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

Stomach Adenocarcinoma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C12Z14BV

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 81 focal events and 10 molecular subtypes across 369 patients, 333 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p36.22 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
amp_1q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1q42.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3q26.2 cnv correlated to 'CN_CNMF'.
amp_5p15.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6p21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6q21 cnv correlated to 'CN_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7p22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7p11.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
amp_7q21.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
amp_8p23.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_9p24.1 cnv correlated to 'CN_CNMF'.
amp_9q34.3 cnv correlated to 'CN_CNMF'.
amp_10p11.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_10q22.2 cnv correlated to 'CN_CNMF'.
amp_10q26.13 cnv correlated to 'CN_CNMF'.
amp_11p13 cnv correlated to 'MIRSEQ_CHIERARCHICAL'.
amp_11q13.3 cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_12p12.1 cnv correlated to 'CN_CNMF'.
amp_12q15 cnv correlated to 'CN_CNMF'.
amp_13q12.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_13q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_15q26.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_17q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_18q11.2 cnv correlated to 'CN_CNMF'.
amp_19p13.2 cnv correlated to 'CN_CNMF'.
amp_19q12 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_xq27.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_1p36.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p13.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_2q37.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_3p26.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3q26.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_4p16.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q23.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6p25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q14.1 cnv correlated to 'CN_CNMF'.
del_6q26 cnv correlated to 'CN_CNMF'.
del_7q31.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_7q36.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p23.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9q21.11 cnv correlated to 'CN_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10p15.3 cnv correlated to 'CN_CNMF'.
del_10q22.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p15.4 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_11q23.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_12p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q12.11 cnv correlated to 'CN_CNMF'.
del_14q23.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q32.33 cnv correlated to 'CN_CNMF'.
del_15q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q15.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16p13.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q23.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
del_17p12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17q24.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_18q21.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_19p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19q13.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_21q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_21q22.13 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_22q13.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp21.1 cnv correlated to 'CN_CNMF'.
del_xq21.33 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 81 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 333 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
amp 1q21 3	135 (37%)	234	1e-05 (0.0081)	1e-05 (0.0081)	0.033 (1.00)	0.027 (1.00)	1e-05 (0.0081)	1e-05 (0.0081)	1e-05 (0.0081)	1e-05 (0.0081)	1e-05 (0.0081)	1e-05 (0.0081)
amp 5p15 33	104 (28%)	265	1e-05 (0.0081)	1e-05 (0.0081)	0.126 (1.00)	0.985 (1.00)	1e-05 (0.0081)	5e-05 (0.0288)	1e-05 (0.0081)	2e-05 (0.0124)	0.0001 (0.055)	1e-05 (0.0081)
amp 13q22 1	149 (40%)	220	1e-05 (0.0081)	1e-05 (0.0081)	0.2 (1.00)	0.679 (1.00)	2e-05 (0.0124)	1e-05 (0.0081)	0.00044 (0.215)	2e-05 (0.0124)	1e-05 (0.0081)	1e-05 (0.0081)
del 3p14 2	131 (36%)	238	1e-05 (0.0081)	1e-05 (0.0081)	0.409 (1.00)	0.371 (1.00)	8e-05 (0.0446)	0.00019 (0.101)	1e-05 (0.0081)	1e-05 (0.0081)	0.00042 (0.207)	1e-05 (0.0081)
del 4p16 3	142 (38%)	227	1e-05 (0.0081)	0.00052 (0.249)	0.46 (1.00)	0.201 (1.00)	3e-05 (0.0179)	5e-05 (0.0288)	0.00046 (0.224)	1e-05 (0.0081)	0.00015 (0.0811)	1e-05 (0.0081)
del 4q34 3	163 (44%)	206	1e-05 (0.0081)	1e-05 (0.0081)	0.0519 (1.00)	0.00887 (1.00)	1e-05 (0.0081)	2e-05 (0.0124)	4e-05 (0.0234)	1e-05 (0.0081)	2e-05 (0.0124)	2e-05 (0.0124)
del 5q11 2	134 (36%)	235	1e-05 (0.0081)	1e-05 (0.0081)	0.24 (1.00)	0.224 (1.00)	1e-05 (0.0081)	1e-05 (0.0081)	1e-05 (0.0081)	1e-05 (0.0081)	1e-05 (0.0081)	1e-05 (0.0081)
del 5q23 2	122 (33%)	247	1e-05 (0.0081)	1e-05 (0.0081)	0.123 (1.00)	0.109 (1.00)	1e-05 (0.0081)	1e-05 (0.0081)	1e-05 (0.0081)	1e-05 (0.0081)	1e-05 (0.0081)	1e-05 (0.0081)
del 10q23 31	90 (24%)	279	1e-05 (0.0081)	0.00015 (0.0811)	0.0634 (1.00)	0.00019 (0.101)	1e-05 (0.0081)	1e-05 (0.0081)	0.00013 (0.0706)	6e-05 (0.0341)	0.00115 (0.509)	1e-05 (0.0081)
del 15q11 2	101 (27%)	268	1e-05 (0.0081)	3e-05 (0.0179)	0.00177 (0.74)	0.267 (1.00)	1e-05 (0.0081)	2e-05 (0.0124)	0.00024 (0.125)	2e-05 (0.0124)	1e-05 (0.0081)	1e-05 (0.0081)
del 17p12	141 (38%)	228	1e-05 (0.0081)	1e-05 (0.0081)	0.401 (1.00)	0.00824 (1.00)	1e-05 (0.0081)	1e-05 (0.0081)	4e-05 (0.0234)	1e-05 (0.0081)	1e-05 (0.0081)	1e-05 (0.0081)
del 19p13 3	127 (34%)	242	1e-05 (0.0081)	1e-05 (0.0081)	0.00364 (1.00)	0.00495 (1.00)	1e-05 (0.0081)	1e-05 (0.0081)	1e-05 (0.0081)	1e-05 (0.0081)	1e-05 (0.0081)	1e-05 (0.0081)
amp 1q42 3	122 (33%)	247	1e-05 (0.0081)	1e-05 (0.0081)	0.402 (1.00)	0.0965 (1.00)	1e-05 (0.0081)	9e-05 (0.0498)	1e-05 (0.0081)	1e-05 (0.0081)	0.00446 (1.00)	1e-05 (0.0081)
amp 5p13 1	103 (28%)	266	1e-05 (0.0081)	1e-05 (0.0081)	0.74 (1.00)	0.86 (1.00)	1e-05 (0.0081)	0.0005 (0.241)	0.00018 (0.0965)	0.00011 (0.0604)	0.00117 (0.516)	1e-05 (0.0081)
amp 19q12	111 (30%)	258	1e-05 (0.0081)	1e-05 (0.0081)	0.00618 (1.00)	0.115 (1.00)	1e-05 (0.0081)	1e-05 (0.0081)	2e-05 (0.0124)	1e-05 (0.0081)	0.00374 (1.00)	1e-05 (0.0081)
amp 20q13 2	243 (66%)	126	1e-05 (0.0081)	1e-05 (0.0081)	0.00637 (1.00)	0.0119 (1.00)	1e-05 (0.0081)	1e-05 (0.0081)	2e-05 (0.0124)	1e-05 (0.0081)	0.00378 (1.00)	1e-05 (0.0081)
del 3p26 1	115 (31%)	254	1e-05 (0.0081)	2e-05 (0.0124)	0.343 (1.00)	0.194 (1.00)	0.00663 (1.00)	5e-05 (0.0288)	9e-05 (0.0498)	4e-05 (0.0234)	0.00043 (0.212)	1e-05 (0.0081)
del 7q36 3	78 (21%)	291	1e-05 (0.0081)	2e-05 (0.0124)	0.38 (1.00)	0.0792 (1.00)	2e-05 (0.0124)	0.00034 (0.17)	0.00021 (0.111)	1e-05 (0.0081)	0.00198 (0.816)	2e-05 (0.0124)
del 8p23 3	102 (28%)	267	1e-05 (0.0081)	1e-05 (0.0081)	0.0756 (1.00)	0.594 (1.00)	1e-05 (0.0081)	1e-05 (0.0081)	0.00111 (0.497)	1e-05 (0.0081)	6e-05 (0.0341)	1e-05 (0.0081)
del 9p21 3	153 (41%)	216	1e-05 (0.0081)	1e-05 (0.0081)	7e-05 (0.0393)	1e-05 (0.0081)	1e-05 (0.0081)	1e-05 (0.0081)	0.00498 (1.00)	0.00075 (0.347)	0.00676 (1.00)	4e-05 (0.0234)
del 15q15 1	103 (28%)	266	1e-05 (0.0081)	1e-05 (0.0081)	0.00356 (1.00)	0.294 (1.00)	1e-05 (0.0081)	2e-05 (0.0124)	0.00117 (0.516)	1e-05 (0.0081)	1e-05 (0.0081)	1e-05 (0.0081)
del 16p13 3	75 (20%)	294	1e-05 (0.0081)	0.00057 (0.27)	0.7 (1.00)	0.817 (1.00)	1e-05 (0.0081)	1e-05 (0.0081)	1e-05 (0.0081)	5e-05 (0.0288)	1e-05 (0.0081)	1e-05 (0.0081)
del 19q13 11	57 (15%)	312	1e-05 (0.0081)	1e-05 (0.0081)	0.0634 (1.00)	0.711 (1.00)	2e-05 (0.0124)	0.00055 (0.262)	0.00024 (0.125)	1e-05 (0.0081)	0.00027 (0.139)	6e-05 (0.0341)
amp 6p21 1	99 (27%)	270	1e-05 (0.0081)	1e-05 (0.0081)	0.348 (1.00)	0.165 (1.00)	0.00065 (0.304)	0.00077 (0.356)	0.00033 (0.167)	0.00029 (0.148)	0.00034 (0.17)	2e-05 (0.0124)
amp 6q12	73 (20%)	296	1e-05 (0.0081)	1e-05 (0.0081)	0.0669 (1.00)	0.883 (1.00)	7e-05 (0.0393)	0.00037 (0.184)	0.00104 (0.468)	0.00032 (0.163)	0.00062 (0.291)	3e-05 (0.0179)
amp 7p22 1	189 (51%)	180	1e-05 (0.0081)	5e-05 (0.0288)	0.636 (1.00)	0.864 (1.00)	0.00021 (0.111)	3e-05 (0.0179)	0.00213 (0.861)	0.00051 (0.245)	0.00172 (0.724)	1e-05 (0.0081)
amp 8q24 21	256 (69%)	113	1e-05 (0.0081)	0.00033 (0.167)	0.385 (1.00)	0.382 (1.00)	0.0058 (1.00)	0.0108 (1.00)	8e-05 (0.0446)	0.00029 (0.148)	1e-05 (0.0081)	1e-05 (0.0081)
amp 13q12 3	144 (39%)	225	1e-05 (0.0081)	1e-05 (0.0081)	0.33 (1.00)	0.153 (1.00)	0.0165 (1.00)	3e-05 (0.0179)	0.00033 (0.167)	0.00461 (1.00)	0.0004 (0.198)	0.00027 (0.139)
