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

Sarcoma (Primary solid tumor)

02 April 2015 | analyses__2015_04_02

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 (2015): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1P26X7J

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 66 focal events and 10 molecular subtypes across 256 patients, 416 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p32.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1q21.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_1q24.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_2p11.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_3p12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_4q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5p15.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_6p21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6q25.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7q31.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8p11.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', and 'RPPA_CHIERARCHICAL'.
amp_11q22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_12q15 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_13q34 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_15q26.3 cnv correlated to 'CN_CNMF'.
amp_17p12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17p11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q24.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.
amp_19p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.
amp_19q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20q13.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_21q21.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_xp21.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_xq21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_1p36.32 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1q44 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2p25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q37.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q37.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_3p21.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3q13.31 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_3q29 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_4q35.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.
del_5p15.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_6p25.3 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_6q14.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', and 'RPPA_CHIERARCHICAL'.
del_7q36.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_8p23.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p24.3 cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10p15.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q26.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p15.5 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.
del_11q24.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_12q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_12q24.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_13q14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q24.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17q25.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_18q23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_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_19q13.43 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_21q11.2 cnv correlated to 'RPPA_CHIERARCHICAL' and 'MIRSEQ_CNMF'.
del_21q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.
del_22q13.32 cnv correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.
del_xp21.1 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xq21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xq22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 66 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 416 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
amp 4q12	78 (30%)	178	1e-05 (6.87e-05)	5e-05 (0.000273)	0.00355 (0.00861)	0.00786 (0.0168)	0.00022 (0.000913)	0.00429 (0.0101)	0.0329 (0.0546)	0.00215 (0.00572)	0.0296 (0.0498)	0.00583 (0.013)
amp 6q25 1	75 (29%)	181	0.00542 (0.0123)	1e-05 (6.87e-05)	7e-05 (0.000347)	0.00036 (0.00135)	1e-05 (6.87e-05)	1e-05 (6.87e-05)	0.00141 (0.00401)	7e-05 (0.000347)	0.00239 (0.00623)	0.00973 (0.0198)
amp 7q31 2	77 (30%)	179	1e-05 (6.87e-05)	4e-05 (0.000226)	0.00363 (0.00878)	0.00031 (0.0012)	1e-05 (6.87e-05)	0.00481 (0.0111)	0.00113 (0.00337)	3e-05 (0.000174)	6e-05 (0.000319)	0.00013 (0.000584)
amp 12q15	94 (37%)	162	1e-05 (6.87e-05)	1e-05 (6.87e-05)	1e-05 (6.87e-05)	1e-05 (6.87e-05)	1e-05 (6.87e-05)	1e-05 (6.87e-05)	1e-05 (6.87e-05)	1e-05 (6.87e-05)	1e-05 (6.87e-05)	1e-05 (6.87e-05)
amp 20q13 33	98 (38%)	158	1e-05 (6.87e-05)	6e-05 (0.000319)	0.00034 (0.00129)	7e-05 (0.000347)	0.00097 (0.00303)	0.00322 (0.00802)	0.0107 (0.0214)	0.00577 (0.013)	0.0227 (0.0401)	0.00479 (0.0111)
del 2p25 3	94 (37%)	162	1e-05 (6.87e-05)	1e-05 (6.87e-05)	0.0283 (0.0481)	0.0043 (0.0101)	1e-05 (6.87e-05)	0.001 (0.00311)	0.00062 (0.00211)	0.00026 (0.00105)	0.00031 (0.0012)	0.00075 (0.00245)
del 3p21 31	65 (25%)	191	0.0201 (0.0362)	1e-05 (6.87e-05)	0.0135 (0.0257)	8e-05 (0.000383)	1e-05 (6.87e-05)	1e-05 (6.87e-05)	0.00041 (0.00149)	0.00063 (0.00213)	0.0015 (0.00421)	1e-05 (6.87e-05)
del 8p23 3	81 (32%)	175	1e-05 (6.87e-05)	2e-05 (0.000122)	0.0015 (0.00421)	9e-05 (0.000418)	7e-05 (0.000347)	0.00096 (0.00302)	0.00227 (0.00597)	0.00083 (0.00265)	0.00965 (0.0197)	0.00078 (0.00254)
del 10q23 31	138 (54%)	118	1e-05 (6.87e-05)	1e-05 (6.87e-05)	1e-05 (6.87e-05)	2e-05 (0.000122)	1e-05 (6.87e-05)	1e-05 (6.87e-05)	1e-05 (6.87e-05)	5e-05 (0.000273)	0.00051 (0.00177)	0.0003 (0.00117)
del 10q26 3	132 (52%)	124	1e-05 (6.87e-05)	1e-05 (6.87e-05)	1e-05 (6.87e-05)	1e-05 (6.87e-05)	1e-05 (6.87e-05)	1e-05 (6.87e-05)	9e-05 (0.000418)	9e-05 (0.000418)	7e-05 (0.000347)	0.00029 (0.00114)
del 13q14 2	180 (70%)	76	1e-05 (6.87e-05)	1e-05 (6.87e-05)	1e-05 (6.87e-05)	0.00075 (0.00245)	1e-05 (6.87e-05)	1e-05 (6.87e-05)	1e-05 (6.87e-05)	1e-05 (6.87e-05)	0.00029 (0.00114)	0.00019 (0.000814)
del 16q11 2	130 (51%)	126	7e-05 (0.000347)	7e-05 (0.000347)	0.00669 (0.0148)	0.00275 (0.00701)	0.00043 (0.00153)	7e-05 (0.000347)	0.00235 (0.00615)	0.00774 (0.0166)	1e-05 (6.87e-05)	3e-05 (0.000174)
del 17p13 1	129 (50%)	127	0.00023 (0.000949)	2e-05 (0.000122)	0.00715 (0.0157)	0.0006 (0.00205)	3e-05 (0.000174)	5e-05 (0.000273)	0.00016 (0.000714)	0.0006 (0.00205)	2e-05 (0.000122)	0.00041 (0.00149)
del 17q11 2	81 (32%)	175	1e-05 (6.87e-05)	1e-05 (6.87e-05)	0.00033 (0.00126)	1e-05 (6.87e-05)	1e-05 (6.87e-05)	8e-05 (0.000383)	0.00433 (0.0102)	0.00745 (0.0161)	0.0126 (0.0243)	0.0252 (0.0438)
del xq21 1	114 (45%)	142	0.00051 (0.00177)	0.00024 (0.000972)	3e-05 (0.000174)	0.00558 (0.0126)	4e-05 (0.000226)	0.0002 (0.000852)	8e-05 (0.000383)	0.00075 (0.00245)	0.0383 (0.0625)	0.0318 (0.0529)
del xq22 3	123 (48%)	133	1e-05 (6.87e-05)	1e-05 (6.87e-05)	0.00143 (0.00405)	0.00324 (0.00804)	1e-05 (6.87e-05)	6e-05 (0.000319)	0.00021 (0.000883)	0.00083 (0.00265)	0.0223 (0.0394)	0.0498 (0.079)
amp 1p32 1	94 (37%)	162	3e-05 (0.000174)	1e-05 (6.87e-05)	0.00069 (0.0023)	0.00017 (0.000738)	2e-05 (0.000122)	1e-05 (6.87e-05)	0.00463 (0.0108)	9e-05 (0.000418)	0.164 (0.215)	0.00045 (0.0016)
amp 3p12 1	69 (27%)	187	1e-05 (6.87e-05)	3e-05 (0.000174)	0.00319 (0.00797)	1e-05 (6.87e-05)	0.00012 (0.000542)	2e-05 (0.000122)	0.311 (0.37)	0.00105 (0.00319)	0.00217 (0.00575)	0.00296 (0.00746)
amp 6p21 1	60 (23%)	196	1e-05 (6.87e-05)	1e-05 (6.87e-05)	0.0008 (0.00259)	0.00038 (0.00141)	0.00024 (0.000972)	0.00042 (0.00151)	0.013 (0.025)	0.00069 (0.0023)	0.308 (0.368)	0.0151 (0.0282)
del 1p36 32	69 (27%)	187	0.123 (0.168)	1e-05 (6.87e-05)	1e-05 (6.87e-05)	1e-05 (6.87e-05)	1e-05 (6.87e-05)	1e-05 (6.87e-05)	1e-05 (6.87e-05)	1e-05 (6.87e-05)	1e-05 (6.87e-05)	0.00104 (0.00318)
del 1q44	80 (31%)	176	1e-05 (6.87e-05)	1e-05 (6.87e-05)	0.0145 (0.0271)	0.00021 (0.000883)	0.00035 (0.00132)	8e-05 (0.000383)	0.0257 (0.0443)	0.00082 (0.00264)	0.0991 (0.139)	0.00128 (0.00372)
del 3q13 31	51 (20%)	205	0.00011 (0.000501)	0.00427 (0.0101)	0.141 (0.187)	0.0108 (0.0214)	0.00511 (0.0117)	0.00996 (0.0202)	0.0101 (0.0204)	0.00887 (0.0185)	0.0177 (0.0326)	0.0297 (0.0499)
del 16q23 1	134 (52%)	122	1e-05 (6.87e-05)	0.00052 (0.0018)	0.00186 (0.00505)	0.165 (0.215)	0.00102 (0.00315)	0.00039 (0.00144)	0.00352 (0.00857)	0.0103 (0.0207)	2e-05 (0.000122)	8e-05 (0.000383)
amp 17p11 2	104 (41%)	152	1e-05 (6.87e-05)	1e-05 (6.87e-05)	0.0294 (0.0496)	0.00486 (0.0112)	0.0383 (0.0625)	0.0231 (0.0406)	0.594 (0.644)	0.00926 (0.0191)	0.0769 (0.115)	0.00434 (0.0102)
del 9p21 3	114 (45%)	142	1e-05 (6.87e-05)	0.0891 (0.128)	0.00135 (0.00387)	0.00065 (0.00219)	0.00415 (0.00989)	0.00255 (0.00657)	0.0317 (0.0529)	0.0848 (0.123)	7e-05 (0.000347)	0.00335 (0.00822)
del 11q24 2	123 (48%)	133	1e-05 (6.87e-05)	1e-05 (6.87e-05)	0.0198 (0.0358)	0.00017 (0.000738)	0.00161 (0.00446)	0.00193 (0.0052)	0.0534 (0.0833)	0.0198 (0.0358)	0.338 (0.397)	0.0163 (0.0302)
del 18q23	86 (34%)	170	0.00104 (0.00318)	2e-05 (0.000122)	0.00028 (0.00111)	0.00033 (0.00126)	0.00663 (0.0147)	0.00183 (0.00503)	0.0141 (0.0267)	0.104 (0.145)	0.0871 (0.126)	0.00017 (0.000738)
del 19p13 3	70 (27%)	186	0.00019 (0.000814)	0.00257 (0.0066)	0.309 (0.369)	0.082 (0.121)	0.00891 (0.0185)	0.0021 (0.00561)	0.0116 (0.0228)	0.00341 (0.00834)	0.00133 (0.00383)	0.0144 (0.0271)
del 2q37 3	108 (42%)	148	1e-05 (6.87e-05)	0.00107 (0.00322)	0.145 (0.193)	0.049 (0.0785)	0.0208 (0.0373)	0.00107 (0.00322)	0.163 (0.214)	0.0242 (0.0423)	0.0843 (0.123)	0.0284 (0.0481)
del 5p15 33	33 (13%)	223	0.0335 (0.0554)	0.0289 (0.0489)	0.0165 (0.0304)	0.00102 (0.00315)	0.0115 (0.0226)	0.00289 (0.00731)	0.195 (0.247)	0.0544 (0.0846)	0.0243 (0.0425)	0.0918 (0.131)
del 9q34 3	61 (24%)	195	1e-05 (6.87e-05)	0.00118 (0.00351)	0.0443 (0.0718)	0.111 (0.153)	0.0498 (0.079)	0.126 (0.171)	0.00152 (0.00423)	0.00037 (0.00138)	0.119 (0.164)	0.0366 (0.06)
amp 5p15 33	119 (46%)	137	1e-05 (6.87e-05)	0.00185 (0.00505)	0.01 (0.0203)	0.00853 (0.0178)	0.00958 (0.0196)	0.00072 (0.00239)	0.334 (0.394)	0.0858 (0.124)	0.769 (0.8)	0.87 (0.884)
amp 17p12	102 (40%)	154	1e-05 (6.87e-05)	2e-05 (0.000122)	0.136 (0.181)	0.0094 (0.0193)	0.0636 (0.0965)	0.00453 (0.0106)	0.233 (0.288)	0.0012 (0.00354)	0.0586 (0.0898)	0.00708 (0.0156)
amp 19q12	93 (36%)	163	1e-05 (6.87e-05)	0.0001 (0.000458)	0.118 (0.162)	0.00022 (0.000913)	0.0314 (0.0526)	0.0188 (0.0344)	0.609 (0.657)	0.051 (0.0802)	0.8 (0.829)	0.00924 (0.0191)
del 6p25 3	81 (32%)	175	0.0726 (0.109)	0.00198 (0.00531)	0.0012 (0.00354)	0.096 (0.135)	0.0005 (0.00176)	0.00222 (0.00586)	0.0144 (0.0271)	0.019 (0.0345)	0.0549 (0.0851)	0.235 (0.289)
del 14q24 1	80 (31%)	176	0.0255 (0.0441)	0.0138 (0.0263)	0.408 (0.467)	0.641 (0.689)	0.206 (0.261)	1e-05 (6.87e-05)	0.0461 (0.0746)	0.0201 (0.0362)	0.19 (0.241)	0.0278 (0.0475)
del xp21 1	55 (21%)	201	0.885 (0.897)	0.00245 (0.00637)	0.0573 (0.0882)	0.16 (0.21)	0.00804 (0.0171)	0.0208 (0.0373)	0.0185 (0.034)	0.0322 (0.0535)	0.361 (0.419)	0.0482 (0.0774)
amp 11q22 2	36 (14%)	220	0.0356 (0.0584)	0.0125 (0.0243)	0.124 (0.169)	0.0268 (0.0459)	0.0151 (0.0282)	0.0181 (0.0333)	0.199 (0.252)	0.0509 (0.0802)	0.609 (0.657)	0.0579 (0.0889)
amp 17q24 3	79 (31%)	177	2e-05 (0.000122)	0.00084 (0.00267)	0.00732 (0.0159)	0.00132 (0.00382)	0.238 (0.292)	0.00375 (0.00903)	0.0564 (0.0869)	0.0534 (0.0833)	0.0999 (0.14)	0.221 (0.275)
amp xq21 1	46 (18%)	210	1e-05 (6.87e-05)	0.00112 (0.00336)	0.0109 (0.0216)	0.233 (0.288)	0.0418 (0.068)	0.00397 (0.00953)	0.115 (0.159)	0.298 (0.359)	0.536 (0.59)	0.466 (0.523)
del 2q37 3	110 (43%)	146	1e-05 (6.87e-05)	0.00042 (0.00151)	0.384 (0.445)	0.00547 (0.0124)	0.0134 (0.0257)	0.00164 (0.00453)	0.565 (0.618)	0.0645 (0.0974)	0.594 (0.644)	0.105 (0.146)
del 12q12	56 (22%)	200	1e-05 (6.87e-05)	0.00252 (0.00652)	0.165 (0.215)	0.447 (0.504)	0.0498 (0.079)	0.0223 (0.0394)	0.0481 (0.0774)	0.41 (0.468)	0.13 (0.176)	0.33 (0.391)
amp 1q24 3	102 (40%)	154	1e-05 (6.87e-05)	0.004 (0.00957)	0.538 (0.592)	0.659 (0.7)	0.0085 (0.0178)	0.0251 (0.0438)	0.802 (0.829)	0.079 (0.117)	0.684 (0.724)	0.589 (0.642)
amp 13q34	54 (21%)	202	1e-05 (6.87e-05)	0.00788 (0.0168)	0.856 (0.873)	0.0159 (0.0295)	0.498 (0.556)	0.0601 (0.0914)	0.557 (0.61)	0.0855 (0.124)	0.803 (0.829)	0.0069 (0.0152)
amp 19p13 2	107 (42%)	149	1e-05 (6.87e-05)	0.00764 (0.0164)	0.39 (0.45)	0.00047 (0.00166)	0.132 (0.178)	0.0343 (0.0565)	0.842 (0.861)	0.155 (0.204)	0.93 (0.937)	0.0914 (0.13)
amp xp21 2	97 (38%)	159	1e-05 (6.87e-05)	0.00017 (0.000738)	0.739 (0.774)	0.0601 (0.0914)	0.401 (0.46)	0.0757 (0.113)	0.861 (0.876)	0.0219 (0.0392)	0.421 (0.479)	0.00808 (0.0171)
del 4q35 1	94 (37%)	162	1e-05 (6.87e-05)	0.00138 (0.00394)	0.232 (0.287)	0.0106 (0.0212)	0.00762 (0.0164)	0.0505 (0.0799)	0.809 (0.834)	0.301 (0.362)	0.946 (0.95)	0.336 (0.396)
del 6q14 1	78 (30%)	178	2e-05 (0.000122)	0.00327 (0.00808)	0.0112 (0.0221)	0.0125 (0.0243)	0.302 (0.362)	0.217 (0.272)	0.59 (0.642)	0.835 (0.858)	0.0561 (0.0867)	0.971 (0.974)
del 10p15 3	128 (50%)	128	0.00854 (0.0178)	0.00184 (0.00504)	0.0876 (0.126)	0.00094 (0.00297)	0.29 (0.35)	0.00332 (0.00818)	0.229 (0.285)	0.0661 (0.0997)	0.713 (0.751)	0.649 (0.694)
del 12p13 1	87 (34%)	169	4e-05 (0.000226)	0.00152 (0.00423)	0.359 (0.419)	0.212 (0.267)	0.00722 (0.0158)	0.00947 (0.0194)	0.153 (0.202)	0.0549 (0.0851)	0.256 (0.313)	0.321 (0.381)
amp 8p11 22	81 (32%)	175	5e-05 (0.000273)	0.0141 (0.0267)	0.185 (0.238)	0.154 (0.204)	0.338 (0.397)	0.0281 (0.048)	0.321 (0.381)	0.0524 (0.0821)	0.523 (0.58)	0.0934 (0.133)
amp 8q24 21	83 (32%)	173	0.00122 (0.00358)	0.0665 (0.1)	0.0135 (0.0257)	0.026 (0.0447)	0.649 (0.694)	0.184 (0.237)	0.518 (0.577)	0.911 (0.92)	0.109 (0.152)	0.465 (0.523)
del 3q29	54 (21%)	202	0.00028 (0.00111)	0.00519 (0.0118)	0.791 (0.821)	0.838 (0.859)	0.343 (0.402)	0.186 (0.238)	0.292 (0.352)	0.0222 (0.0394)	0.309 (0.369)	0.0835 (0.123)
del 7q36 3	71 (28%)	185	1e-05 (6.87e-05)	0.0257 (0.0443)	0.401 (0.46)	0.0641 (0.097)	0.097 (0.136)	0.199 (0.252)	0.133 (0.178)	0.0347 (0.0572)	0.12 (0.164)	0.554 (0.608)
del 11p15 5	110 (43%)	146	1e-05 (6.87e-05)	0.00041 (0.00149)	0.75 (0.784)	0.00602 (0.0134)	0.444 (0.502)	0.288 (0.349)	0.575 (0.628)	0.849 (0.867)	0.812 (0.836)	0.642 (0.689)
del 12q24 33	69 (27%)	187	1e-05 (6.87e-05)	0.0125 (0.0243)	0.706 (0.746)	0.213 (0.267)	0.611 (0.657)	0.0126 (0.0243)	0.523 (0.58)	0.125 (0.17)	0.129 (0.175)	0.4 (0.46)
del 19q13 43	106 (41%)	150	0.013 (0.025)	0.00127 (0.00371)	0.165 (0.215)	0.388 (0.449)	0.179 (0.232)	0.428 (0.486)	0.602 (0.651)	0.0899 (0.128)	0.532 (0.587)	0.00489 (0.0112)
del 21q22 3	66 (26%)	190	0.00024 (0.000972)	0.00741 (0.0161)	0.18 (0.233)	0.00844 (0.0178)	0.0821 (0.121)	0.23 (0.286)	0.388 (0.449)	0.263 (0.321)	0.491 (0.549)	0.529 (0.585)
amp 1q21 3	104 (41%)	152	1e-05 (6.87e-05)	0.00189 (0.00511)	0.284 (0.345)	0.104 (0.145)	0.511 (0.569)	0.0774 (0.115)	0.657 (0.699)	0.189 (0.24)	0.0951 (0.134)	0.275 (0.334)
amp 2p11 2	64 (25%)	192	0.00308 (0.00773)	0.019 (0.0345)	0.72 (0.756)	0.139 (0.185)	0.823 (0.846)	0.254 (0.311)	0.768 (0.8)	0.443 (0.501)	0.788 (0.819)	0.999 (1.00)
amp 21q21 1	73 (29%)	183	1e-05 (6.87e-05)	0.0001 (0.000458)	0.0796 (0.118)	0.187 (0.24)	0.0744 (0.111)	0.396 (0.456)	0.549 (0.603)	0.0842 (0.123)	0.477 (0.534)	0.22 (0.275)
del 9p24 3	100 (39%)	156	1e-05 (6.87e-05)	0.714 (0.751)	0.0228 (0.0401)	0.0899 (0.128)	0.168 (0.219)	0.36 (0.419)	0.119 (0.164)	0.276 (0.335)	0.0846 (0.123)	0.874 (0.887)
del 17q25 3	67 (26%)	189	2e-05 (0.000122)	0.0027 (0.00691)	0.436 (0.494)	0.21 (0.265)	0.132 (0.178)	0.35 (0.409)	0.721 (0.756)	0.134 (0.18)	0.239 (0.293)	0.179 (0.232)
del 21q11 2	51 (20%)	205	0.0589 (0.09)	0.0817 (0.121)	0.134 (0.18)	0.0476 (0.0767)	0.188 (0.24)	0.215 (0.269)	0.00283 (0.00718)	0.187 (0.239)	0.0871 (0.126)	0.331 (0.391)
del 22q13 32	83 (32%)	173	1e-05 (6.87e-05)	0.0938 (0.133)	0.9 (0.909)	0.0491 (0.0785)	0.648 (0.694)	0.0509 (0.0802)	0.345 (0.404)	0.525 (0.581)	0.894 (0.905)	0.651 (0.694)
amp 15q26 3	84 (33%)	172	1e-05 (6.87e-05)	0.139 (0.185)	0.764 (0.798)	0.466 (0.523)	0.671 (0.712)	0.103 (0.144)	1 (1.00)	0.412 (0.47)	0.945 (0.95)	0.697 (0.737)

