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

Prostate Adenocarcinoma (Primary solid tumor)

02 April 2015 | analyses__2015_04_02

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C18914Z7

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 65 focal events and 8 molecular subtypes across 492 patients, 397 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3q26.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_4p16.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
amp_4q13.3 cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_5q35.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_7p14.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8p11.23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_9q33.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_11q13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_13q12.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_14q21.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_15q11.2 cnv correlated to 'CN_CNMF'.
amp_16q11.2 cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_17q23.2 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
amp_19q13.43 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20q13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_xp22.11 cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_xp22.11 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_xp21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_xq21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_xq21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_xq25 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_xq27.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_1p31.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_1q42.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2p21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_3q29 cnv correlated to 'MRNASEQ_CNMF'.
del_4q28.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6p25.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q14.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_7q31.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p23.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p23 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_11q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12q24.32 cnv correlated to 'CN_CNMF'.
del_13q14.13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q24.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17q21.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_18q21.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19q13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_21q22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_21q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 65 focal events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 397 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	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
amp 1q22	40 (8%)	452	1e-05 (4.09e-05)	0.0349 (0.0485)	0.00109 (0.00244)	0.00025 (0.000663)	0.0128 (0.0205)	0.00044 (0.00107)	0.04 (0.0543)	0.0189 (0.0284)
amp 3q21 3	75 (15%)	417	1e-05 (4.09e-05)	0.00084 (0.00195)	0.00039 (0.000966)	9e-05 (0.000272)	0.0179 (0.0272)	0.00031 (0.000794)	0.00904 (0.0152)	0.00021 (0.000566)
amp 7p14 3	104 (21%)	388	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	4e-05 (0.000127)	0.00376 (0.00708)	0.00054 (0.00128)	0.00114 (0.00251)	0.00927 (0.0155)
amp 7q22 1	101 (21%)	391	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	2e-05 (7.03e-05)	0.00648 (0.0115)	1e-05 (4.09e-05)	0.00042 (0.00103)	0.00299 (0.0057)
amp 8p11 23	67 (14%)	425	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	0.00045 (0.00109)	0.0457 (0.0606)	0.00134 (0.00287)	2e-05 (7.03e-05)	0.00052 (0.00124)
amp 8q22 1	157 (32%)	335	1e-05 (4.09e-05)	1e-05 (4.09e-05)	3e-05 (0.000102)	1e-05 (4.09e-05)	4e-05 (0.000127)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	4e-05 (0.000127)
amp 8q24 21	152 (31%)	340	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	2e-05 (7.03e-05)	0.00036 (0.000904)
amp 9q33 3	62 (13%)	430	1e-05 (4.09e-05)	0.0199 (0.0294)	0.00225 (0.00447)	0.0163 (0.0251)	0.0199 (0.0294)	0.00097 (0.00221)	0.0167 (0.0255)	0.00836 (0.0142)
amp 11q13 2	48 (10%)	444	1e-05 (4.09e-05)	0.00831 (0.0142)	0.00707 (0.0125)	0.0004 (0.000986)	0.0315 (0.0444)	0.00021 (0.000566)	0.00742 (0.013)	0.0306 (0.0434)
del 1p22 1	58 (12%)	434	1e-05 (4.09e-05)	2e-05 (7.03e-05)	0.00116 (0.00252)	0.00016 (0.000447)	0.00785 (0.0135)	0.00336 (0.00638)	0.00983 (0.0164)	0.00694 (0.0123)
del 2q22 1	92 (19%)	400	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	4e-05 (0.000127)	0.00174 (0.00359)	0.00091 (0.00209)
del 2q22 3	85 (17%)	407	1e-05 (4.09e-05)	1e-05 (4.09e-05)	3e-05 (0.000102)	1e-05 (4.09e-05)	0.00013 (0.000371)	3e-05 (0.000102)	0.0129 (0.0206)	0.00026 (0.000679)
del 5q11 2	100 (20%)	392	1e-05 (4.09e-05)	1e-05 (4.09e-05)	0.00025 (0.000663)	1e-05 (4.09e-05)	0.00011 (0.000329)	2e-05 (7.03e-05)	0.00093 (0.00213)	0.00017 (0.000473)
del 5q13 2	99 (20%)	393	1e-05 (4.09e-05)	2e-05 (7.03e-05)	0.00089 (0.00206)	0.00285 (0.00547)	0.00026 (0.000679)	1e-05 (4.09e-05)	0.0022 (0.00442)	0.00033 (0.000841)
del 6q14 3	180 (37%)	312	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	0.00211 (0.00425)	0.00498 (0.00912)
del 8p23 2	224 (46%)	268	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	0.00031 (0.000794)	0.00035 (0.000888)	0.0358 (0.0496)	0.00191 (0.00391)
del 8p21 3	294 (60%)	198	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	2e-05 (7.03e-05)	1e-05 (4.09e-05)	0.00844 (0.0143)	2e-05 (7.03e-05)
del 10q23 31	157 (32%)	335	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	0.0142 (0.0223)	1e-05 (4.09e-05)	0.0402 (0.0545)	1e-05 (4.09e-05)
del 13q14 13	227 (46%)	265	1e-05 (4.09e-05)	1e-05 (4.09e-05)	6e-05 (0.000187)	2e-05 (7.03e-05)	4e-05 (0.000127)	0.00037 (0.000925)	0.00015 (0.000424)	4e-05 (0.000127)
del 13q22 1	176 (36%)	316	1e-05 (4.09e-05)	6e-05 (0.000187)	2e-05 (7.03e-05)	9e-05 (0.000272)	0.00464 (0.00859)	0.00129 (0.00277)	0.00164 (0.00342)	0.00012 (0.000357)
del 15q21 3	67 (14%)	425	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	2e-05 (7.03e-05)	2e-05 (7.03e-05)	3e-05 (0.000102)	0.00013 (0.000371)	1e-05 (4.09e-05)
del 16q22 3	191 (39%)	301	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	0.00013 (0.000371)	4e-05 (0.000127)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)
del 16q24 1	213 (43%)	279	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	0.0061 (0.0109)	0.00021 (0.000566)	1e-05 (4.09e-05)	0.00253 (0.00496)	1e-05 (4.09e-05)
del 17p13 1	163 (33%)	329	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	0.00013 (0.000371)	1e-05 (4.09e-05)	0.00148 (0.00312)	1e-05 (4.09e-05)
del 18q21 31	131 (27%)	361	1e-05 (4.09e-05)	0.00195 (0.00396)	0.00016 (0.000447)	0.0118 (0.0192)	0.00022 (0.00059)	0.0183 (0.0278)	0.00375 (0.00708)	1e-05 (4.09e-05)
del 18q23	137 (28%)	355	1e-05 (4.09e-05)	0.0107 (0.0175)	8e-05 (0.000245)	0.0437 (0.0587)	0.0113 (0.0185)	0.00754 (0.0132)	0.00848 (0.0143)	1e-05 (4.09e-05)
del 19q13 2	52 (11%)	440	1e-05 (4.09e-05)	0.00115 (0.00251)	0.00533 (0.00962)	0.0481 (0.0632)	0.00261 (0.00508)	0.00079 (0.00187)	0.00279 (0.00541)	0.00113 (0.0025)
amp 3q26 2	86 (17%)	406	1e-05 (4.09e-05)	0.0451 (0.06)	0.00508 (0.00927)	0.014 (0.0221)	0.0818 (0.101)	0.00776 (0.0134)	0.00749 (0.0131)	1e-05 (4.09e-05)
amp 19q13 43	19 (4%)	473	1e-05 (4.09e-05)	0.0381 (0.0521)	0.00257 (0.00502)	0.0271 (0.0392)	0.00631 (0.0112)	0.0014 (0.00296)	0.151 (0.175)	0.0115 (0.0188)
amp 20q13 2	45 (9%)	447	1e-05 (4.09e-05)	8e-05 (0.000245)	0.00156 (0.00327)	0.00118 (0.00256)	0.00042 (0.00103)	4e-05 (0.000127)	0.161 (0.185)	5e-05 (0.000158)
del 1p31 3	60 (12%)	432	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	0.00167 (0.00347)	0.169 (0.193)	0.00545 (0.00981)	0.0011 (0.00245)
del 2p21	46 (9%)	446	1e-05 (4.09e-05)	2e-05 (7.03e-05)	0.00036 (0.000904)	0.0206 (0.0303)	0.0008 (0.00188)	0.0718 (0.0909)	0.0323 (0.0452)	0.0146 (0.0229)
del 4q28 2	51 (10%)	441	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	2e-05 (7.03e-05)	0.0919 (0.112)	0.015 (0.0232)	0.00082 (0.00192)	0.0256 (0.0372)
del 5q21 1	109 (22%)	383	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	0.00018 (0.000493)	0.00234 (0.00463)	0.102 (0.123)	0.0043 (0.00801)
del 7q31 33	28 (6%)	464	0.0001 (0.000301)	0.0144 (0.0226)	0.00015 (0.000424)	0.00028 (0.000724)	0.00115 (0.00251)	0.00026 (0.000679)	0.752 (0.765)	0.0473 (0.0623)
del 11p11 2	34 (7%)	458	1e-05 (4.09e-05)	0.00252 (0.00496)	0.00139 (0.00295)	0.0257 (0.0374)	0.0292 (0.0417)	0.0244 (0.0356)	0.00809 (0.0138)	0.476 (0.502)
del 12p13 1	124 (25%)	368	2e-05 (7.03e-05)	2e-05 (7.03e-05)	0.00135 (0.00288)	0.00408 (0.00766)	0.0637 (0.0817)	4e-05 (0.000127)	4e-05 (0.000127)	0.00281 (0.00541)
del 21q22 3	147 (30%)	345	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	0.0323 (0.0452)	1e-05 (4.09e-05)	0.77 (0.782)	1e-05 (4.09e-05)
amp 14q21 1	30 (6%)	462	1e-05 (4.09e-05)	0.0774 (0.0962)	0.0116 (0.0189)	0.0383 (0.0523)	0.00803 (0.0138)	0.0102 (0.0168)	0.0647 (0.0829)	0.0282 (0.0406)
amp xp22 11	25 (5%)	467	2e-05 (7.03e-05)	0.368 (0.396)	0.0337 (0.0469)	0.0128 (0.0205)	0.00774 (0.0134)	0.0102 (0.0168)	0.0463 (0.0613)	0.232 (0.261)
amp xp21 1	23 (5%)	469	2e-05 (7.03e-05)	0.0283 (0.0407)	0.0407 (0.055)	0.126 (0.15)	0.0195 (0.029)	0.00936 (0.0157)	0.00519 (0.00944)	0.146 (0.171)
del 1q23 1	28 (6%)	464	0.00521 (0.00944)	7e-05 (0.000217)	0.00018 (0.000493)	0.00084 (0.00195)	0.0442 (0.0591)	0.0544 (0.0708)	0.0191 (0.0286)	0.189 (0.215)
del 6p25 1	46 (9%)	446	1e-05 (4.09e-05)	0.0142 (0.0223)	0.00569 (0.0102)	0.0121 (0.0195)	0.146 (0.171)	0.0491 (0.0644)	0.387 (0.414)	0.0165 (0.0253)
del 21q22 2	52 (11%)	440	0.00052 (0.00124)	0.00013 (0.000371)	4e-05 (0.000127)	0.00018 (0.000493)	0.165 (0.19)	0.04 (0.0543)	0.836 (0.842)	0.00286 (0.00547)
amp 5q35 3	28 (6%)	464	1e-05 (4.09e-05)	0.0135 (0.0215)	0.055 (0.0713)	0.0427 (0.0575)	0.183 (0.208)	0.00104 (0.00234)	0.0161 (0.0249)	0.294 (0.324)
amp 13q12 11	25 (5%)	467	1e-05 (4.09e-05)	0.00225 (0.00447)	0.00484 (0.00889)	0.107 (0.129)	0.0139 (0.0221)	0.0318 (0.0447)	0.0674 (0.0857)	0.0731 (0.0923)
amp xq27 1	19 (4%)	473	0.00425 (0.00795)	0.0375 (0.0515)	0.095 (0.116)	0.113 (0.136)	0.00127 (0.00274)	0.00027 (0.000702)	0.037 (0.0509)	0.126 (0.15)
del 3p13	78 (16%)	414	0.00051 (0.00123)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	1e-05 (4.09e-05)	0.292 (0.321)	0.0665 (0.0848)	0.0296 (0.0422)	0.169 (0.193)
del 9p23	45 (9%)	447	1e-05 (4.09e-05)	0.203 (0.23)	0.00013 (0.000371)	0.00194 (0.00396)	0.0285 (0.0408)	0.0792 (0.0983)	0.0742 (0.0932)	0.0164 (0.0252)
amp 12q23 1	36 (7%)	456	1e-05 (4.09e-05)	0.00177 (0.00364)	0.0611 (0.0786)	0.00039 (0.000966)	0.651 (0.669)	0.0021 (0.00425)	0.285 (0.315)	0.124 (0.148)
amp xp22 11	26 (5%)	466	2e-05 (7.03e-05)	0.142 (0.167)	0.0915 (0.112)	0.0589 (0.076)	0.0161 (0.0249)	0.00481 (0.00887)	0.0443 (0.0591)	0.312 (0.338)
amp xq21 1	16 (3%)	476	0.00112 (0.00249)	0.031 (0.0439)	0.00759 (0.0132)	0.0192 (0.0288)	0.309 (0.337)	0.453 (0.48)	0.452 (0.479)	0.395 (0.421)
del 1q42 3	47 (10%)	445	0.00104 (0.00234)	1e-05 (4.09e-05)	0.35 (0.379)	0.0757 (0.0944)	0.113 (0.136)	0.0308 (0.0436)	0.696 (0.712)	0.0468 (0.0618)
del 17q21 31	96 (20%)	396	1e-05 (4.09e-05)	2e-05 (7.03e-05)	1e-05 (4.09e-05)	0.00013 (0.000371)	0.556 (0.579)	0.054 (0.0704)	0.17 (0.193)	0.311 (0.337)
amp 4p16 3	20 (4%)	472	1e-05 (4.09e-05)	0.0104 (0.0171)	0.0188 (0.0284)	0.137 (0.162)	0.41 (0.436)	0.075 (0.0937)	0.747 (0.761)	0.582 (0.603)
amp 4q13 3	22 (4%)	470	1e-05 (4.09e-05)	0.522 (0.546)	0.1 (0.122)	0.286 (0.315)	0.0273 (0.0395)	0.0662 (0.0846)	0.0367 (0.0506)	0.166 (0.19)
amp 16q11 2	30 (6%)	462	2e-05 (7.03e-05)	0.138 (0.162)	0.149 (0.173)	0.0577 (0.0746)	0.00172 (0.00356)	0.00099 (0.00225)	0.0817 (0.101)	0.245 (0.273)
amp xq21 1	14 (3%)	478	0.00222 (0.00444)	0.0184 (0.0279)	0.206 (0.233)	0.00433 (0.00804)	0.0537 (0.0701)	0.237 (0.265)	0.301 (0.33)	0.774 (0.784)
amp xq25	19 (4%)	473	0.00281 (0.00541)	0.0197 (0.0292)	0.106 (0.128)	0.0241 (0.0353)	0.204 (0.231)	0.149 (0.174)	0.731 (0.747)	0.144 (0.169)
del 11q22 3	43 (9%)	449	0.044 (0.059)	0.021 (0.0308)	0.361 (0.39)	0.104 (0.126)	0.863 (0.868)	0.784 (0.793)	0.161 (0.185)	0.0122 (0.0197)
amp 17q23 2	25 (5%)	467	1e-05 (4.09e-05)	0.789 (0.797)	0.0744 (0.0932)	0.233 (0.262)	0.52 (0.546)	0.0148 (0.0231)	0.378 (0.406)	0.0897 (0.11)
amp 15q11 2	16 (3%)	476	0.0101 (0.0168)	0.505 (0.532)	0.901 (0.905)	0.52 (0.546)	0.133 (0.158)	0.684 (0.702)	0.536 (0.56)	0.152 (0.176)
del 3q29	32 (7%)	460	0.612 (0.631)	0.299 (0.328)	0.0359 (0.0496)	0.0734 (0.0925)	0.311 (0.337)	0.253 (0.281)	0.12 (0.144)	0.602 (0.622)
del 12q24 32	43 (9%)	449	3e-05 (0.000102)	0.376 (0.404)	0.234 (0.262)	0.568 (0.59)	0.629 (0.647)	0.548 (0.571)	0.392 (0.418)	0.0705 (0.0895)
del 11q23 2	48 (10%)	444	0.134 (0.159)	0.0854 (0.105)	1 (1.00)	0.927 (0.929)	0.235 (0.263)	0.468 (0.495)	0.305 (0.333)	0.262 (0.29)