amp 17q12	116 (31%)	253	1e-05 (0.0081)	1e-05 (0.0081)	0.795 (1.00)	0.0398 (1.00)	0.00021 (0.111)	0.00019 (0.101)	4e-05 (0.0234)	0.00021 (0.111)	0.0018 (0.747)	0.00092 (0.42)
del 1p36 11	104 (28%)	265	1e-05 (0.0081)	1e-05 (0.0081)	0.156 (1.00)	0.00095 (0.43)	0.00033 (0.167)	1e-05 (0.0081)	0.00962 (1.00)	0.00011 (0.0604)	0.00218 (0.876)	1e-05 (0.0081)
del 6p25 3	93 (25%)	276	1e-05 (0.0081)	0.0002 (0.106)	0.138 (1.00)	0.821 (1.00)	0.00011 (0.0604)	6e-05 (0.0341)	0.00069 (0.322)	2e-05 (0.0124)	0.00729 (1.00)	0.00043 (0.212)
del 14q23 3	108 (29%)	261	1e-05 (0.0081)	1e-05 (0.0081)	0.752 (1.00)	0.43 (1.00)	4e-05 (0.0234)	0.00043 (0.212)	0.00129 (0.557)	3e-05 (0.0179)	0.00074 (0.344)	0.00012 (0.0654)
del 12p13 1	57 (15%)	312	1e-05 (0.0081)	1e-05 (0.0081)	0.541 (1.00)	0.419 (1.00)	3e-05 (0.0179)	3e-05 (0.0179)	0.0187 (1.00)	0.012 (1.00)	0.0114 (1.00)	5e-05 (0.0288)
del 21q11 2	140 (38%)	229	1e-05 (0.0081)	0.00027 (0.139)	0.342 (1.00)	0.202 (1.00)	0.0024 (0.953)	0.00445 (1.00)	6e-05 (0.0341)	0.0113 (1.00)	4e-05 (0.0234)	0.00032 (0.163)
del 22q13 31	129 (35%)	240	1e-05 (0.0081)	1e-05 (0.0081)	0.0486 (1.00)	0.00646 (1.00)	0.0013 (0.56)	0.00435 (1.00)	3e-05 (0.0179)	1e-05 (0.0081)	0.00086 (0.395)	1e-05 (0.0081)
del xp22 2	67 (18%)	302	1e-05 (0.0081)	2e-05 (0.0124)	0.367 (1.00)	0.059 (1.00)	0.00019 (0.101)	0.00024 (0.125)	0.091 (1.00)	0.00298 (1.00)	0.215 (1.00)	0.00016 (0.0862)
amp 10p11 22	98 (27%)	271	1e-05 (0.0081)	1e-05 (0.0081)	0.147 (1.00)	0.523 (1.00)	0.00112 (0.5)	0.00927 (1.00)	0.00343 (1.00)	0.00013 (0.0706)	0.00184 (0.762)	9e-05 (0.0498)
amp 15q26 1	88 (24%)	281	1e-05 (0.0081)	0.00024 (0.125)	0.464 (1.00)	0.288 (1.00)	1e-05 (0.0081)	2e-05 (0.0124)	0.00797 (1.00)	0.00953 (1.00)	0.00577 (1.00)	0.00305 (1.00)
del 3q26 31	46 (12%)	323	1e-05 (0.0081)	1e-05 (0.0081)	0.134 (1.00)	0.373 (1.00)	0.00043 (0.212)	0.00046 (0.224)	0.00123 (0.536)	0.00056 (0.265)	0.00178 (0.742)	0.00282 (1.00)
del 4q22 1	160 (43%)	209	1e-05 (0.0081)	6e-05 (0.0341)	0.108 (1.00)	0.268 (1.00)	0.00253 (0.999)	3e-05 (0.0179)	0.0291 (1.00)	0.00203 (0.832)	0.0304 (1.00)	0.00047 (0.227)
del 10q22 3	61 (17%)	308	1e-05 (0.0081)	0.0136 (1.00)	0.749 (1.00)	0.0577 (1.00)	0.00018 (0.0965)	0.00035 (0.174)	0.00584 (1.00)	0.00532 (1.00)	0.00332 (1.00)	0.00022 (0.115)
del 11p15 4	79 (21%)	290	1e-05 (0.0081)	1e-05 (0.0081)	2e-05 (0.0124)	0.0008 (0.368)	0.00145 (0.621)	0.0127 (1.00)	0.00108 (0.485)	8e-05 (0.0446)	0.038 (1.00)	0.00118 (0.517)
del 18q21 2	169 (46%)	200	1e-05 (0.0081)	0.00046 (0.224)	0.667 (1.00)	0.452 (1.00)	0.00031 (0.158)	0.0041 (1.00)	0.00115 (0.509)	0.00278 (1.00)	0.0002 (0.106)	0.00374 (1.00)
del 21q22 13	152 (41%)	217	1e-05 (0.0081)	0.0224 (1.00)	0.102 (1.00)	0.24 (1.00)	0.00203 (0.832)	0.00037 (0.184)	0.00023 (0.12)	0.00088 (0.403)	4e-05 (0.0234)	0.00074 (0.344)
amp 6q21	68 (18%)	301	1e-05 (0.0081)	0.00055 (0.262)	0.383 (1.00)	0.406 (1.00)	0.00143 (0.613)	0.00151 (0.645)	0.00125 (0.542)	0.00051 (0.245)	0.00225 (0.9)	1e-05 (0.0081)
amp 11q13 3	90 (24%)	279	1e-05 (0.0081)	0.0181 (1.00)	0.19 (1.00)	0.639 (1.00)	0.127 (1.00)	0.037 (1.00)	0.00032 (0.163)	0.00619 (1.00)	0.00017 (0.0915)	0.00172 (0.724)
del 2q37 2	54 (15%)	315	1e-05 (0.0081)	5e-05 (0.0288)	0.273 (1.00)	0.345 (1.00)	0.00333 (1.00)	0.214 (1.00)	0.0225 (1.00)	1e-05 (0.0081)	0.08 (1.00)	0.00167 (0.706)
del 9p23	156 (42%)	213	1e-05 (0.0081)	2e-05 (0.0124)	0.0291 (1.00)	0.00113 (0.502)	1e-05 (0.0081)	0.00176 (0.737)	0.00159 (0.676)	0.00356 (1.00)	0.0354 (1.00)	0.00092 (0.42)
del 9q21 11	93 (25%)	276	1e-05 (0.0081)	0.00346 (1.00)	0.139 (1.00)	0.0565 (1.00)	0.00155 (0.66)	0.0354 (1.00)	0.00478 (1.00)	0.00049 (0.237)	0.00171 (0.722)	0.00024 (0.125)
del 17q24 3	68 (18%)	301	1e-05 (0.0081)	0.00011 (0.0604)	0.19 (1.00)	0.22 (1.00)	0.00161 (0.683)	0.00235 (0.935)	0.0697 (1.00)	0.00041 (0.203)	0.00363 (1.00)	0.00135 (0.58)
amp 1p36 22	52 (14%)	317	1e-05 (0.0081)	0.0229 (1.00)	0.518 (1.00)	0.242 (1.00)	0.00021 (0.111)	0.119 (1.00)	0.11 (1.00)	0.0425 (1.00)	0.119 (1.00)	0.0301 (1.00)
amp 7p11 2	172 (47%)	197	1e-05 (0.0081)	0.00117 (0.516)	0.906 (1.00)	0.851 (1.00)	0.0437 (1.00)	0.00051 (0.245)	0.00949 (1.00)	0.0408 (1.00)	0.00199 (0.818)	0.00123 (0.536)
amp 7q21 2	168 (46%)	201	1e-05 (0.0081)	0.00063 (0.295)	0.199 (1.00)	0.671 (1.00)	0.516 (1.00)	7e-05 (0.0393)	0.0219 (1.00)	0.0581 (1.00)	0.0493 (1.00)	0.00255 (1.00)
amp 8p23 1	146 (40%)	223	6e-05 (0.0341)	8e-05 (0.0446)	0.591 (1.00)	0.602 (1.00)	0.0548 (1.00)	0.0178 (1.00)	0.364 (1.00)	0.344 (1.00)	0.0371 (1.00)	0.055 (1.00)
amp xq27 3	67 (18%)	302	7e-05 (0.0393)	0.00324 (1.00)	0.598 (1.00)	0.963 (1.00)	0.187 (1.00)	1e-05 (0.0081)	0.0297 (1.00)	0.969 (1.00)	0.0544 (1.00)	0.0723 (1.00)
del 1p13 2	75 (20%)	294	1e-05 (0.0081)	1e-05 (0.0081)	0.0806 (1.00)	0.0636 (1.00)	0.00122 (0.533)	0.00091 (0.416)	0.182 (1.00)	0.017 (1.00)	0.0194 (1.00)	0.00317 (1.00)
del 7q31 1	54 (15%)	315	1e-05 (0.0081)	4e-05 (0.0234)	0.715 (1.00)	0.498 (1.00)	0.00852 (1.00)	0.277 (1.00)	0.0196 (1.00)	0.00707 (1.00)	0.00376 (1.00)	0.00427 (1.00)
del 11q23 2	82 (22%)	287	1e-05 (0.0081)	0.00818 (1.00)	0.701 (1.00)	0.153 (1.00)	0.00112 (0.5)	0.00012 (0.0654)	0.0914 (1.00)	0.204 (1.00)	0.0279 (1.00)	0.0426 (1.00)
del 16q23 1	146 (40%)	223	1e-05 (0.0081)	0.00272 (1.00)	0.47 (1.00)	0.17 (1.00)	0.00187 (0.772)	0.0091 (1.00)	0.00442 (1.00)	0.0185 (1.00)	5e-05 (0.0288)	0.00097 (0.438)
del xq21 33	46 (12%)	323	3e-05 (0.0179)	0.00021 (0.111)	0.815 (1.00)	0.0353 (1.00)	0.00817 (1.00)	0.0521 (1.00)	0.174 (1.00)	0.204 (1.00)	0.523 (1.00)	0.0924 (1.00)
amp 3q26 2	125 (34%)	244	1e-05 (0.0081)	0.00256 (1.00)	0.821 (1.00)	0.0112 (1.00)	0.448 (1.00)	0.0287 (1.00)	0.0141 (1.00)	0.0177 (1.00)	0.0195 (1.00)	0.00437 (1.00)
amp 9p24 1	57 (15%)	312	2e-05 (0.0124)	0.449 (1.00)	0.617 (1.00)	0.219 (1.00)	0.109 (1.00)	0.00557 (1.00)	0.0311 (1.00)	0.308 (1.00)	0.038 (1.00)	0.129 (1.00)
amp 9q34 3	98 (27%)	271	0.00025 (0.129)	0.179 (1.00)	0.712 (1.00)	0.56 (1.00)	0.0286 (1.00)	0.297 (1.00)	0.0287 (1.00)	0.429 (1.00)	0.167 (1.00)	0.094 (1.00)
amp 10q22 2	68 (18%)	301	1e-05 (0.0081)	0.0201 (1.00)	0.0269 (1.00)	0.252 (1.00)	0.0182 (1.00)	0.023 (1.00)	0.202 (1.00)	0.184 (1.00)	0.0976 (1.00)	0.0236 (1.00)
amp 10q26 13	72 (20%)	297	1e-05 (0.0081)	0.0022 (0.882)	0.0363 (1.00)	0.33 (1.00)	0.00556 (1.00)	0.0318 (1.00)	0.633 (1.00)	0.11 (1.00)	0.899 (1.00)	0.0827 (1.00)
amp 11p13	70 (19%)	299	0.00053 (0.253)	0.041 (1.00)	0.643 (1.00)	0.116 (1.00)	0.00057 (0.27)	0.0059 (1.00)	0.0596 (1.00)	0.00017 (0.0915)	0.0642 (1.00)	0.00456 (1.00)
amp 12p12 1	109 (30%)	260	1e-05 (0.0081)	0.0377 (1.00)	0.428 (1.00)	0.348 (1.00)	0.209 (1.00)	0.367 (1.00)	0.00308 (1.00)	0.23 (1.00)	0.00437 (1.00)	0.0511 (1.00)
amp 12q15	92 (25%)	277	1e-05 (0.0081)	0.361 (1.00)	0.22 (1.00)	0.329 (1.00)	0.276 (1.00)	0.0752 (1.00)	0.0895 (1.00)	0.389 (1.00)	0.254 (1.00)	0.716 (1.00)
amp 18q11 2	117 (32%)	252	1e-05 (0.0081)	0.00216 (0.87)	0.294 (1.00)	0.286 (1.00)	0.0152 (1.00)	0.00386 (1.00)	0.00126 (0.546)	0.00208 (0.847)	0.00093 (0.422)	0.0049 (1.00)
amp 19p13 2	41 (11%)	328	0.00033 (0.167)	0.119 (1.00)	0.905 (1.00)	0.757 (1.00)	0.733 (1.00)	0.16 (1.00)	0.977 (1.00)	0.976 (1.00)	0.875 (1.00)	0.744 (1.00)
del 6q14 1	72 (20%)	297	1e-05 (0.0081)	0.00111 (0.497)	0.214 (1.00)	0.844 (1.00)	0.00061 (0.287)	0.00505 (1.00)	0.123 (1.00)	0.0164 (1.00)	0.0722 (1.00)	0.0481 (1.00)
del 6q26	82 (22%)	287	1e-05 (0.0081)	0.00824 (1.00)	0.792 (1.00)	0.702 (1.00)	0.00078 (0.36)	0.00247 (0.978)	0.159 (1.00)	0.0116 (1.00)	0.0775 (1.00)	0.0064 (1.00)
del 10p15 3	62 (17%)	307	3e-05 (0.0179)	0.0188 (1.00)	0.304 (1.00)	0.417 (1.00)	0.06 (1.00)	0.102 (1.00)	0.0603 (1.00)	0.0376 (1.00)	0.00865 (1.00)	0.00664 (1.00)
del 13q12 11	52 (14%)	317	1e-05 (0.0081)	0.109 (1.00)	0.426 (1.00)	0.366 (1.00)	0.0658 (1.00)	0.0222 (1.00)	0.39 (1.00)	0.423 (1.00)	0.179 (1.00)	0.219 (1.00)
del 14q32 33	106 (29%)	263	1e-05 (0.0081)	0.0007 (0.326)	0.928 (1.00)	0.222 (1.00)	0.00209 (0.847)	0.00524 (1.00)	0.0216 (1.00)	0.0319 (1.00)	0.0292 (1.00)	0.0683 (1.00)
del xp21 1	64 (17%)	305	1e-05 (0.0081)	0.00338 (1.00)	0.0929 (1.00)	0.0225 (1.00)	0.0141 (1.00)	0.0254 (1.00)	0.197 (1.00)	0.336 (1.00)	0.217 (1.00)	0.0415 (1.00)
amp 9p13 3	71 (19%)	298	0.00274 (1.00)	0.483 (1.00)	0.267 (1.00)	0.316 (1.00)	0.00983 (1.00)	0.232 (1.00)	0.00732 (1.00)	0.434 (1.00)	0.00179 (0.745)	0.171 (1.00)
del 1q25 1	13 (4%)	356	0.0373 (1.00)	0.0944 (1.00)	0.168 (1.00)	0.895 (1.00)	0.444 (1.00)	0.415 (1.00)	0.207 (1.00)	0.71 (1.00)	0.188 (1.00)	0.0718 (1.00)
del 1q44	23 (6%)	346	0.00313 (1.00)	0.00103 (0.465)	0.309 (1.00)	0.373 (1.00)	0.739 (1.00)	0.337 (1.00)	0.0145 (1.00)	0.443 (1.00)	0.0106 (1.00)	0.155 (1.00)
del 2q32 1	53 (14%)	316	0.0089 (1.00)	0.0988 (1.00)	0.49 (1.00)	0.0826 (1.00)	0.0904 (1.00)	0.24 (1.00)	0.377 (1.00)	0.00206 (0.84)	0.153 (1.00)	0.147 (1.00)
del 20p12 1	31 (8%)	338	0.00208 (0.847)	0.00233 (0.93)	0.658 (1.00)	0.192 (1.00)	0.0154 (1.00)	0.0855 (1.00)	0.0292 (1.00)	0.112 (1.00)	0.0262 (1.00)	0.0663 (1.00)