'amp_1p32.1' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S1. Gene #1: 'amp_1p32.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
AMP PEAK 1(1P32.1) MUTATED	36	14	31	13
AMP PEAK 1(1P32.1) WILD-TYPE	34	72	43	13

Figure S1. Get High-res Image Gene #1: 'amp_1p32.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1p32.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S2. Gene #1: 'amp_1p32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
AMP PEAK 1(1P32.1) MUTATED	18	16	14	3	39	1	3
AMP PEAK 1(1P32.1) WILD-TYPE	30	30	47	31	8	14	2

Figure S2. Get High-res Image Gene #1: 'amp_1p32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1p32.1' versus 'RPPA_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0023

Table S3. Gene #1: 'amp_1p32.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
AMP PEAK 1(1P32.1) MUTATED	19	54	15
AMP PEAK 1(1P32.1) WILD-TYPE	39	46	45

Figure S3. Get High-res Image Gene #1: 'amp_1p32.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_1p32.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00074

Table S4. Gene #1: 'amp_1p32.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
AMP PEAK 1(1P32.1) MUTATED	9	9	29	18	16	7
AMP PEAK 1(1P32.1) WILD-TYPE	15	19	10	50	21	15

Figure S4. Get High-res Image Gene #1: 'amp_1p32.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_1p32.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S5. Gene #1: 'amp_1p32.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
AMP PEAK 1(1P32.1) MUTATED	61	17	16
AMP PEAK 1(1P32.1) WILD-TYPE	53	60	47

Figure S5. Get High-res Image Gene #1: 'amp_1p32.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1p32.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S6. Gene #1: 'amp_1p32.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
AMP PEAK 1(1P32.1) MUTATED	18	9	10	8	21	6	22
AMP PEAK 1(1P32.1) WILD-TYPE	28	14	39	38	7	23	11

Figure S6. Get High-res Image Gene #1: 'amp_1p32.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1p32.1' versus 'MIRSEQ_CNMF'

P value = 0.00463 (Fisher's exact test), Q value = 0.011

Table S7. Gene #1: 'amp_1p32.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
AMP PEAK 1(1P32.1) MUTATED	43	25	24
AMP PEAK 1(1P32.1) WILD-TYPE	64	25	73

Figure S7. Get High-res Image Gene #1: 'amp_1p32.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1p32.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00042

Table S8. Gene #1: 'amp_1p32.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
AMP PEAK 1(1P32.1) MUTATED	41	23	25	3
AMP PEAK 1(1P32.1) WILD-TYPE	38	29	75	20

Figure S8. Get High-res Image Gene #1: 'amp_1p32.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1p32.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0016

Table S9. Gene #1: 'amp_1p32.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
AMP PEAK 1(1P32.1) MUTATED	10	12	11	11	2	17	12	3
AMP PEAK 1(1P32.1) WILD-TYPE	14	20	26	13	9	5	9	19

Figure S9. Get High-res Image Gene #1: 'amp_1p32.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S10. Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
AMP PEAK 2(1Q21.3) MUTATED	44	12	40	8
AMP PEAK 2(1Q21.3) WILD-TYPE	26	74	34	18

Figure S10. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 0.00189 (Fisher's exact test), Q value = 0.0051

Table S11. Gene #2: 'amp_1q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
AMP PEAK 2(1Q21.3) MUTATED	21	11	25	11	30	3	3
AMP PEAK 2(1Q21.3) WILD-TYPE	27	35	36	23	17	12	2

Figure S11. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S12. Gene #3: 'amp_1q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
AMP PEAK 3(1Q24.3) MUTATED	43	15	31	13
AMP PEAK 3(1Q24.3) WILD-TYPE	27	71	43	13

Figure S12. Get High-res Image Gene #3: 'amp_1q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q24.3' versus 'METHLYATION_CNMF'

P value = 0.004 (Fisher's exact test), Q value = 0.0096

Table S13. Gene #3: 'amp_1q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
AMP PEAK 3(1Q24.3) MUTATED	23	14	21	9	29	3	3
AMP PEAK 3(1Q24.3) WILD-TYPE	25	32	40	25	18	12	2

Figure S13. Get High-res Image Gene #3: 'amp_1q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q24.3' versus 'MRNASEQ_CNMF'

P value = 0.0085 (Fisher's exact test), Q value = 0.018

Table S14. Gene #3: 'amp_1q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
AMP PEAK 3(1Q24.3) MUTATED	57	28	17
AMP PEAK 3(1Q24.3) WILD-TYPE	57	49	46

Figure S14. Get High-res Image Gene #3: 'amp_1q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0251 (Fisher's exact test), Q value = 0.044

Table S15. Gene #3: 'amp_1q24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
AMP PEAK 3(1Q24.3) MUTATED	23	9	15	14	8	12	21
AMP PEAK 3(1Q24.3) WILD-TYPE	23	14	34	32	20	17	12

Figure S15. Get High-res Image Gene #3: 'amp_1q24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_2p11.2' versus 'CN_CNMF'

P value = 0.00308 (Fisher's exact test), Q value = 0.0077

Table S16. Gene #4: 'amp_2p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
AMP PEAK 4(2P11.2) MUTATED	21	10	25	8
AMP PEAK 4(2P11.2) WILD-TYPE	49	76	49	18

Figure S16. Get High-res Image Gene #4: 'amp_2p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2p11.2' versus 'METHLYATION_CNMF'

P value = 0.019 (Fisher's exact test), Q value = 0.035

Table S17. Gene #4: 'amp_2p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
AMP PEAK 4(2P11.2) MUTATED	15	8	14	6	16	1	4
AMP PEAK 4(2P11.2) WILD-TYPE	33	38	47	28	31	14	1

Figure S17. Get High-res Image Gene #4: 'amp_2p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S18. Gene #5: 'amp_3p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
AMP PEAK 5(3P12.1) MUTATED	26	8	30	5
AMP PEAK 5(3P12.1) WILD-TYPE	44	78	44	21

Figure S18. Get High-res Image Gene #5: 'amp_3p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3p12.1' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S19. Gene #5: 'amp_3p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
AMP PEAK 5(3P12.1) MUTATED	16	15	16	1	21	0	0
AMP PEAK 5(3P12.1) WILD-TYPE	32	31	45	33	26	15	5

Figure S19. Get High-res Image Gene #5: 'amp_3p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3p12.1' versus 'RPPA_CNMF'

P value = 0.00319 (Fisher's exact test), Q value = 0.008

Table S20. Gene #5: 'amp_3p12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
AMP PEAK 5(3P12.1) MUTATED	12	38	9
AMP PEAK 5(3P12.1) WILD-TYPE	46	62	51

Figure S20. Get High-res Image Gene #5: 'amp_3p12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_3p12.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S21. Gene #5: 'amp_3p12.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
AMP PEAK 5(3P12.1) MUTATED	5	5	21	10	17	1
AMP PEAK 5(3P12.1) WILD-TYPE	19	23	18	58	20	21

Figure S21. Get High-res Image Gene #5: 'amp_3p12.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_3p12.1' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00054

Table S22. Gene #5: 'amp_3p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
AMP PEAK 5(3P12.1) MUTATED	44	17	7
AMP PEAK 5(3P12.1) WILD-TYPE	70	60	56

Figure S22. Get High-res Image Gene #5: 'amp_3p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S23. Gene #5: 'amp_3p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
AMP PEAK 5(3P12.1) MUTATED	17	8	12	2	15	4	10
AMP PEAK 5(3P12.1) WILD-TYPE	29	15	37	44	13	25	23

Figure S23. Get High-res Image Gene #5: 'amp_3p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00105 (Fisher's exact test), Q value = 0.0032

Table S24. Gene #5: 'amp_3p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
AMP PEAK 5(3P12.1) MUTATED	30	14	25	0
AMP PEAK 5(3P12.1) WILD-TYPE	49	38	75	23

Figure S24. Get High-res Image Gene #5: 'amp_3p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3p12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00217 (Fisher's exact test), Q value = 0.0058

Table S25. Gene #5: 'amp_3p12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	64	46
AMP PEAK 5(3P12.1) MUTATED	19	17	24
AMP PEAK 5(3P12.1) WILD-TYPE	64	47	22

Figure S25. Get High-res Image Gene #5: 'amp_3p12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_3p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00296 (Fisher's exact test), Q value = 0.0075

Table S26. Gene #5: 'amp_3p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
AMP PEAK 5(3P12.1) MUTATED	7	9	11	11	2	10	10	0
AMP PEAK 5(3P12.1) WILD-TYPE	17	23	26	13	9	12	11	22

Figure S26. Get High-res Image Gene #5: 'amp_3p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S27. Gene #6: 'amp_4q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
AMP PEAK 6(4Q12) MUTATED	34	10	27	7
AMP PEAK 6(4Q12) WILD-TYPE	36	76	47	19

Figure S27. Get High-res Image Gene #6: 'amp_4q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4q12' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00027

Table S28. Gene #6: 'amp_4q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
AMP PEAK 6(4Q12) MUTATED	17	16	12	5	25	0	3
AMP PEAK 6(4Q12) WILD-TYPE	31	30	49	29	22	15	2

Figure S28. Get High-res Image Gene #6: 'amp_4q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_4q12' versus 'RPPA_CNMF'

P value = 0.00355 (Fisher's exact test), Q value = 0.0086

Table S29. Gene #6: 'amp_4q12' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
AMP PEAK 6(4Q12) MUTATED	21	39	9
AMP PEAK 6(4Q12) WILD-TYPE	37	61	51

Figure S29. Get High-res Image Gene #6: 'amp_4q12' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_4q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00786 (Fisher's exact test), Q value = 0.017

Table S30. Gene #6: 'amp_4q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
AMP PEAK 6(4Q12) MUTATED	11	10	18	13	14	3
AMP PEAK 6(4Q12) WILD-TYPE	13	18	21	55	23	19

Figure S30. Get High-res Image Gene #6: 'amp_4q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_4q12' versus 'MRNASEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00091

Table S31. Gene #6: 'amp_4q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
AMP PEAK 6(4Q12) MUTATED	50	14	14
AMP PEAK 6(4Q12) WILD-TYPE	64	63	49

Figure S31. Get High-res Image Gene #6: 'amp_4q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_4q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00429 (Fisher's exact test), Q value = 0.01

Table S32. Gene #6: 'amp_4q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
AMP PEAK 6(4Q12) MUTATED	18	9	7	9	13	7	15
AMP PEAK 6(4Q12) WILD-TYPE	28	14	42	37	15	22	18

Figure S32. Get High-res Image Gene #6: 'amp_4q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_4q12' versus 'MIRSEQ_CNMF'

P value = 0.0329 (Fisher's exact test), Q value = 0.055

Table S33. Gene #6: 'amp_4q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
AMP PEAK 6(4Q12) MUTATED	29	23	25
AMP PEAK 6(4Q12) WILD-TYPE	78	27	72

Figure S33. Get High-res Image Gene #6: 'amp_4q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_4q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00215 (Fisher's exact test), Q value = 0.0057

Table S34. Gene #6: 'amp_4q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
AMP PEAK 6(4Q12) MUTATED	27	23	26	1
AMP PEAK 6(4Q12) WILD-TYPE	52	29	74	22

Figure S34. Get High-res Image Gene #6: 'amp_4q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_4q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 0.05

Table S35. Gene #6: 'amp_4q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	64	46
AMP PEAK 6(4Q12) MUTATED	22	22	23
AMP PEAK 6(4Q12) WILD-TYPE	61	42	23

Figure S35. Get High-res Image Gene #6: 'amp_4q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_4q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00583 (Fisher's exact test), Q value = 0.013

Table S36. Gene #6: 'amp_4q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
AMP PEAK 6(4Q12) MUTATED	9	9	7	14	4	12	9	3
AMP PEAK 6(4Q12) WILD-TYPE	15	23	30	10	7	10	12	19

Figure S36. Get High-res Image Gene #6: 'amp_4q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S37. Gene #7: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
AMP PEAK 7(5P15.33) MUTATED	29	13	63	14
AMP PEAK 7(5P15.33) WILD-TYPE	41	73	11	12

Figure S37. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 0.00185 (Fisher's exact test), Q value = 0.005

Table S38. Gene #7: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
AMP PEAK 7(5P15.33) MUTATED	29	23	27	10	26	1	3
AMP PEAK 7(5P15.33) WILD-TYPE	19	23	34	24	21	14	2

Figure S38. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'RPPA_CNMF'

P value = 0.01 (Fisher's exact test), Q value = 0.02

Table S39. Gene #7: 'amp_5p15.33' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
AMP PEAK 7(5P15.33) MUTATED	24	58	21
AMP PEAK 7(5P15.33) WILD-TYPE	34	42	39

Figure S39. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_5p15.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.00853 (Fisher's exact test), Q value = 0.018

Table S40. Gene #7: 'amp_5p15.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
AMP PEAK 7(5P15.33) MUTATED	11	9	27	24	21	11
AMP PEAK 7(5P15.33) WILD-TYPE	13	19	12	44	16	11

Figure S40. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 0.00958 (Fisher's exact test), Q value = 0.02

Table S41. Gene #7: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
AMP PEAK 7(5P15.33) MUTATED	65	30	23
AMP PEAK 7(5P15.33) WILD-TYPE	49	47	40

Figure S41. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00072 (Fisher's exact test), Q value = 0.0024

Table S42. Gene #7: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
AMP PEAK 7(5P15.33) MUTATED	32	9	23	16	17	6	15
AMP PEAK 7(5P15.33) WILD-TYPE	14	14	26	30	11	23	18

Figure S42. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S43. Gene #8: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
AMP PEAK 8(6P21.1) MUTATED	27	3	20	10
AMP PEAK 8(6P21.1) WILD-TYPE	43	83	54	16

Figure S43. Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S44. Gene #8: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
AMP PEAK 8(6P21.1) MUTATED	21	7	5	5	19	0	3
AMP PEAK 8(6P21.1) WILD-TYPE	27	39	56	29	28	15	2

Figure S44. Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p21.1' versus 'RPPA_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0026

Table S45. Gene #8: 'amp_6p21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
AMP PEAK 8(6P21.1) MUTATED	17	33	5
AMP PEAK 8(6P21.1) WILD-TYPE	41	67	55

Figure S45. Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_6p21.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.0014

Table S46. Gene #8: 'amp_6p21.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
AMP PEAK 8(6P21.1) MUTATED	12	4	15	7	10	7
AMP PEAK 8(6P21.1) WILD-TYPE	12	24	24	61	27	15

Figure S46. Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_6p21.1' versus 'MRNASEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00097

Table S47. Gene #8: 'amp_6p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
AMP PEAK 8(6P21.1) MUTATED	39	7	14
AMP PEAK 8(6P21.1) WILD-TYPE	75	70	49

Figure S47. Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.0015

Table S48. Gene #8: 'amp_6p21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
AMP PEAK 8(6P21.1) MUTATED	20	4	3	9	8	4	12
AMP PEAK 8(6P21.1) WILD-TYPE	26	19	46	37	20	25	21

Figure S48. Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.025

Table S49. Gene #8: 'amp_6p21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
AMP PEAK 8(6P21.1) MUTATED	31	15	13
AMP PEAK 8(6P21.1) WILD-TYPE	76	35	84