'amp_1q22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S1. Gene #1: 'amp_1q22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 1(1Q22) MUTATED	11	28	1
AMP PEAK 1(1Q22) WILD-TYPE	262	106	84

Figure S1. Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q22' versus 'METHLYATION_CNMF'

P value = 0.0349 (Fisher's exact test), Q value = 0.049

Table S2. Gene #1: 'amp_1q22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
AMP PEAK 1(1Q22) MUTATED	6	17	17
AMP PEAK 1(1Q22) WILD-TYPE	154	148	150

Figure S2. Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q22' versus 'MRNASEQ_CNMF'

P value = 0.00109 (Fisher's exact test), Q value = 0.0024

Table S3. Gene #1: 'amp_1q22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
AMP PEAK 1(1Q22) MUTATED	3	15	22
AMP PEAK 1(1Q22) WILD-TYPE	143	156	152

Figure S3. Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_1q22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.00066

Table S4. Gene #1: 'amp_1q22' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
AMP PEAK 1(1Q22) MUTATED	3	25	12
AMP PEAK 1(1Q22) WILD-TYPE	168	180	103

Figure S4. Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_1q22' versus 'MIRSEQ_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.02

Table S5. Gene #1: 'amp_1q22' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
AMP PEAK 1(1Q22) MUTATED	8	8	24
AMP PEAK 1(1Q22) WILD-TYPE	150	139	159

Figure S5. Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_1q22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.0011

Table S6. Gene #1: 'amp_1q22' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 1(1Q22) MUTATED	5	7	5	22	1
AMP PEAK 1(1Q22) WILD-TYPE	142	91	54	106	55

Figure S6. Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_1q22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.04 (Fisher's exact test), Q value = 0.054

Table S7. Gene #1: 'amp_1q22' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
AMP PEAK 1(1Q22) MUTATED	2	15	2	7
AMP PEAK 1(1Q22) WILD-TYPE	60	91	58	83

Figure S7. Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_1q22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.028

Table S8. Gene #1: 'amp_1q22' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
AMP PEAK 1(1Q22) MUTATED	1	2	5	13	1	4
AMP PEAK 1(1Q22) WILD-TYPE	69	39	35	69	24	56

Figure S8. Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S9. Gene #2: 'amp_3q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 2(3Q21.3) MUTATED	15	48	12
AMP PEAK 2(3Q21.3) WILD-TYPE	258	86	73

Figure S9. Get High-res Image Gene #2: 'amp_3q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q21.3' versus 'METHLYATION_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.0019

Table S10. Gene #2: 'amp_3q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
AMP PEAK 2(3Q21.3) MUTATED	13	38	24
AMP PEAK 2(3Q21.3) WILD-TYPE	147	127	143

Figure S10. Get High-res Image Gene #2: 'amp_3q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q21.3' versus 'MRNASEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.00097

Table S11. Gene #2: 'amp_3q21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
AMP PEAK 2(3Q21.3) MUTATED	10	39	26
AMP PEAK 2(3Q21.3) WILD-TYPE	136	132	148

Figure S11. Get High-res Image Gene #2: 'amp_3q21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_3q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00027

Table S12. Gene #2: 'amp_3q21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
AMP PEAK 2(3Q21.3) MUTATED	11	45	19
AMP PEAK 2(3Q21.3) WILD-TYPE	160	160	96

Figure S12. Get High-res Image Gene #2: 'amp_3q21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_3q21.3' versus 'MIRSEQ_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.027

Table S13. Gene #2: 'amp_3q21.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
AMP PEAK 2(3Q21.3) MUTATED	18	17	39
AMP PEAK 2(3Q21.3) WILD-TYPE	140	130	144

Figure S13. Get High-res Image Gene #2: 'amp_3q21.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_3q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.00079

Table S14. Gene #2: 'amp_3q21.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 2(3Q21.3) MUTATED	12	15	6	35	6
AMP PEAK 2(3Q21.3) WILD-TYPE	135	83	53	93	50

Figure S14. Get High-res Image Gene #2: 'amp_3q21.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_3q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00904 (Fisher's exact test), Q value = 0.015

Table S15. Gene #2: 'amp_3q21.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
AMP PEAK 2(3Q21.3) MUTATED	2	22	10	12
AMP PEAK 2(3Q21.3) WILD-TYPE	60	84	50	78

Figure S15. Get High-res Image Gene #2: 'amp_3q21.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_3q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00057

Table S16. Gene #2: 'amp_3q21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
AMP PEAK 2(3Q21.3) MUTATED	5	4	16	14	1	6
AMP PEAK 2(3Q21.3) WILD-TYPE	65	37	24	68	24	54

Figure S16. Get High-res Image Gene #2: 'amp_3q21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S17. Gene #3: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 3(3Q26.2) MUTATED	22	51	13
AMP PEAK 3(3Q26.2) WILD-TYPE	251	83	72

Figure S17. Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 0.0451 (Fisher's exact test), Q value = 0.06

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
AMP PEAK 3(3Q26.2) MUTATED	20	38	28
AMP PEAK 3(3Q26.2) WILD-TYPE	140	127	139

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

'amp_3q26.2' versus 'MRNASEQ_CNMF'

P value = 0.00508 (Fisher's exact test), Q value = 0.0093

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
AMP PEAK 3(3Q26.2) MUTATED	15	41	30
AMP PEAK 3(3Q26.2) WILD-TYPE	131	130	144

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

'amp_3q26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 0.022

Table S20. Gene #3: 'amp_3q26.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
AMP PEAK 3(3Q26.2) MUTATED	19	46	21
AMP PEAK 3(3Q26.2) WILD-TYPE	152	159	94

Figure S20. Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00776 (Fisher's exact test), Q value = 0.013

Table S21. Gene #3: 'amp_3q26.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 3(3Q26.2) MUTATED	17	16	8	36	8
AMP PEAK 3(3Q26.2) WILD-TYPE	130	82	51	92	48

Figure S21. Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00749 (Fisher's exact test), Q value = 0.013

Table S22. Gene #3: 'amp_3q26.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
AMP PEAK 3(3Q26.2) MUTATED	5	25	14	9
AMP PEAK 3(3Q26.2) WILD-TYPE	57	81	46	81

Figure S22. Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S23. Gene #3: 'amp_3q26.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
AMP PEAK 3(3Q26.2) MUTATED	4	6	17	19	4	3
AMP PEAK 3(3Q26.2) WILD-TYPE	66	35	23	63	21	57

Figure S23. Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4p16.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S24. Gene #4: 'amp_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 4(4P16.3) MUTATED	2	17	1
AMP PEAK 4(4P16.3) WILD-TYPE	271	117	84

Figure S24. Get High-res Image Gene #4: 'amp_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4p16.3' versus 'METHLYATION_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.017

Table S25. Gene #4: 'amp_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
AMP PEAK 4(4P16.3) MUTATED	1	11	8
AMP PEAK 4(4P16.3) WILD-TYPE	159	154	159

Figure S25. Get High-res Image Gene #4: 'amp_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_4p16.3' versus 'MRNASEQ_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.028

Table S26. Gene #4: 'amp_4p16.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
AMP PEAK 4(4P16.3) MUTATED	1	11	8
AMP PEAK 4(4P16.3) WILD-TYPE	145	160	166

Figure S26. Get High-res Image Gene #4: 'amp_4p16.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_4q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S27. Gene #5: 'amp_4q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 5(4Q13.3) MUTATED	5	17	0
AMP PEAK 5(4Q13.3) WILD-TYPE	268	117	85

Figure S27. Get High-res Image Gene #5: 'amp_4q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4q13.3' versus 'MIRSEQ_CNMF'

P value = 0.0273 (Fisher's exact test), Q value = 0.04

Table S28. Gene #5: 'amp_4q13.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
AMP PEAK 5(4Q13.3) MUTATED	4	3	14
AMP PEAK 5(4Q13.3) WILD-TYPE	154	144	169

Figure S28. Get High-res Image Gene #5: 'amp_4q13.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_4q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0367 (Fisher's exact test), Q value = 0.051

Table S29. Gene #5: 'amp_4q13.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
AMP PEAK 5(4Q13.3) MUTATED	1	6	4	0
AMP PEAK 5(4Q13.3) WILD-TYPE	61	100	56	90

Figure S29. Get High-res Image Gene #5: 'amp_4q13.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_5q35.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S30. Gene #6: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 6(5Q35.3) MUTATED	4	24	0
AMP PEAK 6(5Q35.3) WILD-TYPE	269	110	85

Figure S30. Get High-res Image Gene #6: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q35.3' versus 'METHLYATION_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.021

Table S31. Gene #6: 'amp_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
AMP PEAK 6(5Q35.3) MUTATED	3	15	10
AMP PEAK 6(5Q35.3) WILD-TYPE	157	150	157

Figure S31. Get High-res Image Gene #6: 'amp_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5q35.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0427 (Fisher's exact test), Q value = 0.058

Table S32. Gene #6: 'amp_5q35.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
AMP PEAK 6(5Q35.3) MUTATED	4	16	8
AMP PEAK 6(5Q35.3) WILD-TYPE	167	189	107

Figure S32. Get High-res Image Gene #6: 'amp_5q35.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_5q35.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00104 (Fisher's exact test), Q value = 0.0023

Table S33. Gene #6: 'amp_5q35.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 6(5Q35.3) MUTATED	6	6	0	16	0
AMP PEAK 6(5Q35.3) WILD-TYPE	141	92	59	112	56

Figure S33. Get High-res Image Gene #6: 'amp_5q35.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_5q35.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.025

Table S34. Gene #6: 'amp_5q35.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
AMP PEAK 6(5Q35.3) MUTATED	1	13	2	3
AMP PEAK 6(5Q35.3) WILD-TYPE	61	93	58	87

Figure S34. Get High-res Image Gene #6: 'amp_5q35.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_7p14.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S35. Gene #7: 'amp_7p14.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 7(7P14.3) MUTATED	13	69	22
AMP PEAK 7(7P14.3) WILD-TYPE	260	65	63

Figure S35. Get High-res Image Gene #7: 'amp_7p14.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p14.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S36. Gene #7: 'amp_7p14.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
AMP PEAK 7(7P14.3) MUTATED	14	60	30
AMP PEAK 7(7P14.3) WILD-TYPE	146	105	137

Figure S36. Get High-res Image Gene #7: 'amp_7p14.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p14.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S37. Gene #7: 'amp_7p14.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
AMP PEAK 7(7P14.3) MUTATED	11	64	29
AMP PEAK 7(7P14.3) WILD-TYPE	135	107	145

Figure S37. Get High-res Image Gene #7: 'amp_7p14.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_7p14.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00013

Table S38. Gene #7: 'amp_7p14.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
AMP PEAK 7(7P14.3) MUTATED	22	64	18
AMP PEAK 7(7P14.3) WILD-TYPE	149	141	97

Figure S38. Get High-res Image Gene #7: 'amp_7p14.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_7p14.3' versus 'MIRSEQ_CNMF'

P value = 0.00376 (Fisher's exact test), Q value = 0.0071

Table S39. Gene #7: 'amp_7p14.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
AMP PEAK 7(7P14.3) MUTATED	21	31	51
AMP PEAK 7(7P14.3) WILD-TYPE	137	116	132

Figure S39. Get High-res Image Gene #7: 'amp_7p14.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_7p14.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.0013

Table S40. Gene #7: 'amp_7p14.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 7(7P14.3) MUTATED	17	28	13	38	7
AMP PEAK 7(7P14.3) WILD-TYPE	130	70	46	90	49

Figure S40. Get High-res Image Gene #7: 'amp_7p14.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_7p14.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00114 (Fisher's exact test), Q value = 0.0025

Table S41. Gene #7: 'amp_7p14.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
AMP PEAK 7(7P14.3) MUTATED	5	35	10	20
AMP PEAK 7(7P14.3) WILD-TYPE	57	71	50	70

Figure S41. Get High-res Image Gene #7: 'amp_7p14.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_7p14.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00927 (Fisher's exact test), Q value = 0.016

Table S42. Gene #7: 'amp_7p14.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
AMP PEAK 7(7P14.3) MUTATED	6	12	12	24	3	13
AMP PEAK 7(7P14.3) WILD-TYPE	64	29	28	58	22	47

Figure S42. Get High-res Image Gene #7: 'amp_7p14.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S43. Gene #8: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 8(7Q22.1) MUTATED	13	66	22
AMP PEAK 8(7Q22.1) WILD-TYPE	260	68	63

Figure S43. Get High-res Image Gene #8: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S44. Gene #8: 'amp_7q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
AMP PEAK 8(7Q22.1) MUTATED	15	59	27
AMP PEAK 8(7Q22.1) WILD-TYPE	145	106	140

Figure S44. Get High-res Image Gene #8: 'amp_7q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S45. Gene #8: 'amp_7q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
AMP PEAK 8(7Q22.1) MUTATED	11	64	26
AMP PEAK 8(7Q22.1) WILD-TYPE	135	107	148

Figure S45. Get High-res Image Gene #8: 'amp_7q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_7q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S46. Gene #8: 'amp_7q22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
AMP PEAK 8(7Q22.1) MUTATED	22	64	15
AMP PEAK 8(7Q22.1) WILD-TYPE	149	141	100

Figure S46. Get High-res Image Gene #8: 'amp_7q22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_7q22.1' versus 'MIRSEQ_CNMF'

P value = 0.00648 (Fisher's exact test), Q value = 0.012

Table S47. Gene #8: 'amp_7q22.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
AMP PEAK 8(7Q22.1) MUTATED	20	32	48
AMP PEAK 8(7Q22.1) WILD-TYPE	138	115	135

Figure S47. Get High-res Image Gene #8: 'amp_7q22.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_7q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S48. Gene #8: 'amp_7q22.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 8(7Q22.1) MUTATED	13	30	16	36	5
AMP PEAK 8(7Q22.1) WILD-TYPE	134	68	43	92	51

Figure S48. Get High-res Image Gene #8: 'amp_7q22.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_7q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.001

Table S49. Gene #8: 'amp_7q22.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
AMP PEAK 8(7Q22.1) MUTATED	4	35	12	18
AMP PEAK 8(7Q22.1) WILD-TYPE	58	71	48	72

Figure S49. Get High-res Image Gene #8: 'amp_7q22.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_7q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00299 (Fisher's exact test), Q value = 0.0057

Table S50. Gene #8: 'amp_7q22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
AMP PEAK 8(7Q22.1) MUTATED	6	12	12	25	2	12
AMP PEAK 8(7Q22.1) WILD-TYPE	64	29	28	57	23	48

Figure S50. Get High-res Image Gene #8: 'amp_7q22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S51. Gene #9: 'amp_8p11.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 9(8P11.23) MUTATED	9	49	9
AMP PEAK 9(8P11.23) WILD-TYPE	264	85	76

Figure S51. Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p11.23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S52. Gene #9: 'amp_8p11.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
AMP PEAK 9(8P11.23) MUTATED	8	45	14
AMP PEAK 9(8P11.23) WILD-TYPE	152	120	153

Figure S52. Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8p11.23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S53. Gene #9: 'amp_8p11.23' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
AMP PEAK 9(8P11.23) MUTATED	10	43	14
AMP PEAK 9(8P11.23) WILD-TYPE	136	128	160

Figure S53. Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_8p11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0011

Table S54. Gene #9: 'amp_8p11.23' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
AMP PEAK 9(8P11.23) MUTATED	13	43	11
AMP PEAK 9(8P11.23) WILD-TYPE	158	162	104

Figure S54. Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.23' versus 'MIRSEQ_CNMF'

P value = 0.0457 (Fisher's exact test), Q value = 0.061

Table S55. Gene #9: 'amp_8p11.23' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
AMP PEAK 9(8P11.23) MUTATED	14	19	33
AMP PEAK 9(8P11.23) WILD-TYPE	144	128	150

Figure S55. Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_8p11.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00134 (Fisher's exact test), Q value = 0.0029

Table S56. Gene #9: 'amp_8p11.23' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 9(8P11.23) MUTATED	10	12	6	31	7
AMP PEAK 9(8P11.23) WILD-TYPE	137	86	53	97	49

Figure S56. Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.23' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S57. Gene #9: 'amp_8p11.23' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
AMP PEAK 9(8P11.23) MUTATED	2	31	4	8
AMP PEAK 9(8P11.23) WILD-TYPE	60	75	56	82

