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 68 focal events and 12 molecular subtypes across 516 patients, 518 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p22.3 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_1q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_3q26.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', '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', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6p21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7p11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_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', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8p11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_11q13.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12p12.1 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12q14.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12q15 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_14q13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q12 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_18q11.2 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19q12 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20q13.33 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_22q11.22 cnv correlated to 'CN_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_xq28 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_2q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_3p26.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p21.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3q11.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_3q29 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_4p16.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q34.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q12.1 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_5q31.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q11.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_6q22.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_6q26 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_8p23.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p11.21 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_9p23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_9q21.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10p15.3 cnv correlated to 'CN_CNMF', 'METHLYATION_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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p15.5 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q23.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_11q25 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_12p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_12q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12q24.33 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_13q12.11 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q12.13 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q14.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q34 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q32.12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_15q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q15.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q21.32 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_19p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19q11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19q13.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_20p13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_20q13.12 cnv correlated to 'MRNA_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_21q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_22q13.32 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 68 focal events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 518 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
del 4q34 3	188 (36%)	328	0.00476 (0.0102)	0.00558 (0.0118)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.0396 (0.0648)	0.00275 (0.00622)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.024 (0.0424)	1e-05 (4.23e-05)
del 8p23 2	257 (50%)	259	0.0236 (0.0418)	0.0483 (0.0766)	1e-05 (4.23e-05)	0.0358 (0.0595)	0.00937 (0.0188)	0.0015 (0.00369)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.00026 (0.000771)	0.01 (0.02)	0.0217 (0.0392)	0.00098 (0.00251)
amp 3q26 2	171 (33%)	345	0.00025 (0.000747)	0.00184 (0.00439)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.00295 (0.0066)	0.00156 (0.0038)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.459 (0.522)	1e-05 (4.23e-05)
amp 8q24 21	322 (62%)	194	0.00756 (0.0155)	0.0265 (0.0458)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.0211 (0.0384)	0.0885 (0.128)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.00015 (0.000465)	0.0484 (0.0766)	1e-05 (4.23e-05)
amp 19q12	137 (27%)	379	0.0932 (0.135)	0.04 (0.0652)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.00011 (0.000353)	0.00294 (0.00659)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	2e-05 (7.7e-05)	0.00021 (0.000637)	0.0453 (0.0725)	0.00012 (0.00038)
amp 20q13 33	244 (47%)	272	0.00312 (0.00694)	0.0148 (0.0281)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.0875 (0.127)	0.00078 (0.00205)	0.00153 (0.00374)	1e-05 (4.23e-05)	2e-05 (7.7e-05)	1e-05 (4.23e-05)	0.022 (0.0395)	2e-05 (7.7e-05)
del 13q12 11	294 (57%)	222	0.00074 (0.00195)	0.0232 (0.0411)	1e-05 (4.23e-05)	0.00133 (0.0033)	0.00018 (0.000552)	0.0379 (0.0623)	4e-05 (0.000141)	1e-05 (4.23e-05)	0.00329 (0.00726)	0.00387 (0.00844)	0.243 (0.304)	0.00095 (0.00245)
del 13q14 2	282 (55%)	234	0.0125 (0.0242)	0.0226 (0.0405)	1e-05 (4.23e-05)	0.00464 (0.00994)	0.00044 (0.00123)	0.0599 (0.0913)	0.00013 (0.000406)	1e-05 (4.23e-05)	0.00228 (0.0053)	0.005 (0.0107)	0.0488 (0.0769)	9e-05 (0.000297)
del 22q13 32	255 (49%)	261	0.0248 (0.0434)	0.0792 (0.117)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.00442 (0.00959)	0.00045 (0.00126)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.0146 (0.0279)	5e-05 (0.000173)
amp 11q13 3	170 (33%)	346	0.00103 (0.00263)	0.0001 (0.000326)	1e-05 (4.23e-05)	3e-05 (0.000111)	0.224 (0.283)	0.00637 (0.0133)	5e-05 (0.000173)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.467 (0.531)	0.00021 (0.000637)
amp 17q12	226 (44%)	290	0.122 (0.17)	0.0472 (0.0749)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.00223 (0.0052)	0.0007 (0.00187)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.545 (0.601)	1e-05 (4.23e-05)
del 5q12 1	177 (34%)	339	0.221 (0.281)	0.184 (0.243)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	4e-05 (0.000141)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.0126 (0.0242)	1e-05 (4.23e-05)
del 11p15 5	143 (28%)	373	0.268 (0.329)	0.0321 (0.0541)	1e-05 (4.23e-05)	0.00104 (0.00264)	0.0212 (0.0385)	0.00299 (0.00667)	2e-05 (7.7e-05)	1e-05 (4.23e-05)	0.00029 (0.000845)	0.00028 (0.000822)	0.0712 (0.106)	0.00051 (0.00142)
del 13q12 13	293 (57%)	223	0.00893 (0.018)	0.0652 (0.098)	1e-05 (4.23e-05)	0.00163 (0.00395)	0.00011 (0.000353)	0.0259 (0.0449)	8e-05 (0.000268)	1e-05 (4.23e-05)	0.00447 (0.00968)	0.00581 (0.0122)	0.209 (0.269)	0.00068 (0.00183)
amp 7p11 2	272 (53%)	244	0.922 (0.943)	0.817 (0.853)	1e-05 (4.23e-05)	0.0339 (0.0568)	0.0973 (0.14)	0.0138 (0.0263)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	2e-05 (7.7e-05)	8e-05 (0.000268)	1e-05 (4.23e-05)
amp 8p11 21	173 (34%)	343	0.439 (0.503)	0.635 (0.689)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.0817 (0.12)	0.00581 (0.0122)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.0004 (0.00113)	0.00013 (0.000406)	0.0134 (0.0257)	0.00027 (0.000798)
amp 12p12 1	179 (35%)	337	0.196 (0.255)	0.0378 (0.0623)	1e-05 (4.23e-05)	0.00265 (0.00602)	0.057 (0.088)	0.0165 (0.0311)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	4e-05 (0.000141)	1e-05 (4.23e-05)	0.678 (0.731)	1e-05 (4.23e-05)
amp 12q14 1	168 (33%)	348	0.505 (0.567)	0.137 (0.19)	1e-05 (4.23e-05)	0.00019 (0.000581)	0.00028 (0.000822)	0.0306 (0.0518)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.349 (0.413)	1e-05 (4.23e-05)
amp 12q15	171 (33%)	345	0.358 (0.422)	0.0625 (0.095)	1e-05 (4.23e-05)	3e-05 (0.000111)	0.00064 (0.00174)	0.0103 (0.0204)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.434 (0.499)	1e-05 (4.23e-05)
amp 14q13 3	229 (44%)	287	0.481 (0.545)	0.315 (0.376)	1e-05 (4.23e-05)	4e-05 (0.000141)	0.0228 (0.0406)	0.0335 (0.0563)	0.0008 (0.00209)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.188 (0.248)	9e-05 (0.000297)
amp 17q23 1	249 (48%)	267	0.0792 (0.117)	0.3 (0.362)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.0384 (0.0629)	0.00273 (0.00619)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.705 (0.75)	2e-05 (7.7e-05)
del 3p21 31	246 (48%)	270	0.249 (0.311)	0.142 (0.194)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.0247 (0.0434)	0.00092 (0.00238)	0.00157 (0.00381)	1e-05 (4.23e-05)	3e-05 (0.000111)	2e-05 (7.7e-05)	0.598 (0.653)	3e-05 (0.000111)
del 4p16 3	131 (25%)	385	0.804 (0.842)	0.846 (0.879)	0.00129 (0.00322)	0.00038 (0.00108)	0.0218 (0.0392)	0.0269 (0.0463)	0.00961 (0.0192)	2e-05 (7.7e-05)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.729 (0.773)	0.00066 (0.00178)
del 5q31 1	208 (40%)	308	0.2 (0.261)	0.143 (0.195)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	2e-05 (7.7e-05)	4e-05 (0.000141)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.399 (0.466)	1e-05 (4.23e-05)
del 9q21 11	256 (50%)	260	0.0638 (0.0967)	0.537 (0.595)	1e-05 (4.23e-05)	0.0001 (0.000326)	0.0227 (0.0405)	0.00069 (0.00185)	0.00564 (0.0119)	2e-05 (7.7e-05)	6e-05 (0.000206)	1e-05 (4.23e-05)	0.188 (0.248)	0.0003 (0.000868)
del 13q34	243 (47%)	273	0.0241 (0.0424)	0.0843 (0.123)	1e-05 (4.23e-05)	0.0402 (0.0654)	0.00188 (0.00446)	0.272 (0.333)	0.00055 (0.00151)	1e-05 (4.23e-05)	0.00813 (0.0166)	0.0201 (0.0367)	0.223 (0.283)	0.0218 (0.0392)
del 16q23 1	170 (33%)	346	0.0867 (0.126)	1 (1.00)	1e-05 (4.23e-05)	4e-05 (0.000141)	4e-05 (0.000141)	0.00543 (0.0115)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.0213 (0.0387)	0.00327 (0.00723)	0.864 (0.893)	0.00054 (0.00149)
del 19p13 3	283 (55%)	233	0.257 (0.318)	1 (1.00)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.00231 (0.00535)	0.0488 (0.0769)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.103 (0.148)	0.00086 (0.00223)
del 19q13 33	194 (38%)	322	0.519 (0.578)	0.0959 (0.138)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.0122 (0.0237)	0.00043 (0.00121)	4e-05 (0.000141)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.577 (0.632)	0.0119 (0.0231)
amp 1q21 3	372 (72%)	144	0.855 (0.887)	1 (1.00)	2e-05 (7.7e-05)	1e-05 (4.23e-05)	0.00058 (0.00159)	0.209 (0.269)	4e-05 (0.000141)	0.00012 (0.00038)	0.00454 (0.00977)	0.00073 (0.00194)	0.00527 (0.0112)	0.172 (0.228)
amp 18q11 2	103 (20%)	413	0.193 (0.253)	0.0197 (0.0363)	3e-05 (0.000111)	1e-05 (4.23e-05)	0.559 (0.615)	0.218 (0.278)	9e-05 (0.000297)	2e-05 (7.7e-05)	8e-05 (0.000268)	1e-05 (4.23e-05)	0.428 (0.493)	2e-05 (7.7e-05)
del 1p36 11	125 (24%)	391	0.438 (0.502)	0.125 (0.175)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.0172 (0.0321)	0.0748 (0.111)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.0248 (0.0434)	0.0644 (0.0974)	0.0167 (0.0314)	0.0088 (0.0178)
del 3p26 2	236 (46%)	280	0.169 (0.226)	0.31 (0.373)	1e-05 (4.23e-05)	0.00011 (0.000353)	0.0538 (0.0844)	0.00868 (0.0176)	0.035 (0.0584)	1e-05 (4.23e-05)	3e-05 (0.000111)	0.0003 (0.000868)	0.797 (0.835)	0.00051 (0.00142)
del 10q26 3	156 (30%)	360	0.273 (0.333)	0.132 (0.183)	0.00041 (0.00116)	0.0384 (0.0629)	0.00742 (0.0152)	0.788 (0.828)	0.00278 (0.00627)	1e-05 (4.23e-05)	0.0117 (0.0229)	0.00153 (0.00374)	0.0582 (0.0893)	0.00108 (0.00273)
del 15q11 2	262 (51%)	254	0.264 (0.325)	0.142 (0.194)	1e-05 (4.23e-05)	0.00103 (0.00263)	0.0373 (0.0617)	0.505 (0.567)	0.00074 (0.00195)	1e-05 (4.23e-05)	5e-05 (0.000173)	0.00701 (0.0144)	0.307 (0.369)	3e-05 (0.000111)
del 17p13 3	281 (54%)	235	0.664 (0.718)	0.56 (0.615)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.0105 (0.0208)	0.764 (0.807)	4e-05 (0.000141)	1e-05 (4.23e-05)	0.0138 (0.0263)	0.0252 (0.0438)	0.921 (0.943)	0.00199 (0.00469)
del 19p13 2	280 (54%)	236	0.744 (0.788)	0.898 (0.922)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.0103 (0.0205)	0.142 (0.194)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	2e-05 (7.7e-05)	1e-05 (4.23e-05)	0.0576 (0.0885)	0.00111 (0.00279)
del 19p13 2	270 (52%)	246	0.695 (0.743)	1 (1.00)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.0013 (0.00323)	0.155 (0.209)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.0541 (0.0848)	0.00013 (0.000406)
del 19q11	134 (26%)	382	1 (1.00)	0.879 (0.906)	1e-05 (4.23e-05)	0.0008 (0.00209)	0.305 (0.367)	0.00575 (0.0121)	0.00264 (0.00602)	0.00241 (0.00556)	0.00168 (0.00406)	0.00033 (0.000945)	0.409 (0.476)	0.0451 (0.0723)
del 21q11 2	185 (36%)	331	0.222 (0.282)	0.238 (0.298)	1e-05 (4.23e-05)	0.0273 (0.0468)	0.00449 (0.00969)	0.0687 (0.103)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.00024 (0.00072)	0.44 (0.503)	0.00022 (0.000665)
amp 5p15 33	328 (64%)	188	0.0567 (0.0876)	0.228 (0.286)	1e-05 (4.23e-05)	0.00172 (0.00414)	0.351 (0.415)	0.666 (0.72)	0.023 (0.0408)	0.00015 (0.000465)	0.00147 (0.00363)	0.00091 (0.00236)	0.358 (0.422)	1e-05 (4.23e-05)
amp 7q31 2	214 (41%)	302	0.956 (0.971)	0.417 (0.484)	1e-05 (4.23e-05)	0.183 (0.241)	0.0345 (0.0576)	0.08 (0.117)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.00106 (0.00269)	0.00175 (0.0042)	0.113 (0.159)	1e-05 (4.23e-05)
del 10p15 3	126 (24%)	390	1 (1.00)	1 (1.00)	0.00644 (0.0133)	0.0104 (0.0206)	0.433 (0.499)	0.986 (1)	0.136 (0.189)	0.00223 (0.0052)	0.00201 (0.00473)	0.0191 (0.0353)	0.0315 (0.0532)	0.013 (0.025)
del 11q23 2	119 (23%)	397	0.455 (0.52)	0.685 (0.736)	1e-05 (4.23e-05)	0.00026 (0.000771)	0.0176 (0.0329)	0.0583 (0.0893)	1e-05 (4.23e-05)	0.00078 (0.00205)	0.00221 (0.00518)	0.0551 (0.086)	0.0459 (0.0732)	0.312 (0.375)
del 15q15 1	274 (53%)	242	0.161 (0.217)	0.0646 (0.0974)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.077 (0.114)	0.171 (0.227)	0.00012 (0.00038)	1e-05 (4.23e-05)	2e-05 (7.7e-05)	0.00031 (0.000891)	0.233 (0.292)	2e-05 (7.7e-05)
amp 6p21 1	190 (37%)	326	0.64 (0.693)	0.224 (0.283)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.109 (0.154)	0.361 (0.425)	0.0545 (0.0852)	0.0101 (0.0201)	0.0338 (0.0568)	0.00684 (0.0141)	0.348 (0.413)	0.0277 (0.0476)
amp xq28	157 (30%)	359	0.191 (0.251)	0.16 (0.215)	1e-05 (4.23e-05)	0.00068 (0.00183)	0.052 (0.0818)	0.141 (0.194)	5e-05 (0.000173)	0.00018 (0.000552)	0.00884 (0.0179)	0.0858 (0.125)	0.262 (0.323)	0.00024 (0.00072)
del 1p13 1	149 (29%)	367	0.344 (0.409)	0.539 (0.597)	1e-05 (4.23e-05)	0.0004 (0.00113)	0.0198 (0.0364)	0.568 (0.623)	2e-05 (7.7e-05)	8e-05 (0.000268)	0.193 (0.253)	0.00455 (0.00977)	0.837 (0.872)	0.778 (0.82)
del 2q22 1	46 (9%)	470	0.871 (0.899)	0.781 (0.822)	0.0038 (0.00831)	0.00265 (0.00602)	0.102 (0.146)	0.00176 (0.00421)	0.0592 (0.0904)	0.0161 (0.0304)	0.0372 (0.0617)	0.0083 (0.0169)	0.856 (0.887)	0.0883 (0.128)
del 12q12	98 (19%)	418	0.597 (0.652)	0.748 (0.79)	1e-05 (4.23e-05)	0.0246 (0.0432)	0.00199 (0.00469)	0.517 (0.577)	0.0001 (0.000326)	0.0446 (0.0716)	0.0565 (0.0875)	0.214 (0.274)	0.901 (0.924)	0.0266 (0.0459)
del 18q21 32	251 (49%)	265	0.407 (0.474)	0.0903 (0.131)	1e-05 (4.23e-05)	0.95 (0.967)	0.00333 (0.00732)	0.0253 (0.0439)	2e-05 (7.7e-05)	1e-05 (4.23e-05)	0.0197 (0.0363)	0.112 (0.158)	0.87 (0.899)	0.0616 (0.0938)
del 20p13	131 (25%)	385	0.105 (0.15)	0.225 (0.283)	1e-05 (4.23e-05)	0.00052 (0.00144)	0.0352 (0.0586)	0.3 (0.362)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.954 (0.971)	0.705 (0.75)	0.365 (0.43)	0.0149 (0.0282)
amp 1p22 3	141 (27%)	375	1 (1.00)	0.844 (0.877)	1e-05 (4.23e-05)	0.547 (0.603)	0.00111 (0.00279)	0.0168 (0.0314)	0.0564 (0.0875)	0.0426 (0.0689)	0.141 (0.194)	0.0281 (0.0481)	0.423 (0.49)	0.181 (0.24)
del 3q29	135 (26%)	381	0.61 (0.663)	0.689 (0.739)	0.00322 (0.00714)	0.00149 (0.00367)	0.0765 (0.113)	0.0309 (0.0523)	1e-05 (4.23e-05)	1e-05 (4.23e-05)	0.787 (0.828)	0.0649 (0.0977)	0.143 (0.196)	0.246 (0.307)
del 9p23	285 (55%)	231	0.168 (0.226)	0.315 (0.376)	1e-05 (4.23e-05)	0.04 (0.0652)	0.367 (0.431)	0.401 (0.467)	0.0409 (0.0664)	0.00031 (0.000891)	0.171 (0.227)	0.0249 (0.0435)	0.282 (0.344)	0.214 (0.274)
del 9p21 3	291 (56%)	225	0.169 (0.226)	0.315 (0.376)	1e-05 (4.23e-05)	0.018 (0.0334)	0.296 (0.358)	0.222 (0.282)	0.114 (0.16)	1e-05 (4.23e-05)	0.193 (0.253)	0.00186 (0.00442)	0.0439 (0.0707)	0.105 (0.15)
del 11q25	117 (23%)	399	0.108 (0.154)	0.482 (0.545)	4e-05 (0.000141)	0.00018 (0.000552)	0.0158 (0.03)	0.106 (0.151)	3e-05 (0.000111)	0.0028 (0.00629)	0.0681 (0.102)	0.14 (0.194)	0.0984 (0.141)	0.427 (0.493)
del 12p13 2	138 (27%)	378	0.386 (0.451)	1 (1.00)	1e-05 (4.23e-05)	0.0122 (0.0237)	0.0287 (0.049)	0.341 (0.407)	0.00029 (0.000845)	0.00946 (0.019)	0.896 (0.921)	0.979 (0.994)	0.473 (0.537)	0.113 (0.159)
del 12q24 33	137 (27%)	379	0.212 (0.272)	0.203 (0.263)	0.00011 (0.000353)	0.217 (0.277)	0.00255 (0.00584)	0.11 (0.156)	7e-05 (0.000238)	7e-05 (0.000238)	0.204 (0.264)	0.011 (0.0217)	0.504 (0.567)	0.501 (0.565)
del 14q32 12	144 (28%)	372	0.701 (0.748)	0.286 (0.347)	1e-05 (4.23e-05)	0.00337 (0.00739)	0.507 (0.568)	0.378 (0.442)	0.256 (0.317)	0.0117 (0.0229)	0.00719 (0.0148)	0.164 (0.221)	0.0464 (0.0738)	0.0703 (0.105)
del xp22 2	143 (28%)	373	0.691 (0.74)	0.894 (0.92)	1e-05 (4.23e-05)	0.0165 (0.0311)	0.0413 (0.0668)	0.0632 (0.0959)	0.0116 (0.0227)	0.00012 (0.00038)	0.271 (0.332)	0.513 (0.574)	0.99 (1.00)	0.0692 (0.103)
del 3q11 1	140 (27%)	376	0.609 (0.663)	0.685 (0.736)	0.018 (0.0334)	0.00644 (0.0133)	0.212 (0.272)	0.67 (0.723)	0.0207 (0.0379)	0.0376 (0.0622)	0.15 (0.203)	0.74 (0.784)	0.524 (0.582)	0.839 (0.873)
del 6q22 31	252 (49%)	264	0.271 (0.332)	0.147 (0.2)	6e-05 (0.000206)	1e-05 (4.23e-05)	0.0724 (0.108)	0.285 (0.346)	0.176 (0.234)	0.00066 (0.00178)	0.797 (0.835)	0.00117 (0.00293)	0.494 (0.558)	0.346 (0.411)
del 6q26	257 (50%)	259	0.458 (0.522)	0.23 (0.289)	0.0006 (0.00164)	5e-05 (0.000173)	0.295 (0.358)	0.252 (0.313)	0.202 (0.263)	0.00625 (0.013)	0.937 (0.957)	0.0182 (0.0336)	0.514 (0.574)	0.284 (0.346)
amp 22q11 22	88 (17%)	428	0.196 (0.255)	0.146 (0.199)	2e-05 (7.7e-05)	0.442 (0.505)	0.262 (0.323)	0.0558 (0.0867)	0.108 (0.153)	0.0553 (0.0862)	0.0572 (0.0881)	0.0292 (0.0498)	0.596 (0.652)	0.0217 (0.0392)
del 20q13 12	80 (16%)	436	0.0294 (0.0499)	0.522 (0.58)	0.519 (0.578)	0.427 (0.493)	0.119 (0.166)	0.209 (0.27)	0.13 (0.181)	0.00409 (0.0089)	0.157 (0.213)	0.226 (0.285)	0.0433 (0.0698)	0.257 (0.318)
del 6q11 1	134 (26%)	382	0.538 (0.596)	1 (1.00)	0.0458 (0.0731)	0.00232 (0.00536)	0.943 (0.962)	0.609 (0.663)	0.435 (0.5)	0.729 (0.773)	0.0771 (0.114)	0.148 (0.201)	0.69 (0.739)	0.111 (0.156)
del 8p11 21	123 (24%)	393	0.806 (0.842)	0.257 (0.318)	1e-05 (4.23e-05)	0.347 (0.413)	0.484 (0.548)	0.377 (0.442)	0.00246 (0.00565)	0.165 (0.221)	0.208 (0.268)	0.69 (0.739)	0.541 (0.598)	0.129 (0.18)

