MUTATED	90	147	19
AMP PEAK 7(5P13.1) WILD-TYPE	96	62	11

Figure S24. Get High-res Image Gene #7: 'amp_5p13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5q35.1' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.088

Table S25. Gene #8: 'amp_5q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
AMP PEAK 8(5Q35.1) MUTATED	41	27	25	18
AMP PEAK 8(5Q35.1) WILD-TYPE	51	98	90	81

Figure S25. Get High-res Image Gene #8: 'amp_5q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_5q35.1' versus 'MRNASEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.21

Table S26. Gene #8: 'amp_5q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 8(5Q35.1) MUTATED	34	42	8	20	16
AMP PEAK 8(5Q35.1) WILD-TYPE	104	70	68	86	38

Figure S26. Get High-res Image Gene #8: 'amp_5q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5q35.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S27. Gene #8: 'amp_5q35.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
AMP PEAK 8(5Q35.1) MUTATED	36	12	18	32	11	14
AMP PEAK 8(5Q35.1) WILD-TYPE	35	32	100	105	72	21

Figure S27. Get High-res Image Gene #8: 'amp_5q35.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_5q35.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.14

Table S28. Gene #8: 'amp_5q35.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
AMP PEAK 8(5Q35.1) MUTATED	60	36	13
AMP PEAK 8(5Q35.1) WILD-TYPE	126	173	17

Figure S28. Get High-res Image Gene #8: 'amp_5q35.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6p21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S29. Gene #9: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 9(6P21.1) MUTATED	82	55	49
AMP PEAK 9(6P21.1) WILD-TYPE	104	161	42

Figure S29. Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S30. Gene #9: 'amp_6p21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
AMP PEAK 9(6P21.1) MUTATED	28	76	45	16
AMP PEAK 9(6P21.1) WILD-TYPE	64	49	70	83

Figure S30. Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7p21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S31. Gene #10: 'amp_7p21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 10(7P21.1) MUTATED	155	80	35
AMP PEAK 10(7P21.1) WILD-TYPE	31	136	56

Figure S31. Get High-res Image Gene #10: 'amp_7p21.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7p21.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S32. Gene #10: 'amp_7p21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 10(7P21.1) MUTATED	108	43	36	49	29
AMP PEAK 10(7P21.1) WILD-TYPE	30	69	40	57	25

Figure S32. Get High-res Image Gene #10: 'amp_7p21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S33. Gene #10: 'amp_7p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
AMP PEAK 10(7P21.1) MUTATED	57	26	34	51	10	25	28	2	32
AMP PEAK 10(7P21.1) WILD-TYPE	26	31	10	33	36	26	21	16	22

Figure S33. Get High-res Image Gene #10: 'amp_7p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7p21.1' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S34. Gene #10: 'amp_7p21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 10(7P21.1) MUTATED	76	136	55
AMP PEAK 10(7P21.1) WILD-TYPE	103	95	23

Figure S34. Get High-res Image Gene #10: 'amp_7p21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7p21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S35. Gene #10: 'amp_7p21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
AMP PEAK 10(7P21.1) MUTATED	79	127	24
AMP PEAK 10(7P21.1) WILD-TYPE	107	82	6

Figure S35. Get High-res Image Gene #10: 'amp_7p21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S36. Gene #11: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 11(7P11.2) MUTATED	149	76	35
AMP PEAK 11(7P11.2) WILD-TYPE	37	140	56

Figure S36. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S37. Gene #11: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 11(7P11.2) MUTATED	106	36	40	46	28
AMP PEAK 11(7P11.2) WILD-TYPE	32	76	36	60	26

Figure S37. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S38. Gene #11: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
AMP PEAK 11(7P11.2) MUTATED	53	23	35	48	9	23	32	2	31
AMP PEAK 11(7P11.2) WILD-TYPE	30	34	9	36	37	28	17	16	23

Figure S38. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S39. Gene #11: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 11(7P11.2) MUTATED	66	136	55
AMP PEAK 11(7P11.2) WILD-TYPE	113	95	23

Figure S39. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S40. Gene #11: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
AMP PEAK 11(7P11.2) MUTATED	21	23	82	65	43	23
AMP PEAK 11(7P11.2) WILD-TYPE	50	21	36	72	40	12

Figure S40. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S41. Gene #11: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 11(7P11.2) MUTATED	58	113	51
AMP PEAK 11(7P11.2) WILD-TYPE	97	79	27

Figure S41. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S42. Gene #11: 'amp_7p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
AMP PEAK 11(7P11.2) MUTATED	69	130	23
AMP PEAK 11(7P11.2) WILD-TYPE	117	79	7

Figure S42. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S43. Gene #12: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 12(7Q31.2) MUTATED	116	60	30
AMP PEAK 12(7Q31.2) WILD-TYPE	70	156	61

Figure S43. Get High-res Image Gene #12: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S44. Gene #12: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 12(7Q31.2) MUTATED	86	24	33	36	23
AMP PEAK 12(7Q31.2) WILD-TYPE	52	88	43	70	31

Figure S44. Get High-res Image Gene #12: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S45. Gene #12: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
AMP PEAK 12(7Q31.2) MUTATED	46	15	33	39	5	15	23	2	24
AMP PEAK 12(7Q31.2) WILD-TYPE	37	42	11	45	41	36	26	16	30

Figure S45. Get High-res Image Gene #12: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S46. Gene #13: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 13(8P11.23) MUTATED	34	38	62
AMP PEAK 13(8P11.23) WILD-TYPE	152	178	29

Figure S46. Get High-res Image Gene #13: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.23' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.069

Table S47. Gene #13: 'amp_8p11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
AMP PEAK 13(8P11.23) MUTATED	18	53	27	18
AMP PEAK 13(8P11.23) WILD-TYPE	74	72	88	81

Figure S47. Get High-res Image Gene #13: 'amp_8p11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8p11.23' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S48. Gene #13: 'amp_8p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 13(8P11.23) MUTATED	28	16	25	49	12
AMP PEAK 13(8P11.23) WILD-TYPE	110	96	51	57	42

Figure S48. Get High-res Image Gene #13: 'amp_8p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.13

Table S49. Gene #13: 'amp_8p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
AMP PEAK 13(8P11.23) MUTATED	22	7	10	27	12	23	19	0	10
AMP PEAK 13(8P11.23) WILD-TYPE	61	50	34	57	34	28	30	18	44

Figure S49. Get High-res Image Gene #13: 'amp_8p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S50. Gene #14: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 14(8P11.21) MUTATED	49	48	73
AMP PEAK 14(8P11.21) WILD-TYPE	137	168	18

Figure S50. Get High-res Image Gene #14: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S51. Gene #14: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 14(8P11.21) MUTATED	44	19	25	63	14
AMP PEAK 14(8P11.21) WILD-TYPE	94	93	51	43	40

Figure S51. Get High-res Image Gene #14: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S52. Gene #14: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
AMP PEAK 14(8P11.21) MUTATED	26	9	20	35	15	30	18	0	12
AMP PEAK 14(8P11.21) WILD-TYPE	57	48	24	49	31	21	31	18	42

Figure S52. Get High-res Image Gene #14: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.22

Table S53. Gene #14: 'amp_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 14(8P11.21) MUTATED	37	85	27
AMP PEAK 14(8P11.21) WILD-TYPE	118	107	51

Figure S53. Get High-res Image Gene #14: 'amp_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S54. Gene #14: 'amp_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
AMP PEAK 14(8P11.21) MUTATED	45	95	9
AMP PEAK 14(8P11.21) WILD-TYPE	141	114	21

Figure S54. Get High-res Image Gene #14: 'amp_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q11.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S55. Gene #15: 'amp_8q11.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 15(8Q11.1) MUTATED	92	55	77
AMP PEAK 15(8Q11.1) WILD-TYPE	94	161	14

Figure S55. Get High-res Image Gene #15: 'amp_8q11.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q11.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S56. Gene #15: 'amp_8q11.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
AMP PEAK 15(8Q11.1) MUTATED	23	80	62	31
AMP PEAK 15(8Q11.1) WILD-TYPE	69	45	53	68

Figure S56. Get High-res Image Gene #15: 'amp_8q11.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q11.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S57. Gene #15: 'amp_8q11.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 15(8Q11.1) MUTATED	67	28	32	71	21
AMP PEAK 15(8Q11.1) WILD-TYPE	71	84	44	35	33

Figure S57. Get High-res Image Gene #15: 'amp_8q11.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q11.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S58. Gene #15: 'amp_8q11.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
AMP PEAK 15(8Q11.1) MUTATED	35	16	26	42	18	37	24	0	21
AMP PEAK 15(8Q11.1) WILD-TYPE	48	41	18	42	28	14	25	18	33

Figure S58. Get High-res Image Gene #15: 'amp_8q11.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q11.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S59. Gene #15: 'amp_8q11.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 15(8Q11.1) MUTATED	55	130	37
AMP PEAK 15(8Q11.1) WILD-TYPE	124	101	41

Figure S59. Get High-res Image Gene #15: 'amp_8q11.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q11.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S60. Gene #15: 'amp_8q11.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 15(8Q11.1) MUTATED	48	108	38
AMP PEAK 15(8Q11.1) WILD-TYPE	107	84	40

Figure S60. Get High-res Image Gene #15: 'amp_8q11.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q11.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S61. Gene #15: 'amp_8q11.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
AMP PEAK 15(8Q11.1) MUTATED	59	121	14
AMP PEAK 15(8Q11.1) WILD-TYPE	127	88	16

Figure S61. Get High-res Image Gene #15: 'amp_8q11.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S62. Gene #16: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 16(8Q24.21) MUTATED	136	92	82
AMP PEAK 16(8Q24.21) WILD-TYPE	50	124	9

Figure S62. Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S63. Gene #16: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
AMP PEAK 16(8Q24.21) MUTATED	38	95	85	51
AMP PEAK 16(8Q24.21) WILD-TYPE	54	30	30	48

Figure S63. Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S64. Gene #16: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 16(8Q24.21) MUTATED	103	49	39	86	26
AMP PEAK 16(8Q24.21) WILD-TYPE	35	63	37	20	28

Figure S64. Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S65. Gene #16: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
AMP PEAK 16(8Q24.21) MUTATED	52	25	39	57	27	45	30	0	28
AMP PEAK 16(8Q24.21) WILD-TYPE	31	32	5	27	19	6	19	18	26