'amp_1p36.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S1. Gene #1: 'amp_1p36.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 1(1P36.22) MUTATED	5	3	16	1	27
AMP PEAK 1(1P36.22) WILD-TYPE	164	30	50	9	64

Figure S1. Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1p36.22' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.11

Table S2. Gene #1: 'amp_1p36.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 1(1P36.22) MUTATED	2	2	6	6	16
AMP PEAK 1(1P36.22) WILD-TYPE	63	60	40	31	46

Figure S2. Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S3. Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 2(1Q21.3) MUTATED	15	13	31	8	68
AMP PEAK 2(1Q21.3) WILD-TYPE	154	20	35	2	23

Figure S3. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S4. Gene #2: 'amp_1q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
AMP PEAK 2(1Q21.3) MUTATED	35	61	22
AMP PEAK 2(1Q21.3) WILD-TYPE	85	31	87

Figure S4. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S5. Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 2(1Q21.3) MUTATED	12	10	16	13	47
AMP PEAK 2(1Q21.3) WILD-TYPE	53	52	30	24	15

Figure S5. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S6. Gene #2: 'amp_1q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 2(1Q21.3) MUTATED	12	3	7	26	22	27	1
AMP PEAK 2(1Q21.3) WILD-TYPE	26	18	42	36	19	13	20

Figure S6. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S7. Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
AMP PEAK 2(1Q21.3) MUTATED	34	22	78
AMP PEAK 2(1Q21.3) WILD-TYPE	85	86	63

Figure S7. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S8. Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
AMP PEAK 2(1Q21.3) MUTATED	52	21	61
AMP PEAK 2(1Q21.3) WILD-TYPE	127	62	45

Figure S8. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S9. Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
AMP PEAK 2(1Q21.3) MUTATED	17	78	22
AMP PEAK 2(1Q21.3) WILD-TYPE	60	66	78

Figure S9. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S10. Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
AMP PEAK 2(1Q21.3) MUTATED	58	9	50
AMP PEAK 2(1Q21.3) WILD-TYPE	119	53	32

Figure S10. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q42.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S11. Gene #3: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 3(1Q42.3) MUTATED	18	12	23	7	62
AMP PEAK 3(1Q42.3) WILD-TYPE	151	21	43	3	29

Figure S11. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q42.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S12. Gene #3: 'amp_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
AMP PEAK 3(1Q42.3) MUTATED	31	50	25
AMP PEAK 3(1Q42.3) WILD-TYPE	89	42	84

Figure S12. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q42.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S13. Gene #3: 'amp_1q42.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 3(1Q42.3) MUTATED	13	13	12	12	41
AMP PEAK 3(1Q42.3) WILD-TYPE	52	49	34	25	21

Figure S13. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q42.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.05

Table S14. Gene #3: 'amp_1q42.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 3(1Q42.3) MUTATED	12	3	10	20	20	24	2
AMP PEAK 3(1Q42.3) WILD-TYPE	26	18	39	42	21	16	19

Figure S14. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1q42.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S15. Gene #3: 'amp_1q42.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
AMP PEAK 3(1Q42.3) MUTATED	28	25	69
AMP PEAK 3(1Q42.3) WILD-TYPE	91	83	72

Figure S15. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q42.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S16. Gene #3: 'amp_1q42.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
AMP PEAK 3(1Q42.3) MUTATED	41	22	59
AMP PEAK 3(1Q42.3) WILD-TYPE	138	61	47

Figure S16. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1q42.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S17. Gene #3: 'amp_1q42.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
AMP PEAK 3(1Q42.3) MUTATED	49	13	45
AMP PEAK 3(1Q42.3) WILD-TYPE	128	49	37

Figure S17. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S18. Gene #4: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 4(3Q26.2) MUTATED	31	8	36	5	45
AMP PEAK 4(3Q26.2) WILD-TYPE	138	25	30	5	46

Figure S18. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S19. Gene #5: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 5(5P15.33) MUTATED	15	7	18	2	62
AMP PEAK 5(5P15.33) WILD-TYPE	154	26	48	8	29

Figure S19. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S20. Gene #5: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
AMP PEAK 5(5P15.33) MUTATED	19	50	22
AMP PEAK 5(5P15.33) WILD-TYPE	101	42	87

Figure S20. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S21. Gene #5: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 5(5P15.33) MUTATED	11	6	10	10	38
AMP PEAK 5(5P15.33) WILD-TYPE	54	56	36	27	24

Figure S21. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.029

Table S22. Gene #5: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 5(5P15.33) MUTATED	7	5	6	16	16	23	2
AMP PEAK 5(5P15.33) WILD-TYPE	31	16	43	46	25	17	19

Figure S22. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S23. Gene #5: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
AMP PEAK 5(5P15.33) MUTATED	29	16	58
AMP PEAK 5(5P15.33) WILD-TYPE	90	92	83

Figure S23. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S24. Gene #5: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
AMP PEAK 5(5P15.33) MUTATED	39	15	49
AMP PEAK 5(5P15.33) WILD-TYPE	140	68	57

Figure S24. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.055

Table S25. Gene #5: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
AMP PEAK 5(5P15.33) MUTATED	19	56	15
AMP PEAK 5(5P15.33) WILD-TYPE	58	88	85

Figure S25. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S26. Gene #5: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
AMP PEAK 5(5P15.33) MUTATED	42	5	43
AMP PEAK 5(5P15.33) WILD-TYPE	135	57	39

Figure S26. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S27. Gene #6: 'amp_5p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 6(5P13.1) MUTATED	15	7	17	2	62
AMP PEAK 6(5P13.1) WILD-TYPE	154	26	49	8	29

Figure S27. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S28. Gene #6: 'amp_5p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
AMP PEAK 6(5P13.1) MUTATED	22	45	21
AMP PEAK 6(5P13.1) WILD-TYPE	98	47	88

Figure S28. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S29. Gene #6: 'amp_5p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 6(5P13.1) MUTATED	11	8	10	9	37
AMP PEAK 6(5P13.1) WILD-TYPE	54	54	36	28	25

Figure S29. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.24

Table S30. Gene #6: 'amp_5p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 6(5P13.1) MUTATED	9	4	7	17	14	22	2
AMP PEAK 6(5P13.1) WILD-TYPE	29	17	42	45	27	18	19

Figure S30. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5p13.1' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.096

Table S31. Gene #6: 'amp_5p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
AMP PEAK 6(5P13.1) MUTATED	27	19	57
AMP PEAK 6(5P13.1) WILD-TYPE	92	89	84

Figure S31. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.06

Table S32. Gene #6: 'amp_5p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
AMP PEAK 6(5P13.1) MUTATED	39	17	47
AMP PEAK 6(5P13.1) WILD-TYPE	140	66	59

Figure S32. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S33. Gene #6: 'amp_5p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
AMP PEAK 6(5P13.1) MUTATED	40	7	41
AMP PEAK 6(5P13.1) WILD-TYPE	137	55	41

Figure S33. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6p21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S34. Gene #7: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 7(6P21.1) MUTATED	8	10	23	4	54
AMP PEAK 7(6P21.1) WILD-TYPE	161	23	43	6	37

Figure S34. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S35. Gene #7: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
AMP PEAK 7(6P21.1) MUTATED	23	48	12
AMP PEAK 7(6P21.1) WILD-TYPE	97	44	97

Figure S35. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p21.1' versus 'MIRSEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.17

Table S36. Gene #7: 'amp_6p21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
AMP PEAK 7(6P21.1) MUTATED	26	18	54
AMP PEAK 7(6P21.1) WILD-TYPE	93	90	87

Figure S36. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6p21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.15

Table S37. Gene #7: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
AMP PEAK 7(6P21.1) MUTATED	39	15	44
AMP PEAK 7(6P21.1) WILD-TYPE	140	68	62

Figure S37. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.17

Table S38. Gene #7: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
AMP PEAK 7(6P21.1) MUTATED	13	53	17
AMP PEAK 7(6P21.1) WILD-TYPE	64	91	83

Figure S38. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S39. Gene #7: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
AMP PEAK 7(6P21.1) MUTATED	40	7	36
AMP PEAK 7(6P21.1) WILD-TYPE	137	55	46

