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

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 69 focal events and 10 molecular subtypes across 257 patients, 460 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', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5p15.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_6p21.1 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_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', 'RPPA_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', and 'RPPA_CHIERARCHICAL'.
amp_11q22.2 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_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' and 'RPPA_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_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', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.
amp_19q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', 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', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_xq21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_1p36.32 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_1q44 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_2p25.3 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_2q37.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', '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', and 'MIRSEQ_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_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', 'RPPA_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_4q35.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_5p15.33 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6p25.3 cnv correlated to 'CN_CNMF', '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', 'RPPA_CHIERARCHICAL', 'MIRSEQ_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', 'RPPA_CNMF', and 'MIRSEQ_CNMF'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_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', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10p15.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_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' and 'RPPA_CHIERARCHICAL'.
del_11q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q25 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_12q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', 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_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17q25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_18p11.32 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
del_18q23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p13.3 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_19q13.43 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_21q11.2 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_21q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_22q13.32 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_xp21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_xq21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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 69 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, 460 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 1p32 1	94 (37%)	163	2e-05 (0.000116)	1e-05 (6.9e-05)	0.00382 (0.00918)	7e-05 (0.00034)	3e-05 (0.000163)	1e-05 (6.9e-05)	0.0082 (0.0167)	0.00445 (0.0103)	0.0292 (0.0475)	0.00042 (0.00152)
amp 6p21 1	60 (23%)	197	1e-05 (6.9e-05)	1e-05 (6.9e-05)	7e-05 (0.00034)	0.00056 (0.00185)	0.00036 (0.00134)	0.0003 (0.00116)	0.00584 (0.0127)	0.0102 (0.0201)	0.025 (0.0421)	0.0211 (0.036)
amp 6q25 1	75 (29%)	182	0.00135 (0.0038)	8e-05 (0.000373)	0.00031 (0.00118)	0.00019 (0.00078)	1e-05 (6.9e-05)	1e-05 (6.9e-05)	0.00017 (0.000711)	0.00012 (0.000524)	0.00064 (0.00204)	0.00064 (0.00204)
amp 7q31 2	77 (30%)	180	0.00033 (0.00124)	0.00017 (0.000711)	0.0139 (0.0257)	0.00061 (0.00198)	2e-05 (0.000116)	0.00499 (0.0112)	0.00029 (0.00113)	0.0447 (0.0677)	0.0002 (0.000817)	0.00057 (0.00186)
amp 12q15	94 (37%)	163	1e-05 (6.9e-05)	1e-05 (6.9e-05)	1e-05 (6.9e-05)	1e-05 (6.9e-05)	1e-05 (6.9e-05)	1e-05 (6.9e-05)	1e-05 (6.9e-05)	1e-05 (6.9e-05)	1e-05 (6.9e-05)	1e-05 (6.9e-05)
amp 20q13 33	98 (38%)	159	1e-05 (6.9e-05)	2e-05 (0.000116)	0.00482 (0.0109)	7e-05 (0.00034)	0.00123 (0.00357)	0.00141 (0.00392)	0.0116 (0.0222)	0.00049 (0.00171)	0.00035 (0.00131)	0.00037 (0.00137)
del 1p36 32	69 (27%)	188	1e-05 (6.9e-05)	1e-05 (6.9e-05)	1e-05 (6.9e-05)	1e-05 (6.9e-05)	1e-05 (6.9e-05)	1e-05 (6.9e-05)	1e-05 (6.9e-05)	1e-05 (6.9e-05)	6e-05 (0.000304)	5e-05 (0.000261)
del 3p21 31	65 (25%)	192	0.0101 (0.02)	1e-05 (6.9e-05)	0.00067 (0.00212)	0.00013 (0.000564)	1e-05 (6.9e-05)	1e-05 (6.9e-05)	0.0001 (0.000451)	0.00802 (0.0164)	2e-05 (0.000116)	9e-05 (0.000409)
del 3q13 31	51 (20%)	206	0.0063 (0.0135)	0.00161 (0.00437)	0.00078 (0.00239)	0.025 (0.0421)	0.00525 (0.0116)	0.00652 (0.0138)	0.00994 (0.0197)	0.018 (0.0318)	0.00676 (0.0142)	0.0417 (0.0635)
del 8p23 3	81 (32%)	176	3e-05 (0.000163)	2e-05 (0.000116)	0.00042 (0.00152)	0.00076 (0.00237)	7e-05 (0.00034)	0.00047 (0.00167)	0.00632 (0.0135)	0.00416 (0.00976)	0.00031 (0.00118)	0.00011 (0.000483)
del 10q23 31	138 (54%)	119	1e-05 (6.9e-05)	1e-05 (6.9e-05)	1e-05 (6.9e-05)	1e-05 (6.9e-05)	1e-05 (6.9e-05)	1e-05 (6.9e-05)	4e-05 (0.000214)	1e-05 (6.9e-05)	0.00039 (0.00143)	0.00025 (0.000986)
del 10q26 3	132 (51%)	125	1e-05 (6.9e-05)	1e-05 (6.9e-05)	1e-05 (6.9e-05)	1e-05 (6.9e-05)	2e-05 (0.000116)	1e-05 (6.9e-05)	3e-05 (0.000163)	2e-05 (0.000116)	3e-05 (0.000163)	8e-05 (0.000373)
del 13q14 2	180 (70%)	77	1e-05 (6.9e-05)	1e-05 (6.9e-05)	1e-05 (6.9e-05)	0.00171 (0.00461)	1e-05 (6.9e-05)	1e-05 (6.9e-05)	9e-05 (0.000409)	1e-05 (6.9e-05)	0.00087 (0.00261)	8e-05 (0.000373)
del 16q11 2	130 (51%)	127	1e-05 (6.9e-05)	1e-05 (6.9e-05)	0.0237 (0.0402)	0.0027 (0.0068)	0.00064 (0.00204)	8e-05 (0.000373)	0.00407 (0.00962)	0.00048 (0.00168)	0.00097 (0.00286)	2e-05 (0.000116)
del 17p13 1	129 (50%)	128	1e-05 (6.9e-05)	3e-05 (0.000163)	0.00454 (0.0104)	9e-05 (0.000409)	1e-05 (6.9e-05)	8e-05 (0.000373)	2e-05 (0.000116)	6e-05 (0.000304)	0.00077 (0.00239)	0.00011 (0.000483)
del 19p13 3	70 (27%)	187	1e-05 (6.9e-05)	0.0005 (0.00172)	0.00919 (0.0183)	0.0007 (0.0022)	0.00966 (0.0192)	0.00453 (0.0104)	0.0276 (0.0454)	0.00392 (0.00936)	0.00693 (0.0145)	0.00492 (0.0111)
del xq22 3	123 (48%)	134	1e-05 (6.9e-05)	1e-05 (6.9e-05)	0.00041 (0.0015)	0.00627 (0.0135)	1e-05 (6.9e-05)	2e-05 (0.000116)	0.00099 (0.00289)	5e-05 (0.000261)	0.0061 (0.0132)	0.0114 (0.0218)
amp 3p12 1	69 (27%)	188	2e-05 (0.000116)	0.00064 (0.00204)	0.00469 (0.0107)	7e-05 (0.00034)	0.00068 (0.00214)	6e-05 (0.000304)	0.151 (0.196)	0.00318 (0.00786)	0.00211 (0.00549)	0.00019 (0.00078)
amp 4q12	78 (30%)	179	1e-05 (6.9e-05)	1e-05 (6.9e-05)	0.0174 (0.0309)	0.00168 (0.00455)	0.00055 (0.00185)	0.00378 (0.00912)	0.0212 (0.0361)	0.0131 (0.0244)	0.05 (0.0749)	0.00214 (0.00555)
del 1q44	80 (31%)	177	1e-05 (6.9e-05)	0.00056 (0.00185)	0.0582 (0.0854)	7e-05 (0.00034)	0.00093 (0.00277)	0.00021 (0.000847)	0.00175 (0.0047)	0.00694 (0.0145)	0.00124 (0.00358)	0.00048 (0.00168)
del 2p25 3	94 (37%)	163	1e-05 (6.9e-05)	0.00024 (0.000952)	0.0707 (0.102)	0.00385 (0.00922)	2e-05 (0.000116)	0.00128 (0.00363)	0.00021 (0.000847)	2e-05 (0.000116)	0.00204 (0.00533)	3e-05 (0.000163)
del 9p21 3	114 (44%)	143	1e-05 (6.9e-05)	0.00311 (0.00772)	0.00562 (0.0123)	0.00078 (0.00239)	0.00455 (0.0104)	0.00487 (0.011)	0.00151 (0.00417)	0.557 (0.598)	0.00033 (0.00124)	0.00129 (0.00365)
del 11q25	123 (48%)	134	1e-05 (6.9e-05)	0.00107 (0.00312)	0.00673 (0.0142)	0.00043 (0.00155)	0.00139 (0.0039)	0.00327 (0.008)	0.00098 (0.00288)	0.114 (0.155)	0.0304 (0.0493)	0.00434 (0.0101)
del 15q11 2	47 (18%)	210	0.00856 (0.0173)	0.013 (0.0242)	0.0178 (0.0315)	0.0163 (0.0291)	0.00778 (0.0159)	0.00651 (0.0138)	0.0144 (0.0262)	0.196 (0.244)	0.00048 (0.00168)	0.0284 (0.0466)
del 16q23 1	134 (52%)	123	1e-05 (6.9e-05)	1e-05 (6.9e-05)	0.0123 (0.0232)	0.0751 (0.108)	0.00158 (0.00431)	0.00056 (0.00185)	0.00514 (0.0115)	0.00011 (0.000483)	9e-05 (0.000409)	1e-05 (6.9e-05)
del 17q11 2	81 (32%)	176	1e-05 (6.9e-05)	1e-05 (6.9e-05)	0.00058 (0.00189)	1e-05 (6.9e-05)	2e-05 (0.000116)	6e-05 (0.000304)	0.00081 (0.00247)	0.12 (0.161)	0.00084 (0.00254)	0.0018 (0.00477)
del 18q23	86 (33%)	171	1e-05 (6.9e-05)	1e-05 (6.9e-05)	0.00324 (0.00796)	0.00027 (0.00106)	0.0116 (0.0222)	0.00235 (0.00601)	0.00088 (0.00263)	0.147 (0.191)	0.00321 (0.00791)	0.00515 (0.0115)
del xq21 1	114 (44%)	143	1e-05 (6.9e-05)	5e-05 (0.000261)	3e-05 (0.000163)	0.00141 (0.00392)	3e-05 (0.000163)	0.00033 (0.00124)	0.00031 (0.00118)	0.0005 (0.00172)	0.0208 (0.0357)	0.0537 (0.0798)
amp 19q12	93 (36%)	164	1e-05 (6.9e-05)	2e-05 (0.000116)	0.0531 (0.079)	0.00022 (0.000883)	0.0428 (0.065)	0.00864 (0.0174)	0.488 (0.532)	0.00888 (0.0178)	0.0411 (0.0631)	0.00225 (0.00579)
del 2q37 3	108 (42%)	149	1e-05 (6.9e-05)	0.00146 (0.00405)	0.0914 (0.128)	0.0394 (0.0614)	0.0389 (0.0608)	0.00082 (0.00249)	0.13 (0.174)	0.00607 (0.0132)	0.0337 (0.0536)	0.0123 (0.0232)
del 9q34 3	61 (24%)	196	2e-05 (0.000116)	4e-05 (0.000214)	0.0195 (0.0339)	0.0957 (0.133)	0.0425 (0.0646)	0.15 (0.194)	0.0121 (0.023)	0.00293 (0.0073)	0.0402 (0.0619)	0.0221 (0.0376)
del 11q23 1	118 (46%)	139	1e-05 (6.9e-05)	0.00285 (0.00712)	0.0922 (0.129)	0.00433 (0.0101)	0.0125 (0.0235)	0.0154 (0.0276)	0.00343 (0.00833)	0.0769 (0.11)	0.0151 (0.0271)	0.0206 (0.0354)
amp 17p11 2	104 (40%)	153	1e-05 (6.9e-05)	1e-05 (6.9e-05)	0.215 (0.264)	0.00018 (0.000748)	0.0313 (0.0503)	0.02 (0.0345)	0.673 (0.704)	0.00181 (0.00477)	0.279 (0.328)	0.00738 (0.0153)
amp xq21 1	46 (18%)	211	1e-05 (6.9e-05)	0.0178 (0.0315)	0.0335 (0.0535)	0.34 (0.388)	0.0413 (0.0632)	0.00273 (0.00685)	0.0163 (0.0291)	0.403 (0.45)	0.0471 (0.0711)	0.292 (0.341)
del 5p15 33	33 (13%)	224	0.447 (0.492)	0.0141 (0.0259)	0.0141 (0.0259)	0.00056 (0.00185)	0.0137 (0.0253)	0.00154 (0.00423)	0.0559 (0.0827)	0.61 (0.648)	0.0235 (0.0398)	0.0253 (0.0424)
del 6p25 3	81 (32%)	176	1e-05 (6.9e-05)	0.00016 (0.000681)	0.00052 (0.00177)	0.0969 (0.135)	0.00078 (0.00239)	0.00158 (0.00431)	0.0126 (0.0235)	0.0255 (0.0426)	0.0703 (0.102)	0.0734 (0.106)
amp 8p11 22	81 (32%)	176	1e-05 (6.9e-05)	0.00343 (0.00833)	0.0327 (0.0524)	0.0926 (0.129)	0.439 (0.487)	0.0143 (0.0261)	0.161 (0.206)	0.0103 (0.0202)	0.0908 (0.128)	0.0289 (0.0473)
amp 17p12	102 (40%)	155	1e-05 (6.9e-05)	2e-05 (0.000116)	0.239 (0.289)	0.00085 (0.00256)	0.0522 (0.0779)	0.00226 (0.0058)	0.432 (0.48)	0.00181 (0.00477)	0.207 (0.256)	0.00431 (0.0101)
del 2q37 3	110 (43%)	147	1e-05 (6.9e-05)	0.00857 (0.0173)	0.585 (0.627)	0.00409 (0.00963)	0.0255 (0.0426)	0.00127 (0.00362)	0.446 (0.492)	0.0247 (0.0417)	0.081 (0.115)	0.0631 (0.0918)
del 14q24 1	80 (31%)	177	0.00051 (0.00175)	0.229 (0.28)	0.412 (0.459)	0.653 (0.689)	0.222 (0.271)	1e-05 (6.9e-05)	0.04 (0.0619)	0.00472 (0.0107)	0.00044 (0.00157)	0.0485 (0.073)
del xp21 1	55 (21%)	202	0.00178 (0.00474)	0.00251 (0.00639)	0.0329 (0.0526)	0.132 (0.176)	0.00774 (0.0159)	0.0296 (0.0481)	0.0263 (0.0435)	0.101 (0.14)	0.444 (0.491)	0.0705 (0.102)
amp 1q21 3	105 (41%)	152	1e-05 (6.9e-05)	0.00914 (0.0183)	0.239 (0.29)	0.0126 (0.0235)	0.505 (0.55)	0.105 (0.145)	0.687 (0.715)	0.165 (0.21)	0.00125 (0.00359)	0.0383 (0.06)
amp 5p15 33	119 (46%)	138	1e-05 (6.9e-05)	0.00053 (0.00179)	0.138 (0.183)	0.156 (0.201)	0.0181 (0.0318)	0.00017 (0.000711)	0.308 (0.356)	0.014 (0.0258)	0.831 (0.844)	0.752 (0.773)
amp 17q24 3	79 (31%)	178	1e-05 (6.9e-05)	0.00256 (0.00649)	0.031 (0.05)	0.00225 (0.00579)	0.257 (0.307)	0.0054 (0.0119)	0.108 (0.148)	0.154 (0.199)	0.445 (0.491)	0.0843 (0.119)
amp xp21 2	97 (38%)	160	1e-05 (6.9e-05)	0.0338 (0.0536)	0.317 (0.364)	0.0568 (0.0837)	0.363 (0.41)	0.0488 (0.0733)	0.733 (0.756)	0.04 (0.0619)	0.261 (0.311)	0.00397 (0.00945)
del 4q35 1	94 (37%)	163	1e-05 (6.9e-05)	0.00554 (0.0122)	0.659 (0.693)	0.0137 (0.0253)	0.015 (0.0271)	0.029 (0.0474)	0.355 (0.404)	0.107 (0.148)	0.276 (0.326)	0.208 (0.256)
del 7q36 3	71 (28%)	186	1e-05 (6.9e-05)	0.0149 (0.0271)	0.278 (0.328)	0.0385 (0.0602)	0.173 (0.219)	0.138 (0.183)	0.0489 (0.0733)	0.0058 (0.0127)	0.453 (0.497)	0.111 (0.152)
del 10p15 3	128 (50%)	129	1e-05 (6.9e-05)	0.00346 (0.00838)	0.33 (0.377)	0.00024 (0.000952)	0.258 (0.308)	0.00925 (0.0184)	0.559 (0.6)	0.0189 (0.0329)	0.605 (0.644)	0.718 (0.744)
del 12p13 1	87 (34%)	170	1e-05 (6.9e-05)	0.00016 (0.000681)	0.545 (0.588)	0.233 (0.284)	0.0186 (0.0326)	0.00572 (0.0125)	0.206 (0.255)	0.0339 (0.0537)	0.106 (0.147)	0.0617 (0.0902)
amp 1q24 3	102 (40%)	155	1e-05 (6.9e-05)	0.0401 (0.0619)	0.138 (0.183)	0.319 (0.367)	0.0176 (0.0313)	0.0202 (0.0348)	0.804 (0.821)	0.137 (0.182)	0.452 (0.497)	0.114 (0.155)
amp 8q24 21	83 (32%)	174	0.00011 (0.000483)	0.0373 (0.0587)	0.00758 (0.0157)	0.00773 (0.0159)	0.653 (0.689)	0.245 (0.295)	0.359 (0.407)	0.294 (0.342)	0.0549 (0.0813)	0.066 (0.0959)
amp 11q22 2	36 (14%)	221	0.326 (0.374)	0.0119 (0.0225)	0.411 (0.459)	0.191 (0.239)	0.0144 (0.0262)	0.00407 (0.00962)	0.136 (0.181)	0.00451 (0.0104)	0.284 (0.333)	0.189 (0.236)
del 3q29	54 (21%)	203	0.00669 (0.0141)	0.0401 (0.0619)	0.0108 (0.0209)	0.748 (0.769)	0.356 (0.404)	0.077 (0.11)	0.161 (0.206)	0.0379 (0.0595)	0.0852 (0.12)	0.133 (0.178)
del 6q14 1	78 (30%)	179	1e-05 (6.9e-05)	0.0186 (0.0326)	0.00646 (0.0138)	0.0272 (0.0448)	0.459 (0.502)	0.264 (0.313)	0.194 (0.242)	0.591 (0.632)	0.284 (0.333)	0.361 (0.408)
del 12q12	56 (22%)	201	2e-05 (0.000116)	8e-05 (0.000373)	0.628 (0.665)	0.877 (0.886)	0.0775 (0.11)	0.0262 (0.0435)	0.0839 (0.119)	0.0308 (0.0498)	0.263 (0.312)	0.11 (0.151)
del 17q25 3	67 (26%)	190	1e-05 (6.9e-05)	0.00095 (0.00281)	0.391 (0.438)	0.247 (0.297)	0.178 (0.225)	0.254 (0.305)	0.614 (0.652)	0.00838 (0.017)	0.0417 (0.0635)	0.302 (0.349)
del 21q11 2	51 (20%)	206	0.0114 (0.0218)	0.118 (0.159)	0.166 (0.211)	0.0189 (0.0329)	0.211 (0.259)	0.253 (0.303)	0.00057 (0.00186)	0.955 (0.958)	0.0075 (0.0155)	0.225 (0.275)
del 21q22 3	66 (26%)	191	0.00052 (0.00177)	0.0118 (0.0225)	0.295 (0.342)	0.0173 (0.0309)	0.119 (0.16)	0.161 (0.206)	0.14 (0.184)	0.0578 (0.0851)	0.0271 (0.0447)	0.145 (0.189)
amp 19p13 2	108 (42%)	149	1e-05 (6.9e-05)	0.242 (0.292)	0.262 (0.312)	0.00196 (0.00514)	0.194 (0.242)	0.00656 (0.0139)	0.879 (0.886)	0.285 (0.334)	0.784 (0.803)	0.165 (0.21)
del 9p24 3	100 (39%)	157	1e-05 (6.9e-05)	0.197 (0.245)	0.0327 (0.0524)	0.144 (0.188)	0.187 (0.235)	0.334 (0.381)	0.0106 (0.0207)	0.912 (0.917)	0.375 (0.422)	0.552 (0.594)
del 12q24 33	70 (27%)	187	1e-05 (6.9e-05)	0.0198 (0.0343)	0.524 (0.568)	0.875 (0.885)	0.679 (0.709)	0.0105 (0.0205)	0.381 (0.428)	0.115 (0.156)	0.106 (0.147)	0.669 (0.7)
del 19q13 43	106 (41%)	151	1e-05 (6.9e-05)	0.00258 (0.00652)	0.164 (0.209)	0.514 (0.559)	0.166 (0.211)	0.412 (0.459)	0.597 (0.637)	0.0341 (0.0538)	0.916 (0.92)	0.062 (0.0904)
amp 2p11 2	64 (25%)	193	0.00016 (0.000681)	0.0256 (0.0426)	0.33 (0.377)	0.0586 (0.0859)	0.836 (0.849)	0.37 (0.418)	0.878 (0.886)	0.314 (0.362)	0.852 (0.863)	0.989 (0.989)
amp 13q34	54 (21%)	203	1e-05 (6.9e-05)	0.114 (0.155)	0.962 (0.964)	0.0112 (0.0217)	0.459 (0.502)	0.143 (0.186)	0.656 (0.691)	0.14 (0.185)	0.826 (0.841)	0.141 (0.185)
amp 21q21 1	73 (28%)	184	1e-05 (6.9e-05)	2e-05 (0.000116)	0.208 (0.256)	0.158 (0.203)	0.121 (0.163)	0.291 (0.34)	0.663 (0.696)	0.141 (0.185)	0.299 (0.346)	0.118 (0.159)
del 11p15 5	110 (43%)	147	1e-05 (6.9e-05)	0.119 (0.161)	0.294 (0.342)	0.0106 (0.0207)	0.532 (0.574)	0.142 (0.186)	0.379 (0.425)	0.316 (0.364)	0.484 (0.529)	0.734 (0.756)
del 18p11 32	68 (26%)	189	0.00126 (0.00361)	0.0735 (0.106)	0.597 (0.637)	0.179 (0.226)	0.686 (0.715)	0.206 (0.255)	0.724 (0.748)	0.00176 (0.00471)	0.531 (0.574)	0.237 (0.288)
del 22q13 32	83 (32%)	174	1e-05 (6.9e-05)	0.161 (0.206)	0.789 (0.806)	0.249 (0.299)	0.693 (0.72)	0.0408 (0.0627)	0.0894 (0.126)	0.441 (0.489)	0.518 (0.562)	0.707 (0.734)
amp 15q26 3	84 (33%)	173	1e-05 (6.9e-05)	0.0529 (0.0788)	0.722 (0.747)	0.271 (0.321)	0.643 (0.681)	0.0847 (0.12)	0.665 (0.697)	0.185 (0.232)	0.775 (0.794)	0.808 (0.824)