Figure S57. Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_8p11.23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.0012

Table S58. Gene #9: 'amp_8p11.23' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
AMP PEAK 9(8P11.23) MUTATED	5	5	4	25	1	5
AMP PEAK 9(8P11.23) WILD-TYPE	65	36	36	57	24	55

Figure S58. Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S59. Gene #10: 'amp_8q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 10(8Q22.1) MUTATED	45	100	12
AMP PEAK 10(8Q22.1) WILD-TYPE	228	34	73

Figure S59. Get High-res Image Gene #10: 'amp_8q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S60. Gene #10: 'amp_8q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
AMP PEAK 10(8Q22.1) MUTATED	25	83	49
AMP PEAK 10(8Q22.1) WILD-TYPE	135	82	118

Figure S60. Get High-res Image Gene #10: 'amp_8q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q22.1' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 1e-04

Table S61. Gene #10: 'amp_8q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
AMP PEAK 10(8Q22.1) MUTATED	27	74	56
AMP PEAK 10(8Q22.1) WILD-TYPE	119	97	118

Figure S61. Get High-res Image Gene #10: 'amp_8q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_8q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S62. Gene #10: 'amp_8q22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
AMP PEAK 10(8Q22.1) MUTATED	31	90	36
AMP PEAK 10(8Q22.1) WILD-TYPE	140	115	79

Figure S62. Get High-res Image Gene #10: 'amp_8q22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_8q22.1' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00013

Table S63. Gene #10: 'amp_8q22.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
AMP PEAK 10(8Q22.1) MUTATED	38	36	81
AMP PEAK 10(8Q22.1) WILD-TYPE	120	111	102

Figure S63. Get High-res Image Gene #10: 'amp_8q22.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_8q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S64. Gene #10: 'amp_8q22.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 10(8Q22.1) MUTATED	25	29	24	65	12
AMP PEAK 10(8Q22.1) WILD-TYPE	122	69	35	63	44

Figure S64. Get High-res Image Gene #10: 'amp_8q22.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_8q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S65. Gene #10: 'amp_8q22.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
AMP PEAK 10(8Q22.1) MUTATED	10	56	12	23
AMP PEAK 10(8Q22.1) WILD-TYPE	52	50	48	67

Figure S65. Get High-res Image Gene #10: 'amp_8q22.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_8q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00013

Table S66. Gene #10: 'amp_8q22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
AMP PEAK 10(8Q22.1) MUTATED	12	9	16	43	6	15
AMP PEAK 10(8Q22.1) WILD-TYPE	58	32	24	39	19	45

Figure S66. Get High-res Image Gene #10: 'amp_8q22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S67. Gene #11: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 11(8Q24.21) MUTATED	43	98	11
AMP PEAK 11(8Q24.21) WILD-TYPE	230	36	74

Figure S67. Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S68. Gene #11: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
AMP PEAK 11(8Q24.21) MUTATED	25	80	47
AMP PEAK 11(8Q24.21) WILD-TYPE	135	85	120

Figure S68. Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S69. Gene #11: 'amp_8q24.21' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
AMP PEAK 11(8Q24.21) MUTATED	24	76	52
AMP PEAK 11(8Q24.21) WILD-TYPE	122	95	122

Figure S69. Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S70. Gene #11: 'amp_8q24.21' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
AMP PEAK 11(8Q24.21) MUTATED	29	90	33
AMP PEAK 11(8Q24.21) WILD-TYPE	142	115	82

Figure S70. Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S71. Gene #11: 'amp_8q24.21' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
AMP PEAK 11(8Q24.21) MUTATED	33	35	82
AMP PEAK 11(8Q24.21) WILD-TYPE	125	112	101

Figure S71. Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S72. Gene #11: 'amp_8q24.21' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 11(8Q24.21) MUTATED	21	29	23	65	12
AMP PEAK 11(8Q24.21) WILD-TYPE	126	69	36	63	44

Figure S72. Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S73. Gene #11: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
AMP PEAK 11(8Q24.21) MUTATED	10	53	14	21
AMP PEAK 11(8Q24.21) WILD-TYPE	52	53	46	69

Figure S73. Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 9e-04

Table S74. Gene #11: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
AMP PEAK 11(8Q24.21) MUTATED	13	9	15	41	6	14
AMP PEAK 11(8Q24.21) WILD-TYPE	57	32	25	41	19	46

Figure S74. Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9q33.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S75. Gene #12: 'amp_9q33.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 12(9Q33.3) MUTATED	9	53	0
AMP PEAK 12(9Q33.3) WILD-TYPE	264	81	85

Figure S75. Get High-res Image Gene #12: 'amp_9q33.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9q33.3' versus 'METHLYATION_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.029

Table S76. Gene #12: 'amp_9q33.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
AMP PEAK 12(9Q33.3) MUTATED	11	24	27
AMP PEAK 12(9Q33.3) WILD-TYPE	149	141	140

Figure S76. Get High-res Image Gene #12: 'amp_9q33.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9q33.3' versus 'MRNASEQ_CNMF'

P value = 0.00225 (Fisher's exact test), Q value = 0.0045

Table S77. Gene #12: 'amp_9q33.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
AMP PEAK 12(9Q33.3) MUTATED	8	23	31
AMP PEAK 12(9Q33.3) WILD-TYPE	138	148	143

Figure S77. Get High-res Image Gene #12: 'amp_9q33.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_9q33.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0163 (Fisher's exact test), Q value = 0.025

Table S78. Gene #12: 'amp_9q33.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
AMP PEAK 12(9Q33.3) MUTATED	12	34	16
AMP PEAK 12(9Q33.3) WILD-TYPE	159	171	99

Figure S78. Get High-res Image Gene #12: 'amp_9q33.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_9q33.3' versus 'MIRSEQ_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.029

Table S79. Gene #12: 'amp_9q33.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
AMP PEAK 12(9Q33.3) MUTATED	14	14	33
AMP PEAK 12(9Q33.3) WILD-TYPE	144	133	150

Figure S79. Get High-res Image Gene #12: 'amp_9q33.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_9q33.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00097 (Fisher's exact test), Q value = 0.0022

Table S80. Gene #12: 'amp_9q33.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 12(9Q33.3) MUTATED	10	10	7	30	4
AMP PEAK 12(9Q33.3) WILD-TYPE	137	88	52	98	52

Figure S80. Get High-res Image Gene #12: 'amp_9q33.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_9q33.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.026

Table S81. Gene #12: 'amp_9q33.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
AMP PEAK 12(9Q33.3) MUTATED	2	19	4	9
AMP PEAK 12(9Q33.3) WILD-TYPE	60	87	56	81

Figure S81. Get High-res Image Gene #12: 'amp_9q33.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_9q33.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00836 (Fisher's exact test), Q value = 0.014

Table S82. Gene #12: 'amp_9q33.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
AMP PEAK 12(9Q33.3) MUTATED	3	2	10	13	1	5
AMP PEAK 12(9Q33.3) WILD-TYPE	67	39	30	69	24	55

Figure S82. Get High-res Image Gene #12: 'amp_9q33.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S83. Gene #13: 'amp_11q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 13(11Q13.2) MUTATED	7	39	2
AMP PEAK 13(11Q13.2) WILD-TYPE	266	95	83

Figure S83. Get High-res Image Gene #13: 'amp_11q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.2' versus 'METHLYATION_CNMF'

P value = 0.00831 (Fisher's exact test), Q value = 0.014

Table S84. Gene #13: 'amp_11q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
AMP PEAK 13(11Q13.2) MUTATED	8	25	15
AMP PEAK 13(11Q13.2) WILD-TYPE	152	140	152

Figure S84. Get High-res Image Gene #13: 'amp_11q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11q13.2' versus 'MRNASEQ_CNMF'

P value = 0.00707 (Fisher's exact test), Q value = 0.012

Table S85. Gene #13: 'amp_11q13.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
AMP PEAK 13(11Q13.2) MUTATED	7	26	15
AMP PEAK 13(11Q13.2) WILD-TYPE	139	145	159

Figure S85. Get High-res Image Gene #13: 'amp_11q13.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_11q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.00099

Table S86. Gene #13: 'amp_11q13.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
AMP PEAK 13(11Q13.2) MUTATED	8	33	7
AMP PEAK 13(11Q13.2) WILD-TYPE	163	172	108

Figure S86. Get High-res Image Gene #13: 'amp_11q13.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.2' versus 'MIRSEQ_CNMF'

P value = 0.0315 (Fisher's exact test), Q value = 0.044

Table S87. Gene #13: 'amp_11q13.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
AMP PEAK 13(11Q13.2) MUTATED	10	11	26
AMP PEAK 13(11Q13.2) WILD-TYPE	148	136	157

Figure S87. Get High-res Image Gene #13: 'amp_11q13.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_11q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00057

Table S88. Gene #13: 'amp_11q13.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 13(11Q13.2) MUTATED	6	11	5	24	1
AMP PEAK 13(11Q13.2) WILD-TYPE	141	87	54	104	55

Figure S88. Get High-res Image Gene #13: 'amp_11q13.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00742 (Fisher's exact test), Q value = 0.013

Table S89. Gene #13: 'amp_11q13.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
AMP PEAK 13(11Q13.2) MUTATED	1	17	6	5
AMP PEAK 13(11Q13.2) WILD-TYPE	61	89	54	85

Figure S89. Get High-res Image Gene #13: 'amp_11q13.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_11q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0306 (Fisher's exact test), Q value = 0.043

Table S90. Gene #13: 'amp_11q13.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
AMP PEAK 13(11Q13.2) MUTATED	3	2	8	11	0	5
AMP PEAK 13(11Q13.2) WILD-TYPE	67	39	32	71	25	55

Figure S90. Get High-res Image Gene #13: 'amp_11q13.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S91. Gene #14: 'amp_12q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 14(12Q23.1) MUTATED	12	23	1
AMP PEAK 14(12Q23.1) WILD-TYPE	261	111	84

Figure S91. Get High-res Image Gene #14: 'amp_12q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q23.1' versus 'METHLYATION_CNMF'

P value = 0.00177 (Fisher's exact test), Q value = 0.0036

Table S92. Gene #14: 'amp_12q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
AMP PEAK 14(12Q23.1) MUTATED	8	22	6
AMP PEAK 14(12Q23.1) WILD-TYPE	152	143	161

Figure S92. Get High-res Image Gene #14: 'amp_12q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.00097

Table S93. Gene #14: 'amp_12q23.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
AMP PEAK 14(12Q23.1) MUTATED	8	26	2
AMP PEAK 14(12Q23.1) WILD-TYPE	163	179	113

Figure S93. Get High-res Image Gene #14: 'amp_12q23.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_12q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0021 (Fisher's exact test), Q value = 0.0042

Table S94. Gene #14: 'amp_12q23.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 14(12Q23.1) MUTATED	7	6	3	19	0
AMP PEAK 14(12Q23.1) WILD-TYPE	140	92	56	109	56

Figure S94. Get High-res Image Gene #14: 'amp_12q23.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_13q12.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S95. Gene #15: 'amp_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 15(13Q12.11) MUTATED	4	20	1
AMP PEAK 15(13Q12.11) WILD-TYPE	269	114	84

Figure S95. Get High-res Image Gene #15: 'amp_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q12.11' versus 'METHLYATION_CNMF'

P value = 0.00225 (Fisher's exact test), Q value = 0.0045

Table S96. Gene #15: 'amp_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
AMP PEAK 15(13Q12.11) MUTATED	1	11	13
AMP PEAK 15(13Q12.11) WILD-TYPE	159	154	154

Figure S96. Get High-res Image Gene #15: 'amp_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q12.11' versus 'MRNASEQ_CNMF'

P value = 0.00484 (Fisher's exact test), Q value = 0.0089

Table S97. Gene #15: 'amp_13q12.11' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
AMP PEAK 15(13Q12.11) MUTATED	1	13	11
AMP PEAK 15(13Q12.11) WILD-TYPE	145	158	163

Figure S97. Get High-res Image Gene #15: 'amp_13q12.11' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_13q12.11' versus 'MIRSEQ_CNMF'

P value = 0.0139 (Fisher's exact test), Q value = 0.022

Table S98. Gene #15: 'amp_13q12.11' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
AMP PEAK 15(13Q12.11) MUTATED	4	4	16
AMP PEAK 15(13Q12.11) WILD-TYPE	154	143	167

Figure S98. Get High-res Image Gene #15: 'amp_13q12.11' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_13q12.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0318 (Fisher's exact test), Q value = 0.045

Table S99. Gene #15: 'amp_13q12.11' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 15(13Q12.11) MUTATED	2	4	5	11	2
AMP PEAK 15(13Q12.11) WILD-TYPE	145	94	54	117	54

Figure S99. Get High-res Image Gene #15: 'amp_13q12.11' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_14q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S100. Gene #16: 'amp_14q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 16(14Q21.1) MUTATED	1	25	4
AMP PEAK 16(14Q21.1) WILD-TYPE	272	109	81

Figure S100. Get High-res Image Gene #16: 'amp_14q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_14q21.1' versus 'MRNASEQ_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 0.019

Table S101. Gene #16: 'amp_14q21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
AMP PEAK 16(14Q21.1) MUTATED	3	17	10
AMP PEAK 16(14Q21.1) WILD-TYPE	143	154	164

Figure S101. Get High-res Image Gene #16: 'amp_14q21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_14q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0383 (Fisher's exact test), Q value = 0.052

Table S102. Gene #16: 'amp_14q21.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
AMP PEAK 16(14Q21.1) MUTATED	5	19	6
AMP PEAK 16(14Q21.1) WILD-TYPE	166	186	109

Figure S102. Get High-res Image Gene #16: 'amp_14q21.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_14q21.1' versus 'MIRSEQ_CNMF'

P value = 0.00803 (Fisher's exact test), Q value = 0.014

Table S103. Gene #16: 'amp_14q21.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
AMP PEAK 16(14Q21.1) MUTATED	4	7	19
AMP PEAK 16(14Q21.1) WILD-TYPE	154	140	164

Figure S103. Get High-res Image Gene #16: 'amp_14q21.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_14q21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.017

Table S104. Gene #16: 'amp_14q21.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 16(14Q21.1) MUTATED	3	5	3	16	3
AMP PEAK 16(14Q21.1) WILD-TYPE	144	93	56	112	53

Figure S104. Get High-res Image Gene #16: 'amp_14q21.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_14q21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0282 (Fisher's exact test), Q value = 0.041

Table S105. Gene #16: 'amp_14q21.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
AMP PEAK 16(14Q21.1) MUTATED	1	2	7	9	1	3
AMP PEAK 16(14Q21.1) WILD-TYPE	69	39	33	73	24	57

Figure S105. Get High-res Image Gene #16: 'amp_14q21.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_15q11.2' versus 'CN_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.017

Table S106. Gene #17: 'amp_15q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 17(15Q11.2) MUTATED	5	10	1
AMP PEAK 17(15Q11.2) WILD-TYPE	268	124	84

Figure S106. Get High-res Image Gene #17: 'amp_15q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_16q11.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S107. Gene #18: 'amp_16q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 18(16Q11.2) MUTATED	8	21	1
AMP PEAK 18(16Q11.2) WILD-TYPE	265	113	84

Figure S107. Get High-res Image Gene #18: 'amp_16q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_16q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00172 (Fisher's exact test), Q value = 0.0036

Table S108. Gene #18: 'amp_16q11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
AMP PEAK 18(16Q11.2) MUTATED	2	9	18
AMP PEAK 18(16Q11.2) WILD-TYPE	156	138	165

Figure S108. Get High-res Image Gene #18: 'amp_16q11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_16q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00099 (Fisher's exact test), Q value = 0.0022

Table S109. Gene #18: 'amp_16q11.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 18(16Q11.2) MUTATED	1	5	4	15	4
AMP PEAK 18(16Q11.2) WILD-TYPE	146	93	55	113	52

Figure S109. Get High-res Image Gene #18: 'amp_16q11.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_17q23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S110. Gene #19: 'amp_17q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 19(17Q23.2) MUTATED	6	19	0
AMP PEAK 19(17Q23.2) WILD-TYPE	267	115	85

Figure S110. Get High-res Image Gene #19: 'amp_17q23.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0148 (Fisher's exact test), Q value = 0.023

Table S111. Gene #19: 'amp_17q23.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 19(17Q23.2) MUTATED	4	4	7	10	0
AMP PEAK 19(17Q23.2) WILD-TYPE	143	94	52	118	56