Figure S39. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S40. Gene #8: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 8(6Q12) MUTATED	8	7	14	3	41
AMP PEAK 8(6Q12) WILD-TYPE	161	26	52	7	50

Figure S40. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S41. Gene #8: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
AMP PEAK 8(6Q12) MUTATED	15	34	10
AMP PEAK 8(6Q12) WILD-TYPE	105	58	99

Figure S41. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q12' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.039

Table S42. Gene #8: 'amp_6q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 8(6Q12) MUTATED	6	7	9	6	26
AMP PEAK 8(6Q12) WILD-TYPE	59	55	37	31	36

Figure S42. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.18

Table S43. Gene #8: 'amp_6q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 8(6Q12) MUTATED	7	1	3	12	12	17	2
AMP PEAK 8(6Q12) WILD-TYPE	31	20	46	50	29	23	19

Figure S43. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.16

Table S44. Gene #8: 'amp_6q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
AMP PEAK 8(6Q12) MUTATED	26	11	35
AMP PEAK 8(6Q12) WILD-TYPE	153	72	71

Figure S44. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S45. Gene #8: 'amp_6q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
AMP PEAK 8(6Q12) MUTATED	25	4	29
AMP PEAK 8(6Q12) WILD-TYPE	152	58	53

Figure S45. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S46. Gene #9: 'amp_6q21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 9(6Q21) MUTATED	8	6	17	2	35
AMP PEAK 9(6Q21) WILD-TYPE	161	27	49	8	56

Figure S46. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.25

Table S47. Gene #9: 'amp_6q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
AMP PEAK 9(6Q21) MUTATED	27	8	32
AMP PEAK 9(6Q21) WILD-TYPE	152	75	74

Figure S47. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6q21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S48. Gene #9: 'amp_6q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
AMP PEAK 9(6Q21) MUTATED	23	3	28
AMP PEAK 9(6Q21) WILD-TYPE	154	59	54

Figure S48. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S49. Gene #10: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 10(7P22.1) MUTATED	47	32	39	5	66
AMP PEAK 10(7P22.1) WILD-TYPE	122	1	27	5	25

Figure S49. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p22.1' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.029

Table S50. Gene #10: 'amp_7p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
AMP PEAK 10(7P22.1) MUTATED	60	64	41
AMP PEAK 10(7P22.1) WILD-TYPE	60	28	68

Figure S50. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p22.1' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.11

Table S51. Gene #10: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 10(7P22.1) MUTATED	29	25	16	20	46
AMP PEAK 10(7P22.1) WILD-TYPE	36	37	30	17	16

Figure S51. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S52. Gene #10: 'amp_7p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 10(7P22.1) MUTATED	17	11	15	31	30	28	4
AMP PEAK 10(7P22.1) WILD-TYPE	21	10	34	31	11	12	17

Figure S52. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7p22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.25

Table S53. Gene #10: 'amp_7p22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
AMP PEAK 10(7P22.1) MUTATED	82	35	71
AMP PEAK 10(7P22.1) WILD-TYPE	97	48	35

Figure S53. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7p22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S54. Gene #10: 'amp_7p22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
AMP PEAK 10(7P22.1) MUTATED	87	18	59
AMP PEAK 10(7P22.1) WILD-TYPE	90	44	23

Figure S54. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S55. Gene #11: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 11(7P11.2) MUTATED	46	31	38	6	51
AMP PEAK 11(7P11.2) WILD-TYPE	123	2	28	4	40

Figure S55. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.25

Table S56. Gene #11: 'amp_7p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 11(7P11.2) MUTATED	15	11	15	29	28	22	3
AMP PEAK 11(7P11.2) WILD-TYPE	23	10	34	33	13	18	18

Figure S56. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S57. Gene #12: 'amp_7q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 12(7Q21.2) MUTATED	47	30	41	7	43
AMP PEAK 12(7Q21.2) WILD-TYPE	122	3	25	3	48

Figure S57. Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.039

Table S58. Gene #12: 'amp_7q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 12(7Q21.2) MUTATED	15	13	14	26	30	19	3
AMP PEAK 12(7Q21.2) WILD-TYPE	23	8	35	36	11	21	18

Figure S58. Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8p23.1' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.034

Table S59. Gene #13: 'amp_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 13(8P23.1) MUTATED	75	13	22	10	26
AMP PEAK 13(8P23.1) WILD-TYPE	94	20	44	0	65

Figure S59. Get High-res Image Gene #13: 'amp_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p23.1' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.045

Table S60. Gene #13: 'amp_8p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
AMP PEAK 13(8P23.1) MUTATED	64	27	32
AMP PEAK 13(8P23.1) WILD-TYPE	56	65	77

Figure S60. Get High-res Image Gene #13: 'amp_8p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S61. Gene #14: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 14(8Q24.21) MUTATED	96	28	41	10	81
AMP PEAK 14(8Q24.21) WILD-TYPE	73	5	25	0	10

Figure S61. Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.17

Table S62. Gene #14: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
AMP PEAK 14(8Q24.21) MUTATED	87	73	59
AMP PEAK 14(8Q24.21) WILD-TYPE	33	19	50

Figure S62. Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.045

Table S63. Gene #14: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
AMP PEAK 14(8Q24.21) MUTATED	80	60	115
AMP PEAK 14(8Q24.21) WILD-TYPE	39	48	26

Figure S63. Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.15

Table S64. Gene #14: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
AMP PEAK 14(8Q24.21) MUTATED	117	49	89
AMP PEAK 14(8Q24.21) WILD-TYPE	62	34	17

Figure S64. Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S65. Gene #14: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
AMP PEAK 14(8Q24.21) MUTATED	46	121	52
AMP PEAK 14(8Q24.21) WILD-TYPE	31	23	48

Figure S65. Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S66. Gene #14: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
AMP PEAK 14(8Q24.21) MUTATED	122	28	69
AMP PEAK 14(8Q24.21) WILD-TYPE	55	34	13

Figure S66. Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9p24.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S67. Gene #15: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 15(9P24.1) MUTATED	26	1	1	2	27
AMP PEAK 15(9P24.1) WILD-TYPE	143	32	65	8	64

Figure S67. Get High-res Image Gene #15: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9q34.3' versus 'CN_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.13

Table S68. Gene #17: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 17(9Q34.3) MUTATED	28	11	19	2	38
AMP PEAK 17(9Q34.3) WILD-TYPE	141	22	47	8	53

Figure S68. Get High-res Image Gene #17: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10p11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S69. Gene #18: 'amp_10p11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 18(10P11.22) MUTATED	13	8	34	1	42
AMP PEAK 18(10P11.22) WILD-TYPE	156	25	32	9	49

Figure S69. Get High-res Image Gene #18: 'amp_10p11.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10p11.22' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S70. Gene #18: 'amp_10p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
AMP PEAK 18(10P11.22) MUTATED	24	43	19
AMP PEAK 18(10P11.22) WILD-TYPE	96	49	90

Figure S70. Get High-res Image Gene #18: 'amp_10p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_10p11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.071

Table S71. Gene #18: 'amp_10p11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
AMP PEAK 18(10P11.22) MUTATED	34	19	44
AMP PEAK 18(10P11.22) WILD-TYPE	145	64	62

Figure S71. Get High-res Image Gene #18: 'amp_10p11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_10p11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.05

Table S72. Gene #18: 'amp_10p11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
AMP PEAK 18(10P11.22) MUTATED	41	8	36
AMP PEAK 18(10P11.22) WILD-TYPE	136	54	46

Figure S72. Get High-res Image Gene #18: 'amp_10p11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10q22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S73. Gene #19: 'amp_10q22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 19(10Q22.2) MUTATED	11	3	31	2	21
AMP PEAK 19(10Q22.2) WILD-TYPE	158	30	35	8	70

Figure S73. Get High-res Image Gene #19: 'amp_10q22.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10q26.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S74. Gene #20: 'amp_10q26.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 20(10Q26.13) MUTATED	15	7	24	0	26
AMP PEAK 20(10Q26.13) WILD-TYPE	154	26	42	10	65

Figure S74. Get High-res Image Gene #20: 'amp_10q26.13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.091

Table S75. Gene #21: 'amp_11p13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
AMP PEAK 21(11P13) MUTATED	21	14	34
AMP PEAK 21(11P13) WILD-TYPE	158	69	72

Figure S75. Get High-res Image Gene #21: 'amp_11p13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S76. Gene #22: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 22(11Q13.3) MUTATED	16	5	34	4	31
AMP PEAK 22(11Q13.3) WILD-TYPE	153	28	32	6	60

Figure S76. Get High-res Image Gene #22: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.16

Table S77. Gene #22: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
AMP PEAK 22(11Q13.3) MUTATED	23	16	50
AMP PEAK 22(11Q13.3) WILD-TYPE	96	92	91

Figure S77. Get High-res Image Gene #22: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.091

Table S78. Gene #22: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
AMP PEAK 22(11Q13.3) MUTATED	10	51	16
AMP PEAK 22(11Q13.3) WILD-TYPE	67	93	84

Figure S78. Get High-res Image Gene #22: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_12p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S79. Gene #23: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 23(12P12.1) MUTATED	26	12	35	5	31
AMP PEAK 23(12P12.1) WILD-TYPE	143	21	31	5	60

Figure S79. Get High-res Image Gene #23: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S80. Gene #24: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 24(12Q15) MUTATED	26	6	32	2	26
AMP PEAK 24(12Q15) WILD-TYPE	143	27	34	8	65

Figure S80. Get High-res Image Gene #24: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q12.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S81. Gene #25: 'amp_13q12.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 25(13Q12.3) MUTATED	35	29	20	5	55
AMP PEAK 25(13Q12.3) WILD-TYPE	134	4	46	5	36

Figure S81. Get High-res Image Gene #25: 'amp_13q12.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q12.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S82. Gene #25: 'amp_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
AMP PEAK 25(13Q12.3) MUTATED	38	56	31
AMP PEAK 25(13Q12.3) WILD-TYPE	82	36	78

Figure S82. Get High-res Image Gene #25: 'amp_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q12.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S83. Gene #25: 'amp_13q12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 25(13Q12.3) MUTATED	4	5	17	23	25	22	5
AMP PEAK 25(13Q12.3) WILD-TYPE	34	16	32	39	16	18	16

Figure S83. Get High-res Image Gene #25: 'amp_13q12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_13q12.3' versus 'MIRSEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.17

Table S84. Gene #25: 'amp_13q12.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
AMP PEAK 25(13Q12.3) MUTATED	42	29	72
AMP PEAK 25(13Q12.3) WILD-TYPE	77	79	69

Figure S84. Get High-res Image Gene #25: 'amp_13q12.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_13q12.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.2

Table S85. Gene #25: 'amp_13q12.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
AMP PEAK 25(13Q12.3) MUTATED	23	73	28
AMP PEAK 25(13Q12.3) WILD-TYPE	54	71	72

Figure S85. Get High-res Image Gene #25: 'amp_13q12.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_13q12.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.14

Table S86. Gene #25: 'amp_13q12.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
AMP PEAK 25(13Q12.3) MUTATED	63	15	46
AMP PEAK 25(13Q12.3) WILD-TYPE	114	47	36

Figure S86. Get High-res Image Gene #25: 'amp_13q12.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S87. Gene #26: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 26(13Q22.1) MUTATED	39	28	18	4	60
AMP PEAK 26(13Q22.1) WILD-TYPE	130	5	48	6	31

Figure S87. Get High-res Image Gene #26: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S88. Gene #26: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
AMP PEAK 26(13Q22.1) MUTATED	37	57	33
AMP PEAK 26(13Q22.1) WILD-TYPE	83	35	76

Figure S88. Get High-res Image Gene #26: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S89. Gene #26: 'amp_13q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 26(13Q22.1) MUTATED	23	16	9	17	39
AMP PEAK 26(13Q22.1) WILD-TYPE	42	46	37	20	23