Figure S49. Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6p21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00069 (Fisher's exact test), Q value = 0.0023

Table S50. Gene #8: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
AMP PEAK 8(6P21.1) MUTATED	28	16	12	3
AMP PEAK 8(6P21.1) WILD-TYPE	51	36	88	20

Figure S50. Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0151 (Fisher's exact test), Q value = 0.028

Table S51. Gene #8: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
AMP PEAK 8(6P21.1) MUTATED	9	10	4	10	1	9	3	3
AMP PEAK 8(6P21.1) WILD-TYPE	15	22	33	14	10	13	18	19

Figure S51. Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q25.1' versus 'CN_CNMF'

P value = 0.00542 (Fisher's exact test), Q value = 0.012

Table S52. Gene #9: 'amp_6q25.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
AMP PEAK 9(6Q25.1) MUTATED	25	15	22	13
AMP PEAK 9(6Q25.1) WILD-TYPE	45	71	52	13

Figure S52. Get High-res Image Gene #9: 'amp_6q25.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q25.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S53. Gene #9: 'amp_6q25.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
AMP PEAK 9(6Q25.1) MUTATED	29	17	7	3	16	2	1
AMP PEAK 9(6Q25.1) WILD-TYPE	19	29	54	31	31	13	4

Figure S53. Get High-res Image Gene #9: 'amp_6q25.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q25.1' versus 'RPPA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00035

Table S54. Gene #9: 'amp_6q25.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
AMP PEAK 9(6Q25.1) MUTATED	24	37	6
AMP PEAK 9(6Q25.1) WILD-TYPE	34	63	54

Figure S54. Get High-res Image Gene #9: 'amp_6q25.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_6q25.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.0013

Table S55. Gene #9: 'amp_6q25.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
AMP PEAK 9(6Q25.1) MUTATED	13	12	12	8	15	7
AMP PEAK 9(6Q25.1) WILD-TYPE	11	16	27	60	22	15

Figure S55. Get High-res Image Gene #9: 'amp_6q25.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_6q25.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S56. Gene #9: 'amp_6q25.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
AMP PEAK 9(6Q25.1) MUTATED	55	8	11
AMP PEAK 9(6Q25.1) WILD-TYPE	59	69	52

Figure S56. Get High-res Image Gene #9: 'amp_6q25.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6q25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S57. Gene #9: 'amp_6q25.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
AMP PEAK 9(6Q25.1) MUTATED	25	14	5	10	7	3	10
AMP PEAK 9(6Q25.1) WILD-TYPE	21	9	44	36	21	26	23

Figure S57. Get High-res Image Gene #9: 'amp_6q25.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6q25.1' versus 'MIRSEQ_CNMF'

P value = 0.00141 (Fisher's exact test), Q value = 0.004

Table S58. Gene #9: 'amp_6q25.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
AMP PEAK 9(6Q25.1) MUTATED	41	18	16
AMP PEAK 9(6Q25.1) WILD-TYPE	66	32	81

Figure S58. Get High-res Image Gene #9: 'amp_6q25.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6q25.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00035

Table S59. Gene #9: 'amp_6q25.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
AMP PEAK 9(6Q25.1) MUTATED	36	19	17	3
AMP PEAK 9(6Q25.1) WILD-TYPE	43	33	83	20

Figure S59. Get High-res Image Gene #9: 'amp_6q25.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6q25.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00239 (Fisher's exact test), Q value = 0.0062

Table S60. Gene #9: 'amp_6q25.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	64	46
AMP PEAK 9(6Q25.1) MUTATED	28	13	24
AMP PEAK 9(6Q25.1) WILD-TYPE	55	51	22

Figure S60. Get High-res Image Gene #9: 'amp_6q25.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_6q25.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00973 (Fisher's exact test), Q value = 0.02

Table S61. Gene #9: 'amp_6q25.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
AMP PEAK 9(6Q25.1) MUTATED	10	17	6	10	2	8	9	3
AMP PEAK 9(6Q25.1) WILD-TYPE	14	15	31	14	9	14	12	19

Figure S61. Get High-res Image Gene #9: 'amp_6q25.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S62. Gene #10: 'amp_7q31.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
AMP PEAK 10(7Q31.2) MUTATED	22	10	37	8
AMP PEAK 10(7Q31.2) WILD-TYPE	48	76	37	18

Figure S62. Get High-res Image Gene #10: 'amp_7q31.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q31.2' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00023

Table S63. Gene #10: 'amp_7q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
AMP PEAK 10(7Q31.2) MUTATED	25	15	8	6	19	1	3
AMP PEAK 10(7Q31.2) WILD-TYPE	23	31	53	28	28	14	2

Figure S63. Get High-res Image Gene #10: 'amp_7q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q31.2' versus 'RPPA_CNMF'

P value = 0.00363 (Fisher's exact test), Q value = 0.0088

Table S64. Gene #10: 'amp_7q31.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
AMP PEAK 10(7Q31.2) MUTATED	19	42	10
AMP PEAK 10(7Q31.2) WILD-TYPE	39	58	50

Figure S64. Get High-res Image Gene #10: 'amp_7q31.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_7q31.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.0012

Table S65. Gene #10: 'amp_7q31.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
AMP PEAK 10(7Q31.2) MUTATED	11	15	17	10	14	4
AMP PEAK 10(7Q31.2) WILD-TYPE	13	13	22	58	23	18

Figure S65. Get High-res Image Gene #10: 'amp_7q31.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_7q31.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S66. Gene #10: 'amp_7q31.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
AMP PEAK 10(7Q31.2) MUTATED	50	10	17
AMP PEAK 10(7Q31.2) WILD-TYPE	64	67	46

Figure S66. Get High-res Image Gene #10: 'amp_7q31.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00481 (Fisher's exact test), Q value = 0.011

Table S67. Gene #10: 'amp_7q31.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
AMP PEAK 10(7Q31.2) MUTATED	21	8	6	13	11	5	13
AMP PEAK 10(7Q31.2) WILD-TYPE	25	15	43	33	17	24	20

Figure S67. Get High-res Image Gene #10: 'amp_7q31.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_CNMF'

P value = 0.00113 (Fisher's exact test), Q value = 0.0034

Table S68. Gene #10: 'amp_7q31.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
AMP PEAK 10(7Q31.2) MUTATED	33	25	19
AMP PEAK 10(7Q31.2) WILD-TYPE	74	25	78

Figure S68. Get High-res Image Gene #10: 'amp_7q31.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S69. Gene #10: 'amp_7q31.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
AMP PEAK 10(7Q31.2) MUTATED	28	28	17	4
AMP PEAK 10(7Q31.2) WILD-TYPE	51	24	83	19

Figure S69. Get High-res Image Gene #10: 'amp_7q31.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00032

Table S70. Gene #10: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	64	46
AMP PEAK 10(7Q31.2) MUTATED	24	11	26
AMP PEAK 10(7Q31.2) WILD-TYPE	59	53	20

Figure S70. Get High-res Image Gene #10: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00058

Table S71. Gene #10: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
AMP PEAK 10(7Q31.2) MUTATED	11	12	4	13	1	3	12	5
AMP PEAK 10(7Q31.2) WILD-TYPE	13	20	33	11	10	19	9	17

Figure S71. Get High-res Image Gene #10: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p11.22' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00027

Table S72. Gene #11: 'amp_8p11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
AMP PEAK 11(8P11.22) MUTATED	29	12	34	6
AMP PEAK 11(8P11.22) WILD-TYPE	41	74	40	20

Figure S72. Get High-res Image Gene #11: 'amp_8p11.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p11.22' versus 'METHLYATION_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.027

Table S73. Gene #11: 'amp_8p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
AMP PEAK 11(8P11.22) MUTATED	18	15	18	5	22	1	2
AMP PEAK 11(8P11.22) WILD-TYPE	30	31	43	29	25	14	3

Figure S73. Get High-res Image Gene #11: 'amp_8p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8p11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0281 (Fisher's exact test), Q value = 0.048

Table S74. Gene #11: 'amp_8p11.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
AMP PEAK 11(8P11.22) MUTATED	18	6	13	9	16	7	12
AMP PEAK 11(8P11.22) WILD-TYPE	28	17	36	37	12	22	21

Figure S74. Get High-res Image Gene #11: 'amp_8p11.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 0.00122 (Fisher's exact test), Q value = 0.0036

Table S75. Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
AMP PEAK 12(8Q24.21) MUTATED	28	16	33	6
AMP PEAK 12(8Q24.21) WILD-TYPE	42	70	41	20

Figure S75. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'RPPA_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.026

Table S76. Gene #12: 'amp_8q24.21' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
AMP PEAK 12(8Q24.21) MUTATED	16	43	13
AMP PEAK 12(8Q24.21) WILD-TYPE	42	57	47

Figure S76. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_8q24.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.026 (Fisher's exact test), Q value = 0.045

Table S77. Gene #12: 'amp_8q24.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
AMP PEAK 12(8Q24.21) MUTATED	7	5	19	16	15	10
AMP PEAK 12(8Q24.21) WILD-TYPE	17	23	20	52	22	12

Figure S77. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_11q22.2' versus 'CN_CNMF'

P value = 0.0356 (Fisher's exact test), Q value = 0.058

Table S78. Gene #13: 'amp_11q22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
AMP PEAK 13(11Q22.2) MUTATED	10	6	17	3
AMP PEAK 13(11Q22.2) WILD-TYPE	60	80	57	23

Figure S78. Get High-res Image Gene #13: 'amp_11q22.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q22.2' versus 'METHLYATION_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.024

Table S79. Gene #13: 'amp_11q22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
AMP PEAK 13(11Q22.2) MUTATED	7	7	3	2	14	2	1
AMP PEAK 13(11Q22.2) WILD-TYPE	41	39	58	32	33	13	4

Figure S79. Get High-res Image Gene #13: 'amp_11q22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11q22.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0268 (Fisher's exact test), Q value = 0.046

Table S80. Gene #13: 'amp_11q22.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
AMP PEAK 13(11Q22.2) MUTATED	6	8	9	5	3	4
AMP PEAK 13(11Q22.2) WILD-TYPE	18	20	30	63	34	18

Figure S80. Get High-res Image Gene #13: 'amp_11q22.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_11q22.2' versus 'MRNASEQ_CNMF'

P value = 0.0151 (Fisher's exact test), Q value = 0.028

Table S81. Gene #13: 'amp_11q22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
AMP PEAK 13(11Q22.2) MUTATED	22	4	10
AMP PEAK 13(11Q22.2) WILD-TYPE	92	73	53

Figure S81. Get High-res Image Gene #13: 'amp_11q22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_11q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0181 (Fisher's exact test), Q value = 0.033

Table S82. Gene #13: 'amp_11q22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
AMP PEAK 13(11Q22.2) MUTATED	10	3	2	5	9	2	5
AMP PEAK 13(11Q22.2) WILD-TYPE	36	20	47	41	19	27	28

Figure S82. Get High-res Image Gene #13: 'amp_11q22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S83. Gene #14: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
AMP PEAK 14(12Q15) MUTATED	9	25	36	24
AMP PEAK 14(12Q15) WILD-TYPE	61	61	38	2

Figure S83. Get High-res Image Gene #14: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S84. Gene #14: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
AMP PEAK 14(12Q15) MUTATED	29	27	1	13	19	3	2
AMP PEAK 14(12Q15) WILD-TYPE	19	19	60	21	28	12	3

Figure S84. Get High-res Image Gene #14: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12q15' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S85. Gene #14: 'amp_12q15' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
AMP PEAK 14(12Q15) MUTATED	35	48	4
AMP PEAK 14(12Q15) WILD-TYPE	23	52	56

Figure S85. Get High-res Image Gene #14: 'amp_12q15' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_12q15' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S86. Gene #14: 'amp_12q15' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
AMP PEAK 14(12Q15) MUTATED	13	20	19	7	21	7
AMP PEAK 14(12Q15) WILD-TYPE	11	8	20	61	16	15

Figure S86. Get High-res Image Gene #14: 'amp_12q15' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_12q15' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S87. Gene #14: 'amp_12q15' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
AMP PEAK 14(12Q15) MUTATED	59	2	33
AMP PEAK 14(12Q15) WILD-TYPE	55	75	30

Figure S87. Get High-res Image Gene #14: 'amp_12q15' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S88. Gene #14: 'amp_12q15' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
AMP PEAK 14(12Q15) MUTATED	29	14	1	25	13	1	11
AMP PEAK 14(12Q15) WILD-TYPE	17	9	48	21	15	28	22

Figure S88. Get High-res Image Gene #14: 'amp_12q15' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S89. Gene #14: 'amp_12q15' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
AMP PEAK 14(12Q15) MUTATED	58	24	10
AMP PEAK 14(12Q15) WILD-TYPE	49	26	87

Figure S89. Get High-res Image Gene #14: 'amp_12q15' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_12q15' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S90. Gene #14: 'amp_12q15' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
AMP PEAK 14(12Q15) MUTATED	49	26	10	7
AMP PEAK 14(12Q15) WILD-TYPE	30	26	90	16

Figure S90. Get High-res Image Gene #14: 'amp_12q15' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S91. Gene #14: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	64	46
AMP PEAK 14(12Q15) MUTATED	47	7	21
AMP PEAK 14(12Q15) WILD-TYPE	36	57	25

Figure S91. Get High-res Image Gene #14: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_12q15' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S92. Gene #14: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
AMP PEAK 14(12Q15) MUTATED	8	27	0	10	1	10	10	9
AMP PEAK 14(12Q15) WILD-TYPE	16	5	37	14	10	12	11	13

Figure S92. Get High-res Image Gene #14: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S93. Gene #15: 'amp_13q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
AMP PEAK 15(13Q34) MUTATED	38	9	4	3
AMP PEAK 15(13Q34) WILD-TYPE	32	77	70	23

Figure S93. Get High-res Image Gene #15: 'amp_13q34' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q34' versus 'METHLYATION_CNMF'

P value = 0.00788 (Fisher's exact test), Q value = 0.017

Table S94. Gene #15: 'amp_13q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
AMP PEAK 15(13Q34) MUTATED	15	6	13	3	15	0	2
AMP PEAK 15(13Q34) WILD-TYPE	33	40	48	31	32	15	3

Figure S94. Get High-res Image Gene #15: 'amp_13q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q34' versus 'RPPA_CHIERARCHICAL'

P value = 0.0159 (Fisher's exact test), Q value = 0.03

Table S95. Gene #15: 'amp_13q34' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
AMP PEAK 15(13Q34) MUTATED	10	3	10	14	12	1
AMP PEAK 15(13Q34) WILD-TYPE	14	25	29	54	25	21

Figure S95. Get High-res Image Gene #15: 'amp_13q34' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_13q34' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0069 (Fisher's exact test), Q value = 0.015

Table S96. Gene #15: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
AMP PEAK 15(13Q34) MUTATED	11	5	8	6	4	9	2	1
AMP PEAK 15(13Q34) WILD-TYPE	13	27	29	18	7	13	19	21

Figure S96. Get High-res Image Gene #15: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_15q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S97. Gene #16: 'amp_15q26.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
AMP PEAK 16(15Q26.3) MUTATED	25	8	41	10
AMP PEAK 16(15Q26.3) WILD-TYPE	45	78	33	16

Figure S97. Get High-res Image Gene #16: 'amp_15q26.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S98. Gene #17: 'amp_17p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
AMP PEAK 17(17P12) MUTATED	56	12	28	6
AMP PEAK 17(17P12) WILD-TYPE	14	74	46	20

Figure S98. Get High-res Image Gene #17: 'amp_17p12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17p12' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S99. Gene #17: 'amp_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
AMP PEAK 17(17P12) MUTATED	23	10	32	6	28	2	1
AMP PEAK 17(17P12) WILD-TYPE	25	36	29	28	19	13	4

Figure S99. Get High-res Image Gene #17: 'amp_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17p12' versus 'RPPA_CHIERARCHICAL'

P value = 0.0094 (Fisher's exact test), Q value = 0.019

Table S100. Gene #17: 'amp_17p12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
AMP PEAK 17(17P12) MUTATED	14	6	21	27	16	4
AMP PEAK 17(17P12) WILD-TYPE	10	22	18	41	21	18

Figure S100. Get High-res Image Gene #17: 'amp_17p12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00453 (Fisher's exact test), Q value = 0.011

Table S101. Gene #17: 'amp_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
AMP PEAK 17(17P12) MUTATED	23	3	26	11	12	11	15
AMP PEAK 17(17P12) WILD-TYPE	23	20	23	35	16	18	18

Figure S101. Get High-res Image Gene #17: 'amp_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0012 (Fisher's exact test), Q value = 0.0035

Table S102. Gene #17: 'amp_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
AMP PEAK 17(17P12) MUTATED	33	21	45	1
AMP PEAK 17(17P12) WILD-TYPE	46	31	55	22

Figure S102. Get High-res Image Gene #17: 'amp_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_17p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00708 (Fisher's exact test), Q value = 0.016

Table S103. Gene #17: 'amp_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
AMP PEAK 17(17P12) MUTATED	12	9	20	11	5	13	8	2
AMP PEAK 17(17P12) WILD-TYPE	12	23	17	13	6	9	13	20

Figure S103. Get High-res Image Gene #17: 'amp_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S104. Gene #18: 'amp_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
AMP PEAK 18(17P11.2) MUTATED	57	11	31	5
AMP PEAK 18(17P11.2) WILD-TYPE	13	75	43	21

Figure S104. Get High-res Image Gene #18: 'amp_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17p11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S105. Gene #18: 'amp_17p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
AMP PEAK 18(17P11.2) MUTATED	24	10	30	7	31	1	1
AMP PEAK 18(17P11.2) WILD-TYPE	24	36	31	27	16	14	4

Figure S105. Get High-res Image Gene #18: 'amp_17p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17p11.2' versus 'RPPA_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 0.05

Table S106. Gene #18: 'amp_17p11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
AMP PEAK 18(17P11.2) MUTATED	16	49	25
AMP PEAK 18(17P11.2) WILD-TYPE	42	51	35

Figure S106. Get High-res Image Gene #18: 'amp_17p11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_17p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00486 (Fisher's exact test), Q value = 0.011

Table S107. Gene #18: 'amp_17p11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
AMP PEAK 18(17P11.2) MUTATED	15	6	22	25	17	5
AMP PEAK 18(17P11.2) WILD-TYPE	9	22	17	43	20	17

Figure S107. Get High-res Image Gene #18: 'amp_17p11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_17p11.2' versus 'MRNASEQ_CNMF'

P value = 0.0383 (Fisher's exact test), Q value = 0.062

Table S108. Gene #18: 'amp_17p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
AMP PEAK 18(17P11.2) MUTATED	52	34	17
AMP PEAK 18(17P11.2) WILD-TYPE	62	43	46

Figure S108. Get High-res Image Gene #18: 'amp_17p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0231 (Fisher's exact test), Q value = 0.041