Figure S111. Get High-res Image Gene #19: 'amp_17q23.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_19q13.43' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S112. Gene #20: 'amp_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 20(19Q13.43) MUTATED	0	19	0
AMP PEAK 20(19Q13.43) WILD-TYPE	273	115	85

Figure S112. Get High-res Image Gene #20: 'amp_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q13.43' versus 'METHLYATION_CNMF'

P value = 0.0381 (Fisher's exact test), Q value = 0.052

Table S113. Gene #20: 'amp_19q13.43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
AMP PEAK 20(19Q13.43) MUTATED	2	11	6
AMP PEAK 20(19Q13.43) WILD-TYPE	158	154	161

Figure S113. Get High-res Image Gene #20: 'amp_19q13.43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q13.43' versus 'MRNASEQ_CNMF'

P value = 0.00257 (Fisher's exact test), Q value = 0.005

Table S114. Gene #20: 'amp_19q13.43' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
AMP PEAK 20(19Q13.43) MUTATED	0	11	8
AMP PEAK 20(19Q13.43) WILD-TYPE	146	160	166

Figure S114. Get High-res Image Gene #20: 'amp_19q13.43' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_19q13.43' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0271 (Fisher's exact test), Q value = 0.039

Table S115. Gene #20: 'amp_19q13.43' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
AMP PEAK 20(19Q13.43) MUTATED	2	13	4
AMP PEAK 20(19Q13.43) WILD-TYPE	169	192	111

Figure S115. Get High-res Image Gene #20: 'amp_19q13.43' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_19q13.43' versus 'MIRSEQ_CNMF'

P value = 0.00631 (Fisher's exact test), Q value = 0.011

Table S116. Gene #20: 'amp_19q13.43' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
AMP PEAK 20(19Q13.43) MUTATED	1	5	13
AMP PEAK 20(19Q13.43) WILD-TYPE	157	142	170

Figure S116. Get High-res Image Gene #20: 'amp_19q13.43' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_19q13.43' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0014 (Fisher's exact test), Q value = 0.003

Table S117. Gene #20: 'amp_19q13.43' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 20(19Q13.43) MUTATED	0	5	1	11	2
AMP PEAK 20(19Q13.43) WILD-TYPE	147	93	58	117	54

Figure S117. Get High-res Image Gene #20: 'amp_19q13.43' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_19q13.43' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0115 (Fisher's exact test), Q value = 0.019

Table S118. Gene #20: 'amp_19q13.43' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
AMP PEAK 20(19Q13.43) MUTATED	0	0	5	5	0	2
AMP PEAK 20(19Q13.43) WILD-TYPE	70	41	35	77	25	58

Figure S118. Get High-res Image Gene #20: 'amp_19q13.43' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S119. Gene #21: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 21(20Q13.2) MUTATED	5	37	3
AMP PEAK 21(20Q13.2) WILD-TYPE	268	97	82

Figure S119. Get High-res Image Gene #21: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.2' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00024

Table S120. Gene #21: 'amp_20q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
AMP PEAK 21(20Q13.2) MUTATED	5	28	12
AMP PEAK 21(20Q13.2) WILD-TYPE	155	137	155

Figure S120. Get High-res Image Gene #21: 'amp_20q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q13.2' versus 'MRNASEQ_CNMF'

P value = 0.00156 (Fisher's exact test), Q value = 0.0033

Table S121. Gene #21: 'amp_20q13.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
AMP PEAK 21(20Q13.2) MUTATED	4	23	18
AMP PEAK 21(20Q13.2) WILD-TYPE	142	148	156

Figure S121. Get High-res Image Gene #21: 'amp_20q13.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_20q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00118 (Fisher's exact test), Q value = 0.0026

Table S122. Gene #21: 'amp_20q13.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
AMP PEAK 21(20Q13.2) MUTATED	7	30	8
AMP PEAK 21(20Q13.2) WILD-TYPE	164	175	107

Figure S122. Get High-res Image Gene #21: 'amp_20q13.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.001

Table S123. Gene #21: 'amp_20q13.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
AMP PEAK 21(20Q13.2) MUTATED	5	12	28
AMP PEAK 21(20Q13.2) WILD-TYPE	153	135	155

Figure S123. Get High-res Image Gene #21: 'amp_20q13.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_20q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00013

Table S124. Gene #21: 'amp_20q13.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 21(20Q13.2) MUTATED	5	13	1	23	3
AMP PEAK 21(20Q13.2) WILD-TYPE	142	85	58	105	53

Figure S124. Get High-res Image Gene #21: 'amp_20q13.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00016

Table S125. Gene #21: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
AMP PEAK 21(20Q13.2) MUTATED	1	1	12	5	2	6
AMP PEAK 21(20Q13.2) WILD-TYPE	69	40	28	77	23	54

Figure S125. Get High-res Image Gene #21: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xp22.11' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S126. Gene #22: 'amp_xp22.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 22(XP22.11) MUTATED	5	19	2
AMP PEAK 22(XP22.11) WILD-TYPE	268	115	83

Figure S126. Get High-res Image Gene #22: 'amp_xp22.11' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp22.11' versus 'MIRSEQ_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.025

Table S127. Gene #22: 'amp_xp22.11' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
AMP PEAK 22(XP22.11) MUTATED	5	4	17
AMP PEAK 22(XP22.11) WILD-TYPE	153	143	166

Figure S127. Get High-res Image Gene #22: 'amp_xp22.11' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_xp22.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00481 (Fisher's exact test), Q value = 0.0089

Table S128. Gene #22: 'amp_xp22.11' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 22(XP22.11) MUTATED	1	6	3	13	3
AMP PEAK 22(XP22.11) WILD-TYPE	146	92	56	115	53

Figure S128. Get High-res Image Gene #22: 'amp_xp22.11' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_xp22.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0443 (Fisher's exact test), Q value = 0.059

Table S129. Gene #22: 'amp_xp22.11' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
AMP PEAK 22(XP22.11) MUTATED	0	10	2	5
AMP PEAK 22(XP22.11) WILD-TYPE	62	96	58	85

Figure S129. Get High-res Image Gene #22: 'amp_xp22.11' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_xp22.11' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S130. Gene #23: 'amp_xp22.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 23(XP22.11) MUTATED	5	18	2
AMP PEAK 23(XP22.11) WILD-TYPE	268	116	83

Figure S130. Get High-res Image Gene #23: 'amp_xp22.11' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp22.11' versus 'MRNASEQ_CNMF'

P value = 0.0337 (Fisher's exact test), Q value = 0.047

Table S131. Gene #23: 'amp_xp22.11' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
AMP PEAK 23(XP22.11) MUTATED	2	12	11
AMP PEAK 23(XP22.11) WILD-TYPE	144	159	163

Figure S131. Get High-res Image Gene #23: 'amp_xp22.11' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_xp22.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0128 (Fisher's exact test), Q value = 0.02

Table S132. Gene #23: 'amp_xp22.11' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
AMP PEAK 23(XP22.11) MUTATED	3	17	5
AMP PEAK 23(XP22.11) WILD-TYPE	168	188	110

Figure S132. Get High-res Image Gene #23: 'amp_xp22.11' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_xp22.11' versus 'MIRSEQ_CNMF'

P value = 0.00774 (Fisher's exact test), Q value = 0.013

Table S133. Gene #23: 'amp_xp22.11' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
AMP PEAK 23(XP22.11) MUTATED	4	4	17
AMP PEAK 23(XP22.11) WILD-TYPE	154	143	166

Figure S133. Get High-res Image Gene #23: 'amp_xp22.11' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_xp22.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.017

Table S134. Gene #23: 'amp_xp22.11' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 23(XP22.11) MUTATED	2	8	2	12	1
AMP PEAK 23(XP22.11) WILD-TYPE	145	90	57	116	55

Figure S134. Get High-res Image Gene #23: 'amp_xp22.11' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_xp22.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0463 (Fisher's exact test), Q value = 0.061

Table S135. Gene #23: 'amp_xp22.11' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
AMP PEAK 23(XP22.11) MUTATED	2	10	2	1
AMP PEAK 23(XP22.11) WILD-TYPE	60	96	58	89

Figure S135. Get High-res Image Gene #23: 'amp_xp22.11' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_xp21.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S136. Gene #24: 'amp_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 24(XP21.1) MUTATED	4	17	2
AMP PEAK 24(XP21.1) WILD-TYPE	269	117	83

Figure S136. Get High-res Image Gene #24: 'amp_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp21.1' versus 'METHLYATION_CNMF'

P value = 0.0283 (Fisher's exact test), Q value = 0.041

Table S137. Gene #24: 'amp_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
AMP PEAK 24(XP21.1) MUTATED	2	11	10
AMP PEAK 24(XP21.1) WILD-TYPE	158	154	157

Figure S137. Get High-res Image Gene #24: 'amp_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xp21.1' versus 'MRNASEQ_CNMF'

P value = 0.0407 (Fisher's exact test), Q value = 0.055

Table S138. Gene #24: 'amp_xp21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
AMP PEAK 24(XP21.1) MUTATED	2	12	9
AMP PEAK 24(XP21.1) WILD-TYPE	144	159	165

Figure S138. Get High-res Image Gene #24: 'amp_xp21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_xp21.1' versus 'MIRSEQ_CNMF'

P value = 0.0195 (Fisher's exact test), Q value = 0.029

Table S139. Gene #24: 'amp_xp21.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
AMP PEAK 24(XP21.1) MUTATED	5	3	15
AMP PEAK 24(XP21.1) WILD-TYPE	153	144	168

Figure S139. Get High-res Image Gene #24: 'amp_xp21.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_xp21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00936 (Fisher's exact test), Q value = 0.016

Table S140. Gene #24: 'amp_xp21.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 24(XP21.1) MUTATED	3	8	1	11	0
AMP PEAK 24(XP21.1) WILD-TYPE	144	90	58	117	56

Figure S140. Get High-res Image Gene #24: 'amp_xp21.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_xp21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00519 (Fisher's exact test), Q value = 0.0094

Table S141. Gene #24: 'amp_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
AMP PEAK 24(XP21.1) MUTATED	0	8	2	0
AMP PEAK 24(XP21.1) WILD-TYPE	62	98	58	90

Figure S141. Get High-res Image Gene #24: 'amp_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_xq21.1' versus 'CN_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.0025

Table S142. Gene #25: 'amp_xq21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 25(XQ21.1) MUTATED	3	11	2
AMP PEAK 25(XQ21.1) WILD-TYPE	270	123	83

Figure S142. Get High-res Image Gene #25: 'amp_xq21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq21.1' versus 'METHLYATION_CNMF'

P value = 0.031 (Fisher's exact test), Q value = 0.044

Table S143. Gene #25: 'amp_xq21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
AMP PEAK 25(XQ21.1) MUTATED	1	9	6
AMP PEAK 25(XQ21.1) WILD-TYPE	159	156	161

Figure S143. Get High-res Image Gene #25: 'amp_xq21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xq21.1' versus 'MRNASEQ_CNMF'

P value = 0.00759 (Fisher's exact test), Q value = 0.013

Table S144. Gene #25: 'amp_xq21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
AMP PEAK 25(XQ21.1) MUTATED	0	9	7
AMP PEAK 25(XQ21.1) WILD-TYPE	146	162	167

Figure S144. Get High-res Image Gene #25: 'amp_xq21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_xq21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0192 (Fisher's exact test), Q value = 0.029

Table S145. Gene #25: 'amp_xq21.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
AMP PEAK 25(XQ21.1) MUTATED	1	11	4
AMP PEAK 25(XQ21.1) WILD-TYPE	170	194	111

Figure S145. Get High-res Image Gene #25: 'amp_xq21.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_xq21.1' versus 'CN_CNMF'

P value = 0.00222 (Fisher's exact test), Q value = 0.0044

Table S146. Gene #26: 'amp_xq21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 26(XQ21.1) MUTATED	2	9	3
AMP PEAK 26(XQ21.1) WILD-TYPE	271	125	82

Figure S146. Get High-res Image Gene #26: 'amp_xq21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq21.1' versus 'METHLYATION_CNMF'

P value = 0.0184 (Fisher's exact test), Q value = 0.028

Table S147. Gene #26: 'amp_xq21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
AMP PEAK 26(XQ21.1) MUTATED	2	10	2
AMP PEAK 26(XQ21.1) WILD-TYPE	158	155	165

Figure S147. Get High-res Image Gene #26: 'amp_xq21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xq21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00433 (Fisher's exact test), Q value = 0.008

Table S148. Gene #26: 'amp_xq21.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
AMP PEAK 26(XQ21.1) MUTATED	1	12	1
AMP PEAK 26(XQ21.1) WILD-TYPE	170	193	114

Figure S148. Get High-res Image Gene #26: 'amp_xq21.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_xq25' versus 'CN_CNMF'

P value = 0.00281 (Fisher's exact test), Q value = 0.0054

Table S149. Gene #27: 'amp_xq25' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 27(XQ25) MUTATED	4	11	4
AMP PEAK 27(XQ25) WILD-TYPE	269	123	81

Figure S149. Get High-res Image Gene #27: 'amp_xq25' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq25' versus 'METHLYATION_CNMF'

P value = 0.0197 (Fisher's exact test), Q value = 0.029

Table S150. Gene #27: 'amp_xq25' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
AMP PEAK 27(XQ25) MUTATED	2	12	5
AMP PEAK 27(XQ25) WILD-TYPE	158	153	162

Figure S150. Get High-res Image Gene #27: 'amp_xq25' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xq25' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0241 (Fisher's exact test), Q value = 0.035

Table S151. Gene #27: 'amp_xq25' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
AMP PEAK 27(XQ25) MUTATED	3	14	2
AMP PEAK 27(XQ25) WILD-TYPE	168	191	113

Figure S151. Get High-res Image Gene #27: 'amp_xq25' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_xq27.1' versus 'CN_CNMF'

P value = 0.00425 (Fisher's exact test), Q value = 0.0079

Table S152. Gene #28: 'amp_xq27.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 28(XQ27.1) MUTATED	4	10	5
AMP PEAK 28(XQ27.1) WILD-TYPE	269	124	80

Figure S152. Get High-res Image Gene #28: 'amp_xq27.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq27.1' versus 'METHLYATION_CNMF'

P value = 0.0375 (Fisher's exact test), Q value = 0.051

Table S153. Gene #28: 'amp_xq27.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
AMP PEAK 28(XQ27.1) MUTATED	2	11	6
AMP PEAK 28(XQ27.1) WILD-TYPE	158	154	161

Figure S153. Get High-res Image Gene #28: 'amp_xq27.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xq27.1' versus 'MIRSEQ_CNMF'

P value = 0.00127 (Fisher's exact test), Q value = 0.0027

Table S154. Gene #28: 'amp_xq27.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
AMP PEAK 28(XQ27.1) MUTATED	0	10	9
AMP PEAK 28(XQ27.1) WILD-TYPE	158	137	174

Figure S154. Get High-res Image Gene #28: 'amp_xq27.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_xq27.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 7e-04

Table S155. Gene #28: 'amp_xq27.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 28(XQ27.1) MUTATED	0	7	0	6	6
AMP PEAK 28(XQ27.1) WILD-TYPE	147	91	59	122	50

Figure S155. Get High-res Image Gene #28: 'amp_xq27.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_xq27.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.037 (Fisher's exact test), Q value = 0.051

Table S156. Gene #28: 'amp_xq27.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
AMP PEAK 28(XQ27.1) MUTATED	0	4	1	8
AMP PEAK 28(XQ27.1) WILD-TYPE	62	102	59	82

Figure S156. Get High-res Image Gene #28: 'amp_xq27.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_1p31.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S157. Gene #29: 'del_1p31.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 1(1P31.3) MUTATED	17	39	4
DEL PEAK 1(1P31.3) WILD-TYPE	256	95	81

Figure S157. Get High-res Image Gene #29: 'del_1p31.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p31.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S158. Gene #29: 'del_1p31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 1(1P31.3) MUTATED	3	19	38
DEL PEAK 1(1P31.3) WILD-TYPE	157	146	129

Figure S158. Get High-res Image Gene #29: 'del_1p31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p31.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S159. Gene #29: 'del_1p31.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 1(1P31.3) MUTATED	3	18	39
DEL PEAK 1(1P31.3) WILD-TYPE	143	153	135

Figure S159. Get High-res Image Gene #29: 'del_1p31.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_1p31.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S160. Gene #29: 'del_1p31.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 1(1P31.3) MUTATED	5	26	29
DEL PEAK 1(1P31.3) WILD-TYPE	166	179	86

Figure S160. Get High-res Image Gene #29: 'del_1p31.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_1p31.3' versus 'MIRSEQ_CNMF'