'amp_1p32.1' versus 'CN_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
AMP PEAK 1(1P32.1) MUTATED	43	12	6	33
AMP PEAK 1(1P32.1) WILD-TYPE	52	48	33	30

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
ALL	54	56	72	75
AMP PEAK 1(1P32.1) MUTATED	17	8	16	53
AMP PEAK 1(1P32.1) WILD-TYPE	37	48	56	22

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 = 0.00382 (Fisher's exact test), Q value = 0.0092

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
AMP PEAK 1(1P32.1) MUTATED	21	26	15	26
AMP PEAK 1(1P32.1) WILD-TYPE	37	19	46	30

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 = 7e-05 (Fisher's exact test), Q value = 0.00034

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	35	49	68	22	22
AMP PEAK 1(1P32.1) MUTATED	9	12	35	18	7	7
AMP PEAK 1(1P32.1) WILD-TYPE	15	23	14	50	15	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 = 3e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
AMP PEAK 1(1P32.1) MUTATED	60	17	17
AMP PEAK 1(1P32.1) WILD-TYPE	54	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	47	21	49	46	30	29	33
AMP PEAK 1(1P32.1) MUTATED	19	7	10	8	22	6	22
AMP PEAK 1(1P32.1) WILD-TYPE	28	14	39	38	8	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 = 0.0082 (Fisher's exact test), Q value = 0.017

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
AMP PEAK 1(1P32.1) MUTATED	43	24	25
AMP PEAK 1(1P32.1) WILD-TYPE	62	26	75

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 = 0.00445 (Fisher's exact test), Q value = 0.01

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
AMP PEAK 1(1P32.1) MUTATED	40	15	34	3
AMP PEAK 1(1P32.1) WILD-TYPE	42	22	80	19

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

'amp_1p32.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0292 (Fisher's exact test), Q value = 0.048

Table S9. Gene #1: 'amp_1p32.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
AMP PEAK 1(1P32.1) MUTATED	21	11	13	9	24
AMP PEAK 1(1P32.1) WILD-TYPE	37	16	34	14	15

Figure S9. Get High-res Image Gene #1: 'amp_1p32.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_1p32.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S10. Gene #1: 'amp_1p32.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
AMP PEAK 1(1P32.1) MUTATED	27	13	10	25	3
AMP PEAK 1(1P32.1) WILD-TYPE	31	36	11	17	21

Figure S10. 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 S11. Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
AMP PEAK 2(1Q21.3) MUTATED	49	6	9	41
AMP PEAK 2(1Q21.3) WILD-TYPE	46	54	30	22

Figure S11. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 0.00914 (Fisher's exact test), Q value = 0.018

Table S12. Gene #2: 'amp_1q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
AMP PEAK 2(1Q21.3) MUTATED	17	17	29	42
AMP PEAK 2(1Q21.3) WILD-TYPE	37	39	43	33

Figure S12. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0126 (Fisher's exact test), Q value = 0.024

Table S13. Gene #2: 'amp_1q21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	35	49	68	22	22
AMP PEAK 2(1Q21.3) MUTATED	14	10	28	25	5	11
AMP PEAK 2(1Q21.3) WILD-TYPE	10	25	21	43	17	11

Figure S13. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00125 (Fisher's exact test), Q value = 0.0036

Table S14. Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
AMP PEAK 2(1Q21.3) MUTATED	21	8	19	18	23
AMP PEAK 2(1Q21.3) WILD-TYPE	37	19	28	5	16

Figure S14. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0383 (Fisher's exact test), Q value = 0.06

Table S15. Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
AMP PEAK 2(1Q21.3) MUTATED	24	21	13	25	6
AMP PEAK 2(1Q21.3) WILD-TYPE	34	28	8	17	18

Figure S15. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q24.3' versus 'CN_CNMF'

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

Table S16. Gene #3: 'amp_1q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
AMP PEAK 3(1Q24.3) MUTATED	48	12	6	36
AMP PEAK 3(1Q24.3) WILD-TYPE	47	48	33	27

Figure S16. Get High-res Image Gene #3: 'amp_1q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q24.3' versus 'METHLYATION_CNMF'

P value = 0.0401 (Fisher's exact test), Q value = 0.062

Table S17. Gene #3: 'amp_1q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
AMP PEAK 3(1Q24.3) MUTATED	17	20	25	40
AMP PEAK 3(1Q24.3) WILD-TYPE	37	36	47	35

Figure S17. Get High-res Image Gene #3: 'amp_1q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q24.3' versus 'MRNASEQ_CNMF'

P value = 0.0176 (Fisher's exact test), Q value = 0.031

Table S18. Gene #3: 'amp_1q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
AMP PEAK 3(1Q24.3) MUTATED	56	28	18
AMP PEAK 3(1Q24.3) WILD-TYPE	58	49	46

Figure S18. Get High-res Image Gene #3: 'amp_1q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0202 (Fisher's exact test), Q value = 0.035

Table S19. 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	47	21	49	46	30	29	33
AMP PEAK 3(1Q24.3) MUTATED	24	7	15	14	9	12	21
AMP PEAK 3(1Q24.3) WILD-TYPE	23	14	34	32	21	17	12

Figure S19. Get High-res Image Gene #3: 'amp_1q24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_2p11.2' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00068

Table S20. Gene #4: 'amp_2p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
AMP PEAK 4(2P11.2) MUTATED	35	4	9	16
AMP PEAK 4(2P11.2) WILD-TYPE	60	56	30	47

Figure S20. Get High-res Image Gene #4: 'amp_2p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2p11.2' versus 'METHLYATION_CNMF'

P value = 0.0256 (Fisher's exact test), Q value = 0.043

Table S21. Gene #4: 'amp_2p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
AMP PEAK 4(2P11.2) MUTATED	10	9	17	28
AMP PEAK 4(2P11.2) WILD-TYPE	44	47	55	47

Figure S21. Get High-res Image Gene #4: 'amp_2p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3p12.1' versus 'CN_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
AMP PEAK 5(3P12.1) MUTATED	38	5	4	22
AMP PEAK 5(3P12.1) WILD-TYPE	57	55	35	41

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

'amp_3p12.1' versus 'METHLYATION_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.002

Table S23. Gene #5: 'amp_3p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
AMP PEAK 5(3P12.1) MUTATED	16	6	16	31
AMP PEAK 5(3P12.1) WILD-TYPE	38	50	56	44

Figure S23. Get High-res Image Gene #5: 'amp_3p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3p12.1' versus 'RPPA_CNMF'

P value = 0.00469 (Fisher's exact test), Q value = 0.011

Table S24. Gene #5: 'amp_3p12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
AMP PEAK 5(3P12.1) MUTATED	12	12	10	25
AMP PEAK 5(3P12.1) WILD-TYPE	46	33	51	31

Figure S24. Get High-res Image Gene #5: 'amp_3p12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_3p12.1' versus 'RPPA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00034

Table S25. 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	35	49	68	22	22
AMP PEAK 5(3P12.1) MUTATED	5	9	25	10	9	1
AMP PEAK 5(3P12.1) WILD-TYPE	19	26	24	58	13	21

Figure S25. Get High-res Image Gene #5: 'amp_3p12.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_3p12.1' versus 'MRNASEQ_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.0021

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
AMP PEAK 5(3P12.1) MUTATED	43	17	8
AMP PEAK 5(3P12.1) WILD-TYPE	71	60	56

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

'amp_3p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 3e-04

Table S27. 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	47	21	49	46	30	29	33
AMP PEAK 5(3P12.1) MUTATED	18	6	12	2	15	4	11
AMP PEAK 5(3P12.1) WILD-TYPE	29	15	37	44	15	25	22

Figure S27. Get High-res Image Gene #5: 'amp_3p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00318 (Fisher's exact test), Q value = 0.0079

Table S28. Gene #5: 'amp_3p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
AMP PEAK 5(3P12.1) MUTATED	29	9	31	0
AMP PEAK 5(3P12.1) WILD-TYPE	53	28	83	22

Figure S28. Get High-res Image Gene #5: 'amp_3p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3p12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00211 (Fisher's exact test), Q value = 0.0055

Table S29. Gene #5: 'amp_3p12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
AMP PEAK 5(3P12.1) MUTATED	14	7	12	4	23
AMP PEAK 5(3P12.1) WILD-TYPE	44	20	35	19	16

Figure S29. 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 = 0.00019 (Fisher's exact test), Q value = 0.00078

Table S30. Gene #5: 'amp_3p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
AMP PEAK 5(3P12.1) MUTATED	18	13	10	19	0
AMP PEAK 5(3P12.1) WILD-TYPE	40	36	11	23	24

Figure S30. 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 S31. Gene #6: 'amp_4q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
AMP PEAK 6(4Q12) MUTATED	38	4	8	28
AMP PEAK 6(4Q12) WILD-TYPE	57	56	31	35

Figure S31. Get High-res Image Gene #6: 'amp_4q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4q12' versus 'METHLYATION_CNMF'

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

Table S32. Gene #6: 'amp_4q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
AMP PEAK 6(4Q12) MUTATED	15	10	14	39
AMP PEAK 6(4Q12) WILD-TYPE	39	46	58	36

Figure S32. Get High-res Image Gene #6: 'amp_4q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_4q12' versus 'RPPA_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.031

Table S33. Gene #6: 'amp_4q12' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
AMP PEAK 6(4Q12) MUTATED	21	18	10	21
AMP PEAK 6(4Q12) WILD-TYPE	37	27	51	35

Figure S33. Get High-res Image Gene #6: 'amp_4q12' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_4q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00168 (Fisher's exact test), Q value = 0.0045

Table S34. 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	35	49	68	22	22
AMP PEAK 6(4Q12) MUTATED	11	14	24	13	5	3
AMP PEAK 6(4Q12) WILD-TYPE	13	21	25	55	17	19

Figure S34. Get High-res Image Gene #6: 'amp_4q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_4q12' versus 'MRNASEQ_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0018

Table S35. Gene #6: 'amp_4q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
AMP PEAK 6(4Q12) MUTATED	49	14	15
AMP PEAK 6(4Q12) WILD-TYPE	65	63	49

Figure S35. Get High-res Image Gene #6: 'amp_4q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_4q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00378 (Fisher's exact test), Q value = 0.0091

Table S36. 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	47	21	49	46	30	29	33
AMP PEAK 6(4Q12) MUTATED	19	8	7	9	15	7	13
AMP PEAK 6(4Q12) WILD-TYPE	28	13	42	37	15	22	20

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

'amp_4q12' versus 'MIRSEQ_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.036

Table S37. Gene #6: 'amp_4q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
AMP PEAK 6(4Q12) MUTATED	30	23	24
AMP PEAK 6(4Q12) WILD-TYPE	75	27	76

Figure S37. Get High-res Image Gene #6: 'amp_4q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_4q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0131 (Fisher's exact test), Q value = 0.024

Table S38. Gene #6: 'amp_4q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
AMP PEAK 6(4Q12) MUTATED	28	15	33	1
AMP PEAK 6(4Q12) WILD-TYPE	54	22	81	21

Figure S38. Get High-res Image Gene #6: 'amp_4q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_4q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00214 (Fisher's exact test), Q value = 0.0056

Table S39. Gene #6: 'amp_4q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
AMP PEAK 6(4Q12) MUTATED	19	12	12	21	3
AMP PEAK 6(4Q12) WILD-TYPE	39	37	9	21	21

Figure S39. 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 S40. Gene #7: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
AMP PEAK 7(5P15.33) MUTATED	71	8	14	26
AMP PEAK 7(5P15.33) WILD-TYPE	24	52	25	37

Figure S40. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.0018

Table S41. Gene #7: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
AMP PEAK 7(5P15.33) MUTATED	24	17	29	49
AMP PEAK 7(5P15.33) WILD-TYPE	30	39	43	26

Figure S41. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.032

Table S42. Gene #7: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
AMP PEAK 7(5P15.33) MUTATED	64	30	24
AMP PEAK 7(5P15.33) WILD-TYPE	50	47	40

Figure S42. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00071

Table S43. 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	47	21	49	46	30	29	33
AMP PEAK 7(5P15.33) MUTATED	33	8	23	16	19	6	13
AMP PEAK 7(5P15.33) WILD-TYPE	14	13	26	30	11	23	20

Figure S43. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 0.026

Table S44. Gene #7: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
AMP PEAK 7(5P15.33) MUTATED	48	15	50	5
AMP PEAK 7(5P15.33) WILD-TYPE	34	22	64	17

Figure S44. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'CN_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
AMP PEAK 8(6P21.1) MUTATED	29	5	1	25
AMP PEAK 8(6P21.1) WILD-TYPE	66	55	38	38

Figure S45. 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 S46. Gene #8: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
AMP PEAK 8(6P21.1) MUTATED	9	11	7	33
AMP PEAK 8(6P21.1) WILD-TYPE	45	45	65	42

Figure S46. Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p21.1' versus 'RPPA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00034

Table S47. Gene #8: 'amp_6p21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
AMP PEAK 8(6P21.1) MUTATED	18	21	5	11
AMP PEAK 8(6P21.1) WILD-TYPE	40	24	56	45

Figure S47. Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_6p21.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0018

Table S48. 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	35	49	68	22	22
AMP PEAK 8(6P21.1) MUTATED	12	7	18	7	4	7
AMP PEAK 8(6P21.1) WILD-TYPE	12	28	31	61	18	15

Figure S48. Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_6p21.1' versus 'MRNASEQ_CNMF'

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

Table S49. Gene #8: 'amp_6p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
AMP PEAK 8(6P21.1) MUTATED	38	7	15
AMP PEAK 8(6P21.1) WILD-TYPE	76	70	49

Figure S49. Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0012

Table S50. 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	47	21	49	46	30	29	33
AMP PEAK 8(6P21.1) MUTATED	21	3	3	9	9	4	11
AMP PEAK 8(6P21.1) WILD-TYPE	26	18	46	37	21	25	22

Figure S50. Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_CNMF'

P value = 0.00584 (Fisher's exact test), Q value = 0.013

Table S51. Gene #8: 'amp_6p21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
AMP PEAK 8(6P21.1) MUTATED	30	16	13
AMP PEAK 8(6P21.1) WILD-TYPE	75	34	87

Figure S51. Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6p21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.02

Table S52. Gene #8: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
AMP PEAK 8(6P21.1) MUTATED	29	9	18	3
AMP PEAK 8(6P21.1) WILD-TYPE	53	28	96	19

Figure S52. Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 0.042

Table S53. Gene #8: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
AMP PEAK 8(6P21.1) MUTATED	14	9	5	10	11
AMP PEAK 8(6P21.1) WILD-TYPE	44	18	42	13	28

Figure S53. Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0211 (Fisher's exact test), Q value = 0.036

Table S54. Gene #8: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
AMP PEAK 8(6P21.1) MUTATED	20	6	8	12	3
AMP PEAK 8(6P21.1) WILD-TYPE	38	43	13	30	21

Figure S54. Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q25.1' versus 'CN_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.0038

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
AMP PEAK 9(6Q25.1) MUTATED	37	14	3	21
AMP PEAK 9(6Q25.1) WILD-TYPE	58	46	36	42

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

'amp_6q25.1' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00037

Table S56. Gene #9: 'amp_6q25.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
AMP PEAK 9(6Q25.1) MUTATED	20	15	8	32
AMP PEAK 9(6Q25.1) WILD-TYPE	34	41	64	43

Figure S56. Get High-res Image Gene #9: 'amp_6q25.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q25.1' versus 'RPPA_CNMF'

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

Table S57. Gene #9: 'amp_6q25.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
AMP PEAK 9(6Q25.1) MUTATED	25	13	7	23
AMP PEAK 9(6Q25.1) WILD-TYPE	33	32	54	33

Figure S57. Get High-res Image Gene #9: 'amp_6q25.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_6q25.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00078

Table S58. 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	35	49	68	22	22
AMP PEAK 9(6Q25.1) MUTATED	13	13	16	8	11	7
AMP PEAK 9(6Q25.1) WILD-TYPE	11	22	33	60	11	15

Figure S58. 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 S59. Gene #9: 'amp_6q25.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
AMP PEAK 9(6Q25.1) MUTATED	54	8	12
AMP PEAK 9(6Q25.1) WILD-TYPE	60	69	52

Figure S59. 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 S60. 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	47	21	49	46	30	29	33
AMP PEAK 9(6Q25.1) MUTATED	26	12	5	10	8	3	10
AMP PEAK 9(6Q25.1) WILD-TYPE	21	9	44	36	22	26	23

Figure S60. Get High-res Image Gene #9: 'amp_6q25.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6q25.1' versus 'MIRSEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00071

Table S61. Gene #9: 'amp_6q25.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
AMP PEAK 9(6Q25.1) MUTATED	42	18	15
AMP PEAK 9(6Q25.1) WILD-TYPE	63	32	85

Figure S61. Get High-res Image Gene #9: 'amp_6q25.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6q25.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00052

Table S62. Gene #9: 'amp_6q25.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
AMP PEAK 9(6Q25.1) MUTATED	37	14	22	2
AMP PEAK 9(6Q25.1) WILD-TYPE	45	23	92	20

Figure S62. Get High-res Image Gene #9: 'amp_6q25.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6q25.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.002