Table S109. Gene #18: 'amp_17p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
AMP PEAK 18(17P11.2) MUTATED	23	6	24	10	13	10	17
AMP PEAK 18(17P11.2) WILD-TYPE	23	17	25	36	15	19	16

Figure S109. Get High-res Image Gene #18: 'amp_17p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00926 (Fisher's exact test), Q value = 0.019

Table S110. Gene #18: 'amp_17p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
AMP PEAK 18(17P11.2) MUTATED	34	23	43	2
AMP PEAK 18(17P11.2) WILD-TYPE	45	29	57	21

Figure S110. Get High-res Image Gene #18: 'amp_17p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_17p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00434 (Fisher's exact test), Q value = 0.01

Table S111. Gene #18: 'amp_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
AMP PEAK 18(17P11.2) MUTATED	14	8	17	13	5	14	9	3
AMP PEAK 18(17P11.2) WILD-TYPE	10	24	20	11	6	8	12	19

Figure S111. Get High-res Image Gene #18: 'amp_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q24.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S112. Gene #19: 'amp_17q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
AMP PEAK 19(17Q24.3) MUTATED	32	10	29	8
AMP PEAK 19(17Q24.3) WILD-TYPE	38	76	45	18

Figure S112. Get High-res Image Gene #19: 'amp_17q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q24.3' versus 'METHLYATION_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.0027

Table S113. Gene #19: 'amp_17q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
AMP PEAK 19(17Q24.3) MUTATED	21	11	11	9	19	3	5
AMP PEAK 19(17Q24.3) WILD-TYPE	27	35	50	25	28	12	0

Figure S113. Get High-res Image Gene #19: 'amp_17q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q24.3' versus 'RPPA_CNMF'

P value = 0.00732 (Fisher's exact test), Q value = 0.016

Table S114. Gene #19: 'amp_17q24.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
AMP PEAK 19(17Q24.3) MUTATED	18	40	10
AMP PEAK 19(17Q24.3) WILD-TYPE	40	60	50

Figure S114. Get High-res Image Gene #19: 'amp_17q24.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_17q24.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00132 (Fisher's exact test), Q value = 0.0038

Table S115. Gene #19: 'amp_17q24.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
AMP PEAK 19(17Q24.3) MUTATED	14	5	12	12	16	9
AMP PEAK 19(17Q24.3) WILD-TYPE	10	23	27	56	21	13

Figure S115. Get High-res Image Gene #19: 'amp_17q24.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_17q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00375 (Fisher's exact test), Q value = 0.009

Table S116. Gene #19: 'amp_17q24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
AMP PEAK 19(17Q24.3) MUTATED	17	4	5	15	12	13	12
AMP PEAK 19(17Q24.3) WILD-TYPE	29	19	44	31	16	16	21

Figure S116. Get High-res Image Gene #19: 'amp_17q24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S117. Gene #20: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
AMP PEAK 20(19P13.2) MUTATED	31	17	50	9
AMP PEAK 20(19P13.2) WILD-TYPE	39	69	24	17

Figure S117. Get High-res Image Gene #20: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19p13.2' versus 'METHLYATION_CNMF'

P value = 0.00764 (Fisher's exact test), Q value = 0.016

Table S118. Gene #20: 'amp_19p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
AMP PEAK 20(19P13.2) MUTATED	31	17	27	8	18	4	2
AMP PEAK 20(19P13.2) WILD-TYPE	17	29	34	26	29	11	3

Figure S118. Get High-res Image Gene #20: 'amp_19p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.0017

Table S119. Gene #20: 'amp_19p13.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
AMP PEAK 20(19P13.2) MUTATED	16	7	23	28	16	3
AMP PEAK 20(19P13.2) WILD-TYPE	8	21	16	40	21	19

Figure S119. Get High-res Image Gene #20: 'amp_19p13.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0343 (Fisher's exact test), Q value = 0.057

Table S120. Gene #20: 'amp_19p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
AMP PEAK 20(19P13.2) MUTATED	28	11	21	17	11	12	7
AMP PEAK 20(19P13.2) WILD-TYPE	18	12	28	29	17	17	26

Figure S120. Get High-res Image Gene #20: 'amp_19p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S121. Gene #21: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
AMP PEAK 21(19Q12) MUTATED	44	5	35	9
AMP PEAK 21(19Q12) WILD-TYPE	26	81	39	17

Figure S121. Get High-res Image Gene #21: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00046

Table S122. Gene #21: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
AMP PEAK 21(19Q12) MUTATED	28	13	16	8	25	1	2
AMP PEAK 21(19Q12) WILD-TYPE	20	33	45	26	22	14	3

Figure S122. Get High-res Image Gene #21: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.00091

Table S123. Gene #21: 'amp_19q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
AMP PEAK 21(19Q12) MUTATED	18	8	19	16	17	8
AMP PEAK 21(19Q12) WILD-TYPE	6	20	20	52	20	14

Figure S123. Get High-res Image Gene #21: 'amp_19q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 0.0314 (Fisher's exact test), Q value = 0.053

Table S124. Gene #21: 'amp_19q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
AMP PEAK 21(19Q12) MUTATED	51	20	22
AMP PEAK 21(19Q12) WILD-TYPE	63	57	41

Figure S124. Get High-res Image Gene #21: 'amp_19q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0188 (Fisher's exact test), Q value = 0.034

Table S125. Gene #21: 'amp_19q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
AMP PEAK 21(19Q12) MUTATED	27	8	13	15	11	6	13
AMP PEAK 21(19Q12) WILD-TYPE	19	15	36	31	17	23	20

Figure S125. Get High-res Image Gene #21: 'amp_19q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00924 (Fisher's exact test), Q value = 0.019

Table S126. Gene #21: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
AMP PEAK 21(19Q12) MUTATED	12	17	9	13	1	10	8	4
AMP PEAK 21(19Q12) WILD-TYPE	12	15	28	11	10	12	13	18

Figure S126. Get High-res Image Gene #21: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S127. Gene #22: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
AMP PEAK 22(20Q13.33) MUTATED	32	13	41	12
AMP PEAK 22(20Q13.33) WILD-TYPE	38	73	33	14

Figure S127. Get High-res Image Gene #22: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.33' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00032

Table S128. Gene #22: 'amp_20q13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
AMP PEAK 22(20Q13.33) MUTATED	28	14	14	10	29	2	1
AMP PEAK 22(20Q13.33) WILD-TYPE	20	32	47	24	18	13	4

Figure S128. Get High-res Image Gene #22: 'amp_20q13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q13.33' versus 'RPPA_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0013

Table S129. Gene #22: 'amp_20q13.33' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
AMP PEAK 22(20Q13.33) MUTATED	24	55	14
AMP PEAK 22(20Q13.33) WILD-TYPE	34	45	46

Figure S129. Get High-res Image Gene #22: 'amp_20q13.33' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_20q13.33' versus 'RPPA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00035

Table S130. Gene #22: 'amp_20q13.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
AMP PEAK 22(20Q13.33) MUTATED	14	11	27	15	17	9
AMP PEAK 22(20Q13.33) WILD-TYPE	10	17	12	53	20	13

Figure S130. Get High-res Image Gene #22: 'amp_20q13.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_20q13.33' versus 'MRNASEQ_CNMF'

P value = 0.00097 (Fisher's exact test), Q value = 0.003

Table S131. Gene #22: 'amp_20q13.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
AMP PEAK 22(20Q13.33) MUTATED	55	17	25
AMP PEAK 22(20Q13.33) WILD-TYPE	59	60	38

Figure S131. Get High-res Image Gene #22: 'amp_20q13.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00322 (Fisher's exact test), Q value = 0.008

Table S132. Gene #22: 'amp_20q13.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
AMP PEAK 22(20Q13.33) MUTATED	24	8	10	18	16	6	15
AMP PEAK 22(20Q13.33) WILD-TYPE	22	15	39	28	12	23	18

Figure S132. Get High-res Image Gene #22: 'amp_20q13.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.021

Table S133. Gene #22: 'amp_20q13.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
AMP PEAK 22(20Q13.33) MUTATED	45	26	27
AMP PEAK 22(20Q13.33) WILD-TYPE	62	24	70

Figure S133. Get High-res Image Gene #22: 'amp_20q13.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_20q13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00577 (Fisher's exact test), Q value = 0.013

Table S134. Gene #22: 'amp_20q13.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
AMP PEAK 22(20Q13.33) MUTATED	40	23	31	4
AMP PEAK 22(20Q13.33) WILD-TYPE	39	29	69	19

Figure S134. Get High-res Image Gene #22: 'amp_20q13.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.04

Table S135. Gene #22: 'amp_20q13.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	64	46
AMP PEAK 22(20Q13.33) MUTATED	33	21	27
AMP PEAK 22(20Q13.33) WILD-TYPE	50	43	19

Figure S135. Get High-res Image Gene #22: 'amp_20q13.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00479 (Fisher's exact test), Q value = 0.011

Table S136. Gene #22: 'amp_20q13.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
AMP PEAK 22(20Q13.33) MUTATED	12	15	7	13	4	11	14	5
AMP PEAK 22(20Q13.33) WILD-TYPE	12	17	30	11	7	11	7	17

Figure S136. Get High-res Image Gene #22: 'amp_20q13.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_21q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S137. Gene #23: 'amp_21q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
AMP PEAK 23(21Q21.1) MUTATED	30	7	27	9
AMP PEAK 23(21Q21.1) WILD-TYPE	40	79	47	17

Figure S137. Get High-res Image Gene #23: 'amp_21q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_21q21.1' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00046

Table S138. Gene #23: 'amp_21q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
AMP PEAK 23(21Q21.1) MUTATED	21	7	15	6	22	0	2
AMP PEAK 23(21Q21.1) WILD-TYPE	27	39	46	28	25	15	3

Figure S138. Get High-res Image Gene #23: 'amp_21q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xp21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S139. Gene #24: 'amp_xp21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
AMP PEAK 24(XP21.2) MUTATED	43	10	32	12
AMP PEAK 24(XP21.2) WILD-TYPE	27	76	42	14

Figure S139. Get High-res Image Gene #24: 'amp_xp21.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp21.2' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00074

Table S140. Gene #24: 'amp_xp21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
AMP PEAK 24(XP21.2) MUTATED	29	12	24	7	21	1	3
AMP PEAK 24(XP21.2) WILD-TYPE	19	34	37	27	26	14	2

Figure S140. Get High-res Image Gene #24: 'amp_xp21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xp21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0219 (Fisher's exact test), Q value = 0.039

Table S141. Gene #24: 'amp_xp21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
AMP PEAK 24(XP21.2) MUTATED	37	17	38	3
AMP PEAK 24(XP21.2) WILD-TYPE	42	35	62	20

Figure S141. Get High-res Image Gene #24: 'amp_xp21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_xp21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00808 (Fisher's exact test), Q value = 0.017

Table S142. Gene #24: 'amp_xp21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
AMP PEAK 24(XP21.2) MUTATED	13	18	12	13	4	7	8	2
AMP PEAK 24(XP21.2) WILD-TYPE	11	14	25	11	7	15	13	20

Figure S142. Get High-res Image Gene #24: 'amp_xp21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xq21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S143. Gene #25: 'amp_xq21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
AMP PEAK 25(XQ21.1) MUTATED	10	3	26	7
AMP PEAK 25(XQ21.1) WILD-TYPE	60	83	48	19

Figure S143. Get High-res Image Gene #25: 'amp_xq21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq21.1' versus 'METHLYATION_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.0034

Table S144. Gene #25: 'amp_xq21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
AMP PEAK 25(XQ21.1) MUTATED	15	5	5	6	12	0	3
AMP PEAK 25(XQ21.1) WILD-TYPE	33	41	56	28	35	15	2

Figure S144. Get High-res Image Gene #25: 'amp_xq21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xq21.1' versus 'RPPA_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.022

Table S145. Gene #25: 'amp_xq21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
AMP PEAK 25(XQ21.1) MUTATED	13	24	4
AMP PEAK 25(XQ21.1) WILD-TYPE	45	76	56

Figure S145. Get High-res Image Gene #25: 'amp_xq21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_xq21.1' versus 'MRNASEQ_CNMF'

P value = 0.0418 (Fisher's exact test), Q value = 0.068

Table S146. Gene #25: 'amp_xq21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
AMP PEAK 25(XQ21.1) MUTATED	28	8	10
AMP PEAK 25(XQ21.1) WILD-TYPE	86	69	53

Figure S146. Get High-res Image Gene #25: 'amp_xq21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_xq21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00397 (Fisher's exact test), Q value = 0.0095

Table S147. Gene #25: 'amp_xq21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
AMP PEAK 25(XQ21.1) MUTATED	16	2	3	7	9	5	4
AMP PEAK 25(XQ21.1) WILD-TYPE	30	21	46	39	19	24	29

Figure S147. Get High-res Image Gene #25: 'amp_xq21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S148. Gene #26: 'del_1p36.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 1(1P36.32) MUTATED	9	1	37	8	6	5	3
DEL PEAK 1(1P36.32) WILD-TYPE	39	45	24	26	41	10	2

Figure S148. Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.32' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S149. Gene #26: 'del_1p36.32' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
DEL PEAK 1(1P36.32) MUTATED	11	10	35
DEL PEAK 1(1P36.32) WILD-TYPE	47	90	25

Figure S149. Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_1p36.32' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S150. Gene #26: 'del_1p36.32' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
DEL PEAK 1(1P36.32) MUTATED	6	2	6	37	1	4
DEL PEAK 1(1P36.32) WILD-TYPE	18	26	33	31	36	18

Figure S150. Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_1p36.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S151. Gene #26: 'del_1p36.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
DEL PEAK 1(1P36.32) MUTATED	13	45	10
DEL PEAK 1(1P36.32) WILD-TYPE	101	32	53

Figure S151. Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p36.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S152. Gene #26: 'del_1p36.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
DEL PEAK 1(1P36.32) MUTATED	8	1	30	7	4	15	3
DEL PEAK 1(1P36.32) WILD-TYPE	38	22	19	39	24	14	30

Figure S152. Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S153. Gene #26: 'del_1p36.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
DEL PEAK 1(1P36.32) MUTATED	15	6	48
DEL PEAK 1(1P36.32) WILD-TYPE	92	44	49

Figure S153. Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p36.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S154. Gene #26: 'del_1p36.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
DEL PEAK 1(1P36.32) MUTATED	11	5	49	4
DEL PEAK 1(1P36.32) WILD-TYPE	68	47	51	19

Figure S154. Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S155. Gene #26: 'del_1p36.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	64	46
DEL PEAK 1(1P36.32) MUTATED	14	31	4
DEL PEAK 1(1P36.32) WILD-TYPE	69	33	42

Figure S155. Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p36.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00104 (Fisher's exact test), Q value = 0.0032

Table S156. Gene #26: 'del_1p36.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
DEL PEAK 1(1P36.32) MUTATED	4	5	18	5	7	2	3	5
DEL PEAK 1(1P36.32) WILD-TYPE	20	27	19	19	4	20	18	17

Figure S156. Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1q44' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S157. Gene #27: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 2(1Q44) MUTATED	31	5	33	11
DEL PEAK 2(1Q44) WILD-TYPE	39	81	41	15

Figure S157. Get High-res Image Gene #27: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q44' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S158. Gene #27: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 2(1Q44) MUTATED	27	14	11	3	22	1	2
DEL PEAK 2(1Q44) WILD-TYPE	21	32	50	31	25	14	3

Figure S158. Get High-res Image Gene #27: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1q44' versus 'RPPA_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.027

Table S159. Gene #27: 'del_1q44' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
DEL PEAK 2(1Q44) MUTATED	20	40	11
DEL PEAK 2(1Q44) WILD-TYPE	38	60	49

Figure S159. Get High-res Image Gene #27: 'del_1q44' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_1q44' versus 'RPPA_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00088

Table S160. Gene #27: 'del_1q44' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
DEL PEAK 2(1Q44) MUTATED	15	7	18	11	15	5
DEL PEAK 2(1Q44) WILD-TYPE	9	21	21	57	22	17

Figure S160. Get High-res Image Gene #27: 'del_1q44' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_1q44' versus 'MRNASEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0013

Table S161. Gene #27: 'del_1q44' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
DEL PEAK 2(1Q44) MUTATED	50	14	16
DEL PEAK 2(1Q44) WILD-TYPE	64	63	47

Figure S161. Get High-res Image Gene #27: 'del_1q44' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1q44' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00038

Table S162. Gene #27: 'del_1q44' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
DEL PEAK 2(1Q44) MUTATED	27	6	10	10	11	3	13
DEL PEAK 2(1Q44) WILD-TYPE	19	17	39	36	17	26	20

Figure S162. Get High-res Image Gene #27: 'del_1q44' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1q44' versus 'MIRSEQ_CNMF'

P value = 0.0257 (Fisher's exact test), Q value = 0.044

Table S163. Gene #27: 'del_1q44' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
DEL PEAK 2(1Q44) MUTATED	36	22	22
DEL PEAK 2(1Q44) WILD-TYPE	71	28	75

Figure S163. Get High-res Image Gene #27: 'del_1q44' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1q44' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00082 (Fisher's exact test), Q value = 0.0026

Table S164. Gene #27: 'del_1q44' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
DEL PEAK 2(1Q44) MUTATED	35	20	23	2
DEL PEAK 2(1Q44) WILD-TYPE	44	32	77	21

Figure S164. Get High-res Image Gene #27: 'del_1q44' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1q44' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00128 (Fisher's exact test), Q value = 0.0037

Table S165. Gene #27: 'del_1q44' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
DEL PEAK 2(1Q44) MUTATED	11	16	9	12	0	9	9	2
DEL PEAK 2(1Q44) WILD-TYPE	13	16	28	12	11	13	12	20

Figure S165. Get High-res Image Gene #27: 'del_1q44' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2p25.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S166. Gene #28: 'del_2p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 3(2P25.3) MUTATED	40	12	36	6
DEL PEAK 3(2P25.3) WILD-TYPE	30	74	38	20

Figure S166. Get High-res Image Gene #28: 'del_2p25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2p25.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S167. Gene #28: 'del_2p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 3(2P25.3) MUTATED	23	11	35	3	15	4	3
DEL PEAK 3(2P25.3) WILD-TYPE	25	35	26	31	32	11	2

Figure S167. Get High-res Image Gene #28: 'del_2p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2p25.3' versus 'RPPA_CNMF'

P value = 0.0283 (Fisher's exact test), Q value = 0.048

Table S168. Gene #28: 'del_2p25.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
DEL PEAK 3(2P25.3) MUTATED	16	33	30
DEL PEAK 3(2P25.3) WILD-TYPE	42	67	30

Figure S168. Get High-res Image Gene #28: 'del_2p25.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_2p25.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0043 (Fisher's exact test), Q value = 0.01

Table S169. Gene #28: 'del_2p25.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
DEL PEAK 3(2P25.3) MUTATED	12	5	13	34	12	3
DEL PEAK 3(2P25.3) WILD-TYPE	12	23	26	34	25	19