P value = 0.00167 (Fisher's exact test), Q value = 0.0035

Table S161. Gene #29: 'del_1p31.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 1(1P31.3) MUTATED	9	17	33
DEL PEAK 1(1P31.3) WILD-TYPE	149	130	150

Figure S161. Get High-res Image Gene #29: 'del_1p31.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_1p31.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00545 (Fisher's exact test), Q value = 0.0098

Table S162. Gene #29: 'del_1p31.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
DEL PEAK 1(1P31.3) MUTATED	3	25	6	12
DEL PEAK 1(1P31.3) WILD-TYPE	59	81	54	78

Figure S162. Get High-res Image Gene #29: 'del_1p31.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_1p31.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0011 (Fisher's exact test), Q value = 0.0025

Table S163. Gene #29: 'del_1p31.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 1(1P31.3) MUTATED	2	4	11	18	2	9
DEL PEAK 1(1P31.3) WILD-TYPE	68	37	29	64	23	51

Figure S163. Get High-res Image Gene #29: 'del_1p31.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S164. Gene #30: 'del_1p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 2(1P22.1) MUTATED	11	38	9
DEL PEAK 2(1P22.1) WILD-TYPE	262	96	76

Figure S164. Get High-res Image Gene #30: 'del_1p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p22.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S165. Gene #30: 'del_1p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 2(1P22.1) MUTATED	4	29	25
DEL PEAK 2(1P22.1) WILD-TYPE	156	136	142

Figure S165. Get High-res Image Gene #30: 'del_1p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p22.1' versus 'MRNASEQ_CNMF'

P value = 0.00116 (Fisher's exact test), Q value = 0.0025

Table S166. Gene #30: 'del_1p22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 2(1P22.1) MUTATED	6	24	28
DEL PEAK 2(1P22.1) WILD-TYPE	140	147	146

Figure S166. Get High-res Image Gene #30: 'del_1p22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_1p22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00045

Table S167. Gene #30: 'del_1p22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 2(1P22.1) MUTATED	7	31	20
DEL PEAK 2(1P22.1) WILD-TYPE	164	174	95

Figure S167. Get High-res Image Gene #30: 'del_1p22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_1p22.1' versus 'MIRSEQ_CNMF'

P value = 0.00785 (Fisher's exact test), Q value = 0.014

Table S168. Gene #30: 'del_1p22.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 2(1P22.1) MUTATED	11	14	32
DEL PEAK 2(1P22.1) WILD-TYPE	147	133	151

Figure S168. Get High-res Image Gene #30: 'del_1p22.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_1p22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00336 (Fisher's exact test), Q value = 0.0064

Table S169. Gene #30: 'del_1p22.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 2(1P22.1) MUTATED	10	6	9	26	6
DEL PEAK 2(1P22.1) WILD-TYPE	137	92	50	102	50

Figure S169. Get High-res Image Gene #30: 'del_1p22.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_1p22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00983 (Fisher's exact test), Q value = 0.016

Table S170. Gene #30: 'del_1p22.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
DEL PEAK 2(1P22.1) MUTATED	3	22	4	12
DEL PEAK 2(1P22.1) WILD-TYPE	59	84	56	78

Figure S170. Get High-res Image Gene #30: 'del_1p22.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_1p22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00694 (Fisher's exact test), Q value = 0.012

Table S171. Gene #30: 'del_1p22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 2(1P22.1) MUTATED	4	5	9	17	0	6
DEL PEAK 2(1P22.1) WILD-TYPE	66	36	31	65	25	54

Figure S171. Get High-res Image Gene #30: 'del_1p22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1q23.1' versus 'CN_CNMF'

P value = 0.00521 (Fisher's exact test), Q value = 0.0094

Table S172. Gene #31: 'del_1q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 3(1Q23.1) MUTATED	8	10	10
DEL PEAK 3(1Q23.1) WILD-TYPE	265	124	75

Figure S172. Get High-res Image Gene #31: 'del_1q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q23.1' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00022

Table S173. Gene #31: 'del_1q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 3(1Q23.1) MUTATED	1	19	8
DEL PEAK 3(1Q23.1) WILD-TYPE	159	146	159

Figure S173. Get High-res Image Gene #31: 'del_1q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1q23.1' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00049

Table S174. Gene #31: 'del_1q23.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 3(1Q23.1) MUTATED	2	20	6
DEL PEAK 3(1Q23.1) WILD-TYPE	144	151	168

Figure S174. Get High-res Image Gene #31: 'del_1q23.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_1q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00084 (Fisher's exact test), Q value = 0.0019

Table S175. Gene #31: 'del_1q23.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 3(1Q23.1) MUTATED	2	20	6
DEL PEAK 3(1Q23.1) WILD-TYPE	169	185	109

Figure S175. Get High-res Image Gene #31: 'del_1q23.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_1q23.1' versus 'MIRSEQ_CNMF'

P value = 0.0442 (Fisher's exact test), Q value = 0.059

Table S176. Gene #31: 'del_1q23.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 3(1Q23.1) MUTATED	4	8	16
DEL PEAK 3(1Q23.1) WILD-TYPE	154	139	167

Figure S176. Get High-res Image Gene #31: 'del_1q23.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_1q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.029

Table S177. Gene #31: 'del_1q23.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
DEL PEAK 3(1Q23.1) MUTATED	0	12	3	5
DEL PEAK 3(1Q23.1) WILD-TYPE	62	94	57	85

Figure S177. Get High-res Image Gene #31: 'del_1q23.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_1q42.3' versus 'CN_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.0023

Table S178. Gene #32: 'del_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 4(1Q42.3) MUTATED	15	23	9
DEL PEAK 4(1Q42.3) WILD-TYPE	258	111	76

Figure S178. Get High-res Image Gene #32: 'del_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q42.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S179. Gene #32: 'del_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 4(1Q42.3) MUTATED	7	30	10
DEL PEAK 4(1Q42.3) WILD-TYPE	153	135	157

Figure S179. Get High-res Image Gene #32: 'del_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1q42.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0308 (Fisher's exact test), Q value = 0.044

Table S180. Gene #32: 'del_1q42.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 4(1Q42.3) MUTATED	10	6	3	21	7
DEL PEAK 4(1Q42.3) WILD-TYPE	137	92	56	107	49

Figure S180. Get High-res Image Gene #32: 'del_1q42.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_1q42.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0468 (Fisher's exact test), Q value = 0.062

Table S181. Gene #32: 'del_1q42.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 4(1Q42.3) MUTATED	3	2	6	15	1	6
DEL PEAK 4(1Q42.3) WILD-TYPE	67	39	34	67	24	54

Figure S181. Get High-res Image Gene #32: 'del_1q42.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2p21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S182. Gene #33: 'del_2p21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 5(2P21) MUTATED	14	28	4
DEL PEAK 5(2P21) WILD-TYPE	259	106	81

Figure S182. Get High-res Image Gene #33: 'del_2p21' versus Molecular Subtype #1: 'CN_CNMF'

'del_2p21' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S183. Gene #33: 'del_2p21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 5(2P21) MUTATED	2	21	23
DEL PEAK 5(2P21) WILD-TYPE	158	144	144

Figure S183. Get High-res Image Gene #33: 'del_2p21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2p21' versus 'MRNASEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 9e-04

Table S184. Gene #33: 'del_2p21' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 5(2P21) MUTATED	5	13	28
DEL PEAK 5(2P21) WILD-TYPE	141	158	146

Figure S184. Get High-res Image Gene #33: 'del_2p21' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_2p21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0206 (Fisher's exact test), Q value = 0.03

Table S185. Gene #33: 'del_2p21' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 5(2P21) MUTATED	8	23	15
DEL PEAK 5(2P21) WILD-TYPE	163	182	100

Figure S185. Get High-res Image Gene #33: 'del_2p21' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_2p21' versus 'MIRSEQ_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0019

Table S186. Gene #33: 'del_2p21' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 5(2P21) MUTATED	13	4	26
DEL PEAK 5(2P21) WILD-TYPE	145	143	157

Figure S186. Get High-res Image Gene #33: 'del_2p21' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_2p21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0323 (Fisher's exact test), Q value = 0.045

Table S187. Gene #33: 'del_2p21' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
DEL PEAK 5(2P21) MUTATED	3	15	2	4
DEL PEAK 5(2P21) WILD-TYPE	59	91	58	86

Figure S187. Get High-res Image Gene #33: 'del_2p21' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_2p21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0146 (Fisher's exact test), Q value = 0.023

Table S188. Gene #33: 'del_2p21' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 5(2P21) MUTATED	2	0	4	12	3	3
DEL PEAK 5(2P21) WILD-TYPE	68	41	36	70	22	57

Figure S188. Get High-res Image Gene #33: 'del_2p21' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S189. Gene #34: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 6(2Q22.1) MUTATED	13	49	30
DEL PEAK 6(2Q22.1) WILD-TYPE	260	85	55

Figure S189. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S190. Gene #34: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 6(2Q22.1) MUTATED	7	64	21
DEL PEAK 6(2Q22.1) WILD-TYPE	153	101	146

Figure S190. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S191. Gene #34: 'del_2q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 6(2Q22.1) MUTATED	10	55	27
DEL PEAK 6(2Q22.1) WILD-TYPE	136	116	147

Figure S191. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_2q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S192. Gene #34: 'del_2q22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 6(2Q22.1) MUTATED	10	64	18
DEL PEAK 6(2Q22.1) WILD-TYPE	161	141	97

Figure S192. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S193. Gene #34: 'del_2q22.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 6(2Q22.1) MUTATED	15	21	56
DEL PEAK 6(2Q22.1) WILD-TYPE	143	126	127

Figure S193. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00013

Table S194. Gene #34: 'del_2q22.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 6(2Q22.1) MUTATED	16	20	3	39	14
DEL PEAK 6(2Q22.1) WILD-TYPE	131	78	56	89	42

Figure S194. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00174 (Fisher's exact test), Q value = 0.0036

Table S195. Gene #34: 'del_2q22.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
DEL PEAK 6(2Q22.1) MUTATED	5	32	7	17
DEL PEAK 6(2Q22.1) WILD-TYPE	57	74	53	73

Figure S195. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_2q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00091 (Fisher's exact test), Q value = 0.0021

Table S196. Gene #34: 'del_2q22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 6(2Q22.1) MUTATED	6	6	10	27	1	11
DEL PEAK 6(2Q22.1) WILD-TYPE	64	35	30	55	24	49

Figure S196. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S197. Gene #35: 'del_2q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 7(2Q22.3) MUTATED	11	46	28
DEL PEAK 7(2Q22.3) WILD-TYPE	262	88	57

Figure S197. Get High-res Image Gene #35: 'del_2q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S198. Gene #35: 'del_2q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 7(2Q22.3) MUTATED	8	56	21
DEL PEAK 7(2Q22.3) WILD-TYPE	152	109	146

Figure S198. Get High-res Image Gene #35: 'del_2q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.3' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 1e-04

Table S199. Gene #35: 'del_2q22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 7(2Q22.3) MUTATED	11	49	25
DEL PEAK 7(2Q22.3) WILD-TYPE	135	122	149

Figure S199. Get High-res Image Gene #35: 'del_2q22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_2q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S200. Gene #35: 'del_2q22.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 7(2Q22.3) MUTATED	12	56	17
DEL PEAK 7(2Q22.3) WILD-TYPE	159	149	98

Figure S200. Get High-res Image Gene #35: 'del_2q22.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.3' versus 'MIRSEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00037

Table S201. Gene #35: 'del_2q22.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 7(2Q22.3) MUTATED	17	19	49
DEL PEAK 7(2Q22.3) WILD-TYPE	141	128	134

Figure S201. Get High-res Image Gene #35: 'del_2q22.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_2q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 1e-04

Table S202. Gene #35: 'del_2q22.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 7(2Q22.3) MUTATED	14	15	4	36	16
DEL PEAK 7(2Q22.3) WILD-TYPE	133	83	55	92	40

Figure S202. Get High-res Image Gene #35: 'del_2q22.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_2q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.021

Table S203. Gene #35: 'del_2q22.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
DEL PEAK 7(2Q22.3) MUTATED	5	26	6	19
DEL PEAK 7(2Q22.3) WILD-TYPE	57	80	54	71

Figure S203. Get High-res Image Gene #35: 'del_2q22.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_2q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.00068

Table S204. Gene #35: 'del_2q22.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 7(2Q22.3) MUTATED	5	5	11	24	0	11
DEL PEAK 7(2Q22.3) WILD-TYPE	65	36	29	58	25	49

Figure S204. Get High-res Image Gene #35: 'del_2q22.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p13' versus 'CN_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0012

Table S205. Gene #36: 'del_3p13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 8(3P13) MUTATED	58	15	5
DEL PEAK 8(3P13) WILD-TYPE	215	119	80

Figure S205. Get High-res Image Gene #36: 'del_3p13' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S206. Gene #36: 'del_3p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 8(3P13) MUTATED	18	12	48
DEL PEAK 8(3P13) WILD-TYPE	142	153	119

Figure S206. Get High-res Image Gene #36: 'del_3p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S207. Gene #36: 'del_3p13' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 8(3P13) MUTATED	15	12	51
DEL PEAK 8(3P13) WILD-TYPE	131	159	123

Figure S207. Get High-res Image Gene #36: 'del_3p13' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S208. Gene #36: 'del_3p13' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 8(3P13) MUTATED	20	19	39
DEL PEAK 8(3P13) WILD-TYPE	151	186	76

Figure S208. Get High-res Image Gene #36: 'del_3p13' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 0.042

Table S209. Gene #36: 'del_3p13' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
DEL PEAK 8(3P13) MUTATED	13	19	6	6
DEL PEAK 8(3P13) WILD-TYPE	49	87	54	84

Figure S209. Get High-res Image Gene #36: 'del_3p13' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3q29' versus 'MRNASEQ_CNMF'

P value = 0.0359 (Fisher's exact test), Q value = 0.05

Table S210. Gene #37: 'del_3q29' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 9(3Q29) MUTATED	5	9	18
DEL PEAK 9(3Q29) WILD-TYPE	141	162	156

Figure S210. Get High-res Image Gene #37: 'del_3q29' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_4q28.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S211. Gene #38: 'del_4q28.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 10(4Q28.2) MUTATED	7	30	14
DEL PEAK 10(4Q28.2) WILD-TYPE	266	104	71

Figure S211. Get High-res Image Gene #38: 'del_4q28.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q28.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S212. Gene #38: 'del_4q28.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 10(4Q28.2) MUTATED	3	35	13
DEL PEAK 10(4Q28.2) WILD-TYPE	157	130	154

Figure S212. Get High-res Image Gene #38: 'del_4q28.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q28.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S213. Gene #38: 'del_4q28.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 10(4Q28.2) MUTATED	4	35	12
DEL PEAK 10(4Q28.2) WILD-TYPE	142	136	162

Figure S213. Get High-res Image Gene #38: 'del_4q28.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_4q28.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S214. Gene #38: 'del_4q28.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 10(4Q28.2) MUTATED	5	37	9
DEL PEAK 10(4Q28.2) WILD-TYPE	166	168	106

Figure S214. Get High-res Image Gene #38: 'del_4q28.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_4q28.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.015 (Fisher's exact test), Q value = 0.023

Table S215. Gene #38: 'del_4q28.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 10(4Q28.2) MUTATED	11	8	3	24	4
DEL PEAK 10(4Q28.2) WILD-TYPE	136	90	56	104	52

Figure S215. Get High-res Image Gene #38: 'del_4q28.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_4q28.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00082 (Fisher's exact test), Q value = 0.0019

Table S216. Gene #38: 'del_4q28.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
DEL PEAK 10(4Q28.2) MUTATED	0	18	5	6
DEL PEAK 10(4Q28.2) WILD-TYPE	62	88	55	84

Figure S216. Get High-res Image Gene #38: 'del_4q28.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_4q28.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0256 (Fisher's exact test), Q value = 0.037

Table S217. Gene #38: 'del_4q28.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 10(4Q28.2) MUTATED	4	2	7	13	0	3
DEL PEAK 10(4Q28.2) WILD-TYPE	66	39	33	69	25	57

Figure S217. Get High-res Image Gene #38: 'del_4q28.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S218. Gene #39: 'del_5q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 11(5Q11.2) MUTATED	23	64	13
DEL PEAK 11(5Q11.2) WILD-TYPE	250	70	72

Figure S218. Get High-res Image Gene #39: 'del_5q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S219. Gene #39: 'del_5q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 11(5Q11.2) MUTATED	11	51	38
DEL PEAK 11(5Q11.2) WILD-TYPE	149	114	129