Table S63. Gene #9: 'amp_6q25.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
AMP PEAK 9(6Q25.1) MUTATED	17	15	7	6	20
AMP PEAK 9(6Q25.1) WILD-TYPE	41	12	40	17	19

Figure S63. 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 = 0.00064 (Fisher's exact test), Q value = 0.002

Table S64. Gene #9: 'amp_6q25.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
AMP PEAK 9(6Q25.1) MUTATED	24	8	9	21	3
AMP PEAK 9(6Q25.1) WILD-TYPE	34	41	12	21	21

Figure S64. Get High-res Image Gene #9: 'amp_6q25.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q31.2' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0012

Table S65. Gene #10: 'amp_7q31.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
AMP PEAK 10(7Q31.2) MUTATED	43	9	9	16
AMP PEAK 10(7Q31.2) WILD-TYPE	52	51	30	47

Figure S65. Get High-res Image Gene #10: 'amp_7q31.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q31.2' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00071

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
AMP PEAK 10(7Q31.2) MUTATED	20	13	10	34
AMP PEAK 10(7Q31.2) WILD-TYPE	34	43	62	41

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

'amp_7q31.2' versus 'RPPA_CNMF'

P value = 0.0139 (Fisher's exact test), Q value = 0.026

Table S67. Gene #10: 'amp_7q31.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
AMP PEAK 10(7Q31.2) MUTATED	18	17	11	25
AMP PEAK 10(7Q31.2) WILD-TYPE	40	28	50	31

Figure S67. Get High-res Image Gene #10: 'amp_7q31.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_7q31.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.002

Table S68. 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	35	49	68	22	22
AMP PEAK 10(7Q31.2) MUTATED	11	16	22	10	8	4
AMP PEAK 10(7Q31.2) WILD-TYPE	13	19	27	58	14	18

Figure S68. Get High-res Image Gene #10: 'amp_7q31.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_7q31.2' versus 'MRNASEQ_CNMF'

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

Table S69. Gene #10: 'amp_7q31.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
AMP PEAK 10(7Q31.2) MUTATED	49	10	18
AMP PEAK 10(7Q31.2) WILD-TYPE	65	67	46

Figure S69. Get High-res Image Gene #10: 'amp_7q31.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00499 (Fisher's exact test), Q value = 0.011

Table S70. 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	47	21	49	46	30	29	33
AMP PEAK 10(7Q31.2) MUTATED	21	7	6	13	13	5	12
AMP PEAK 10(7Q31.2) WILD-TYPE	26	14	43	33	17	24	21

Figure S70. Get High-res Image Gene #10: 'amp_7q31.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0011

Table S71. Gene #10: 'amp_7q31.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
AMP PEAK 10(7Q31.2) MUTATED	32	26	19
AMP PEAK 10(7Q31.2) WILD-TYPE	73	24	81

Figure S71. Get High-res Image Gene #10: 'amp_7q31.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0447 (Fisher's exact test), Q value = 0.068

Table S72. Gene #10: 'amp_7q31.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
AMP PEAK 10(7Q31.2) MUTATED	28	17	28	4
AMP PEAK 10(7Q31.2) WILD-TYPE	54	20	86	18

Figure S72. Get High-res Image Gene #10: 'amp_7q31.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.00082

Table S73. Gene #10: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
AMP PEAK 10(7Q31.2) MUTATED	15	9	5	11	21
AMP PEAK 10(7Q31.2) WILD-TYPE	43	18	42	12	18

Figure S73. 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 = 0.00057 (Fisher's exact test), Q value = 0.0019

Table S74. Gene #10: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
AMP PEAK 10(7Q31.2) MUTATED	19	6	10	21	5
AMP PEAK 10(7Q31.2) WILD-TYPE	39	43	11	21	19

Figure S74. Get High-res Image Gene #10: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p11.22' versus 'CN_CNMF'

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

Table S75. Gene #11: 'amp_8p11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
AMP PEAK 11(8P11.22) MUTATED	44	5	10	22
AMP PEAK 11(8P11.22) WILD-TYPE	51	55	29	41

Figure S75. Get High-res Image Gene #11: 'amp_8p11.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p11.22' versus 'METHLYATION_CNMF'

P value = 0.00343 (Fisher's exact test), Q value = 0.0083

Table S76. Gene #11: 'amp_8p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
AMP PEAK 11(8P11.22) MUTATED	18	9	20	34
AMP PEAK 11(8P11.22) WILD-TYPE	36	47	52	41

Figure S76. Get High-res Image Gene #11: 'amp_8p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8p11.22' versus 'RPPA_CNMF'

P value = 0.0327 (Fisher's exact test), Q value = 0.052

Table S77. Gene #11: 'amp_8p11.22' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
AMP PEAK 11(8P11.22) MUTATED	17	23	15	17
AMP PEAK 11(8P11.22) WILD-TYPE	41	22	46	39

Figure S77. Get High-res Image Gene #11: 'amp_8p11.22' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_8p11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.026

Table S78. 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	47	21	49	46	30	29	33
AMP PEAK 11(8P11.22) MUTATED	18	6	13	9	18	7	10
AMP PEAK 11(8P11.22) WILD-TYPE	29	15	36	37	12	22	23

Figure S78. Get High-res Image Gene #11: 'amp_8p11.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.02

Table S79. Gene #11: 'amp_8p11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
AMP PEAK 11(8P11.22) MUTATED	32	10	37	1
AMP PEAK 11(8P11.22) WILD-TYPE	50	27	77	21

Figure S79. Get High-res Image Gene #11: 'amp_8p11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0289 (Fisher's exact test), Q value = 0.047

Table S80. Gene #11: 'amp_8p11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
AMP PEAK 11(8P11.22) MUTATED	22	15	12	15	3
AMP PEAK 11(8P11.22) WILD-TYPE	36	34	9	27	21

Figure S80. Get High-res Image Gene #11: 'amp_8p11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00048

Table S81. Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
AMP PEAK 12(8Q24.21) MUTATED	40	6	15	22
AMP PEAK 12(8Q24.21) WILD-TYPE	55	54	24	41

Figure S81. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 0.0373 (Fisher's exact test), Q value = 0.059

Table S82. Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
AMP PEAK 12(8Q24.21) MUTATED	15	13	21	34
AMP PEAK 12(8Q24.21) WILD-TYPE	39	43	51	41

Figure S82. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'RPPA_CNMF'

P value = 0.00758 (Fisher's exact test), Q value = 0.016

Table S83. Gene #12: 'amp_8q24.21' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
AMP PEAK 12(8Q24.21) MUTATED	14	20	13	25
AMP PEAK 12(8Q24.21) WILD-TYPE	44	25	48	31

Figure S83. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_8q24.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.00773 (Fisher's exact test), Q value = 0.016

Table S84. 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	35	49	68	22	22
AMP PEAK 12(8Q24.21) MUTATED	7	6	25	16	8	10
AMP PEAK 12(8Q24.21) WILD-TYPE	17	29	24	52	14	12

Figure S84. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_11q22.2' versus 'METHLYATION_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.023

Table S85. Gene #13: 'amp_11q22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
AMP PEAK 13(11Q22.2) MUTATED	8	6	4	18
AMP PEAK 13(11Q22.2) WILD-TYPE	46	50	68	57

Figure S85. Get High-res Image Gene #13: 'amp_11q22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11q22.2' versus 'MRNASEQ_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.026

Table S86. Gene #13: 'amp_11q22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
AMP PEAK 13(11Q22.2) MUTATED	22	4	10
AMP PEAK 13(11Q22.2) WILD-TYPE	92	73	54

Figure S86. Get High-res Image Gene #13: 'amp_11q22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_11q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00407 (Fisher's exact test), Q value = 0.0096

Table S87. 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	47	21	49	46	30	29	33
AMP PEAK 13(11Q22.2) MUTATED	10	2	2	5	11	2	4
AMP PEAK 13(11Q22.2) WILD-TYPE	37	19	47	41	19	27	29

Figure S87. Get High-res Image Gene #13: 'amp_11q22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11q22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00451 (Fisher's exact test), Q value = 0.01

Table S88. Gene #13: 'amp_11q22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
AMP PEAK 13(11Q22.2) MUTATED	19	7	10	0
AMP PEAK 13(11Q22.2) WILD-TYPE	63	30	104	22

Figure S88. Get High-res Image Gene #13: 'amp_11q22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

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

Table S89. Gene #14: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
AMP PEAK 14(12Q15) MUTATED	56	28	5	5
AMP PEAK 14(12Q15) WILD-TYPE	39	32	34	58

Figure S89. 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 S90. Gene #14: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
AMP PEAK 14(12Q15) MUTATED	30	24	2	38
AMP PEAK 14(12Q15) WILD-TYPE	24	32	70	37

Figure S90. 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 S91. Gene #14: 'amp_12q15' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
AMP PEAK 14(12Q15) MUTATED	37	20	2	29
AMP PEAK 14(12Q15) WILD-TYPE	21	25	59	27

Figure S91. 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 S92. 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	35	49	68	22	22
AMP PEAK 14(12Q15) MUTATED	13	24	23	7	14	7
AMP PEAK 14(12Q15) WILD-TYPE	11	11	26	61	8	15

Figure S92. 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 S93. Gene #14: 'amp_12q15' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
AMP PEAK 14(12Q15) MUTATED	59	2	33
AMP PEAK 14(12Q15) WILD-TYPE	55	75	31

Figure S93. 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 S94. 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	47	21	49	46	30	29	33
AMP PEAK 14(12Q15) MUTATED	30	12	1	25	14	1	11
AMP PEAK 14(12Q15) WILD-TYPE	17	9	48	21	16	28	22

Figure S94. 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 S95. Gene #14: 'amp_12q15' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
AMP PEAK 14(12Q15) MUTATED	58	24	10
AMP PEAK 14(12Q15) WILD-TYPE	47	26	90

Figure S95. 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 S96. Gene #14: 'amp_12q15' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
AMP PEAK 14(12Q15) MUTATED	50	19	16	7
AMP PEAK 14(12Q15) WILD-TYPE	32	18	98	15

Figure S96. 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 S97. Gene #14: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
AMP PEAK 14(12Q15) MUTATED	35	17	1	6	16
AMP PEAK 14(12Q15) WILD-TYPE	23	10	46	17	23

Figure S97. 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 S98. Gene #14: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
AMP PEAK 14(12Q15) MUTATED	37	1	8	20	9
AMP PEAK 14(12Q15) WILD-TYPE	21	48	13	22	15

Figure S98. 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 S99. Gene #15: 'amp_13q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
AMP PEAK 15(13Q34) MUTATED	11	3	5	35
AMP PEAK 15(13Q34) WILD-TYPE	84	57	34	28

Figure S99. Get High-res Image Gene #15: 'amp_13q34' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q34' versus 'RPPA_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 0.022

Table S100. 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	35	49	68	22	22
AMP PEAK 15(13Q34) MUTATED	10	4	16	14	5	1
AMP PEAK 15(13Q34) WILD-TYPE	14	31	33	54	17	21

Figure S100. Get High-res Image Gene #15: 'amp_13q34' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_15q26.3' versus 'CN_CNMF'

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

Table S101. Gene #16: 'amp_15q26.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
AMP PEAK 16(15Q26.3) MUTATED	48	3	12	21
AMP PEAK 16(15Q26.3) WILD-TYPE	47	57	27	42

Figure S101. 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 S102. Gene #17: 'amp_17p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
AMP PEAK 17(17P12) MUTATED	42	1	15	44
AMP PEAK 17(17P12) WILD-TYPE	53	59	24	19

Figure S102. 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 S103. Gene #17: 'amp_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
AMP PEAK 17(17P12) MUTATED	13	11	34	44
AMP PEAK 17(17P12) WILD-TYPE	41	45	38	31

Figure S103. Get High-res Image Gene #17: 'amp_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17p12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00085 (Fisher's exact test), Q value = 0.0026

Table S104. 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	35	49	68	22	22
AMP PEAK 17(17P12) MUTATED	14	8	29	27	6	4
AMP PEAK 17(17P12) WILD-TYPE	10	27	20	41	16	18

Figure S104. Get High-res Image Gene #17: 'amp_17p12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00226 (Fisher's exact test), Q value = 0.0058

Table S105. 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	47	21	49	46	30	29	33
AMP PEAK 17(17P12) MUTATED	24	2	26	11	14	11	13
AMP PEAK 17(17P12) WILD-TYPE	23	19	23	35	16	18	20

Figure S105. Get High-res Image Gene #17: 'amp_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00181 (Fisher's exact test), Q value = 0.0048

Table S106. Gene #17: 'amp_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
AMP PEAK 17(17P12) MUTATED	32	17	50	1
AMP PEAK 17(17P12) WILD-TYPE	50	20	64	21

Figure S106. Get High-res Image Gene #17: 'amp_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_17p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00431 (Fisher's exact test), Q value = 0.01

Table S107. Gene #17: 'amp_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
AMP PEAK 17(17P12) MUTATED	24	25	11	18	2
AMP PEAK 17(17P12) WILD-TYPE	34	24	10	24	22

Figure S107. 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 S108. Gene #18: 'amp_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
AMP PEAK 18(17P11.2) MUTATED	46	1	13	44
AMP PEAK 18(17P11.2) WILD-TYPE	49	59	26	19

Figure S108. 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 S109. Gene #18: 'amp_17p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
AMP PEAK 18(17P11.2) MUTATED	15	9	31	49
AMP PEAK 18(17P11.2) WILD-TYPE	39	47	41	26

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

'amp_17p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00075

Table S110. 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	35	49	68	22	22
AMP PEAK 18(17P11.2) MUTATED	15	8	31	25	6	5
AMP PEAK 18(17P11.2) WILD-TYPE	9	27	18	43	16	17

Figure S110. Get High-res Image Gene #18: 'amp_17p11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_17p11.2' versus 'MRNASEQ_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.05

Table S111. Gene #18: 'amp_17p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
AMP PEAK 18(17P11.2) MUTATED	52	34	17
AMP PEAK 18(17P11.2) WILD-TYPE	62	43	47

Figure S111. Get High-res Image Gene #18: 'amp_17p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.02 (Fisher's exact test), Q value = 0.035

Table S112. 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	47	21	49	46	30	29	33
AMP PEAK 18(17P11.2) MUTATED	24	5	24	10	15	10	15
AMP PEAK 18(17P11.2) WILD-TYPE	23	16	25	36	15	19	18

Figure S112. Get High-res Image Gene #18: 'amp_17p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00181 (Fisher's exact test), Q value = 0.0048

Table S113. Gene #18: 'amp_17p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
AMP PEAK 18(17P11.2) MUTATED	35	16	50	1
AMP PEAK 18(17P11.2) WILD-TYPE	47	21	64	21

Figure S113. Get High-res Image Gene #18: 'amp_17p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_17p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00738 (Fisher's exact test), Q value = 0.015

Table S114. Gene #18: 'amp_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
AMP PEAK 18(17P11.2) MUTATED	24	22	13	21	3
AMP PEAK 18(17P11.2) WILD-TYPE	34	27	8	21	21

Figure S114. Get High-res Image Gene #18: 'amp_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q24.3' versus 'CN_CNMF'

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

Table S115. Gene #19: 'amp_17q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
AMP PEAK 19(17Q24.3) MUTATED	36	2	13	28
AMP PEAK 19(17Q24.3) WILD-TYPE	59	58	26	35

Figure S115. Get High-res Image Gene #19: 'amp_17q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q24.3' versus 'METHLYATION_CNMF'

P value = 0.00256 (Fisher's exact test), Q value = 0.0065

Table S116. Gene #19: 'amp_17q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
AMP PEAK 19(17Q24.3) MUTATED	14	13	16	36
AMP PEAK 19(17Q24.3) WILD-TYPE	40	43	56	39

Figure S116. Get High-res Image Gene #19: 'amp_17q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q24.3' versus 'RPPA_CNMF'

P value = 0.031 (Fisher's exact test), Q value = 0.05

Table S117. Gene #19: 'amp_17q24.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
AMP PEAK 19(17Q24.3) MUTATED	17	19	11	21
AMP PEAK 19(17Q24.3) WILD-TYPE	41	26	50	35

Figure S117. Get High-res Image Gene #19: 'amp_17q24.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_17q24.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00225 (Fisher's exact test), Q value = 0.0058

Table S118. 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	35	49	68	22	22
AMP PEAK 19(17Q24.3) MUTATED	14	7	19	12	7	9
AMP PEAK 19(17Q24.3) WILD-TYPE	10	28	30	56	15	13

Figure S118. Get High-res Image Gene #19: 'amp_17q24.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_17q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0054 (Fisher's exact test), Q value = 0.012

Table S119. 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	47	21	49	46	30	29	33
AMP PEAK 19(17Q24.3) MUTATED	17	4	5	15	13	13	11
AMP PEAK 19(17Q24.3) WILD-TYPE	30	17	44	31	17	16	22

Figure S119. 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 S120. Gene #20: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
AMP PEAK 20(19P13.2) MUTATED	62	6	14	26
AMP PEAK 20(19P13.2) WILD-TYPE	33	54	25	37

Figure S120. Get High-res Image Gene #20: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19p13.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00196 (Fisher's exact test), Q value = 0.0051

Table S121. 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	35	49	68	22	22
AMP PEAK 20(19P13.2) MUTATED	17	12	25	28	8	3
AMP PEAK 20(19P13.2) WILD-TYPE	7	23	24	40	14	19

Figure S121. Get High-res Image Gene #20: 'amp_19p13.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00656 (Fisher's exact test), Q value = 0.014

Table S122. 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	47	21	49	46	30	29	33
AMP PEAK 20(19P13.2) MUTATED	30	9	21	17	12	13	6
AMP PEAK 20(19P13.2) WILD-TYPE	17	12	28	29	18	16	27

Figure S122. 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 S123. Gene #21: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
AMP PEAK 21(19Q12) MUTATED	50	3	5	35
AMP PEAK 21(19Q12) WILD-TYPE	45	57	34	28

Figure S123. Get High-res Image Gene #21: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

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

Table S124. Gene #21: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
AMP PEAK 21(19Q12) MUTATED	15	15	18	45
AMP PEAK 21(19Q12) WILD-TYPE	39	41	54	30

Figure S124. 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 = 0.00088

Table S125. 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	35	49	68	22	22
AMP PEAK 21(19Q12) MUTATED	18	11	25	16	8	8
AMP PEAK 21(19Q12) WILD-TYPE	6	24	24	52	14	14

Figure S125. Get High-res Image Gene #21: 'amp_19q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 0.0428 (Fisher's exact test), Q value = 0.065

Table S126. Gene #21: 'amp_19q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
AMP PEAK 21(19Q12) MUTATED	50	20	23
AMP PEAK 21(19Q12) WILD-TYPE	64	57	41

Figure S126. Get High-res Image Gene #21: 'amp_19q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00864 (Fisher's exact test), Q value = 0.017

Table S127. 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	47	21	49	46	30	29	33
AMP PEAK 21(19Q12) MUTATED	28	6	13	15	13	6	12
AMP PEAK 21(19Q12) WILD-TYPE	19	15	36	31	17	23	21

Figure S127. Get High-res Image Gene #21: 'amp_19q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00888 (Fisher's exact test), Q value = 0.018

Table S128. Gene #21: 'amp_19q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
AMP PEAK 21(19Q12) MUTATED	38	14	39	2
AMP PEAK 21(19Q12) WILD-TYPE	44	23	75	20

Figure S128. Get High-res Image Gene #21: 'amp_19q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0411 (Fisher's exact test), Q value = 0.063

Table S129. Gene #21: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
AMP PEAK 21(19Q12) MUTATED	21	14	11	13	15
AMP PEAK 21(19Q12) WILD-TYPE	37	13	36	10	24

Figure S129. Get High-res Image Gene #21: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00225 (Fisher's exact test), Q value = 0.0058

Table S130. Gene #21: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
AMP PEAK 21(19Q12) MUTATED	29	11	11	19	4
AMP PEAK 21(19Q12) WILD-TYPE	29	38	10	23	20

Figure S130. 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 S131. Gene #22: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
AMP PEAK 22(20Q13.33) MUTATED	61	3	11	23
AMP PEAK 22(20Q13.33) WILD-TYPE	34	57	28	40

Figure S131. Get High-res Image Gene #22: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.33' versus 'METHLYATION_CNMF'