Figure S169. Get High-res Image Gene #28: 'del_2p25.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_2p25.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S170. Gene #28: 'del_2p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
DEL PEAK 3(2P25.3) MUTATED	42	42	9
DEL PEAK 3(2P25.3) WILD-TYPE	72	35	54

Figure S170. Get High-res Image Gene #28: 'del_2p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.001 (Fisher's exact test), Q value = 0.0031

Table S171. Gene #28: 'del_2p25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
DEL PEAK 3(2P25.3) MUTATED	20	5	28	8	8	14	10
DEL PEAK 3(2P25.3) WILD-TYPE	26	18	21	38	20	15	23

Figure S171. Get High-res Image Gene #28: 'del_2p25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2p25.3' versus 'MIRSEQ_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.0021

Table S172. Gene #28: 'del_2p25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
DEL PEAK 3(2P25.3) MUTATED	25	21	47
DEL PEAK 3(2P25.3) WILD-TYPE	82	29	50

Figure S172. Get High-res Image Gene #28: 'del_2p25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.001

Table S173. Gene #28: 'del_2p25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
DEL PEAK 3(2P25.3) MUTATED	26	17	49	1
DEL PEAK 3(2P25.3) WILD-TYPE	53	35	51	22

Figure S173. Get High-res Image Gene #28: 'del_2p25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2p25.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0012

Table S174. Gene #28: 'del_2p25.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	64	46
DEL PEAK 3(2P25.3) MUTATED	19	35	19
DEL PEAK 3(2P25.3) WILD-TYPE	64	29	27

Figure S174. Get High-res Image Gene #28: 'del_2p25.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_2p25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00075 (Fisher's exact test), Q value = 0.0025

Table S175. Gene #28: 'del_2p25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
DEL PEAK 3(2P25.3) MUTATED	9	12	23	11	5	5	7	1
DEL PEAK 3(2P25.3) WILD-TYPE	15	20	14	13	6	17	14	21

Figure S175. Get High-res Image Gene #28: 'del_2p25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S176. Gene #29: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 4(2Q37.3) MUTATED	55	10	32	11
DEL PEAK 4(2Q37.3) WILD-TYPE	15	76	42	15

Figure S176. Get High-res Image Gene #29: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 0.00107 (Fisher's exact test), Q value = 0.0032

Table S177. Gene #29: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 4(2Q37.3) MUTATED	29	14	28	7	25	3	2
DEL PEAK 4(2Q37.3) WILD-TYPE	19	32	33	27	22	12	3

Figure S177. Get High-res Image Gene #29: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.049 (Fisher's exact test), Q value = 0.079

Table S178. Gene #29: 'del_2q37.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
DEL PEAK 4(2Q37.3) MUTATED	15	7	19	29	19	6
DEL PEAK 4(2Q37.3) WILD-TYPE	9	21	20	39	18	16

Figure S178. Get High-res Image Gene #29: 'del_2q37.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 0.0208 (Fisher's exact test), Q value = 0.037

Table S179. Gene #29: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
DEL PEAK 4(2Q37.3) MUTATED	54	35	17
DEL PEAK 4(2Q37.3) WILD-TYPE	60	42	46

Figure S179. Get High-res Image Gene #29: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00107 (Fisher's exact test), Q value = 0.0032

Table S180. Gene #29: 'del_2q37.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
DEL PEAK 4(2Q37.3) MUTATED	26	7	16	10	12	19	16
DEL PEAK 4(2Q37.3) WILD-TYPE	20	16	33	36	16	10	17

Figure S180. Get High-res Image Gene #29: 'del_2q37.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0242 (Fisher's exact test), Q value = 0.042

Table S181. Gene #29: 'del_2q37.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
DEL PEAK 4(2Q37.3) MUTATED	38	18	47	4
DEL PEAK 4(2Q37.3) WILD-TYPE	41	34	53	19

Figure S181. Get High-res Image Gene #29: 'del_2q37.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0284 (Fisher's exact test), Q value = 0.048

Table S182. Gene #29: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
DEL PEAK 4(2Q37.3) MUTATED	12	16	14	16	7	7	9	4
DEL PEAK 4(2Q37.3) WILD-TYPE	12	16	23	8	4	15	12	18

Figure S182. Get High-res Image Gene #29: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S183. Gene #30: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 5(2Q37.3) MUTATED	55	8	34	13
DEL PEAK 5(2Q37.3) WILD-TYPE	15	78	40	13

Figure S183. Get High-res Image Gene #30: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0015

Table S184. Gene #30: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 5(2Q37.3) MUTATED	31	13	28	8	25	3	2
DEL PEAK 5(2Q37.3) WILD-TYPE	17	33	33	26	22	12	3

Figure S184. Get High-res Image Gene #30: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00547 (Fisher's exact test), Q value = 0.012

Table S185. Gene #30: 'del_2q37.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
DEL PEAK 5(2Q37.3) MUTATED	17	7	19	29	19	5
DEL PEAK 5(2Q37.3) WILD-TYPE	7	21	20	39	18	17

Figure S185. Get High-res Image Gene #30: 'del_2q37.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.026

Table S186. Gene #30: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
DEL PEAK 5(2Q37.3) MUTATED	56	35	17
DEL PEAK 5(2Q37.3) WILD-TYPE	58	42	46

Figure S186. Get High-res Image Gene #30: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00164 (Fisher's exact test), Q value = 0.0045

Table S187. Gene #30: 'del_2q37.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
DEL PEAK 5(2Q37.3) MUTATED	28	7	16	12	12	19	14
DEL PEAK 5(2Q37.3) WILD-TYPE	18	16	33	34	16	10	19

Figure S187. Get High-res Image Gene #30: 'del_2q37.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.31' versus 'CN_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.036

Table S188. Gene #31: 'del_3p21.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 6(3P21.31) MUTATED	22	12	24	7
DEL PEAK 6(3P21.31) WILD-TYPE	48	74	50	19

Figure S188. Get High-res Image Gene #31: 'del_3p21.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p21.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S189. Gene #31: 'del_3p21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 6(3P21.31) MUTATED	24	10	3	12	13	2	1
DEL PEAK 6(3P21.31) WILD-TYPE	24	36	58	22	34	13	4

Figure S189. Get High-res Image Gene #31: 'del_3p21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p21.31' versus 'RPPA_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.026

Table S190. Gene #31: 'del_3p21.31' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
DEL PEAK 6(3P21.31) MUTATED	16	34	8
DEL PEAK 6(3P21.31) WILD-TYPE	42	66	52

Figure S190. Get High-res Image Gene #31: 'del_3p21.31' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_3p21.31' versus 'RPPA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00038

Table S191. Gene #31: 'del_3p21.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
DEL PEAK 6(3P21.31) MUTATED	10	8	10	5	17	8
DEL PEAK 6(3P21.31) WILD-TYPE	14	20	29	63	20	14

Figure S191. Get High-res Image Gene #31: 'del_3p21.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_3p21.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S192. Gene #31: 'del_3p21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
DEL PEAK 6(3P21.31) MUTATED	35	5	25
DEL PEAK 6(3P21.31) WILD-TYPE	79	72	38

Figure S192. Get High-res Image Gene #31: 'del_3p21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S193. Gene #31: 'del_3p21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
DEL PEAK 6(3P21.31) MUTATED	22	6	2	19	5	3	8
DEL PEAK 6(3P21.31) WILD-TYPE	24	17	47	27	23	26	25

Figure S193. Get High-res Image Gene #31: 'del_3p21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0015

Table S194. Gene #31: 'del_3p21.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
DEL PEAK 6(3P21.31) MUTATED	38	15	12
DEL PEAK 6(3P21.31) WILD-TYPE	69	35	85

Figure S194. Get High-res Image Gene #31: 'del_3p21.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00063 (Fisher's exact test), Q value = 0.0021

Table S195. Gene #31: 'del_3p21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
DEL PEAK 6(3P21.31) MUTATED	28	14	13	10
DEL PEAK 6(3P21.31) WILD-TYPE	51	38	87	13

Figure S195. Get High-res Image Gene #31: 'del_3p21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0015 (Fisher's exact test), Q value = 0.0042

Table S196. Gene #31: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	64	46
DEL PEAK 6(3P21.31) MUTATED	31	8	16
DEL PEAK 6(3P21.31) WILD-TYPE	52	56	30

Figure S196. Get High-res Image Gene #31: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S197. Gene #31: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
DEL PEAK 6(3P21.31) MUTATED	12	14	0	8	2	4	5	10
DEL PEAK 6(3P21.31) WILD-TYPE	12	18	37	16	9	18	16	12

Figure S197. Get High-res Image Gene #31: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q13.31' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 5e-04

Table S198. Gene #32: 'del_3q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 7(3Q13.31) MUTATED	9	8	24	10
DEL PEAK 7(3Q13.31) WILD-TYPE	61	78	50	16

Figure S198. Get High-res Image Gene #32: 'del_3q13.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q13.31' versus 'METHLYATION_CNMF'

P value = 0.00427 (Fisher's exact test), Q value = 0.01

Table S199. Gene #32: 'del_3q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 7(3Q13.31) MUTATED	13	6	4	9	13	3	3
DEL PEAK 7(3Q13.31) WILD-TYPE	35	40	57	25	34	12	2

Figure S199. Get High-res Image Gene #32: 'del_3q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3q13.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0108 (Fisher's exact test), Q value = 0.021

Table S200. Gene #32: 'del_3q13.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
DEL PEAK 7(3Q13.31) MUTATED	5	6	12	6	6	9
DEL PEAK 7(3Q13.31) WILD-TYPE	19	22	27	62	31	13

Figure S200. Get High-res Image Gene #32: 'del_3q13.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_3q13.31' versus 'MRNASEQ_CNMF'

P value = 0.00511 (Fisher's exact test), Q value = 0.012

Table S201. Gene #32: 'del_3q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
DEL PEAK 7(3Q13.31) MUTATED	25	7	19
DEL PEAK 7(3Q13.31) WILD-TYPE	89	70	44

Figure S201. Get High-res Image Gene #32: 'del_3q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00996 (Fisher's exact test), Q value = 0.02

Table S202. Gene #32: 'del_3q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
DEL PEAK 7(3Q13.31) MUTATED	13	3	3	16	7	4	5
DEL PEAK 7(3Q13.31) WILD-TYPE	33	20	46	30	21	25	28

Figure S202. Get High-res Image Gene #32: 'del_3q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3q13.31' versus 'MIRSEQ_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.02

Table S203. Gene #32: 'del_3q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
DEL PEAK 7(3Q13.31) MUTATED	30	9	11
DEL PEAK 7(3Q13.31) WILD-TYPE	77	41	86

Figure S203. Get High-res Image Gene #32: 'del_3q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00887 (Fisher's exact test), Q value = 0.018

Table S204. Gene #32: 'del_3q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
DEL PEAK 7(3Q13.31) MUTATED	23	9	11	7
DEL PEAK 7(3Q13.31) WILD-TYPE	56	43	89	16

Figure S204. Get High-res Image Gene #32: 'del_3q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3q13.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.033

Table S205. Gene #32: 'del_3q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	64	46
DEL PEAK 7(3Q13.31) MUTATED	25	7	10
DEL PEAK 7(3Q13.31) WILD-TYPE	58	57	36

Figure S205. Get High-res Image Gene #32: 'del_3q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3q13.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0297 (Fisher's exact test), Q value = 0.05

Table S206. Gene #32: 'del_3q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
DEL PEAK 7(3Q13.31) MUTATED	4	13	2	4	2	5	5	7
DEL PEAK 7(3Q13.31) WILD-TYPE	20	19	35	20	9	17	16	15

Figure S206. Get High-res Image Gene #32: 'del_3q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q29' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0011

Table S207. Gene #33: 'del_3q29' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 8(3Q29) MUTATED	18	7	18	11
DEL PEAK 8(3Q29) WILD-TYPE	52	79	56	15

Figure S207. Get High-res Image Gene #33: 'del_3q29' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q29' versus 'METHLYATION_CNMF'

P value = 0.00519 (Fisher's exact test), Q value = 0.012

Table S208. Gene #33: 'del_3q29' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 8(3Q29) MUTATED	15	5	10	6	13	1	4
DEL PEAK 8(3Q29) WILD-TYPE	33	41	51	28	34	14	1

Figure S208. Get High-res Image Gene #33: 'del_3q29' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3q29' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0222 (Fisher's exact test), Q value = 0.039

Table S209. Gene #33: 'del_3q29' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
DEL PEAK 8(3Q29) MUTATED	26	7	16	4
DEL PEAK 8(3Q29) WILD-TYPE	53	45	84	19

Figure S209. Get High-res Image Gene #33: 'del_3q29' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q35.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S210. Gene #34: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 9(4Q35.1) MUTATED	38	8	41	7
DEL PEAK 9(4Q35.1) WILD-TYPE	32	78	33	19

Figure S210. Get High-res Image Gene #34: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q35.1' versus 'METHLYATION_CNMF'

P value = 0.00138 (Fisher's exact test), Q value = 0.0039

Table S211. Gene #34: 'del_4q35.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 9(4Q35.1) MUTATED	21	13	20	9	26	1	4
DEL PEAK 9(4Q35.1) WILD-TYPE	27	33	41	25	21	14	1

Figure S211. Get High-res Image Gene #34: 'del_4q35.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q35.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0106 (Fisher's exact test), Q value = 0.021

Table S212. Gene #34: 'del_4q35.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
DEL PEAK 9(4Q35.1) MUTATED	10	8	23	19	19	6
DEL PEAK 9(4Q35.1) WILD-TYPE	14	20	16	49	18	16

Figure S212. Get High-res Image Gene #34: 'del_4q35.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_4q35.1' versus 'MRNASEQ_CNMF'

P value = 0.00762 (Fisher's exact test), Q value = 0.016

Table S213. Gene #34: 'del_4q35.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
DEL PEAK 9(4Q35.1) MUTATED	54	24	16
DEL PEAK 9(4Q35.1) WILD-TYPE	60	53	47

Figure S213. Get High-res Image Gene #34: 'del_4q35.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5p15.33' versus 'CN_CNMF'

P value = 0.0335 (Fisher's exact test), Q value = 0.055

Table S214. Gene #35: 'del_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 10(5P15.33) MUTATED	12	14	3	4
DEL PEAK 10(5P15.33) WILD-TYPE	58	72	71	22

Figure S214. Get High-res Image Gene #35: 'del_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_5p15.33' versus 'METHLYATION_CNMF'

P value = 0.0289 (Fisher's exact test), Q value = 0.049

Table S215. Gene #35: 'del_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 10(5P15.33) MUTATED	5	8	3	3	13	1	0
DEL PEAK 10(5P15.33) WILD-TYPE	43	38	58	31	34	14	5

Figure S215. Get High-res Image Gene #35: 'del_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5p15.33' versus 'RPPA_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.03

Table S216. Gene #35: 'del_5p15.33' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
DEL PEAK 10(5P15.33) MUTATED	7	21	3
DEL PEAK 10(5P15.33) WILD-TYPE	51	79	57

Figure S216. Get High-res Image Gene #35: 'del_5p15.33' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_5p15.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.00102 (Fisher's exact test), Q value = 0.0031

Table S217. Gene #35: 'del_5p15.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
DEL PEAK 10(5P15.33) MUTATED	2	5	9	2	11	2
DEL PEAK 10(5P15.33) WILD-TYPE	22	23	30	66	26	20

Figure S217. Get High-res Image Gene #35: 'del_5p15.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_5p15.33' versus 'MRNASEQ_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.023

Table S218. Gene #35: 'del_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
DEL PEAK 10(5P15.33) MUTATED	18	3	11
DEL PEAK 10(5P15.33) WILD-TYPE	96	74	52

Figure S218. Get High-res Image Gene #35: 'del_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00289 (Fisher's exact test), Q value = 0.0073

Table S219. Gene #35: 'del_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
DEL PEAK 10(5P15.33) MUTATED	4	3	3	5	8	0	9
DEL PEAK 10(5P15.33) WILD-TYPE	42	20	46	41	20	29	24

Figure S219. Get High-res Image Gene #35: 'del_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0243 (Fisher's exact test), Q value = 0.042

Table S220. Gene #35: 'del_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	64	46
DEL PEAK 10(5P15.33) MUTATED	10	5	12
DEL PEAK 10(5P15.33) WILD-TYPE	73	59	34

Figure S220. Get High-res Image Gene #35: 'del_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 0.00198 (Fisher's exact test), Q value = 0.0053

Table S221. Gene #36: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 11(6P25.3) MUTATED	12	9	32	6	17	3	2
DEL PEAK 11(6P25.3) WILD-TYPE	36	37	29	28	30	12	3

Figure S221. Get High-res Image Gene #36: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p25.3' versus 'RPPA_CNMF'

P value = 0.0012 (Fisher's exact test), Q value = 0.0035

Table S222. Gene #36: 'del_6p25.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
DEL PEAK 11(6P25.3) MUTATED	10	28	29
DEL PEAK 11(6P25.3) WILD-TYPE	48	72	31

Figure S222. Get High-res Image Gene #36: 'del_6p25.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_6p25.3' versus 'MRNASEQ_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0018

Table S223. Gene #36: 'del_6p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
DEL PEAK 11(6P25.3) MUTATED	29	37	13
DEL PEAK 11(6P25.3) WILD-TYPE	85	40	50

Figure S223. Get High-res Image Gene #36: 'del_6p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00222 (Fisher's exact test), Q value = 0.0059

Table S224. Gene #36: 'del_6p25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
DEL PEAK 11(6P25.3) MUTATED	7	6	26	9	8	11	12
DEL PEAK 11(6P25.3) WILD-TYPE	39	17	23	37	20	18	21

Figure S224. Get High-res Image Gene #36: 'del_6p25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6p25.3' versus 'MIRSEQ_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.027

Table S225. Gene #36: 'del_6p25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
DEL PEAK 11(6P25.3) MUTATED	25	15	41
DEL PEAK 11(6P25.3) WILD-TYPE	82	35	56

Figure S225. Get High-res Image Gene #36: 'del_6p25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.019 (Fisher's exact test), Q value = 0.035

Table S226. Gene #36: 'del_6p25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
DEL PEAK 11(6P25.3) MUTATED	20	16	42	3
DEL PEAK 11(6P25.3) WILD-TYPE	59	36	58	20

Figure S226. Get High-res Image Gene #36: 'del_6p25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q14.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S227. Gene #37: 'del_6q14.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 12(6Q14.1) MUTATED	26	11	36	5
DEL PEAK 12(6Q14.1) WILD-TYPE	44	75	38	21

Figure S227. Get High-res Image Gene #37: 'del_6q14.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q14.1' versus 'METHLYATION_CNMF'

P value = 0.00327 (Fisher's exact test), Q value = 0.0081

Table S228. Gene #37: 'del_6q14.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 12(6Q14.1) MUTATED	15	9	21	6	23	1	3
DEL PEAK 12(6Q14.1) WILD-TYPE	33	37	40	28	24	14	2