Figure S89. Get High-res Image Gene #26: 'amp_13q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S90. Gene #26: 'amp_13q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 26(13Q22.1) MUTATED	7	7	15	18	24	28	5
AMP PEAK 26(13Q22.1) WILD-TYPE	31	14	34	44	17	12	16

Figure S90. Get High-res Image Gene #26: 'amp_13q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.21

Table S91. Gene #26: 'amp_13q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
AMP PEAK 26(13Q22.1) MUTATED	44	30	74
AMP PEAK 26(13Q22.1) WILD-TYPE	75	78	67

Figure S91. Get High-res Image Gene #26: 'amp_13q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_13q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S92. Gene #26: 'amp_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
AMP PEAK 26(13Q22.1) MUTATED	58	26	64
AMP PEAK 26(13Q22.1) WILD-TYPE	121	57	42

Figure S92. Get High-res Image Gene #26: 'amp_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S93. Gene #26: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
AMP PEAK 26(13Q22.1) MUTATED	23	77	27
AMP PEAK 26(13Q22.1) WILD-TYPE	54	67	73

Figure S93. Get High-res Image Gene #26: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_13q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S94. Gene #26: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
AMP PEAK 26(13Q22.1) MUTATED	59	15	53
AMP PEAK 26(13Q22.1) WILD-TYPE	118	47	29

Figure S94. Get High-res Image Gene #26: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_15q26.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S95. Gene #27: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 27(15Q26.1) MUTATED	11	5	26	0	46
AMP PEAK 27(15Q26.1) WILD-TYPE	158	28	40	10	45

Figure S95. Get High-res Image Gene #27: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_15q26.1' versus 'METHLYATION_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.12

Table S96. Gene #27: 'amp_15q26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
AMP PEAK 27(15Q26.1) MUTATED	21	37	19
AMP PEAK 27(15Q26.1) WILD-TYPE	99	55	90

Figure S96. Get High-res Image Gene #27: 'amp_15q26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_15q26.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S97. Gene #27: 'amp_15q26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 27(15Q26.1) MUTATED	12	4	11	9	28
AMP PEAK 27(15Q26.1) WILD-TYPE	53	58	35	28	34

Figure S97. Get High-res Image Gene #27: 'amp_15q26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_15q26.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S98. Gene #27: 'amp_15q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 27(15Q26.1) MUTATED	13	1	4	14	11	20	1
AMP PEAK 27(15Q26.1) WILD-TYPE	25	20	45	48	30	20	20

Figure S98. Get High-res Image Gene #27: 'amp_15q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S99. Gene #28: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 28(17Q12) MUTATED	17	15	21	2	61
AMP PEAK 28(17Q12) WILD-TYPE	152	18	45	8	30

Figure S99. Get High-res Image Gene #28: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S100. Gene #28: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
AMP PEAK 28(17Q12) MUTATED	31	52	19
AMP PEAK 28(17Q12) WILD-TYPE	89	40	90

Figure S100. Get High-res Image Gene #28: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.11

Table S101. Gene #28: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 28(17Q12) MUTATED	14	10	15	8	32
AMP PEAK 28(17Q12) WILD-TYPE	51	52	31	29	30

Figure S101. Get High-res Image Gene #28: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.1

Table S102. Gene #28: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 28(17Q12) MUTATED	13	7	5	20	13	20	1
AMP PEAK 28(17Q12) WILD-TYPE	25	14	44	42	28	20	20

Figure S102. Get High-res Image Gene #28: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.023

Table S103. Gene #28: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
AMP PEAK 28(17Q12) MUTATED	31	21	63
AMP PEAK 28(17Q12) WILD-TYPE	88	87	78

Figure S103. Get High-res Image Gene #28: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.11

Table S104. Gene #28: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
AMP PEAK 28(17Q12) MUTATED	47	18	50
AMP PEAK 28(17Q12) WILD-TYPE	132	65	56

Figure S104. Get High-res Image Gene #28: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S105. Gene #29: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 29(18Q11.2) MUTATED	24	11	34	4	44
AMP PEAK 29(18Q11.2) WILD-TYPE	145	22	32	6	47

Figure S105. Get High-res Image Gene #29: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19p13.2' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.17

Table S106. Gene #30: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 30(19P13.2) MUTATED	8	9	12	0	12
AMP PEAK 30(19P13.2) WILD-TYPE	161	24	54	10	79

Figure S106. Get High-res Image Gene #30: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S107. Gene #31: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 31(19Q12) MUTATED	18	9	17	1	66
AMP PEAK 31(19Q12) WILD-TYPE	151	24	49	9	25

Figure S107. Get High-res Image Gene #31: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S108. Gene #31: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
AMP PEAK 31(19Q12) MUTATED	21	50	28
AMP PEAK 31(19Q12) WILD-TYPE	99	42	81

Figure S108. Get High-res Image Gene #31: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S109. Gene #31: 'amp_19q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 31(19Q12) MUTATED	10	9	10	6	44
AMP PEAK 31(19Q12) WILD-TYPE	55	53	36	31	18

Figure S109. Get High-res Image Gene #31: 'amp_19q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S110. Gene #31: 'amp_19q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 31(19Q12) MUTATED	10	5	6	15	11	29	3
AMP PEAK 31(19Q12) WILD-TYPE	28	16	43	47	30	11	18

Figure S110. Get High-res Image Gene #31: 'amp_19q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S111. Gene #31: 'amp_19q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
AMP PEAK 31(19Q12) MUTATED	25	22	63
AMP PEAK 31(19Q12) WILD-TYPE	94	86	78

Figure S111. Get High-res Image Gene #31: 'amp_19q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S112. Gene #31: 'amp_19q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
AMP PEAK 31(19Q12) MUTATED	29	18	63
AMP PEAK 31(19Q12) WILD-TYPE	150	65	43

Figure S112. Get High-res Image Gene #31: 'amp_19q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S113. Gene #31: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
AMP PEAK 31(19Q12) MUTATED	33	11	55
AMP PEAK 31(19Q12) WILD-TYPE	144	51	27

Figure S113. Get High-res Image Gene #31: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S114. Gene #32: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 32(20Q13.2) MUTATED	65	31	55	9	83
AMP PEAK 32(20Q13.2) WILD-TYPE	104	2	11	1	8

Figure S114. Get High-res Image Gene #32: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S115. Gene #32: 'amp_20q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
AMP PEAK 32(20Q13.2) MUTATED	64	84	63
AMP PEAK 32(20Q13.2) WILD-TYPE	56	8	46

Figure S115. Get High-res Image Gene #32: 'amp_20q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S116. Gene #32: 'amp_20q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 32(20Q13.2) MUTATED	31	31	31	24	59
AMP PEAK 32(20Q13.2) WILD-TYPE	34	31	15	13	3

Figure S116. Get High-res Image Gene #32: 'amp_20q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_20q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S117. Gene #32: 'amp_20q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 32(20Q13.2) MUTATED	23	19	19	43	31	38	3
AMP PEAK 32(20Q13.2) WILD-TYPE	15	2	30	19	10	2	18

Figure S117. Get High-res Image Gene #32: 'amp_20q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S118. Gene #32: 'amp_20q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
AMP PEAK 32(20Q13.2) MUTATED	71	56	115
AMP PEAK 32(20Q13.2) WILD-TYPE	48	52	26

Figure S118. Get High-res Image Gene #32: 'amp_20q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_20q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S119. Gene #32: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
AMP PEAK 32(20Q13.2) MUTATED	103	44	95
AMP PEAK 32(20Q13.2) WILD-TYPE	76	39	11

Figure S119. Get High-res Image Gene #32: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S120. Gene #32: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
AMP PEAK 32(20Q13.2) MUTATED	106	29	76
AMP PEAK 32(20Q13.2) WILD-TYPE	71	33	6

Figure S120. Get High-res Image Gene #32: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xq27.3' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.039

Table S121. Gene #33: 'amp_xq27.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
AMP PEAK 33(XQ27.3) MUTATED	15	13	14	3	22
AMP PEAK 33(XQ27.3) WILD-TYPE	154	20	52	7	69

Figure S121. Get High-res Image Gene #33: 'amp_xq27.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq27.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S122. Gene #33: 'amp_xq27.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 33(XQ27.3) MUTATED	8	4	2	9	20	3	2
AMP PEAK 33(XQ27.3) WILD-TYPE	30	17	47	53	21	37	19

Figure S122. Get High-res Image Gene #33: 'amp_xq27.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S123. Gene #34: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 1(1P36.11) MUTATED	10	8	32	4	50
DEL PEAK 1(1P36.11) WILD-TYPE	159	25	34	6	41

Figure S123. Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S124. Gene #34: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 1(1P36.11) MUTATED	23	48	15
DEL PEAK 1(1P36.11) WILD-TYPE	97	44	94

Figure S124. Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.17

Table S125. Gene #34: 'del_1p36.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 1(1P36.11) MUTATED	12	8	17	11	28
DEL PEAK 1(1P36.11) WILD-TYPE	53	54	29	26	34

Figure S125. Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S126. Gene #34: 'del_1p36.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 1(1P36.11) MUTATED	10	2	4	21	15	22	2
DEL PEAK 1(1P36.11) WILD-TYPE	28	19	45	41	26	18	19

Figure S126. Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.06

Table S127. Gene #34: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
DEL PEAK 1(1P36.11) MUTATED	43	14	46
DEL PEAK 1(1P36.11) WILD-TYPE	136	69	60

Figure S127. Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S128. Gene #34: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
DEL PEAK 1(1P36.11) MUTATED	41	7	38
DEL PEAK 1(1P36.11) WILD-TYPE	136	55	44

Figure S128. Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S129. Gene #35: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 2(1P13.2) MUTATED	5	7	19	3	41
DEL PEAK 2(1P13.2) WILD-TYPE	164	26	47	7	50

Figure S129. Get High-res Image Gene #35: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S130. Gene #35: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 2(1P13.2) MUTATED	21	36	9
DEL PEAK 2(1P13.2) WILD-TYPE	99	56	100

Figure S130. Get High-res Image Gene #35: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S131. Gene #39: 'del_2q37.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 6(2Q37.2) MUTATED	9	4	14	3	24
DEL PEAK 6(2Q37.2) WILD-TYPE	160	29	52	7	67

Figure S131. Get High-res Image Gene #39: 'del_2q37.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.2' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.029

Table S132. Gene #39: 'del_2q37.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 6(2Q37.2) MUTATED	10	28	11
DEL PEAK 6(2Q37.2) WILD-TYPE	110	64	98

Figure S132. Get High-res Image Gene #39: 'del_2q37.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S133. Gene #39: 'del_2q37.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
DEL PEAK 6(2Q37.2) MUTATED	17	6	31
DEL PEAK 6(2Q37.2) WILD-TYPE	162	77	75

Figure S133. Get High-res Image Gene #39: 'del_2q37.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S134. Gene #40: 'del_3p26.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 7(3P26.1) MUTATED	19	18	29	4	45
DEL PEAK 7(3P26.1) WILD-TYPE	150	15	37	6	46

Figure S134. Get High-res Image Gene #40: 'del_3p26.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p26.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S135. Gene #40: 'del_3p26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 7(3P26.1) MUTATED	29	47	25
DEL PEAK 7(3P26.1) WILD-TYPE	91	45	84

Figure S135. Get High-res Image Gene #40: 'del_3p26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p26.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.029

Table S136. Gene #40: 'del_3p26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 7(3P26.1) MUTATED	8	5	8	16	20	18	0
DEL PEAK 7(3P26.1) WILD-TYPE	30	16	41	46	21	22	21

Figure S136. Get High-res Image Gene #40: 'del_3p26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.1' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.05

Table S137. Gene #40: 'del_3p26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
DEL PEAK 7(3P26.1) MUTATED	31	21	62
DEL PEAK 7(3P26.1) WILD-TYPE	88	87	79

Figure S137. Get High-res Image Gene #40: 'del_3p26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p26.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.023