'amp_1p22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S1. Gene #1: 'amp_1p22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
AMP PEAK 1(1P22.3) MUTATED	17	45	10	69
AMP PEAK 1(1P22.3) WILD-TYPE	52	183	69	71

Figure S1. Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1p22.3' versus 'RPPA_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0028

Table S2. Gene #1: 'amp_1p22.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
AMP PEAK 1(1P22.3) MUTATED	38	6	22	20	17
AMP PEAK 1(1P22.3) WILD-TYPE	53	16	44	55	92

Figure S2. Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_1p22.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.031

Table S3. Gene #1: 'amp_1p22.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
AMP PEAK 1(1P22.3) MUTATED	51	43	9
AMP PEAK 1(1P22.3) WILD-TYPE	116	90	54

Figure S3. Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_1p22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0426 (Fisher's exact test), Q value = 0.069

Table S4. Gene #1: 'amp_1p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
AMP PEAK 1(1P22.3) MUTATED	20	34	38	8	12	13	15
AMP PEAK 1(1P22.3) WILD-TYPE	58	76	59	40	41	36	62

Figure S4. Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1p22.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S5. Gene #1: 'amp_1p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
AMP PEAK 1(1P22.3) MUTATED	15	52	33	39
AMP PEAK 1(1P22.3) WILD-TYPE	56	146	108	61

Figure S5. Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.7e-05

Table S6. Gene #2: 'amp_1q21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
AMP PEAK 2(1Q21.3) MUTATED	63	140	58	111
AMP PEAK 2(1Q21.3) WILD-TYPE	6	88	21	29

Figure S6. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S7. Gene #2: 'amp_1q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
AMP PEAK 2(1Q21.3) MUTATED	80	124	127
AMP PEAK 2(1Q21.3) WILD-TYPE	64	25	35

Figure S7. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q21.3' versus 'RPPA_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.0016

Table S8. Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
AMP PEAK 2(1Q21.3) MUTATED	70	17	59	58	66
AMP PEAK 2(1Q21.3) WILD-TYPE	21	5	7	17	43

Figure S8. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S9. Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
AMP PEAK 2(1Q21.3) MUTATED	106	134	129
AMP PEAK 2(1Q21.3) WILD-TYPE	60	61	22

Figure S9. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00038

Table S10. Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
AMP PEAK 2(1Q21.3) MUTATED	54	74	69	45	45	38	44
AMP PEAK 2(1Q21.3) WILD-TYPE	24	36	28	3	8	11	33

Figure S10. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_CNMF'

P value = 0.00454 (Fisher's exact test), Q value = 0.0098

Table S11. Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
AMP PEAK 2(1Q21.3) MUTATED	122	180	65
AMP PEAK 2(1Q21.3) WILD-TYPE	67	48	28

Figure S11. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00073 (Fisher's exact test), Q value = 0.0019

Table S12. Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
AMP PEAK 2(1Q21.3) MUTATED	52	155	83	77
AMP PEAK 2(1Q21.3) WILD-TYPE	19	43	58	23

Figure S12. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00527 (Fisher's exact test), Q value = 0.011

Table S13. Gene #2: 'amp_1q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	198	91
AMP PEAK 2(1Q21.3) MUTATED	111	152	54
AMP PEAK 2(1Q21.3) WILD-TYPE	34	46	37

Figure S13. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.2' versus 'MRNA_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.00075

Table S14. Gene #3: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S14. Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00184 (Fisher's exact test), Q value = 0.0044

Table S15. Gene #3: 'amp_3q26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	11	7
AMP PEAK 3(3Q26.2) MUTATED	0	6	4
AMP PEAK 3(3Q26.2) WILD-TYPE	14	5	3

Figure S15. Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_3q26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S16. Gene #3: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
AMP PEAK 3(3Q26.2) MUTATED	22	46	44	59
AMP PEAK 3(3Q26.2) WILD-TYPE	47	182	35	81

Figure S16. Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S17. Gene #3: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
AMP PEAK 3(3Q26.2) MUTATED	27	70	50
AMP PEAK 3(3Q26.2) WILD-TYPE	117	79	112

Figure S17. Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'RPPA_CNMF'

P value = 0.00295 (Fisher's exact test), Q value = 0.0066

Table S18. Gene #3: 'amp_3q26.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
AMP PEAK 3(3Q26.2) MUTATED	30	7	17	40	30
AMP PEAK 3(3Q26.2) WILD-TYPE	61	15	49	35	79

Figure S18. Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_3q26.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00156 (Fisher's exact test), Q value = 0.0038

Table S19. Gene #3: 'amp_3q26.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
AMP PEAK 3(3Q26.2) MUTATED	44	61	19
AMP PEAK 3(3Q26.2) WILD-TYPE	123	72	44

Figure S19. Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_3q26.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S20. Gene #3: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
AMP PEAK 3(3Q26.2) MUTATED	26	92	53
AMP PEAK 3(3Q26.2) WILD-TYPE	140	103	98

Figure S20. Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S21. Gene #3: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
AMP PEAK 3(3Q26.2) MUTATED	8	39	65	5	17	19	18
AMP PEAK 3(3Q26.2) WILD-TYPE	70	71	32	43	36	30	59

Figure S21. Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S22. Gene #3: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
AMP PEAK 3(3Q26.2) MUTATED	41	103	25
AMP PEAK 3(3Q26.2) WILD-TYPE	148	125	68

Figure S22. Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S23. Gene #3: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
AMP PEAK 3(3Q26.2) MUTATED	12	67	36	54
AMP PEAK 3(3Q26.2) WILD-TYPE	59	131	105	46

Figure S23. Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S24. Gene #3: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
AMP PEAK 3(3Q26.2) MUTATED	15	101	26
AMP PEAK 3(3Q26.2) WILD-TYPE	88	147	57

Figure S24. Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S25. Gene #4: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
AMP PEAK 4(5P15.33) MUTATED	47	109	48	124
AMP PEAK 4(5P15.33) WILD-TYPE	22	119	31	16

Figure S25. Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 0.00172 (Fisher's exact test), Q value = 0.0041

Table S26. Gene #4: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
AMP PEAK 4(5P15.33) MUTATED	76	108	108
AMP PEAK 4(5P15.33) WILD-TYPE	68	41	54

Figure S26. Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 0.023 (Fisher's exact test), Q value = 0.041

Table S27. Gene #4: 'amp_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
AMP PEAK 4(5P15.33) MUTATED	96	138	91
AMP PEAK 4(5P15.33) WILD-TYPE	70	57	60

Figure S27. Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00047

Table S28. Gene #4: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
AMP PEAK 4(5P15.33) MUTATED	48	76	77	22	35	30	37
AMP PEAK 4(5P15.33) WILD-TYPE	30	34	20	26	18	19	40

Figure S28. Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 0.00147 (Fisher's exact test), Q value = 0.0036

Table S29. Gene #4: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
AMP PEAK 4(5P15.33) MUTATED	103	163	61
AMP PEAK 4(5P15.33) WILD-TYPE	86	65	32

Figure S29. Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00091 (Fisher's exact test), Q value = 0.0024

Table S30. Gene #4: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
AMP PEAK 4(5P15.33) MUTATED	44	134	73	76
AMP PEAK 4(5P15.33) WILD-TYPE	27	64	68	24

Figure S30. Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S31. Gene #4: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
AMP PEAK 4(5P15.33) MUTATED	42	187	56
AMP PEAK 4(5P15.33) WILD-TYPE	61	61	27

Figure S31. Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6p21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S32. Gene #5: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
AMP PEAK 5(6P21.1) MUTATED	43	61	28	58
AMP PEAK 5(6P21.1) WILD-TYPE	26	167	51	82

Figure S32. Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S33. Gene #5: 'amp_6p21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
AMP PEAK 5(6P21.1) MUTATED	28	72	70
AMP PEAK 5(6P21.1) WILD-TYPE	116	77	92

Figure S33. Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S34. Gene #5: 'amp_6p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
AMP PEAK 5(6P21.1) MUTATED	26	35	44	24	25	17	18
AMP PEAK 5(6P21.1) WILD-TYPE	52	75	53	24	28	32	59

Figure S34. Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_CNMF'

P value = 0.0338 (Fisher's exact test), Q value = 0.057

Table S35. Gene #5: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
AMP PEAK 5(6P21.1) MUTATED	58	97	31
AMP PEAK 5(6P21.1) WILD-TYPE	131	131	62

Figure S35. Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_6p21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00684 (Fisher's exact test), Q value = 0.014

Table S36. Gene #5: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
AMP PEAK 5(6P21.1) MUTATED	21	85	38	42
AMP PEAK 5(6P21.1) WILD-TYPE	50	113	103	58

Figure S36. Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0277 (Fisher's exact test), Q value = 0.048

Table S37. Gene #5: 'amp_6p21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
AMP PEAK 5(6P21.1) MUTATED	27	97	36
AMP PEAK 5(6P21.1) WILD-TYPE	76	151	47

Figure S37. Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S38. Gene #6: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
AMP PEAK 6(7P11.2) MUTATED	26	87	46	113
AMP PEAK 6(7P11.2) WILD-TYPE	43	141	33	27

Figure S38. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

P value = 0.0339 (Fisher's exact test), Q value = 0.057

Table S39. Gene #6: 'amp_7p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
AMP PEAK 6(7P11.2) MUTATED	64	79	96
AMP PEAK 6(7P11.2) WILD-TYPE	80	70	66

Figure S39. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0138 (Fisher's exact test), Q value = 0.026

Table S40. Gene #6: 'amp_7p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
AMP PEAK 6(7P11.2) MUTATED	82	85	29
AMP PEAK 6(7P11.2) WILD-TYPE	85	48	34

Figure S40. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S41. Gene #6: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
AMP PEAK 6(7P11.2) MUTATED	75	135	58
AMP PEAK 6(7P11.2) WILD-TYPE	91	60	93

Figure S41. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S42. Gene #6: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
AMP PEAK 6(7P11.2) MUTATED	31	81	57	9	24	32	34
AMP PEAK 6(7P11.2) WILD-TYPE	47	29	40	39	29	17	43

Figure S42. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S43. Gene #6: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
AMP PEAK 6(7P11.2) MUTATED	71	133	64
AMP PEAK 6(7P11.2) WILD-TYPE	118	95	29

Figure S43. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7.7e-05

Table S44. Gene #6: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
AMP PEAK 6(7P11.2) MUTATED	22	126	63	57
AMP PEAK 6(7P11.2) WILD-TYPE	49	72	78	43

Figure S44. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00027

Table S45. Gene #6: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	198	91
AMP PEAK 6(7P11.2) MUTATED	61	107	65
AMP PEAK 6(7P11.2) WILD-TYPE	84	91	26

Figure S45. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S46. Gene #6: 'amp_7p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
AMP PEAK 6(7P11.2) MUTATED	31	153	49
AMP PEAK 6(7P11.2) WILD-TYPE	72	95	34

Figure S46. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S47. Gene #7: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
AMP PEAK 7(7Q31.2) MUTATED	19	67	30	98
AMP PEAK 7(7Q31.2) WILD-TYPE	50	161	49	42

Figure S47. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q31.2' versus 'RPPA_CNMF'

P value = 0.0345 (Fisher's exact test), Q value = 0.058

Table S48. Gene #7: 'amp_7q31.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
AMP PEAK 7(7Q31.2) MUTATED	41	8	20	42	44
AMP PEAK 7(7Q31.2) WILD-TYPE	50	14	46	33	65

Figure S48. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S49. Gene #7: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
AMP PEAK 7(7Q31.2) MUTATED	55	106	49
AMP PEAK 7(7Q31.2) WILD-TYPE	111	89	102

Figure S49. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S50. Gene #7: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
AMP PEAK 7(7Q31.2) MUTATED	22	71	46	5	16	22	28
AMP PEAK 7(7Q31.2) WILD-TYPE	56	39	51	43	37	27	49

Figure S50. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.0027

Table S51. Gene #7: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
AMP PEAK 7(7Q31.2) MUTATED	59	103	48
AMP PEAK 7(7Q31.2) WILD-TYPE	130	125	45

Figure S51. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00175 (Fisher's exact test), Q value = 0.0042

Table S52. Gene #7: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
AMP PEAK 7(7Q31.2) MUTATED	18	97	50	45
AMP PEAK 7(7Q31.2) WILD-TYPE	53	101	91	55

Figure S52. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S53. Gene #7: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
AMP PEAK 7(7Q31.2) MUTATED	22	123	37
AMP PEAK 7(7Q31.2) WILD-TYPE	81	125	46

Figure S53. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S54. Gene #8: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
AMP PEAK 8(8P11.21) MUTATED	55	43	30	45
AMP PEAK 8(8P11.21) WILD-TYPE	14	185	49	95

Figure S54. Get High-res Image Gene #8: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S55. Gene #8: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
AMP PEAK 8(8P11.21) MUTATED	27	69	57
AMP PEAK 8(8P11.21) WILD-TYPE	117	80	105

Figure S55. Get High-res Image Gene #8: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8p11.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.00581 (Fisher's exact test), Q value = 0.012

Table S56. Gene #8: 'amp_8p11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
AMP PEAK 8(8P11.21) MUTATED	48	60	17
AMP PEAK 8(8P11.21) WILD-TYPE	119	73	46

Figure S56. Get High-res Image Gene #8: 'amp_8p11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_8p11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S57. Gene #8: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
AMP PEAK 8(8P11.21) MUTATED	32	67	71
AMP PEAK 8(8P11.21) WILD-TYPE	134	128	80

Figure S57. Get High-res Image Gene #8: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S58. Gene #8: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
AMP PEAK 8(8P11.21) MUTATED	17	37	39	15	32	18	12
AMP PEAK 8(8P11.21) WILD-TYPE	61	73	58	33	21	31	65

Figure S58. Get High-res Image Gene #8: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0011

Table S59. Gene #8: 'amp_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
AMP PEAK 8(8P11.21) MUTATED	45	96	30
AMP PEAK 8(8P11.21) WILD-TYPE	144	132	63

Figure S59. Get High-res Image Gene #8: 'amp_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00041

Table S60. Gene #8: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
AMP PEAK 8(8P11.21) MUTATED	18	74	31	48
AMP PEAK 8(8P11.21) WILD-TYPE	53	124	110	52

Figure S60. Get High-res Image Gene #8: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_MATURE_CNMF'

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

Table S61. Gene #8: 'amp_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	198	91
AMP PEAK 8(8P11.21) MUTATED	36	79	32
AMP PEAK 8(8P11.21) WILD-TYPE	109	119	59

Figure S61. Get High-res Image Gene #8: 'amp_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 8e-04

Table S62. Gene #8: 'amp_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
AMP PEAK 8(8P11.21) MUTATED	19	101	27
AMP PEAK 8(8P11.21) WILD-TYPE	84	147	56

Figure S62. Get High-res Image Gene #8: 'amp_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNA_CNMF'

P value = 0.00756 (Fisher's exact test), Q value = 0.015

Table S63. Gene #9: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	5	9	12	6
AMP PEAK 9(8Q24.21) MUTATED	5	7	3	5
AMP PEAK 9(8Q24.21) WILD-TYPE	0	2	9	1

Figure S63. Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8q24.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.0265 (Fisher's exact test), Q value = 0.046

Table S64. Gene #9: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	11	7
AMP PEAK 9(8Q24.21) MUTATED	5	9	6
AMP PEAK 9(8Q24.21) WILD-TYPE	9	2	1

Figure S64. Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S65. Gene #9: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
AMP PEAK 9(8Q24.21) MUTATED	66	94	53	109
AMP PEAK 9(8Q24.21) WILD-TYPE	3	134	26	31

Figure S65. Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S66. Gene #9: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
AMP PEAK 9(8Q24.21) MUTATED	63	101	117
AMP PEAK 9(8Q24.21) WILD-TYPE	81	48	45

Figure S66. Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'RPPA_CNMF'

P value = 0.0211 (Fisher's exact test), Q value = 0.038

Table S67. Gene #9: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
AMP PEAK 9(8Q24.21) MUTATED	58	11	48	56	60
AMP PEAK 9(8Q24.21) WILD-TYPE	33	11	18	19	49

Figure S67. Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S68. Gene #9: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
AMP PEAK 9(8Q24.21) MUTATED	76	136	106
AMP PEAK 9(8Q24.21) WILD-TYPE	90	59	45

Figure S68. Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S69. Gene #9: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
AMP PEAK 9(8Q24.21) MUTATED	39	77	67	28	47	31	29
AMP PEAK 9(8Q24.21) WILD-TYPE	39	33	30	20	6	18	48

Figure S69. Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S70. Gene #9: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
AMP PEAK 9(8Q24.21) MUTATED	89	167	62
AMP PEAK 9(8Q24.21) WILD-TYPE	100	61	31

Figure S70. Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00047

Table S71. Gene #9: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
AMP PEAK 9(8Q24.21) MUTATED	36	139	72	71
AMP PEAK 9(8Q24.21) WILD-TYPE	35	59	69	29

Figure S71. Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0484 (Fisher's exact test), Q value = 0.077

Table S72. Gene #9: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	198	91
AMP PEAK 9(8Q24.21) MUTATED	78	132	58
AMP PEAK 9(8Q24.21) WILD-TYPE	67	66	33

Figure S72. Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S73. Gene #9: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
AMP PEAK 9(8Q24.21) MUTATED	42	175	51
AMP PEAK 9(8Q24.21) WILD-TYPE	61	73	32

Figure S73. Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q13.3' versus 'MRNA_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.0026

Table S74. Gene #10: 'amp_11q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	5	9	12	6
AMP PEAK 10(11Q13.3) MUTATED	2	1	2	6
AMP PEAK 10(11Q13.3) WILD-TYPE	3	8	10	0

Figure S74. Get High-res Image Gene #10: 'amp_11q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11q13.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00033

Table S75. Gene #10: 'amp_11q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	11	7
AMP PEAK 10(11Q13.3) MUTATED	3	1	7
AMP PEAK 10(11Q13.3) WILD-TYPE	11	10	0

Figure S75. Get High-res Image Gene #10: 'amp_11q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S76. Gene #10: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
AMP PEAK 10(11Q13.3) MUTATED	36	32	29	73
AMP PEAK 10(11Q13.3) WILD-TYPE	33	196	50	67