Figure S228. Get High-res Image Gene #37: 'del_6q14.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q14.1' versus 'RPPA_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.022

Table S229. Gene #37: 'del_6q14.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
DEL PEAK 12(6Q14.1) MUTATED	10	39	15
DEL PEAK 12(6Q14.1) WILD-TYPE	48	61	45

Figure S229. Get High-res Image Gene #37: 'del_6q14.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_6q14.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0125 (Fisher's exact test), Q value = 0.024

Table S230. Gene #37: 'del_6q14.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
DEL PEAK 12(6Q14.1) MUTATED	4	8	21	15	9	7
DEL PEAK 12(6Q14.1) WILD-TYPE	20	20	18	53	28	15

Figure S230. Get High-res Image Gene #37: 'del_6q14.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_7q36.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S231. Gene #38: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 13(7Q36.3) MUTATED	26	5	32	8
DEL PEAK 13(7Q36.3) WILD-TYPE	44	81	42	18

Figure S231. Get High-res Image Gene #38: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q36.3' versus 'METHLYATION_CNMF'

P value = 0.0257 (Fisher's exact test), Q value = 0.044

Table S232. Gene #38: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 13(7Q36.3) MUTATED	16	8	18	5	21	2	1
DEL PEAK 13(7Q36.3) WILD-TYPE	32	38	43	29	26	13	4

Figure S232. Get High-res Image Gene #38: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q36.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0347 (Fisher's exact test), Q value = 0.057

Table S233. Gene #38: 'del_7q36.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
DEL PEAK 13(7Q36.3) MUTATED	18	20	30	2
DEL PEAK 13(7Q36.3) WILD-TYPE	61	32	70	21

Figure S233. Get High-res Image Gene #38: 'del_7q36.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S234. Gene #39: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 14(8P23.3) MUTATED	31	9	26	15
DEL PEAK 14(8P23.3) WILD-TYPE	39	77	48	11

Figure S234. Get High-res Image Gene #39: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S235. Gene #39: 'del_8p23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 14(8P23.3) MUTATED	25	10	7	10	25	1	3
DEL PEAK 14(8P23.3) WILD-TYPE	23	36	54	24	22	14	2

Figure S235. Get High-res Image Gene #39: 'del_8p23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.3' versus 'RPPA_CNMF'

P value = 0.0015 (Fisher's exact test), Q value = 0.0042

Table S236. Gene #39: 'del_8p23.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
DEL PEAK 14(8P23.3) MUTATED	20	44	10
DEL PEAK 14(8P23.3) WILD-TYPE	38	56	50

Figure S236. Get High-res Image Gene #39: 'del_8p23.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_8p23.3' versus 'RPPA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00042

Table S237. Gene #39: 'del_8p23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
DEL PEAK 14(8P23.3) MUTATED	13	4	21	13	17	6
DEL PEAK 14(8P23.3) WILD-TYPE	11	24	18	55	20	16

Figure S237. Get High-res Image Gene #39: 'del_8p23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_8p23.3' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00035

Table S238. Gene #39: 'del_8p23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
DEL PEAK 14(8P23.3) MUTATED	51	12	17
DEL PEAK 14(8P23.3) WILD-TYPE	63	65	46

Figure S238. Get High-res Image Gene #39: 'del_8p23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00096 (Fisher's exact test), Q value = 0.003

Table S239. Gene #39: 'del_8p23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
DEL PEAK 14(8P23.3) MUTATED	22	8	6	10	13	7	14
DEL PEAK 14(8P23.3) WILD-TYPE	24	15	43	36	15	22	19

Figure S239. Get High-res Image Gene #39: 'del_8p23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.3' versus 'MIRSEQ_CNMF'

P value = 0.00227 (Fisher's exact test), Q value = 0.006

Table S240. Gene #39: 'del_8p23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
DEL PEAK 14(8P23.3) MUTATED	41	20	18
DEL PEAK 14(8P23.3) WILD-TYPE	66	30	79

Figure S240. Get High-res Image Gene #39: 'del_8p23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00083 (Fisher's exact test), Q value = 0.0026

Table S241. Gene #39: 'del_8p23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
DEL PEAK 14(8P23.3) MUTATED	37	18	20	4
DEL PEAK 14(8P23.3) WILD-TYPE	42	34	80	19

Figure S241. Get High-res Image Gene #39: 'del_8p23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00965 (Fisher's exact test), Q value = 0.02

Table S242. Gene #39: 'del_8p23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	64	46
DEL PEAK 14(8P23.3) MUTATED	34	12	18
DEL PEAK 14(8P23.3) WILD-TYPE	49	52	28

Figure S242. Get High-res Image Gene #39: 'del_8p23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8p23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.0025

Table S243. Gene #39: 'del_8p23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
DEL PEAK 14(8P23.3) MUTATED	10	16	4	8	1	13	7	5
DEL PEAK 14(8P23.3) WILD-TYPE	14	16	33	16	10	9	14	17

Figure S243. Get High-res Image Gene #39: 'del_8p23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S244. Gene #40: 'del_9p24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 15(9P24.3) MUTATED	20	20	53	7
DEL PEAK 15(9P24.3) WILD-TYPE	50	66	21	19

Figure S244. Get High-res Image Gene #40: 'del_9p24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p24.3' versus 'RPPA_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 0.04

Table S245. Gene #40: 'del_9p24.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
DEL PEAK 15(9P24.3) MUTATED	18	50	19
DEL PEAK 15(9P24.3) WILD-TYPE	40	50	41

Figure S245. Get High-res Image Gene #40: 'del_9p24.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S246. Gene #41: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 16(9P21.3) MUTATED	18	25	61	10
DEL PEAK 16(9P21.3) WILD-TYPE	52	61	13	16

Figure S246. Get High-res Image Gene #41: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.0039

Table S247. Gene #41: 'del_9p21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
DEL PEAK 16(9P21.3) MUTATED	23	61	20
DEL PEAK 16(9P21.3) WILD-TYPE	35	39	40

Figure S247. Get High-res Image Gene #41: 'del_9p21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00065 (Fisher's exact test), Q value = 0.0022

Table S248. Gene #41: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
DEL PEAK 16(9P21.3) MUTATED	7	13	28	22	21	13
DEL PEAK 16(9P21.3) WILD-TYPE	17	15	11	46	16	9

Figure S248. Get High-res Image Gene #41: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 0.00415 (Fisher's exact test), Q value = 0.0099

Table S249. Gene #41: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
DEL PEAK 16(9P21.3) MUTATED	58	22	32
DEL PEAK 16(9P21.3) WILD-TYPE	56	55	31

Figure S249. Get High-res Image Gene #41: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00255 (Fisher's exact test), Q value = 0.0066

Table S250. Gene #41: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
DEL PEAK 16(9P21.3) MUTATED	24	7	17	24	18	5	17
DEL PEAK 16(9P21.3) WILD-TYPE	22	16	32	22	10	24	16

Figure S250. Get High-res Image Gene #41: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 0.0317 (Fisher's exact test), Q value = 0.053

Table S251. Gene #41: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
DEL PEAK 16(9P21.3) MUTATED	47	30	36
DEL PEAK 16(9P21.3) WILD-TYPE	60	20	61

Figure S251. Get High-res Image Gene #41: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00035

Table S252. Gene #41: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	64	46
DEL PEAK 16(9P21.3) MUTATED	40	19	33
DEL PEAK 16(9P21.3) WILD-TYPE	43	45	13

Figure S252. Get High-res Image Gene #41: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00335 (Fisher's exact test), Q value = 0.0082

Table S253. Gene #41: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
DEL PEAK 16(9P21.3) MUTATED	11	17	10	16	2	10	16	10
DEL PEAK 16(9P21.3) WILD-TYPE	13	15	27	8	9	12	5	12

Figure S253. Get High-res Image Gene #41: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S254. Gene #42: 'del_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 17(9Q34.3) MUTATED	27	6	26	2
DEL PEAK 17(9Q34.3) WILD-TYPE	43	80	48	24

Figure S254. Get High-res Image Gene #42: 'del_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q34.3' versus 'METHLYATION_CNMF'

P value = 0.00118 (Fisher's exact test), Q value = 0.0035

Table S255. Gene #42: 'del_9q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 17(9Q34.3) MUTATED	9	3	24	6	15	2	2
DEL PEAK 17(9Q34.3) WILD-TYPE	39	43	37	28	32	13	3

Figure S255. Get High-res Image Gene #42: 'del_9q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9q34.3' versus 'RPPA_CNMF'

P value = 0.0443 (Fisher's exact test), Q value = 0.072

Table S256. Gene #42: 'del_9q34.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
DEL PEAK 17(9Q34.3) MUTATED	9	23	21
DEL PEAK 17(9Q34.3) WILD-TYPE	49	77	39

Figure S256. Get High-res Image Gene #42: 'del_9q34.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_9q34.3' versus 'MRNASEQ_CNMF'

P value = 0.0498 (Fisher's exact test), Q value = 0.079

Table S257. Gene #42: 'del_9q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
DEL PEAK 17(9Q34.3) MUTATED	22	26	12
DEL PEAK 17(9Q34.3) WILD-TYPE	92	51	51

Figure S257. Get High-res Image Gene #42: 'del_9q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9q34.3' versus 'MIRSEQ_CNMF'

P value = 0.00152 (Fisher's exact test), Q value = 0.0042

Table S258. Gene #42: 'del_9q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
DEL PEAK 17(9Q34.3) MUTATED	20	6	35
DEL PEAK 17(9Q34.3) WILD-TYPE	87	44	62

Figure S258. Get High-res Image Gene #42: 'del_9q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.0014

Table S259. Gene #42: 'del_9q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
DEL PEAK 17(9Q34.3) MUTATED	13	5	37	6
DEL PEAK 17(9Q34.3) WILD-TYPE	66	47	63	17

Figure S259. Get High-res Image Gene #42: 'del_9q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0366 (Fisher's exact test), Q value = 0.06

Table S260. Gene #42: 'del_9q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
DEL PEAK 17(9Q34.3) MUTATED	1	5	12	9	5	4	5	7
DEL PEAK 17(9Q34.3) WILD-TYPE	23	27	25	15	6	18	16	15

Figure S260. Get High-res Image Gene #42: 'del_9q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 0.00854 (Fisher's exact test), Q value = 0.018

Table S261. Gene #43: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 18(10P15.3) MUTATED	40	31	45	12
DEL PEAK 18(10P15.3) WILD-TYPE	30	55	29	14

Figure S261. Get High-res Image Gene #43: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 0.00184 (Fisher's exact test), Q value = 0.005

Table S262. Gene #43: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 18(10P15.3) MUTATED	29	14	39	15	25	3	3
DEL PEAK 18(10P15.3) WILD-TYPE	19	32	22	19	22	12	2

Figure S262. Get High-res Image Gene #43: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p15.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00094 (Fisher's exact test), Q value = 0.003

Table S263. Gene #43: 'del_10p15.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
DEL PEAK 18(10P15.3) MUTATED	15	5	27	34	16	13
DEL PEAK 18(10P15.3) WILD-TYPE	9	23	12	34	21	9

Figure S263. Get High-res Image Gene #43: 'del_10p15.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00332 (Fisher's exact test), Q value = 0.0082

Table S264. Gene #43: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
DEL PEAK 18(10P15.3) MUTATED	26	5	34	20	12	11	19
DEL PEAK 18(10P15.3) WILD-TYPE	20	18	15	26	16	18	14

Figure S264. Get High-res Image Gene #43: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S265. Gene #44: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 19(10Q23.31) MUTATED	56	29	47	6
DEL PEAK 19(10Q23.31) WILD-TYPE	14	57	27	20

Figure S265. Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S266. Gene #44: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 19(10Q23.31) MUTATED	28	10	52	8	32	4	4
DEL PEAK 19(10Q23.31) WILD-TYPE	20	36	9	26	15	11	1

Figure S266. Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S267. Gene #44: 'del_10q23.31' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
DEL PEAK 19(10Q23.31) MUTATED	18	53	46
DEL PEAK 19(10Q23.31) WILD-TYPE	40	47	14

Figure S267. Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_10q23.31' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S268. Gene #44: 'del_10q23.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
DEL PEAK 19(10Q23.31) MUTATED	13	5	28	47	18	6
DEL PEAK 19(10Q23.31) WILD-TYPE	11	23	11	21	19	16

Figure S268. Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S269. Gene #44: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
DEL PEAK 19(10Q23.31) MUTATED	57	61	19
DEL PEAK 19(10Q23.31) WILD-TYPE	57	16	44

Figure S269. Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S270. Gene #44: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
DEL PEAK 19(10Q23.31) MUTATED	25	7	46	10	12	15	22
DEL PEAK 19(10Q23.31) WILD-TYPE	21	16	3	36	16	14	11

Figure S270. Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S271. Gene #44: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
DEL PEAK 19(10Q23.31) MUTATED	41	27	69
DEL PEAK 19(10Q23.31) WILD-TYPE	66	23	28

Figure S271. Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00027

Table S272. Gene #44: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
DEL PEAK 19(10Q23.31) MUTATED	38	24	70	5
DEL PEAK 19(10Q23.31) WILD-TYPE	41	28	30	18

Figure S272. Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0018

Table S273. Gene #44: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	64	46
DEL PEAK 19(10Q23.31) MUTATED	34	47	25
DEL PEAK 19(10Q23.31) WILD-TYPE	49	17	21

Figure S273. Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0012

Table S274. Gene #44: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
DEL PEAK 19(10Q23.31) MUTATED	15	12	30	14	7	14	9	5
DEL PEAK 19(10Q23.31) WILD-TYPE	9	20	7	10	4	8	12	17

Figure S274. Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S275. Gene #45: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 20(10Q26.3) MUTATED	53	30	43	6
DEL PEAK 20(10Q26.3) WILD-TYPE	17	56	31	20

Figure S275. Get High-res Image Gene #45: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q26.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S276. Gene #45: 'del_10q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 20(10Q26.3) MUTATED	25	10	50	6	33	4	4
DEL PEAK 20(10Q26.3) WILD-TYPE	23	36	11	28	14	11	1

Figure S276. Get High-res Image Gene #45: 'del_10q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q26.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S277. Gene #45: 'del_10q26.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
DEL PEAK 20(10Q26.3) MUTATED	16	52	45
DEL PEAK 20(10Q26.3) WILD-TYPE	42	48	15

Figure S277. Get High-res Image Gene #45: 'del_10q26.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_10q26.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S278. Gene #45: 'del_10q26.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
DEL PEAK 20(10Q26.3) MUTATED	13	5	28	46	15	6
DEL PEAK 20(10Q26.3) WILD-TYPE	11	23	11	22	22	16

Figure S278. Get High-res Image Gene #45: 'del_10q26.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S279. Gene #45: 'del_10q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
DEL PEAK 20(10Q26.3) MUTATED	54	57	19
DEL PEAK 20(10Q26.3) WILD-TYPE	60	20	44

Figure S279. Get High-res Image Gene #45: 'del_10q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S280. Gene #45: 'del_10q26.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
DEL PEAK 20(10Q26.3) MUTATED	21	7	41	9	15	16	21
DEL PEAK 20(10Q26.3) WILD-TYPE	25	16	8	37	13	13	12

Figure S280. Get High-res Image Gene #45: 'del_10q26.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00042

Table S281. Gene #45: 'del_10q26.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
DEL PEAK 20(10Q26.3) MUTATED	38	28	64
DEL PEAK 20(10Q26.3) WILD-TYPE	69	22	33

Figure S281. Get High-res Image Gene #45: 'del_10q26.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00042

Table S282. Gene #45: 'del_10q26.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
DEL PEAK 20(10Q26.3) MUTATED	37	23	66	4
DEL PEAK 20(10Q26.3) WILD-TYPE	42	29	34	19

Figure S282. Get High-res Image Gene #45: 'del_10q26.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00035

Table S283. Gene #45: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	64	46
DEL PEAK 20(10Q26.3) MUTATED	31	47	25
DEL PEAK 20(10Q26.3) WILD-TYPE	52	17	21

Figure S283. Get High-res Image Gene #45: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.0011

Table S284. Gene #45: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
DEL PEAK 20(10Q26.3) MUTATED	14	10	29	13	8	14	10	5
DEL PEAK 20(10Q26.3) WILD-TYPE	10	22	8	11	3	8	11	17

Figure S284. Get High-res Image Gene #45: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S285. Gene #46: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 21(11P15.5) MUTATED	40	9	47	14
DEL PEAK 21(11P15.5) WILD-TYPE	30	77	27	12

Figure S285. Get High-res Image Gene #46: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0015

Table S286. Gene #46: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 21(11P15.5) MUTATED	30	12	30	10	23	2	3
DEL PEAK 21(11P15.5) WILD-TYPE	18	34	31	24	24	13	2

Figure S286. Get High-res Image Gene #46: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.5' versus 'RPPA_CHIERARCHICAL'

P value = 0.00602 (Fisher's exact test), Q value = 0.013

Table S287. Gene #46: 'del_11p15.5' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
DEL PEAK 21(11P15.5) MUTATED	19	7	17	29	16	9
DEL PEAK 21(11P15.5) WILD-TYPE	5	21	22	39	21	13

Figure S287. Get High-res Image Gene #46: 'del_11p15.5' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_11q24.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S288. Gene #47: 'del_11q24.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 22(11Q24.2) MUTATED	48	14	42	19
DEL PEAK 22(11Q24.2) WILD-TYPE	22	72	32	7

Figure S288. Get High-res Image Gene #47: 'del_11q24.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q24.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S289. Gene #47: 'del_11q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 22(11Q24.2) MUTATED	39	16	23	11	28	2	4
DEL PEAK 22(11Q24.2) WILD-TYPE	9	30	38	23	19	13	1

Figure S289. Get High-res Image Gene #47: 'del_11q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q24.2' versus 'RPPA_CNMF'

P value = 0.0198 (Fisher's exact test), Q value = 0.036

Table S290. Gene #47: 'del_11q24.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
DEL PEAK 22(11Q24.2) MUTATED	29	58	21
DEL PEAK 22(11Q24.2) WILD-TYPE	29	42	39

Figure S290. Get High-res Image Gene #47: 'del_11q24.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_11q24.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00074

Table S291. Gene #47: 'del_11q24.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
DEL PEAK 22(11Q24.2) MUTATED	18	13	22	21	26	8
DEL PEAK 22(11Q24.2) WILD-TYPE	6	15	17	47	11	14

Figure S291. Get High-res Image Gene #47: 'del_11q24.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_11q24.2' versus 'MRNASEQ_CNMF'

P value = 0.00161 (Fisher's exact test), Q value = 0.0045

Table S292. Gene #47: 'del_11q24.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
DEL PEAK 22(11Q24.2) MUTATED	69	29	24
DEL PEAK 22(11Q24.2) WILD-TYPE	45	48	39

Figure S292. Get High-res Image Gene #47: 'del_11q24.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q24.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00193 (Fisher's exact test), Q value = 0.0052