Table S138. Gene #40: 'del_3p26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
DEL PEAK 7(3P26.1) MUTATED	44	18	52
DEL PEAK 7(3P26.1) WILD-TYPE	135	65	54

Figure S138. Get High-res Image Gene #40: 'del_3p26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.21

Table S139. Gene #40: 'del_3p26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
DEL PEAK 7(3P26.1) MUTATED	19	61	20
DEL PEAK 7(3P26.1) WILD-TYPE	58	83	80

Figure S139. Get High-res Image Gene #40: 'del_3p26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p26.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S140. Gene #40: 'del_3p26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
DEL PEAK 7(3P26.1) MUTATED	48	8	44
DEL PEAK 7(3P26.1) WILD-TYPE	129	54	38

Figure S140. Get High-res Image Gene #40: 'del_3p26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S141. Gene #41: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 8(3P14.2) MUTATED	27	15	36	5	48
DEL PEAK 8(3P14.2) WILD-TYPE	142	18	30	5	43

Figure S141. Get High-res Image Gene #41: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S142. Gene #41: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 8(3P14.2) MUTATED	42	52	24
DEL PEAK 8(3P14.2) WILD-TYPE	78	40	85

Figure S142. Get High-res Image Gene #41: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p14.2' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.045

Table S143. Gene #41: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 8(3P14.2) MUTATED	16	10	15	13	34
DEL PEAK 8(3P14.2) WILD-TYPE	49	52	31	24	28

Figure S143. Get High-res Image Gene #41: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.1

Table S144. Gene #41: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 8(3P14.2) MUTATED	11	6	6	21	19	22	3
DEL PEAK 8(3P14.2) WILD-TYPE	27	15	43	41	22	18	18

Figure S144. Get High-res Image Gene #41: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S145. Gene #41: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
DEL PEAK 8(3P14.2) MUTATED	36	25	70
DEL PEAK 8(3P14.2) WILD-TYPE	83	83	71

Figure S145. Get High-res Image Gene #41: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S146. Gene #41: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
DEL PEAK 8(3P14.2) MUTATED	53	19	59
DEL PEAK 8(3P14.2) WILD-TYPE	126	64	47

Figure S146. Get High-res Image Gene #41: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.21

Table S147. Gene #41: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
DEL PEAK 8(3P14.2) MUTATED	27	68	23
DEL PEAK 8(3P14.2) WILD-TYPE	50	76	77

Figure S147. Get High-res Image Gene #41: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S148. Gene #41: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
DEL PEAK 8(3P14.2) MUTATED	59	11	48
DEL PEAK 8(3P14.2) WILD-TYPE	118	51	34

Figure S148. Get High-res Image Gene #41: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q26.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S149. Gene #42: 'del_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 9(3Q26.31) MUTATED	4	9	12	1	20
DEL PEAK 9(3Q26.31) WILD-TYPE	165	24	54	9	71

Figure S149. Get High-res Image Gene #42: 'del_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q26.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S150. Gene #42: 'del_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 9(3Q26.31) MUTATED	12	26	3
DEL PEAK 9(3Q26.31) WILD-TYPE	108	66	106

Figure S150. Get High-res Image Gene #42: 'del_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3q26.31' versus 'MRNASEQ_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.21

Table S151. Gene #42: 'del_3q26.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 9(3Q26.31) MUTATED	2	3	3	7	15
DEL PEAK 9(3Q26.31) WILD-TYPE	63	59	43	30	47

Figure S151. Get High-res Image Gene #42: 'del_3q26.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3q26.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.22

Table S152. Gene #42: 'del_3q26.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 9(3Q26.31) MUTATED	4	1	1	4	11	9	0
DEL PEAK 9(3Q26.31) WILD-TYPE	34	20	48	58	30	31	21

Figure S152. Get High-res Image Gene #42: 'del_3q26.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S153. Gene #43: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 10(4P16.3) MUTATED	29	13	40	3	57
DEL PEAK 10(4P16.3) WILD-TYPE	140	20	26	7	34

Figure S153. Get High-res Image Gene #43: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4p16.3' versus 'METHLYATION_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.25

Table S154. Gene #43: 'del_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 10(4P16.3) MUTATED	34	50	39
DEL PEAK 10(4P16.3) WILD-TYPE	86	42	70

Figure S154. Get High-res Image Gene #43: 'del_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4p16.3' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S155. Gene #43: 'del_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 10(4P16.3) MUTATED	11	23	15	11	38
DEL PEAK 10(4P16.3) WILD-TYPE	54	39	31	26	24

Figure S155. Get High-res Image Gene #43: 'del_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.029

Table S156. Gene #43: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 10(4P16.3) MUTATED	10	4	18	18	17	28	3
DEL PEAK 10(4P16.3) WILD-TYPE	28	17	31	44	24	12	18

Figure S156. Get High-res Image Gene #43: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.22

Table S157. Gene #43: 'del_4p16.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
DEL PEAK 10(4P16.3) MUTATED	30	43	69
DEL PEAK 10(4P16.3) WILD-TYPE	89	65	72

Figure S157. Get High-res Image Gene #43: 'del_4p16.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S158. Gene #43: 'del_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
DEL PEAK 10(4P16.3) MUTATED	49	29	64
DEL PEAK 10(4P16.3) WILD-TYPE	130	54	42

Figure S158. Get High-res Image Gene #43: 'del_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.081

Table S159. Gene #43: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
DEL PEAK 10(4P16.3) MUTATED	15	68	41
DEL PEAK 10(4P16.3) WILD-TYPE	62	76	59

Figure S159. Get High-res Image Gene #43: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S160. Gene #43: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
DEL PEAK 10(4P16.3) MUTATED	51	19	54
DEL PEAK 10(4P16.3) WILD-TYPE	126	43	28

Figure S160. Get High-res Image Gene #43: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S161. Gene #44: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 11(4Q22.1) MUTATED	25	17	50	4	64
DEL PEAK 11(4Q22.1) WILD-TYPE	144	16	16	6	27

Figure S161. Get High-res Image Gene #44: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.034

Table S162. Gene #44: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 11(4Q22.1) MUTATED	45	58	36
DEL PEAK 11(4Q22.1) WILD-TYPE	75	34	73

Figure S162. Get High-res Image Gene #44: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S163. Gene #44: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 11(4Q22.1) MUTATED	16	4	16	23	25	27	3
DEL PEAK 11(4Q22.1) WILD-TYPE	22	17	33	39	16	13	18

Figure S163. Get High-res Image Gene #44: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.23

Table S164. Gene #44: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
DEL PEAK 11(4Q22.1) MUTATED	70	19	50
DEL PEAK 11(4Q22.1) WILD-TYPE	107	43	32

Figure S164. Get High-res Image Gene #44: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S165. Gene #45: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 12(4Q34.3) MUTATED	27	15	50	4	67
DEL PEAK 12(4Q34.3) WILD-TYPE	142	18	16	6	24

Figure S165. Get High-res Image Gene #45: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S166. Gene #45: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 12(4Q34.3) MUTATED	40	63	41
DEL PEAK 12(4Q34.3) WILD-TYPE	80	29	68

Figure S166. Get High-res Image Gene #45: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S167. Gene #45: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 12(4Q34.3) MUTATED	14	21	21	16	41
DEL PEAK 12(4Q34.3) WILD-TYPE	51	41	25	21	21

Figure S167. Get High-res Image Gene #45: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S168. Gene #45: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 12(4Q34.3) MUTATED	16	2	17	23	21	30	4
DEL PEAK 12(4Q34.3) WILD-TYPE	22	19	32	39	20	10	17

Figure S168. Get High-res Image Gene #45: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.023

Table S169. Gene #45: 'del_4q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
DEL PEAK 12(4Q34.3) MUTATED	40	39	84
DEL PEAK 12(4Q34.3) WILD-TYPE	79	69	57

Figure S169. Get High-res Image Gene #45: 'del_4q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S170. Gene #45: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
DEL PEAK 12(4Q34.3) MUTATED	65	29	69
DEL PEAK 12(4Q34.3) WILD-TYPE	114	54	37

Figure S170. Get High-res Image Gene #45: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S171. Gene #45: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
DEL PEAK 12(4Q34.3) MUTATED	23	85	37
DEL PEAK 12(4Q34.3) WILD-TYPE	54	59	63

Figure S171. Get High-res Image Gene #45: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S172. Gene #45: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
DEL PEAK 12(4Q34.3) MUTATED	69	20	56
DEL PEAK 12(4Q34.3) WILD-TYPE	108	42	26

Figure S172. Get High-res Image Gene #45: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S173. Gene #46: 'del_5q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 13(5Q11.2) MUTATED	13	13	34	5	69
DEL PEAK 13(5Q11.2) WILD-TYPE	156	20	32	5	22

Figure S173. Get High-res Image Gene #46: '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 = 0.0081

Table S174. Gene #46: 'del_5q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 13(5Q11.2) MUTATED	32	67	21
DEL PEAK 13(5Q11.2) WILD-TYPE	88	25	88

Figure S174. Get High-res Image Gene #46: 'del_5q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S175. Gene #46: 'del_5q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 13(5Q11.2) MUTATED	17	4	11	14	44
DEL PEAK 13(5Q11.2) WILD-TYPE	48	58	35	23	18

Figure S175. Get High-res Image Gene #46: 'del_5q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S176. Gene #46: 'del_5q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 13(5Q11.2) MUTATED	12	4	3	23	18	28	2
DEL PEAK 13(5Q11.2) WILD-TYPE	26	17	46	39	23	12	19

Figure S176. Get High-res Image Gene #46: 'del_5q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S177. Gene #46: 'del_5q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
DEL PEAK 13(5Q11.2) MUTATED	38	18	78
DEL PEAK 13(5Q11.2) WILD-TYPE	81	90	63

Figure S177. Get High-res Image Gene #46: 'del_5q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S178. Gene #46: 'del_5q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
DEL PEAK 13(5Q11.2) MUTATED	53	14	67
DEL PEAK 13(5Q11.2) WILD-TYPE	126	69	39

Figure S178. Get High-res Image Gene #46: 'del_5q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S179. Gene #46: 'del_5q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
DEL PEAK 13(5Q11.2) MUTATED	22	82	17
DEL PEAK 13(5Q11.2) WILD-TYPE	55	62	83

Figure S179. Get High-res Image Gene #46: 'del_5q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S180. Gene #46: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
DEL PEAK 13(5Q11.2) MUTATED	55	6	60
DEL PEAK 13(5Q11.2) WILD-TYPE	122	56	22

Figure S180. Get High-res Image Gene #46: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S181. Gene #47: 'del_5q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 14(5Q23.2) MUTATED	10	13	26	5	68
DEL PEAK 14(5Q23.2) WILD-TYPE	159	20	40	5	23

Figure S181. Get High-res Image Gene #47: 'del_5q23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S182. Gene #47: 'del_5q23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 14(5Q23.2) MUTATED	27	63	19
DEL PEAK 14(5Q23.2) WILD-TYPE	93	29	90

Figure S182. Get High-res Image Gene #47: 'del_5q23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q23.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S183. Gene #47: 'del_5q23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 14(5Q23.2) MUTATED	15	3	10	11	42
DEL PEAK 14(5Q23.2) WILD-TYPE	50	59	36	26	20

Figure S183. Get High-res Image Gene #47: 'del_5q23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S184. Gene #47: 'del_5q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 14(5Q23.2) MUTATED	7	5	2	21	17	27	2
DEL PEAK 14(5Q23.2) WILD-TYPE	31	16	47	41	24	13	19

Figure S184. Get High-res Image Gene #47: 'del_5q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q23.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S185. Gene #47: 'del_5q23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
DEL PEAK 14(5Q23.2) MUTATED	30	15	76
DEL PEAK 14(5Q23.2) WILD-TYPE	89	93	65