Figure S65. Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S66. Gene #16: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 16(8Q24.21) MUTATED	88	168	51
AMP PEAK 16(8Q24.21) WILD-TYPE	91	63	27

Figure S66. Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S67. Gene #16: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
AMP PEAK 16(8Q24.21) MUTATED	94	155	16
AMP PEAK 16(8Q24.21) WILD-TYPE	92	54	14

Figure S67. Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10p15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S68. Gene #17: 'amp_10p15.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 17(10P15.1) MUTATED	60	37	39
AMP PEAK 17(10P15.1) WILD-TYPE	126	179	52

Figure S68. Get High-res Image Gene #17: 'amp_10p15.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_10p15.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S69. Gene #17: 'amp_10p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
AMP PEAK 17(10P15.1) MUTATED	5	51	41	20
AMP PEAK 17(10P15.1) WILD-TYPE	87	74	74	79

Figure S69. Get High-res Image Gene #17: 'amp_10p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_10p15.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S70. Gene #17: 'amp_10p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 17(10P15.1) MUTATED	37	17	27	45	8
AMP PEAK 17(10P15.1) WILD-TYPE	101	95	49	61	46

Figure S70. Get High-res Image Gene #17: 'amp_10p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_10p15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S71. Gene #17: 'amp_10p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
AMP PEAK 17(10P15.1) MUTATED	22	4	13	22	14	23	25	0	11
AMP PEAK 17(10P15.1) WILD-TYPE	61	53	31	62	32	28	24	18	43

Figure S71. Get High-res Image Gene #17: 'amp_10p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10p15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.028

Table S72. Gene #17: 'amp_10p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
AMP PEAK 17(10P15.1) MUTATED	17	17	44	21	30	4
AMP PEAK 17(10P15.1) WILD-TYPE	54	27	74	116	53	31

Figure S72. Get High-res Image Gene #17: 'amp_10p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_10p15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.062

Table S73. Gene #17: 'amp_10p15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
AMP PEAK 17(10P15.1) MUTATED	37	77	3
AMP PEAK 17(10P15.1) WILD-TYPE	149	132	27

Figure S73. Get High-res Image Gene #17: 'amp_10p15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S74. Gene #18: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 18(11Q13.3) MUTATED	90	30	45
AMP PEAK 18(11Q13.3) WILD-TYPE	96	186	46

Figure S74. Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S75. Gene #18: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
AMP PEAK 18(11Q13.3) MUTATED	14	55	49	25
AMP PEAK 18(11Q13.3) WILD-TYPE	78	70	66	74

Figure S75. Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S76. Gene #18: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 18(11Q13.3) MUTATED	58	21	17	56	12
AMP PEAK 18(11Q13.3) WILD-TYPE	80	91	59	50	42

Figure S76. Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S77. Gene #18: 'amp_11q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
AMP PEAK 18(11Q13.3) MUTATED	31	15	18	33	4	34	15	2	12
AMP PEAK 18(11Q13.3) WILD-TYPE	52	42	26	51	42	17	34	16	42

Figure S77. Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S78. Gene #18: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 18(11Q13.3) MUTATED	31	105	26
AMP PEAK 18(11Q13.3) WILD-TYPE	148	126	52

Figure S78. Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S79. Gene #18: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
AMP PEAK 18(11Q13.3) MUTATED	11	23	44	35	40	9
AMP PEAK 18(11Q13.3) WILD-TYPE	60	21	74	102	43	26

Figure S79. Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S80. Gene #18: 'amp_11q13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 18(11Q13.3) MUTATED	29	83	28
AMP PEAK 18(11Q13.3) WILD-TYPE	126	109	50

Figure S80. Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S81. Gene #18: 'amp_11q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
AMP PEAK 18(11Q13.3) MUTATED	35	94	11
AMP PEAK 18(11Q13.3) WILD-TYPE	151	115	19

Figure S81. Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S82. Gene #19: 'amp_12p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 19(12P12.1) MUTATED	70	54	50
AMP PEAK 19(12P12.1) WILD-TYPE	116	162	41

Figure S82. Get High-res Image Gene #19: 'amp_12p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12p12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S83. Gene #19: 'amp_12p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
AMP PEAK 19(12P12.1) MUTATED	10	57	44	37
AMP PEAK 19(12P12.1) WILD-TYPE	82	68	71	62

Figure S83. Get High-res Image Gene #19: 'amp_12p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S84. Gene #19: 'amp_12p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 19(12P12.1) MUTATED	55	10	38	53	16
AMP PEAK 19(12P12.1) WILD-TYPE	83	102	38	53	38

Figure S84. Get High-res Image Gene #19: 'amp_12p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S85. Gene #19: 'amp_12p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
AMP PEAK 19(12P12.1) MUTATED	28	7	21	31	5	32	28	5	15
AMP PEAK 19(12P12.1) WILD-TYPE	55	50	23	53	41	19	21	13	39

Figure S85. Get High-res Image Gene #19: 'amp_12p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S86. Gene #19: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 19(12P12.1) MUTATED	42	106	23
AMP PEAK 19(12P12.1) WILD-TYPE	137	125	55

Figure S86. Get High-res Image Gene #19: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S87. Gene #19: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
AMP PEAK 19(12P12.1) MUTATED	12	26	47	38	39	9
AMP PEAK 19(12P12.1) WILD-TYPE	59	18	71	99	44	26

Figure S87. Get High-res Image Gene #19: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S88. Gene #19: 'amp_12p12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 19(12P12.1) MUTATED	31	88	28
AMP PEAK 19(12P12.1) WILD-TYPE	124	104	50

Figure S88. Get High-res Image Gene #19: 'amp_12p12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S89. Gene #19: 'amp_12p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
AMP PEAK 19(12P12.1) MUTATED	40	99	8
AMP PEAK 19(12P12.1) WILD-TYPE	146	110	22

Figure S89. Get High-res Image Gene #19: 'amp_12p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S90. Gene #20: 'amp_12q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 20(12Q14.1) MUTATED	60	49	52
AMP PEAK 20(12Q14.1) WILD-TYPE	126	167	39

Figure S90. Get High-res Image Gene #20: 'amp_12q14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q14.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S91. Gene #20: 'amp_12q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
AMP PEAK 20(12Q14.1) MUTATED	10	62	34	34
AMP PEAK 20(12Q14.1) WILD-TYPE	82	63	81	65

Figure S91. Get High-res Image Gene #20: 'amp_12q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S92. Gene #20: 'amp_12q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 20(12Q14.1) MUTATED	42	13	34	58	12
AMP PEAK 20(12Q14.1) WILD-TYPE	96	99	42	48	42

Figure S92. Get High-res Image Gene #20: 'amp_12q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S93. Gene #20: 'amp_12q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
AMP PEAK 20(12Q14.1) MUTATED	18	11	18	28	6	36	30	2	10
AMP PEAK 20(12Q14.1) WILD-TYPE	65	46	26	56	40	15	19	16	44

Figure S93. Get High-res Image Gene #20: 'amp_12q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S94. Gene #20: 'amp_12q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 20(12Q14.1) MUTATED	33	105	21
AMP PEAK 20(12Q14.1) WILD-TYPE	146	126	57

Figure S94. Get High-res Image Gene #20: 'amp_12q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S95. Gene #20: 'amp_12q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
AMP PEAK 20(12Q14.1) MUTATED	12	28	43	25	41	10
AMP PEAK 20(12Q14.1) WILD-TYPE	59	16	75	112	42	25

Figure S95. Get High-res Image Gene #20: 'amp_12q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S96. Gene #20: 'amp_12q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 20(12Q14.1) MUTATED	24	83	30
AMP PEAK 20(12Q14.1) WILD-TYPE	131	109	48

Figure S96. Get High-res Image Gene #20: 'amp_12q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S97. Gene #20: 'amp_12q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
AMP PEAK 20(12Q14.1) MUTATED	29	98	10
AMP PEAK 20(12Q14.1) WILD-TYPE	157	111	20

Figure S97. Get High-res Image Gene #20: 'amp_12q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S98. Gene #21: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 21(12Q15) MUTATED	59	52	51
AMP PEAK 21(12Q15) WILD-TYPE	127	164	40

Figure S98. Get High-res Image Gene #21: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S99. Gene #21: 'amp_12q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
AMP PEAK 21(12Q15) MUTATED	11	63	36	31
AMP PEAK 21(12Q15) WILD-TYPE	81	62	79	68

Figure S99. Get High-res Image Gene #21: 'amp_12q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q15' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S100. Gene #21: 'amp_12q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 21(12Q15) MUTATED	41	13	35	58	12
AMP PEAK 21(12Q15) WILD-TYPE	97	99	41	48	42

Figure S100. Get High-res Image Gene #21: 'amp_12q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S101. Gene #21: 'amp_12q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
AMP PEAK 21(12Q15) MUTATED	18	11	17	28	6	36	29	4	10
AMP PEAK 21(12Q15) WILD-TYPE	65	46	27	56	40	15	20	14	44

Figure S101. Get High-res Image Gene #21: 'amp_12q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S102. Gene #21: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 21(12Q15) MUTATED	33	106	22
AMP PEAK 21(12Q15) WILD-TYPE	146	125	56

Figure S102. Get High-res Image Gene #21: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q15' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S103. Gene #21: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
AMP PEAK 21(12Q15) MUTATED	10	29	38	28	44	12
AMP PEAK 21(12Q15) WILD-TYPE	61	15	80	109	39	23

Figure S103. Get High-res Image Gene #21: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S104. Gene #21: 'amp_12q15' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 21(12Q15) MUTATED	24	84	31
AMP PEAK 21(12Q15) WILD-TYPE	131	108	47

Figure S104. Get High-res Image Gene #21: 'amp_12q15' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12q15' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S105. Gene #21: 'amp_12q15' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
AMP PEAK 21(12Q15) MUTATED	30	97	12
AMP PEAK 21(12Q15) WILD-TYPE	156	112	18

Figure S105. Get High-res Image Gene #21: 'amp_12q15' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q33.3' versus 'METHLYATION_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.15

Table S106. Gene #22: 'amp_13q33.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
AMP PEAK 22(13Q33.3) MUTATED	13	34	11	8
AMP PEAK 22(13Q33.3) WILD-TYPE	79	91	104	91

Figure S106. Get High-res Image Gene #22: 'amp_13q33.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_14q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S107. Gene #23: 'amp_14q13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 23(14Q13.3) MUTATED	101	57	64
AMP PEAK 23(14Q13.3) WILD-TYPE	85	159	27