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

Table S132. Gene #22: 'amp_20q13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
AMP PEAK 22(20Q13.33) MUTATED	16	19	16	47
AMP PEAK 22(20Q13.33) WILD-TYPE	38	37	56	28

Figure S132. Get High-res Image Gene #22: 'amp_20q13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q13.33' versus 'RPPA_CNMF'

P value = 0.00482 (Fisher's exact test), Q value = 0.011

Table S133. Gene #22: 'amp_20q13.33' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
AMP PEAK 22(20Q13.33) MUTATED	25	25	15	28
AMP PEAK 22(20Q13.33) WILD-TYPE	33	20	46	28

Figure S133. 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 = 0.00034

Table S134. 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	35	49	68	22	22
AMP PEAK 22(20Q13.33) MUTATED	14	14	32	15	9	9
AMP PEAK 22(20Q13.33) WILD-TYPE	10	21	17	53	13	13

Figure S134. Get High-res Image Gene #22: 'amp_20q13.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_20q13.33' versus 'MRNASEQ_CNMF'

P value = 0.00123 (Fisher's exact test), Q value = 0.0036

Table S135. Gene #22: 'amp_20q13.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
AMP PEAK 22(20Q13.33) MUTATED	54	17	26
AMP PEAK 22(20Q13.33) WILD-TYPE	60	60	38

Figure S135. Get High-res Image Gene #22: 'amp_20q13.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00141 (Fisher's exact test), Q value = 0.0039

Table S136. 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	47	21	49	46	30	29	33
AMP PEAK 22(20Q13.33) MUTATED	25	7	10	18	18	6	13
AMP PEAK 22(20Q13.33) WILD-TYPE	22	14	39	28	12	23	20

Figure S136. Get High-res Image Gene #22: 'amp_20q13.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 0.022

Table S137. Gene #22: 'amp_20q13.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
AMP PEAK 22(20Q13.33) MUTATED	42	27	29
AMP PEAK 22(20Q13.33) WILD-TYPE	63	23	71

Figure S137. Get High-res Image Gene #22: 'amp_20q13.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_20q13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.0017

Table S138. Gene #22: 'amp_20q13.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
AMP PEAK 22(20Q13.33) MUTATED	43	15	38	2
AMP PEAK 22(20Q13.33) WILD-TYPE	39	22	76	20

Figure S138. Get High-res Image Gene #22: 'amp_20q13.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_MATURE_CNMF'

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

Table S139. Gene #22: 'amp_20q13.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
AMP PEAK 22(20Q13.33) MUTATED	19	15	10	12	25
AMP PEAK 22(20Q13.33) WILD-TYPE	39	12	37	11	14

Figure S139. 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 = 0.00037 (Fisher's exact test), Q value = 0.0014

Table S140. Gene #22: 'amp_20q13.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
AMP PEAK 22(20Q13.33) MUTATED	26	12	11	27	5
AMP PEAK 22(20Q13.33) WILD-TYPE	32	37	10	15	19

Figure S140. 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 S141. Gene #23: 'amp_21q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
AMP PEAK 23(21Q21.1) MUTATED	37	4	5	27
AMP PEAK 23(21Q21.1) WILD-TYPE	58	56	34	36

Figure S141. Get High-res Image Gene #23: 'amp_21q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_21q21.1' versus 'METHLYATION_CNMF'

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

Table S142. Gene #23: 'amp_21q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
AMP PEAK 23(21Q21.1) MUTATED	6	13	17	37
AMP PEAK 23(21Q21.1) WILD-TYPE	48	43	55	38

Figure S142. 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 S143. Gene #24: 'amp_xp21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
AMP PEAK 24(XP21.2) MUTATED	52	6	8	31
AMP PEAK 24(XP21.2) WILD-TYPE	43	54	31	32

Figure S143. Get High-res Image Gene #24: 'amp_xp21.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp21.2' versus 'METHLYATION_CNMF'

P value = 0.0338 (Fisher's exact test), Q value = 0.054

Table S144. Gene #24: 'amp_xp21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
AMP PEAK 24(XP21.2) MUTATED	15	17	27	38
AMP PEAK 24(XP21.2) WILD-TYPE	39	39	45	37

Figure S144. Get High-res Image Gene #24: 'amp_xp21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xp21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0488 (Fisher's exact test), Q value = 0.073

Table S145. Gene #24: 'amp_xp21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	47	21	49	46	30	29	33
AMP PEAK 24(XP21.2) MUTATED	26	5	21	13	13	7	12
AMP PEAK 24(XP21.2) WILD-TYPE	21	16	28	33	17	22	21

Figure S145. Get High-res Image Gene #24: 'amp_xp21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_xp21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.04 (Fisher's exact test), Q value = 0.062

Table S146. Gene #24: 'amp_xp21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
AMP PEAK 24(XP21.2) MUTATED	36	11	45	3
AMP PEAK 24(XP21.2) WILD-TYPE	46	26	69	19

Figure S146. Get High-res Image Gene #24: 'amp_xp21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_xp21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00397 (Fisher's exact test), Q value = 0.0094

Table S147. Gene #24: 'amp_xp21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
AMP PEAK 24(XP21.2) MUTATED	27	17	11	20	2
AMP PEAK 24(XP21.2) WILD-TYPE	31	32	10	22	22

Figure S147. 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 S148. Gene #25: 'amp_xq21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
AMP PEAK 25(XQ21.1) MUTATED	33	3	3	7
AMP PEAK 25(XQ21.1) WILD-TYPE	62	57	36	56

Figure S148. Get High-res Image Gene #25: 'amp_xq21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq21.1' versus 'METHLYATION_CNMF'

P value = 0.0178 (Fisher's exact test), Q value = 0.031

Table S149. Gene #25: 'amp_xq21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
AMP PEAK 25(XQ21.1) MUTATED	6	10	8	22
AMP PEAK 25(XQ21.1) WILD-TYPE	48	46	64	53

Figure S149. Get High-res Image Gene #25: 'amp_xq21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xq21.1' versus 'RPPA_CNMF'

P value = 0.0335 (Fisher's exact test), Q value = 0.053

Table S150. Gene #25: 'amp_xq21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
AMP PEAK 25(XQ21.1) MUTATED	15	12	5	10
AMP PEAK 25(XQ21.1) WILD-TYPE	43	33	56	46

Figure S150. Get High-res Image Gene #25: 'amp_xq21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_xq21.1' versus 'MRNASEQ_CNMF'

P value = 0.0413 (Fisher's exact test), Q value = 0.063

Table S151. Gene #25: 'amp_xq21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
AMP PEAK 25(XQ21.1) MUTATED	28	8	10
AMP PEAK 25(XQ21.1) WILD-TYPE	86	69	54

Figure S151. Get High-res Image Gene #25: 'amp_xq21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_xq21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00273 (Fisher's exact test), Q value = 0.0068

Table S152. 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	47	21	49	46	30	29	33
AMP PEAK 25(XQ21.1) MUTATED	16	2	3	7	10	5	3
AMP PEAK 25(XQ21.1) WILD-TYPE	31	19	46	39	20	24	30

Figure S152. Get High-res Image Gene #25: 'amp_xq21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_xq21.1' versus 'MIRSEQ_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 0.029

Table S153. Gene #25: 'amp_xq21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
AMP PEAK 25(XQ21.1) MUTATED	19	15	11
AMP PEAK 25(XQ21.1) WILD-TYPE	86	35	89

Figure S153. Get High-res Image Gene #25: 'amp_xq21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_xq21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0471 (Fisher's exact test), Q value = 0.071

Table S154. Gene #25: 'amp_xq21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
AMP PEAK 25(XQ21.1) MUTATED	11	10	4	6	7
AMP PEAK 25(XQ21.1) WILD-TYPE	47	17	43	17	32

Figure S154. Get High-res Image Gene #25: 'amp_xq21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p36.32' versus 'CN_CNMF'

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

Table S155. Gene #26: 'del_1p36.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 1(1P36.32) MUTATED	21	4	26	18
DEL PEAK 1(1P36.32) WILD-TYPE	74	56	13	45

Figure S155. Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.32' versus 'METHLYATION_CNMF'

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

Table S156. Gene #26: 'del_1p36.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 1(1P36.32) MUTATED	3	11	43	12
DEL PEAK 1(1P36.32) WILD-TYPE	51	45	29	63

Figure S156. 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 S157. Gene #26: 'del_1p36.32' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
DEL PEAK 1(1P36.32) MUTATED	10	5	37	4
DEL PEAK 1(1P36.32) WILD-TYPE	48	40	24	52

Figure S157. 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 S158. 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	35	49	68	22	22
DEL PEAK 1(1P36.32) MUTATED	6	2	6	37	1	4
DEL PEAK 1(1P36.32) WILD-TYPE	18	33	43	31	21	18

Figure S158. 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 S159. Gene #26: 'del_1p36.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
DEL PEAK 1(1P36.32) MUTATED	13	45	10
DEL PEAK 1(1P36.32) WILD-TYPE	101	32	54

Figure S159. 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 S160. 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	47	21	49	46	30	29	33
DEL PEAK 1(1P36.32) MUTATED	8	1	30	7	4	15	3
DEL PEAK 1(1P36.32) WILD-TYPE	39	20	19	39	26	14	30

Figure S160. 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 S161. Gene #26: 'del_1p36.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
DEL PEAK 1(1P36.32) MUTATED	14	6	49
DEL PEAK 1(1P36.32) WILD-TYPE	91	44	51

Figure S161. 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 S162. Gene #26: 'del_1p36.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
DEL PEAK 1(1P36.32) MUTATED	11	3	51	4
DEL PEAK 1(1P36.32) WILD-TYPE	71	34	63	18

Figure S162. Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 3e-04

Table S163. Gene #26: 'del_1p36.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
DEL PEAK 1(1P36.32) MUTATED	8	5	24	8	4
DEL PEAK 1(1P36.32) WILD-TYPE	50	22	23	15	35

Figure S163. 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 = 5e-05 (Fisher's exact test), Q value = 0.00026

Table S164. Gene #26: 'del_1p36.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
DEL PEAK 1(1P36.32) MUTATED	9	26	4	5	5
DEL PEAK 1(1P36.32) WILD-TYPE	49	23	17	37	19

Figure S164. 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 S165. Gene #27: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 2(1Q44) MUTATED	50	1	5	24
DEL PEAK 2(1Q44) WILD-TYPE	45	59	34	39

Figure S165. Get High-res Image Gene #27: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q44' versus 'METHLYATION_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0018

Table S166. Gene #27: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 2(1Q44) MUTATED	20	13	12	35
DEL PEAK 2(1Q44) WILD-TYPE	34	43	60	40

Figure S166. Get High-res Image Gene #27: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1q44' versus 'RPPA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00034

Table S167. 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	35	49	68	22	22
DEL PEAK 2(1Q44) MUTATED	15	10	25	11	6	5
DEL PEAK 2(1Q44) WILD-TYPE	9	25	24	57	16	17

Figure S167. Get High-res Image Gene #27: 'del_1q44' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_1q44' versus 'MRNASEQ_CNMF'

P value = 0.00093 (Fisher's exact test), Q value = 0.0028

Table S168. Gene #27: 'del_1q44' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
DEL PEAK 2(1Q44) MUTATED	49	14	17
DEL PEAK 2(1Q44) WILD-TYPE	65	63	47

Figure S168. Get High-res Image Gene #27: 'del_1q44' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1q44' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00085

Table S169. 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	47	21	49	46	30	29	33
DEL PEAK 2(1Q44) MUTATED	27	6	10	10	12	3	12
DEL PEAK 2(1Q44) WILD-TYPE	20	15	39	36	18	26	21

Figure S169. Get High-res Image Gene #27: 'del_1q44' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1q44' versus 'MIRSEQ_CNMF'

P value = 0.00175 (Fisher's exact test), Q value = 0.0047

Table S170. Gene #27: 'del_1q44' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
DEL PEAK 2(1Q44) MUTATED	34	25	21
DEL PEAK 2(1Q44) WILD-TYPE	71	25	79

Figure S170. Get High-res Image Gene #27: 'del_1q44' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1q44' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00694 (Fisher's exact test), Q value = 0.014

Table S171. Gene #27: 'del_1q44' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
DEL PEAK 2(1Q44) MUTATED	36	11	31	2
DEL PEAK 2(1Q44) WILD-TYPE	46	26	83	20

Figure S171. Get High-res Image Gene #27: 'del_1q44' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1q44' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00124 (Fisher's exact test), Q value = 0.0036

Table S172. Gene #27: 'del_1q44' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
DEL PEAK 2(1Q44) MUTATED	18	18	9	7	16
DEL PEAK 2(1Q44) WILD-TYPE	40	9	38	16	23

Figure S172. Get High-res Image Gene #27: 'del_1q44' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1q44' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00048 (Fisher's exact test), Q value = 0.0017

Table S173. Gene #27: 'del_1q44' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
DEL PEAK 2(1Q44) MUTATED	26	10	10	20	2
DEL PEAK 2(1Q44) WILD-TYPE	32	39	11	22	22

Figure S173. 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 S174. Gene #28: 'del_2p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 3(2P25.3) MUTATED	39	2	17	36
DEL PEAK 3(2P25.3) WILD-TYPE	56	58	22	27

Figure S174. Get High-res Image Gene #28: 'del_2p25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2p25.3' versus 'METHLYATION_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00095

Table S175. Gene #28: 'del_2p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 3(2P25.3) MUTATED	12	14	40	28
DEL PEAK 3(2P25.3) WILD-TYPE	42	42	32	47

Figure S175. Get High-res Image Gene #28: 'del_2p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2p25.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00385 (Fisher's exact test), Q value = 0.0092

Table S176. 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	35	49	68	22	22
DEL PEAK 3(2P25.3) MUTATED	12	7	18	34	6	3
DEL PEAK 3(2P25.3) WILD-TYPE	12	28	31	34	16	19

Figure S176. Get High-res Image Gene #28: 'del_2p25.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_2p25.3' versus 'MRNASEQ_CNMF'

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

Table S177. Gene #28: 'del_2p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
DEL PEAK 3(2P25.3) MUTATED	41	42	10
DEL PEAK 3(2P25.3) WILD-TYPE	73	35	54

Figure S177. Get High-res Image Gene #28: 'del_2p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00128 (Fisher's exact test), Q value = 0.0036

Table S178. 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	47	21	49	46	30	29	33
DEL PEAK 3(2P25.3) MUTATED	20	5	28	8	9	14	9
DEL PEAK 3(2P25.3) WILD-TYPE	27	16	21	38	21	15	24

Figure S178. Get High-res Image Gene #28: 'del_2p25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2p25.3' versus 'MIRSEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00085

Table S179. Gene #28: 'del_2p25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
DEL PEAK 3(2P25.3) MUTATED	23	22	48
DEL PEAK 3(2P25.3) WILD-TYPE	82	28	52

Figure S179. Get High-res Image Gene #28: 'del_2p25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2p25.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S180. Gene #28: 'del_2p25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
DEL PEAK 3(2P25.3) MUTATED	27	10	56	0
DEL PEAK 3(2P25.3) WILD-TYPE	55	27	58	22

Figure S180. Get High-res Image Gene #28: 'del_2p25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2p25.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00204 (Fisher's exact test), Q value = 0.0053

Table S181. Gene #28: 'del_2p25.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
DEL PEAK 3(2P25.3) MUTATED	12	13	27	7	14
DEL PEAK 3(2P25.3) WILD-TYPE	46	14	20	16	25

Figure S181. 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 = 3e-05 (Fisher's exact test), Q value = 0.00016

Table S182. Gene #28: 'del_2p25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
DEL PEAK 3(2P25.3) MUTATED	17	29	9	17	1
DEL PEAK 3(2P25.3) WILD-TYPE	41	20	12	25	23

Figure S182. 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 S183. Gene #29: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 4(2Q37.3) MUTATED	53	3	6	46
DEL PEAK 4(2Q37.3) WILD-TYPE	42	57	33	17

Figure S183. Get High-res Image Gene #29: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 0.00146 (Fisher's exact test), Q value = 0.004

Table S184. Gene #29: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 4(2Q37.3) MUTATED	16	16	33	43
DEL PEAK 4(2Q37.3) WILD-TYPE	38	40	39	32

Figure S184. Get High-res Image Gene #29: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0394 (Fisher's exact test), Q value = 0.061

Table S185. 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	35	49	68	22	22
DEL PEAK 4(2Q37.3) MUTATED	15	11	27	29	7	6
DEL PEAK 4(2Q37.3) WILD-TYPE	9	24	22	39	15	16

Figure S185. Get High-res Image Gene #29: 'del_2q37.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 0.0389 (Fisher's exact test), Q value = 0.061

Table S186. Gene #29: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
DEL PEAK 4(2Q37.3) MUTATED	53	35	18
DEL PEAK 4(2Q37.3) WILD-TYPE	61	42	46

Figure S186. Get High-res Image Gene #29: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00082 (Fisher's exact test), Q value = 0.0025

Table S187. 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	47	21	49	46	30	29	33
DEL PEAK 4(2Q37.3) MUTATED	27	6	16	10	13	19	15
DEL PEAK 4(2Q37.3) WILD-TYPE	20	15	33	36	17	10	18

Figure S187. Get High-res Image Gene #29: 'del_2q37.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00607 (Fisher's exact test), Q value = 0.013

Table S188. Gene #29: 'del_2q37.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
DEL PEAK 4(2Q37.3) MUTATED	39	11	54	3
DEL PEAK 4(2Q37.3) WILD-TYPE	43	26	60	19

Figure S188. Get High-res Image Gene #29: 'del_2q37.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0337 (Fisher's exact test), Q value = 0.054

Table S189. Gene #29: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
DEL PEAK 4(2Q37.3) MUTATED	17	15	19	14	20
DEL PEAK 4(2Q37.3) WILD-TYPE	41	12	28	9	19

Figure S189. Get High-res Image Gene #29: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_2q37.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0123 (Fisher's exact test), Q value = 0.023

Table S190. Gene #29: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
DEL PEAK 4(2Q37.3) MUTATED	24	22	14	21	4
DEL PEAK 4(2Q37.3) WILD-TYPE	34	27	7	21	20

Figure S190. 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 S191. Gene #30: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 5(2Q37.3) MUTATED	56	3	6	45
DEL PEAK 5(2Q37.3) WILD-TYPE	39	57	33	18

Figure S191. Get High-res Image Gene #30: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 0.00857 (Fisher's exact test), Q value = 0.017

Table S192. Gene #30: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 5(2Q37.3) MUTATED	15	20	33	42
DEL PEAK 5(2Q37.3) WILD-TYPE	39	36	39	33

Figure S192. Get High-res Image Gene #30: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00409 (Fisher's exact test), Q value = 0.0096

Table S193. 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	35	49	68	22	22
DEL PEAK 5(2Q37.3) MUTATED	17	11	27	29	7	5
DEL PEAK 5(2Q37.3) WILD-TYPE	7	24	22	39	15	17

Figure S193. Get High-res Image Gene #30: 'del_2q37.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 0.0255 (Fisher's exact test), Q value = 0.043

Table S194. Gene #30: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
DEL PEAK 5(2Q37.3) MUTATED	55	35	18
DEL PEAK 5(2Q37.3) WILD-TYPE	59	42	46

Figure S194. Get High-res Image Gene #30: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00127 (Fisher's exact test), Q value = 0.0036

Table S195. 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	47	21	49	46	30	29	33
DEL PEAK 5(2Q37.3) MUTATED	29	6	16	12	13	19	13
DEL PEAK 5(2Q37.3) WILD-TYPE	18	15	33	34	17	10	20

Figure S195. Get High-res Image Gene #30: 'del_2q37.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0247 (Fisher's exact test), Q value = 0.042

Table S196. Gene #30: 'del_2q37.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
DEL PEAK 5(2Q37.3) MUTATED	41	12	52	4
DEL PEAK 5(2Q37.3) WILD-TYPE	41	25	62	18

Figure S196. Get High-res Image Gene #30: 'del_2q37.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p21.31' versus 'CN_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.02

Table S197. Gene #31: 'del_3p21.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 6(3P21.31) MUTATED	35	11	5	14
DEL PEAK 6(3P21.31) WILD-TYPE	60	49	34	49

Figure S197. 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 S198. Gene #31: 'del_3p21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 6(3P21.31) MUTATED	13	22	4	26
DEL PEAK 6(3P21.31) WILD-TYPE	41	34	68	49