Figure S76. Get High-res Image Gene #10: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S77. Gene #10: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
AMP PEAK 10(11Q13.3) MUTATED	27	56	66
AMP PEAK 10(11Q13.3) WILD-TYPE	117	93	96

Figure S77. Get High-res Image Gene #10: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00637 (Fisher's exact test), Q value = 0.013

Table S78. Gene #10: 'amp_11q13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
AMP PEAK 10(11Q13.3) MUTATED	44	58	19
AMP PEAK 10(11Q13.3) WILD-TYPE	123	75	44

Figure S78. Get High-res Image Gene #10: 'amp_11q13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00017

Table S79. Gene #10: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
AMP PEAK 10(11Q13.3) MUTATED	35	70	65
AMP PEAK 10(11Q13.3) WILD-TYPE	131	125	86

Figure S79. Get High-res Image Gene #10: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S80. Gene #10: 'amp_11q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
AMP PEAK 10(11Q13.3) MUTATED	20	43	38	4	35	16	14
AMP PEAK 10(11Q13.3) WILD-TYPE	58	67	59	44	18	33	63

Figure S80. Get High-res Image Gene #10: 'amp_11q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S81. Gene #10: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
AMP PEAK 10(11Q13.3) MUTATED	35	102	30
AMP PEAK 10(11Q13.3) WILD-TYPE	154	126	63

Figure S81. Get High-res Image Gene #10: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S82. Gene #10: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
AMP PEAK 10(11Q13.3) MUTATED	10	81	29	47
AMP PEAK 10(11Q13.3) WILD-TYPE	61	117	112	53

Figure S82. Get High-res Image Gene #10: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00064

Table S83. Gene #10: 'amp_11q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
AMP PEAK 10(11Q13.3) MUTATED	18	98	29
AMP PEAK 10(11Q13.3) WILD-TYPE	85	150	54

Figure S83. Get High-res Image Gene #10: 'amp_11q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p12.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0378 (Fisher's exact test), Q value = 0.062

Table S84. Gene #11: 'amp_12p12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	11	7
AMP PEAK 11(12P12.1) MUTATED	2	3	5
AMP PEAK 11(12P12.1) WILD-TYPE	12	8	2

Figure S84. Get High-res Image Gene #11: 'amp_12p12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_12p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S85. Gene #11: 'amp_12p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
AMP PEAK 11(12P12.1) MUTATED	26	45	62	46
AMP PEAK 11(12P12.1) WILD-TYPE	43	183	17	94

Figure S85. Get High-res Image Gene #11: 'amp_12p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12p12.1' versus 'METHLYATION_CNMF'

P value = 0.00265 (Fisher's exact test), Q value = 0.006

Table S86. Gene #11: 'amp_12p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
AMP PEAK 11(12P12.1) MUTATED	33	61	59
AMP PEAK 11(12P12.1) WILD-TYPE	111	88	103

Figure S86. Get High-res Image Gene #11: 'amp_12p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12p12.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0165 (Fisher's exact test), Q value = 0.031

Table S87. Gene #11: 'amp_12p12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
AMP PEAK 11(12P12.1) MUTATED	43	55	21
AMP PEAK 11(12P12.1) WILD-TYPE	124	78	42

Figure S87. Get High-res Image Gene #11: 'amp_12p12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_12p12.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S88. Gene #11: 'amp_12p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
AMP PEAK 11(12P12.1) MUTATED	31	83	65
AMP PEAK 11(12P12.1) WILD-TYPE	135	112	86

Figure S88. Get High-res Image Gene #11: 'amp_12p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S89. Gene #11: 'amp_12p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
AMP PEAK 11(12P12.1) MUTATED	12	43	35	5	33	30	21
AMP PEAK 11(12P12.1) WILD-TYPE	66	67	62	43	20	19	56

Figure S89. Get High-res Image Gene #11: 'amp_12p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S90. Gene #11: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
AMP PEAK 11(12P12.1) MUTATED	44	103	29
AMP PEAK 11(12P12.1) WILD-TYPE	145	125	64

Figure S90. Get High-res Image Gene #11: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S91. Gene #11: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
AMP PEAK 11(12P12.1) MUTATED	13	81	35	47
AMP PEAK 11(12P12.1) WILD-TYPE	58	117	106	53

Figure S91. Get High-res Image Gene #11: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S92. Gene #11: 'amp_12p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
AMP PEAK 11(12P12.1) MUTATED	17	107	25
AMP PEAK 11(12P12.1) WILD-TYPE	86	141	58

Figure S92. Get High-res Image Gene #11: 'amp_12p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S93. Gene #12: 'amp_12q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
AMP PEAK 12(12Q14.1) MUTATED	30	42	64	32
AMP PEAK 12(12Q14.1) WILD-TYPE	39	186	15	108

Figure S93. Get High-res Image Gene #12: 'amp_12q14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q14.1' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00058

Table S94. Gene #12: 'amp_12q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
AMP PEAK 12(12Q14.1) MUTATED	32	67	48
AMP PEAK 12(12Q14.1) WILD-TYPE	112	82	114

Figure S94. Get High-res Image Gene #12: 'amp_12q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q14.1' versus 'RPPA_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.00082

Table S95. Gene #12: 'amp_12q14.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
AMP PEAK 12(12Q14.1) MUTATED	23	5	23	42	31
AMP PEAK 12(12Q14.1) WILD-TYPE	68	17	43	33	78

Figure S95. Get High-res Image Gene #12: 'amp_12q14.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_12q14.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0306 (Fisher's exact test), Q value = 0.052

Table S96. Gene #12: 'amp_12q14.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
AMP PEAK 12(12Q14.1) MUTATED	48	57	19
AMP PEAK 12(12Q14.1) WILD-TYPE	119	76	44

Figure S96. Get High-res Image Gene #12: 'amp_12q14.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_12q14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S97. Gene #12: 'amp_12q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
AMP PEAK 12(12Q14.1) MUTATED	24	72	72
AMP PEAK 12(12Q14.1) WILD-TYPE	142	123	79

Figure S97. Get High-res Image Gene #12: 'amp_12q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S98. Gene #12: 'amp_12q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
AMP PEAK 12(12Q14.1) MUTATED	13	31	37	6	37	31	13
AMP PEAK 12(12Q14.1) WILD-TYPE	65	79	60	42	16	18	64

Figure S98. Get High-res Image Gene #12: 'amp_12q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S99. Gene #12: 'amp_12q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
AMP PEAK 12(12Q14.1) MUTATED	34	105	27
AMP PEAK 12(12Q14.1) WILD-TYPE	155	123	66

Figure S99. Get High-res Image Gene #12: 'amp_12q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S100. Gene #12: 'amp_12q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
AMP PEAK 12(12Q14.1) MUTATED	12	78	25	51
AMP PEAK 12(12Q14.1) WILD-TYPE	59	120	116	49

Figure S100. Get High-res Image Gene #12: 'amp_12q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S101. Gene #12: 'amp_12q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
AMP PEAK 12(12Q14.1) MUTATED	11	108	24
AMP PEAK 12(12Q14.1) WILD-TYPE	92	140	59

Figure S101. Get High-res Image Gene #12: 'amp_12q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S102. Gene #13: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
AMP PEAK 13(12Q15) MUTATED	30	44	63	34
AMP PEAK 13(12Q15) WILD-TYPE	39	184	16	106

Figure S102. Get High-res Image Gene #13: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S103. Gene #13: 'amp_12q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
AMP PEAK 13(12Q15) MUTATED	31	69	50
AMP PEAK 13(12Q15) WILD-TYPE	113	80	112

Figure S103. Get High-res Image Gene #13: 'amp_12q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q15' versus 'RPPA_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.0017

Table S104. Gene #13: 'amp_12q15' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
AMP PEAK 13(12Q15) MUTATED	25	7	24	41	27
AMP PEAK 13(12Q15) WILD-TYPE	66	15	42	34	82

Figure S104. Get High-res Image Gene #13: 'amp_12q15' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_12q15' versus 'RPPA_CHIERARCHICAL'

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

Table S105. Gene #13: 'amp_12q15' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
AMP PEAK 13(12Q15) MUTATED	51	58	15
AMP PEAK 13(12Q15) WILD-TYPE	116	75	48

Figure S105. Get High-res Image Gene #13: 'amp_12q15' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_12q15' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S106. Gene #13: 'amp_12q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
AMP PEAK 13(12Q15) MUTATED	31	66	74
AMP PEAK 13(12Q15) WILD-TYPE	135	129	77

Figure S106. Get High-res Image Gene #13: 'amp_12q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S107. Gene #13: 'amp_12q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
AMP PEAK 13(12Q15) MUTATED	17	28	37	6	37	31	15
AMP PEAK 13(12Q15) WILD-TYPE	61	82	60	42	16	18	62

Figure S107. Get High-res Image Gene #13: 'amp_12q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S108. Gene #13: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
AMP PEAK 13(12Q15) MUTATED	37	108	25
AMP PEAK 13(12Q15) WILD-TYPE	152	120	68

Figure S108. Get High-res Image Gene #13: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q15' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S109. Gene #13: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
AMP PEAK 13(12Q15) MUTATED	11	76	31	52
AMP PEAK 13(12Q15) WILD-TYPE	60	122	110	48

Figure S109. Get High-res Image Gene #13: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S110. Gene #13: 'amp_12q15' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
AMP PEAK 13(12Q15) MUTATED	14	106	26
AMP PEAK 13(12Q15) WILD-TYPE	89	142	57

Figure S110. Get High-res Image Gene #13: 'amp_12q15' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_14q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S111. Gene #14: 'amp_14q13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
AMP PEAK 14(14Q13.3) MUTATED	52	64	35	78
AMP PEAK 14(14Q13.3) WILD-TYPE	17	164	44	62

Figure S111. Get High-res Image Gene #14: 'amp_14q13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_14q13.3' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S112. Gene #14: 'amp_14q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
AMP PEAK 14(14Q13.3) MUTATED	42	80	79
AMP PEAK 14(14Q13.3) WILD-TYPE	102	69	83

Figure S112. Get High-res Image Gene #14: 'amp_14q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_14q13.3' versus 'RPPA_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 0.041

Table S113. Gene #14: 'amp_14q13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
AMP PEAK 14(14Q13.3) MUTATED	38	5	27	44	45
AMP PEAK 14(14Q13.3) WILD-TYPE	53	17	39	31	64

Figure S113. Get High-res Image Gene #14: 'amp_14q13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_14q13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0335 (Fisher's exact test), Q value = 0.056

Table S114. Gene #14: 'amp_14q13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
AMP PEAK 14(14Q13.3) MUTATED	63	70	26
AMP PEAK 14(14Q13.3) WILD-TYPE	104	63	37

Figure S114. Get High-res Image Gene #14: 'amp_14q13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_14q13.3' versus 'MRNASEQ_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0021

Table S115. Gene #14: 'amp_14q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
AMP PEAK 14(14Q13.3) MUTATED	54	100	74
AMP PEAK 14(14Q13.3) WILD-TYPE	112	95	77

Figure S115. Get High-res Image Gene #14: 'amp_14q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_14q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S116. Gene #14: 'amp_14q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
AMP PEAK 14(14Q13.3) MUTATED	34	57	63	9	42	8	15
AMP PEAK 14(14Q13.3) WILD-TYPE	44	53	34	39	11	41	62

Figure S116. Get High-res Image Gene #14: 'amp_14q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_14q13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S117. Gene #14: 'amp_14q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
AMP PEAK 14(14Q13.3) MUTATED	54	125	46
AMP PEAK 14(14Q13.3) WILD-TYPE	135	103	47

Figure S117. Get High-res Image Gene #14: 'amp_14q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_14q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S118. Gene #14: 'amp_14q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
AMP PEAK 14(14Q13.3) MUTATED	27	111	34	53
AMP PEAK 14(14Q13.3) WILD-TYPE	44	87	107	47

Figure S118. Get High-res Image Gene #14: 'amp_14q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_14q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 3e-04

Table S119. Gene #14: 'amp_14q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
AMP PEAK 14(14Q13.3) MUTATED	27	125	41
AMP PEAK 14(14Q13.3) WILD-TYPE	76	123	42

Figure S119. Get High-res Image Gene #14: 'amp_14q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.0472 (Fisher's exact test), Q value = 0.075

Table S120. Gene #15: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	11	7
AMP PEAK 15(17Q12) MUTATED	4	6	6
AMP PEAK 15(17Q12) WILD-TYPE	10	5	1

Figure S120. Get High-res Image Gene #15: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S121. Gene #15: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
AMP PEAK 15(17Q12) MUTATED	38	52	42	94
AMP PEAK 15(17Q12) WILD-TYPE	31	176	37	46

Figure S121. Get High-res Image Gene #15: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S122. Gene #15: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
AMP PEAK 15(17Q12) MUTATED	31	73	88
AMP PEAK 15(17Q12) WILD-TYPE	113	76	74

Figure S122. Get High-res Image Gene #15: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q12' versus 'RPPA_CNMF'

P value = 0.00223 (Fisher's exact test), Q value = 0.0052

Table S123. Gene #15: 'amp_17q12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
AMP PEAK 15(17Q12) MUTATED	46	10	28	43	32
AMP PEAK 15(17Q12) WILD-TYPE	45	12	38	32	77

Figure S123. Get High-res Image Gene #15: 'amp_17q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_17q12' versus 'RPPA_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.0019

Table S124. Gene #15: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
AMP PEAK 15(17Q12) MUTATED	67	74	18
AMP PEAK 15(17Q12) WILD-TYPE	100	59	45

Figure S124. Get High-res Image Gene #15: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S125. Gene #15: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
AMP PEAK 15(17Q12) MUTATED	52	111	62
AMP PEAK 15(17Q12) WILD-TYPE	114	84	89

Figure S125. Get High-res Image Gene #15: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S126. Gene #15: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
AMP PEAK 15(17Q12) MUTATED	30	62	57	8	29	17	22
AMP PEAK 15(17Q12) WILD-TYPE	48	48	40	40	24	32	55

Figure S126. Get High-res Image Gene #15: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S127. Gene #15: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
AMP PEAK 15(17Q12) MUTATED	58	129	37
AMP PEAK 15(17Q12) WILD-TYPE	131	99	56

Figure S127. Get High-res Image Gene #15: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S128. Gene #15: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
AMP PEAK 15(17Q12) MUTATED	21	102	40	61
AMP PEAK 15(17Q12) WILD-TYPE	50	96	101	39

Figure S128. Get High-res Image Gene #15: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S129. Gene #15: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
AMP PEAK 15(17Q12) MUTATED	24	125	38
AMP PEAK 15(17Q12) WILD-TYPE	79	123	45

Figure S129. Get High-res Image Gene #15: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S130. Gene #16: 'amp_17q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
AMP PEAK 16(17Q23.1) MUTATED	35	67	47	100
AMP PEAK 16(17Q23.1) WILD-TYPE	34	161	32	40

Figure S130. Get High-res Image Gene #16: 'amp_17q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S131. Gene #16: 'amp_17q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
AMP PEAK 16(17Q23.1) MUTATED	40	73	100
AMP PEAK 16(17Q23.1) WILD-TYPE	104	76	62

Figure S131. Get High-res Image Gene #16: 'amp_17q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q23.1' versus 'RPPA_CNMF'

P value = 0.0384 (Fisher's exact test), Q value = 0.063

Table S132. Gene #16: 'amp_17q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
AMP PEAK 16(17Q23.1) MUTATED	50	11	30	45	42
AMP PEAK 16(17Q23.1) WILD-TYPE	41	11	36	30	67

Figure S132. Get High-res Image Gene #16: 'amp_17q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_17q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00273 (Fisher's exact test), Q value = 0.0062

Table S133. Gene #16: 'amp_17q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
AMP PEAK 16(17Q23.1) MUTATED	75	80	23
AMP PEAK 16(17Q23.1) WILD-TYPE	92	53	40

Figure S133. Get High-res Image Gene #16: 'amp_17q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S134. Gene #16: 'amp_17q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
AMP PEAK 16(17Q23.1) MUTATED	62	127	59
AMP PEAK 16(17Q23.1) WILD-TYPE	104	68	92

Figure S134. Get High-res Image Gene #16: 'amp_17q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S135. Gene #16: 'amp_17q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
AMP PEAK 16(17Q23.1) MUTATED	36	74	55	7	29	22	25
AMP PEAK 16(17Q23.1) WILD-TYPE	42	36	42	41	24	27	52

Figure S135. Get High-res Image Gene #16: 'amp_17q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q23.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S136. Gene #16: 'amp_17q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
AMP PEAK 16(17Q23.1) MUTATED	68	136	43
AMP PEAK 16(17Q23.1) WILD-TYPE	121	92	50

Figure S136. Get High-res Image Gene #16: 'amp_17q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S137. Gene #16: 'amp_17q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
AMP PEAK 16(17Q23.1) MUTATED	26	111	48	62
AMP PEAK 16(17Q23.1) WILD-TYPE	45	87	93	38

Figure S137. Get High-res Image Gene #16: 'amp_17q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7.7e-05

Table S138. Gene #16: 'amp_17q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
AMP PEAK 16(17Q23.1) MUTATED	28	134	43
AMP PEAK 16(17Q23.1) WILD-TYPE	75	114	40

Figure S138. Get High-res Image Gene #16: 'amp_17q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0197 (Fisher's exact test), Q value = 0.036

Table S139. Gene #17: 'amp_18q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	11	7
AMP PEAK 17(18Q11.2) MUTATED	1	1	4
AMP PEAK 17(18Q11.2) WILD-TYPE	13	10	3

Figure S139. Get High-res Image Gene #17: 'amp_18q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_18q11.2' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S140. Gene #17: 'amp_18q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
AMP PEAK 17(18Q11.2) MUTATED	22	26	24	31
AMP PEAK 17(18Q11.2) WILD-TYPE	47	202	55	109

Figure S140. Get High-res Image Gene #17: 'amp_18q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S141. Gene #17: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
AMP PEAK 17(18Q11.2) MUTATED	11	51	31
AMP PEAK 17(18Q11.2) WILD-TYPE	133	98	131

Figure S141. Get High-res Image Gene #17: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 3e-04

Table S142. Gene #17: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
AMP PEAK 17(18Q11.2) MUTATED	17	41	44
AMP PEAK 17(18Q11.2) WILD-TYPE	149	154	107

Figure S142. Get High-res Image Gene #17: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7.7e-05

Table S143. Gene #17: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
AMP PEAK 17(18Q11.2) MUTATED	7	17	30	7	22	9	10
AMP PEAK 17(18Q11.2) WILD-TYPE	71	93	67	41	31	40	67

Figure S143. Get High-res Image Gene #17: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00027

Table S144. Gene #17: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
AMP PEAK 17(18Q11.2) MUTATED	20	62	20
AMP PEAK 17(18Q11.2) WILD-TYPE	169	166	73

Figure S144. Get High-res Image Gene #17: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S145. Gene #17: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
AMP PEAK 17(18Q11.2) MUTATED	6	43	18	35
AMP PEAK 17(18Q11.2) WILD-TYPE	65	155	123	65

Figure S145. Get High-res Image Gene #17: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7.7e-05

Table S146. Gene #17: 'amp_18q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
AMP PEAK 17(18Q11.2) MUTATED	9	70	12
AMP PEAK 17(18Q11.2) WILD-TYPE	94	178	71

Figure S146. Get High-res Image Gene #17: 'amp_18q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.04 (Fisher's exact test), Q value = 0.065

Table S147. Gene #18: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	11	7
AMP PEAK 18(19Q12) MUTATED	0	4	2
AMP PEAK 18(19Q12) WILD-TYPE	14	7	5

Figure S147. Get High-res Image Gene #18: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S148. Gene #18: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
AMP PEAK 18(19Q12) MUTATED	22	34	41	40
AMP PEAK 18(19Q12) WILD-TYPE	47	194	38	100

Figure S148. Get High-res Image Gene #18: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S149. Gene #18: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
AMP PEAK 18(19Q12) MUTATED	26	63	35
AMP PEAK 18(19Q12) WILD-TYPE	118	86	127

Figure S149. Get High-res Image Gene #18: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19q12' versus 'RPPA_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00035

Table S150. Gene #18: 'amp_19q12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
AMP PEAK 18(19Q12) MUTATED	16	7	17	36	22
AMP PEAK 18(19Q12) WILD-TYPE	75	15	49	39	87

Figure S150. Get High-res Image Gene #18: 'amp_19q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00294 (Fisher's exact test), Q value = 0.0066