Figure S107. Get High-res Image Gene #23: 'amp_14q13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_14q13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S108. Gene #23: 'amp_14q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
AMP PEAK 23(14Q13.3) MUTATED	28	77	56	33
AMP PEAK 23(14Q13.3) WILD-TYPE	64	48	59	66

Figure S108. Get High-res Image Gene #23: 'amp_14q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_14q13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S109. Gene #23: 'amp_14q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 23(14Q13.3) MUTATED	81	39	10	74	15
AMP PEAK 23(14Q13.3) WILD-TYPE	57	73	66	32	39

Figure S109. Get High-res Image Gene #23: 'amp_14q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_14q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S110. Gene #23: 'amp_14q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
AMP PEAK 23(14Q13.3) MUTATED	47	25	21	55	9	40	8	0	14
AMP PEAK 23(14Q13.3) WILD-TYPE	36	32	23	29	37	11	41	18	40

Figure S110. Get High-res Image Gene #23: 'amp_14q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_14q13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S111. Gene #23: 'amp_14q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 23(14Q13.3) MUTATED	50	131	38
AMP PEAK 23(14Q13.3) WILD-TYPE	129	100	40

Figure S111. Get High-res Image Gene #23: 'amp_14q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_14q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S112. Gene #23: 'amp_14q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
AMP PEAK 23(14Q13.3) MUTATED	29	36	55	35	46	18
AMP PEAK 23(14Q13.3) WILD-TYPE	42	8	63	102	37	17

Figure S112. Get High-res Image Gene #23: 'amp_14q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_14q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.075

Table S113. Gene #23: 'amp_14q13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 23(14Q13.3) MUTATED	48	100	42
AMP PEAK 23(14Q13.3) WILD-TYPE	107	92	36

Figure S113. Get High-res Image Gene #23: 'amp_14q13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_14q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S114. Gene #23: 'amp_14q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
AMP PEAK 23(14Q13.3) MUTATED	57	116	17
AMP PEAK 23(14Q13.3) WILD-TYPE	129	93	13

Figure S114. Get High-res Image Gene #23: 'amp_14q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_16p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S115. Gene #24: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 24(16P11.2) MUTATED	84	45	30
AMP PEAK 24(16P11.2) WILD-TYPE	102	171	61

Figure S115. Get High-res Image Gene #24: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S116. Gene #25: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 25(17Q12) MUTATED	111	56	52
AMP PEAK 25(17Q12) WILD-TYPE	75	160	39

Figure S116. Get High-res Image Gene #25: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S117. Gene #25: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
AMP PEAK 25(17Q12) MUTATED	20	68	63	33
AMP PEAK 25(17Q12) WILD-TYPE	72	57	52	66

Figure S117. Get High-res Image Gene #25: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S118. Gene #25: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 25(17Q12) MUTATED	84	30	24	57	20
AMP PEAK 25(17Q12) WILD-TYPE	54	82	52	49	34

Figure S118. Get High-res Image Gene #25: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S119. Gene #25: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
AMP PEAK 25(17Q12) MUTATED	43	20	26	51	8	28	19	1	19
AMP PEAK 25(17Q12) WILD-TYPE	40	37	18	33	38	23	30	17	35

Figure S119. Get High-res Image Gene #25: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S120. Gene #25: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 25(17Q12) MUTATED	54	134	29
AMP PEAK 25(17Q12) WILD-TYPE	125	97	49

Figure S120. Get High-res Image Gene #25: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S121. Gene #25: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
AMP PEAK 25(17Q12) MUTATED	21	26	62	43	52	13
AMP PEAK 25(17Q12) WILD-TYPE	50	18	56	94	31	22

Figure S121. Get High-res Image Gene #25: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S122. Gene #25: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
AMP PEAK 25(17Q12) MUTATED	55	117	11
AMP PEAK 25(17Q12) WILD-TYPE	131	92	19

Figure S122. Get High-res Image Gene #25: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S123. Gene #26: 'amp_17q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 26(17Q23.1) MUTATED	123	65	53
AMP PEAK 26(17Q23.1) WILD-TYPE	63	151	38

Figure S123. Get High-res Image Gene #26: 'amp_17q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S124. Gene #26: 'amp_17q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
AMP PEAK 26(17Q23.1) MUTATED	21	68	77	39
AMP PEAK 26(17Q23.1) WILD-TYPE	71	57	38	60

Figure S124. Get High-res Image Gene #26: 'amp_17q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.049

Table S125. Gene #26: 'amp_17q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	112	71	52
AMP PEAK 26(17Q23.1) MUTATED	67	20	29
AMP PEAK 26(17Q23.1) WILD-TYPE	45	51	23

Figure S125. Get High-res Image Gene #26: 'amp_17q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S126. Gene #26: 'amp_17q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 26(17Q23.1) MUTATED	95	37	30	54	21
AMP PEAK 26(17Q23.1) WILD-TYPE	43	75	46	52	33

Figure S126. Get High-res Image Gene #26: 'amp_17q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S127. Gene #26: 'amp_17q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
AMP PEAK 26(17Q23.1) MUTATED	52	25	30	49	7	28	24	0	22
AMP PEAK 26(17Q23.1) WILD-TYPE	31	32	14	35	39	23	25	18	32

Figure S127. Get High-res Image Gene #26: 'amp_17q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q23.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S128. Gene #26: 'amp_17q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 26(17Q23.1) MUTATED	63	143	33
AMP PEAK 26(17Q23.1) WILD-TYPE	116	88	45

Figure S128. Get High-res Image Gene #26: 'amp_17q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.028

Table S129. Gene #26: 'amp_17q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
AMP PEAK 26(17Q23.1) MUTATED	25	25	68	52	55	14
AMP PEAK 26(17Q23.1) WILD-TYPE	46	19	50	85	28	21

Figure S129. Get High-res Image Gene #26: 'amp_17q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.035

Table S130. Gene #26: 'amp_17q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
AMP PEAK 26(17Q23.1) MUTATED	68	122	12
AMP PEAK 26(17Q23.1) WILD-TYPE	118	87	18

Figure S130. Get High-res Image Gene #26: 'amp_17q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S131. Gene #27: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
AMP PEAK 27(18Q11.2) MUTATED	6	48	24	11
AMP PEAK 27(18Q11.2) WILD-TYPE	86	77	91	88

Figure S131. Get High-res Image Gene #27: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.049

Table S132. Gene #27: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 27(18Q11.2) MUTATED	24	12	19	37	6
AMP PEAK 27(18Q11.2) WILD-TYPE	114	100	57	69	48

Figure S132. Get High-res Image Gene #27: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.094

Table S133. Gene #27: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
AMP PEAK 27(18Q11.2) MUTATED	12	5	7	27	6	21	10	4	6
AMP PEAK 27(18Q11.2) WILD-TYPE	71	52	37	57	40	30	39	14	48

Figure S133. Get High-res Image Gene #27: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.15

Table S134. Gene #27: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 27(18Q11.2) MUTATED	20	63	15
AMP PEAK 27(18Q11.2) WILD-TYPE	159	168	63

Figure S134. Get High-res Image Gene #27: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S135. Gene #27: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
AMP PEAK 27(18Q11.2) MUTATED	6	14	26	16	32	4
AMP PEAK 27(18Q11.2) WILD-TYPE	65	30	92	121	51	31

Figure S135. Get High-res Image Gene #27: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S136. Gene #27: 'amp_18q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
AMP PEAK 27(18Q11.2) MUTATED	25	61	3
AMP PEAK 27(18Q11.2) WILD-TYPE	161	148	27

Figure S136. Get High-res Image Gene #27: 'amp_18q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S137. Gene #28: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
AMP PEAK 28(19Q12) MUTATED	13	58	22	27
AMP PEAK 28(19Q12) WILD-TYPE	79	67	93	72

Figure S137. Get High-res Image Gene #28: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.14

Table S138. Gene #28: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 28(19Q12) MUTATED	38	17	28	40	8
AMP PEAK 28(19Q12) WILD-TYPE	100	95	48	66	46

Figure S138. Get High-res Image Gene #28: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S139. Gene #28: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
AMP PEAK 28(19Q12) MUTATED	18	5	14	32	12	17	23	1	9
AMP PEAK 28(19Q12) WILD-TYPE	65	52	30	52	34	34	26	17	45

Figure S139. Get High-res Image Gene #28: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S140. Gene #28: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 28(19Q12) MUTATED	30	85	18
AMP PEAK 28(19Q12) WILD-TYPE	149	146	60

Figure S140. Get High-res Image Gene #28: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S141. Gene #28: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
AMP PEAK 28(19Q12) MUTATED	16	14	45	20	33	5
AMP PEAK 28(19Q12) WILD-TYPE	55	30	73	117	50	30

Figure S141. Get High-res Image Gene #28: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.028

Table S142. Gene #28: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 28(19Q12) MUTATED	28	75	16
AMP PEAK 28(19Q12) WILD-TYPE	127	117	62

Figure S142. Get High-res Image Gene #28: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S143. Gene #28: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
AMP PEAK 28(19Q12) MUTATED	34	81	4
AMP PEAK 28(19Q12) WILD-TYPE	152	128	26

Figure S143. Get High-res Image Gene #28: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20p11.21' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S144. Gene #29: 'amp_20p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 29(20P11.21) MUTATED	73	62	53
AMP PEAK 29(20P11.21) WILD-TYPE	113	154	38

Figure S144. Get High-res Image Gene #29: 'amp_20p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S145. Gene #29: 'amp_20p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
AMP PEAK 29(20P11.21) MUTATED	21	69	35	36
AMP PEAK 29(20P11.21) WILD-TYPE	71	56	80	63

Figure S145. Get High-res Image Gene #29: 'amp_20p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20p11.21' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.055

Table S146. Gene #29: 'amp_20p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 29(20P11.21) MUTATED	47	34	25	62	16
AMP PEAK 29(20P11.21) WILD-TYPE	91	78	51	44	38

Figure S146. Get High-res Image Gene #29: 'amp_20p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S147. Gene #29: 'amp_20p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
AMP PEAK 29(20P11.21) MUTATED	22	14	18	52	17	29	16	1	15
AMP PEAK 29(20P11.21) WILD-TYPE	61	43	26	32	29	22	33	17	39

Figure S147. Get High-res Image Gene #29: 'amp_20p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20p11.21' versus 'MIRSEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.1