Figure S185. Get High-res Image Gene #47: 'del_5q23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5q23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S186. Gene #47: 'del_5q23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
DEL PEAK 14(5Q23.2) MUTATED	49	10	62
DEL PEAK 14(5Q23.2) WILD-TYPE	130	73	44

Figure S186. Get High-res Image Gene #47: 'del_5q23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S187. Gene #47: 'del_5q23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
DEL PEAK 14(5Q23.2) MUTATED	16	77	16
DEL PEAK 14(5Q23.2) WILD-TYPE	61	67	84

Figure S187. Get High-res Image Gene #47: 'del_5q23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5q23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S188. Gene #47: 'del_5q23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
DEL PEAK 14(5Q23.2) MUTATED	50	4	55
DEL PEAK 14(5Q23.2) WILD-TYPE	127	58	27

Figure S188. Get High-res Image Gene #47: 'del_5q23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S189. Gene #48: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 15(6P25.3) MUTATED	17	8	29	1	38
DEL PEAK 15(6P25.3) WILD-TYPE	152	25	37	9	53

Figure S189. Get High-res Image Gene #48: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.11

Table S190. Gene #48: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 15(6P25.3) MUTATED	28	39	19
DEL PEAK 15(6P25.3) WILD-TYPE	92	53	90

Figure S190. Get High-res Image Gene #48: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p25.3' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.06

Table S191. Gene #48: 'del_6p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 15(6P25.3) MUTATED	7	6	14	6	24
DEL PEAK 15(6P25.3) WILD-TYPE	58	56	32	31	38

Figure S191. Get High-res Image Gene #48: 'del_6p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.034

Table S192. Gene #48: 'del_6p25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 15(6P25.3) MUTATED	10	0	4	15	9	18	1
DEL PEAK 15(6P25.3) WILD-TYPE	28	21	45	47	32	22	20

Figure S192. Get High-res Image Gene #48: 'del_6p25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S193. Gene #48: 'del_6p25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
DEL PEAK 15(6P25.3) MUTATED	38	11	44
DEL PEAK 15(6P25.3) WILD-TYPE	141	72	62

Figure S193. Get High-res Image Gene #48: 'del_6p25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6p25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.21

Table S194. Gene #48: 'del_6p25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
DEL PEAK 15(6P25.3) MUTATED	49	6	31
DEL PEAK 15(6P25.3) WILD-TYPE	128	56	51

Figure S194. Get High-res Image Gene #48: 'del_6p25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S195. Gene #49: 'del_6q14.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 16(6Q14.1) MUTATED	11	6	26	1	28
DEL PEAK 16(6Q14.1) WILD-TYPE	158	27	40	9	63

Figure S195. Get High-res Image Gene #49: 'del_6q14.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S196. Gene #50: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 17(6Q26) MUTATED	18	10	29	0	25
DEL PEAK 17(6Q26) WILD-TYPE	151	23	37	10	66

Figure S196. Get High-res Image Gene #50: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S197. Gene #51: 'del_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 18(7Q31.1) MUTATED	8	2	19	1	24
DEL PEAK 18(7Q31.1) WILD-TYPE	161	31	47	9	67

Figure S197. Get High-res Image Gene #51: 'del_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q31.1' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.023

Table S198. Gene #51: 'del_7q31.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 18(7Q31.1) MUTATED	18	24	4
DEL PEAK 18(7Q31.1) WILD-TYPE	102	68	105

Figure S198. Get High-res Image Gene #51: 'del_7q31.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q36.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S199. Gene #52: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 19(7Q36.3) MUTATED	5	1	32	2	38
DEL PEAK 19(7Q36.3) WILD-TYPE	164	32	34	8	53

Figure S199. Get High-res Image Gene #52: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q36.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S200. Gene #52: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 19(7Q36.3) MUTATED	21	35	13
DEL PEAK 19(7Q36.3) WILD-TYPE	99	57	96

Figure S200. Get High-res Image Gene #52: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q36.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S201. Gene #52: 'del_7q36.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 19(7Q36.3) MUTATED	7	8	8	3	27
DEL PEAK 19(7Q36.3) WILD-TYPE	58	54	38	34	35

Figure S201. Get High-res Image Gene #52: 'del_7q36.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_7q36.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.17

Table S202. Gene #52: 'del_7q36.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 19(7Q36.3) MUTATED	12	0	6	13	7	15	0
DEL PEAK 19(7Q36.3) WILD-TYPE	26	21	43	49	34	25	21

Figure S202. Get High-res Image Gene #52: 'del_7q36.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_7q36.3' versus 'MIRSEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.11

Table S203. Gene #52: 'del_7q36.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
DEL PEAK 19(7Q36.3) MUTATED	23	11	44
DEL PEAK 19(7Q36.3) WILD-TYPE	96	97	97

Figure S203. Get High-res Image Gene #52: 'del_7q36.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_7q36.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S204. Gene #52: 'del_7q36.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
DEL PEAK 19(7Q36.3) MUTATED	29	8	41
DEL PEAK 19(7Q36.3) WILD-TYPE	150	75	65

Figure S204. Get High-res Image Gene #52: 'del_7q36.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_7q36.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S205. Gene #52: 'del_7q36.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
DEL PEAK 19(7Q36.3) MUTATED	33	4	33
DEL PEAK 19(7Q36.3) WILD-TYPE	144	58	49

Figure S205. Get High-res Image Gene #52: 'del_7q36.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S206. Gene #53: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 20(8P23.3) MUTATED	12	15	29	0	46
DEL PEAK 20(8P23.3) WILD-TYPE	157	18	37	10	45

Figure S206. Get High-res Image Gene #53: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S207. Gene #53: 'del_8p23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 20(8P23.3) MUTATED	22	44	23
DEL PEAK 20(8P23.3) WILD-TYPE	98	48	86

Figure S207. Get High-res Image Gene #53: 'del_8p23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S208. Gene #53: 'del_8p23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 20(8P23.3) MUTATED	11	9	8	10	34
DEL PEAK 20(8P23.3) WILD-TYPE	54	53	38	27	28

Figure S208. Get High-res Image Gene #53: 'del_8p23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S209. Gene #53: 'del_8p23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 20(8P23.3) MUTATED	9	2	6	13	15	25	2
DEL PEAK 20(8P23.3) WILD-TYPE	29	19	43	49	26	15	19

Figure S209. Get High-res Image Gene #53: 'del_8p23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S210. Gene #53: 'del_8p23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
DEL PEAK 20(8P23.3) MUTATED	36	16	49
DEL PEAK 20(8P23.3) WILD-TYPE	143	67	57

Figure S210. Get High-res Image Gene #53: 'del_8p23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.034

Table S211. Gene #53: 'del_8p23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
DEL PEAK 20(8P23.3) MUTATED	18	56	15
DEL PEAK 20(8P23.3) WILD-TYPE	59	88	85

Figure S211. Get High-res Image Gene #53: 'del_8p23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8p23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S212. Gene #53: 'del_8p23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
DEL PEAK 20(8P23.3) MUTATED	40	8	41
DEL PEAK 20(8P23.3) WILD-TYPE	137	54	41

Figure S212. Get High-res Image Gene #53: 'del_8p23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S213. Gene #54: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 21(9P23) MUTATED	24	21	55	5	51
DEL PEAK 21(9P23) WILD-TYPE	145	12	11	5	40

Figure S213. Get High-res Image Gene #54: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S214. Gene #54: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 21(9P23) MUTATED	40	58	39
DEL PEAK 21(9P23) WILD-TYPE	80	34	70

Figure S214. Get High-res Image Gene #54: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S215. Gene #54: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 21(9P23) MUTATED	14	18	23	13	40
DEL PEAK 21(9P23) WILD-TYPE	51	44	23	24	22

Figure S215. Get High-res Image Gene #54: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S216. Gene #55: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 22(9P21.3) MUTATED	23	19	54	6	51
DEL PEAK 22(9P21.3) WILD-TYPE	146	14	12	4	40

Figure S216. Get High-res Image Gene #55: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S217. Gene #55: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 22(9P21.3) MUTATED	36	61	38
DEL PEAK 22(9P21.3) WILD-TYPE	84	31	71

Figure S217. Get High-res Image Gene #55: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.039

Table S218. Gene #55: 'del_9p21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	90	91
DEL PEAK 22(9P21.3) MUTATED	17	41	47
DEL PEAK 22(9P21.3) WILD-TYPE	65	49	44

Figure S218. Get High-res Image Gene #55: 'del_9p21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S219. Gene #55: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
DEL PEAK 22(9P21.3) MUTATED	8	45	10	42
DEL PEAK 22(9P21.3) WILD-TYPE	26	38	45	49

Figure S219. Get High-res Image Gene #55: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S220. Gene #55: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 22(9P21.3) MUTATED	9	18	23	15	43
DEL PEAK 22(9P21.3) WILD-TYPE	56	44	23	22	19

Figure S220. Get High-res Image Gene #55: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S221. Gene #55: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 22(9P21.3) MUTATED	19	1	11	30	18	27	2
DEL PEAK 22(9P21.3) WILD-TYPE	19	20	38	32	23	13	19

Figure S221. Get High-res Image Gene #55: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.023

Table S222. Gene #55: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
DEL PEAK 22(9P21.3) MUTATED	63	20	52
DEL PEAK 22(9P21.3) WILD-TYPE	114	42	30

Figure S222. Get High-res Image Gene #55: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q21.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S223. Gene #56: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 23(9Q21.11) MUTATED	11	11	34	2	35
DEL PEAK 23(9Q21.11) WILD-TYPE	158	22	32	8	56

Figure S223. Get High-res Image Gene #56: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q21.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.24

Table S224. Gene #56: 'del_9q21.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
DEL PEAK 23(9Q21.11) MUTATED	34	17	42
DEL PEAK 23(9Q21.11) WILD-TYPE	145	66	64

Figure S224. Get High-res Image Gene #56: 'del_9q21.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.12

Table S225. Gene #56: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
DEL PEAK 23(9Q21.11) MUTATED	38	10	36
DEL PEAK 23(9Q21.11) WILD-TYPE	139	52	46

Figure S225. Get High-res Image Gene #56: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S226. Gene #57: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 24(10P15.3) MUTATED	11	8	17	2	24
DEL PEAK 24(10P15.3) WILD-TYPE	158	25	49	8	67

Figure S226. Get High-res Image Gene #57: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S227. Gene #58: 'del_10q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 25(10Q22.3) MUTATED	6	14	7	3	31
DEL PEAK 25(10Q22.3) WILD-TYPE	163	19	59	7	60

Figure S227. Get High-res Image Gene #58: 'del_10q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q22.3' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.096

Table S228. Gene #58: 'del_10q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 25(10Q22.3) MUTATED	7	2	4	8	19
DEL PEAK 25(10Q22.3) WILD-TYPE	58	60	42	29	43

Figure S228. Get High-res Image Gene #58: 'del_10q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.17

Table S229. Gene #58: 'del_10q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 25(10Q22.3) MUTATED	2	1	3	8	14	11	1
DEL PEAK 25(10Q22.3) WILD-TYPE	36	20	46	54	27	29	20

Figure S229. Get High-res Image Gene #58: 'del_10q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.11

Table S230. Gene #58: 'del_10q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
DEL PEAK 25(10Q22.3) MUTATED	27	2	23
DEL PEAK 25(10Q22.3) WILD-TYPE	150	60	59

Figure S230. Get High-res Image Gene #58: 'del_10q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S231. Gene #59: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 26(10Q23.31) MUTATED	11	13	15	4	47
DEL PEAK 26(10Q23.31) WILD-TYPE	158	20	51	6	44

Figure S231. Get High-res Image Gene #59: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.081

Table S232. Gene #59: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 26(10Q23.31) MUTATED	22	37	17
DEL PEAK 26(10Q23.31) WILD-TYPE	98	55	92

Figure S232. Get High-res Image Gene #59: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.1