Table S151. Gene #18: 'amp_19q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
AMP PEAK 18(19Q12) MUTATED	35	50	13
AMP PEAK 18(19Q12) WILD-TYPE	132	83	50

Figure S151. Get High-res Image Gene #18: 'amp_19q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S152. Gene #18: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
AMP PEAK 18(19Q12) MUTATED	19	62	54
AMP PEAK 18(19Q12) WILD-TYPE	147	133	97

Figure S152. Get High-res Image Gene #18: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S153. Gene #18: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
AMP PEAK 18(19Q12) MUTATED	8	30	36	13	17	21	10
AMP PEAK 18(19Q12) WILD-TYPE	70	80	61	35	36	28	67

Figure S153. Get High-res Image Gene #18: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.7e-05

Table S154. Gene #18: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
AMP PEAK 18(19Q12) MUTATED	30	85	22
AMP PEAK 18(19Q12) WILD-TYPE	159	143	71

Figure S154. Get High-res Image Gene #18: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00064

Table S155. Gene #18: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
AMP PEAK 18(19Q12) MUTATED	14	60	23	40
AMP PEAK 18(19Q12) WILD-TYPE	57	138	118	60

Figure S155. Get High-res Image Gene #18: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0453 (Fisher's exact test), Q value = 0.072

Table S156. Gene #18: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	198	91
AMP PEAK 18(19Q12) MUTATED	31	66	23
AMP PEAK 18(19Q12) WILD-TYPE	114	132	68

Figure S156. Get High-res Image Gene #18: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00038

Table S157. Gene #18: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
AMP PEAK 18(19Q12) MUTATED	19	88	13
AMP PEAK 18(19Q12) WILD-TYPE	84	160	70

Figure S157. Get High-res Image Gene #18: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.33' versus 'MRNA_CNMF'

P value = 0.00312 (Fisher's exact test), Q value = 0.0069

Table S158. Gene #19: 'amp_20q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	5	9	12	6
AMP PEAK 19(20Q13.33) MUTATED	2	2	2	6
AMP PEAK 19(20Q13.33) WILD-TYPE	3	7	10	0

Figure S158. Get High-res Image Gene #19: 'amp_20q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q13.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.0148 (Fisher's exact test), Q value = 0.028

Table S159. Gene #19: 'amp_20q13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	11	7
AMP PEAK 19(20Q13.33) MUTATED	3	3	6
AMP PEAK 19(20Q13.33) WILD-TYPE	11	8	1

Figure S159. Get High-res Image Gene #19: 'amp_20q13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S160. Gene #19: 'amp_20q13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
AMP PEAK 19(20Q13.33) MUTATED	45	69	47	83
AMP PEAK 19(20Q13.33) WILD-TYPE	24	159	32	57

Figure S160. Get High-res Image Gene #19: 'amp_20q13.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S161. Gene #19: 'amp_20q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
AMP PEAK 19(20Q13.33) MUTATED	48	90	75
AMP PEAK 19(20Q13.33) WILD-TYPE	96	59	87

Figure S161. Get High-res Image Gene #19: 'amp_20q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.002

Table S162. Gene #19: 'amp_20q13.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
AMP PEAK 19(20Q13.33) MUTATED	64	80	32
AMP PEAK 19(20Q13.33) WILD-TYPE	103	53	31

Figure S162. Get High-res Image Gene #19: 'amp_20q13.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_20q13.33' versus 'MRNASEQ_CNMF'

P value = 0.00153 (Fisher's exact test), Q value = 0.0037

Table S163. Gene #19: 'amp_20q13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
AMP PEAK 19(20Q13.33) MUTATED	60	97	84
AMP PEAK 19(20Q13.33) WILD-TYPE	106	98	67

Figure S163. Get High-res Image Gene #19: 'amp_20q13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S164. Gene #19: 'amp_20q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
AMP PEAK 19(20Q13.33) MUTATED	27	48	67	22	38	18	21
AMP PEAK 19(20Q13.33) WILD-TYPE	51	62	30	26	15	31	56

Figure S164. Get High-res Image Gene #19: 'amp_20q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.7e-05

Table S165. Gene #19: 'amp_20q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
AMP PEAK 19(20Q13.33) MUTATED	65	135	40
AMP PEAK 19(20Q13.33) WILD-TYPE	124	93	53

Figure S165. Get High-res Image Gene #19: 'amp_20q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S166. Gene #19: 'amp_20q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
AMP PEAK 19(20Q13.33) MUTATED	23	104	50	63
AMP PEAK 19(20Q13.33) WILD-TYPE	48	94	91	37

Figure S166. Get High-res Image Gene #19: 'amp_20q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.022 (Fisher's exact test), Q value = 0.04

Table S167. Gene #19: 'amp_20q13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	198	91
AMP PEAK 19(20Q13.33) MUTATED	56	106	42
AMP PEAK 19(20Q13.33) WILD-TYPE	89	92	49

Figure S167. Get High-res Image Gene #19: 'amp_20q13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7.7e-05

Table S168. Gene #19: 'amp_20q13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
AMP PEAK 19(20Q13.33) MUTATED	29	139	36
AMP PEAK 19(20Q13.33) WILD-TYPE	74	109	47

Figure S168. Get High-res Image Gene #19: 'amp_20q13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_22q11.22' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.7e-05

Table S169. Gene #20: 'amp_22q11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
AMP PEAK 20(22Q11.22) MUTATED	7	22	17	42
AMP PEAK 20(22Q11.22) WILD-TYPE	62	206	62	98

Figure S169. Get High-res Image Gene #20: 'amp_22q11.22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_22q11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0292 (Fisher's exact test), Q value = 0.05

Table S170. Gene #20: 'amp_22q11.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
AMP PEAK 20(22Q11.22) MUTATED	11	33	17	27
AMP PEAK 20(22Q11.22) WILD-TYPE	60	165	124	73

Figure S170. Get High-res Image Gene #20: 'amp_22q11.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_22q11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0217 (Fisher's exact test), Q value = 0.039

Table S171. Gene #20: 'amp_22q11.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
AMP PEAK 20(22Q11.22) MUTATED	10	54	13
AMP PEAK 20(22Q11.22) WILD-TYPE	93	194	70

Figure S171. Get High-res Image Gene #20: 'amp_22q11.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xq28' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S172. Gene #21: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
AMP PEAK 21(XQ28) MUTATED	24	37	26	70
AMP PEAK 21(XQ28) WILD-TYPE	45	191	53	70

Figure S172. Get High-res Image Gene #21: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xq28' versus 'METHLYATION_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.0018

Table S173. Gene #21: 'amp_xq28' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
AMP PEAK 21(XQ28) MUTATED	27	45	62
AMP PEAK 21(XQ28) WILD-TYPE	117	104	100

Figure S173. Get High-res Image Gene #21: 'amp_xq28' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xq28' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00017

Table S174. Gene #21: 'amp_xq28' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
AMP PEAK 21(XQ28) MUTATED	37	83	36
AMP PEAK 21(XQ28) WILD-TYPE	129	112	115

Figure S174. Get High-res Image Gene #21: 'amp_xq28' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xq28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00055

Table S175. Gene #21: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
AMP PEAK 21(XQ28) MUTATED	20	49	38	6	14	14	15
AMP PEAK 21(XQ28) WILD-TYPE	58	61	59	42	39	35	62

Figure S175. Get High-res Image Gene #21: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_CNMF'

P value = 0.00884 (Fisher's exact test), Q value = 0.018

Table S176. Gene #21: 'amp_xq28' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
AMP PEAK 21(XQ28) MUTATED	43	74	37
AMP PEAK 21(XQ28) WILD-TYPE	146	154	56

Figure S176. Get High-res Image Gene #21: 'amp_xq28' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_xq28' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.00072

Table S177. Gene #21: 'amp_xq28' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
AMP PEAK 21(XQ28) MUTATED	15	85	30
AMP PEAK 21(XQ28) WILD-TYPE	88	163	53

Figure S177. Get High-res Image Gene #21: 'amp_xq28' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S178. Gene #22: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 1(1P36.11) MUTATED	31	45	29	20
DEL PEAK 1(1P36.11) WILD-TYPE	38	183	50	120

Figure S178. Get High-res Image Gene #22: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S179. Gene #22: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 1(1P36.11) MUTATED	14	45	48
DEL PEAK 1(1P36.11) WILD-TYPE	130	104	114

Figure S179. Get High-res Image Gene #22: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.11' versus 'RPPA_CNMF'

P value = 0.0172 (Fisher's exact test), Q value = 0.032

Table S180. Gene #22: 'del_1p36.11' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 1(1P36.11) MUTATED	17	2	18	29	27
DEL PEAK 1(1P36.11) WILD-TYPE	74	20	48	46	82

Figure S180. Get High-res Image Gene #22: 'del_1p36.11' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S181. Gene #22: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 1(1P36.11) MUTATED	18	49	55
DEL PEAK 1(1P36.11) WILD-TYPE	148	146	96

Figure S181. Get High-res Image Gene #22: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S182. Gene #22: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 1(1P36.11) MUTATED	11	27	20	11	26	21	6
DEL PEAK 1(1P36.11) WILD-TYPE	67	83	77	37	27	28	71

Figure S182. Get High-res Image Gene #22: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CNMF'

P value = 0.0248 (Fisher's exact test), Q value = 0.043

Table S183. Gene #22: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 1(1P36.11) MUTATED	38	67	16
DEL PEAK 1(1P36.11) WILD-TYPE	151	161	77

Figure S183. Get High-res Image Gene #22: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.031

Table S184. Gene #22: 'del_1p36.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	198	91
DEL PEAK 1(1P36.11) MUTATED	33	56	12
DEL PEAK 1(1P36.11) WILD-TYPE	112	142	79

Figure S184. Get High-res Image Gene #22: 'del_1p36.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0088 (Fisher's exact test), Q value = 0.018

Table S185. Gene #22: 'del_1p36.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
DEL PEAK 1(1P36.11) MUTATED	18	71	12
DEL PEAK 1(1P36.11) WILD-TYPE	85	177	71

Figure S185. Get High-res Image Gene #22: 'del_1p36.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S186. Gene #23: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 2(1P13.1) MUTATED	35	46	36	32
DEL PEAK 2(1P13.1) WILD-TYPE	34	182	43	108

Figure S186. Get High-res Image Gene #23: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p13.1' versus 'METHLYATION_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0011

Table S187. Gene #23: 'del_1p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 2(1P13.1) MUTATED	22	51	50
DEL PEAK 2(1P13.1) WILD-TYPE	122	98	112

Figure S187. Get High-res Image Gene #23: 'del_1p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p13.1' versus 'RPPA_CNMF'

P value = 0.0198 (Fisher's exact test), Q value = 0.036

Table S188. Gene #23: 'del_1p13.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 2(1P13.1) MUTATED	16	8	23	29	29
DEL PEAK 2(1P13.1) WILD-TYPE	75	14	43	46	80

Figure S188. Get High-res Image Gene #23: 'del_1p13.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p13.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.7e-05

Table S189. Gene #23: 'del_1p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 2(1P13.1) MUTATED	34	47	66
DEL PEAK 2(1P13.1) WILD-TYPE	132	148	85

Figure S189. Get High-res Image Gene #23: 'del_1p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00027

Table S190. Gene #23: 'del_1p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 2(1P13.1) MUTATED	21	26	27	20	27	17	9
DEL PEAK 2(1P13.1) WILD-TYPE	57	84	70	28	26	32	68

Figure S190. Get High-res Image Gene #23: 'del_1p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00455 (Fisher's exact test), Q value = 0.0098

Table S191. Gene #23: 'del_1p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 2(1P13.1) MUTATED	15	73	29	29
DEL PEAK 2(1P13.1) WILD-TYPE	56	125	112	71

Figure S191. Get High-res Image Gene #23: 'del_1p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q22.1' versus 'CN_CNMF'

P value = 0.0038 (Fisher's exact test), Q value = 0.0083

Table S192. Gene #24: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 3(2Q22.1) MUTATED	10	10	12	14
DEL PEAK 3(2Q22.1) WILD-TYPE	59	218	67	126

Figure S192. Get High-res Image Gene #24: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 0.00265 (Fisher's exact test), Q value = 0.006

Table S193. Gene #24: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 3(2Q22.1) MUTATED	5	22	13
DEL PEAK 3(2Q22.1) WILD-TYPE	139	127	149

Figure S193. Get High-res Image Gene #24: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q22.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00176 (Fisher's exact test), Q value = 0.0042

Table S194. Gene #24: 'del_2q22.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
DEL PEAK 3(2Q22.1) MUTATED	7	21	4
DEL PEAK 3(2Q22.1) WILD-TYPE	160	112	59

Figure S194. Get High-res Image Gene #24: 'del_2q22.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_2q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0161 (Fisher's exact test), Q value = 0.03

Table S195. Gene #24: 'del_2q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 3(2Q22.1) MUTATED	6	8	10	2	8	10	2
DEL PEAK 3(2Q22.1) WILD-TYPE	72	102	87	46	45	39	75

Figure S195. Get High-res Image Gene #24: 'del_2q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_CNMF'

P value = 0.0372 (Fisher's exact test), Q value = 0.062

Table S196. Gene #24: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 3(2Q22.1) MUTATED	9	26	10
DEL PEAK 3(2Q22.1) WILD-TYPE	180	202	83

Figure S196. Get High-res Image Gene #24: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0083 (Fisher's exact test), Q value = 0.017

Table S197. Gene #24: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 3(2Q22.1) MUTATED	3	18	7	17
DEL PEAK 3(2Q22.1) WILD-TYPE	68	180	134	83

Figure S197. Get High-res Image Gene #24: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S198. Gene #25: 'del_3p26.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 4(3P26.2) MUTATED	40	76	45	75
DEL PEAK 4(3P26.2) WILD-TYPE	29	152	34	65

Figure S198. Get High-res Image Gene #25: 'del_3p26.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p26.2' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00035

Table S199. Gene #25: 'del_3p26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 4(3P26.2) MUTATED	51	88	68
DEL PEAK 4(3P26.2) WILD-TYPE	93	61	94

Figure S199. Get High-res Image Gene #25: 'del_3p26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p26.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00868 (Fisher's exact test), Q value = 0.018

Table S200. Gene #25: 'del_3p26.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
DEL PEAK 4(3P26.2) MUTATED	66	76	32
DEL PEAK 4(3P26.2) WILD-TYPE	101	57	31

Figure S200. Get High-res Image Gene #25: 'del_3p26.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p26.2' versus 'MRNASEQ_CNMF'

P value = 0.035 (Fisher's exact test), Q value = 0.058

Table S201. Gene #25: 'del_3p26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 4(3P26.2) MUTATED	62	95	76
DEL PEAK 4(3P26.2) WILD-TYPE	104	100	75

Figure S201. Get High-res Image Gene #25: 'del_3p26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S202. Gene #25: 'del_3p26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 4(3P26.2) MUTATED	31	40	66	15	35	26	20
DEL PEAK 4(3P26.2) WILD-TYPE	47	70	31	33	18	23	57

Figure S202. Get High-res Image Gene #25: 'del_3p26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S203. Gene #25: 'del_3p26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 4(3P26.2) MUTATED	62	115	54
DEL PEAK 4(3P26.2) WILD-TYPE	127	113	39

Figure S203. Get High-res Image Gene #25: 'del_3p26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.00087

Table S204. Gene #25: 'del_3p26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 4(3P26.2) MUTATED	29	86	52	64
DEL PEAK 4(3P26.2) WILD-TYPE	42	112	89	36

Figure S204. Get High-res Image Gene #25: 'del_3p26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.0014

Table S205. Gene #25: 'del_3p26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
DEL PEAK 4(3P26.2) MUTATED	31	131	38
DEL PEAK 4(3P26.2) WILD-TYPE	72	117	45

Figure S205. Get High-res Image Gene #25: 'del_3p26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p21.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S206. Gene #26: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 5(3P21.31) MUTATED	42	74	50	80
DEL PEAK 5(3P21.31) WILD-TYPE	27	154	29	60

Figure S206. Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p21.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S207. Gene #26: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 5(3P21.31) MUTATED	44	101	71
DEL PEAK 5(3P21.31) WILD-TYPE	100	48	91

Figure S207. Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p21.31' versus 'RPPA_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.043

Table S208. Gene #26: 'del_3p21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 5(3P21.31) MUTATED	39	9	28	49	54
DEL PEAK 5(3P21.31) WILD-TYPE	52	13	38	26	55

Figure S208. Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p21.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00092 (Fisher's exact test), Q value = 0.0024

Table S209. Gene #26: 'del_3p21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
DEL PEAK 5(3P21.31) MUTATED	66	81	32
DEL PEAK 5(3P21.31) WILD-TYPE	101	52	31

Figure S209. Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p21.31' versus 'MRNASEQ_CNMF'

P value = 0.00157 (Fisher's exact test), Q value = 0.0038

Table S210. Gene #26: 'del_3p21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 5(3P21.31) MUTATED	60	100	82
DEL PEAK 5(3P21.31) WILD-TYPE	106	95	69

Figure S210. Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S211. Gene #26: 'del_3p21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 5(3P21.31) MUTATED	28	44	70	15	37	29	19
DEL PEAK 5(3P21.31) WILD-TYPE	50	66	27	33	16	20	58

Figure S211. Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S212. Gene #26: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 5(3P21.31) MUTATED	64	125	52
DEL PEAK 5(3P21.31) WILD-TYPE	125	103	41

Figure S212. Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7.7e-05

Table S213. Gene #26: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 5(3P21.31) MUTATED	31	93	48	69
DEL PEAK 5(3P21.31) WILD-TYPE	40	105	93	31

Figure S213. Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S214. Gene #26: 'del_3p21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
DEL PEAK 5(3P21.31) MUTATED	31	140	39
DEL PEAK 5(3P21.31) WILD-TYPE	72	108	44

Figure S214. Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q11.1' versus 'CN_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.033

Table S215. Gene #27: 'del_3q11.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 6(3Q11.1) MUTATED	29	54	17	40
DEL PEAK 6(3Q11.1) WILD-TYPE	40	174	62	100

Figure S215. Get High-res Image Gene #27: 'del_3q11.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q11.1' versus 'METHLYATION_CNMF'

P value = 0.00644 (Fisher's exact test), Q value = 0.013

Table S216. Gene #27: 'del_3q11.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 6(3Q11.1) MUTATED	29	55	47
DEL PEAK 6(3Q11.1) WILD-TYPE	115	94	115

Figure S216. Get High-res Image Gene #27: 'del_3q11.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3q11.1' versus 'MRNASEQ_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.038

Table S217. Gene #27: 'del_3q11.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 6(3Q11.1) MUTATED	45	41	52
DEL PEAK 6(3Q11.1) WILD-TYPE	121	154	99

Figure S217. Get High-res Image Gene #27: 'del_3q11.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3q11.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0376 (Fisher's exact test), Q value = 0.062

Table S218. Gene #27: 'del_3q11.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 6(3Q11.1) MUTATED	20	25	23	17	22	17	14
DEL PEAK 6(3Q11.1) WILD-TYPE	58	85	74	31	31	32	63

Figure S218. Get High-res Image Gene #27: 'del_3q11.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3q29' versus 'CN_CNMF'

P value = 0.00322 (Fisher's exact test), Q value = 0.0071

Table S219. Gene #28: 'del_3q29' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 7(3Q29) MUTATED	31	50	20	34
DEL PEAK 7(3Q29) WILD-TYPE	38	178	59	106

Figure S219. Get High-res Image Gene #28: 'del_3q29' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q29' versus 'METHLYATION_CNMF'

P value = 0.00149 (Fisher's exact test), Q value = 0.0037

Table S220. Gene #28: 'del_3q29' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 7(3Q29) MUTATED	24	51	49
DEL PEAK 7(3Q29) WILD-TYPE	120	98	113

Figure S220. Get High-res Image Gene #28: 'del_3q29' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3q29' versus 'RPPA_CHIERARCHICAL'

P value = 0.0309 (Fisher's exact test), Q value = 0.052

Table S221. Gene #28: 'del_3q29' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
DEL PEAK 7(3Q29) MUTATED	51	24	19
DEL PEAK 7(3Q29) WILD-TYPE	116	109	44

Figure S221. Get High-res Image Gene #28: 'del_3q29' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3q29' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S222. Gene #28: 'del_3q29' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 7(3Q29) MUTATED	44	27	61
DEL PEAK 7(3Q29) WILD-TYPE	122	168	90

Figure S222. Get High-res Image Gene #28: 'del_3q29' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3q29' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S223. Gene #28: 'del_3q29' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 7(3Q29) MUTATED	24	19	13	23	29	13	11
DEL PEAK 7(3Q29) WILD-TYPE	54	91	84	25	24	36	66