Table S148. Gene #29: 'amp_20p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 29(20P11.21) MUTATED	47	108	31
AMP PEAK 29(20P11.21) WILD-TYPE	132	123	47

Figure S148. Get High-res Image Gene #29: 'amp_20p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20p11.21' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S149. Gene #29: 'amp_20p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
AMP PEAK 29(20P11.21) MUTATED	19	20	45	40	48	14
AMP PEAK 29(20P11.21) WILD-TYPE	52	24	73	97	35	21

Figure S149. Get High-res Image Gene #29: 'amp_20p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.028

Table S150. Gene #29: 'amp_20p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
AMP PEAK 29(20P11.21) MUTATED	49	100	13
AMP PEAK 29(20P11.21) WILD-TYPE	137	109	17

Figure S150. Get High-res Image Gene #29: 'amp_20p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S151. Gene #30: 'amp_20q13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 30(20Q13.33) MUTATED	103	73	61
AMP PEAK 30(20Q13.33) WILD-TYPE	83	143	30

Figure S151. Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.33' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.055

Table S152. Gene #30: 'amp_20q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
AMP PEAK 30(20Q13.33) MUTATED	32	80	51	41
AMP PEAK 30(20Q13.33) WILD-TYPE	60	45	64	58

Figure S152. Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S153. Gene #30: 'amp_20q13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 30(20Q13.33) MUTATED	71	41	27	75	19
AMP PEAK 30(20Q13.33) WILD-TYPE	67	71	49	31	35

Figure S153. Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S154. Gene #30: 'amp_20q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
AMP PEAK 30(20Q13.33) MUTATED	34	21	28	56	21	36	17	2	18
AMP PEAK 30(20Q13.33) WILD-TYPE	49	36	16	28	25	15	32	16	36

Figure S154. Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S155. Gene #30: 'amp_20q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 30(20Q13.33) MUTATED	63	135	35
AMP PEAK 30(20Q13.33) WILD-TYPE	116	96	43

Figure S155. Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q13.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.035

Table S156. Gene #30: 'amp_20q13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 30(20Q13.33) MUTATED	54	113	36
AMP PEAK 30(20Q13.33) WILD-TYPE	101	79	42

Figure S156. Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S157. Gene #30: 'amp_20q13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
AMP PEAK 30(20Q13.33) MUTATED	64	122	17
AMP PEAK 30(20Q13.33) WILD-TYPE	122	87	13

Figure S157. Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_22q11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S158. Gene #31: 'amp_22q11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 31(22Q11.22) MUTATED	52	20	15
AMP PEAK 31(22Q11.22) WILD-TYPE	134	196	76

Figure S158. Get High-res Image Gene #31: 'amp_22q11.22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xq28' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S159. Gene #32: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 32(XQ28) MUTATED	91	33	25
AMP PEAK 32(XQ28) WILD-TYPE	95	183	66

Figure S159. Get High-res Image Gene #32: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xq28' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S160. Gene #32: 'amp_xq28' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 32(XQ28) MUTATED	65	23	17	32	12
AMP PEAK 32(XQ28) WILD-TYPE	73	89	59	74	42

Figure S160. Get High-res Image Gene #32: 'amp_xq28' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xq28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S161. Gene #32: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
AMP PEAK 32(XQ28) MUTATED	32	13	23	34	6	13	13	0	15
AMP PEAK 32(XQ28) WILD-TYPE	51	44	21	50	40	38	36	18	39

Figure S161. Get High-res Image Gene #32: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.13' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.075

Table S162. Gene #33: 'del_1p36.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 1(1P36.13) MUTATED	32	47	37
DEL PEAK 1(1P36.13) WILD-TYPE	154	169	54

Figure S162. Get High-res Image Gene #33: 'del_1p36.13' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.13' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.062

Table S163. Gene #33: 'del_1p36.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 1(1P36.13) MUTATED	31	15	23	38	5
DEL PEAK 1(1P36.13) WILD-TYPE	107	97	53	68	49

Figure S163. Get High-res Image Gene #33: 'del_1p36.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S164. Gene #33: 'del_1p36.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 1(1P36.13) MUTATED	12	9	15	17	11	25	17	2	4
DEL PEAK 1(1P36.13) WILD-TYPE	71	48	29	67	35	26	32	16	50

Figure S164. Get High-res Image Gene #33: 'del_1p36.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S165. Gene #34: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 2(1P13.1) MUTATED	44	51	49
DEL PEAK 2(1P13.1) WILD-TYPE	142	165	42

Figure S165. Get High-res Image Gene #34: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p13.1' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.1

Table S166. Gene #34: 'del_1p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 2(1P13.1) MUTATED	33	25	23	50	10
DEL PEAK 2(1P13.1) WILD-TYPE	105	87	53	56	44

Figure S166. Get High-res Image Gene #34: 'del_1p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.075

Table S167. Gene #34: 'del_1p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 2(1P13.1) MUTATED	16	15	15	22	20	27	16	2	8
DEL PEAK 2(1P13.1) WILD-TYPE	67	42	29	62	26	24	33	16	46

Figure S167. Get High-res Image Gene #34: 'del_1p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.081

Table S168. Gene #34: 'del_1p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
DEL PEAK 2(1P13.1) MUTATED	16	25	31	28	25	16
DEL PEAK 2(1P13.1) WILD-TYPE	55	19	87	109	58	19

Figure S168. Get High-res Image Gene #34: 'del_1p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S169. Gene #36: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 4(2Q37.3) MUTATED	36	11	16
DEL PEAK 4(2Q37.3) WILD-TYPE	150	205	75

Figure S169. Get High-res Image Gene #36: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S170. Gene #37: 'del_3p26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 5(3P26.3) MUTATED	96	72	55
DEL PEAK 5(3P26.3) WILD-TYPE	90	144	36

Figure S170. Get High-res Image Gene #37: 'del_3p26.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p26.3' versus 'RPPA_CHIERARCHICAL'

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

Table S171. Gene #37: 'del_3p26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	112	71	52
DEL PEAK 5(3P26.3) MUTATED	54	24	37
DEL PEAK 5(3P26.3) WILD-TYPE	58	47	15

Figure S171. Get High-res Image Gene #37: 'del_3p26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S172. Gene #37: 'del_3p26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 5(3P26.3) MUTATED	28	24	17	58	13	35	28	0	18
DEL PEAK 5(3P26.3) WILD-TYPE	55	33	27	26	33	16	21	18	36

Figure S172. Get High-res Image Gene #37: 'del_3p26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.3' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.042

Table S173. Gene #37: 'del_3p26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 5(3P26.3) MUTATED	57	118	44
DEL PEAK 5(3P26.3) WILD-TYPE	122	113	34

Figure S173. Get High-res Image Gene #37: 'del_3p26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p21.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S174. Gene #38: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 6(3P21.31) MUTATED	101	77	59
DEL PEAK 6(3P21.31) WILD-TYPE	85	139	32

Figure S174. Get High-res Image Gene #38: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p21.31' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.075

Table S175. Gene #38: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
DEL PEAK 6(3P21.31) MUTATED	35	82	48	43
DEL PEAK 6(3P21.31) WILD-TYPE	57	43	67	56

Figure S175. Get High-res Image Gene #38: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p21.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.15

Table S176. Gene #38: 'del_3p21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	112	71	52
DEL PEAK 6(3P21.31) MUTATED	60	24	37
DEL PEAK 6(3P21.31) WILD-TYPE	52	47	15

Figure S176. Get High-res Image Gene #38: 'del_3p21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S177. Gene #38: 'del_3p21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 6(3P21.31) MUTATED	28	25	19	61	13	37	30	1	19
DEL PEAK 6(3P21.31) WILD-TYPE	55	32	25	23	33	14	19	17	35

Figure S177. Get High-res Image Gene #38: 'del_3p21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S178. Gene #38: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 6(3P21.31) MUTATED	61	127	45
DEL PEAK 6(3P21.31) WILD-TYPE	118	104	33

Figure S178. Get High-res Image Gene #38: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.069

Table S179. Gene #38: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
DEL PEAK 6(3P21.31) MUTATED	33	26	51	51	58	14
DEL PEAK 6(3P21.31) WILD-TYPE	38	18	67	86	25	21

Figure S179. Get High-res Image Gene #38: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.069

Table S180. Gene #38: 'del_3p21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
DEL PEAK 6(3P21.31) MUTATED	69	122	13
DEL PEAK 6(3P21.31) WILD-TYPE	117	87	17

Figure S180. Get High-res Image Gene #38: 'del_3p21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q29' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.14

Table S181. Gene #40: 'del_3q29' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
DEL PEAK 8(3Q29) MUTATED	32	46	32	12
DEL PEAK 8(3Q29) WILD-TYPE	60	79	83	87

Figure S181. Get High-res Image Gene #40: 'del_3q29' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3q29' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.088

Table S182. Gene #40: 'del_3q29' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 8(3Q29) MUTATED	22	40	13	41	15
DEL PEAK 8(3Q29) WILD-TYPE	116	72	63	65	39

Figure S182. Get High-res Image Gene #40: 'del_3q29' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3q29' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S183. Gene #40: 'del_3q29' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 8(3Q29) MUTATED	17	19	5	12	22	29	14	0	13
DEL PEAK 8(3Q29) WILD-TYPE	66	38	39	72	24	22	35	18	41

Figure S183. Get High-res Image Gene #40: 'del_3q29' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S184. Gene #41: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 9(4P16.3) MUTATED	49	36	41
DEL PEAK 9(4P16.3) WILD-TYPE	137	180	50

Figure S184. Get High-res Image Gene #41: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S185. Gene #41: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
DEL PEAK 9(4P16.3) MUTATED	8	46	26	30
DEL PEAK 9(4P16.3) WILD-TYPE	84	79	89	69

Figure S185. Get High-res Image Gene #41: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p16.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S186. Gene #41: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 9(4P16.3) MUTATED	35	12	20	45	13
DEL PEAK 9(4P16.3) WILD-TYPE	103	100	56	61	41

Figure S186. Get High-res Image Gene #41: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S187. Gene #41: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 9(4P16.3) MUTATED	18	9	9	39	4	23	11	2	10
DEL PEAK 9(4P16.3) WILD-TYPE	65	48	35	45	42	28	38	16	44

Figure S187. Get High-res Image Gene #41: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S188. Gene #41: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 9(4P16.3) MUTATED	25	80	20
DEL PEAK 9(4P16.3) WILD-TYPE	154	151	58