Figure S198. Get High-res Image Gene #31: 'del_3p21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p21.31' versus 'RPPA_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0021

Table S199. Gene #31: 'del_3p21.31' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
DEL PEAK 6(3P21.31) MUTATED	16	20	6	17
DEL PEAK 6(3P21.31) WILD-TYPE	42	25	55	39

Figure S199. Get High-res Image Gene #31: 'del_3p21.31' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_3p21.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00056

Table S200. 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	35	49	68	22	22
DEL PEAK 6(3P21.31) MUTATED	10	12	14	5	10	8
DEL PEAK 6(3P21.31) WILD-TYPE	14	23	35	63	12	14

Figure S200. 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 S201. Gene #31: 'del_3p21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
DEL PEAK 6(3P21.31) MUTATED	34	5	26
DEL PEAK 6(3P21.31) WILD-TYPE	80	72	38

Figure S201. 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 S202. 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	47	21	49	46	30	29	33
DEL PEAK 6(3P21.31) MUTATED	23	5	2	19	6	3	7
DEL PEAK 6(3P21.31) WILD-TYPE	24	16	47	27	24	26	26

Figure S202. Get High-res Image Gene #31: 'del_3p21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00045

Table S203. Gene #31: 'del_3p21.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
DEL PEAK 6(3P21.31) MUTATED	37	17	11
DEL PEAK 6(3P21.31) WILD-TYPE	68	33	89

Figure S203. Get High-res Image Gene #31: 'del_3p21.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00802 (Fisher's exact test), Q value = 0.016

Table S204. Gene #31: 'del_3p21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
DEL PEAK 6(3P21.31) MUTATED	29	10	18	8
DEL PEAK 6(3P21.31) WILD-TYPE	53	27	96	14

Figure S204. Get High-res Image Gene #31: 'del_3p21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_MATURE_CNMF'

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

Table S205. Gene #31: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
DEL PEAK 6(3P21.31) MUTATED	18	15	2	9	11
DEL PEAK 6(3P21.31) WILD-TYPE	40	12	45	14	28

Figure S205. 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 = 9e-05 (Fisher's exact test), Q value = 0.00041

Table S206. Gene #31: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
DEL PEAK 6(3P21.31) MUTATED	20	2	8	15	10
DEL PEAK 6(3P21.31) WILD-TYPE	38	47	13	27	14

Figure S206. Get High-res Image Gene #31: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q13.31' versus 'CN_CNMF'

P value = 0.0063 (Fisher's exact test), Q value = 0.014

Table S207. Gene #32: 'del_3q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 7(3Q13.31) MUTATED	28	5	9	9
DEL PEAK 7(3Q13.31) WILD-TYPE	67	55	30	54

Figure S207. Get High-res Image Gene #32: 'del_3q13.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q13.31' versus 'METHLYATION_CNMF'

P value = 0.00161 (Fisher's exact test), Q value = 0.0044

Table S208. Gene #32: 'del_3q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 7(3Q13.31) MUTATED	7	15	6	23
DEL PEAK 7(3Q13.31) WILD-TYPE	47	41	66	52

Figure S208. Get High-res Image Gene #32: 'del_3q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3q13.31' versus 'RPPA_CNMF'

P value = 0.00078 (Fisher's exact test), Q value = 0.0024

Table S209. Gene #32: 'del_3q13.31' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
DEL PEAK 7(3Q13.31) MUTATED	17	16	7	5
DEL PEAK 7(3Q13.31) WILD-TYPE	41	29	54	51

Figure S209. Get High-res Image Gene #32: 'del_3q13.31' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_3q13.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.025 (Fisher's exact test), Q value = 0.042

Table S210. 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	35	49	68	22	22
DEL PEAK 7(3Q13.31) MUTATED	5	8	12	6	5	9
DEL PEAK 7(3Q13.31) WILD-TYPE	19	27	37	62	17	13

Figure S210. Get High-res Image Gene #32: 'del_3q13.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_3q13.31' versus 'MRNASEQ_CNMF'

P value = 0.00525 (Fisher's exact test), Q value = 0.012

Table S211. Gene #32: 'del_3q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
DEL PEAK 7(3Q13.31) MUTATED	25	7	19
DEL PEAK 7(3Q13.31) WILD-TYPE	89	70	45

Figure S211. Get High-res Image Gene #32: 'del_3q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00652 (Fisher's exact test), Q value = 0.014

Table S212. 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	47	21	49	46	30	29	33
DEL PEAK 7(3Q13.31) MUTATED	13	2	3	16	8	4	5
DEL PEAK 7(3Q13.31) WILD-TYPE	34	19	46	30	22	25	28

Figure S212. Get High-res Image Gene #32: 'del_3q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3q13.31' versus 'MIRSEQ_CNMF'

P value = 0.00994 (Fisher's exact test), Q value = 0.02

Table S213. Gene #32: 'del_3q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
DEL PEAK 7(3Q13.31) MUTATED	29	10	11
DEL PEAK 7(3Q13.31) WILD-TYPE	76	40	89

Figure S213. Get High-res Image Gene #32: 'del_3q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.018 (Fisher's exact test), Q value = 0.032

Table S214. Gene #32: 'del_3q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
DEL PEAK 7(3Q13.31) MUTATED	24	6	14	6
DEL PEAK 7(3Q13.31) WILD-TYPE	58	31	100	16

Figure S214. Get High-res Image Gene #32: 'del_3q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3q13.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00676 (Fisher's exact test), Q value = 0.014

Table S215. Gene #32: 'del_3q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
DEL PEAK 7(3Q13.31) MUTATED	13	12	4	3	10
DEL PEAK 7(3Q13.31) WILD-TYPE	45	15	43	20	29

Figure S215. 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 = 0.0417 (Fisher's exact test), Q value = 0.064

Table S216. Gene #32: 'del_3q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
DEL PEAK 7(3Q13.31) MUTATED	16	4	3	12	7
DEL PEAK 7(3Q13.31) WILD-TYPE	42	45	18	30	17

Figure S216. Get High-res Image Gene #32: 'del_3q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q29' versus 'CN_CNMF'

P value = 0.00669 (Fisher's exact test), Q value = 0.014

Table S217. Gene #33: 'del_3q29' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 8(3Q29) MUTATED	29	5	6	14
DEL PEAK 8(3Q29) WILD-TYPE	66	55	33	49

Figure S217. Get High-res Image Gene #33: 'del_3q29' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q29' versus 'METHLYATION_CNMF'

P value = 0.0401 (Fisher's exact test), Q value = 0.062

Table S218. Gene #33: 'del_3q29' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 8(3Q29) MUTATED	6	13	12	23
DEL PEAK 8(3Q29) WILD-TYPE	48	43	60	52

Figure S218. Get High-res Image Gene #33: 'del_3q29' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3q29' versus 'RPPA_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.021

Table S219. Gene #33: 'del_3q29' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
DEL PEAK 8(3Q29) MUTATED	16	15	11	5
DEL PEAK 8(3Q29) WILD-TYPE	42	30	50	51

Figure S219. Get High-res Image Gene #33: 'del_3q29' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_3q29' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0379 (Fisher's exact test), Q value = 0.06

Table S220. Gene #33: 'del_3q29' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
DEL PEAK 8(3Q29) MUTATED	26	5	18	4
DEL PEAK 8(3Q29) WILD-TYPE	56	32	96	18

Figure S220. 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 S221. Gene #34: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 9(4Q35.1) MUTATED	47	7	9	31
DEL PEAK 9(4Q35.1) WILD-TYPE	48	53	30	32

Figure S221. Get High-res Image Gene #34: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q35.1' versus 'METHLYATION_CNMF'

P value = 0.00554 (Fisher's exact test), Q value = 0.012

Table S222. Gene #34: 'del_4q35.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 9(4Q35.1) MUTATED	15	16	23	40
DEL PEAK 9(4Q35.1) WILD-TYPE	39	40	49	35

Figure S222. Get High-res Image Gene #34: 'del_4q35.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q35.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 0.025

Table S223. 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	35	49	68	22	22
DEL PEAK 9(4Q35.1) MUTATED	10	11	29	19	10	6
DEL PEAK 9(4Q35.1) WILD-TYPE	14	24	20	49	12	16

Figure S223. Get High-res Image Gene #34: 'del_4q35.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_4q35.1' versus 'MRNASEQ_CNMF'

P value = 0.015 (Fisher's exact test), Q value = 0.027

Table S224. Gene #34: 'del_4q35.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
DEL PEAK 9(4Q35.1) MUTATED	53	24	17
DEL PEAK 9(4Q35.1) WILD-TYPE	61	53	47

Figure S224. Get High-res Image Gene #34: 'del_4q35.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.029 (Fisher's exact test), Q value = 0.047

Table S225. Gene #34: 'del_4q35.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	47	21	49	46	30	29	33
DEL PEAK 9(4Q35.1) MUTATED	24	4	15	13	16	8	14
DEL PEAK 9(4Q35.1) WILD-TYPE	23	17	34	33	14	21	19

Figure S225. Get High-res Image Gene #34: 'del_4q35.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5p15.33' versus 'METHLYATION_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.026

Table S226. Gene #35: 'del_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 10(5P15.33) MUTATED	8	6	3	16
DEL PEAK 10(5P15.33) WILD-TYPE	46	50	69	59

Figure S226. Get High-res Image Gene #35: 'del_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5p15.33' versus 'RPPA_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.026

Table S227. Gene #35: 'del_5p15.33' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
DEL PEAK 10(5P15.33) MUTATED	6	9	3	13
DEL PEAK 10(5P15.33) WILD-TYPE	52	36	58	43

Figure S227. Get High-res Image Gene #35: 'del_5p15.33' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_5p15.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0018

Table S228. 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	35	49	68	22	22
DEL PEAK 10(5P15.33) MUTATED	2	5	15	2	5	2
DEL PEAK 10(5P15.33) WILD-TYPE	22	30	34	66	17	20

Figure S228. Get High-res Image Gene #35: 'del_5p15.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_5p15.33' versus 'MRNASEQ_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.025

Table S229. Gene #35: 'del_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
DEL PEAK 10(5P15.33) MUTATED	18	3	11
DEL PEAK 10(5P15.33) WILD-TYPE	96	74	53

Figure S229. Get High-res Image Gene #35: 'del_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00154 (Fisher's exact test), Q value = 0.0042

Table S230. 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	47	21	49	46	30	29	33
DEL PEAK 10(5P15.33) MUTATED	4	2	3	5	8	0	10
DEL PEAK 10(5P15.33) WILD-TYPE	43	19	46	41	22	29	23

Figure S230. Get High-res Image Gene #35: 'del_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 0.04

Table S231. Gene #35: 'del_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
DEL PEAK 10(5P15.33) MUTATED	6	4	2	4	11
DEL PEAK 10(5P15.33) WILD-TYPE	52	23	45	19	28

Figure S231. Get High-res Image Gene #35: 'del_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0253 (Fisher's exact test), Q value = 0.042

Table S232. Gene #35: 'del_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
DEL PEAK 10(5P15.33) MUTATED	10	2	5	9	1
DEL PEAK 10(5P15.33) WILD-TYPE	48	47	16	33	23

Figure S232. Get High-res Image Gene #35: 'del_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

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

Table S233. Gene #36: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 11(6P25.3) MUTATED	31	4	20	26
DEL PEAK 11(6P25.3) WILD-TYPE	64	56	19	37

Figure S233. Get High-res Image Gene #36: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00068

Table S234. Gene #36: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 11(6P25.3) MUTATED	9	11	36	25
DEL PEAK 11(6P25.3) WILD-TYPE	45	45	36	50

Figure S234. Get High-res Image Gene #36: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p25.3' versus 'RPPA_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0018

Table S235. Gene #36: 'del_6p25.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
DEL PEAK 11(6P25.3) MUTATED	7	13	28	20
DEL PEAK 11(6P25.3) WILD-TYPE	51	32	33	36

Figure S235. Get High-res Image Gene #36: 'del_6p25.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_6p25.3' versus 'MRNASEQ_CNMF'

P value = 0.00078 (Fisher's exact test), Q value = 0.0024

Table S236. Gene #36: 'del_6p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
DEL PEAK 11(6P25.3) MUTATED	28	37	14
DEL PEAK 11(6P25.3) WILD-TYPE	86	40	50

Figure S236. Get High-res Image Gene #36: 'del_6p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00158 (Fisher's exact test), Q value = 0.0043

Table S237. 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	47	21	49	46	30	29	33
DEL PEAK 11(6P25.3) MUTATED	7	5	26	9	9	11	12
DEL PEAK 11(6P25.3) WILD-TYPE	40	16	23	37	21	18	21

Figure S237. Get High-res Image Gene #36: 'del_6p25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6p25.3' versus 'MIRSEQ_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.024

Table S238. Gene #36: 'del_6p25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
DEL PEAK 11(6P25.3) MUTATED	24	15	42
DEL PEAK 11(6P25.3) WILD-TYPE	81	35	58

Figure S238. Get High-res Image Gene #36: 'del_6p25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0255 (Fisher's exact test), Q value = 0.043

Table S239. Gene #36: 'del_6p25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
DEL PEAK 11(6P25.3) MUTATED	20	12	46	3
DEL PEAK 11(6P25.3) WILD-TYPE	62	25	68	19

Figure S239. Get High-res Image Gene #36: 'del_6p25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q14.1' versus 'CN_CNMF'

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

Table S240. Gene #37: 'del_6q14.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 12(6Q14.1) MUTATED	40	3	14	21
DEL PEAK 12(6Q14.1) WILD-TYPE	55	57	25	42

Figure S240. Get High-res Image Gene #37: 'del_6q14.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q14.1' versus 'METHLYATION_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.033

Table S241. Gene #37: 'del_6q14.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 12(6Q14.1) MUTATED	11	12	23	32
DEL PEAK 12(6Q14.1) WILD-TYPE	43	44	49	43

Figure S241. Get High-res Image Gene #37: 'del_6q14.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q14.1' versus 'RPPA_CNMF'

P value = 0.00646 (Fisher's exact test), Q value = 0.014

Table S242. Gene #37: 'del_6q14.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
DEL PEAK 12(6Q14.1) MUTATED	10	22	16	17
DEL PEAK 12(6Q14.1) WILD-TYPE	48	23	45	39

Figure S242. Get High-res Image Gene #37: 'del_6q14.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_6q14.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0272 (Fisher's exact test), Q value = 0.045

Table S243. 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	35	49	68	22	22
DEL PEAK 12(6Q14.1) MUTATED	4	10	24	15	5	7
DEL PEAK 12(6Q14.1) WILD-TYPE	20	25	25	53	17	15

Figure S243. 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 S244. Gene #38: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 13(7Q36.3) MUTATED	41	3	6	21
DEL PEAK 13(7Q36.3) WILD-TYPE	54	57	33	42

Figure S244. Get High-res Image Gene #38: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q36.3' versus 'METHLYATION_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.027

Table S245. Gene #38: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 13(7Q36.3) MUTATED	8	12	22	29
DEL PEAK 13(7Q36.3) WILD-TYPE	46	44	50	46

Figure S245. Get High-res Image Gene #38: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q36.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0385 (Fisher's exact test), Q value = 0.06

Table S246. Gene #38: 'del_7q36.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	35	49	68	22	22
DEL PEAK 13(7Q36.3) MUTATED	5	10	22	17	5	2
DEL PEAK 13(7Q36.3) WILD-TYPE	19	25	27	51	17	20

Figure S246. Get High-res Image Gene #38: 'del_7q36.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_7q36.3' versus 'MIRSEQ_CNMF'

P value = 0.0489 (Fisher's exact test), Q value = 0.073

Table S247. Gene #38: 'del_7q36.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
DEL PEAK 13(7Q36.3) MUTATED	21	19	30
DEL PEAK 13(7Q36.3) WILD-TYPE	84	31	70

Figure S247. Get High-res Image Gene #38: 'del_7q36.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_7q36.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0058 (Fisher's exact test), Q value = 0.013

Table S248. Gene #38: 'del_7q36.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
DEL PEAK 13(7Q36.3) MUTATED	22	11	37	0
DEL PEAK 13(7Q36.3) WILD-TYPE	60	26	77	22

Figure S248. Get High-res Image Gene #38: 'del_7q36.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.3' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00016

Table S249. Gene #39: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 14(8P23.3) MUTATED	43	6	7	25
DEL PEAK 14(8P23.3) WILD-TYPE	52	54	32	38

Figure S249. 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 S250. Gene #39: 'del_8p23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 14(8P23.3) MUTATED	13	16	11	41
DEL PEAK 14(8P23.3) WILD-TYPE	41	40	61	34

Figure S250. Get High-res Image Gene #39: 'del_8p23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.3' versus 'RPPA_CNMF'

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

Table S251. Gene #39: 'del_8p23.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
DEL PEAK 14(8P23.3) MUTATED	20	23	9	22
DEL PEAK 14(8P23.3) WILD-TYPE	38	22	52	34

Figure S251. Get High-res Image Gene #39: 'del_8p23.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_8p23.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00076 (Fisher's exact test), Q value = 0.0024

Table S252. 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	35	49	68	22	22
DEL PEAK 14(8P23.3) MUTATED	13	8	26	13	8	6
DEL PEAK 14(8P23.3) WILD-TYPE	11	27	23	55	14	16

Figure S252. 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 = 0.00034

Table S253. Gene #39: 'del_8p23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
DEL PEAK 14(8P23.3) MUTATED	51	12	17
DEL PEAK 14(8P23.3) WILD-TYPE	63	65	47

Figure S253. Get High-res Image Gene #39: 'del_8p23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p23.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S254. 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	47	21	49	46	30	29	33
DEL PEAK 14(8P23.3) MUTATED	23	6	6	10	14	7	14
DEL PEAK 14(8P23.3) WILD-TYPE	24	15	43	36	16	22	19

Figure S254. Get High-res Image Gene #39: 'del_8p23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.3' versus 'MIRSEQ_CNMF'

P value = 0.00632 (Fisher's exact test), Q value = 0.014

Table S255. Gene #39: 'del_8p23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
DEL PEAK 14(8P23.3) MUTATED	38	21	20
DEL PEAK 14(8P23.3) WILD-TYPE	67	29	80

Figure S255. Get High-res Image Gene #39: 'del_8p23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00416 (Fisher's exact test), Q value = 0.0098

Table S256. Gene #39: 'del_8p23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
DEL PEAK 14(8P23.3) MUTATED	36	14	25	4
DEL PEAK 14(8P23.3) WILD-TYPE	46	23	89	18

Figure S256. Get High-res Image Gene #39: 'del_8p23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.3' versus 'MIRSEQ_MATURE_CNMF'

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

Table S257. Gene #39: 'del_8p23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
DEL PEAK 14(8P23.3) MUTATED	17	16	6	8	17
DEL PEAK 14(8P23.3) WILD-TYPE	41	11	41	15	22

Figure S257. 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 = 0.00011 (Fisher's exact test), Q value = 0.00048

Table S258. Gene #39: 'del_8p23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
DEL PEAK 14(8P23.3) MUTATED	29	5	8	17	5
DEL PEAK 14(8P23.3) WILD-TYPE	29	44	13	25	19

Figure S258. 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 S259. Gene #40: 'del_9p24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 15(9P24.3) MUTATED	59	11	17	13
DEL PEAK 15(9P24.3) WILD-TYPE	36	49	22	50

Figure S259. Get High-res Image Gene #40: 'del_9p24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p24.3' versus 'RPPA_CNMF'

P value = 0.0327 (Fisher's exact test), Q value = 0.052

Table S260. Gene #40: 'del_9p24.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
DEL PEAK 15(9P24.3) MUTATED	17	22	20	29
DEL PEAK 15(9P24.3) WILD-TYPE	41	23	41	27

Figure S260. Get High-res Image Gene #40: 'del_9p24.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_9p24.3' versus 'MIRSEQ_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.021

Table S261. Gene #40: 'del_9p24.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
DEL PEAK 15(9P24.3) MUTATED	38	29	33
DEL PEAK 15(9P24.3) WILD-TYPE	67	21	67

Figure S261. Get High-res Image Gene #40: 'del_9p24.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'CN_CNMF'

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

Table S262. Gene #41: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 16(9P21.3) MUTATED	74	12	18	10
DEL PEAK 16(9P21.3) WILD-TYPE	21	48	21	53