Table S293. Gene #47: 'del_11q24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
DEL PEAK 22(11Q24.2) MUTATED	35	12	19	20	12	9	15
DEL PEAK 22(11Q24.2) WILD-TYPE	11	11	30	26	16	20	18

Figure S293. Get High-res Image Gene #47: 'del_11q24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q24.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0198 (Fisher's exact test), Q value = 0.036

Table S294. Gene #47: 'del_11q24.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
DEL PEAK 22(11Q24.2) MUTATED	47	27	40	7
DEL PEAK 22(11Q24.2) WILD-TYPE	32	25	60	16

Figure S294. Get High-res Image Gene #47: 'del_11q24.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11q24.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0163 (Fisher's exact test), Q value = 0.03

Table S295. Gene #47: 'del_11q24.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
DEL PEAK 22(11Q24.2) MUTATED	16	23	15	17	3	13	9	9
DEL PEAK 22(11Q24.2) WILD-TYPE	8	9	22	7	8	9	12	13

Figure S295. Get High-res Image Gene #47: 'del_11q24.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12p13.1' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00023

Table S296. Gene #48: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 23(12P13.1) MUTATED	32	13	30	12
DEL PEAK 23(12P13.1) WILD-TYPE	38	73	44	14

Figure S296. Get High-res Image Gene #48: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

P value = 0.00152 (Fisher's exact test), Q value = 0.0042

Table S297. Gene #48: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 23(12P13.1) MUTATED	26	10	19	6	22	3	1
DEL PEAK 23(12P13.1) WILD-TYPE	22	36	42	28	25	12	4

Figure S297. Get High-res Image Gene #48: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12p13.1' versus 'MRNASEQ_CNMF'

P value = 0.00722 (Fisher's exact test), Q value = 0.016

Table S298. Gene #48: 'del_12p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
DEL PEAK 23(12P13.1) MUTATED	49	23	13
DEL PEAK 23(12P13.1) WILD-TYPE	65	54	50

Figure S298. Get High-res Image Gene #48: 'del_12p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00947 (Fisher's exact test), Q value = 0.019

Table S299. Gene #48: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
DEL PEAK 23(12P13.1) MUTATED	26	8	14	8	10	9	10
DEL PEAK 23(12P13.1) WILD-TYPE	20	15	35	38	18	20	23

Figure S299. Get High-res Image Gene #48: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S300. Gene #49: 'del_12q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 24(12Q12) MUTATED	26	5	18	7
DEL PEAK 24(12Q12) WILD-TYPE	44	81	56	19

Figure S300. Get High-res Image Gene #49: 'del_12q12' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q12' versus 'METHLYATION_CNMF'

P value = 0.00252 (Fisher's exact test), Q value = 0.0065

Table S301. Gene #49: 'del_12q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 24(12Q12) MUTATED	13	5	21	2	14	1	0
DEL PEAK 24(12Q12) WILD-TYPE	35	41	40	32	33	14	5

Figure S301. Get High-res Image Gene #49: 'del_12q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12q12' versus 'MRNASEQ_CNMF'

P value = 0.0498 (Fisher's exact test), Q value = 0.079

Table S302. Gene #49: 'del_12q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
DEL PEAK 24(12Q12) MUTATED	25	23	8
DEL PEAK 24(12Q12) WILD-TYPE	89	54	55

Figure S302. Get High-res Image Gene #49: 'del_12q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_12q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0223 (Fisher's exact test), Q value = 0.039

Table S303. Gene #49: 'del_12q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
DEL PEAK 24(12Q12) MUTATED	13	3	17	3	7	5	8
DEL PEAK 24(12Q12) WILD-TYPE	33	20	32	43	21	24	25

Figure S303. Get High-res Image Gene #49: 'del_12q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12q12' versus 'MIRSEQ_CNMF'

P value = 0.0481 (Fisher's exact test), Q value = 0.077

Table S304. Gene #49: 'del_12q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
DEL PEAK 24(12Q12) MUTATED	16	15	25
DEL PEAK 24(12Q12) WILD-TYPE	91	35	72

Figure S304. Get High-res Image Gene #49: 'del_12q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_12q24.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S305. Gene #50: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 25(12Q24.33) MUTATED	29	6	26	8
DEL PEAK 25(12Q24.33) WILD-TYPE	41	80	48	18

Figure S305. Get High-res Image Gene #50: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q24.33' versus 'METHLYATION_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.024

Table S306. Gene #50: 'del_12q24.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 25(12Q24.33) MUTATED	17	6	23	7	15	1	0
DEL PEAK 25(12Q24.33) WILD-TYPE	31	40	38	27	32	14	5

Figure S306. Get High-res Image Gene #50: 'del_12q24.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12q24.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0126 (Fisher's exact test), Q value = 0.024

Table S307. Gene #50: 'del_12q24.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
DEL PEAK 25(12Q24.33) MUTATED	17	3	21	9	8	3	8
DEL PEAK 25(12Q24.33) WILD-TYPE	29	20	28	37	20	26	25

Figure S307. Get High-res Image Gene #50: 'del_12q24.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S308. Gene #51: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 26(13Q14.2) MUTATED	67	36	63	14
DEL PEAK 26(13Q14.2) WILD-TYPE	3	50	11	12

Figure S308. Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S309. Gene #51: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 26(13Q14.2) MUTATED	36	23	59	13	38	6	5
DEL PEAK 26(13Q14.2) WILD-TYPE	12	23	2	21	9	9	0

Figure S309. Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q14.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S310. Gene #51: 'del_13q14.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
DEL PEAK 26(13Q14.2) MUTATED	27	73	53
DEL PEAK 26(13Q14.2) WILD-TYPE	31	27	7

Figure S310. Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_13q14.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00075 (Fisher's exact test), Q value = 0.0025

Table S311. Gene #51: 'del_13q14.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
DEL PEAK 26(13Q14.2) MUTATED	15	14	31	55	29	9
DEL PEAK 26(13Q14.2) WILD-TYPE	9	14	8	13	8	13

Figure S311. Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S312. Gene #51: 'del_13q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
DEL PEAK 26(13Q14.2) MUTATED	80	69	29
DEL PEAK 26(13Q14.2) WILD-TYPE	34	8	34

Figure S312. Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S313. Gene #51: 'del_13q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
DEL PEAK 26(13Q14.2) MUTATED	33	12	47	19	21	22	24
DEL PEAK 26(13Q14.2) WILD-TYPE	13	11	2	27	7	7	9

Figure S313. Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S314. Gene #51: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
DEL PEAK 26(13Q14.2) MUTATED	61	33	84
DEL PEAK 26(13Q14.2) WILD-TYPE	46	17	13

Figure S314. Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S315. Gene #51: 'del_13q14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
DEL PEAK 26(13Q14.2) MUTATED	53	32	85	8
DEL PEAK 26(13Q14.2) WILD-TYPE	26	20	15	15

Figure S315. Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0011

Table S316. Gene #51: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	64	46
DEL PEAK 26(13Q14.2) MUTATED	49	56	36
DEL PEAK 26(13Q14.2) WILD-TYPE	34	8	10

Figure S316. Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00081

Table S317. Gene #51: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
DEL PEAK 26(13Q14.2) MUTATED	17	21	36	20	7	16	15	9
DEL PEAK 26(13Q14.2) WILD-TYPE	7	11	1	4	4	6	6	13

Figure S317. Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q24.1' versus 'CN_CNMF'

P value = 0.0255 (Fisher's exact test), Q value = 0.044

Table S318. Gene #52: 'del_14q24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 27(14Q24.1) MUTATED	29	17	25	9
DEL PEAK 27(14Q24.1) WILD-TYPE	41	69	49	17

Figure S318. Get High-res Image Gene #52: 'del_14q24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q24.1' versus 'METHLYATION_CNMF'

P value = 0.0138 (Fisher's exact test), Q value = 0.026

Table S319. Gene #52: 'del_14q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 27(14Q24.1) MUTATED	23	7	19	7	15	7	2
DEL PEAK 27(14Q24.1) WILD-TYPE	25	39	42	27	32	8	3

Figure S319. Get High-res Image Gene #52: 'del_14q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S320. Gene #52: 'del_14q24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
DEL PEAK 27(14Q24.1) MUTATED	21	5	9	11	2	21	11
DEL PEAK 27(14Q24.1) WILD-TYPE	25	18	40	35	26	8	22

Figure S320. Get High-res Image Gene #52: 'del_14q24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q24.1' versus 'MIRSEQ_CNMF'

P value = 0.0461 (Fisher's exact test), Q value = 0.075

Table S321. Gene #52: 'del_14q24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
DEL PEAK 27(14Q24.1) MUTATED	25	17	38
DEL PEAK 27(14Q24.1) WILD-TYPE	82	33	59

Figure S321. Get High-res Image Gene #52: 'del_14q24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_14q24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0201 (Fisher's exact test), Q value = 0.036

Table S322. Gene #52: 'del_14q24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
DEL PEAK 27(14Q24.1) MUTATED	22	16	40	2
DEL PEAK 27(14Q24.1) WILD-TYPE	57	36	60	21

Figure S322. Get High-res Image Gene #52: 'del_14q24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_14q24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0278 (Fisher's exact test), Q value = 0.048

Table S323. Gene #52: 'del_14q24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
DEL PEAK 27(14Q24.1) MUTATED	13	11	12	10	5	5	4	2
DEL PEAK 27(14Q24.1) WILD-TYPE	11	21	25	14	6	17	17	20

Figure S323. Get High-res Image Gene #52: 'del_14q24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q11.2' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00035

Table S324. Gene #53: 'del_16q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 28(16Q11.2) MUTATED	48	28	44	10
DEL PEAK 28(16Q11.2) WILD-TYPE	22	58	30	16

Figure S324. Get High-res Image Gene #53: 'del_16q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q11.2' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00035

Table S325. Gene #53: 'del_16q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 28(16Q11.2) MUTATED	23	16	43	9	31	6	2
DEL PEAK 28(16Q11.2) WILD-TYPE	25	30	18	25	16	9	3

Figure S325. Get High-res Image Gene #53: 'del_16q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q11.2' versus 'RPPA_CNMF'

P value = 0.00669 (Fisher's exact test), Q value = 0.015

Table S326. Gene #53: 'del_16q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
DEL PEAK 28(16Q11.2) MUTATED	20	51	38
DEL PEAK 28(16Q11.2) WILD-TYPE	38	49	22

Figure S326. Get High-res Image Gene #53: 'del_16q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_16q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00275 (Fisher's exact test), Q value = 0.007

Table S327. Gene #53: 'del_16q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
DEL PEAK 28(16Q11.2) MUTATED	13	7	27	39	16	7
DEL PEAK 28(16Q11.2) WILD-TYPE	11	21	12	29	21	15

Figure S327. Get High-res Image Gene #53: 'del_16q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_16q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.0015

Table S328. Gene #53: 'del_16q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
DEL PEAK 28(16Q11.2) MUTATED	59	50	20
DEL PEAK 28(16Q11.2) WILD-TYPE	55	27	43

Figure S328. Get High-res Image Gene #53: 'del_16q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00035

Table S329. Gene #53: 'del_16q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
DEL PEAK 28(16Q11.2) MUTATED	24	8	34	10	17	17	19
DEL PEAK 28(16Q11.2) WILD-TYPE	22	15	15	36	11	12	14

Figure S329. Get High-res Image Gene #53: 'del_16q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00235 (Fisher's exact test), Q value = 0.0062

Table S330. Gene #53: 'del_16q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
DEL PEAK 28(16Q11.2) MUTATED	41	28	60
DEL PEAK 28(16Q11.2) WILD-TYPE	66	22	37

Figure S330. Get High-res Image Gene #53: 'del_16q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00774 (Fisher's exact test), Q value = 0.017

Table S331. Gene #53: 'del_16q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
DEL PEAK 28(16Q11.2) MUTATED	37	22	63	7
DEL PEAK 28(16Q11.2) WILD-TYPE	42	30	37	16

Figure S331. Get High-res Image Gene #53: 'del_16q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S332. Gene #53: 'del_16q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	64	46
DEL PEAK 28(16Q11.2) MUTATED	30	47	30
DEL PEAK 28(16Q11.2) WILD-TYPE	53	17	16

Figure S332. Get High-res Image Gene #53: 'del_16q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S333. Gene #53: 'del_16q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
DEL PEAK 28(16Q11.2) MUTATED	12	10	31	15	7	13	14	5
DEL PEAK 28(16Q11.2) WILD-TYPE	12	22	6	9	4	9	7	17

Figure S333. Get High-res Image Gene #53: 'del_16q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S334. Gene #54: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 29(16Q23.1) MUTATED	49	29	46	10
DEL PEAK 29(16Q23.1) WILD-TYPE	21	57	28	16

Figure S334. Get High-res Image Gene #54: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0018

Table S335. Gene #54: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 29(16Q23.1) MUTATED	27	17	43	10	29	6	2
DEL PEAK 29(16Q23.1) WILD-TYPE	21	29	18	24	18	9	3

Figure S335. Get High-res Image Gene #54: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.1' versus 'RPPA_CNMF'

P value = 0.00186 (Fisher's exact test), Q value = 0.0051

Table S336. Gene #54: 'del_16q23.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
DEL PEAK 29(16Q23.1) MUTATED	20	55	40
DEL PEAK 29(16Q23.1) WILD-TYPE	38	45	20

Figure S336. Get High-res Image Gene #54: 'del_16q23.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.0031

Table S337. Gene #54: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
DEL PEAK 29(16Q23.1) MUTATED	60	51	22
DEL PEAK 29(16Q23.1) WILD-TYPE	54	26	41

Figure S337. Get High-res Image Gene #54: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0014

Table S338. Gene #54: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
DEL PEAK 29(16Q23.1) MUTATED	28	8	34	12	17	17	17
DEL PEAK 29(16Q23.1) WILD-TYPE	18	15	15	34	11	12	16

Figure S338. Get High-res Image Gene #54: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 0.00352 (Fisher's exact test), Q value = 0.0086

Table S339. Gene #54: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
DEL PEAK 29(16Q23.1) MUTATED	43	29	61
DEL PEAK 29(16Q23.1) WILD-TYPE	64	21	36

Figure S339. Get High-res Image Gene #54: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.021

Table S340. Gene #54: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
DEL PEAK 29(16Q23.1) MUTATED	38	24	64	7
DEL PEAK 29(16Q23.1) WILD-TYPE	41	28	36	16

Figure S340. Get High-res Image Gene #54: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S341. Gene #54: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	64	46
DEL PEAK 29(16Q23.1) MUTATED	30	47	32
DEL PEAK 29(16Q23.1) WILD-TYPE	53	17	14

Figure S341. Get High-res Image Gene #54: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00038

Table S342. Gene #54: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
DEL PEAK 29(16Q23.1) MUTATED	14	10	30	16	8	10	15	6
DEL PEAK 29(16Q23.1) WILD-TYPE	10	22	7	8	3	12	6	16

Figure S342. Get High-res Image Gene #54: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p13.1' versus 'CN_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00095

Table S343. Gene #55: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 30(17P13.1) MUTATED	48	34	40	7
DEL PEAK 30(17P13.1) WILD-TYPE	22	52	34	19

Figure S343. Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S344. Gene #55: 'del_17p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 30(17P13.1) MUTATED	18	18	50	12	25	4	2
DEL PEAK 30(17P13.1) WILD-TYPE	30	28	11	22	22	11	3

Figure S344. Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p13.1' versus 'RPPA_CNMF'

P value = 0.00715 (Fisher's exact test), Q value = 0.016

Table S345. Gene #55: 'del_17p13.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
DEL PEAK 30(17P13.1) MUTATED	21	48	39
DEL PEAK 30(17P13.1) WILD-TYPE	37	52	21

Figure S345. Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_17p13.1' versus 'RPPA_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.0021

Table S346. Gene #55: 'del_17p13.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
DEL PEAK 30(17P13.1) MUTATED	10	8	28	41	12	9
DEL PEAK 30(17P13.1) WILD-TYPE	14	20	11	27	25	13

Figure S346. Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_17p13.1' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S347. Gene #55: 'del_17p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
DEL PEAK 30(17P13.1) MUTATED	51	55	21
DEL PEAK 30(17P13.1) WILD-TYPE	63	22	42

Figure S347. Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00027

Table S348. Gene #55: 'del_17p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
DEL PEAK 30(17P13.1) MUTATED	18	9	40	16	16	14	14
DEL PEAK 30(17P13.1) WILD-TYPE	28	14	9	30	12	15	19

Figure S348. Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.1' versus 'MIRSEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00071

Table S349. Gene #55: 'del_17p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
DEL PEAK 30(17P13.1) MUTATED	38	27	62
DEL PEAK 30(17P13.1) WILD-TYPE	69	23	35

Figure S349. Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.0021

Table S350. Gene #55: 'del_17p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
DEL PEAK 30(17P13.1) MUTATED	28	27	64	8
DEL PEAK 30(17P13.1) WILD-TYPE	51	25	36	15

Figure S350. Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S351. Gene #55: 'del_17p13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	64	46
DEL PEAK 30(17P13.1) MUTATED	27	44	29
DEL PEAK 30(17P13.1) WILD-TYPE	56	20	17

Figure S351. Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0015

Table S352. Gene #55: 'del_17p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
DEL PEAK 30(17P13.1) MUTATED	12	8	30	14	6	10	12	8
DEL PEAK 30(17P13.1) WILD-TYPE	12	24	7	10	5	12	9	14

Figure S352. Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S353. Gene #56: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 31(17Q11.2) MUTATED	28	7	37	9
DEL PEAK 31(17Q11.2) WILD-TYPE	42	79	37	17

Figure S353. Get High-res Image Gene #56: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S354. Gene #56: 'del_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 31(17Q11.2) MUTATED	25	11	9	9	25	0	2
DEL PEAK 31(17Q11.2) WILD-TYPE	23	35	52	25	22	15	3

Figure S354. Get High-res Image Gene #56: 'del_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q11.2' versus 'RPPA_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0013

Table S355. Gene #56: 'del_17q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
DEL PEAK 31(17Q11.2) MUTATED	21	45	9
DEL PEAK 31(17Q11.2) WILD-TYPE	37	55	51

Figure S355. Get High-res Image Gene #56: 'del_17q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_17q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S356. Gene #56: 'del_17q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
DEL PEAK 31(17Q11.2) MUTATED	12	4	26	9	18	6
DEL PEAK 31(17Q11.2) WILD-TYPE	12	24	13	59	19	16

Figure S356. Get High-res Image Gene #56: 'del_17q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_17q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S357. Gene #56: 'del_17q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
DEL PEAK 31(17Q11.2) MUTATED	53	10	18
DEL PEAK 31(17Q11.2) WILD-TYPE	61	67	45

Figure S357. Get High-res Image Gene #56: 'del_17q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00038

Table S358. Gene #56: 'del_17q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
DEL PEAK 31(17Q11.2) MUTATED	23	8	7	12	14	3	14
DEL PEAK 31(17Q11.2) WILD-TYPE	23	15	42	34	14	26	19