Figure S188. Get High-res Image Gene #41: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S189. Gene #41: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
DEL PEAK 9(4P16.3) MUTATED	6	16	39	26	33	5
DEL PEAK 9(4P16.3) WILD-TYPE	65	28	79	111	50	30

Figure S189. Get High-res Image Gene #41: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S190. Gene #41: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
DEL PEAK 9(4P16.3) MUTATED	33	72	4
DEL PEAK 9(4P16.3) WILD-TYPE	153	137	26

Figure S190. Get High-res Image Gene #41: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.1' versus 'MRNA_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.15

Table S191. Gene #42: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	5	9	12	6
DEL PEAK 10(4Q22.1) MUTATED	3	1	0	5
DEL PEAK 10(4Q22.1) WILD-TYPE	2	8	12	1

Figure S191. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S192. Gene #42: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 10(4Q22.1) MUTATED	64	44	46
DEL PEAK 10(4Q22.1) WILD-TYPE	122	172	45

Figure S192. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S193. Gene #42: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
DEL PEAK 10(4Q22.1) MUTATED	8	61	28	33
DEL PEAK 10(4Q22.1) WILD-TYPE	84	64	87	66

Figure S193. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S194. Gene #42: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 10(4Q22.1) MUTATED	40	15	31	52	14
DEL PEAK 10(4Q22.1) WILD-TYPE	98	97	45	54	40

Figure S194. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S195. Gene #42: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 10(4Q22.1) MUTATED	21	8	6	43	6	29	25	1	13
DEL PEAK 10(4Q22.1) WILD-TYPE	62	49	38	41	40	22	24	17	41

Figure S195. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S196. Gene #42: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 10(4Q22.1) MUTATED	31	96	26
DEL PEAK 10(4Q22.1) WILD-TYPE	148	135	52

Figure S196. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S197. Gene #42: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
DEL PEAK 10(4Q22.1) MUTATED	11	17	47	27	42	9
DEL PEAK 10(4Q22.1) WILD-TYPE	60	27	71	110	41	26

Figure S197. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S198. Gene #42: 'del_4q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
DEL PEAK 10(4Q22.1) MUTATED	37	86	7
DEL PEAK 10(4Q22.1) WILD-TYPE	149	123	23

Figure S198. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q35.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S199. Gene #43: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 11(4Q35.1) MUTATED	75	51	56
DEL PEAK 11(4Q35.1) WILD-TYPE	111	165	35

Figure S199. Get High-res Image Gene #43: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q35.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S200. Gene #43: 'del_4q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
DEL PEAK 11(4Q35.1) MUTATED	7	74	38	38
DEL PEAK 11(4Q35.1) WILD-TYPE	85	51	77	61

Figure S200. Get High-res Image Gene #43: 'del_4q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q35.1' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S201. Gene #43: 'del_4q35.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	112	71	52
DEL PEAK 11(4Q35.1) MUTATED	47	16	33
DEL PEAK 11(4Q35.1) WILD-TYPE	65	55	19

Figure S201. Get High-res Image Gene #43: 'del_4q35.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4q35.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S202. Gene #43: 'del_4q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 11(4Q35.1) MUTATED	45	18	37	63	16
DEL PEAK 11(4Q35.1) WILD-TYPE	93	94	39	43	38

Figure S202. Get High-res Image Gene #43: 'del_4q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S203. Gene #43: 'del_4q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 11(4Q35.1) MUTATED	24	9	6	50	8	36	29	1	16
DEL PEAK 11(4Q35.1) WILD-TYPE	59	48	38	34	38	15	20	17	38

Figure S203. Get High-res Image Gene #43: 'del_4q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S204. Gene #43: 'del_4q35.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 11(4Q35.1) MUTATED	40	118	23
DEL PEAK 11(4Q35.1) WILD-TYPE	139	113	55

Figure S204. Get High-res Image Gene #43: 'del_4q35.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q35.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S205. Gene #43: 'del_4q35.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
DEL PEAK 11(4Q35.1) MUTATED	12	22	53	35	53	6
DEL PEAK 11(4Q35.1) WILD-TYPE	59	22	65	102	30	29

Figure S205. Get High-res Image Gene #43: 'del_4q35.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S206. Gene #43: 'del_4q35.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
DEL PEAK 11(4Q35.1) MUTATED	40	95	22
DEL PEAK 11(4Q35.1) WILD-TYPE	115	97	56

Figure S206. Get High-res Image Gene #43: 'del_4q35.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q35.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S207. Gene #43: 'del_4q35.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
DEL PEAK 11(4Q35.1) MUTATED	43	109	5
DEL PEAK 11(4Q35.1) WILD-TYPE	143	100	25

Figure S207. Get High-res Image Gene #43: 'del_4q35.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S208. Gene #44: 'del_5q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 12(5Q11.2) MUTATED	95	34	43
DEL PEAK 12(5Q11.2) WILD-TYPE	91	182	48

Figure S208. Get High-res Image Gene #44: 'del_5q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S209. Gene #44: 'del_5q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
DEL PEAK 12(5Q11.2) MUTATED	12	63	39	31
DEL PEAK 12(5Q11.2) WILD-TYPE	80	62	76	68

Figure S209. Get High-res Image Gene #44: 'del_5q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S210. Gene #44: 'del_5q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 12(5Q11.2) MUTATED	57	19	29	52	12
DEL PEAK 12(5Q11.2) WILD-TYPE	81	93	47	54	42

Figure S210. Get High-res Image Gene #44: 'del_5q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S211. Gene #44: 'del_5q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 12(5Q11.2) MUTATED	30	11	13	46	6	24	24	1	14
DEL PEAK 12(5Q11.2) WILD-TYPE	53	46	31	38	40	27	25	17	40

Figure S211. Get High-res Image Gene #44: 'del_5q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S212. Gene #44: 'del_5q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 12(5Q11.2) MUTATED	33	112	24
DEL PEAK 12(5Q11.2) WILD-TYPE	146	119	54

Figure S212. Get High-res Image Gene #44: 'del_5q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S213. Gene #44: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
DEL PEAK 12(5Q11.2) MUTATED	12	19	47	37	48	6
DEL PEAK 12(5Q11.2) WILD-TYPE	59	25	71	100	35	29

Figure S213. Get High-res Image Gene #44: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S214. Gene #44: 'del_5q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
DEL PEAK 12(5Q11.2) MUTATED	30	90	23
DEL PEAK 12(5Q11.2) WILD-TYPE	125	102	55

Figure S214. Get High-res Image Gene #44: 'del_5q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S215. Gene #44: 'del_5q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
DEL PEAK 12(5Q11.2) MUTATED	33	103	7
DEL PEAK 12(5Q11.2) WILD-TYPE	153	106	23

Figure S215. Get High-res Image Gene #44: 'del_5q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S216. Gene #45: 'del_5q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 13(5Q31.1) MUTATED	102	45	52
DEL PEAK 13(5Q31.1) WILD-TYPE	84	171	39

Figure S216. Get High-res Image Gene #45: 'del_5q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q31.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S217. Gene #45: 'del_5q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
DEL PEAK 13(5Q31.1) MUTATED	14	70	49	39
DEL PEAK 13(5Q31.1) WILD-TYPE	78	55	66	60

Figure S217. Get High-res Image Gene #45: 'del_5q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q31.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S218. Gene #45: 'del_5q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 13(5Q31.1) MUTATED	66	23	33	59	15
DEL PEAK 13(5Q31.1) WILD-TYPE	72	89	43	47	39

Figure S218. Get High-res Image Gene #45: 'del_5q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S219. Gene #45: 'del_5q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 13(5Q31.1) MUTATED	36	12	16	47	10	30	26	1	18
DEL PEAK 13(5Q31.1) WILD-TYPE	47	45	28	37	36	21	23	17	36

Figure S219. Get High-res Image Gene #45: 'del_5q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q31.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S220. Gene #45: 'del_5q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 13(5Q31.1) MUTATED	43	127	26
DEL PEAK 13(5Q31.1) WILD-TYPE	136	104	52

Figure S220. Get High-res Image Gene #45: 'del_5q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S221. Gene #45: 'del_5q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
DEL PEAK 13(5Q31.1) MUTATED	19	20	57	40	53	7
DEL PEAK 13(5Q31.1) WILD-TYPE	52	24	61	97	30	28

Figure S221. Get High-res Image Gene #45: 'del_5q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q31.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S222. Gene #45: 'del_5q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
DEL PEAK 13(5Q31.1) MUTATED	42	101	27
DEL PEAK 13(5Q31.1) WILD-TYPE	113	91	51

Figure S222. Get High-res Image Gene #45: 'del_5q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S223. Gene #45: 'del_5q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
DEL PEAK 13(5Q31.1) MUTATED	48	114	8
DEL PEAK 13(5Q31.1) WILD-TYPE	138	95	22

Figure S223. Get High-res Image Gene #45: 'del_5q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q22.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S224. Gene #47: 'del_6q22.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
DEL PEAK 15(6Q22.31) MUTATED	48	66	75	30
DEL PEAK 15(6Q22.31) WILD-TYPE	44	59	40	69

Figure S224. Get High-res Image Gene #47: 'del_6q22.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q22.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.055

Table S225. Gene #47: 'del_6q22.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 15(6Q22.31) MUTATED	46	24	21	31	34	33	19	4	29
DEL PEAK 15(6Q22.31) WILD-TYPE	37	33	23	53	12	18	30	14	25

Figure S225. Get High-res Image Gene #47: 'del_6q22.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S226. Gene #49: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 17(8P23.2) MUTATED	141	58	42
DEL PEAK 17(8P23.2) WILD-TYPE	45	158	49

Figure S226. Get High-res Image Gene #49: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'RPPA_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.13

Table S227. Gene #49: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	112	71	52
DEL PEAK 17(8P23.2) MUTATED	69	21	27
DEL PEAK 17(8P23.2) WILD-TYPE	43	50	25

Figure S227. Get High-res Image Gene #49: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S228. Gene #49: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 17(8P23.2) MUTATED	96	39	32	50	21
DEL PEAK 17(8P23.2) WILD-TYPE	42	73	44	56	33

Figure S228. Get High-res Image Gene #49: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S229. Gene #49: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 17(8P23.2) MUTATED	49	22	31	56	10	20	24	2	24
DEL PEAK 17(8P23.2) WILD-TYPE	34	35	13	28	36	31	25	16	30