Figure S262. Get High-res Image Gene #41: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 0.00311 (Fisher's exact test), Q value = 0.0077

Table S263. Gene #41: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 16(9P21.3) MUTATED	26	23	21	44
DEL PEAK 16(9P21.3) WILD-TYPE	28	33	51	31

Figure S263. Get High-res Image Gene #41: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

P value = 0.00562 (Fisher's exact test), Q value = 0.012

Table S264. Gene #41: 'del_9p21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
DEL PEAK 16(9P21.3) MUTATED	23	26	21	35
DEL PEAK 16(9P21.3) WILD-TYPE	35	19	40	21

Figure S264. Get High-res Image Gene #41: 'del_9p21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.0024

Table S265. 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	35	49	68	22	22
DEL PEAK 16(9P21.3) MUTATED	7	17	34	22	12	13
DEL PEAK 16(9P21.3) WILD-TYPE	17	18	15	46	10	9

Figure S265. Get High-res Image Gene #41: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 0.00455 (Fisher's exact test), Q value = 0.01

Table S266. Gene #41: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
DEL PEAK 16(9P21.3) MUTATED	58	22	32
DEL PEAK 16(9P21.3) WILD-TYPE	56	55	32

Figure S266. Get High-res Image Gene #41: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00487 (Fisher's exact test), Q value = 0.011

Table S267. 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	47	21	49	46	30	29	33
DEL PEAK 16(9P21.3) MUTATED	24	7	17	24	19	5	16
DEL PEAK 16(9P21.3) WILD-TYPE	23	14	32	22	11	24	17

Figure S267. Get High-res Image Gene #41: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 0.00151 (Fisher's exact test), Q value = 0.0042

Table S268. Gene #41: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
DEL PEAK 16(9P21.3) MUTATED	45	33	35
DEL PEAK 16(9P21.3) WILD-TYPE	60	17	65

Figure S268. Get High-res Image Gene #41: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0012

Table S269. Gene #41: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
DEL PEAK 16(9P21.3) MUTATED	25	17	13	9	28
DEL PEAK 16(9P21.3) WILD-TYPE	33	10	34	14	11

Figure S269. 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 = 0.00129 (Fisher's exact test), Q value = 0.0036

Table S270. Gene #41: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
DEL PEAK 16(9P21.3) MUTATED	30	12	14	26	10
DEL PEAK 16(9P21.3) WILD-TYPE	28	37	7	16	14

Figure S270. Get High-res Image Gene #41: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q34.3' versus 'CN_CNMF'

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

Table S271. Gene #42: 'del_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 17(9Q34.3) MUTATED	27	2	9	23
DEL PEAK 17(9Q34.3) WILD-TYPE	68	58	30	40

Figure S271. Get High-res Image Gene #42: 'del_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q34.3' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00021

Table S272. Gene #42: 'del_9q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 17(9Q34.3) MUTATED	3	8	26	24
DEL PEAK 17(9Q34.3) WILD-TYPE	51	48	46	51

Figure S272. Get High-res Image Gene #42: 'del_9q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9q34.3' versus 'RPPA_CNMF'

P value = 0.0195 (Fisher's exact test), Q value = 0.034

Table S273. Gene #42: 'del_9q34.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
DEL PEAK 17(9Q34.3) MUTATED	8	13	22	10
DEL PEAK 17(9Q34.3) WILD-TYPE	50	32	39	46

Figure S273. Get High-res Image Gene #42: 'del_9q34.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_9q34.3' versus 'MRNASEQ_CNMF'

P value = 0.0425 (Fisher's exact test), Q value = 0.065

Table S274. Gene #42: 'del_9q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
DEL PEAK 17(9Q34.3) MUTATED	21	26	13
DEL PEAK 17(9Q34.3) WILD-TYPE	93	51	51

Figure S274. Get High-res Image Gene #42: 'del_9q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9q34.3' versus 'MIRSEQ_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.023

Table S275. Gene #42: 'del_9q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
DEL PEAK 17(9Q34.3) MUTATED	18	9	34
DEL PEAK 17(9Q34.3) WILD-TYPE	87	41	66

Figure S275. Get High-res Image Gene #42: 'del_9q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00293 (Fisher's exact test), Q value = 0.0073

Table S276. Gene #42: 'del_9q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
DEL PEAK 17(9Q34.3) MUTATED	14	3	39	5
DEL PEAK 17(9Q34.3) WILD-TYPE	68	34	75	17

Figure S276. Get High-res Image Gene #42: 'del_9q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0402 (Fisher's exact test), Q value = 0.062

Table S277. Gene #42: 'del_9q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
DEL PEAK 17(9Q34.3) MUTATED	9	5	14	11	9
DEL PEAK 17(9Q34.3) WILD-TYPE	49	22	33	12	30

Figure S277. Get High-res Image Gene #42: 'del_9q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0221 (Fisher's exact test), Q value = 0.038

Table S278. Gene #42: 'del_9q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
DEL PEAK 17(9Q34.3) MUTATED	8	18	8	7	7
DEL PEAK 17(9Q34.3) WILD-TYPE	50	31	13	35	17

Figure S278. Get High-res Image Gene #42: 'del_9q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

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

Table S279. Gene #43: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 18(10P15.3) MUTATED	60	6	27	35
DEL PEAK 18(10P15.3) WILD-TYPE	35	54	12	28

Figure S279. Get High-res Image Gene #43: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 0.00346 (Fisher's exact test), Q value = 0.0084

Table S280. Gene #43: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 18(10P15.3) MUTATED	17	24	43	44
DEL PEAK 18(10P15.3) WILD-TYPE	37	32	29	31

Figure S280. Get High-res Image Gene #43: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p15.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.00095

Table S281. 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	35	49	68	22	22
DEL PEAK 18(10P15.3) MUTATED	15	8	34	34	7	13
DEL PEAK 18(10P15.3) WILD-TYPE	9	27	15	34	15	9

Figure S281. Get High-res Image Gene #43: 'del_10p15.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00925 (Fisher's exact test), Q value = 0.018

Table S282. 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	47	21	49	46	30	29	33
DEL PEAK 18(10P15.3) MUTATED	26	5	34	20	13	11	18
DEL PEAK 18(10P15.3) WILD-TYPE	21	16	15	26	17	18	15

Figure S282. Get High-res Image Gene #43: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.033

Table S283. Gene #43: 'del_10p15.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
DEL PEAK 18(10P15.3) MUTATED	43	12	65	7
DEL PEAK 18(10P15.3) WILD-TYPE	39	25	49	15

Figure S283. Get High-res Image Gene #43: 'del_10p15.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

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

Table S284. Gene #44: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 19(10Q23.31) MUTATED	50	4	32	52
DEL PEAK 19(10Q23.31) WILD-TYPE	45	56	7	11

Figure S284. 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 S285. Gene #44: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 19(10Q23.31) MUTATED	14	15	58	51
DEL PEAK 19(10Q23.31) WILD-TYPE	40	41	14	24

Figure S285. 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 S286. Gene #44: 'del_10q23.31' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
DEL PEAK 19(10Q23.31) MUTATED	17	25	48	27
DEL PEAK 19(10Q23.31) WILD-TYPE	41	20	13	29

Figure S286. Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_10q23.31' versus 'RPPA_CHIERARCHICAL'

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

Table S287. 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	35	49	68	22	22
DEL PEAK 19(10Q23.31) MUTATED	13	7	35	47	9	6
DEL PEAK 19(10Q23.31) WILD-TYPE	11	28	14	21	13	16

Figure S287. 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 S288. Gene #44: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
DEL PEAK 19(10Q23.31) MUTATED	56	61	20
DEL PEAK 19(10Q23.31) WILD-TYPE	58	16	44

Figure S288. 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 S289. 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	47	21	49	46	30	29	33
DEL PEAK 19(10Q23.31) MUTATED	25	7	46	10	13	15	21
DEL PEAK 19(10Q23.31) WILD-TYPE	22	14	3	36	17	14	12

Figure S289. Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00021

Table S290. Gene #44: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
DEL PEAK 19(10Q23.31) MUTATED	40	28	69
DEL PEAK 19(10Q23.31) WILD-TYPE	65	22	31

Figure S290. Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S291. Gene #44: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
DEL PEAK 19(10Q23.31) MUTATED	38	14	81	4
DEL PEAK 19(10Q23.31) WILD-TYPE	44	23	33	18

Figure S291. Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0014

Table S292. Gene #44: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
DEL PEAK 19(10Q23.31) MUTATED	20	15	36	15	20
DEL PEAK 19(10Q23.31) WILD-TYPE	38	12	11	8	19

Figure S292. 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 = 0.00025 (Fisher's exact test), Q value = 0.00099

Table S293. Gene #44: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
DEL PEAK 19(10Q23.31) MUTATED	27	38	11	24	6
DEL PEAK 19(10Q23.31) WILD-TYPE	31	11	10	18	18

Figure S293. 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 S294. Gene #45: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 20(10Q26.3) MUTATED	47	2	33	50
DEL PEAK 20(10Q26.3) WILD-TYPE	48	58	6	13

Figure S294. 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 S295. Gene #45: 'del_10q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 20(10Q26.3) MUTATED	12	13	56	51
DEL PEAK 20(10Q26.3) WILD-TYPE	42	43	16	24

Figure S295. 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 S296. Gene #45: 'del_10q26.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
DEL PEAK 20(10Q26.3) MUTATED	18	24	46	26
DEL PEAK 20(10Q26.3) WILD-TYPE	40	21	15	30

Figure S296. 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 S297. 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	35	49	68	22	22
DEL PEAK 20(10Q26.3) MUTATED	13	5	37	46	7	6
DEL PEAK 20(10Q26.3) WILD-TYPE	11	30	12	22	15	16

Figure S297. Get High-res Image Gene #45: 'del_10q26.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_10q26.3' versus 'MRNASEQ_CNMF'

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

Table S298. Gene #45: 'del_10q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
DEL PEAK 20(10Q26.3) MUTATED	53	57	20
DEL PEAK 20(10Q26.3) WILD-TYPE	61	20	44

Figure S298. 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 S299. 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	47	21	49	46	30	29	33
DEL PEAK 20(10Q26.3) MUTATED	21	7	41	9	16	16	20
DEL PEAK 20(10Q26.3) WILD-TYPE	26	14	8	37	14	13	13

Figure S299. Get High-res Image Gene #45: 'del_10q26.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00016

Table S300. Gene #45: 'del_10q26.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
DEL PEAK 20(10Q26.3) MUTATED	37	27	66
DEL PEAK 20(10Q26.3) WILD-TYPE	68	23	34

Figure S300. Get High-res Image Gene #45: 'del_10q26.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q26.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S301. Gene #45: 'del_10q26.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
DEL PEAK 20(10Q26.3) MUTATED	37	14	76	3
DEL PEAK 20(10Q26.3) WILD-TYPE	45	23	38	19

Figure S301. Get High-res Image Gene #45: 'del_10q26.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00016

Table S302. Gene #45: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
DEL PEAK 20(10Q26.3) MUTATED	16	14	36	15	22
DEL PEAK 20(10Q26.3) WILD-TYPE	42	13	11	8	17

Figure S302. 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 = 8e-05 (Fisher's exact test), Q value = 0.00037

Table S303. Gene #45: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
DEL PEAK 20(10Q26.3) MUTATED	25	38	11	24	5
DEL PEAK 20(10Q26.3) WILD-TYPE	33	11	10	18	19

Figure S303. 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 S304. Gene #46: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 21(11P15.5) MUTATED	60	3	13	34
DEL PEAK 21(11P15.5) WILD-TYPE	35	57	26	29

Figure S304. Get High-res Image Gene #46: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.5' versus 'RPPA_CHIERARCHICAL'

P value = 0.0106 (Fisher's exact test), Q value = 0.021

Table S305. 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	35	49	68	22	22
DEL PEAK 21(11P15.5) MUTATED	19	12	22	29	7	9
DEL PEAK 21(11P15.5) WILD-TYPE	5	23	27	39	15	13

Figure S305. Get High-res Image Gene #46: 'del_11p15.5' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_11q23.1' versus 'CN_CNMF'

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

Table S306. Gene #47: 'del_11q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 22(11Q23.1) MUTATED	63	7	8	40
DEL PEAK 22(11Q23.1) WILD-TYPE	32	53	31	23

Figure S306. Get High-res Image Gene #47: 'del_11q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q23.1' versus 'METHLYATION_CNMF'

P value = 0.00285 (Fisher's exact test), Q value = 0.0071

Table S307. Gene #47: 'del_11q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 22(11Q23.1) MUTATED	22	21	27	48
DEL PEAK 22(11Q23.1) WILD-TYPE	32	35	45	27

Figure S307. Get High-res Image Gene #47: 'del_11q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00433 (Fisher's exact test), Q value = 0.01

Table S308. Gene #47: 'del_11q23.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	35	49	68	22	22
DEL PEAK 22(11Q23.1) MUTATED	17	19	26	20	12	8
DEL PEAK 22(11Q23.1) WILD-TYPE	7	16	23	48	10	14

Figure S308. Get High-res Image Gene #47: 'del_11q23.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_11q23.1' versus 'MRNASEQ_CNMF'

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

Table S309. Gene #47: 'del_11q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
DEL PEAK 22(11Q23.1) MUTATED	64	28	25
DEL PEAK 22(11Q23.1) WILD-TYPE	50	49	39

Figure S309. Get High-res Image Gene #47: 'del_11q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0154 (Fisher's exact test), Q value = 0.028

Table S310. Gene #47: 'del_11q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	47	21	49	46	30	29	33
DEL PEAK 22(11Q23.1) MUTATED	32	12	18	21	11	9	14
DEL PEAK 22(11Q23.1) WILD-TYPE	15	9	31	25	19	20	19

Figure S310. Get High-res Image Gene #47: 'del_11q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.1' versus 'MIRSEQ_CNMF'

P value = 0.00343 (Fisher's exact test), Q value = 0.0083

Table S311. Gene #47: 'del_11q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
DEL PEAK 22(11Q23.1) MUTATED	51	31	34
DEL PEAK 22(11Q23.1) WILD-TYPE	54	19	66

Figure S311. Get High-res Image Gene #47: 'del_11q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0151 (Fisher's exact test), Q value = 0.027

Table S312. Gene #47: 'del_11q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
DEL PEAK 22(11Q23.1) MUTATED	30	21	17	12	22
DEL PEAK 22(11Q23.1) WILD-TYPE	28	6	30	11	17

Figure S312. Get High-res Image Gene #47: 'del_11q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0206 (Fisher's exact test), Q value = 0.035

Table S313. Gene #47: 'del_11q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
DEL PEAK 22(11Q23.1) MUTATED	35	18	14	26	9
DEL PEAK 22(11Q23.1) WILD-TYPE	23	31	7	16	15

Figure S313. Get High-res Image Gene #47: 'del_11q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q25' versus 'CN_CNMF'

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

Table S314. Gene #48: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 23(11Q25) MUTATED	67	7	10	39
DEL PEAK 23(11Q25) WILD-TYPE	28	53	29	24

Figure S314. Get High-res Image Gene #48: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q25' versus 'METHLYATION_CNMF'

P value = 0.00107 (Fisher's exact test), Q value = 0.0031

Table S315. Gene #48: 'del_11q25' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 23(11Q25) MUTATED	25	21	27	50
DEL PEAK 23(11Q25) WILD-TYPE	29	35	45	25

Figure S315. Get High-res Image Gene #48: 'del_11q25' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q25' versus 'RPPA_CNMF'

P value = 0.00673 (Fisher's exact test), Q value = 0.014

Table S316. Gene #48: 'del_11q25' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
DEL PEAK 23(11Q25) MUTATED	27	26	20	35
DEL PEAK 23(11Q25) WILD-TYPE	31	19	41	21

Figure S316. Get High-res Image Gene #48: 'del_11q25' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_11q25' versus 'RPPA_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.0015

Table S317. Gene #48: 'del_11q25' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	35	49	68	22	22
DEL PEAK 23(11Q25) MUTATED	16	18	31	20	15	8
DEL PEAK 23(11Q25) WILD-TYPE	8	17	18	48	7	14

Figure S317. Get High-res Image Gene #48: 'del_11q25' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_11q25' versus 'MRNASEQ_CNMF'

P value = 0.00139 (Fisher's exact test), Q value = 0.0039

Table S318. Gene #48: 'del_11q25' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
DEL PEAK 23(11Q25) MUTATED	69	28	25
DEL PEAK 23(11Q25) WILD-TYPE	45	49	39

Figure S318. Get High-res Image Gene #48: 'del_11q25' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q25' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00327 (Fisher's exact test), Q value = 0.008

Table S319. Gene #48: 'del_11q25' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	47	21	49	46	30	29	33
DEL PEAK 23(11Q25) MUTATED	34	12	19	20	15	8	14
DEL PEAK 23(11Q25) WILD-TYPE	13	9	30	26	15	21	19

Figure S319. Get High-res Image Gene #48: 'del_11q25' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q25' versus 'MIRSEQ_CNMF'

P value = 0.00098 (Fisher's exact test), Q value = 0.0029

Table S320. Gene #48: 'del_11q25' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
DEL PEAK 23(11Q25) MUTATED	51	34	36
DEL PEAK 23(11Q25) WILD-TYPE	54	16	64

Figure S320. Get High-res Image Gene #48: 'del_11q25' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11q25' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0304 (Fisher's exact test), Q value = 0.049

Table S321. Gene #48: 'del_11q25' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
DEL PEAK 23(11Q25) MUTATED	29	20	18	14	24
DEL PEAK 23(11Q25) WILD-TYPE	29	7	29	9	15

Figure S321. Get High-res Image Gene #48: 'del_11q25' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q25' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S322. Gene #48: 'del_11q25' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
DEL PEAK 23(11Q25) MUTATED	35	19	17	25	9
DEL PEAK 23(11Q25) WILD-TYPE	23	30	4	17	15

Figure S322. Get High-res Image Gene #48: 'del_11q25' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12p13.1' versus 'CN_CNMF'

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

Table S323. Gene #49: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 24(12P13.1) MUTATED	48	5	6	28
DEL PEAK 24(12P13.1) WILD-TYPE	47	55	33	35

Figure S323. Get High-res Image Gene #49: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00068

Table S324. Gene #49: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 24(12P13.1) MUTATED	11	13	23	40
DEL PEAK 24(12P13.1) WILD-TYPE	43	43	49	35

Figure S324. Get High-res Image Gene #49: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12p13.1' versus 'MRNASEQ_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.033

Table S325. Gene #49: 'del_12p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
DEL PEAK 24(12P13.1) MUTATED	48	23	14
DEL PEAK 24(12P13.1) WILD-TYPE	66	54	50

Figure S325. Get High-res Image Gene #49: 'del_12p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00572 (Fisher's exact test), Q value = 0.013

Table S326. Gene #49: '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	47	21	49	46	30	29	33
DEL PEAK 24(12P13.1) MUTATED	27	6	14	8	11	9	10
DEL PEAK 24(12P13.1) WILD-TYPE	20	15	35	38	19	20	23

Figure S326. Get High-res Image Gene #49: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0339 (Fisher's exact test), Q value = 0.054

Table S327. Gene #49: 'del_12p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
DEL PEAK 24(12P13.1) MUTATED	36	13	34	3
DEL PEAK 24(12P13.1) WILD-TYPE	46	24	80	19

Figure S327. Get High-res Image Gene #49: 'del_12p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_12q12' versus 'CN_CNMF'

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

Table S328. Gene #50: 'del_12q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 25(12Q12) MUTATED	21	2	9	24
DEL PEAK 25(12Q12) WILD-TYPE	74	58	30	39

Figure S328. Get High-res Image Gene #50: 'del_12q12' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q12' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00037

Table S329. Gene #50: 'del_12q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 25(12Q12) MUTATED	4	5	22	25
DEL PEAK 25(12Q12) WILD-TYPE	50	51	50	50

Figure S329. Get High-res Image Gene #50: 'del_12q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0262 (Fisher's exact test), Q value = 0.043

Table S330. Gene #50: 'del_12q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	47	21	49	46	30	29	33
DEL PEAK 25(12Q12) MUTATED	13	3	17	3	8	5	7
DEL PEAK 25(12Q12) WILD-TYPE	34	18	32	43	22	24	26