Figure S223. Get High-res Image Gene #28: 'del_3q29' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'CN_CNMF'

P value = 0.00129 (Fisher's exact test), Q value = 0.0032

Table S224. Gene #29: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 8(4P16.3) MUTATED	23	39	26	43
DEL PEAK 8(4P16.3) WILD-TYPE	46	189	53	97

Figure S224. Get High-res Image Gene #29: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.3' versus 'METHLYATION_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0011

Table S225. Gene #29: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 8(4P16.3) MUTATED	27	55	33
DEL PEAK 8(4P16.3) WILD-TYPE	117	94	129

Figure S225. Get High-res Image Gene #29: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p16.3' versus 'RPPA_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.039

Table S226. Gene #29: 'del_4p16.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 8(4P16.3) MUTATED	20	8	14	31	25
DEL PEAK 8(4P16.3) WILD-TYPE	71	14	52	44	84

Figure S226. Get High-res Image Gene #29: 'del_4p16.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4p16.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0269 (Fisher's exact test), Q value = 0.046

Table S227. Gene #29: 'del_4p16.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
DEL PEAK 8(4P16.3) MUTATED	43	45	10
DEL PEAK 8(4P16.3) WILD-TYPE	124	88	53

Figure S227. Get High-res Image Gene #29: 'del_4p16.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4p16.3' versus 'MRNASEQ_CNMF'

P value = 0.00961 (Fisher's exact test), Q value = 0.019

Table S228. Gene #29: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 8(4P16.3) MUTATED	29	53	48
DEL PEAK 8(4P16.3) WILD-TYPE	137	142	103

Figure S228. Get High-res Image Gene #29: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7.7e-05

Table S229. Gene #29: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 8(4P16.3) MUTATED	14	21	43	5	23	11	13
DEL PEAK 8(4P16.3) WILD-TYPE	64	89	54	43	30	38	64

Figure S229. Get High-res Image Gene #29: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S230. Gene #29: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 8(4P16.3) MUTATED	26	79	25
DEL PEAK 8(4P16.3) WILD-TYPE	163	149	68

Figure S230. Get High-res Image Gene #29: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S231. Gene #29: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 8(4P16.3) MUTATED	6	56	27	41
DEL PEAK 8(4P16.3) WILD-TYPE	65	142	114	59

Figure S231. Get High-res Image Gene #29: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.0018

Table S232. Gene #29: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
DEL PEAK 8(4P16.3) MUTATED	14	80	18
DEL PEAK 8(4P16.3) WILD-TYPE	89	168	65

Figure S232. Get High-res Image Gene #29: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.3' versus 'MRNA_CNMF'

P value = 0.00476 (Fisher's exact test), Q value = 0.01

Table S233. Gene #30: 'del_4q34.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	5	9	12	6
DEL PEAK 9(4Q34.3) MUTATED	3	2	1	5
DEL PEAK 9(4Q34.3) WILD-TYPE	2	7	11	1

Figure S233. Get High-res Image Gene #30: 'del_4q34.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q34.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00558 (Fisher's exact test), Q value = 0.012

Table S234. Gene #30: 'del_4q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	11	7
DEL PEAK 9(4Q34.3) MUTATED	2	3	6
DEL PEAK 9(4Q34.3) WILD-TYPE	12	8	1

Figure S234. Get High-res Image Gene #30: 'del_4q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S235. Gene #30: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 9(4Q34.3) MUTATED	40	49	42	57
DEL PEAK 9(4Q34.3) WILD-TYPE	29	179	37	83

Figure S235. Get High-res Image Gene #30: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S236. Gene #30: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 9(4Q34.3) MUTATED	27	87	49
DEL PEAK 9(4Q34.3) WILD-TYPE	117	62	113

Figure S236. Get High-res Image Gene #30: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q34.3' versus 'RPPA_CNMF'

P value = 0.0396 (Fisher's exact test), Q value = 0.065

Table S237. Gene #30: 'del_4q34.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 9(4Q34.3) MUTATED	31	7	20	40	39
DEL PEAK 9(4Q34.3) WILD-TYPE	60	15	46	35	70

Figure S237. Get High-res Image Gene #30: 'del_4q34.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4q34.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00275 (Fisher's exact test), Q value = 0.0062

Table S238. Gene #30: 'del_4q34.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
DEL PEAK 9(4Q34.3) MUTATED	55	65	17
DEL PEAK 9(4Q34.3) WILD-TYPE	112	68	46

Figure S238. Get High-res Image Gene #30: 'del_4q34.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S239. Gene #30: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 9(4Q34.3) MUTATED	35	73	78
DEL PEAK 9(4Q34.3) WILD-TYPE	131	122	73

Figure S239. Get High-res Image Gene #30: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S240. Gene #30: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 9(4Q34.3) MUTATED	15	26	56	8	36	29	16
DEL PEAK 9(4Q34.3) WILD-TYPE	63	84	41	40	17	20	61

Figure S240. Get High-res Image Gene #30: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S241. Gene #30: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 9(4Q34.3) MUTATED	39	117	30
DEL PEAK 9(4Q34.3) WILD-TYPE	150	111	63

Figure S241. Get High-res Image Gene #30: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S242. Gene #30: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 9(4Q34.3) MUTATED	12	81	29	64
DEL PEAK 9(4Q34.3) WILD-TYPE	59	117	112	36

Figure S242. Get High-res Image Gene #30: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.024 (Fisher's exact test), Q value = 0.042

Table S243. Gene #30: 'del_4q34.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	198	91
DEL PEAK 9(4Q34.3) MUTATED	43	86	30
DEL PEAK 9(4Q34.3) WILD-TYPE	102	112	61

Figure S243. Get High-res Image Gene #30: 'del_4q34.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S244. Gene #30: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
DEL PEAK 9(4Q34.3) MUTATED	20	119	20
DEL PEAK 9(4Q34.3) WILD-TYPE	83	129	63

Figure S244. Get High-res Image Gene #30: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S245. Gene #31: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 10(5Q12.1) MUTATED	27	38	38	74
DEL PEAK 10(5Q12.1) WILD-TYPE	42	190	41	66

Figure S245. Get High-res Image Gene #31: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S246. Gene #31: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 10(5Q12.1) MUTATED	25	70	55
DEL PEAK 10(5Q12.1) WILD-TYPE	119	79	107

Figure S246. Get High-res Image Gene #31: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q12.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S247. Gene #31: 'del_5q12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 10(5Q12.1) MUTATED	30	8	13	44	28
DEL PEAK 10(5Q12.1) WILD-TYPE	61	14	53	31	81

Figure S247. Get High-res Image Gene #31: 'del_5q12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_5q12.1' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S248. Gene #31: 'del_5q12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
DEL PEAK 10(5Q12.1) MUTATED	39	65	19
DEL PEAK 10(5Q12.1) WILD-TYPE	128	68	44

Figure S248. Get High-res Image Gene #31: 'del_5q12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_5q12.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S249. Gene #31: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 10(5Q12.1) MUTATED	33	80	62
DEL PEAK 10(5Q12.1) WILD-TYPE	133	115	89

Figure S249. Get High-res Image Gene #31: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S250. Gene #31: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 10(5Q12.1) MUTATED	13	40	50	7	25	24	16
DEL PEAK 10(5Q12.1) WILD-TYPE	65	70	47	41	28	25	61

Figure S250. Get High-res Image Gene #31: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S251. Gene #31: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 10(5Q12.1) MUTATED	36	114	23
DEL PEAK 10(5Q12.1) WILD-TYPE	153	114	70

Figure S251. Get High-res Image Gene #31: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S252. Gene #31: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 10(5Q12.1) MUTATED	12	74	31	56
DEL PEAK 10(5Q12.1) WILD-TYPE	59	124	110	44

Figure S252. Get High-res Image Gene #31: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_MATURE_CNMF'

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

Table S253. Gene #31: 'del_5q12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	198	91
DEL PEAK 10(5Q12.1) MUTATED	38	81	27
DEL PEAK 10(5Q12.1) WILD-TYPE	107	117	64

Figure S253. Get High-res Image Gene #31: 'del_5q12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S254. Gene #31: 'del_5q12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
DEL PEAK 10(5Q12.1) MUTATED	14	112	20
DEL PEAK 10(5Q12.1) WILD-TYPE	89	136	63

Figure S254. Get High-res Image Gene #31: 'del_5q12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S255. Gene #32: 'del_5q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 11(5Q31.1) MUTATED	34	49	46	79
DEL PEAK 11(5Q31.1) WILD-TYPE	35	179	33	61

Figure S255. Get High-res Image Gene #32: 'del_5q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q31.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S256. Gene #32: 'del_5q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 11(5Q31.1) MUTATED	31	81	72
DEL PEAK 11(5Q31.1) WILD-TYPE	113	68	90

Figure S256. Get High-res Image Gene #32: 'del_5q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q31.1' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.7e-05

Table S257. Gene #32: 'del_5q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 11(5Q31.1) MUTATED	39	9	18	49	33
DEL PEAK 11(5Q31.1) WILD-TYPE	52	13	48	26	76

Figure S257. Get High-res Image Gene #32: 'del_5q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_5q31.1' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S258. Gene #32: 'del_5q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
DEL PEAK 11(5Q31.1) MUTATED	49	75	24
DEL PEAK 11(5Q31.1) WILD-TYPE	118	58	39

Figure S258. Get High-res Image Gene #32: 'del_5q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_5q31.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S259. Gene #32: 'del_5q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 11(5Q31.1) MUTATED	36	97	73
DEL PEAK 11(5Q31.1) WILD-TYPE	130	98	78

Figure S259. Get High-res Image Gene #32: 'del_5q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S260. Gene #32: 'del_5q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 11(5Q31.1) MUTATED	13	51	54	11	30	27	20
DEL PEAK 11(5Q31.1) WILD-TYPE	65	59	43	37	23	22	57

Figure S260. Get High-res Image Gene #32: 'del_5q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q31.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S261. Gene #32: 'del_5q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 11(5Q31.1) MUTATED	44	127	33
DEL PEAK 11(5Q31.1) WILD-TYPE	145	101	60

Figure S261. Get High-res Image Gene #32: 'del_5q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S262. Gene #32: 'del_5q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 11(5Q31.1) MUTATED	16	87	36	65
DEL PEAK 11(5Q31.1) WILD-TYPE	55	111	105	35

Figure S262. Get High-res Image Gene #32: 'del_5q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S263. Gene #32: 'del_5q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
DEL PEAK 11(5Q31.1) MUTATED	21	131	28
DEL PEAK 11(5Q31.1) WILD-TYPE	82	117	55

Figure S263. Get High-res Image Gene #32: 'del_5q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q11.1' versus 'CN_CNMF'

P value = 0.0458 (Fisher's exact test), Q value = 0.073

Table S264. Gene #33: 'del_6q11.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 12(6Q11.1) MUTATED	25	50	26	33
DEL PEAK 12(6Q11.1) WILD-TYPE	44	178	53	107

Figure S264. Get High-res Image Gene #33: 'del_6q11.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q11.1' versus 'METHLYATION_CNMF'

P value = 0.00232 (Fisher's exact test), Q value = 0.0054

Table S265. Gene #33: 'del_6q11.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 12(6Q11.1) MUTATED	32	30	59
DEL PEAK 12(6Q11.1) WILD-TYPE	112	119	103

Figure S265. Get High-res Image Gene #33: 'del_6q11.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q22.31' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00021

Table S266. Gene #34: 'del_6q22.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 13(6Q22.31) MUTATED	50	93	40	69
DEL PEAK 13(6Q22.31) WILD-TYPE	19	135	39	71

Figure S266. Get High-res Image Gene #34: 'del_6q22.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q22.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S267. Gene #34: 'del_6q22.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 13(6Q22.31) MUTATED	48	67	111
DEL PEAK 13(6Q22.31) WILD-TYPE	96	82	51

Figure S267. Get High-res Image Gene #34: 'del_6q22.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q22.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.0018

Table S268. Gene #34: 'del_6q22.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 13(6Q22.31) MUTATED	33	58	37	34	34	21	32
DEL PEAK 13(6Q22.31) WILD-TYPE	45	52	60	14	19	28	45

Figure S268. Get High-res Image Gene #34: 'del_6q22.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q22.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00117 (Fisher's exact test), Q value = 0.0029

Table S269. Gene #34: 'del_6q22.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 13(6Q22.31) MUTATED	35	118	58	39
DEL PEAK 13(6Q22.31) WILD-TYPE	36	80	83	61

Figure S269. Get High-res Image Gene #34: 'del_6q22.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'CN_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0016

Table S270. Gene #35: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 14(6Q26) MUTATED	49	98	42	68
DEL PEAK 14(6Q26) WILD-TYPE	20	130	37	72

Figure S270. Get High-res Image Gene #35: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00017

Table S271. Gene #35: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 14(6Q26) MUTATED	53	70	102
DEL PEAK 14(6Q26) WILD-TYPE	91	79	60

Figure S271. Get High-res Image Gene #35: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00625 (Fisher's exact test), Q value = 0.013

Table S272. Gene #35: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 14(6Q26) MUTATED	31	62	39	32	32	25	33
DEL PEAK 14(6Q26) WILD-TYPE	47	48	58	16	21	24	44

Figure S272. Get High-res Image Gene #35: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0182 (Fisher's exact test), Q value = 0.034

Table S273. Gene #35: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 14(6Q26) MUTATED	35	115	63	41
DEL PEAK 14(6Q26) WILD-TYPE	36	83	78	59

Figure S273. Get High-res Image Gene #35: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MRNA_CNMF'

P value = 0.0236 (Fisher's exact test), Q value = 0.042

Table S274. Gene #36: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	5	9	12	6
DEL PEAK 15(8P23.2) MUTATED	5	7	5	6
DEL PEAK 15(8P23.2) WILD-TYPE	0	2	7	0

Figure S274. Get High-res Image Gene #36: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p23.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0483 (Fisher's exact test), Q value = 0.077

Table S275. Gene #36: 'del_8p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	11	7
DEL PEAK 15(8P23.2) MUTATED	7	9	7
DEL PEAK 15(8P23.2) WILD-TYPE	7	2	0

Figure S275. Get High-res Image Gene #36: 'del_8p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S276. Gene #36: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 15(8P23.2) MUTATED	32	78	47	100
DEL PEAK 15(8P23.2) WILD-TYPE	37	150	32	40

Figure S276. Get High-res Image Gene #36: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 0.0358 (Fisher's exact test), Q value = 0.06

Table S277. Gene #36: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 15(8P23.2) MUTATED	59	75	90
DEL PEAK 15(8P23.2) WILD-TYPE	85	74	72

Figure S277. Get High-res Image Gene #36: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.2' versus 'RPPA_CNMF'

P value = 0.00937 (Fisher's exact test), Q value = 0.019

Table S278. Gene #36: 'del_8p23.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 15(8P23.2) MUTATED	54	11	26	46	45
DEL PEAK 15(8P23.2) WILD-TYPE	37	11	40	29	64

Figure S278. Get High-res Image Gene #36: 'del_8p23.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_8p23.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0015 (Fisher's exact test), Q value = 0.0037

Table S279. Gene #36: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
DEL PEAK 15(8P23.2) MUTATED	70	83	29
DEL PEAK 15(8P23.2) WILD-TYPE	97	50	34

Figure S279. Get High-res Image Gene #36: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S280. Gene #36: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 15(8P23.2) MUTATED	63	135	57
DEL PEAK 15(8P23.2) WILD-TYPE	103	60	94

Figure S280. Get High-res Image Gene #36: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S281. Gene #36: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 15(8P23.2) MUTATED	34	72	64	11	20	24	30
DEL PEAK 15(8P23.2) WILD-TYPE	44	38	33	37	33	25	47

Figure S281. Get High-res Image Gene #36: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.00077

Table S282. Gene #36: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 15(8P23.2) MUTATED	72	127	54
DEL PEAK 15(8P23.2) WILD-TYPE	117	101	39

Figure S282. Get High-res Image Gene #36: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S283. Gene #36: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 15(8P23.2) MUTATED	27	108	60	58
DEL PEAK 15(8P23.2) WILD-TYPE	44	90	81	42

Figure S283. Get High-res Image Gene #36: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.039

Table S284. Gene #36: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	198	91
DEL PEAK 15(8P23.2) MUTATED	57	104	50
DEL PEAK 15(8P23.2) WILD-TYPE	88	94	41

Figure S284. Get High-res Image Gene #36: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00098 (Fisher's exact test), Q value = 0.0025

Table S285. Gene #36: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
DEL PEAK 15(8P23.2) MUTATED	34	136	41
DEL PEAK 15(8P23.2) WILD-TYPE	69	112	42

Figure S285. Get High-res Image Gene #36: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S286. Gene #37: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 16(8P11.21) MUTATED	5	34	24	60
DEL PEAK 16(8P11.21) WILD-TYPE	64	194	55	80

Figure S286. Get High-res Image Gene #37: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p11.21' versus 'MRNASEQ_CNMF'

P value = 0.00246 (Fisher's exact test), Q value = 0.0057

Table S287. Gene #37: 'del_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 16(8P11.21) MUTATED	35	62	25
DEL PEAK 16(8P11.21) WILD-TYPE	131	133	126

Figure S287. Get High-res Image Gene #37: 'del_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S288. Gene #38: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 17(9P23) MUTATED	34	100	63	88
DEL PEAK 17(9P23) WILD-TYPE	35	128	16	52

Figure S288. Get High-res Image Gene #38: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 0.04 (Fisher's exact test), Q value = 0.065

Table S289. Gene #38: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 17(9P23) MUTATED	69	93	86
DEL PEAK 17(9P23) WILD-TYPE	75	56	76

Figure S289. Get High-res Image Gene #38: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 0.0409 (Fisher's exact test), Q value = 0.066

Table S290. Gene #38: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 17(9P23) MUTATED	81	107	95
DEL PEAK 17(9P23) WILD-TYPE	85	88	56

Figure S290. Get High-res Image Gene #38: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.00089

Table S291. Gene #38: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 17(9P23) MUTATED	42	51	63	24	27	40	36
DEL PEAK 17(9P23) WILD-TYPE	36	59	34	24	26	9	41

Figure S291. Get High-res Image Gene #38: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0249 (Fisher's exact test), Q value = 0.043

Table S292. Gene #38: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 17(9P23) MUTATED	35	106	71	68
DEL PEAK 17(9P23) WILD-TYPE	36	92	70	32

Figure S292. Get High-res Image Gene #38: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S293. Gene #39: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 18(9P21.3) MUTATED	32	104	65	90
DEL PEAK 18(9P21.3) WILD-TYPE	37	124	14	50

Figure S293. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.033

Table S294. Gene #39: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 18(9P21.3) MUTATED	67	94	89
DEL PEAK 18(9P21.3) WILD-TYPE	77	55	73

Figure S294. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S295. Gene #39: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 18(9P21.3) MUTATED	45	54	63	23	25	43	36
DEL PEAK 18(9P21.3) WILD-TYPE	33	56	34	25	28	6	41

Figure S295. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00186 (Fisher's exact test), Q value = 0.0044

Table S296. Gene #39: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 18(9P21.3) MUTATED	35	104	75	73
DEL PEAK 18(9P21.3) WILD-TYPE	36	94	66	27

Figure S296. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0439 (Fisher's exact test), Q value = 0.071

Table S297. Gene #39: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	198	91
DEL PEAK 18(9P21.3) MUTATED	91	98	53
DEL PEAK 18(9P21.3) WILD-TYPE	54	100	38

Figure S297. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9q21.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S298. Gene #40: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 19(9Q21.11) MUTATED	39	81	58	78
DEL PEAK 19(9Q21.11) WILD-TYPE	30	147	21	62

Figure S298. Get High-res Image Gene #40: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_9q21.11' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00033

Table S299. Gene #40: 'del_9q21.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 19(9Q21.11) MUTATED	57	94	70
DEL PEAK 19(9Q21.11) WILD-TYPE	87	55	92

Figure S299. Get High-res Image Gene #40: 'del_9q21.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q21.11' versus 'RPPA_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.041

Table S300. Gene #40: 'del_9q21.11' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 19(9Q21.11) MUTATED	46	10	30	48	43
DEL PEAK 19(9Q21.11) WILD-TYPE	45	12	36	27	66

Figure S300. Get High-res Image Gene #40: 'del_9q21.11' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9q21.11' versus 'RPPA_CHIERARCHICAL'