Figure S229. Get High-res Image Gene #49: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.035

Table S230. Gene #49: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 17(8P23.2) MUTATED	63	130	45
DEL PEAK 17(8P23.2) WILD-TYPE	116	101	33

Figure S230. Get High-res Image Gene #49: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S231. Gene #50: 'del_8p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 18(8P12) MUTATED	129	51	35
DEL PEAK 18(8P12) WILD-TYPE	57	165	56

Figure S231. Get High-res Image Gene #50: 'del_8p12' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p12' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.12

Table S232. Gene #50: 'del_8p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
DEL PEAK 18(8P12) MUTATED	23	57	64	46
DEL PEAK 18(8P12) WILD-TYPE	69	68	51	53

Figure S232. Get High-res Image Gene #50: 'del_8p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S233. Gene #50: 'del_8p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 18(8P12) MUTATED	89	35	29	44	16
DEL PEAK 18(8P12) WILD-TYPE	49	77	47	62	38

Figure S233. Get High-res Image Gene #50: 'del_8p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.094

Table S234. Gene #50: 'del_8p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 18(8P12) MUTATED	45	23	27	45	10	20	21	2	20
DEL PEAK 18(8P12) WILD-TYPE	38	34	17	39	36	31	28	16	34

Figure S234. Get High-res Image Gene #50: 'del_8p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p12' versus 'MIRSEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.16

Table S235. Gene #50: 'del_8p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 18(8P12) MUTATED	57	120	35
DEL PEAK 18(8P12) WILD-TYPE	122	111	43

Figure S235. Get High-res Image Gene #50: 'del_8p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S236. Gene #51: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 19(8P11.21) MUTATED	82	28	3
DEL PEAK 19(8P11.21) WILD-TYPE	104	188	88

Figure S236. Get High-res Image Gene #51: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S237. Gene #53: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 21(9P23) MUTATED	41	31	19	54	22	26	42	10	23
DEL PEAK 21(9P23) WILD-TYPE	42	26	25	30	24	25	7	8	31

Figure S237. Get High-res Image Gene #53: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S238. Gene #54: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 22(9P21.3) MUTATED	73	60	64	51	27
DEL PEAK 22(9P21.3) WILD-TYPE	65	52	12	55	27

Figure S238. Get High-res Image Gene #54: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S239. Gene #54: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 22(9P21.3) MUTATED	43	33	21	54	22	24	44	11	23
DEL PEAK 22(9P21.3) WILD-TYPE	40	24	23	30	24	27	5	7	31

Figure S239. Get High-res Image Gene #54: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S240. Gene #55: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 23(9Q21.11) MUTATED	100	82	64
DEL PEAK 23(9Q21.11) WILD-TYPE	86	134	27

Figure S240. Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_9q21.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S241. Gene #55: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 23(9Q21.11) MUTATED	34	27	19	52	15	37	32	4	24
DEL PEAK 23(9Q21.11) WILD-TYPE	49	30	25	32	31	14	17	14	30

Figure S241. Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.069

Table S242. Gene #55: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 23(9Q21.11) MUTATED	67	128	48
DEL PEAK 23(9Q21.11) WILD-TYPE	112	103	30

Figure S242. Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9q21.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S243. Gene #55: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
DEL PEAK 23(9Q21.11) MUTATED	26	28	60	53	58	18
DEL PEAK 23(9Q21.11) WILD-TYPE	45	16	58	84	25	17

Figure S243. Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.049

Table S244. Gene #56: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 24(10P15.3) MUTATED	62	33	27
DEL PEAK 24(10P15.3) WILD-TYPE	124	183	64

Figure S244. Get High-res Image Gene #56: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10p15.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.042

Table S245. Gene #56: 'del_10p15.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
DEL PEAK 24(10P15.3) MUTATED	9	13	20	31	31	17
DEL PEAK 24(10P15.3) WILD-TYPE	62	31	98	106	52	18

Figure S245. Get High-res Image Gene #56: 'del_10p15.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.21

Table S246. Gene #56: 'del_10p15.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
DEL PEAK 24(10P15.3) MUTATED	24	52	30
DEL PEAK 24(10P15.3) WILD-TYPE	131	140	48

Figure S246. Get High-res Image Gene #56: 'del_10p15.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10p15.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.14

Table S247. Gene #56: 'del_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
DEL PEAK 24(10P15.3) MUTATED	32	59	15
DEL PEAK 24(10P15.3) WILD-TYPE	154	150	15

Figure S247. Get High-res Image Gene #56: 'del_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S248. Gene #57: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 25(10Q26.3) MUTATED	77	36	29
DEL PEAK 25(10Q26.3) WILD-TYPE	109	180	62

Figure S248. Get High-res Image Gene #57: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S249. Gene #57: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 25(10Q26.3) MUTATED	59	19	13	34	16
DEL PEAK 25(10Q26.3) WILD-TYPE	79	93	63	72	38

Figure S249. Get High-res Image Gene #57: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S250. Gene #57: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 25(10Q26.3) MUTATED	30	16	15	43	1	11	9	2	14
DEL PEAK 25(10Q26.3) WILD-TYPE	53	41	29	41	45	40	40	16	40

Figure S250. Get High-res Image Gene #57: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S251. Gene #57: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
DEL PEAK 25(10Q26.3) MUTATED	10	9	31	33	40	17
DEL PEAK 25(10Q26.3) WILD-TYPE	61	35	87	104	43	18

Figure S251. Get High-res Image Gene #57: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.049

Table S252. Gene #57: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
DEL PEAK 25(10Q26.3) MUTATED	25	61	34
DEL PEAK 25(10Q26.3) WILD-TYPE	130	131	44

Figure S252. Get High-res Image Gene #57: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.12

Table S253. Gene #57: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
DEL PEAK 25(10Q26.3) MUTATED	35	71	14
DEL PEAK 25(10Q26.3) WILD-TYPE	151	138	16

Figure S253. Get High-res Image Gene #57: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S254. Gene #58: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 26(11P15.5) MUTATED	72	34	29
DEL PEAK 26(11P15.5) WILD-TYPE	114	182	62

Figure S254. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.23

Table S255. Gene #58: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 26(11P15.5) MUTATED	45	13	24	35	14
DEL PEAK 26(11P15.5) WILD-TYPE	93	99	52	71	40

Figure S255. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S256. Gene #58: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 26(11P15.5) MUTATED	23	6	11	34	8	13	23	0	13
DEL PEAK 26(11P15.5) WILD-TYPE	60	51	33	50	38	38	26	18	41

Figure S256. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.1

Table S257. Gene #58: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 26(11P15.5) MUTATED	33	84	16
DEL PEAK 26(11P15.5) WILD-TYPE	146	147	62

Figure S257. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S258. Gene #58: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
DEL PEAK 26(11P15.5) MUTATED	12	10	51	27	30	3
DEL PEAK 26(11P15.5) WILD-TYPE	59	34	67	110	53	32

Figure S258. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S259. Gene #58: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
DEL PEAK 26(11P15.5) MUTATED	27	75	14
DEL PEAK 26(11P15.5) WILD-TYPE	128	117	64

Figure S259. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S260. Gene #58: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
DEL PEAK 26(11P15.5) MUTATED	38	77	1
DEL PEAK 26(11P15.5) WILD-TYPE	148	132	29

Figure S260. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q23.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S261. Gene #59: 'del_11q23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 27(11Q23.2) MUTATED	41	36	39
DEL PEAK 27(11Q23.2) WILD-TYPE	145	180	52

Figure S261. Get High-res Image Gene #59: 'del_11q23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q23.2' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.13

Table S262. Gene #59: 'del_11q23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
DEL PEAK 27(11Q23.2) MUTATED	11	44	29	17
DEL PEAK 27(11Q23.2) WILD-TYPE	81	81	86	82

Figure S262. Get High-res Image Gene #59: 'del_11q23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q23.2' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.075

Table S263. Gene #59: 'del_11q23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 27(11Q23.2) MUTATED	26	13	25	38	10
DEL PEAK 27(11Q23.2) WILD-TYPE	112	99	51	68	44

Figure S263. Get High-res Image Gene #59: 'del_11q23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q25' versus 'CN_CNMF'

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

Table S264. Gene #60: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 28(11Q25) MUTATED	44	34	34
DEL PEAK 28(11Q25) WILD-TYPE	142	182	57

Figure S264. Get High-res Image Gene #60: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q25' versus 'MRNASEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.24

Table S265. Gene #60: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 28(11Q25) MUTATED	24	14	26	34	10
DEL PEAK 28(11Q25) WILD-TYPE	114	98	50	72	44

Figure S265. Get High-res Image Gene #60: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12q12' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.1

Table S266. Gene #62: 'del_12q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 30(12Q12) MUTATED	53	31	10
DEL PEAK 30(12Q12) WILD-TYPE	133	185	81

Figure S266. Get High-res Image Gene #62: 'del_12q12' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q24.33' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S267. Gene #63: 'del_12q24.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 31(12Q24.33) MUTATED	64	50	9
DEL PEAK 31(12Q24.33) WILD-TYPE	122	166	82

Figure S267. Get High-res Image Gene #63: 'del_12q24.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q24.33' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S268. Gene #63: 'del_12q24.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 31(12Q24.33) MUTATED	46	35	7	16	18
DEL PEAK 31(12Q24.33) WILD-TYPE	92	77	69	90	36

Figure S268. Get High-res Image Gene #63: 'del_12q24.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12q24.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S269. Gene #63: 'del_12q24.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 31(12Q24.33) MUTATED	31	18	4	24	15	2	6	2	20
DEL PEAK 31(12Q24.33) WILD-TYPE	52	39	40	60	31	49	43	16	34

Figure S269. Get High-res Image Gene #63: 'del_12q24.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q12.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S270. Gene #64: 'del_13q12.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 32(13Q12.11) MUTATED	142	72	68
DEL PEAK 32(13Q12.11) WILD-TYPE	44	144	23

Figure S270. Get High-res Image Gene #64: 'del_13q12.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q12.11' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S271. Gene #64: 'del_13q12.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	112	71	52
DEL PEAK 32(13Q12.11) MUTATED	81	22	30
DEL PEAK 32(13Q12.11) WILD-TYPE	31	49	22

Figure S271. Get High-res Image Gene #64: 'del_13q12.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_13q12.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S272. Gene #64: 'del_13q12.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 32(13Q12.11) MUTATED	100	45	30	76	27
DEL PEAK 32(13Q12.11) WILD-TYPE	38	67	46	30	27