Figure S219. Get High-res Image Gene #39: 'del_5q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.00066

Table S220. Gene #39: 'del_5q11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 11(5Q11.2) MUTATED	14	44	42
DEL PEAK 11(5Q11.2) WILD-TYPE	132	127	132

Figure S220. Get High-res Image Gene #39: 'del_5q11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_5q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S221. Gene #39: 'del_5q11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 11(5Q11.2) MUTATED	15	55	30
DEL PEAK 11(5Q11.2) WILD-TYPE	156	150	85

Figure S221. Get High-res Image Gene #39: 'del_5q11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00033

Table S222. Gene #39: 'del_5q11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 11(5Q11.2) MUTATED	23	20	56
DEL PEAK 11(5Q11.2) WILD-TYPE	135	127	127

Figure S222. Get High-res Image Gene #39: 'del_5q11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_5q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S223. Gene #39: 'del_5q11.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 11(5Q11.2) MUTATED	19	9	15	45	11
DEL PEAK 11(5Q11.2) WILD-TYPE	128	89	44	83	45

Figure S223. Get High-res Image Gene #39: 'del_5q11.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00093 (Fisher's exact test), Q value = 0.0021

Table S224. Gene #39: 'del_5q11.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
DEL PEAK 11(5Q11.2) MUTATED	6	36	9	18
DEL PEAK 11(5Q11.2) WILD-TYPE	56	70	51	72

Figure S224. Get High-res Image Gene #39: 'del_5q11.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_5q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00047

Table S225. Gene #39: 'del_5q11.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 11(5Q11.2) MUTATED	9	4	16	28	2	10
DEL PEAK 11(5Q11.2) WILD-TYPE	61	37	24	54	23	50

Figure S225. Get High-res Image Gene #39: 'del_5q11.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S226. Gene #40: 'del_5q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 12(5Q13.2) MUTATED	19	67	13
DEL PEAK 12(5Q13.2) WILD-TYPE	254	67	72

Figure S226. Get High-res Image Gene #40: 'del_5q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q13.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S227. Gene #40: 'del_5q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 12(5Q13.2) MUTATED	12	53	34
DEL PEAK 12(5Q13.2) WILD-TYPE	148	112	133

Figure S227. Get High-res Image Gene #40: 'del_5q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q13.2' versus 'MRNASEQ_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.0021

Table S228. Gene #40: 'del_5q13.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 12(5Q13.2) MUTATED	15	44	40
DEL PEAK 12(5Q13.2) WILD-TYPE	131	127	134

Figure S228. Get High-res Image Gene #40: 'del_5q13.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_5q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00285 (Fisher's exact test), Q value = 0.0055

Table S229. Gene #40: 'del_5q13.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 12(5Q13.2) MUTATED	21	54	24
DEL PEAK 12(5Q13.2) WILD-TYPE	150	151	91

Figure S229. Get High-res Image Gene #40: 'del_5q13.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_5q13.2' versus 'MIRSEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.00068

Table S230. Gene #40: 'del_5q13.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 12(5Q13.2) MUTATED	32	15	51
DEL PEAK 12(5Q13.2) WILD-TYPE	126	132	132

Figure S230. Get High-res Image Gene #40: 'del_5q13.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_5q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S231. Gene #40: 'del_5q13.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 12(5Q13.2) MUTATED	27	7	14	44	6
DEL PEAK 12(5Q13.2) WILD-TYPE	120	91	45	84	50

Figure S231. Get High-res Image Gene #40: 'del_5q13.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_5q13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0022 (Fisher's exact test), Q value = 0.0044

Table S232. Gene #40: 'del_5q13.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
DEL PEAK 12(5Q13.2) MUTATED	7	34	7	16
DEL PEAK 12(5Q13.2) WILD-TYPE	55	72	53	74

Figure S232. Get High-res Image Gene #40: 'del_5q13.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_5q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.00084

Table S233. Gene #40: 'del_5q13.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 12(5Q13.2) MUTATED	10	3	14	27	4	6
DEL PEAK 12(5Q13.2) WILD-TYPE	60	38	26	55	21	54

Figure S233. Get High-res Image Gene #40: 'del_5q13.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S234. Gene #41: 'del_5q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 13(5Q21.1) MUTATED	13	60	36
DEL PEAK 13(5Q21.1) WILD-TYPE	260	74	49

Figure S234. Get High-res Image Gene #41: 'del_5q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S235. Gene #41: 'del_5q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 13(5Q21.1) MUTATED	11	73	25
DEL PEAK 13(5Q21.1) WILD-TYPE	149	92	142

Figure S235. Get High-res Image Gene #41: 'del_5q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q21.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S236. Gene #41: 'del_5q21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 13(5Q21.1) MUTATED	13	69	27
DEL PEAK 13(5Q21.1) WILD-TYPE	133	102	147

Figure S236. Get High-res Image Gene #41: 'del_5q21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_5q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S237. Gene #41: 'del_5q21.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 13(5Q21.1) MUTATED	17	72	20
DEL PEAK 13(5Q21.1) WILD-TYPE	154	133	95

Figure S237. Get High-res Image Gene #41: 'del_5q21.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_5q21.1' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00049

Table S238. Gene #41: 'del_5q21.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 13(5Q21.1) MUTATED	30	20	58
DEL PEAK 13(5Q21.1) WILD-TYPE	128	127	125

Figure S238. Get High-res Image Gene #41: 'del_5q21.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_5q21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00234 (Fisher's exact test), Q value = 0.0046

Table S239. Gene #41: 'del_5q21.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 13(5Q21.1) MUTATED	26	14	14	44	10
DEL PEAK 13(5Q21.1) WILD-TYPE	121	84	45	84	46

Figure S239. Get High-res Image Gene #41: 'del_5q21.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_5q21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0043 (Fisher's exact test), Q value = 0.008

Table S240. Gene #41: 'del_5q21.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 13(5Q21.1) MUTATED	8	7	10	29	2	11
DEL PEAK 13(5Q21.1) WILD-TYPE	62	34	30	53	23	49

Figure S240. Get High-res Image Gene #41: 'del_5q21.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p25.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S241. Gene #42: 'del_6p25.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 14(6P25.1) MUTATED	12	30	4
DEL PEAK 14(6P25.1) WILD-TYPE	261	104	81

Figure S241. Get High-res Image Gene #42: 'del_6p25.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.1' versus 'METHLYATION_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.022

Table S242. Gene #42: 'del_6p25.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 14(6P25.1) MUTATED	8	14	24
DEL PEAK 14(6P25.1) WILD-TYPE	152	151	143

Figure S242. Get High-res Image Gene #42: 'del_6p25.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p25.1' versus 'MRNASEQ_CNMF'

P value = 0.00569 (Fisher's exact test), Q value = 0.01

Table S243. Gene #42: 'del_6p25.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 14(6P25.1) MUTATED	6	15	25
DEL PEAK 14(6P25.1) WILD-TYPE	140	156	149

Figure S243. Get High-res Image Gene #42: 'del_6p25.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_6p25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0121 (Fisher's exact test), Q value = 0.019

Table S244. Gene #42: 'del_6p25.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 14(6P25.1) MUTATED	10	17	19
DEL PEAK 14(6P25.1) WILD-TYPE	161	188	96

Figure S244. Get High-res Image Gene #42: 'del_6p25.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_6p25.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0491 (Fisher's exact test), Q value = 0.064

Table S245. Gene #42: 'del_6p25.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 14(6P25.1) MUTATED	9	5	8	19	5
DEL PEAK 14(6P25.1) WILD-TYPE	138	93	51	109	51

Figure S245. Get High-res Image Gene #42: 'del_6p25.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_6p25.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0165 (Fisher's exact test), Q value = 0.025

Table S246. Gene #42: 'del_6p25.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 14(6P25.1) MUTATED	3	1	9	12	2	5
DEL PEAK 14(6P25.1) WILD-TYPE	67	40	31	70	23	55

Figure S246. Get High-res Image Gene #42: 'del_6p25.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q14.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S247. Gene #43: 'del_6q14.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 15(6Q14.3) MUTATED	50	76	54
DEL PEAK 15(6Q14.3) WILD-TYPE	223	58	31

Figure S247. Get High-res Image Gene #43: 'del_6q14.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q14.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S248. Gene #43: 'del_6q14.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 15(6Q14.3) MUTATED	24	118	38
DEL PEAK 15(6Q14.3) WILD-TYPE	136	47	129

Figure S248. Get High-res Image Gene #43: 'del_6q14.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q14.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S249. Gene #43: 'del_6q14.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 15(6Q14.3) MUTATED	31	102	47
DEL PEAK 15(6Q14.3) WILD-TYPE	115	69	127

Figure S249. Get High-res Image Gene #43: 'del_6q14.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_6q14.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S250. Gene #43: 'del_6q14.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 15(6Q14.3) MUTATED	33	117	30
DEL PEAK 15(6Q14.3) WILD-TYPE	138	88	85

Figure S250. Get High-res Image Gene #43: 'del_6q14.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_6q14.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S251. Gene #43: 'del_6q14.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 15(6Q14.3) MUTATED	43	42	94
DEL PEAK 15(6Q14.3) WILD-TYPE	115	105	89

Figure S251. Get High-res Image Gene #43: 'del_6q14.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_6q14.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S252. Gene #43: 'del_6q14.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 15(6Q14.3) MUTATED	38	35	14	68	24
DEL PEAK 15(6Q14.3) WILD-TYPE	109	63	45	60	32

Figure S252. Get High-res Image Gene #43: 'del_6q14.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_6q14.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00211 (Fisher's exact test), Q value = 0.0043

Table S253. Gene #43: 'del_6q14.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
DEL PEAK 15(6Q14.3) MUTATED	13	51	18	27
DEL PEAK 15(6Q14.3) WILD-TYPE	49	55	42	63

Figure S253. Get High-res Image Gene #43: 'del_6q14.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_6q14.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00498 (Fisher's exact test), Q value = 0.0091

Table S254. Gene #43: 'del_6q14.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 15(6Q14.3) MUTATED	17	13	16	41	4	18
DEL PEAK 15(6Q14.3) WILD-TYPE	53	28	24	41	21	42

Figure S254. Get High-res Image Gene #43: 'del_6q14.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q31.33' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 3e-04

Table S255. Gene #44: 'del_7q31.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 16(7Q31.33) MUTATED	7	18	3
DEL PEAK 16(7Q31.33) WILD-TYPE	266	116	82

Figure S255. Get High-res Image Gene #44: 'del_7q31.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q31.33' versus 'METHLYATION_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.023

Table S256. Gene #44: 'del_7q31.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 16(7Q31.33) MUTATED	3	15	10
DEL PEAK 16(7Q31.33) WILD-TYPE	157	150	157

Figure S256. Get High-res Image Gene #44: 'del_7q31.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q31.33' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00042

Table S257. Gene #44: 'del_7q31.33' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 16(7Q31.33) MUTATED	0	15	13
DEL PEAK 16(7Q31.33) WILD-TYPE	146	156	161

Figure S257. Get High-res Image Gene #44: 'del_7q31.33' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_7q31.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.00072

Table S258. Gene #44: 'del_7q31.33' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 16(7Q31.33) MUTATED	1	17	10
DEL PEAK 16(7Q31.33) WILD-TYPE	170	188	105

Figure S258. Get High-res Image Gene #44: 'del_7q31.33' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_7q31.33' versus 'MIRSEQ_CNMF'

P value = 0.00115 (Fisher's exact test), Q value = 0.0025

Table S259. Gene #44: 'del_7q31.33' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 16(7Q31.33) MUTATED	4	4	20
DEL PEAK 16(7Q31.33) WILD-TYPE	154	143	163

Figure S259. Get High-res Image Gene #44: 'del_7q31.33' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_7q31.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.00068

Table S260. Gene #44: 'del_7q31.33' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 16(7Q31.33) MUTATED	4	1	2	18	3
DEL PEAK 16(7Q31.33) WILD-TYPE	143	97	57	110	53

Figure S260. Get High-res Image Gene #44: 'del_7q31.33' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_7q31.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0473 (Fisher's exact test), Q value = 0.062

Table S261. Gene #44: 'del_7q31.33' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 16(7Q31.33) MUTATED	3	0	5	7	0	1
DEL PEAK 16(7Q31.33) WILD-TYPE	67	41	35	75	25	59

Figure S261. Get High-res Image Gene #44: 'del_7q31.33' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S262. Gene #45: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 17(8P23.2) MUTATED	123	90	11
DEL PEAK 17(8P23.2) WILD-TYPE	150	44	74

Figure S262. Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S263. Gene #45: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 17(8P23.2) MUTATED	43	80	101
DEL PEAK 17(8P23.2) WILD-TYPE	117	85	66

Figure S263. Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S264. Gene #45: 'del_8p23.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 17(8P23.2) MUTATED	46	75	103
DEL PEAK 17(8P23.2) WILD-TYPE	100	96	71

Figure S264. Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S265. Gene #45: 'del_8p23.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 17(8P23.2) MUTATED	52	101	71
DEL PEAK 17(8P23.2) WILD-TYPE	119	104	44

Figure S265. Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.00079

Table S266. Gene #45: 'del_8p23.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 17(8P23.2) MUTATED	61	56	105
DEL PEAK 17(8P23.2) WILD-TYPE	97	91	78

Figure S266. Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.00089

Table S267. Gene #45: 'del_8p23.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 17(8P23.2) MUTATED	53	34	31	75	29
DEL PEAK 17(8P23.2) WILD-TYPE	94	64	28	53	27

Figure S267. Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0358 (Fisher's exact test), Q value = 0.05

Table S268. Gene #45: 'del_8p23.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
DEL PEAK 17(8P23.2) MUTATED	17	51	22	42
DEL PEAK 17(8P23.2) WILD-TYPE	45	55	38	48

Figure S268. Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00191 (Fisher's exact test), Q value = 0.0039

Table S269. Gene #45: 'del_8p23.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 17(8P23.2) MUTATED	22	11	25	39	6	29
DEL PEAK 17(8P23.2) WILD-TYPE	48	30	15	43	19	31

Figure S269. Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S270. Gene #46: 'del_8p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 18(8P21.3) MUTATED	161	107	26
DEL PEAK 18(8P21.3) WILD-TYPE	112	27	59

Figure S270. Get High-res Image Gene #46: 'del_8p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S271. Gene #46: 'del_8p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 18(8P21.3) MUTATED	60	106	128
DEL PEAK 18(8P21.3) WILD-TYPE	100	59	39

Figure S271. Get High-res Image Gene #46: 'del_8p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S272. Gene #46: 'del_8p21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 18(8P21.3) MUTATED	62	97	135
DEL PEAK 18(8P21.3) WILD-TYPE	84	74	39

Figure S272. Get High-res Image Gene #46: 'del_8p21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_8p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S273. Gene #46: 'del_8p21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 18(8P21.3) MUTATED	77	128	89
DEL PEAK 18(8P21.3) WILD-TYPE	94	77	26

Figure S273. Get High-res Image Gene #46: 'del_8p21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_8p21.3' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S274. Gene #46: 'del_8p21.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 18(8P21.3) MUTATED	81	77	134
DEL PEAK 18(8P21.3) WILD-TYPE	77	70	49

Figure S274. Get High-res Image Gene #46: 'del_8p21.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_8p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S275. Gene #46: 'del_8p21.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 18(8P21.3) MUTATED	67	50	42	97	36
DEL PEAK 18(8P21.3) WILD-TYPE	80	48	17	31	20

Figure S275. Get High-res Image Gene #46: 'del_8p21.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_8p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00844 (Fisher's exact test), Q value = 0.014

Table S276. Gene #46: 'del_8p21.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
DEL PEAK 18(8P21.3) MUTATED	26	69	28	55
DEL PEAK 18(8P21.3) WILD-TYPE	36	37	32	35

Figure S276. Get High-res Image Gene #46: 'del_8p21.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_8p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S277. Gene #46: 'del_8p21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 18(8P21.3) MUTATED	24	17	32	53	14	38
DEL PEAK 18(8P21.3) WILD-TYPE	46	24	8	29	11	22

Figure S277. Get High-res Image Gene #46: 'del_8p21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S278. Gene #47: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 19(9P23) MUTATED	15	28	2
DEL PEAK 19(9P23) WILD-TYPE	258	106	83

Figure S278. Get High-res Image Gene #47: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00037

Table S279. Gene #47: 'del_9p23' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 19(9P23) MUTATED	3	16	26
DEL PEAK 19(9P23) WILD-TYPE	143	155	148