Figure S330. Get High-res Image Gene #50: 'del_12q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0308 (Fisher's exact test), Q value = 0.05

Table S331. Gene #50: 'del_12q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
DEL PEAK 25(12Q12) MUTATED	16	4	34	2
DEL PEAK 25(12Q12) WILD-TYPE	66	33	80	20

Figure S331. Get High-res Image Gene #50: 'del_12q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_12q24.33' versus 'CN_CNMF'

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

Table S332. Gene #51: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 26(12Q24.33) MUTATED	34	2	7	27
DEL PEAK 26(12Q24.33) WILD-TYPE	61	58	32	36

Figure S332. Get High-res Image Gene #51: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q24.33' versus 'METHLYATION_CNMF'

P value = 0.0198 (Fisher's exact test), Q value = 0.034

Table S333. Gene #51: 'del_12q24.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 26(12Q24.33) MUTATED	7	13	24	26
DEL PEAK 26(12Q24.33) WILD-TYPE	47	43	48	49

Figure S333. Get High-res Image Gene #51: 'del_12q24.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12q24.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.021

Table S334. Gene #51: '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	47	21	49	46	30	29	33
DEL PEAK 26(12Q24.33) MUTATED	18	3	21	9	9	3	7
DEL PEAK 26(12Q24.33) WILD-TYPE	29	18	28	37	21	26	26

Figure S334. Get High-res Image Gene #51: '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 S335. Gene #52: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 27(13Q14.2) MUTATED	78	8	35	59
DEL PEAK 27(13Q14.2) WILD-TYPE	17	52	4	4

Figure S335. Get High-res Image Gene #52: '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 S336. Gene #52: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 27(13Q14.2) MUTATED	26	24	67	63
DEL PEAK 27(13Q14.2) WILD-TYPE	28	32	5	12

Figure S336. Get High-res Image Gene #52: '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 S337. Gene #52: 'del_13q14.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
DEL PEAK 27(13Q14.2) MUTATED	27	34	54	39
DEL PEAK 27(13Q14.2) WILD-TYPE	31	11	7	17

Figure S337. Get High-res Image Gene #52: 'del_13q14.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_13q14.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00171 (Fisher's exact test), Q value = 0.0046

Table S338. Gene #52: 'del_13q14.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	35	49	68	22	22
DEL PEAK 27(13Q14.2) MUTATED	15	20	40	55	15	9
DEL PEAK 27(13Q14.2) WILD-TYPE	9	15	9	13	7	13

Figure S338. Get High-res Image Gene #52: '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 S339. Gene #52: 'del_13q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
DEL PEAK 27(13Q14.2) MUTATED	79	69	30
DEL PEAK 27(13Q14.2) WILD-TYPE	35	8	34

Figure S339. Get High-res Image Gene #52: '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 S340. Gene #52: '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	47	21	49	46	30	29	33
DEL PEAK 27(13Q14.2) MUTATED	34	10	47	19	23	22	23
DEL PEAK 27(13Q14.2) WILD-TYPE	13	11	2	27	7	7	10

Figure S340. Get High-res Image Gene #52: 'del_13q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00041

Table S341. Gene #52: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
DEL PEAK 27(13Q14.2) MUTATED	59	36	83
DEL PEAK 27(13Q14.2) WILD-TYPE	46	14	17

Figure S341. Get High-res Image Gene #52: '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 S342. Gene #52: 'del_13q14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
DEL PEAK 27(13Q14.2) MUTATED	54	20	97	7
DEL PEAK 27(13Q14.2) WILD-TYPE	28	17	17	15

Figure S342. Get High-res Image Gene #52: 'del_13q14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0026

Table S343. Gene #52: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
DEL PEAK 27(13Q14.2) MUTATED	31	21	42	16	31
DEL PEAK 27(13Q14.2) WILD-TYPE	27	6	5	7	8

Figure S343. Get High-res Image Gene #52: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00037

Table S344. Gene #52: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
DEL PEAK 27(13Q14.2) MUTATED	39	44	17	32	9
DEL PEAK 27(13Q14.2) WILD-TYPE	19	5	4	10	15

Figure S344. Get High-res Image Gene #52: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q24.1' versus 'CN_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0018

Table S345. Gene #53: 'del_14q24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 28(14Q24.1) MUTATED	31	7	14	28
DEL PEAK 28(14Q24.1) WILD-TYPE	64	53	25	35

Figure S345. Get High-res Image Gene #53: 'del_14q24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q24.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S346. Gene #53: '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	47	21	49	46	30	29	33
DEL PEAK 28(14Q24.1) MUTATED	21	4	9	11	3	21	11
DEL PEAK 28(14Q24.1) WILD-TYPE	26	17	40	35	27	8	22

Figure S346. Get High-res Image Gene #53: 'del_14q24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q24.1' versus 'MIRSEQ_CNMF'

P value = 0.04 (Fisher's exact test), Q value = 0.062

Table S347. Gene #53: 'del_14q24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
DEL PEAK 28(14Q24.1) MUTATED	24	20	36
DEL PEAK 28(14Q24.1) WILD-TYPE	81	30	64

Figure S347. Get High-res Image Gene #53: 'del_14q24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_14q24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00472 (Fisher's exact test), Q value = 0.011

Table S348. Gene #53: 'del_14q24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
DEL PEAK 28(14Q24.1) MUTATED	22	12	45	1
DEL PEAK 28(14Q24.1) WILD-TYPE	60	25	69	21

Figure S348. Get High-res Image Gene #53: 'del_14q24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_14q24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0016

Table S349. Gene #53: 'del_14q24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
DEL PEAK 28(14Q24.1) MUTATED	10	17	16	10	9
DEL PEAK 28(14Q24.1) WILD-TYPE	48	10	31	13	30

Figure S349. Get High-res Image Gene #53: 'del_14q24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_14q24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0485 (Fisher's exact test), Q value = 0.073

Table S350. Gene #53: 'del_14q24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
DEL PEAK 28(14Q24.1) MUTATED	19	17	10	14	2
DEL PEAK 28(14Q24.1) WILD-TYPE	39	32	11	28	22

Figure S350. Get High-res Image Gene #53: 'del_14q24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q11.2' versus 'CN_CNMF'

P value = 0.00856 (Fisher's exact test), Q value = 0.017

Table S351. Gene #54: 'del_15q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 29(15Q11.2) MUTATED	23	5	3	16
DEL PEAK 29(15Q11.2) WILD-TYPE	72	55	36	47

Figure S351. Get High-res Image Gene #54: 'del_15q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q11.2' versus 'METHLYATION_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.024

Table S352. Gene #54: 'del_15q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 29(15Q11.2) MUTATED	11	7	7	22
DEL PEAK 29(15Q11.2) WILD-TYPE	43	49	65	53

Figure S352. Get High-res Image Gene #54: 'del_15q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q11.2' versus 'RPPA_CNMF'

P value = 0.0178 (Fisher's exact test), Q value = 0.031

Table S353. Gene #54: 'del_15q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
DEL PEAK 29(15Q11.2) MUTATED	7	12	7	17
DEL PEAK 29(15Q11.2) WILD-TYPE	51	33	54	39

Figure S353. Get High-res Image Gene #54: 'del_15q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_15q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0163 (Fisher's exact test), Q value = 0.029

Table S354. Gene #54: 'del_15q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	35	49	68	22	22
DEL PEAK 29(15Q11.2) MUTATED	5	5	17	6	4	6
DEL PEAK 29(15Q11.2) WILD-TYPE	19	30	32	62	18	16

Figure S354. Get High-res Image Gene #54: 'del_15q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_15q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00778 (Fisher's exact test), Q value = 0.016

Table S355. Gene #54: 'del_15q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
DEL PEAK 29(15Q11.2) MUTATED	30	7	10
DEL PEAK 29(15Q11.2) WILD-TYPE	84	70	54

Figure S355. Get High-res Image Gene #54: 'del_15q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00651 (Fisher's exact test), Q value = 0.014

Table S356. Gene #54: 'del_15q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	47	21	49	46	30	29	33
DEL PEAK 29(15Q11.2) MUTATED	8	4	2	7	9	5	12
DEL PEAK 29(15Q11.2) WILD-TYPE	39	17	47	39	21	24	21

Figure S356. Get High-res Image Gene #54: 'del_15q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.026

Table S357. Gene #54: 'del_15q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
DEL PEAK 29(15Q11.2) MUTATED	19	16	12
DEL PEAK 29(15Q11.2) WILD-TYPE	86	34	88

Figure S357. Get High-res Image Gene #54: 'del_15q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_15q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.0017

Table S358. Gene #54: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
DEL PEAK 29(15Q11.2) MUTATED	5	8	4	8	14
DEL PEAK 29(15Q11.2) WILD-TYPE	53	19	43	15	25

Figure S358. Get High-res Image Gene #54: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_15q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0284 (Fisher's exact test), Q value = 0.047

Table S359. Gene #54: 'del_15q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
DEL PEAK 29(15Q11.2) MUTATED	10	5	7	14	3
DEL PEAK 29(15Q11.2) WILD-TYPE	48	44	14	28	21

Figure S359. Get High-res Image Gene #54: 'del_15q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q11.2' versus 'CN_CNMF'

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

Table S360. Gene #55: 'del_16q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 30(16Q11.2) MUTATED	50	6	30	44
DEL PEAK 30(16Q11.2) WILD-TYPE	45	54	9	19

Figure S360. Get High-res Image Gene #55: 'del_16q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q11.2' versus 'METHLYATION_CNMF'

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

Table S361. Gene #55: 'del_16q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 30(16Q11.2) MUTATED	20	14	50	46
DEL PEAK 30(16Q11.2) WILD-TYPE	34	42	22	29

Figure S361. Get High-res Image Gene #55: 'del_16q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q11.2' versus 'RPPA_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 0.04

Table S362. Gene #55: 'del_16q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
DEL PEAK 30(16Q11.2) MUTATED	20	23	38	29
DEL PEAK 30(16Q11.2) WILD-TYPE	38	22	23	27

Figure S362. Get High-res Image Gene #55: 'del_16q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_16q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0027 (Fisher's exact test), Q value = 0.0068

Table S363. Gene #55: 'del_16q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	35	49	68	22	22
DEL PEAK 30(16Q11.2) MUTATED	13	11	33	39	7	7
DEL PEAK 30(16Q11.2) WILD-TYPE	11	24	16	29	15	15

Figure S363. Get High-res Image Gene #55: 'del_16q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_16q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.002

Table S364. Gene #55: 'del_16q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
DEL PEAK 30(16Q11.2) MUTATED	58	50	21
DEL PEAK 30(16Q11.2) WILD-TYPE	56	27	43

Figure S364. Get High-res Image Gene #55: 'del_16q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00037

Table S365. Gene #55: '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	47	21	49	46	30	29	33
DEL PEAK 30(16Q11.2) MUTATED	24	7	34	10	18	17	19
DEL PEAK 30(16Q11.2) WILD-TYPE	23	14	15	36	12	12	14

Figure S365. Get High-res Image Gene #55: 'del_16q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00407 (Fisher's exact test), Q value = 0.0096

Table S366. Gene #55: 'del_16q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
DEL PEAK 30(16Q11.2) MUTATED	40	30	59
DEL PEAK 30(16Q11.2) WILD-TYPE	65	20	41

Figure S366. Get High-res Image Gene #55: 'del_16q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00048 (Fisher's exact test), Q value = 0.0017

Table S367. Gene #55: 'del_16q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
DEL PEAK 30(16Q11.2) MUTATED	38	11	73	7
DEL PEAK 30(16Q11.2) WILD-TYPE	44	26	41	15

Figure S367. Get High-res Image Gene #55: 'del_16q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00097 (Fisher's exact test), Q value = 0.0029

Table S368. Gene #55: 'del_16q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
DEL PEAK 30(16Q11.2) MUTATED	21	13	36	14	23
DEL PEAK 30(16Q11.2) WILD-TYPE	37	14	11	9	16

Figure S368. Get High-res Image Gene #55: 'del_16q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S369. Gene #55: 'del_16q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
DEL PEAK 30(16Q11.2) MUTATED	25	39	13	25	5
DEL PEAK 30(16Q11.2) WILD-TYPE	33	10	8	17	19

Figure S369. Get High-res Image Gene #55: '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 S370. Gene #56: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 31(16Q23.1) MUTATED	56	6	29	43
DEL PEAK 31(16Q23.1) WILD-TYPE	39	54	10	20

Figure S370. Get High-res Image Gene #56: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

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

Table S371. Gene #56: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 31(16Q23.1) MUTATED	21	16	50	47
DEL PEAK 31(16Q23.1) WILD-TYPE	33	40	22	28

Figure S371. Get High-res Image Gene #56: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.1' versus 'RPPA_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.023

Table S372. Gene #56: 'del_16q23.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
DEL PEAK 31(16Q23.1) MUTATED	21	26	40	29
DEL PEAK 31(16Q23.1) WILD-TYPE	37	19	21	27

Figure S372. Get High-res Image Gene #56: 'del_16q23.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 0.00158 (Fisher's exact test), Q value = 0.0043

Table S373. Gene #56: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
DEL PEAK 31(16Q23.1) MUTATED	59	51	23
DEL PEAK 31(16Q23.1) WILD-TYPE	55	26	41

Figure S373. Get High-res Image Gene #56: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0018

Table S374. Gene #56: '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	47	21	49	46	30	29	33
DEL PEAK 31(16Q23.1) MUTATED	28	7	34	12	18	17	17
DEL PEAK 31(16Q23.1) WILD-TYPE	19	14	15	34	12	12	16

Figure S374. Get High-res Image Gene #56: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 0.00514 (Fisher's exact test), Q value = 0.011

Table S375. Gene #56: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
DEL PEAK 31(16Q23.1) MUTATED	42	31	60
DEL PEAK 31(16Q23.1) WILD-TYPE	63	19	40

Figure S375. Get High-res Image Gene #56: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00048

Table S376. Gene #56: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
DEL PEAK 31(16Q23.1) MUTATED	40	12	75	6
DEL PEAK 31(16Q23.1) WILD-TYPE	42	25	39	16

Figure S376. Get High-res Image Gene #56: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00041

Table S377. Gene #56: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
DEL PEAK 31(16Q23.1) MUTATED	19	14	37	14	25
DEL PEAK 31(16Q23.1) WILD-TYPE	39	13	10	9	14

Figure S377. Get High-res Image Gene #56: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S378. Gene #56: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
DEL PEAK 31(16Q23.1) MUTATED	23	39	13	28	6
DEL PEAK 31(16Q23.1) WILD-TYPE	35	10	8	14	18

Figure S378. Get High-res Image Gene #56: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p13.1' versus 'CN_CNMF'

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

Table S379. Gene #57: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 32(17P13.1) MUTATED	46	7	31	45
DEL PEAK 32(17P13.1) WILD-TYPE	49	53	8	18

Figure S379. Get High-res Image Gene #57: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.1' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00016

Table S380. Gene #57: 'del_17p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 32(17P13.1) MUTATED	22	19	54	34
DEL PEAK 32(17P13.1) WILD-TYPE	32	37	18	41

Figure S380. Get High-res Image Gene #57: 'del_17p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p13.1' versus 'RPPA_CNMF'

P value = 0.00454 (Fisher's exact test), Q value = 0.01

Table S381. Gene #57: 'del_17p13.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
DEL PEAK 32(17P13.1) MUTATED	19	21	40	28
DEL PEAK 32(17P13.1) WILD-TYPE	39	24	21	28

Figure S381. Get High-res Image Gene #57: 'del_17p13.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_17p13.1' versus 'RPPA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00041

Table S382. Gene #57: 'del_17p13.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	35	49	68	22	22
DEL PEAK 32(17P13.1) MUTATED	10	8	34	41	6	9
DEL PEAK 32(17P13.1) WILD-TYPE	14	27	15	27	16	13

Figure S382. Get High-res Image Gene #57: 'del_17p13.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_17p13.1' versus 'MRNASEQ_CNMF'

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

Table S383. Gene #57: 'del_17p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
DEL PEAK 32(17P13.1) MUTATED	51	55	21
DEL PEAK 32(17P13.1) WILD-TYPE	63	22	43

Figure S383. Get High-res Image Gene #57: 'del_17p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00037

Table S384. Gene #57: '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	47	21	49	46	30	29	33
DEL PEAK 32(17P13.1) MUTATED	18	8	40	16	16	14	15
DEL PEAK 32(17P13.1) WILD-TYPE	29	13	9	30	14	15	18

Figure S384. Get High-res Image Gene #57: 'del_17p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.1' versus 'MIRSEQ_CNMF'

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

Table S385. Gene #57: 'del_17p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
DEL PEAK 32(17P13.1) MUTATED	34	29	64
DEL PEAK 32(17P13.1) WILD-TYPE	71	21	36

Figure S385. Get High-res Image Gene #57: 'del_17p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 3e-04

Table S386. Gene #57: 'del_17p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
DEL PEAK 32(17P13.1) MUTATED	30	16	75	6
DEL PEAK 32(17P13.1) WILD-TYPE	52	21	39	16

Figure S386. Get High-res Image Gene #57: 'del_17p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.0024

Table S387. Gene #57: 'del_17p13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
DEL PEAK 32(17P13.1) MUTATED	19	11	34	14	22
DEL PEAK 32(17P13.1) WILD-TYPE	39	16	13	9	17

Figure S387. Get High-res Image Gene #57: 'del_17p13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00048

Table S388. Gene #57: 'del_17p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
DEL PEAK 32(17P13.1) MUTATED	19	36	12	25	8
DEL PEAK 32(17P13.1) WILD-TYPE	39	13	9	17	16

Figure S388. Get High-res Image Gene #57: '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 S389. Gene #58: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 33(17Q11.2) MUTATED	50	3	8	20
DEL PEAK 33(17Q11.2) WILD-TYPE	45	57	31	43

Figure S389. Get High-res Image Gene #58: '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 S390. Gene #58: 'del_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 33(17Q11.2) MUTATED	13	16	10	42
DEL PEAK 33(17Q11.2) WILD-TYPE	41	40	62	33

Figure S390. Get High-res Image Gene #58: 'del_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q11.2' versus 'RPPA_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.0019

Table S391. Gene #58: 'del_17q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
DEL PEAK 33(17Q11.2) MUTATED	21	23	9	22
DEL PEAK 33(17Q11.2) WILD-TYPE	37	22	52	34

Figure S391. Get High-res Image Gene #58: '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 S392. Gene #58: 'del_17q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	35	49	68	22	22
DEL PEAK 33(17Q11.2) MUTATED	12	8	32	9	8	6
DEL PEAK 33(17Q11.2) WILD-TYPE	12	27	17	59	14	16

Figure S392. Get High-res Image Gene #58: 'del_17q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_17q11.2' versus 'MRNASEQ_CNMF'

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

Table S393. Gene #58: 'del_17q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
DEL PEAK 33(17Q11.2) MUTATED	52	10	19
DEL PEAK 33(17Q11.2) WILD-TYPE	62	67	45

Figure S393. Get High-res Image Gene #58: 'del_17q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 3e-04

Table S394. Gene #58: '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	47	21	49	46	30	29	33
DEL PEAK 33(17Q11.2) MUTATED	24	6	7	12	15	3	14
DEL PEAK 33(17Q11.2) WILD-TYPE	23	15	42	34	15	26	19

Figure S394. Get High-res Image Gene #58: 'del_17q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.0025

Table S395. Gene #58: 'del_17q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
DEL PEAK 33(17Q11.2) MUTATED	37	24	19
DEL PEAK 33(17Q11.2) WILD-TYPE	68	26	81

Figure S395. Get High-res Image Gene #58: 'del_17q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.0025

Table S396. Gene #58: 'del_17q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
DEL PEAK 33(17Q11.2) MUTATED	17	15	6	10	17
DEL PEAK 33(17Q11.2) WILD-TYPE	41	12	41	13	22

Figure S396. Get High-res Image Gene #58: 'del_17q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0018 (Fisher's exact test), Q value = 0.0048

Table S397. Gene #58: 'del_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
DEL PEAK 33(17Q11.2) MUTATED	21	6	10	20	8
DEL PEAK 33(17Q11.2) WILD-TYPE	37	43	11	22	16

Figure S397. Get High-res Image Gene #58: 'del_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q25.3' versus 'CN_CNMF'