Figure S272. Get High-res Image Gene #64: 'del_13q12.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q12.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S273. Gene #64: 'del_13q12.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 32(13Q12.11) MUTATED	60	24	28	61	14	37	24	1	29
DEL PEAK 32(13Q12.11) WILD-TYPE	23	33	16	23	32	14	25	17	25

Figure S273. Get High-res Image Gene #64: 'del_13q12.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q12.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S274. Gene #65: 'del_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 33(13Q12.13) MUTATED	144	70	68
DEL PEAK 33(13Q12.13) WILD-TYPE	42	146	23

Figure S274. Get High-res Image Gene #65: 'del_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q12.13' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S275. Gene #65: 'del_13q12.13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	112	71	52
DEL PEAK 33(13Q12.13) MUTATED	80	22	31
DEL PEAK 33(13Q12.13) WILD-TYPE	32	49	21

Figure S275. Get High-res Image Gene #65: 'del_13q12.13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_13q12.13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S276. Gene #65: 'del_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 33(13Q12.13) MUTATED	99	47	29	76	27
DEL PEAK 33(13Q12.13) WILD-TYPE	39	65	47	30	27

Figure S276. Get High-res Image Gene #65: 'del_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q12.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S277. Gene #65: 'del_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 33(13Q12.13) MUTATED	60	26	28	58	14	39	23	1	29
DEL PEAK 33(13Q12.13) WILD-TYPE	23	31	16	26	32	12	26	17	25

Figure S277. Get High-res Image Gene #65: 'del_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S278. Gene #66: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 34(13Q14.2) MUTATED	139	66	66
DEL PEAK 34(13Q14.2) WILD-TYPE	47	150	25

Figure S278. Get High-res Image Gene #66: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'RPPA_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.23

Table S279. Gene #66: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	68	73
DEL PEAK 34(13Q14.2) MUTATED	61	23	41
DEL PEAK 34(13Q14.2) WILD-TYPE	33	45	32

Figure S279. Get High-res Image Gene #66: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q14.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S280. Gene #66: 'del_13q14.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	112	71	52
DEL PEAK 34(13Q14.2) MUTATED	74	19	32
DEL PEAK 34(13Q14.2) WILD-TYPE	38	52	20

Figure S280. Get High-res Image Gene #66: 'del_13q14.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S281. Gene #66: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 34(13Q14.2) MUTATED	98	43	28	74	25
DEL PEAK 34(13Q14.2) WILD-TYPE	40	69	48	32	29

Figure S281. Get High-res Image Gene #66: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S282. Gene #66: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 34(13Q14.2) MUTATED	59	24	29	54	11	40	23	1	27
DEL PEAK 34(13Q14.2) WILD-TYPE	24	33	15	30	35	11	26	17	27

Figure S282. Get High-res Image Gene #66: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.094

Table S283. Gene #66: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
DEL PEAK 34(13Q14.2) MUTATED	82	136	16
DEL PEAK 34(13Q14.2) WILD-TYPE	104	73	14

Figure S283. Get High-res Image Gene #66: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S284. Gene #67: 'del_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 35(13Q34) MUTATED	114	59	59
DEL PEAK 35(13Q34) WILD-TYPE	72	157	32

Figure S284. Get High-res Image Gene #67: 'del_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q34' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S285. Gene #67: 'del_13q34' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	112	71	52
DEL PEAK 35(13Q34) MUTATED	60	15	29
DEL PEAK 35(13Q34) WILD-TYPE	52	56	23

Figure S285. Get High-res Image Gene #67: 'del_13q34' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_13q34' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S286. Gene #67: 'del_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 35(13Q34) MUTATED	80	38	25	65	22
DEL PEAK 35(13Q34) WILD-TYPE	58	74	51	41	32

Figure S286. Get High-res Image Gene #67: 'del_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S287. Gene #67: 'del_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 35(13Q34) MUTATED	53	19	24	43	13	33	21	1	23
DEL PEAK 35(13Q34) WILD-TYPE	30	38	20	41	33	18	28	17	31

Figure S287. Get High-res Image Gene #67: 'del_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S288. Gene #69: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 37(15Q11.2) MUTATED	122	74	57
DEL PEAK 37(15Q11.2) WILD-TYPE	64	142	34

Figure S288. Get High-res Image Gene #69: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S289. Gene #69: 'del_15q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
DEL PEAK 37(15Q11.2) MUTATED	28	69	74	47
DEL PEAK 37(15Q11.2) WILD-TYPE	64	56	41	52

Figure S289. Get High-res Image Gene #69: 'del_15q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S290. Gene #69: 'del_15q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 37(15Q11.2) MUTATED	96	43	15	68	26
DEL PEAK 37(15Q11.2) WILD-TYPE	42	69	61	38	28

Figure S290. Get High-res Image Gene #69: 'del_15q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S291. Gene #69: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 37(15Q11.2) MUTATED	55	26	30	54	11	35	10	0	27
DEL PEAK 37(15Q11.2) WILD-TYPE	28	31	14	30	35	16	39	18	27

Figure S291. Get High-res Image Gene #69: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.028

Table S292. Gene #69: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 37(15Q11.2) MUTATED	68	136	47
DEL PEAK 37(15Q11.2) WILD-TYPE	111	95	31

Figure S292. Get High-res Image Gene #69: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S293. Gene #70: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 38(16Q23.1) MUTATED	81	48	38
DEL PEAK 38(16Q23.1) WILD-TYPE	105	168	53

Figure S293. Get High-res Image Gene #70: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S294. Gene #70: 'del_16q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
DEL PEAK 38(16Q23.1) MUTATED	11	50	53	30
DEL PEAK 38(16Q23.1) WILD-TYPE	81	75	62	69

Figure S294. Get High-res Image Gene #70: 'del_16q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S295. Gene #70: 'del_16q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 38(16Q23.1) MUTATED	69	19	26	40	11
DEL PEAK 38(16Q23.1) WILD-TYPE	69	93	50	66	43

Figure S295. Get High-res Image Gene #70: 'del_16q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S296. Gene #70: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 38(16Q23.1) MUTATED	42	10	24	35	9	17	17	0	11
DEL PEAK 38(16Q23.1) WILD-TYPE	41	47	20	49	37	34	32	18	43

Figure S296. Get High-res Image Gene #70: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S297. Gene #71: 'del_17p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 39(17P13.3) MUTATED	142	71	52
DEL PEAK 39(17P13.3) WILD-TYPE	44	145	39

Figure S297. Get High-res Image Gene #71: 'del_17p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S298. Gene #71: 'del_17p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
DEL PEAK 39(17P13.3) MUTATED	30	70	83	46
DEL PEAK 39(17P13.3) WILD-TYPE	62	55	32	53

Figure S298. Get High-res Image Gene #71: 'del_17p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S299. Gene #71: 'del_17p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 39(17P13.3) MUTATED	98	42	36	61	24
DEL PEAK 39(17P13.3) WILD-TYPE	40	70	40	45	30

Figure S299. Get High-res Image Gene #71: 'del_17p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S300. Gene #71: 'del_17p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 39(17P13.3) MUTATED	59	26	27	51	10	33	22	6	27
DEL PEAK 39(17P13.3) WILD-TYPE	24	31	17	33	36	18	27	12	27

Figure S300. Get High-res Image Gene #71: 'del_17p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S301. Gene #72: 'del_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 40(17P11.2) MUTATED	119	50	47
DEL PEAK 40(17P11.2) WILD-TYPE	67	166	44

Figure S301. Get High-res Image Gene #72: 'del_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S302. Gene #72: 'del_17p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
DEL PEAK 40(17P11.2) MUTATED	27	49	75	34
DEL PEAK 40(17P11.2) WILD-TYPE	65	76	40	65

Figure S302. Get High-res Image Gene #72: 'del_17p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p11.2' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S303. Gene #72: 'del_17p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 40(17P11.2) MUTATED	84	32	32	48	18
DEL PEAK 40(17P11.2) WILD-TYPE	54	80	44	58	36

Figure S303. Get High-res Image Gene #72: 'del_17p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S304. Gene #72: 'del_17p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 40(17P11.2) MUTATED	52	19	25	47	8	21	17	6	19
DEL PEAK 40(17P11.2) WILD-TYPE	31	38	19	37	38	30	32	12	35

Figure S304. Get High-res Image Gene #72: 'del_17p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S305. Gene #73: 'del_18q21.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 41(18Q21.32) MUTATED	131	77	33
DEL PEAK 41(18Q21.32) WILD-TYPE	55	139	58

Figure S305. Get High-res Image Gene #73: 'del_18q21.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q21.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S306. Gene #73: 'del_18q21.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 41(18Q21.32) MUTATED	91	42	40	42	23
DEL PEAK 41(18Q21.32) WILD-TYPE	47	70	36	64	31

Figure S306. Get High-res Image Gene #73: 'del_18q21.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q21.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S307. Gene #73: 'del_18q21.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 41(18Q21.32) MUTATED	44	28	28	51	9	17	30	9	22
DEL PEAK 41(18Q21.32) WILD-TYPE	39	29	16	33	37	34	19	9	32

Figure S307. Get High-res Image Gene #73: 'del_18q21.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S308. Gene #74: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 42(18Q23) MUTATED	133	75	30
DEL PEAK 42(18Q23) WILD-TYPE	53	141	61

Figure S308. Get High-res Image Gene #74: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q23' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S309. Gene #74: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 42(18Q23) MUTATED	92	42	40	38	23
DEL PEAK 42(18Q23) WILD-TYPE	46	70	36	68	31

Figure S309. Get High-res Image Gene #74: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.028

Table S310. Gene #74: 'del_18q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 42(18Q23) MUTATED	42	27	29	50	9	17	30	9	22
DEL PEAK 42(18Q23) WILD-TYPE	41	30	15	34	37	34	19	9	32

Figure S310. Get High-res Image Gene #74: 'del_18q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S311. Gene #75: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 43(19P13.3) MUTATED	105	92	68
DEL PEAK 43(19P13.3) WILD-TYPE	81	124	23

Figure S311. Get High-res Image Gene #75: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S312. Gene #75: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
DEL PEAK 43(19P13.3) MUTATED	35	96	50	49
DEL PEAK 43(19P13.3) WILD-TYPE	57	29	65	50