P value = 0.00069 (Fisher's exact test), Q value = 0.0018

Table S301. Gene #40: 'del_9q21.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
DEL PEAK 19(9Q21.11) MUTATED	80	78	19
DEL PEAK 19(9Q21.11) WILD-TYPE	87	55	44

Figure S301. Get High-res Image Gene #40: 'del_9q21.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9q21.11' versus 'MRNASEQ_CNMF'

P value = 0.00564 (Fisher's exact test), Q value = 0.012

Table S302. Gene #40: 'del_9q21.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 19(9Q21.11) MUTATED	67	99	88
DEL PEAK 19(9Q21.11) WILD-TYPE	99	96	63

Figure S302. Get High-res Image Gene #40: 'del_9q21.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9q21.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7.7e-05

Table S303. Gene #40: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 19(9Q21.11) MUTATED	35	47	59	16	38	31	28
DEL PEAK 19(9Q21.11) WILD-TYPE	43	63	38	32	15	18	49

Figure S303. Get High-res Image Gene #40: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00021

Table S304. Gene #40: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 19(9Q21.11) MUTATED	70	125	57
DEL PEAK 19(9Q21.11) WILD-TYPE	119	103	36

Figure S304. Get High-res Image Gene #40: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9q21.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S305. Gene #40: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 19(9Q21.11) MUTATED	26	101	54	71
DEL PEAK 19(9Q21.11) WILD-TYPE	45	97	87	29

Figure S305. Get High-res Image Gene #40: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.00087

Table S306. Gene #40: 'del_9q21.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
DEL PEAK 19(9Q21.11) MUTATED	34	141	40
DEL PEAK 19(9Q21.11) WILD-TYPE	69	107	43

Figure S306. Get High-res Image Gene #40: 'del_9q21.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 0.00644 (Fisher's exact test), Q value = 0.013

Table S307. Gene #41: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 20(10P15.3) MUTATED	15	41	25	45
DEL PEAK 20(10P15.3) WILD-TYPE	54	187	54	95

Figure S307. Get High-res Image Gene #41: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.021

Table S308. Gene #41: 'del_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 20(10P15.3) MUTATED	23	46	41
DEL PEAK 20(10P15.3) WILD-TYPE	121	103	121

Figure S308. Get High-res Image Gene #41: 'del_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00223 (Fisher's exact test), Q value = 0.0052

Table S309. Gene #41: 'del_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 20(10P15.3) MUTATED	16	26	39	6	16	8	14
DEL PEAK 20(10P15.3) WILD-TYPE	62	84	58	42	37	41	63

Figure S309. Get High-res Image Gene #41: 'del_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_CNMF'

P value = 0.00201 (Fisher's exact test), Q value = 0.0047

Table S310. Gene #41: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 20(10P15.3) MUTATED	33	58	34
DEL PEAK 20(10P15.3) WILD-TYPE	156	170	59

Figure S310. Get High-res Image Gene #41: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10p15.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0191 (Fisher's exact test), Q value = 0.035

Table S311. Gene #41: 'del_10p15.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 20(10P15.3) MUTATED	9	51	32	33
DEL PEAK 20(10P15.3) WILD-TYPE	62	147	109	67

Figure S311. Get High-res Image Gene #41: 'del_10p15.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0315 (Fisher's exact test), Q value = 0.053

Table S312. Gene #41: 'del_10p15.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	198	91
DEL PEAK 20(10P15.3) MUTATED	26	54	29
DEL PEAK 20(10P15.3) WILD-TYPE	119	144	62

Figure S312. Get High-res Image Gene #41: 'del_10p15.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10p15.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S313. Gene #41: 'del_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
DEL PEAK 20(10P15.3) MUTATED	15	69	25
DEL PEAK 20(10P15.3) WILD-TYPE	88	179	58

Figure S313. Get High-res Image Gene #41: 'del_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q26.3' versus 'CN_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0012

Table S314. Gene #42: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 21(10Q26.3) MUTATED	18	53	23	62
DEL PEAK 21(10Q26.3) WILD-TYPE	51	175	56	78

Figure S314. Get High-res Image Gene #42: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q26.3' versus 'METHLYATION_CNMF'

P value = 0.0384 (Fisher's exact test), Q value = 0.063

Table S315. Gene #42: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 21(10Q26.3) MUTATED	32	53	50
DEL PEAK 21(10Q26.3) WILD-TYPE	112	96	112

Figure S315. Get High-res Image Gene #42: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q26.3' versus 'RPPA_CNMF'

P value = 0.00742 (Fisher's exact test), Q value = 0.015

Table S316. Gene #42: 'del_10q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 21(10Q26.3) MUTATED	40	7	16	26	23
DEL PEAK 21(10Q26.3) WILD-TYPE	51	15	50	49	86

Figure S316. Get High-res Image Gene #42: 'del_10q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 0.00278 (Fisher's exact test), Q value = 0.0063

Table S317. Gene #42: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 21(10Q26.3) MUTATED	42	76	36
DEL PEAK 21(10Q26.3) WILD-TYPE	124	119	115

Figure S317. Get High-res Image Gene #42: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S318. Gene #42: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 21(10Q26.3) MUTATED	23	44	48	1	11	9	18
DEL PEAK 21(10Q26.3) WILD-TYPE	55	66	49	47	42	40	59

Figure S318. Get High-res Image Gene #42: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 0.023

Table S319. Gene #42: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 21(10Q26.3) MUTATED	43	74	36
DEL PEAK 21(10Q26.3) WILD-TYPE	146	154	57

Figure S319. Get High-res Image Gene #42: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00153 (Fisher's exact test), Q value = 0.0037

Table S320. Gene #42: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 21(10Q26.3) MUTATED	12	62	36	43
DEL PEAK 21(10Q26.3) WILD-TYPE	59	136	105	57

Figure S320. Get High-res Image Gene #42: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00108 (Fisher's exact test), Q value = 0.0027

Table S321. Gene #42: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
DEL PEAK 21(10Q26.3) MUTATED	16	85	26
DEL PEAK 21(10Q26.3) WILD-TYPE	87	163	57

Figure S321. Get High-res Image Gene #42: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'MRNA_CHIERARCHICAL'

P value = 0.0321 (Fisher's exact test), Q value = 0.054

Table S322. Gene #43: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	11	7
DEL PEAK 22(11P15.5) MUTATED	1	2	4
DEL PEAK 22(11P15.5) WILD-TYPE	13	9	3

Figure S322. Get High-res Image Gene #43: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S323. Gene #43: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 22(11P15.5) MUTATED	20	31	30	62
DEL PEAK 22(11P15.5) WILD-TYPE	49	197	49	78

Figure S323. Get High-res Image Gene #43: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.0026

Table S324. Gene #43: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 22(11P15.5) MUTATED	27	57	42
DEL PEAK 22(11P15.5) WILD-TYPE	117	92	120

Figure S324. Get High-res Image Gene #43: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11p15.5' versus 'RPPA_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.039

Table S325. Gene #43: 'del_11p15.5' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 22(11P15.5) MUTATED	20	6	13	32	31
DEL PEAK 22(11P15.5) WILD-TYPE	71	16	53	43	78

Figure S325. Get High-res Image Gene #43: 'del_11p15.5' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_11p15.5' versus 'RPPA_CHIERARCHICAL'

P value = 0.00299 (Fisher's exact test), Q value = 0.0067

Table S326. Gene #43: 'del_11p15.5' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
DEL PEAK 22(11P15.5) MUTATED	34	51	17
DEL PEAK 22(11P15.5) WILD-TYPE	133	82	46

Figure S326. Get High-res Image Gene #43: 'del_11p15.5' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.7e-05

Table S327. Gene #43: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 22(11P15.5) MUTATED	26	72	42
DEL PEAK 22(11P15.5) WILD-TYPE	140	123	109

Figure S327. Get High-res Image Gene #43: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S328. Gene #43: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 22(11P15.5) MUTATED	8	36	38	8	14	23	13
DEL PEAK 22(11P15.5) WILD-TYPE	70	74	59	40	39	26	64

Figure S328. Get High-res Image Gene #43: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.00085

Table S329. Gene #43: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 22(11P15.5) MUTATED	35	82	23
DEL PEAK 22(11P15.5) WILD-TYPE	154	146	70

Figure S329. Get High-res Image Gene #43: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.00082

Table S330. Gene #43: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 22(11P15.5) MUTATED	14	63	24	39
DEL PEAK 22(11P15.5) WILD-TYPE	57	135	117	61

Figure S330. Get High-res Image Gene #43: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.0014

Table S331. Gene #43: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
DEL PEAK 22(11P15.5) MUTATED	17	87	17
DEL PEAK 22(11P15.5) WILD-TYPE	86	161	66

Figure S331. Get High-res Image Gene #43: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S332. Gene #44: 'del_11q23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 23(11Q23.2) MUTATED	31	34	30	24
DEL PEAK 23(11Q23.2) WILD-TYPE	38	194	49	116

Figure S332. Get High-res Image Gene #44: 'del_11q23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q23.2' versus 'METHLYATION_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.00077

Table S333. Gene #44: 'del_11q23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 23(11Q23.2) MUTATED	21	51	32
DEL PEAK 23(11Q23.2) WILD-TYPE	123	98	130

Figure S333. Get High-res Image Gene #44: 'del_11q23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q23.2' versus 'RPPA_CNMF'

P value = 0.0176 (Fisher's exact test), Q value = 0.033

Table S334. Gene #44: 'del_11q23.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 23(11Q23.2) MUTATED	12	3	14	26	26
DEL PEAK 23(11Q23.2) WILD-TYPE	79	19	52	49	83

Figure S334. Get High-res Image Gene #44: 'del_11q23.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_11q23.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S335. Gene #44: 'del_11q23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 23(11Q23.2) MUTATED	20	44	53
DEL PEAK 23(11Q23.2) WILD-TYPE	146	151	98

Figure S335. Get High-res Image Gene #44: 'del_11q23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.002

Table S336. Gene #44: 'del_11q23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 23(11Q23.2) MUTATED	10	26	22	15	20	16	8
DEL PEAK 23(11Q23.2) WILD-TYPE	68	84	75	33	33	33	69

Figure S336. Get High-res Image Gene #44: 'del_11q23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.2' versus 'MIRSEQ_CNMF'

P value = 0.00221 (Fisher's exact test), Q value = 0.0052

Table S337. Gene #44: 'del_11q23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 23(11Q23.2) MUTATED	35	69	14
DEL PEAK 23(11Q23.2) WILD-TYPE	154	159	79

Figure S337. Get High-res Image Gene #44: 'del_11q23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11q23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0459 (Fisher's exact test), Q value = 0.073

Table S338. Gene #44: 'del_11q23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	198	91
DEL PEAK 23(11Q23.2) MUTATED	29	55	14
DEL PEAK 23(11Q23.2) WILD-TYPE	116	143	77

Figure S338. Get High-res Image Gene #44: 'del_11q23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11q25' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S339. Gene #45: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 24(11Q25) MUTATED	27	34	26	30
DEL PEAK 24(11Q25) WILD-TYPE	42	194	53	110

Figure S339. Get High-res Image Gene #45: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q25' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00055

Table S340. Gene #45: 'del_11q25' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 24(11Q25) MUTATED	19	50	36
DEL PEAK 24(11Q25) WILD-TYPE	125	99	126

Figure S340. Get High-res Image Gene #45: 'del_11q25' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q25' versus 'RPPA_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.03

Table S341. Gene #45: 'del_11q25' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 24(11Q25) MUTATED	11	3	15	25	27
DEL PEAK 24(11Q25) WILD-TYPE	80	19	51	50	82

Figure S341. Get High-res Image Gene #45: 'del_11q25' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_11q25' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S342. Gene #45: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 24(11Q25) MUTATED	19	47	49
DEL PEAK 24(11Q25) WILD-TYPE	147	148	102

Figure S342. Get High-res Image Gene #45: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q25' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0028 (Fisher's exact test), Q value = 0.0063

Table S343. Gene #45: 'del_11q25' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 24(11Q25) MUTATED	11	25	22	14	19	16	8
DEL PEAK 24(11Q25) WILD-TYPE	67	85	75	34	34	33	69

Figure S343. Get High-res Image Gene #45: 'del_11q25' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S344. Gene #46: 'del_12p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 25(12P13.2) MUTATED	18	50	9	61
DEL PEAK 25(12P13.2) WILD-TYPE	51	178	70	79

Figure S344. Get High-res Image Gene #46: 'del_12p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_12p13.2' versus 'METHLYATION_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.024

Table S345. Gene #46: 'del_12p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 25(12P13.2) MUTATED	26	41	53
DEL PEAK 25(12P13.2) WILD-TYPE	118	108	109

Figure S345. Get High-res Image Gene #46: 'del_12p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12p13.2' versus 'RPPA_CNMF'

P value = 0.0287 (Fisher's exact test), Q value = 0.049

Table S346. Gene #46: 'del_12p13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 25(12P13.2) MUTATED	28	11	16	18	20
DEL PEAK 25(12P13.2) WILD-TYPE	63	11	50	57	89

Figure S346. Get High-res Image Gene #46: 'del_12p13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_12p13.2' versus 'MRNASEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.00085

Table S347. Gene #46: 'del_12p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 25(12P13.2) MUTATED	54	60	22
DEL PEAK 25(12P13.2) WILD-TYPE	112	135	129

Figure S347. Get High-res Image Gene #46: 'del_12p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00946 (Fisher's exact test), Q value = 0.019

Table S348. Gene #46: 'del_12p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 25(12P13.2) MUTATED	23	35	34	11	8	5	20
DEL PEAK 25(12P13.2) WILD-TYPE	55	75	63	37	45	44	57

Figure S348. Get High-res Image Gene #46: 'del_12p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S349. Gene #47: 'del_12q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 26(12Q12) MUTATED	8	37	5	48
DEL PEAK 26(12Q12) WILD-TYPE	61	191	74	92

Figure S349. Get High-res Image Gene #47: 'del_12q12' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q12' versus 'METHLYATION_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 0.043

Table S350. Gene #47: 'del_12q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 26(12Q12) MUTATED	25	21	42
DEL PEAK 26(12Q12) WILD-TYPE	119	128	120

Figure S350. Get High-res Image Gene #47: 'del_12q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12q12' versus 'RPPA_CNMF'

P value = 0.00199 (Fisher's exact test), Q value = 0.0047

Table S351. Gene #47: 'del_12q12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 26(12Q12) MUTATED	27	3	18	7	14
DEL PEAK 26(12Q12) WILD-TYPE	64	19	48	68	95

Figure S351. Get High-res Image Gene #47: 'del_12q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_12q12' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00033

Table S352. Gene #47: 'del_12q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 26(12Q12) MUTATED	42	43	12
DEL PEAK 26(12Q12) WILD-TYPE	124	152	139

Figure S352. Get High-res Image Gene #47: 'del_12q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0446 (Fisher's exact test), Q value = 0.072

Table S353. Gene #47: 'del_12q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 26(12Q12) MUTATED	16	26	20	10	2	7	16
DEL PEAK 26(12Q12) WILD-TYPE	62	84	77	38	51	42	61

Figure S353. Get High-res Image Gene #47: 'del_12q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0266 (Fisher's exact test), Q value = 0.046

Table S354. Gene #47: 'del_12q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
DEL PEAK 26(12Q12) MUTATED	16	43	25
DEL PEAK 26(12Q12) WILD-TYPE	87	205	58

Figure S354. Get High-res Image Gene #47: 'del_12q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q24.33' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00035

Table S355. Gene #48: 'del_12q24.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 27(12Q24.33) MUTATED	10	60	12	55
DEL PEAK 27(12Q24.33) WILD-TYPE	59	168	67	85

Figure S355. Get High-res Image Gene #48: 'del_12q24.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q24.33' versus 'RPPA_CNMF'

P value = 0.00255 (Fisher's exact test), Q value = 0.0058

Table S356. Gene #48: 'del_12q24.33' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 27(12Q24.33) MUTATED	33	8	20	10	21
DEL PEAK 27(12Q24.33) WILD-TYPE	58	14	46	65	88

Figure S356. Get High-res Image Gene #48: 'del_12q24.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_12q24.33' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00024

Table S357. Gene #48: 'del_12q24.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 27(12Q24.33) MUTATED	55	60	21
DEL PEAK 27(12Q24.33) WILD-TYPE	111	135	130

Figure S357. Get High-res Image Gene #48: 'del_12q24.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12q24.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00024

Table S358. Gene #48: 'del_12q24.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 27(12Q24.33) MUTATED	22	34	31	16	2	6	25
DEL PEAK 27(12Q24.33) WILD-TYPE	56	76	66	32	51	43	52

Figure S358. Get High-res Image Gene #48: 'del_12q24.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q24.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.022

Table S359. Gene #48: 'del_12q24.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 27(12Q24.33) MUTATED	20	50	49	16
DEL PEAK 27(12Q24.33) WILD-TYPE	51	148	92	84

Figure S359. Get High-res Image Gene #48: 'del_12q24.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q12.11' versus 'MRNA_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.002

Table S360. Gene #49: 'del_13q12.11' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	5	9	12	6
DEL PEAK 28(13Q12.11) MUTATED	5	6	1	4
DEL PEAK 28(13Q12.11) WILD-TYPE	0	3	11	2

Figure S360. Get High-res Image Gene #49: 'del_13q12.11' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q12.11' versus 'MRNA_CHIERARCHICAL'

P value = 0.0232 (Fisher's exact test), Q value = 0.041

Table S361. Gene #49: 'del_13q12.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	11	7
DEL PEAK 28(13Q12.11) MUTATED	3	8	5
DEL PEAK 28(13Q12.11) WILD-TYPE	11	3	2

Figure S361. Get High-res Image Gene #49: 'del_13q12.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q12.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S362. Gene #49: 'del_13q12.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 28(13Q12.11) MUTATED	49	86	48	111
DEL PEAK 28(13Q12.11) WILD-TYPE	20	142	31	29

Figure S362. Get High-res Image Gene #49: 'del_13q12.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q12.11' versus 'METHLYATION_CNMF'

P value = 0.00133 (Fisher's exact test), Q value = 0.0033

Table S363. Gene #49: 'del_13q12.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 28(13Q12.11) MUTATED	65	94	103
DEL PEAK 28(13Q12.11) WILD-TYPE	79	55	59

Figure S363. Get High-res Image Gene #49: 'del_13q12.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q12.11' versus 'RPPA_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00055

Table S364. Gene #49: 'del_13q12.11' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 28(13Q12.11) MUTATED	65	12	34	53	48
DEL PEAK 28(13Q12.11) WILD-TYPE	26	10	32	22	61

Figure S364. Get High-res Image Gene #49: 'del_13q12.11' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q12.11' versus 'RPPA_CHIERARCHICAL'

P value = 0.0379 (Fisher's exact test), Q value = 0.062

Table S365. Gene #49: 'del_13q12.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
DEL PEAK 28(13Q12.11) MUTATED	94	88	30
DEL PEAK 28(13Q12.11) WILD-TYPE	73	45	33

Figure S365. Get High-res Image Gene #49: 'del_13q12.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_13q12.11' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S366. Gene #49: 'del_13q12.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 28(13Q12.11) MUTATED	73	133	85
DEL PEAK 28(13Q12.11) WILD-TYPE	93	62	66

Figure S366. Get High-res Image Gene #49: 'del_13q12.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q12.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S367. Gene #49: 'del_13q12.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 28(13Q12.11) MUTATED	38	80	67	15	39	22	30
DEL PEAK 28(13Q12.11) WILD-TYPE	40	30	30	33	14	27	47

Figure S367. Get High-res Image Gene #49: 'del_13q12.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q12.11' versus 'MIRSEQ_CNMF'

P value = 0.00329 (Fisher's exact test), Q value = 0.0073

Table S368. Gene #49: 'del_13q12.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 28(13Q12.11) MUTATED	90	143	59
DEL PEAK 28(13Q12.11) WILD-TYPE	99	85	34

Figure S368. Get High-res Image Gene #49: 'del_13q12.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q12.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00387 (Fisher's exact test), Q value = 0.0084

Table S369. Gene #49: 'del_13q12.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 28(13Q12.11) MUTATED	37	124	65	66
DEL PEAK 28(13Q12.11) WILD-TYPE	34	74	76	34

Figure S369. Get High-res Image Gene #49: 'del_13q12.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q12.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00095 (Fisher's exact test), Q value = 0.0024

Table S370. Gene #49: 'del_13q12.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
DEL PEAK 28(13Q12.11) MUTATED	44	160	48
DEL PEAK 28(13Q12.11) WILD-TYPE	59	88	35