Figure S279. Get High-res Image Gene #47: 'del_9p23' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00194 (Fisher's exact test), Q value = 0.004

Table S280. Gene #47: 'del_9p23' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 19(9P23) MUTATED	7	19	19
DEL PEAK 19(9P23) WILD-TYPE	164	186	96

Figure S280. Get High-res Image Gene #47: 'del_9p23' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 0.0285 (Fisher's exact test), Q value = 0.041

Table S281. Gene #47: 'del_9p23' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 19(9P23) MUTATED	13	7	24
DEL PEAK 19(9P23) WILD-TYPE	145	140	159

Figure S281. Get High-res Image Gene #47: 'del_9p23' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 0.025

Table S282. Gene #47: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 19(9P23) MUTATED	1	3	8	10	3	4
DEL PEAK 19(9P23) WILD-TYPE	69	38	32	72	22	56

Figure S282. Get High-res Image Gene #47: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S283. Gene #48: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 20(10Q23.31) MUTATED	78	68	11
DEL PEAK 20(10Q23.31) WILD-TYPE	195	66	74

Figure S283. Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S284. Gene #48: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 20(10Q23.31) MUTATED	28	39	90
DEL PEAK 20(10Q23.31) WILD-TYPE	132	126	77

Figure S284. Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S285. Gene #48: 'del_10q23.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 20(10Q23.31) MUTATED	21	31	105
DEL PEAK 20(10Q23.31) WILD-TYPE	125	140	69

Figure S285. Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S286. Gene #48: 'del_10q23.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 20(10Q23.31) MUTATED	33	47	77
DEL PEAK 20(10Q23.31) WILD-TYPE	138	158	38

Figure S286. Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.022

Table S287. Gene #48: 'del_10q23.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 20(10Q23.31) MUTATED	47	36	72
DEL PEAK 20(10Q23.31) WILD-TYPE	111	111	111

Figure S287. Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S288. Gene #48: 'del_10q23.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 20(10Q23.31) MUTATED	41	12	25	57	20
DEL PEAK 20(10Q23.31) WILD-TYPE	106	86	34	71	36

Figure S288. Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0402 (Fisher's exact test), Q value = 0.054

Table S289. Gene #48: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
DEL PEAK 20(10Q23.31) MUTATED	16	41	15	39
DEL PEAK 20(10Q23.31) WILD-TYPE	46	65	45	51

Figure S289. Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S290. Gene #48: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 20(10Q23.31) MUTATED	10	3	32	31	9	26
DEL PEAK 20(10Q23.31) WILD-TYPE	60	38	8	51	16	34

Figure S290. Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S291. Gene #49: 'del_11p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 21(11P11.2) MUTATED	5	23	6
DEL PEAK 21(11P11.2) WILD-TYPE	268	111	79

Figure S291. Get High-res Image Gene #49: 'del_11p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p11.2' versus 'METHLYATION_CNMF'

P value = 0.00252 (Fisher's exact test), Q value = 0.005

Table S292. Gene #49: 'del_11p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 21(11P11.2) MUTATED	6	21	7
DEL PEAK 21(11P11.2) WILD-TYPE	154	144	160

Figure S292. Get High-res Image Gene #49: 'del_11p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p11.2' versus 'MRNASEQ_CNMF'

P value = 0.00139 (Fisher's exact test), Q value = 0.003

Table S293. Gene #49: 'del_11p11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 21(11P11.2) MUTATED	6	22	6
DEL PEAK 21(11P11.2) WILD-TYPE	140	149	168

Figure S293. Get High-res Image Gene #49: 'del_11p11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_11p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0257 (Fisher's exact test), Q value = 0.037

Table S294. Gene #49: 'del_11p11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 21(11P11.2) MUTATED	7	22	5
DEL PEAK 21(11P11.2) WILD-TYPE	164	183	110

Figure S294. Get High-res Image Gene #49: 'del_11p11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_11p11.2' versus 'MIRSEQ_CNMF'

P value = 0.0292 (Fisher's exact test), Q value = 0.042

Table S295. Gene #49: 'del_11p11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 21(11P11.2) MUTATED	6	8	20
DEL PEAK 21(11P11.2) WILD-TYPE	152	139	163

Figure S295. Get High-res Image Gene #49: 'del_11p11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_11p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0244 (Fisher's exact test), Q value = 0.036

Table S296. Gene #49: 'del_11p11.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 21(11P11.2) MUTATED	5	7	2	17	3
DEL PEAK 21(11P11.2) WILD-TYPE	142	91	57	111	53

Figure S296. Get High-res Image Gene #49: 'del_11p11.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_11p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00809 (Fisher's exact test), Q value = 0.014

Table S297. Gene #49: 'del_11p11.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
DEL PEAK 21(11P11.2) MUTATED	0	13	3	4
DEL PEAK 21(11P11.2) WILD-TYPE	62	93	57	86

Figure S297. Get High-res Image Gene #49: 'del_11p11.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_11q22.3' versus 'CN_CNMF'

P value = 0.044 (Fisher's exact test), Q value = 0.059

Table S298. Gene #50: 'del_11q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 22(11Q22.3) MUTATED	19	19	5
DEL PEAK 22(11Q22.3) WILD-TYPE	254	115	80

Figure S298. Get High-res Image Gene #50: 'del_11q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q22.3' versus 'METHLYATION_CNMF'

P value = 0.021 (Fisher's exact test), Q value = 0.031

Table S299. Gene #50: 'del_11q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 22(11Q22.3) MUTATED	10	23	10
DEL PEAK 22(11Q22.3) WILD-TYPE	150	142	157

Figure S299. Get High-res Image Gene #50: 'del_11q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0122 (Fisher's exact test), Q value = 0.02

Table S300. Gene #50: 'del_11q22.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 22(11Q22.3) MUTATED	2	0	1	12	1	6
DEL PEAK 22(11Q22.3) WILD-TYPE	68	41	39	70	24	54

Figure S300. Get High-res Image Gene #50: 'del_11q22.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12p13.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S301. Gene #52: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 24(12P13.1) MUTATED	59	54	11
DEL PEAK 24(12P13.1) WILD-TYPE	214	80	74

Figure S301. Get High-res Image Gene #52: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S302. Gene #52: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 24(12P13.1) MUTATED	20	53	51
DEL PEAK 24(12P13.1) WILD-TYPE	140	112	116

Figure S302. Get High-res Image Gene #52: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12p13.1' versus 'MRNASEQ_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.0029

Table S303. Gene #52: 'del_12p13.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 24(12P13.1) MUTATED	25	39	60
DEL PEAK 24(12P13.1) WILD-TYPE	121	132	114

Figure S303. Get High-res Image Gene #52: 'del_12p13.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00408 (Fisher's exact test), Q value = 0.0077

Table S304. Gene #52: 'del_12p13.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 24(12P13.1) MUTATED	31	52	41
DEL PEAK 24(12P13.1) WILD-TYPE	140	153	74

Figure S304. Get High-res Image Gene #52: 'del_12p13.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00013

Table S305. Gene #52: 'del_12p13.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 24(12P13.1) MUTATED	31	10	18	47	15
DEL PEAK 24(12P13.1) WILD-TYPE	116	88	41	81	41

Figure S305. Get High-res Image Gene #52: 'del_12p13.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00013

Table S306. Gene #52: 'del_12p13.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
DEL PEAK 24(12P13.1) MUTATED	5	41	12	21
DEL PEAK 24(12P13.1) WILD-TYPE	57	65	48	69

Figure S306. Get High-res Image Gene #52: 'del_12p13.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_12p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00281 (Fisher's exact test), Q value = 0.0054

Table S307. Gene #52: 'del_12p13.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 24(12P13.1) MUTATED	14	4	16	29	3	13
DEL PEAK 24(12P13.1) WILD-TYPE	56	37	24	53	22	47

Figure S307. Get High-res Image Gene #52: 'del_12p13.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q24.32' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 1e-04

Table S308. Gene #53: 'del_12q24.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 25(12Q24.32) MUTATED	15	25	3
DEL PEAK 25(12Q24.32) WILD-TYPE	258	109	82

Figure S308. Get High-res Image Gene #53: 'del_12q24.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S309. Gene #54: 'del_13q14.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 26(13Q14.13) MUTATED	86	90	51
DEL PEAK 26(13Q14.13) WILD-TYPE	187	44	34

Figure S309. Get High-res Image Gene #54: 'del_13q14.13' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S310. Gene #54: 'del_13q14.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 26(13Q14.13) MUTATED	43	98	86
DEL PEAK 26(13Q14.13) WILD-TYPE	117	67	81

Figure S310. Get High-res Image Gene #54: 'del_13q14.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q14.13' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00019

Table S311. Gene #54: 'del_13q14.13' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 26(13Q14.13) MUTATED	45	89	93
DEL PEAK 26(13Q14.13) WILD-TYPE	101	82	81

Figure S311. Get High-res Image Gene #54: 'del_13q14.13' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_13q14.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S312. Gene #54: 'del_13q14.13' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 26(13Q14.13) MUTATED	56	105	66
DEL PEAK 26(13Q14.13) WILD-TYPE	115	100	49

Figure S312. Get High-res Image Gene #54: 'del_13q14.13' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.13' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00013

Table S313. Gene #54: 'del_13q14.13' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 26(13Q14.13) MUTATED	60	58	108
DEL PEAK 26(13Q14.13) WILD-TYPE	98	89	75

Figure S313. Get High-res Image Gene #54: 'del_13q14.13' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_13q14.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.00092

Table S314. Gene #54: 'del_13q14.13' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 26(13Q14.13) MUTATED	55	37	25	78	31
DEL PEAK 26(13Q14.13) WILD-TYPE	92	61	34	50	25

Figure S314. Get High-res Image Gene #54: 'del_13q14.13' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00042

Table S315. Gene #54: 'del_13q14.13' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
DEL PEAK 26(13Q14.13) MUTATED	19	66	21	46
DEL PEAK 26(13Q14.13) WILD-TYPE	43	40	39	44

Figure S315. Get High-res Image Gene #54: 'del_13q14.13' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_13q14.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00013

Table S316. Gene #54: 'del_13q14.13' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 26(13Q14.13) MUTATED	19	14	23	53	11	32
DEL PEAK 26(13Q14.13) WILD-TYPE	51	27	17	29	14	28

Figure S316. Get High-res Image Gene #54: 'del_13q14.13' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S317. Gene #55: 'del_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 27(13Q22.1) MUTATED	56	88	32
DEL PEAK 27(13Q22.1) WILD-TYPE	217	46	53

Figure S317. Get High-res Image Gene #55: 'del_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q22.1' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00019

Table S318. Gene #55: 'del_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 27(13Q22.1) MUTATED	35	74	67
DEL PEAK 27(13Q22.1) WILD-TYPE	125	91	100

Figure S318. Get High-res Image Gene #55: 'del_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q22.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S319. Gene #55: 'del_13q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 27(13Q22.1) MUTATED	29	72	75
DEL PEAK 27(13Q22.1) WILD-TYPE	117	99	99

Figure S319. Get High-res Image Gene #55: 'del_13q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_13q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00027

Table S320. Gene #55: 'del_13q22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 27(13Q22.1) MUTATED	40	86	50
DEL PEAK 27(13Q22.1) WILD-TYPE	131	119	65

Figure S320. Get High-res Image Gene #55: 'del_13q22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_13q22.1' versus 'MIRSEQ_CNMF'

P value = 0.00464 (Fisher's exact test), Q value = 0.0086

Table S321. Gene #55: 'del_13q22.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 27(13Q22.1) MUTATED	46	46	82
DEL PEAK 27(13Q22.1) WILD-TYPE	112	101	101

Figure S321. Get High-res Image Gene #55: 'del_13q22.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_13q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00129 (Fisher's exact test), Q value = 0.0028

Table S322. Gene #55: 'del_13q22.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 27(13Q22.1) MUTATED	42	27	19	64	22
DEL PEAK 27(13Q22.1) WILD-TYPE	105	71	40	64	34

Figure S322. Get High-res Image Gene #55: 'del_13q22.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_13q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00164 (Fisher's exact test), Q value = 0.0034

Table S323. Gene #55: 'del_13q22.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
DEL PEAK 27(13Q22.1) MUTATED	13	50	17	39
DEL PEAK 27(13Q22.1) WILD-TYPE	49	56	43	51

Figure S323. Get High-res Image Gene #55: 'del_13q22.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_13q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00036

Table S324. Gene #55: 'del_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 27(13Q22.1) MUTATED	17	9	22	44	6	21
DEL PEAK 27(13Q22.1) WILD-TYPE	53	32	18	38	19	39

Figure S324. Get High-res Image Gene #55: 'del_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S325. Gene #56: 'del_15q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 28(15Q21.3) MUTATED	17	47	3
DEL PEAK 28(15Q21.3) WILD-TYPE	256	87	82

Figure S325. Get High-res Image Gene #56: 'del_15q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S326. Gene #56: 'del_15q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 28(15Q21.3) MUTATED	5	29	33
DEL PEAK 28(15Q21.3) WILD-TYPE	155	136	134

Figure S326. Get High-res Image Gene #56: 'del_15q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S327. Gene #56: 'del_15q21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 28(15Q21.3) MUTATED	3	28	36
DEL PEAK 28(15Q21.3) WILD-TYPE	143	143	138

Figure S327. Get High-res Image Gene #56: 'del_15q21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_15q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S328. Gene #56: 'del_15q21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 28(15Q21.3) MUTATED	7	37	23
DEL PEAK 28(15Q21.3) WILD-TYPE	164	168	92

Figure S328. Get High-res Image Gene #56: 'del_15q21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_15q21.3' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S329. Gene #56: 'del_15q21.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 28(15Q21.3) MUTATED	8	15	42
DEL PEAK 28(15Q21.3) WILD-TYPE	150	132	141

Figure S329. Get High-res Image Gene #56: 'del_15q21.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_15q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 1e-04

Table S330. Gene #56: 'del_15q21.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 28(15Q21.3) MUTATED	7	8	10	28	12
DEL PEAK 28(15Q21.3) WILD-TYPE	140	90	49	100	44

Figure S330. Get High-res Image Gene #56: 'del_15q21.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_15q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00037

Table S331. Gene #56: 'del_15q21.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
DEL PEAK 28(15Q21.3) MUTATED	1	26	5	12
DEL PEAK 28(15Q21.3) WILD-TYPE	61	80	55	78

Figure S331. Get High-res Image Gene #56: 'del_15q21.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_15q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S332. Gene #56: 'del_15q21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 28(15Q21.3) MUTATED	0	2	14	18	1	9
DEL PEAK 28(15Q21.3) WILD-TYPE	70	39	26	64	24	51

Figure S332. Get High-res Image Gene #56: 'del_15q21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S333. Gene #57: 'del_16q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 29(16Q22.3) MUTATED	88	93	10
DEL PEAK 29(16Q22.3) WILD-TYPE	185	41	75

Figure S333. Get High-res Image Gene #57: 'del_16q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S334. Gene #57: 'del_16q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 29(16Q22.3) MUTATED	32	72	87
DEL PEAK 29(16Q22.3) WILD-TYPE	128	93	80

Figure S334. Get High-res Image Gene #57: 'del_16q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S335. Gene #57: 'del_16q22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 29(16Q22.3) MUTATED	35	60	96
DEL PEAK 29(16Q22.3) WILD-TYPE	111	111	78

Figure S335. Get High-res Image Gene #57: 'del_16q22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_16q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00037

Table S336. Gene #57: 'del_16q22.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 29(16Q22.3) MUTATED	51	77	63
DEL PEAK 29(16Q22.3) WILD-TYPE	120	128	52

Figure S336. Get High-res Image Gene #57: 'del_16q22.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_16q22.3' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00013

Table S337. Gene #57: 'del_16q22.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 29(16Q22.3) MUTATED	56	39	94
DEL PEAK 29(16Q22.3) WILD-TYPE	102	108	89

Figure S337. Get High-res Image Gene #57: 'del_16q22.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_16q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S338. Gene #57: 'del_16q22.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 29(16Q22.3) MUTATED	44	22	28	78	17
DEL PEAK 29(16Q22.3) WILD-TYPE	103	76	31	50	39

Figure S338. Get High-res Image Gene #57: 'del_16q22.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_16q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S339. Gene #57: 'del_16q22.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
DEL PEAK 29(16Q22.3) MUTATED	10	57	16	31
DEL PEAK 29(16Q22.3) WILD-TYPE	52	49	44	59