Figure S358. Get High-res Image Gene #56: 'del_17q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00433 (Fisher's exact test), Q value = 0.01

Table S359. Gene #56: 'del_17q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
DEL PEAK 31(17Q11.2) MUTATED	40	21	19
DEL PEAK 31(17Q11.2) WILD-TYPE	67	29	78

Figure S359. Get High-res Image Gene #56: 'del_17q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00745 (Fisher's exact test), Q value = 0.016

Table S360. Gene #56: 'del_17q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
DEL PEAK 31(17Q11.2) MUTATED	34	19	20	7
DEL PEAK 31(17Q11.2) WILD-TYPE	45	33	80	16

Figure S360. Get High-res Image Gene #56: 'del_17q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.024

Table S361. Gene #56: 'del_17q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	64	46
DEL PEAK 31(17Q11.2) MUTATED	31	13	21
DEL PEAK 31(17Q11.2) WILD-TYPE	52	51	25

Figure S361. Get High-res Image Gene #56: 'del_17q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0252 (Fisher's exact test), Q value = 0.044

Table S362. Gene #56: 'del_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
DEL PEAK 31(17Q11.2) MUTATED	11	13	5	12	1	7	8	8
DEL PEAK 31(17Q11.2) WILD-TYPE	13	19	32	12	10	15	13	14

Figure S362. Get High-res Image Gene #56: 'del_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q25.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S363. Gene #57: 'del_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 32(17Q25.3) MUTATED	30	7	22	8
DEL PEAK 32(17Q25.3) WILD-TYPE	40	79	52	18

Figure S363. Get High-res Image Gene #57: 'del_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q25.3' versus 'METHLYATION_CNMF'

P value = 0.0027 (Fisher's exact test), Q value = 0.0069

Table S364. Gene #57: 'del_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 32(17Q25.3) MUTATED	14	6	22	4	19	1	1
DEL PEAK 32(17Q25.3) WILD-TYPE	34	40	39	30	28	14	4

Figure S364. Get High-res Image Gene #57: 'del_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q23' versus 'CN_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.0032

Table S365. Gene #58: 'del_18q23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 33(18Q23) MUTATED	30	15	31	10
DEL PEAK 33(18Q23) WILD-TYPE	40	71	43	16

Figure S365. Get High-res Image Gene #58: 'del_18q23' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q23' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S366. Gene #58: 'del_18q23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 33(18Q23) MUTATED	15	15	14	6	32	3	1
DEL PEAK 33(18Q23) WILD-TYPE	33	31	47	28	15	12	4

Figure S366. Get High-res Image Gene #58: 'del_18q23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q23' versus 'RPPA_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0011

Table S367. Gene #58: 'del_18q23' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
DEL PEAK 33(18Q23) MUTATED	13	49	14
DEL PEAK 33(18Q23) WILD-TYPE	45	51	46

Figure S367. Get High-res Image Gene #58: 'del_18q23' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_18q23' versus 'RPPA_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.0013

Table S368. Gene #58: 'del_18q23' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
DEL PEAK 33(18Q23) MUTATED	7	7	24	13	17	8
DEL PEAK 33(18Q23) WILD-TYPE	17	21	15	55	20	14

Figure S368. Get High-res Image Gene #58: 'del_18q23' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_18q23' versus 'MRNASEQ_CNMF'

P value = 0.00663 (Fisher's exact test), Q value = 0.015

Table S369. Gene #58: 'del_18q23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
DEL PEAK 33(18Q23) MUTATED	50	18	17
DEL PEAK 33(18Q23) WILD-TYPE	64	59	46

Figure S369. Get High-res Image Gene #58: 'del_18q23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00183 (Fisher's exact test), Q value = 0.005

Table S370. Gene #58: 'del_18q23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
DEL PEAK 33(18Q23) MUTATED	16	7	12	11	17	5	17
DEL PEAK 33(18Q23) WILD-TYPE	30	16	37	35	11	24	16

Figure S370. Get High-res Image Gene #58: 'del_18q23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.027

Table S371. Gene #58: 'del_18q23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
DEL PEAK 33(18Q23) MUTATED	35	25	25
DEL PEAK 33(18Q23) WILD-TYPE	72	25	72

Figure S371. Get High-res Image Gene #58: 'del_18q23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00074

Table S372. Gene #58: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
DEL PEAK 33(18Q23) MUTATED	6	8	10	11	1	14	15	5
DEL PEAK 33(18Q23) WILD-TYPE	18	24	27	13	10	8	6	17

Figure S372. Get High-res Image Gene #58: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00081

Table S373. Gene #59: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 34(19P13.3) MUTATED	27	12	28	3
DEL PEAK 34(19P13.3) WILD-TYPE	43	74	46	23

Figure S373. Get High-res Image Gene #59: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 0.00257 (Fisher's exact test), Q value = 0.0066

Table S374. Gene #59: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 34(19P13.3) MUTATED	9	6	23	5	19	5	3
DEL PEAK 34(19P13.3) WILD-TYPE	39	40	38	29	28	10	2

Figure S374. Get High-res Image Gene #59: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00891 (Fisher's exact test), Q value = 0.018

Table S375. Gene #59: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
DEL PEAK 34(19P13.3) MUTATED	23	31	16
DEL PEAK 34(19P13.3) WILD-TYPE	91	46	47

Figure S375. Get High-res Image Gene #59: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0021 (Fisher's exact test), Q value = 0.0056

Table S376. Gene #59: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
DEL PEAK 34(19P13.3) MUTATED	8	1	20	9	7	11	14
DEL PEAK 34(19P13.3) WILD-TYPE	38	22	29	37	21	18	19

Figure S376. Get High-res Image Gene #59: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 0.023

Table S377. Gene #59: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
DEL PEAK 34(19P13.3) MUTATED	20	12	36
DEL PEAK 34(19P13.3) WILD-TYPE	87	38	61

Figure S377. Get High-res Image Gene #59: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00341 (Fisher's exact test), Q value = 0.0083

Table S378. Gene #59: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
DEL PEAK 34(19P13.3) MUTATED	18	7	39	4
DEL PEAK 34(19P13.3) WILD-TYPE	61	45	61	19

Figure S378. Get High-res Image Gene #59: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00133 (Fisher's exact test), Q value = 0.0038

Table S379. Gene #59: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	64	46
DEL PEAK 34(19P13.3) MUTATED	18	29	8
DEL PEAK 34(19P13.3) WILD-TYPE	65	35	38

Figure S379. Get High-res Image Gene #59: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.027

Table S380. Gene #59: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
DEL PEAK 34(19P13.3) MUTATED	3	5	18	10	3	8	4	4
DEL PEAK 34(19P13.3) WILD-TYPE	21	27	19	14	8	14	17	18

Figure S380. Get High-res Image Gene #59: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.43' versus 'CN_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.025

Table S381. Gene #60: 'del_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 35(19Q13.43) MUTATED	36	24	33	13
DEL PEAK 35(19Q13.43) WILD-TYPE	34	62	41	13

Figure S381. Get High-res Image Gene #60: 'del_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.43' versus 'METHLYATION_CNMF'

P value = 0.00127 (Fisher's exact test), Q value = 0.0037

Table S382. Gene #60: 'del_19q13.43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 35(19Q13.43) MUTATED	26	9	31	8	22	7	3
DEL PEAK 35(19Q13.43) WILD-TYPE	22	37	30	26	25	8	2

Figure S382. Get High-res Image Gene #60: 'del_19q13.43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19q13.43' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00489 (Fisher's exact test), Q value = 0.011

Table S383. Gene #60: 'del_19q13.43' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
DEL PEAK 35(19Q13.43) MUTATED	14	17	22	8	1	6	10	5
DEL PEAK 35(19Q13.43) WILD-TYPE	10	15	15	16	10	16	11	17

Figure S383. Get High-res Image Gene #60: 'del_19q13.43' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0476 (Fisher's exact test), Q value = 0.077

Table S384. Gene #61: 'del_21q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
DEL PEAK 36(21Q11.2) MUTATED	4	4	13	7	10	6
DEL PEAK 36(21Q11.2) WILD-TYPE	20	24	26	61	27	16

Figure S384. Get High-res Image Gene #61: 'del_21q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00283 (Fisher's exact test), Q value = 0.0072

Table S385. Gene #61: 'del_21q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
DEL PEAK 36(21Q11.2) MUTATED	19	19	13
DEL PEAK 36(21Q11.2) WILD-TYPE	88	31	84

Figure S385. Get High-res Image Gene #61: 'del_21q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_21q22.3' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00097

Table S386. Gene #62: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 37(21Q22.3) MUTATED	20	9	26	11
DEL PEAK 37(21Q22.3) WILD-TYPE	50	77	48	15

Figure S386. Get High-res Image Gene #62: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q22.3' versus 'METHLYATION_CNMF'

P value = 0.00741 (Fisher's exact test), Q value = 0.016

Table S387. Gene #62: 'del_21q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 37(21Q22.3) MUTATED	19	9	13	4	18	1	2
DEL PEAK 37(21Q22.3) WILD-TYPE	29	37	48	30	29	14	3

Figure S387. Get High-res Image Gene #62: 'del_21q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q22.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00844 (Fisher's exact test), Q value = 0.018

Table S388. Gene #62: 'del_21q22.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
DEL PEAK 37(21Q22.3) MUTATED	6	7	18	10	14	4
DEL PEAK 37(21Q22.3) WILD-TYPE	18	21	21	58	23	18

Figure S388. Get High-res Image Gene #62: 'del_21q22.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S389. Gene #63: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 38(22Q13.32) MUTATED	41	11	22	9
DEL PEAK 38(22Q13.32) WILD-TYPE	29	75	52	17

Figure S389. Get High-res Image Gene #63: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.32' versus 'RPPA_CHIERARCHICAL'

P value = 0.0491 (Fisher's exact test), Q value = 0.079

Table S390. Gene #63: 'del_22q13.32' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
DEL PEAK 38(22Q13.32) MUTATED	13	4	13	21	16	7
DEL PEAK 38(22Q13.32) WILD-TYPE	11	24	26	47	21	15

Figure S390. Get High-res Image Gene #63: 'del_22q13.32' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 0.00245 (Fisher's exact test), Q value = 0.0064

Table S391. Gene #64: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 39(XP21.1) MUTATED	7	2	21	8	10	5	2
DEL PEAK 39(XP21.1) WILD-TYPE	41	44	40	26	37	10	3

Figure S391. Get High-res Image Gene #64: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp21.1' versus 'MRNASEQ_CNMF'

P value = 0.00804 (Fisher's exact test), Q value = 0.017

Table S392. Gene #64: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
DEL PEAK 39(XP21.1) MUTATED	18	26	10
DEL PEAK 39(XP21.1) WILD-TYPE	96	51	53

Figure S392. Get High-res Image Gene #64: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0208 (Fisher's exact test), Q value = 0.037

Table S393. Gene #64: 'del_xp21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
DEL PEAK 39(XP21.1) MUTATED	7	1	15	7	8	11	5
DEL PEAK 39(XP21.1) WILD-TYPE	39	22	34	39	20	18	28

Figure S393. Get High-res Image Gene #64: 'del_xp21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.034

Table S394. Gene #64: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
DEL PEAK 39(XP21.1) MUTATED	16	9	30
DEL PEAK 39(XP21.1) WILD-TYPE	91	41	67

Figure S394. Get High-res Image Gene #64: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xp21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0322 (Fisher's exact test), Q value = 0.054

Table S395. Gene #64: 'del_xp21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
DEL PEAK 39(XP21.1) MUTATED	10	9	30	6
DEL PEAK 39(XP21.1) WILD-TYPE	69	43	70	17

Figure S395. Get High-res Image Gene #64: 'del_xp21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0482 (Fisher's exact test), Q value = 0.077

Table S396. Gene #64: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
DEL PEAK 39(XP21.1) MUTATED	5	2	14	3	1	4	4	7
DEL PEAK 39(XP21.1) WILD-TYPE	19	30	23	21	10	18	17	15

Figure S396. Get High-res Image Gene #64: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xq21.1' versus 'CN_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0018

Table S397. Gene #65: 'del_xq21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 40(XQ21.1) MUTATED	43	25	32	14
DEL PEAK 40(XQ21.1) WILD-TYPE	27	61	42	12

Figure S397. Get High-res Image Gene #65: 'del_xq21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq21.1' versus 'METHLYATION_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00097

Table S398. Gene #65: 'del_xq21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 40(XQ21.1) MUTATED	21	12	43	12	17	7	2
DEL PEAK 40(XQ21.1) WILD-TYPE	27	34	18	22	30	8	3

Figure S398. Get High-res Image Gene #65: 'del_xq21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq21.1' versus 'RPPA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S399. Gene #65: 'del_xq21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
DEL PEAK 40(XQ21.1) MUTATED	18	35	42
DEL PEAK 40(XQ21.1) WILD-TYPE	40	65	18

Figure S399. Get High-res Image Gene #65: 'del_xq21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_xq21.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00558 (Fisher's exact test), Q value = 0.013

Table S400. Gene #65: 'del_xq21.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
DEL PEAK 40(XQ21.1) MUTATED	10	8	14	43	13	7
DEL PEAK 40(XQ21.1) WILD-TYPE	14	20	25	25	24	15

Figure S400. Get High-res Image Gene #65: 'del_xq21.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_xq21.1' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00023

Table S401. Gene #65: 'del_xq21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
DEL PEAK 40(XQ21.1) MUTATED	38	51	24
DEL PEAK 40(XQ21.1) WILD-TYPE	76	26	39

Figure S401. Get High-res Image Gene #65: 'del_xq21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xq21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00085

Table S402. Gene #65: 'del_xq21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
DEL PEAK 40(XQ21.1) MUTATED	18	7	36	16	7	15	14
DEL PEAK 40(XQ21.1) WILD-TYPE	28	16	13	30	21	14	19

Figure S402. Get High-res Image Gene #65: 'del_xq21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xq21.1' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00038

Table S403. Gene #65: 'del_xq21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
DEL PEAK 40(XQ21.1) MUTATED	35	18	60
DEL PEAK 40(XQ21.1) WILD-TYPE	72	32	37

Figure S403. Get High-res Image Gene #65: 'del_xq21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xq21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00075 (Fisher's exact test), Q value = 0.0025

Table S404. Gene #65: 'del_xq21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
DEL PEAK 40(XQ21.1) MUTATED	28	19	60	6
DEL PEAK 40(XQ21.1) WILD-TYPE	51	33	40	17

Figure S404. Get High-res Image Gene #65: 'del_xq21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xq21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0383 (Fisher's exact test), Q value = 0.062

Table S405. Gene #65: 'del_xq21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	64	46
DEL PEAK 40(XQ21.1) MUTATED	29	36	21
DEL PEAK 40(XQ21.1) WILD-TYPE	54	28	25

Figure S405. Get High-res Image Gene #65: 'del_xq21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xq21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0318 (Fisher's exact test), Q value = 0.053

Table S406. Gene #65: 'del_xq21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
DEL PEAK 40(XQ21.1) MUTATED	11	16	23	12	6	4	8	6
DEL PEAK 40(XQ21.1) WILD-TYPE	13	16	14	12	5	18	13	16

Figure S406. Get High-res Image Gene #65: 'del_xq21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xq22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S407. Gene #66: 'del_xq22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	86	74	26
DEL PEAK 41(XQ22.3) MUTATED	48	26	40	9
DEL PEAK 41(XQ22.3) WILD-TYPE	22	60	34	17

Figure S407. Get High-res Image Gene #66: 'del_xq22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S408. Gene #66: 'del_xq22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	48	46	61	34	47	15	5
DEL PEAK 41(XQ22.3) MUTATED	27	11	45	9	21	6	4
DEL PEAK 41(XQ22.3) WILD-TYPE	21	35	16	25	26	9	1

Figure S408. Get High-res Image Gene #66: 'del_xq22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq22.3' versus 'RPPA_CNMF'

P value = 0.00143 (Fisher's exact test), Q value = 0.0041

Table S409. Gene #66: 'del_xq22.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	100	60
DEL PEAK 41(XQ22.3) MUTATED	25	40	41
DEL PEAK 41(XQ22.3) WILD-TYPE	33	60	19

Figure S409. Get High-res Image Gene #66: 'del_xq22.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_xq22.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00324 (Fisher's exact test), Q value = 0.008

Table S410. Gene #66: 'del_xq22.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	28	39	68	37	22
DEL PEAK 41(XQ22.3) MUTATED	12	9	17	45	18	5
DEL PEAK 41(XQ22.3) WILD-TYPE	12	19	22	23	19	17

Figure S410. Get High-res Image Gene #66: 'del_xq22.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_xq22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.9e-05

Table S411. Gene #66: 'del_xq22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	63
DEL PEAK 41(XQ22.3) MUTATED	48	55	19
DEL PEAK 41(XQ22.3) WILD-TYPE	66	22	44

Figure S411. Get High-res Image Gene #66: 'del_xq22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xq22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00032

Table S412. Gene #66: 'del_xq22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	23	49	46	28	29	33
DEL PEAK 41(XQ22.3) MUTATED	26	6	35	13	9	19	14
DEL PEAK 41(XQ22.3) WILD-TYPE	20	17	14	33	19	10	19

Figure S412. Get High-res Image Gene #66: 'del_xq22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xq22.3' versus 'MIRSEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00088

Table S413. Gene #66: 'del_xq22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	50	97
DEL PEAK 41(XQ22.3) MUTATED	39	20	62
DEL PEAK 41(XQ22.3) WILD-TYPE	68	30	35

Figure S413. Get High-res Image Gene #66: 'del_xq22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xq22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00083 (Fisher's exact test), Q value = 0.0026

Table S414. Gene #66: 'del_xq22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	52	100	23
DEL PEAK 41(XQ22.3) MUTATED	32	19	63	7
DEL PEAK 41(XQ22.3) WILD-TYPE	47	33	37	16

Figure S414. Get High-res Image Gene #66: 'del_xq22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xq22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0223 (Fisher's exact test), Q value = 0.039

Table S415. Gene #66: 'del_xq22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	64	46
DEL PEAK 41(XQ22.3) MUTATED	33	40	22
DEL PEAK 41(XQ22.3) WILD-TYPE	50	24	24

Figure S415. Get High-res Image Gene #66: 'del_xq22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xq22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0498 (Fisher's exact test), Q value = 0.079

Table S416. Gene #66: 'del_xq22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	24	32	37	24	11	22	21	22
DEL PEAK 41(XQ22.3) MUTATED	14	15	25	12	7	7	9	6
DEL PEAK 41(XQ22.3) WILD-TYPE	10	17	12	12	4	15	12	16

Figure S416. Get High-res Image Gene #66: 'del_xq22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SARC-TP/15098582/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/SARC-TP/15111074/SARC-TP.transferedmergedcluster.txt
Number of patients = 256
Number of significantly focal cnvs = 66
Number of molecular subtypes = 10
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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