Figure S370. Get High-res Image Gene #49: 'del_13q12.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q12.13' versus 'MRNA_CNMF'

P value = 0.00893 (Fisher's exact test), Q value = 0.018

Table S371. Gene #50: 'del_13q12.13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	5	9	12	6
DEL PEAK 29(13Q12.13) MUTATED	4	5	1	4
DEL PEAK 29(13Q12.13) WILD-TYPE	1	4	11	2

Figure S371. Get High-res Image Gene #50: 'del_13q12.13' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q12.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S372. Gene #50: 'del_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 29(13Q12.13) MUTATED	51	85	46	111
DEL PEAK 29(13Q12.13) WILD-TYPE	18	143	33	29

Figure S372. Get High-res Image Gene #50: 'del_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q12.13' versus 'METHLYATION_CNMF'

P value = 0.00163 (Fisher's exact test), Q value = 0.0039

Table S373. Gene #50: 'del_13q12.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 29(13Q12.13) MUTATED	65	93	103
DEL PEAK 29(13Q12.13) WILD-TYPE	79	56	59

Figure S373. Get High-res Image Gene #50: 'del_13q12.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q12.13' versus 'RPPA_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00035

Table S374. Gene #50: 'del_13q12.13' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 29(13Q12.13) MUTATED	64	13	34	55	47
DEL PEAK 29(13Q12.13) WILD-TYPE	27	9	32	20	62

Figure S374. Get High-res Image Gene #50: 'del_13q12.13' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q12.13' versus 'RPPA_CHIERARCHICAL'

P value = 0.0259 (Fisher's exact test), Q value = 0.045

Table S375. Gene #50: 'del_13q12.13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
DEL PEAK 29(13Q12.13) MUTATED	94	89	30
DEL PEAK 29(13Q12.13) WILD-TYPE	73	44	33

Figure S375. Get High-res Image Gene #50: 'del_13q12.13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_13q12.13' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00027

Table S376. Gene #50: 'del_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 29(13Q12.13) MUTATED	74	131	85
DEL PEAK 29(13Q12.13) WILD-TYPE	92	64	66

Figure S376. Get High-res Image Gene #50: 'del_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q12.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S377. Gene #50: 'del_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 29(13Q12.13) MUTATED	40	79	63	15	41	23	29
DEL PEAK 29(13Q12.13) WILD-TYPE	38	31	34	33	12	26	48

Figure S377. Get High-res Image Gene #50: 'del_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q12.13' versus 'MIRSEQ_CNMF'

P value = 0.00447 (Fisher's exact test), Q value = 0.0097

Table S378. Gene #50: 'del_13q12.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 29(13Q12.13) MUTATED	90	142	59
DEL PEAK 29(13Q12.13) WILD-TYPE	99	86	34

Figure S378. Get High-res Image Gene #50: 'del_13q12.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q12.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00581 (Fisher's exact test), Q value = 0.012

Table S379. Gene #50: 'del_13q12.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 29(13Q12.13) MUTATED	36	123	66	66
DEL PEAK 29(13Q12.13) WILD-TYPE	35	75	75	34

Figure S379. Get High-res Image Gene #50: 'del_13q12.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q12.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00068 (Fisher's exact test), Q value = 0.0018

Table S380. Gene #50: 'del_13q12.13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
DEL PEAK 29(13Q12.13) MUTATED	44	161	49
DEL PEAK 29(13Q12.13) WILD-TYPE	59	87	34

Figure S380. Get High-res Image Gene #50: 'del_13q12.13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q14.2' versus 'MRNA_CNMF'

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

Table S381. Gene #51: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	5	9	12	6
DEL PEAK 30(13Q14.2) MUTATED	4	4	1	4
DEL PEAK 30(13Q14.2) WILD-TYPE	1	5	11	2

Figure S381. Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q14.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0226 (Fisher's exact test), Q value = 0.041

Table S382. Gene #51: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	11	7
DEL PEAK 30(13Q14.2) MUTATED	2	6	5
DEL PEAK 30(13Q14.2) WILD-TYPE	12	5	2

Figure S382. Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S383. Gene #51: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 30(13Q14.2) MUTATED	51	77	43	111
DEL PEAK 30(13Q14.2) WILD-TYPE	18	151	36	29

Figure S383. Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 0.00464 (Fisher's exact test), Q value = 0.0099

Table S384. Gene #51: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 30(13Q14.2) MUTATED	62	89	96
DEL PEAK 30(13Q14.2) WILD-TYPE	82	60	66

Figure S384. Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'RPPA_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0012

Table S385. Gene #51: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 30(13Q14.2) MUTATED	60	12	32	53	46
DEL PEAK 30(13Q14.2) WILD-TYPE	31	10	34	22	63

Figure S385. Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00041

Table S386. Gene #51: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 30(13Q14.2) MUTATED	70	126	83
DEL PEAK 30(13Q14.2) WILD-TYPE	96	69	68

Figure S386. Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S387. Gene #51: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 30(13Q14.2) MUTATED	38	78	61	12	41	21	28
DEL PEAK 30(13Q14.2) WILD-TYPE	40	32	36	36	12	28	49

Figure S387. Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 0.00228 (Fisher's exact test), Q value = 0.0053

Table S388. Gene #51: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 30(13Q14.2) MUTATED	84	139	55
DEL PEAK 30(13Q14.2) WILD-TYPE	105	89	38

Figure S388. Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.005 (Fisher's exact test), Q value = 0.011

Table S389. Gene #51: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 30(13Q14.2) MUTATED	33	123	63	59
DEL PEAK 30(13Q14.2) WILD-TYPE	38	75	78	41

Figure S389. Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0488 (Fisher's exact test), Q value = 0.077

Table S390. Gene #51: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	198	91
DEL PEAK 30(13Q14.2) MUTATED	71	122	47
DEL PEAK 30(13Q14.2) WILD-TYPE	74	76	44

Figure S390. Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 3e-04

Table S391. Gene #51: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
DEL PEAK 30(13Q14.2) MUTATED	39	156	45
DEL PEAK 30(13Q14.2) WILD-TYPE	64	92	38

Figure S391. Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q34' versus 'MRNA_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.042

Table S392. Gene #52: 'del_13q34' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	5	9	12	6
DEL PEAK 31(13Q34) MUTATED	3	5	1	4
DEL PEAK 31(13Q34) WILD-TYPE	2	4	11	2

Figure S392. Get High-res Image Gene #52: 'del_13q34' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S393. Gene #52: 'del_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 31(13Q34) MUTATED	49	67	37	90
DEL PEAK 31(13Q34) WILD-TYPE	20	161	42	50

Figure S393. Get High-res Image Gene #52: 'del_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q34' versus 'METHLYATION_CNMF'

P value = 0.0402 (Fisher's exact test), Q value = 0.065

Table S394. Gene #52: 'del_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 31(13Q34) MUTATED	55	74	84
DEL PEAK 31(13Q34) WILD-TYPE	89	75	78

Figure S394. Get High-res Image Gene #52: 'del_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q34' versus 'RPPA_CNMF'

P value = 0.00188 (Fisher's exact test), Q value = 0.0045

Table S395. Gene #52: 'del_13q34' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 31(13Q34) MUTATED	53	8	26	45	40
DEL PEAK 31(13Q34) WILD-TYPE	38	14	40	30	69

Figure S395. Get High-res Image Gene #52: 'del_13q34' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q34' versus 'MRNASEQ_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0015

Table S396. Gene #52: 'del_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 31(13Q34) MUTATED	58	108	74
DEL PEAK 31(13Q34) WILD-TYPE	108	87	77

Figure S396. Get High-res Image Gene #52: 'del_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S397. Gene #52: 'del_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 31(13Q34) MUTATED	31	70	49	14	34	19	23
DEL PEAK 31(13Q34) WILD-TYPE	47	40	48	34	19	30	54

Figure S397. Get High-res Image Gene #52: 'del_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q34' versus 'MIRSEQ_CNMF'

P value = 0.00813 (Fisher's exact test), Q value = 0.017

Table S398. Gene #52: 'del_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 31(13Q34) MUTATED	73	113	53
DEL PEAK 31(13Q34) WILD-TYPE	116	115	40

Figure S398. Get High-res Image Gene #52: 'del_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0201 (Fisher's exact test), Q value = 0.037

Table S399. Gene #52: 'del_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 31(13Q34) MUTATED	31	108	53	47
DEL PEAK 31(13Q34) WILD-TYPE	40	90	88	53

Figure S399. Get High-res Image Gene #52: 'del_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q34' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 0.039

Table S400. Gene #52: 'del_13q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
DEL PEAK 31(13Q34) MUTATED	37	129	39
DEL PEAK 31(13Q34) WILD-TYPE	66	119	44

Figure S400. Get High-res Image Gene #52: 'del_13q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q32.12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S401. Gene #53: 'del_14q32.12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 32(14Q32.12) MUTATED	15	44	41	44
DEL PEAK 32(14Q32.12) WILD-TYPE	54	184	38	96

Figure S401. Get High-res Image Gene #53: 'del_14q32.12' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q32.12' versus 'METHLYATION_CNMF'

P value = 0.00337 (Fisher's exact test), Q value = 0.0074

Table S402. Gene #53: 'del_14q32.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 32(14Q32.12) MUTATED	27	54	44
DEL PEAK 32(14Q32.12) WILD-TYPE	117	95	118

Figure S402. Get High-res Image Gene #53: 'del_14q32.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q32.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0117 (Fisher's exact test), Q value = 0.023

Table S403. Gene #53: 'del_14q32.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 32(14Q32.12) MUTATED	17	31	27	12	16	25	15
DEL PEAK 32(14Q32.12) WILD-TYPE	61	79	70	36	37	24	62

Figure S403. Get High-res Image Gene #53: 'del_14q32.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.12' versus 'MIRSEQ_CNMF'

P value = 0.00719 (Fisher's exact test), Q value = 0.015

Table S404. Gene #53: 'del_14q32.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 32(14Q32.12) MUTATED	48	79	17
DEL PEAK 32(14Q32.12) WILD-TYPE	141	149	76

Figure S404. Get High-res Image Gene #53: 'del_14q32.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_14q32.12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0464 (Fisher's exact test), Q value = 0.074

Table S405. Gene #53: 'del_14q32.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	198	91
DEL PEAK 32(14Q32.12) MUTATED	48	58	17
DEL PEAK 32(14Q32.12) WILD-TYPE	97	140	74

Figure S405. Get High-res Image Gene #53: 'del_14q32.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S406. Gene #54: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 33(15Q11.2) MUTATED	46	77	37	102
DEL PEAK 33(15Q11.2) WILD-TYPE	23	151	42	38

Figure S406. Get High-res Image Gene #54: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q11.2' versus 'METHLYATION_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.0026

Table S407. Gene #54: 'del_15q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 33(15Q11.2) MUTATED	54	79	94
DEL PEAK 33(15Q11.2) WILD-TYPE	90	70	68

Figure S407. Get High-res Image Gene #54: 'del_15q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q11.2' versus 'RPPA_CNMF'

P value = 0.0373 (Fisher's exact test), Q value = 0.062

Table S408. Gene #54: 'del_15q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 33(15Q11.2) MUTATED	58	11	31	41	46
DEL PEAK 33(15Q11.2) WILD-TYPE	33	11	35	34	63

Figure S408. Get High-res Image Gene #54: 'del_15q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_15q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.002

Table S409. Gene #54: 'del_15q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 33(15Q11.2) MUTATED	72	119	67
DEL PEAK 33(15Q11.2) WILD-TYPE	94	76	84

Figure S409. Get High-res Image Gene #54: 'del_15q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S410. Gene #54: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 33(15Q11.2) MUTATED	39	73	62	11	36	9	28
DEL PEAK 33(15Q11.2) WILD-TYPE	39	37	35	37	17	40	49

Figure S410. Get High-res Image Gene #54: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00017

Table S411. Gene #54: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 33(15Q11.2) MUTATED	71	133	55
DEL PEAK 33(15Q11.2) WILD-TYPE	118	95	38

Figure S411. Get High-res Image Gene #54: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00701 (Fisher's exact test), Q value = 0.014

Table S412. Gene #54: 'del_15q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 33(15Q11.2) MUTATED	28	116	61	54
DEL PEAK 33(15Q11.2) WILD-TYPE	43	82	80	46

Figure S412. Get High-res Image Gene #54: 'del_15q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S413. Gene #54: 'del_15q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
DEL PEAK 33(15Q11.2) MUTATED	33	136	51
DEL PEAK 33(15Q11.2) WILD-TYPE	70	112	32

Figure S413. Get High-res Image Gene #54: 'del_15q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S414. Gene #55: 'del_15q15.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 34(15Q15.1) MUTATED	51	79	36	108
DEL PEAK 34(15Q15.1) WILD-TYPE	18	149	43	32

Figure S414. Get High-res Image Gene #55: 'del_15q15.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q15.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S415. Gene #55: 'del_15q15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 34(15Q15.1) MUTATED	52	82	101
DEL PEAK 34(15Q15.1) WILD-TYPE	92	67	61

Figure S415. Get High-res Image Gene #55: 'del_15q15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q15.1' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00038

Table S416. Gene #55: 'del_15q15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 34(15Q15.1) MUTATED	73	126	71
DEL PEAK 34(15Q15.1) WILD-TYPE	93	69	80

Figure S416. Get High-res Image Gene #55: 'del_15q15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S417. Gene #55: 'del_15q15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 34(15Q15.1) MUTATED	39	76	64	12	39	11	29
DEL PEAK 34(15Q15.1) WILD-TYPE	39	34	33	36	14	38	48

Figure S417. Get High-res Image Gene #55: 'del_15q15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.7e-05

Table S418. Gene #55: 'del_15q15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 34(15Q15.1) MUTATED	73	141	57
DEL PEAK 34(15Q15.1) WILD-TYPE	116	87	36

Figure S418. Get High-res Image Gene #55: 'del_15q15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.00089

Table S419. Gene #55: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 34(15Q15.1) MUTATED	30	125	59	57
DEL PEAK 34(15Q15.1) WILD-TYPE	41	73	82	43

Figure S419. Get High-res Image Gene #55: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7.7e-05

Table S420. Gene #55: 'del_15q15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
DEL PEAK 34(15Q15.1) MUTATED	33	146	49
DEL PEAK 34(15Q15.1) WILD-TYPE	70	102	34

Figure S420. Get High-res Image Gene #55: 'del_15q15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S421. Gene #56: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 35(16Q23.1) MUTATED	30	48	34	58
DEL PEAK 35(16Q23.1) WILD-TYPE	39	180	45	82

Figure S421. Get High-res Image Gene #56: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S422. Gene #56: 'del_16q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 35(16Q23.1) MUTATED	26	55	66
DEL PEAK 35(16Q23.1) WILD-TYPE	118	94	96

Figure S422. Get High-res Image Gene #56: 'del_16q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16q23.1' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S423. Gene #56: 'del_16q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 35(16Q23.1) MUTATED	35	8	14	40	23
DEL PEAK 35(16Q23.1) WILD-TYPE	56	14	52	35	86

Figure S423. Get High-res Image Gene #56: 'del_16q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_16q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00543 (Fisher's exact test), Q value = 0.012

Table S424. Gene #56: 'del_16q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
DEL PEAK 35(16Q23.1) MUTATED	47	58	15
DEL PEAK 35(16Q23.1) WILD-TYPE	120	75	48

Figure S424. Get High-res Image Gene #56: 'del_16q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S425. Gene #56: 'del_16q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 35(16Q23.1) MUTATED	36	92	42
DEL PEAK 35(16Q23.1) WILD-TYPE	130	103	109

Figure S425. Get High-res Image Gene #56: 'del_16q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S426. Gene #56: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 35(16Q23.1) MUTATED	20	60	37	9	17	17	10
DEL PEAK 35(16Q23.1) WILD-TYPE	58	50	60	39	36	32	67

Figure S426. Get High-res Image Gene #56: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 0.0213 (Fisher's exact test), Q value = 0.039

Table S427. Gene #56: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 35(16Q23.1) MUTATED	49	87	34
DEL PEAK 35(16Q23.1) WILD-TYPE	140	141	59

Figure S427. Get High-res Image Gene #56: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00327 (Fisher's exact test), Q value = 0.0072

Table S428. Gene #56: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 35(16Q23.1) MUTATED	20	77	32	41
DEL PEAK 35(16Q23.1) WILD-TYPE	51	121	109	59

Figure S428. Get High-res Image Gene #56: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.0015

Table S429. Gene #56: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
DEL PEAK 35(16Q23.1) MUTATED	18	94	29
DEL PEAK 35(16Q23.1) WILD-TYPE	85	154	54

Figure S429. Get High-res Image Gene #56: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S430. Gene #57: 'del_17p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 36(17P13.3) MUTATED	39	84	45	113
DEL PEAK 36(17P13.3) WILD-TYPE	30	144	34	27

Figure S430. Get High-res Image Gene #57: 'del_17p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S431. Gene #57: 'del_17p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 36(17P13.3) MUTATED	54	82	108
DEL PEAK 36(17P13.3) WILD-TYPE	90	67	54

Figure S431. Get High-res Image Gene #57: 'del_17p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p13.3' versus 'RPPA_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.021

Table S432. Gene #57: 'del_17p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 36(17P13.3) MUTATED	62	12	28	47	55
DEL PEAK 36(17P13.3) WILD-TYPE	29	10	38	28	54

Figure S432. Get High-res Image Gene #57: 'del_17p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_17p13.3' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S433. Gene #57: 'del_17p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 36(17P13.3) MUTATED	78	132	69
DEL PEAK 36(17P13.3) WILD-TYPE	88	63	82

Figure S433. Get High-res Image Gene #57: 'del_17p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S434. Gene #57: 'del_17p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 36(17P13.3) MUTATED	39	75	62	10	33	24	36
DEL PEAK 36(17P13.3) WILD-TYPE	39	35	35	38	20	25	41

Figure S434. Get High-res Image Gene #57: 'del_17p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.3' versus 'MIRSEQ_CNMF'

P value = 0.0138 (Fisher's exact test), Q value = 0.026

Table S435. Gene #57: 'del_17p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 36(17P13.3) MUTATED	90	140	47
DEL PEAK 36(17P13.3) WILD-TYPE	99	88	46

Figure S435. Get High-res Image Gene #57: 'del_17p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0252 (Fisher's exact test), Q value = 0.044

Table S436. Gene #57: 'del_17p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 36(17P13.3) MUTATED	30	118	69	60
DEL PEAK 36(17P13.3) WILD-TYPE	41	80	72	40

Figure S436. Get High-res Image Gene #57: 'del_17p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00199 (Fisher's exact test), Q value = 0.0047

Table S437. Gene #57: 'del_17p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
DEL PEAK 36(17P13.3) MUTATED	40	147	47
DEL PEAK 36(17P13.3) WILD-TYPE	63	101	36

Figure S437. Get High-res Image Gene #57: 'del_17p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q21.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S438. Gene #58: 'del_18q21.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 37(18Q21.32) MUTATED	21	88	44	98
DEL PEAK 37(18Q21.32) WILD-TYPE	48	140	35	42

Figure S438. Get High-res Image Gene #58: 'del_18q21.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q21.32' versus 'RPPA_CNMF'

P value = 0.00333 (Fisher's exact test), Q value = 0.0073

Table S439. Gene #58: 'del_18q21.32' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 37(18Q21.32) MUTATED	48	12	30	49	40
DEL PEAK 37(18Q21.32) WILD-TYPE	43	10	36	26	69

Figure S439. Get High-res Image Gene #58: 'del_18q21.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_18q21.32' versus 'RPPA_CHIERARCHICAL'

P value = 0.0253 (Fisher's exact test), Q value = 0.044

Table S440. Gene #58: 'del_18q21.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
DEL PEAK 37(18Q21.32) MUTATED	72	78	29
DEL PEAK 37(18Q21.32) WILD-TYPE	95	55	34

Figure S440. Get High-res Image Gene #58: 'del_18q21.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_18q21.32' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.7e-05

Table S441. Gene #58: 'del_18q21.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 37(18Q21.32) MUTATED	69	121	59
DEL PEAK 37(18Q21.32) WILD-TYPE	97	74	92

Figure S441. Get High-res Image Gene #58: 'del_18q21.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q21.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S442. Gene #58: 'del_18q21.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 37(18Q21.32) MUTATED	39	63	57	10	17	29	34
DEL PEAK 37(18Q21.32) WILD-TYPE	39	47	40	38	36	20	43

Figure S442. Get High-res Image Gene #58: 'del_18q21.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.32' versus 'MIRSEQ_CNMF'