Figure S339. Get High-res Image Gene #57: 'del_16q22.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_16q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S340. Gene #57: 'del_16q22.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 29(16Q22.3) MUTATED	16	4	20	46	4	24
DEL PEAK 29(16Q22.3) WILD-TYPE	54	37	20	36	21	36

Figure S340. Get High-res Image Gene #57: 'del_16q22.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S341. Gene #58: 'del_16q24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 30(16Q24.1) MUTATED	105	101	7
DEL PEAK 30(16Q24.1) WILD-TYPE	168	33	78

Figure S341. Get High-res Image Gene #58: 'del_16q24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q24.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S342. Gene #58: 'del_16q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 30(16Q24.1) MUTATED	39	79	95
DEL PEAK 30(16Q24.1) WILD-TYPE	121	86	72

Figure S342. Get High-res Image Gene #58: 'del_16q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q24.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S343. Gene #58: 'del_16q24.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 30(16Q24.1) MUTATED	44	65	104
DEL PEAK 30(16Q24.1) WILD-TYPE	102	106	70

Figure S343. Get High-res Image Gene #58: 'del_16q24.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_16q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0061 (Fisher's exact test), Q value = 0.011

Table S344. Gene #58: 'del_16q24.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 30(16Q24.1) MUTATED	63	86	64
DEL PEAK 30(16Q24.1) WILD-TYPE	108	119	51

Figure S344. Get High-res Image Gene #58: 'del_16q24.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_16q24.1' versus 'MIRSEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00057

Table S345. Gene #58: 'del_16q24.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 30(16Q24.1) MUTATED	64	47	99
DEL PEAK 30(16Q24.1) WILD-TYPE	94	100	84

Figure S345. Get High-res Image Gene #58: 'del_16q24.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_16q24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S346. Gene #58: 'del_16q24.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 30(16Q24.1) MUTATED	50	25	32	86	17
DEL PEAK 30(16Q24.1) WILD-TYPE	97	73	27	42	39

Figure S346. Get High-res Image Gene #58: 'del_16q24.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_16q24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00253 (Fisher's exact test), Q value = 0.005

Table S347. Gene #58: 'del_16q24.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
DEL PEAK 30(16Q24.1) MUTATED	16	57	21	35
DEL PEAK 30(16Q24.1) WILD-TYPE	46	49	39	55

Figure S347. Get High-res Image Gene #58: 'del_16q24.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_16q24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S348. Gene #58: 'del_16q24.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 30(16Q24.1) MUTATED	16	7	22	49	8	27
DEL PEAK 30(16Q24.1) WILD-TYPE	54	34	18	33	17	33

Figure S348. Get High-res Image Gene #58: 'del_16q24.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S349. Gene #59: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 31(17P13.1) MUTATED	71	85	7
DEL PEAK 31(17P13.1) WILD-TYPE	202	49	78

Figure S349. Get High-res Image Gene #59: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S350. Gene #59: 'del_17p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 31(17P13.1) MUTATED	32	44	87
DEL PEAK 31(17P13.1) WILD-TYPE	128	121	80

Figure S350. Get High-res Image Gene #59: 'del_17p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S351. Gene #59: 'del_17p13.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 31(17P13.1) MUTATED	27	37	99
DEL PEAK 31(17P13.1) WILD-TYPE	119	134	75

Figure S351. Get High-res Image Gene #59: 'del_17p13.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_17p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S352. Gene #59: 'del_17p13.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 31(17P13.1) MUTATED	38	54	71
DEL PEAK 31(17P13.1) WILD-TYPE	133	151	44

Figure S352. Get High-res Image Gene #59: 'del_17p13.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.1' versus 'MIRSEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00037

Table S353. Gene #59: 'del_17p13.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 31(17P13.1) MUTATED	46	34	81
DEL PEAK 31(17P13.1) WILD-TYPE	112	113	102

Figure S353. Get High-res Image Gene #59: 'del_17p13.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_17p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S354. Gene #59: 'del_17p13.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 31(17P13.1) MUTATED	36	15	34	60	16
DEL PEAK 31(17P13.1) WILD-TYPE	111	83	25	68	40

Figure S354. Get High-res Image Gene #59: 'del_17p13.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_17p13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00148 (Fisher's exact test), Q value = 0.0031

Table S355. Gene #59: 'del_17p13.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
DEL PEAK 31(17P13.1) MUTATED	14	52	15	32
DEL PEAK 31(17P13.1) WILD-TYPE	48	54	45	58

Figure S355. Get High-res Image Gene #59: 'del_17p13.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_17p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S356. Gene #59: 'del_17p13.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 31(17P13.1) MUTATED	16	3	28	40	8	18
DEL PEAK 31(17P13.1) WILD-TYPE	54	38	12	42	17	42

Figure S356. Get High-res Image Gene #59: 'del_17p13.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q21.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S357. Gene #60: 'del_17q21.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 32(17Q21.31) MUTATED	52	41	3
DEL PEAK 32(17Q21.31) WILD-TYPE	221	93	82

Figure S357. Get High-res Image Gene #60: 'del_17q21.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q21.31' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S358. Gene #60: 'del_17q21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 32(17Q21.31) MUTATED	21	17	58
DEL PEAK 32(17Q21.31) WILD-TYPE	139	148	109

Figure S358. Get High-res Image Gene #60: 'del_17q21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q21.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S359. Gene #60: 'del_17q21.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 32(17Q21.31) MUTATED	19	14	63
DEL PEAK 32(17Q21.31) WILD-TYPE	127	157	111

Figure S359. Get High-res Image Gene #60: 'del_17q21.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_17q21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00037

Table S360. Gene #60: 'del_17q21.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 32(17Q21.31) MUTATED	33	26	37
DEL PEAK 32(17Q21.31) WILD-TYPE	138	179	78

Figure S360. Get High-res Image Gene #60: 'del_17q21.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S361. Gene #61: 'del_18q21.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 33(18Q21.31) MUTATED	45	72	14
DEL PEAK 33(18Q21.31) WILD-TYPE	228	62	71

Figure S361. Get High-res Image Gene #61: 'del_18q21.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q21.31' versus 'METHLYATION_CNMF'

P value = 0.00195 (Fisher's exact test), Q value = 0.004

Table S362. Gene #61: 'del_18q21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 33(18Q21.31) MUTATED	27	54	50
DEL PEAK 33(18Q21.31) WILD-TYPE	133	111	117

Figure S362. Get High-res Image Gene #61: 'del_18q21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q21.31' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00045

Table S363. Gene #61: 'del_18q21.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 33(18Q21.31) MUTATED	21	53	57
DEL PEAK 33(18Q21.31) WILD-TYPE	125	118	117

Figure S363. Get High-res Image Gene #61: 'del_18q21.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_18q21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0118 (Fisher's exact test), Q value = 0.019

Table S364. Gene #61: 'del_18q21.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 33(18Q21.31) MUTATED	32	63	36
DEL PEAK 33(18Q21.31) WILD-TYPE	139	142	79

Figure S364. Get High-res Image Gene #61: 'del_18q21.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.31' versus 'MIRSEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00059

Table S365. Gene #61: 'del_18q21.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 33(18Q21.31) MUTATED	31	30	68
DEL PEAK 33(18Q21.31) WILD-TYPE	127	117	115

Figure S365. Get High-res Image Gene #61: 'del_18q21.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_18q21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0183 (Fisher's exact test), Q value = 0.028

Table S366. Gene #61: 'del_18q21.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 33(18Q21.31) MUTATED	29	20	20	45	15
DEL PEAK 33(18Q21.31) WILD-TYPE	118	78	39	83	41

Figure S366. Get High-res Image Gene #61: 'del_18q21.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00375 (Fisher's exact test), Q value = 0.0071

Table S367. Gene #61: 'del_18q21.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
DEL PEAK 33(18Q21.31) MUTATED	9	41	12	24
DEL PEAK 33(18Q21.31) WILD-TYPE	53	65	48	66

Figure S367. Get High-res Image Gene #61: 'del_18q21.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_18q21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S368. Gene #61: 'del_18q21.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 33(18Q21.31) MUTATED	9	4	21	33	5	14
DEL PEAK 33(18Q21.31) WILD-TYPE	61	37	19	49	20	46

Figure S368. Get High-res Image Gene #61: 'del_18q21.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S369. Gene #62: 'del_18q23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 34(18Q23) MUTATED	48	77	12
DEL PEAK 34(18Q23) WILD-TYPE	225	57	73

Figure S369. Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q23' versus 'METHLYATION_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.018

Table S370. Gene #62: 'del_18q23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 34(18Q23) MUTATED	31	50	56
DEL PEAK 34(18Q23) WILD-TYPE	129	115	111

Figure S370. Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q23' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00024

Table S371. Gene #62: 'del_18q23' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 34(18Q23) MUTATED	23	49	65
DEL PEAK 34(18Q23) WILD-TYPE	123	122	109

Figure S371. Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_18q23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0437 (Fisher's exact test), Q value = 0.059

Table S372. Gene #62: 'del_18q23' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 34(18Q23) MUTATED	37	60	40
DEL PEAK 34(18Q23) WILD-TYPE	134	145	75

Figure S372. Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.018

Table S373. Gene #62: 'del_18q23' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 34(18Q23) MUTATED	35	35	65
DEL PEAK 34(18Q23) WILD-TYPE	123	112	118

Figure S373. Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_18q23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00754 (Fisher's exact test), Q value = 0.013

Table S374. Gene #62: 'del_18q23' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 34(18Q23) MUTATED	29	21	22	46	17
DEL PEAK 34(18Q23) WILD-TYPE	118	77	37	82	39

Figure S374. Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00848 (Fisher's exact test), Q value = 0.014

Table S375. Gene #62: 'del_18q23' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
DEL PEAK 34(18Q23) MUTATED	11	40	11	29
DEL PEAK 34(18Q23) WILD-TYPE	51	66	49	61

Figure S375. Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_18q23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S376. Gene #62: 'del_18q23' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 34(18Q23) MUTATED	11	3	21	32	6	18
DEL PEAK 34(18Q23) WILD-TYPE	59	38	19	50	19	42

Figure S376. Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S377. Gene #63: 'del_19q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 35(19Q13.2) MUTATED	14	32	6
DEL PEAK 35(19Q13.2) WILD-TYPE	259	102	79

Figure S377. Get High-res Image Gene #63: 'del_19q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.2' versus 'METHLYATION_CNMF'

P value = 0.00115 (Fisher's exact test), Q value = 0.0025

Table S378. Gene #63: 'del_19q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 35(19Q13.2) MUTATED	6	24	22
DEL PEAK 35(19Q13.2) WILD-TYPE	154	141	145

Figure S378. Get High-res Image Gene #63: 'del_19q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19q13.2' versus 'MRNASEQ_CNMF'

P value = 0.00533 (Fisher's exact test), Q value = 0.0096

Table S379. Gene #63: 'del_19q13.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 35(19Q13.2) MUTATED	6	22	24
DEL PEAK 35(19Q13.2) WILD-TYPE	140	149	150

Figure S379. Get High-res Image Gene #63: 'del_19q13.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_19q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0481 (Fisher's exact test), Q value = 0.063

Table S380. Gene #63: 'del_19q13.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 35(19Q13.2) MUTATED	11	29	12
DEL PEAK 35(19Q13.2) WILD-TYPE	160	176	103

Figure S380. Get High-res Image Gene #63: 'del_19q13.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.2' versus 'MIRSEQ_CNMF'

P value = 0.00261 (Fisher's exact test), Q value = 0.0051

Table S381. Gene #63: 'del_19q13.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 35(19Q13.2) MUTATED	12	8	30
DEL PEAK 35(19Q13.2) WILD-TYPE	146	139	153

Figure S381. Get High-res Image Gene #63: 'del_19q13.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_19q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.0019

Table S382. Gene #63: 'del_19q13.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 35(19Q13.2) MUTATED	6	7	13	19	5
DEL PEAK 35(19Q13.2) WILD-TYPE	141	91	46	109	51

Figure S382. Get High-res Image Gene #63: 'del_19q13.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00279 (Fisher's exact test), Q value = 0.0054

Table S383. Gene #63: 'del_19q13.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
DEL PEAK 35(19Q13.2) MUTATED	2	20	2	9
DEL PEAK 35(19Q13.2) WILD-TYPE	60	86	58	81

Figure S383. Get High-res Image Gene #63: 'del_19q13.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_19q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00113 (Fisher's exact test), Q value = 0.0025

Table S384. Gene #63: 'del_19q13.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 35(19Q13.2) MUTATED	1	2	5	18	2	5
DEL PEAK 35(19Q13.2) WILD-TYPE	69	39	35	64	23	55

Figure S384. Get High-res Image Gene #63: 'del_19q13.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q22.2' versus 'CN_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0012

Table S385. Gene #64: 'del_21q22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 36(21Q22.2) MUTATED	29	22	1
DEL PEAK 36(21Q22.2) WILD-TYPE	244	112	84

Figure S385. Get High-res Image Gene #64: 'del_21q22.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q22.2' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00037

Table S386. Gene #64: 'del_21q22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 36(21Q22.2) MUTATED	11	9	32
DEL PEAK 36(21Q22.2) WILD-TYPE	149	156	135

Figure S386. Get High-res Image Gene #64: 'del_21q22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q22.2' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00013

Table S387. Gene #64: 'del_21q22.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 36(21Q22.2) MUTATED	11	7	34
DEL PEAK 36(21Q22.2) WILD-TYPE	135	164	140

Figure S387. Get High-res Image Gene #64: 'del_21q22.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_21q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00049

Table S388. Gene #64: 'del_21q22.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 36(21Q22.2) MUTATED	12	15	25
DEL PEAK 36(21Q22.2) WILD-TYPE	159	190	90

Figure S388. Get High-res Image Gene #64: 'del_21q22.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_21q22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.04 (Fisher's exact test), Q value = 0.054

Table S389. Gene #64: 'del_21q22.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 36(21Q22.2) MUTATED	11	7	13	15	5
DEL PEAK 36(21Q22.2) WILD-TYPE	136	91	46	113	51

Figure S389. Get High-res Image Gene #64: 'del_21q22.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_21q22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00286 (Fisher's exact test), Q value = 0.0055

Table S390. Gene #64: 'del_21q22.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 36(21Q22.2) MUTATED	4	2	13	9	3	6
DEL PEAK 36(21Q22.2) WILD-TYPE	66	39	27	73	22	54

Figure S390. Get High-res Image Gene #64: 'del_21q22.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S391. Gene #65: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 37(21Q22.3) MUTATED	95	49	3
DEL PEAK 37(21Q22.3) WILD-TYPE	178	85	82

Figure S391. Get High-res Image Gene #65: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S392. Gene #65: 'del_21q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	165	167
DEL PEAK 37(21Q22.3) MUTATED	30	13	104
DEL PEAK 37(21Q22.3) WILD-TYPE	130	152	63

Figure S392. Get High-res Image Gene #65: 'del_21q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S393. Gene #65: 'del_21q22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	171	174
DEL PEAK 37(21Q22.3) MUTATED	26	12	109
DEL PEAK 37(21Q22.3) WILD-TYPE	120	159	65

Figure S393. Get High-res Image Gene #65: 'del_21q22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_21q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S394. Gene #65: 'del_21q22.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 37(21Q22.3) MUTATED	43	21	83
DEL PEAK 37(21Q22.3) WILD-TYPE	128	184	32

Figure S394. Get High-res Image Gene #65: 'del_21q22.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_21q22.3' versus 'MIRSEQ_CNMF'

P value = 0.0323 (Fisher's exact test), Q value = 0.045

Table S395. Gene #65: 'del_21q22.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 37(21Q22.3) MUTATED	50	32	63
DEL PEAK 37(21Q22.3) WILD-TYPE	108	115	120

Figure S395. Get High-res Image Gene #65: 'del_21q22.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_21q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S396. Gene #65: 'del_21q22.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 37(21Q22.3) MUTATED	44	15	33	39	14
DEL PEAK 37(21Q22.3) WILD-TYPE	103	83	26	89	42

Figure S396. Get High-res Image Gene #65: 'del_21q22.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_21q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.1e-05

Table S397. Gene #65: 'del_21q22.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 37(21Q22.3) MUTATED	17	3	26	19	13	19
DEL PEAK 37(21Q22.3) WILD-TYPE	53	38	14	63	12	41

Figure S397. Get High-res Image Gene #65: 'del_21q22.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PRAD-TP/15098590/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PRAD-TP/15115159/PRAD-TP.transferedmergedcluster.txt
Number of patients = 492
Number of significantly focal cnvs = 65
Number of molecular subtypes = 8
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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