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

Table S398. Gene #59: 'del_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 34(17Q25.3) MUTATED	32	3	5	27
DEL PEAK 34(17Q25.3) WILD-TYPE	63	57	34	36

Figure S398. Get High-res Image Gene #59: 'del_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q25.3' versus 'METHLYATION_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.0028

Table S399. Gene #59: 'del_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 34(17Q25.3) MUTATED	7	8	24	28
DEL PEAK 34(17Q25.3) WILD-TYPE	47	48	48	47

Figure S399. Get High-res Image Gene #59: 'del_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00838 (Fisher's exact test), Q value = 0.017

Table S400. Gene #59: 'del_17q25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
DEL PEAK 34(17Q25.3) MUTATED	23	5	37	1
DEL PEAK 34(17Q25.3) WILD-TYPE	59	32	77	21

Figure S400. Get High-res Image Gene #59: 'del_17q25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17q25.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0417 (Fisher's exact test), Q value = 0.064

Table S401. Gene #59: 'del_17q25.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
DEL PEAK 34(17Q25.3) MUTATED	9	11	14	10	10
DEL PEAK 34(17Q25.3) WILD-TYPE	49	16	33	13	29

Figure S401. Get High-res Image Gene #59: 'del_17q25.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_18p11.32' versus 'CN_CNMF'

P value = 0.00126 (Fisher's exact test), Q value = 0.0036

Table S402. Gene #60: 'del_18p11.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 35(18P11.32) MUTATED	33	5	11	19
DEL PEAK 35(18P11.32) WILD-TYPE	62	55	28	44

Figure S402. Get High-res Image Gene #60: 'del_18p11.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_18p11.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00176 (Fisher's exact test), Q value = 0.0047

Table S403. Gene #60: 'del_18p11.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
DEL PEAK 35(18P11.32) MUTATED	25	2	37	3
DEL PEAK 35(18P11.32) WILD-TYPE	57	35	77	19

Figure S403. Get High-res Image Gene #60: 'del_18p11.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q23' versus 'CN_CNMF'

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

Table S404. Gene #61: 'del_18q23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 36(18Q23) MUTATED	41	5	12	28
DEL PEAK 36(18Q23) WILD-TYPE	54	55	27	35

Figure S404. Get High-res Image Gene #61: 'del_18q23' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q23' versus 'METHLYATION_CNMF'

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

Table S405. Gene #61: 'del_18q23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 36(18Q23) MUTATED	14	8	16	48
DEL PEAK 36(18Q23) WILD-TYPE	40	48	56	27

Figure S405. Get High-res Image Gene #61: 'del_18q23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q23' versus 'RPPA_CNMF'

P value = 0.00324 (Fisher's exact test), Q value = 0.008

Table S406. Gene #61: 'del_18q23' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
DEL PEAK 36(18Q23) MUTATED	13	21	15	27
DEL PEAK 36(18Q23) WILD-TYPE	45	24	46	29

Figure S406. Get High-res Image Gene #61: 'del_18q23' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_18q23' versus 'RPPA_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.0011

Table S407. Gene #61: 'del_18q23' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	35	49	68	22	22
DEL PEAK 36(18Q23) MUTATED	7	10	30	13	8	8
DEL PEAK 36(18Q23) WILD-TYPE	17	25	19	55	14	14

Figure S407. Get High-res Image Gene #61: 'del_18q23' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_18q23' versus 'MRNASEQ_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 0.022

Table S408. Gene #61: 'del_18q23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
DEL PEAK 36(18Q23) MUTATED	49	18	18
DEL PEAK 36(18Q23) WILD-TYPE	65	59	46

Figure S408. Get High-res Image Gene #61: 'del_18q23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00235 (Fisher's exact test), Q value = 0.006

Table S409. Gene #61: 'del_18q23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	47	21	49	46	30	29	33
DEL PEAK 36(18Q23) MUTATED	16	6	12	11	17	5	18
DEL PEAK 36(18Q23) WILD-TYPE	31	15	37	35	13	24	15

Figure S409. Get High-res Image Gene #61: 'del_18q23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_CNMF'

P value = 0.00088 (Fisher's exact test), Q value = 0.0026

Table S410. Gene #61: 'del_18q23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
DEL PEAK 36(18Q23) MUTATED	35	27	23
DEL PEAK 36(18Q23) WILD-TYPE	70	23	77

Figure S410. Get High-res Image Gene #61: 'del_18q23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00321 (Fisher's exact test), Q value = 0.0079

Table S411. Gene #61: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
DEL PEAK 36(18Q23) MUTATED	18	8	10	11	23
DEL PEAK 36(18Q23) WILD-TYPE	40	19	37	12	16

Figure S411. Get High-res Image Gene #61: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_18q23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00515 (Fisher's exact test), Q value = 0.011

Table S412. Gene #61: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
DEL PEAK 36(18Q23) MUTATED	20	11	11	23	5
DEL PEAK 36(18Q23) WILD-TYPE	38	38	10	19	19

Figure S412. Get High-res Image Gene #61: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

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

Table S413. Gene #62: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 37(19P13.3) MUTATED	25	2	17	26
DEL PEAK 37(19P13.3) WILD-TYPE	70	58	22	37

Figure S413. Get High-res Image Gene #62: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0017

Table S414. Gene #62: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 37(19P13.3) MUTATED	6	10	29	25
DEL PEAK 37(19P13.3) WILD-TYPE	48	46	43	50

Figure S414. Get High-res Image Gene #62: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'RPPA_CNMF'

P value = 0.00919 (Fisher's exact test), Q value = 0.018

Table S415. Gene #62: 'del_19p13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
DEL PEAK 37(19P13.3) MUTATED	11	18	22	9
DEL PEAK 37(19P13.3) WILD-TYPE	47	27	39	47

Figure S415. Get High-res Image Gene #62: 'del_19p13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_19p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.0022

Table S416. Gene #62: 'del_19p13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	35	49	68	22	22
DEL PEAK 37(19P13.3) MUTATED	7	4	18	23	0	8
DEL PEAK 37(19P13.3) WILD-TYPE	17	31	31	45	22	14

Figure S416. Get High-res Image Gene #62: 'del_19p13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00966 (Fisher's exact test), Q value = 0.019

Table S417. Gene #62: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
DEL PEAK 37(19P13.3) MUTATED	23	31	16
DEL PEAK 37(19P13.3) WILD-TYPE	91	46	48

Figure S417. Get High-res Image Gene #62: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00453 (Fisher's exact test), Q value = 0.01

Table S418. Gene #62: '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	47	21	49	46	30	29	33
DEL PEAK 37(19P13.3) MUTATED	8	1	20	9	8	11	13
DEL PEAK 37(19P13.3) WILD-TYPE	39	20	29	37	22	18	20

Figure S418. Get High-res Image Gene #62: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 0.0276 (Fisher's exact test), Q value = 0.045

Table S419. Gene #62: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
DEL PEAK 37(19P13.3) MUTATED	21	11	36
DEL PEAK 37(19P13.3) WILD-TYPE	84	39	64

Figure S419. Get High-res Image Gene #62: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00392 (Fisher's exact test), Q value = 0.0094

Table S420. Gene #62: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
DEL PEAK 37(19P13.3) MUTATED	19	4	42	3
DEL PEAK 37(19P13.3) WILD-TYPE	63	33	72	19

Figure S420. Get High-res Image Gene #62: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00693 (Fisher's exact test), Q value = 0.014

Table S421. Gene #62: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
DEL PEAK 37(19P13.3) MUTATED	8	6	20	10	11
DEL PEAK 37(19P13.3) WILD-TYPE	50	21	27	13	28

Figure S421. Get High-res Image Gene #62: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00492 (Fisher's exact test), Q value = 0.011

Table S422. Gene #62: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
DEL PEAK 37(19P13.3) MUTATED	14	22	9	6	4
DEL PEAK 37(19P13.3) WILD-TYPE	44	27	12	36	20

Figure S422. Get High-res Image Gene #62: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.43' versus 'CN_CNMF'

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

Table S423. Gene #63: 'del_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 38(19Q13.43) MUTATED	47	4	25	30
DEL PEAK 38(19Q13.43) WILD-TYPE	48	56	14	33

Figure S423. Get High-res Image Gene #63: 'del_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.43' versus 'METHLYATION_CNMF'

P value = 0.00258 (Fisher's exact test), Q value = 0.0065

Table S424. Gene #63: 'del_19q13.43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 38(19Q13.43) MUTATED	12	20	36	38
DEL PEAK 38(19Q13.43) WILD-TYPE	42	36	36	37

Figure S424. Get High-res Image Gene #63: 'del_19q13.43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19q13.43' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0341 (Fisher's exact test), Q value = 0.054

Table S425. Gene #63: 'del_19q13.43' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
DEL PEAK 38(19Q13.43) MUTATED	37	14	51	3
DEL PEAK 38(19Q13.43) WILD-TYPE	45	23	63	19

Figure S425. Get High-res Image Gene #63: 'del_19q13.43' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_21q11.2' versus 'CN_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.022

Table S426. Gene #64: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 39(21Q11.2) MUTATED	24	4	11	12
DEL PEAK 39(21Q11.2) WILD-TYPE	71	56	28	51

Figure S426. Get High-res Image Gene #64: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.033

Table S427. Gene #64: 'del_21q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	35	49	68	22	22
DEL PEAK 39(21Q11.2) MUTATED	4	7	18	7	3	6
DEL PEAK 39(21Q11.2) WILD-TYPE	20	28	31	61	19	16

Figure S427. Get High-res Image Gene #64: 'del_21q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0019

Table S428. Gene #64: 'del_21q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
DEL PEAK 39(21Q11.2) MUTATED	18	20	13
DEL PEAK 39(21Q11.2) WILD-TYPE	87	30	87

Figure S428. Get High-res Image Gene #64: 'del_21q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_21q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0075 (Fisher's exact test), Q value = 0.016

Table S429. Gene #64: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
DEL PEAK 39(21Q11.2) MUTATED	9	7	5	10	13
DEL PEAK 39(21Q11.2) WILD-TYPE	49	20	42	13	26

Figure S429. Get High-res Image Gene #64: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_21q22.3' versus 'CN_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0018

Table S430. Gene #65: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 40(21Q22.3) MUTATED	35	5	8	18
DEL PEAK 40(21Q22.3) WILD-TYPE	60	55	31	45

Figure S430. Get High-res Image Gene #65: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q22.3' versus 'METHLYATION_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.023

Table S431. Gene #65: 'del_21q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 40(21Q22.3) MUTATED	12	10	14	30
DEL PEAK 40(21Q22.3) WILD-TYPE	42	46	58	45

Figure S431. Get High-res Image Gene #65: 'del_21q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q22.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0173 (Fisher's exact test), Q value = 0.031

Table S432. Gene #65: 'del_21q22.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	35	49	68	22	22
DEL PEAK 40(21Q22.3) MUTATED	6	12	21	10	7	4
DEL PEAK 40(21Q22.3) WILD-TYPE	18	23	28	58	15	18

Figure S432. Get High-res Image Gene #65: 'del_21q22.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_21q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0271 (Fisher's exact test), Q value = 0.045

Table S433. Gene #65: 'del_21q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
DEL PEAK 40(21Q22.3) MUTATED	14	14	9	6	15
DEL PEAK 40(21Q22.3) WILD-TYPE	44	13	38	17	24

Figure S433. Get High-res Image Gene #65: 'del_21q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.32' versus 'CN_CNMF'

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

Table S434. Gene #66: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 41(22Q13.32) MUTATED	31	8	7	37
DEL PEAK 41(22Q13.32) WILD-TYPE	64	52	32	26

Figure S434. Get High-res Image Gene #66: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0408 (Fisher's exact test), Q value = 0.063

Table S435. Gene #66: 'del_22q13.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	47	21	49	46	30	29	33
DEL PEAK 41(22Q13.32) MUTATED	20	4	10	16	7	15	10
DEL PEAK 41(22Q13.32) WILD-TYPE	27	17	39	30	23	14	23

Figure S435. Get High-res Image Gene #66: 'del_22q13.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp21.1' versus 'CN_CNMF'

P value = 0.00178 (Fisher's exact test), Q value = 0.0047

Table S436. Gene #67: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 42(XP21.1) MUTATED	15	6	14	20
DEL PEAK 42(XP21.1) WILD-TYPE	80	54	25	43

Figure S436. Get High-res Image Gene #67: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 0.00251 (Fisher's exact test), Q value = 0.0064

Table S437. Gene #67: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 42(XP21.1) MUTATED	4	11	25	15
DEL PEAK 42(XP21.1) WILD-TYPE	50	45	47	60

Figure S437. Get High-res Image Gene #67: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp21.1' versus 'RPPA_CNMF'

P value = 0.0329 (Fisher's exact test), Q value = 0.053

Table S438. Gene #67: 'del_xp21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
DEL PEAK 42(XP21.1) MUTATED	7	11	20	9
DEL PEAK 42(XP21.1) WILD-TYPE	51	34	41	47

Figure S438. Get High-res Image Gene #67: 'del_xp21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_xp21.1' versus 'MRNASEQ_CNMF'

P value = 0.00774 (Fisher's exact test), Q value = 0.016

Table S439. Gene #67: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
DEL PEAK 42(XP21.1) MUTATED	18	26	10
DEL PEAK 42(XP21.1) WILD-TYPE	96	51	54

Figure S439. Get High-res Image Gene #67: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0296 (Fisher's exact test), Q value = 0.048

Table S440. Gene #67: '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	47	21	49	46	30	29	33
DEL PEAK 42(XP21.1) MUTATED	7	1	15	7	8	11	5
DEL PEAK 42(XP21.1) WILD-TYPE	40	20	34	39	22	18	28

Figure S440. Get High-res Image Gene #67: 'del_xp21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_CNMF'

P value = 0.0263 (Fisher's exact test), Q value = 0.044

Table S441. Gene #67: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
DEL PEAK 42(XP21.1) MUTATED	15	10	30
DEL PEAK 42(XP21.1) WILD-TYPE	90	40	70

Figure S441. Get High-res Image Gene #67: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xq21.1' versus 'CN_CNMF'

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

Table S442. Gene #68: 'del_xq21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 43(XQ21.1) MUTATED	45	7	24	38
DEL PEAK 43(XQ21.1) WILD-TYPE	50	53	15	25

Figure S442. Get High-res Image Gene #68: 'del_xq21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq21.1' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00026

Table S443. Gene #68: 'del_xq21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 43(XQ21.1) MUTATED	15	24	48	27
DEL PEAK 43(XQ21.1) WILD-TYPE	39	32	24	48

Figure S443. Get High-res Image Gene #68: '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 = 0.00016

Table S444. Gene #68: 'del_xq21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
DEL PEAK 43(XQ21.1) MUTATED	17	20	41	17
DEL PEAK 43(XQ21.1) WILD-TYPE	41	25	20	39

Figure S444. Get High-res Image Gene #68: 'del_xq21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_xq21.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00141 (Fisher's exact test), Q value = 0.0039

Table S445. Gene #68: 'del_xq21.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	35	49	68	22	22
DEL PEAK 43(XQ21.1) MUTATED	10	12	19	43	4	7
DEL PEAK 43(XQ21.1) WILD-TYPE	14	23	30	25	18	15

Figure S445. Get High-res Image Gene #68: 'del_xq21.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_xq21.1' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00016

Table S446. Gene #68: 'del_xq21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
DEL PEAK 43(XQ21.1) MUTATED	38	51	24
DEL PEAK 43(XQ21.1) WILD-TYPE	76	26	40

Figure S446. Get High-res Image Gene #68: 'del_xq21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xq21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.0012

Table S447. Gene #68: '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	47	21	49	46	30	29	33
DEL PEAK 43(XQ21.1) MUTATED	19	6	36	16	9	15	12
DEL PEAK 43(XQ21.1) WILD-TYPE	28	15	13	30	21	14	21

Figure S447. Get High-res Image Gene #68: 'del_xq21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xq21.1' versus 'MIRSEQ_CNMF'

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

Table S448. Gene #68: 'del_xq21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
DEL PEAK 43(XQ21.1) MUTATED	33	21	59
DEL PEAK 43(XQ21.1) WILD-TYPE	72	29	41

Figure S448. Get High-res Image Gene #68: 'del_xq21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xq21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.0017

Table S449. Gene #68: 'del_xq21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
DEL PEAK 43(XQ21.1) MUTATED	28	12	67	6
DEL PEAK 43(XQ21.1) WILD-TYPE	54	25	47	16

Figure S449. Get High-res Image Gene #68: 'del_xq21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xq21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0208 (Fisher's exact test), Q value = 0.036

Table S450. Gene #68: 'del_xq21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
DEL PEAK 43(XQ21.1) MUTATED	17	14	28	12	15
DEL PEAK 43(XQ21.1) WILD-TYPE	41	13	19	11	24

Figure S450. Get High-res Image Gene #68: 'del_xq21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xq22.3' versus 'CN_CNMF'

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

Table S451. Gene #69: 'del_xq22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	60	39	63
DEL PEAK 44(XQ22.3) MUTATED	49	9	23	42
DEL PEAK 44(XQ22.3) WILD-TYPE	46	51	16	21

Figure S451. Get High-res Image Gene #69: '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 S452. Gene #69: 'del_xq22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	56	72	75
DEL PEAK 44(XQ22.3) MUTATED	15	22	52	34
DEL PEAK 44(XQ22.3) WILD-TYPE	39	34	20	41

Figure S452. Get High-res Image Gene #69: 'del_xq22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq22.3' versus 'RPPA_CNMF'

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

Table S453. Gene #69: 'del_xq22.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	45	61	56
DEL PEAK 44(XQ22.3) MUTATED	24	23	42	18
DEL PEAK 44(XQ22.3) WILD-TYPE	34	22	19	38

Figure S453. Get High-res Image Gene #69: 'del_xq22.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_xq22.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00627 (Fisher's exact test), Q value = 0.014

Table S454. Gene #69: 'del_xq22.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	35	49	68	22	22
DEL PEAK 44(XQ22.3) MUTATED	12	15	21	45	9	5
DEL PEAK 44(XQ22.3) WILD-TYPE	12	20	28	23	13	17

Figure S454. Get High-res Image Gene #69: '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 S455. Gene #69: 'del_xq22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	77	64
DEL PEAK 44(XQ22.3) MUTATED	47	55	20
DEL PEAK 44(XQ22.3) WILD-TYPE	67	22	44

Figure S455. Get High-res Image Gene #69: 'del_xq22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xq22.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S456. Gene #69: '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	47	21	49	46	30	29	33
DEL PEAK 44(XQ22.3) MUTATED	27	5	35	13	10	19	13
DEL PEAK 44(XQ22.3) WILD-TYPE	20	16	14	33	20	10	20

Figure S456. Get High-res Image Gene #69: 'del_xq22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xq22.3' versus 'MIRSEQ_CNMF'

P value = 0.00099 (Fisher's exact test), Q value = 0.0029

Table S457. Gene #69: 'del_xq22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	50	100
DEL PEAK 44(XQ22.3) MUTATED	37	23	61
DEL PEAK 44(XQ22.3) WILD-TYPE	68	27	39

Figure S457. Get High-res Image Gene #69: 'del_xq22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xq22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00026

Table S458. Gene #69: 'del_xq22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	82	37	114	22
DEL PEAK 44(XQ22.3) MUTATED	32	10	72	7
DEL PEAK 44(XQ22.3) WILD-TYPE	50	27	42	15

Figure S458. Get High-res Image Gene #69: 'del_xq22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xq22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0061 (Fisher's exact test), Q value = 0.013

Table S459. Gene #69: 'del_xq22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	27	47	23	39
DEL PEAK 44(XQ22.3) MUTATED	18	17	29	14	17
DEL PEAK 44(XQ22.3) WILD-TYPE	40	10	18	9	22

Figure S459. Get High-res Image Gene #69: 'del_xq22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xq22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0114 (Fisher's exact test), Q value = 0.022

Table S460. Gene #69: 'del_xq22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	49	21	42	24
DEL PEAK 44(XQ22.3) MUTATED	25	33	10	21	6
DEL PEAK 44(XQ22.3) WILD-TYPE	33	16	11	21	18

Figure S460. Get High-res Image Gene #69: '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/22534094/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/SARC-TP/22542442/SARC-TP.transferedmergedcluster.txt
Number of patients = 257
Number of significantly focal cnvs = 69
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.

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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