P value = 0.0197 (Fisher's exact test), Q value = 0.036

Table S443. Gene #58: 'del_18q21.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 37(18Q21.32) MUTATED	78	116	54
DEL PEAK 37(18Q21.32) WILD-TYPE	111	112	39

Figure S443. Get High-res Image Gene #58: 'del_18q21.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S444. Gene #59: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 38(19P13.3) MUTATED	48	85	67	83
DEL PEAK 38(19P13.3) WILD-TYPE	21	143	12	57

Figure S444. Get High-res Image Gene #59: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S445. Gene #59: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 38(19P13.3) MUTATED	54	118	76
DEL PEAK 38(19P13.3) WILD-TYPE	90	31	86

Figure S445. Get High-res Image Gene #59: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p13.3' versus 'RPPA_CNMF'

P value = 0.00231 (Fisher's exact test), Q value = 0.0054

Table S446. Gene #59: 'del_19p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 38(19P13.3) MUTATED	44	12	45	53	51
DEL PEAK 38(19P13.3) WILD-TYPE	47	10	21	22	58

Figure S446. Get High-res Image Gene #59: 'del_19p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0488 (Fisher's exact test), Q value = 0.077

Table S447. Gene #59: 'del_19p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
DEL PEAK 38(19P13.3) MUTATED	91	85	29
DEL PEAK 38(19P13.3) WILD-TYPE	76	48	34

Figure S447. Get High-res Image Gene #59: 'del_19p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S448. Gene #59: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 38(19P13.3) MUTATED	56	113	111
DEL PEAK 38(19P13.3) WILD-TYPE	110	82	40

Figure S448. Get High-res Image Gene #59: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S449. Gene #59: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 38(19P13.3) MUTATED	26	53	64	39	34	42	22
DEL PEAK 38(19P13.3) WILD-TYPE	52	57	33	9	19	7	55

Figure S449. Get High-res Image Gene #59: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S450. Gene #59: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 38(19P13.3) MUTATED	81	153	43
DEL PEAK 38(19P13.3) WILD-TYPE	108	75	50

Figure S450. Get High-res Image Gene #59: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S451. Gene #59: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 38(19P13.3) MUTATED	36	116	52	73
DEL PEAK 38(19P13.3) WILD-TYPE	35	82	89	27

Figure S451. Get High-res Image Gene #59: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00086 (Fisher's exact test), Q value = 0.0022

Table S452. Gene #59: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
DEL PEAK 38(19P13.3) MUTATED	47	153	34
DEL PEAK 38(19P13.3) WILD-TYPE	56	95	49

Figure S452. Get High-res Image Gene #59: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S453. Gene #60: 'del_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 39(19P13.2) MUTATED	49	82	66	83
DEL PEAK 39(19P13.2) WILD-TYPE	20	146	13	57

Figure S453. Get High-res Image Gene #60: 'del_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S454. Gene #60: 'del_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 39(19P13.2) MUTATED	50	118	78
DEL PEAK 39(19P13.2) WILD-TYPE	94	31	84

Figure S454. Get High-res Image Gene #60: 'del_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p13.2' versus 'RPPA_CNMF'

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

Table S455. Gene #60: 'del_19p13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 39(19P13.2) MUTATED	43	13	43	51	51
DEL PEAK 39(19P13.2) WILD-TYPE	48	9	23	24	58

Figure S455. Get High-res Image Gene #60: 'del_19p13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19p13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S456. Gene #60: 'del_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 39(19P13.2) MUTATED	54	110	113
DEL PEAK 39(19P13.2) WILD-TYPE	112	85	38

Figure S456. Get High-res Image Gene #60: 'del_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S457. Gene #60: 'del_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 39(19P13.2) MUTATED	25	55	61	39	37	38	22
DEL PEAK 39(19P13.2) WILD-TYPE	53	55	36	9	16	11	55

Figure S457. Get High-res Image Gene #60: 'del_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.2' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.7e-05

Table S458. Gene #60: 'del_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 39(19P13.2) MUTATED	79	151	44
DEL PEAK 39(19P13.2) WILD-TYPE	110	77	49

Figure S458. Get High-res Image Gene #60: 'del_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S459. Gene #60: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 39(19P13.2) MUTATED	37	114	50	73
DEL PEAK 39(19P13.2) WILD-TYPE	34	84	91	27

Figure S459. Get High-res Image Gene #60: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00111 (Fisher's exact test), Q value = 0.0028

Table S460. Gene #60: 'del_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
DEL PEAK 39(19P13.2) MUTATED	46	153	35
DEL PEAK 39(19P13.2) WILD-TYPE	57	95	48

Figure S460. Get High-res Image Gene #60: 'del_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S461. Gene #61: 'del_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 40(19P13.2) MUTATED	50	76	64	80
DEL PEAK 40(19P13.2) WILD-TYPE	19	152	15	60

Figure S461. Get High-res Image Gene #61: 'del_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S462. Gene #61: 'del_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 40(19P13.2) MUTATED	45	115	77
DEL PEAK 40(19P13.2) WILD-TYPE	99	34	85

Figure S462. Get High-res Image Gene #61: 'del_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p13.2' versus 'RPPA_CNMF'

P value = 0.0013 (Fisher's exact test), Q value = 0.0032

Table S463. Gene #61: 'del_19p13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 40(19P13.2) MUTATED	40	12	44	50	47
DEL PEAK 40(19P13.2) WILD-TYPE	51	10	22	25	62

Figure S463. Get High-res Image Gene #61: 'del_19p13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19p13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S464. Gene #61: 'del_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 40(19P13.2) MUTATED	51	103	113
DEL PEAK 40(19P13.2) WILD-TYPE	115	92	38

Figure S464. Get High-res Image Gene #61: 'del_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S465. Gene #61: 'del_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 40(19P13.2) MUTATED	22	52	55	38	40	38	22
DEL PEAK 40(19P13.2) WILD-TYPE	56	58	42	10	13	11	55

Figure S465. Get High-res Image Gene #61: 'del_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S466. Gene #61: 'del_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 40(19P13.2) MUTATED	76	148	40
DEL PEAK 40(19P13.2) WILD-TYPE	113	80	53

Figure S466. Get High-res Image Gene #61: 'del_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S467. Gene #61: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 40(19P13.2) MUTATED	36	108	48	72
DEL PEAK 40(19P13.2) WILD-TYPE	35	90	93	28

Figure S467. Get High-res Image Gene #61: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00041

Table S468. Gene #61: 'del_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
DEL PEAK 40(19P13.2) MUTATED	43	152	33
DEL PEAK 40(19P13.2) WILD-TYPE	60	96	50

Figure S468. Get High-res Image Gene #61: 'del_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S469. Gene #62: 'del_19q11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 41(19Q11) MUTATED	24	37	19	54
DEL PEAK 41(19Q11) WILD-TYPE	45	191	60	86

Figure S469. Get High-res Image Gene #62: 'del_19q11' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q11' versus 'METHLYATION_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0021

Table S470. Gene #62: 'del_19q11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 41(19Q11) MUTATED	21	44	51
DEL PEAK 41(19Q11) WILD-TYPE	123	105	111

Figure S470. Get High-res Image Gene #62: 'del_19q11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q11' versus 'RPPA_CHIERARCHICAL'

P value = 0.00575 (Fisher's exact test), Q value = 0.012

Table S471. Gene #62: 'del_19q11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
DEL PEAK 41(19Q11) MUTATED	51	44	8
DEL PEAK 41(19Q11) WILD-TYPE	116	89	55

Figure S471. Get High-res Image Gene #62: 'del_19q11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_19q11' versus 'MRNASEQ_CNMF'

P value = 0.00264 (Fisher's exact test), Q value = 0.006

Table S472. Gene #62: 'del_19q11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 41(19Q11) MUTATED	29	65	39
DEL PEAK 41(19Q11) WILD-TYPE	137	130	112

Figure S472. Get High-res Image Gene #62: 'del_19q11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19q11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00241 (Fisher's exact test), Q value = 0.0056

Table S473. Gene #62: 'del_19q11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 41(19Q11) MUTATED	15	39	31	11	15	14	8
DEL PEAK 41(19Q11) WILD-TYPE	63	71	66	37	38	35	69

Figure S473. Get High-res Image Gene #62: 'del_19q11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19q11' versus 'MIRSEQ_CNMF'

P value = 0.00168 (Fisher's exact test), Q value = 0.0041

Table S474. Gene #62: 'del_19q11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 41(19Q11) MUTATED	31	67	30
DEL PEAK 41(19Q11) WILD-TYPE	158	161	63

Figure S474. Get High-res Image Gene #62: 'del_19q11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19q11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.00094

Table S475. Gene #62: 'del_19q11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 41(19Q11) MUTATED	13	61	20	34
DEL PEAK 41(19Q11) WILD-TYPE	58	137	121	66

Figure S475. Get High-res Image Gene #62: 'del_19q11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19q11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0451 (Fisher's exact test), Q value = 0.072

Table S476. Gene #62: 'del_19q11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
DEL PEAK 41(19Q11) MUTATED	18	74	19
DEL PEAK 41(19Q11) WILD-TYPE	85	174	64

Figure S476. Get High-res Image Gene #62: 'del_19q11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S477. Gene #63: 'del_19q13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 42(19Q13.33) MUTATED	30	52	38	74
DEL PEAK 42(19Q13.33) WILD-TYPE	39	176	41	66

Figure S477. Get High-res Image Gene #63: 'del_19q13.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q13.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S478. Gene #63: 'del_19q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 42(19Q13.33) MUTATED	25	72	66
DEL PEAK 42(19Q13.33) WILD-TYPE	119	77	96

Figure S478. Get High-res Image Gene #63: 'del_19q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q13.33' versus 'RPPA_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.024

Table S479. Gene #63: 'del_19q13.33' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 42(19Q13.33) MUTATED	31	9	35	34	31
DEL PEAK 42(19Q13.33) WILD-TYPE	60	13	31	41	78

Figure S479. Get High-res Image Gene #63: 'del_19q13.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19q13.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.0012

Table S480. Gene #63: 'del_19q13.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
DEL PEAK 42(19Q13.33) MUTATED	65	63	12
DEL PEAK 42(19Q13.33) WILD-TYPE	102	70	51

Figure S480. Get High-res Image Gene #63: 'del_19q13.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_19q13.33' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S481. Gene #63: 'del_19q13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 42(19Q13.33) MUTATED	38	85	68
DEL PEAK 42(19Q13.33) WILD-TYPE	128	110	83

Figure S481. Get High-res Image Gene #63: 'del_19q13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S482. Gene #63: 'del_19q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 42(19Q13.33) MUTATED	19	46	45	23	24	23	11
DEL PEAK 42(19Q13.33) WILD-TYPE	59	64	52	25	29	26	66

Figure S482. Get High-res Image Gene #63: 'del_19q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S483. Gene #63: 'del_19q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 42(19Q13.33) MUTATED	47	107	35
DEL PEAK 42(19Q13.33) WILD-TYPE	142	121	58

Figure S483. Get High-res Image Gene #63: 'del_19q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19q13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S484. Gene #63: 'del_19q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 42(19Q13.33) MUTATED	22	87	28	52
DEL PEAK 42(19Q13.33) WILD-TYPE	49	111	113	48

Figure S484. Get High-res Image Gene #63: 'del_19q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S485. Gene #63: 'del_19q13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
DEL PEAK 42(19Q13.33) MUTATED	27	103	25
DEL PEAK 42(19Q13.33) WILD-TYPE	76	145	58

Figure S485. Get High-res Image Gene #63: 'del_19q13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S486. Gene #64: 'del_20p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 43(20P13) MUTATED	10	40	24	57
DEL PEAK 43(20P13) WILD-TYPE	59	188	55	83

Figure S486. Get High-res Image Gene #64: 'del_20p13' versus Molecular Subtype #3: 'CN_CNMF'

'del_20p13' versus 'METHLYATION_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0014

Table S487. Gene #64: 'del_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 43(20P13) MUTATED	32	26	58
DEL PEAK 43(20P13) WILD-TYPE	112	123	104

Figure S487. Get High-res Image Gene #64: 'del_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_20p13' versus 'RPPA_CNMF'

P value = 0.0352 (Fisher's exact test), Q value = 0.059

Table S488. Gene #64: 'del_20p13' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 43(20P13) MUTATED	33	2	15	22	23
DEL PEAK 43(20P13) WILD-TYPE	58	20	51	53	86

Figure S488. Get High-res Image Gene #64: 'del_20p13' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_20p13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S489. Gene #64: 'del_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 43(20P13) MUTATED	39	72	19
DEL PEAK 43(20P13) WILD-TYPE	127	123	132

Figure S489. Get High-res Image Gene #64: 'del_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_20p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S490. Gene #64: 'del_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 43(20P13) MUTATED	23	44	20	0	10	16	17
DEL PEAK 43(20P13) WILD-TYPE	55	66	77	48	43	33	60

Figure S490. Get High-res Image Gene #64: 'del_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_20p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0149 (Fisher's exact test), Q value = 0.028

Table S491. Gene #64: 'del_20p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
DEL PEAK 43(20P13) MUTATED	15	65	26
DEL PEAK 43(20P13) WILD-TYPE	88	183	57

Figure S491. Get High-res Image Gene #64: 'del_20p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20q13.12' versus 'MRNA_CNMF'

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

Table S492. Gene #65: 'del_20q13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	5	9	12	6
DEL PEAK 44(20Q13.12) MUTATED	3	0	3	0
DEL PEAK 44(20Q13.12) WILD-TYPE	2	9	9	6

Figure S492. Get High-res Image Gene #65: 'del_20q13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_20q13.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00409 (Fisher's exact test), Q value = 0.0089

Table S493. Gene #65: 'del_20q13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 44(20Q13.12) MUTATED	18	15	6	12	9	12	8
DEL PEAK 44(20Q13.12) WILD-TYPE	60	95	91	36	44	37	69

Figure S493. Get High-res Image Gene #65: 'del_20q13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_20q13.12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0433 (Fisher's exact test), Q value = 0.07

Table S494. Gene #65: 'del_20q13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	198	91
DEL PEAK 44(20Q13.12) MUTATED	28	30	7
DEL PEAK 44(20Q13.12) WILD-TYPE	117	168	84

Figure S494. Get High-res Image Gene #65: 'del_20q13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_21q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S495. Gene #66: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 45(21Q11.2) MUTATED	38	60	45	42
DEL PEAK 45(21Q11.2) WILD-TYPE	31	168	34	98

Figure S495. Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 0.0273 (Fisher's exact test), Q value = 0.047

Table S496. Gene #66: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 45(21Q11.2) MUTATED	38	61	59
DEL PEAK 45(21Q11.2) WILD-TYPE	106	88	103

Figure S496. Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_21q11.2' versus 'RPPA_CNMF'

P value = 0.00449 (Fisher's exact test), Q value = 0.0097

Table S497. Gene #66: 'del_21q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 45(21Q11.2) MUTATED	24	5	22	40	37
DEL PEAK 45(21Q11.2) WILD-TYPE	67	17	44	35	72

Figure S497. Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_21q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S498. Gene #66: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 45(21Q11.2) MUTATED	28	77	77
DEL PEAK 45(21Q11.2) WILD-TYPE	138	118	74

Figure S498. Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_21q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S499. Gene #66: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 45(21Q11.2) MUTATED	11	39	41	12	35	22	22
DEL PEAK 45(21Q11.2) WILD-TYPE	67	71	56	36	18	27	55

Figure S499. Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S500. Gene #66: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 45(21Q11.2) MUTATED	46	109	26
DEL PEAK 45(21Q11.2) WILD-TYPE	143	119	67

Figure S500. Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_21q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.00072

Table S501. Gene #66: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 45(21Q11.2) MUTATED	17	76	37	51
DEL PEAK 45(21Q11.2) WILD-TYPE	54	122	104	49

Figure S501. Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.00066

Table S502. Gene #66: 'del_21q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
DEL PEAK 45(21Q11.2) MUTATED	22	106	23
DEL PEAK 45(21Q11.2) WILD-TYPE	81	142	60

Figure S502. Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.32' versus 'MRNA_CNMF'

P value = 0.0248 (Fisher's exact test), Q value = 0.043

Table S503. Gene #67: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	5	9	12	6
DEL PEAK 46(22Q13.32) MUTATED	3	7	2	4
DEL PEAK 46(22Q13.32) WILD-TYPE	2	2	10	2

Figure S503. Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S504. Gene #67: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 46(22Q13.32) MUTATED	52	72	45	86
DEL PEAK 46(22Q13.32) WILD-TYPE	17	156	34	54

Figure S504. Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S505. Gene #67: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 46(22Q13.32) MUTATED	41	94	90
DEL PEAK 46(22Q13.32) WILD-TYPE	103	55	72

Figure S505. Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q13.32' versus 'RPPA_CNMF'

P value = 0.00442 (Fisher's exact test), Q value = 0.0096

Table S506. Gene #67: 'del_22q13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 46(22Q13.32) MUTATED	48	7	24	49	54
DEL PEAK 46(22Q13.32) WILD-TYPE	43	15	42	26	55

Figure S506. Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_22q13.32' versus 'RPPA_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0013

Table S507. Gene #67: 'del_22q13.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	133	63
DEL PEAK 46(22Q13.32) MUTATED	66	83	33
DEL PEAK 46(22Q13.32) WILD-TYPE	101	50	30

Figure S507. Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S508. Gene #67: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 46(22Q13.32) MUTATED	53	113	86
DEL PEAK 46(22Q13.32) WILD-TYPE	113	82	65

Figure S508. Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S509. Gene #67: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 46(22Q13.32) MUTATED	26	67	54	15	42	28	20
DEL PEAK 46(22Q13.32) WILD-TYPE	52	43	43	33	11	21	57

Figure S509. Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S510. Gene #67: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
DEL PEAK 46(22Q13.32) MUTATED	67	139	45
DEL PEAK 46(22Q13.32) WILD-TYPE	122	89	48

Figure S510. Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_22q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S511. Gene #67: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
DEL PEAK 46(22Q13.32) MUTATED	24	116	49	62
DEL PEAK 46(22Q13.32) WILD-TYPE	47	82	92	38

Figure S511. Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0146 (Fisher's exact test), Q value = 0.028

Table S512. Gene #67: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	198	91
DEL PEAK 46(22Q13.32) MUTATED	70	110	34
DEL PEAK 46(22Q13.32) WILD-TYPE	75	88	57

Figure S512. Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_22q13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00017

Table S513. Gene #67: 'del_22q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
DEL PEAK 46(22Q13.32) MUTATED	34	145	35
DEL PEAK 46(22Q13.32) WILD-TYPE	69	103	48

Figure S513. Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.2e-05

Table S514. Gene #68: 'del_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	228	79	140
DEL PEAK 47(XP22.2) MUTATED	18	37	21	67
DEL PEAK 47(XP22.2) WILD-TYPE	51	191	58	73

Figure S514. Get High-res Image Gene #68: 'del_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_xp22.2' versus 'METHLYATION_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.031

Table S515. Gene #68: 'del_xp22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	149	162
DEL PEAK 47(XP22.2) MUTATED	28	41	55
DEL PEAK 47(XP22.2) WILD-TYPE	116	108	107

Figure S515. Get High-res Image Gene #68: 'del_xp22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xp22.2' versus 'RPPA_CNMF'

P value = 0.0413 (Fisher's exact test), Q value = 0.067

Table S516. Gene #68: 'del_xp22.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	22	66	75	109
DEL PEAK 47(XP22.2) MUTATED	32	5	10	25	27
DEL PEAK 47(XP22.2) WILD-TYPE	59	17	56	50	82

Figure S516. Get High-res Image Gene #68: 'del_xp22.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_xp22.2' versus 'MRNASEQ_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 0.023

Table S517. Gene #68: 'del_xp22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	195	151
DEL PEAK 47(XP22.2) MUTATED	39	69	34
DEL PEAK 47(XP22.2) WILD-TYPE	127	126	117

Figure S517. Get High-res Image Gene #68: 'del_xp22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_xp22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00038

Table S518. Gene #68: 'del_xp22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	110	97	48	53	49	77
DEL PEAK 47(XP22.2) MUTATED	23	48	33	9	8	8	13
DEL PEAK 47(XP22.2) WILD-TYPE	55	62	64	39	45	41	64

Figure S518. Get High-res Image Gene #68: 'del_xp22.2' versus Molecular Subtype #8: 'MRNASEQ_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/LUAD-TP/20146410/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LUAD-TP/20140677/LUAD-TP.transferedmergedcluster.txt
Number of patients = 516
Number of significantly focal cnvs = 68
Number of molecular subtypes = 12
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

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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