Figure S312. Get High-res Image Gene #75: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S313. Gene #75: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 43(19P13.3) MUTATED	70	49	50	76	17
DEL PEAK 43(19P13.3) WILD-TYPE	68	63	26	30	37

Figure S313. Get High-res Image Gene #75: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S314. Gene #75: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 43(19P13.3) MUTATED	29	20	22	56	37	34	43	4	17
DEL PEAK 43(19P13.3) WILD-TYPE	54	37	22	28	9	17	6	14	37

Figure S314. Get High-res Image Gene #75: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S315. Gene #75: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 43(19P13.3) MUTATED	78	149	33
DEL PEAK 43(19P13.3) WILD-TYPE	101	82	45

Figure S315. Get High-res Image Gene #75: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S316. Gene #75: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
DEL PEAK 43(19P13.3) MUTATED	36	27	74	49	60	14
DEL PEAK 43(19P13.3) WILD-TYPE	35	17	44	88	23	21

Figure S316. Get High-res Image Gene #75: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.075

Table S317. Gene #75: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
DEL PEAK 43(19P13.3) MUTATED	71	125	33
DEL PEAK 43(19P13.3) WILD-TYPE	84	67	45

Figure S317. Get High-res Image Gene #75: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S318. Gene #75: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
DEL PEAK 43(19P13.3) MUTATED	80	139	10
DEL PEAK 43(19P13.3) WILD-TYPE	106	70	20

Figure S318. Get High-res Image Gene #75: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S319. Gene #76: 'del_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 44(19P13.2) MUTATED	107	87	66
DEL PEAK 44(19P13.2) WILD-TYPE	79	129	25

Figure S319. Get High-res Image Gene #76: 'del_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S320. Gene #76: 'del_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
DEL PEAK 44(19P13.2) MUTATED	32	97	53	44
DEL PEAK 44(19P13.2) WILD-TYPE	60	28	62	55

Figure S320. Get High-res Image Gene #76: 'del_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S321. Gene #76: 'del_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 44(19P13.2) MUTATED	71	47	45	77	17
DEL PEAK 44(19P13.2) WILD-TYPE	67	65	31	29	37

Figure S321. Get High-res Image Gene #76: 'del_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S322. Gene #76: 'del_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 44(19P13.2) MUTATED	31	18	23	48	36	40	39	4	18
DEL PEAK 44(19P13.2) WILD-TYPE	52	39	21	36	10	11	10	14	36

Figure S322. Get High-res Image Gene #76: 'del_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S323. Gene #76: 'del_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 44(19P13.2) MUTATED	76	147	32
DEL PEAK 44(19P13.2) WILD-TYPE	103	84	46

Figure S323. Get High-res Image Gene #76: 'del_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S324. Gene #76: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
DEL PEAK 44(19P13.2) MUTATED	37	27	72	49	58	12
DEL PEAK 44(19P13.2) WILD-TYPE	34	17	46	88	25	23

Figure S324. Get High-res Image Gene #76: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.075

Table S325. Gene #76: 'del_19p13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
DEL PEAK 44(19P13.2) MUTATED	68	124	33
DEL PEAK 44(19P13.2) WILD-TYPE	87	68	45

Figure S325. Get High-res Image Gene #76: 'del_19p13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S326. Gene #76: 'del_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
DEL PEAK 44(19P13.2) MUTATED	79	137	9
DEL PEAK 44(19P13.2) WILD-TYPE	107	72	21

Figure S326. Get High-res Image Gene #76: 'del_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S327. Gene #77: 'del_19q13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 45(19Q13.33) MUTATED	97	51	39
DEL PEAK 45(19Q13.33) WILD-TYPE	89	165	52

Figure S327. Get High-res Image Gene #77: 'del_19q13.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S328. Gene #77: 'del_19q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 45(19Q13.33) MUTATED	29	16	21	40	22	24	23	0	10
DEL PEAK 45(19Q13.33) WILD-TYPE	54	41	23	44	24	27	26	18	44

Figure S328. Get High-res Image Gene #77: 'del_19q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.33' versus 'MIRSEQ_CNMF'

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

Table S329. Gene #77: 'del_19q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 45(19Q13.33) MUTATED	47	106	30
DEL PEAK 45(19Q13.33) WILD-TYPE	132	125	48

Figure S329. Get High-res Image Gene #77: 'del_19q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19q13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.035

Table S330. Gene #77: 'del_19q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
DEL PEAK 45(19Q13.33) MUTATED	23	24	53	30	39	14
DEL PEAK 45(19Q13.33) WILD-TYPE	48	20	65	107	44	21

Figure S330. Get High-res Image Gene #77: 'del_19q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.13

Table S331. Gene #77: 'del_19q13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
DEL PEAK 45(19Q13.33) MUTATED	47	94	11
DEL PEAK 45(19Q13.33) WILD-TYPE	139	115	19

Figure S331. Get High-res Image Gene #77: 'del_19q13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S332. Gene #78: 'del_20p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 46(20P13) MUTATED	71	39	16
DEL PEAK 46(20P13) WILD-TYPE	115	177	75

Figure S332. Get High-res Image Gene #78: 'del_20p13' versus Molecular Subtype #3: 'CN_CNMF'

'del_20p13' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.042

Table S333. Gene #78: 'del_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 46(20P13) MUTATED	56	23	21	14	12
DEL PEAK 46(20P13) WILD-TYPE	82	89	55	92	42

Figure S333. Get High-res Image Gene #78: 'del_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_20p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S334. Gene #78: 'del_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 46(20P13) MUTATED	32	16	20	15	0	10	16	3	14
DEL PEAK 46(20P13) WILD-TYPE	51	41	24	69	46	41	33	15	40

Figure S334. Get High-res Image Gene #78: 'del_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_21q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S335. Gene #80: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 48(21Q11.2) MUTATED	54	60	53
DEL PEAK 48(21Q11.2) WILD-TYPE	132	156	38

Figure S335. Get High-res Image Gene #80: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.17

Table S336. Gene #80: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
DEL PEAK 48(21Q11.2) MUTATED	14	52	39	35
DEL PEAK 48(21Q11.2) WILD-TYPE	78	73	76	64

Figure S336. Get High-res Image Gene #80: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_21q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S337. Gene #80: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 48(21Q11.2) MUTATED	49	13	30	59	12
DEL PEAK 48(21Q11.2) WILD-TYPE	89	99	46	47	42

Figure S337. Get High-res Image Gene #80: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_21q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S338. Gene #80: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 48(21Q11.2) MUTATED	18	9	18	33	10	34	24	3	14
DEL PEAK 48(21Q11.2) WILD-TYPE	65	48	26	51	36	17	25	15	40

Figure S338. Get High-res Image Gene #80: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.028

Table S339. Gene #80: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 48(21Q11.2) MUTATED	41	102	21
DEL PEAK 48(21Q11.2) WILD-TYPE	138	129	57

Figure S339. Get High-res Image Gene #80: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_21q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S340. Gene #80: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
DEL PEAK 48(21Q11.2) MUTATED	17	19	47	31	43	7
DEL PEAK 48(21Q11.2) WILD-TYPE	54	25	71	106	40	28

Figure S340. Get High-res Image Gene #80: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.21

Table S341. Gene #80: 'del_21q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
DEL PEAK 48(21Q11.2) MUTATED	49	87	4
DEL PEAK 48(21Q11.2) WILD-TYPE	137	122	26

Figure S341. Get High-res Image Gene #80: 'del_21q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S342. Gene #81: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 49(22Q13.32) MUTATED	110	66	64
DEL PEAK 49(22Q13.32) WILD-TYPE	76	150	27

Figure S342. Get High-res Image Gene #81: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S343. Gene #81: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	125	115	99
DEL PEAK 49(22Q13.32) MUTATED	18	75	71	46
DEL PEAK 49(22Q13.32) WILD-TYPE	74	50	44	53

Figure S343. Get High-res Image Gene #81: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S344. Gene #81: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 49(22Q13.32) MUTATED	80	33	36	74	12
DEL PEAK 49(22Q13.32) WILD-TYPE	58	79	40	32	42

Figure S344. Get High-res Image Gene #81: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S345. Gene #81: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 49(22Q13.32) MUTATED	52	14	24	47	14	39	28	4	13
DEL PEAK 49(22Q13.32) WILD-TYPE	31	43	20	37	32	12	21	14	41

Figure S345. Get High-res Image Gene #81: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S346. Gene #81: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 49(22Q13.32) MUTATED	62	138	37
DEL PEAK 49(22Q13.32) WILD-TYPE	117	93	41

Figure S346. Get High-res Image Gene #81: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_22q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S347. Gene #81: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	44	118	137	83	35
DEL PEAK 49(22Q13.32) MUTATED	26	26	71	49	53	12
DEL PEAK 49(22Q13.32) WILD-TYPE	45	18	47	88	30	23

Figure S347. Get High-res Image Gene #81: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S348. Gene #81: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
DEL PEAK 49(22Q13.32) MUTATED	59	117	29
DEL PEAK 49(22Q13.32) WILD-TYPE	96	75	49

Figure S348. Get High-res Image Gene #81: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_22q13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S349. Gene #81: 'del_22q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	209	30
DEL PEAK 49(22Q13.32) MUTATED	65	131	9
DEL PEAK 49(22Q13.32) WILD-TYPE	121	78	21

Figure S349. Get High-res Image Gene #81: 'del_22q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0098

Table S350. Gene #82: 'del_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 50(XP22.2) MUTATED	79	34	22
DEL PEAK 50(XP22.2) WILD-TYPE	107	182	69

Figure S350. Get High-res Image Gene #82: 'del_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_xp22.2' versus 'MRNASEQ_CNMF'

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

Table S351. Gene #82: 'del_xp22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 50(XP22.2) MUTATED	58	28	13	25	10
DEL PEAK 50(XP22.2) WILD-TYPE	80	84	63	81	44

Figure S351. Get High-res Image Gene #82: 'del_xp22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_xp22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.24

Table S352. Gene #82: 'del_xp22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
DEL PEAK 50(XP22.2) MUTATED	36	16	17	27	8	8	8	1	13
DEL PEAK 50(XP22.2) WILD-TYPE	47	41	27	57	38	43	41	17	41

Figure S352. Get High-res Image Gene #82: 'del_xp22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = LUAD-TP.transferedmergedcluster.txt
Number of patients = 493
Number of significantly focal cnvs = 82
Number of molecular subtypes = 12
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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