Table S233. Gene #59: 'del_10q23.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
DEL PEAK 26(10Q23.31) MUTATED	7	34	8	13
DEL PEAK 26(10Q23.31) WILD-TYPE	27	49	47	78

Figure S233. Get High-res Image Gene #59: 'del_10q23.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S234. Gene #59: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 26(10Q23.31) MUTATED	8	4	9	12	28
DEL PEAK 26(10Q23.31) WILD-TYPE	57	58	37	25	34

Figure S234. Get High-res Image Gene #59: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S235. Gene #59: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 26(10Q23.31) MUTATED	2	3	4	16	18	17	1
DEL PEAK 26(10Q23.31) WILD-TYPE	36	18	45	46	23	23	20

Figure S235. Get High-res Image Gene #59: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.071

Table S236. Gene #59: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
DEL PEAK 26(10Q23.31) MUTATED	28	13	49
DEL PEAK 26(10Q23.31) WILD-TYPE	91	95	92

Figure S236. Get High-res Image Gene #59: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.034

Table S237. Gene #59: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
DEL PEAK 26(10Q23.31) MUTATED	43	8	39
DEL PEAK 26(10Q23.31) WILD-TYPE	136	75	67

Figure S237. Get High-res Image Gene #59: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S238. Gene #59: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
DEL PEAK 26(10Q23.31) MUTATED	40	3	33
DEL PEAK 26(10Q23.31) WILD-TYPE	137	59	49

Figure S238. Get High-res Image Gene #59: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.4' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S239. Gene #60: 'del_11p15.4' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 27(11P15.4) MUTATED	10	6	21	2	40
DEL PEAK 27(11P15.4) WILD-TYPE	159	27	45	8	51

Figure S239. Get High-res Image Gene #60: 'del_11p15.4' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.4' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S240. Gene #60: 'del_11p15.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 27(11P15.4) MUTATED	16	35	14
DEL PEAK 27(11P15.4) WILD-TYPE	104	57	95

Figure S240. Get High-res Image Gene #60: 'del_11p15.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.4' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S241. Gene #60: 'del_11p15.4' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	90	91
DEL PEAK 27(11P15.4) MUTATED	6	15	35
DEL PEAK 27(11P15.4) WILD-TYPE	76	75	56

Figure S241. Get High-res Image Gene #60: 'del_11p15.4' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_11p15.4' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.045

Table S242. Gene #60: 'del_11p15.4' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
DEL PEAK 27(11P15.4) MUTATED	31	10	38
DEL PEAK 27(11P15.4) WILD-TYPE	148	73	68

Figure S242. Get High-res Image Gene #60: 'del_11p15.4' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11q23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S243. Gene #61: 'del_11q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 28(11Q23.2) MUTATED	17	8	24	2	31
DEL PEAK 28(11Q23.2) WILD-TYPE	152	25	42	8	60

Figure S243. Get High-res Image Gene #61: 'del_11q23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.065

Table S244. Gene #61: 'del_11q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 28(11Q23.2) MUTATED	4	1	7	24	7	12	0
DEL PEAK 28(11Q23.2) WILD-TYPE	34	20	42	38	34	28	21

Figure S244. Get High-res Image Gene #61: 'del_11q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S245. Gene #62: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 29(12P13.1) MUTATED	4	2	13	4	34
DEL PEAK 29(12P13.1) WILD-TYPE	165	31	53	6	57

Figure S245. Get High-res Image Gene #62: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S246. Gene #62: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 29(12P13.1) MUTATED	10	33	6
DEL PEAK 29(12P13.1) WILD-TYPE	110	59	103

Figure S246. Get High-res Image Gene #62: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12p13.1' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S247. Gene #62: 'del_12p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 29(12P13.1) MUTATED	4	5	5	4	23
DEL PEAK 29(12P13.1) WILD-TYPE	61	57	41	33	39

Figure S247. Get High-res Image Gene #62: 'del_12p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S248. Gene #62: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 29(12P13.1) MUTATED	7	0	3	8	6	17	0
DEL PEAK 29(12P13.1) WILD-TYPE	31	21	46	54	35	23	21

Figure S248. Get High-res Image Gene #62: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.029

Table S249. Gene #62: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
DEL PEAK 29(12P13.1) MUTATED	21	3	25
DEL PEAK 29(12P13.1) WILD-TYPE	156	59	57

Figure S249. Get High-res Image Gene #62: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q12.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S250. Gene #63: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 30(13Q12.11) MUTATED	7	1	23	2	19
DEL PEAK 30(13Q12.11) WILD-TYPE	162	32	43	8	72

Figure S250. Get High-res Image Gene #63: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S251. Gene #64: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 31(14Q23.3) MUTATED	19	9	34	4	42
DEL PEAK 31(14Q23.3) WILD-TYPE	150	24	32	6	49

Figure S251. Get High-res Image Gene #64: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q23.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S252. Gene #64: 'del_14q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 31(14Q23.3) MUTATED	26	46	23
DEL PEAK 31(14Q23.3) WILD-TYPE	94	46	86

Figure S252. Get High-res Image Gene #64: 'del_14q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q23.3' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.023

Table S253. Gene #64: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 31(14Q23.3) MUTATED	11	14	13	6	33
DEL PEAK 31(14Q23.3) WILD-TYPE	54	48	33	31	29

Figure S253. Get High-res Image Gene #64: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.21

Table S254. Gene #64: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 31(14Q23.3) MUTATED	9	5	10	15	10	25	3
DEL PEAK 31(14Q23.3) WILD-TYPE	29	16	39	47	31	15	18

Figure S254. Get High-res Image Gene #64: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S255. Gene #64: 'del_14q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
DEL PEAK 31(14Q23.3) MUTATED	40	18	50
DEL PEAK 31(14Q23.3) WILD-TYPE	139	65	56

Figure S255. Get High-res Image Gene #64: 'del_14q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_14q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.065

Table S256. Gene #64: 'del_14q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
DEL PEAK 31(14Q23.3) MUTATED	44	12	39
DEL PEAK 31(14Q23.3) WILD-TYPE	133	50	43

Figure S256. Get High-res Image Gene #64: 'del_14q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q32.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S257. Gene #65: 'del_14q32.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 32(14Q32.33) MUTATED	21	9	36	2	38
DEL PEAK 32(14Q32.33) WILD-TYPE	148	24	30	8	53

Figure S257. Get High-res Image Gene #65: 'del_14q32.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S258. Gene #66: 'del_15q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 33(15Q11.2) MUTATED	12	13	25	4	47
DEL PEAK 33(15Q11.2) WILD-TYPE	157	20	41	6	44

Figure S258. Get High-res Image Gene #66: 'del_15q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q11.2' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S259. Gene #66: 'del_15q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 33(15Q11.2) MUTATED	25	44	22
DEL PEAK 33(15Q11.2) WILD-TYPE	95	48	87

Figure S259. Get High-res Image Gene #66: 'del_15q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S260. Gene #66: 'del_15q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 33(15Q11.2) MUTATED	9	3	15	8	31
DEL PEAK 33(15Q11.2) WILD-TYPE	56	59	31	29	31

Figure S260. Get High-res Image Gene #66: 'del_15q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S261. Gene #66: 'del_15q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 33(15Q11.2) MUTATED	8	3	2	19	16	17	1
DEL PEAK 33(15Q11.2) WILD-TYPE	30	18	47	43	25	23	20

Figure S261. Get High-res Image Gene #66: 'del_15q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.12

Table S262. Gene #66: 'del_15q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
DEL PEAK 33(15Q11.2) MUTATED	28	18	55
DEL PEAK 33(15Q11.2) WILD-TYPE	91	90	86

Figure S262. Get High-res Image Gene #66: 'del_15q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_15q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S263. Gene #66: 'del_15q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
DEL PEAK 33(15Q11.2) MUTATED	44	10	47
DEL PEAK 33(15Q11.2) WILD-TYPE	135	73	59

Figure S263. Get High-res Image Gene #66: 'del_15q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S264. Gene #66: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
DEL PEAK 33(15Q11.2) MUTATED	16	61	14
DEL PEAK 33(15Q11.2) WILD-TYPE	61	83	86

Figure S264. Get High-res Image Gene #66: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_15q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S265. Gene #66: 'del_15q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
DEL PEAK 33(15Q11.2) MUTATED	49	4	38
DEL PEAK 33(15Q11.2) WILD-TYPE	128	58	44

Figure S265. Get High-res Image Gene #66: 'del_15q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S266. Gene #67: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 34(15Q15.1) MUTATED	13	12	27	4	47
DEL PEAK 34(15Q15.1) WILD-TYPE	156	21	39	6	44

Figure S266. Get High-res Image Gene #67: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q15.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S267. Gene #67: 'del_15q15.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 34(15Q15.1) MUTATED	24	46	20
DEL PEAK 34(15Q15.1) WILD-TYPE	96	46	89

Figure S267. Get High-res Image Gene #67: 'del_15q15.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q15.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S268. Gene #67: 'del_15q15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 34(15Q15.1) MUTATED	11	3	16	7	31
DEL PEAK 34(15Q15.1) WILD-TYPE	54	59	30	30	31

Figure S268. Get High-res Image Gene #67: 'del_15q15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S269. Gene #67: 'del_15q15.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 34(15Q15.1) MUTATED	10	4	1	19	14	19	1
DEL PEAK 34(15Q15.1) WILD-TYPE	28	17	48	43	27	21	20

Figure S269. Get High-res Image Gene #67: 'del_15q15.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S270. Gene #67: 'del_15q15.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
DEL PEAK 34(15Q15.1) MUTATED	46	9	48
DEL PEAK 34(15Q15.1) WILD-TYPE	133	74	58

Figure S270. Get High-res Image Gene #67: 'del_15q15.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S271. Gene #67: 'del_15q15.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
DEL PEAK 34(15Q15.1) MUTATED	18	59	13
DEL PEAK 34(15Q15.1) WILD-TYPE	59	85	87

Figure S271. Get High-res Image Gene #67: 'del_15q15.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_15q15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S272. Gene #67: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
DEL PEAK 34(15Q15.1) MUTATED	49	4	37
DEL PEAK 34(15Q15.1) WILD-TYPE	128	58	45

Figure S272. Get High-res Image Gene #67: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S273. Gene #68: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 35(16P13.3) MUTATED	7	4	23	0	41
DEL PEAK 35(16P13.3) WILD-TYPE	162	29	43	10	50

Figure S273. Get High-res Image Gene #68: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S274. Gene #68: 'del_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 35(16P13.3) MUTATED	8	6	4	3	29
DEL PEAK 35(16P13.3) WILD-TYPE	57	56	42	34	33

Figure S274. Get High-res Image Gene #68: 'del_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S275. Gene #68: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 35(16P13.3) MUTATED	8	0	4	7	6	22	3
DEL PEAK 35(16P13.3) WILD-TYPE	30	21	45	55	35	18	18

Figure S275. Get High-res Image Gene #68: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S276. Gene #68: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
DEL PEAK 35(16P13.3) MUTATED	13	14	48
DEL PEAK 35(16P13.3) WILD-TYPE	106	94	93

Figure S276. Get High-res Image Gene #68: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.029

Table S277. Gene #68: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
DEL PEAK 35(16P13.3) MUTATED	27	10	38
DEL PEAK 35(16P13.3) WILD-TYPE	152	73	68

Figure S277. Get High-res Image Gene #68: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S278. Gene #68: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
DEL PEAK 35(16P13.3) MUTATED	5	47	15
DEL PEAK 35(16P13.3) WILD-TYPE	72	97	85

Figure S278. Get High-res Image Gene #68: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S279. Gene #68: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
DEL PEAK 35(16P13.3) MUTATED	28	5	34
DEL PEAK 35(16P13.3) WILD-TYPE	149	57	48

Figure S279. Get High-res Image Gene #68: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S280. Gene #69: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 36(16Q23.1) MUTATED	37	16	36	3	54
DEL PEAK 36(16Q23.1) WILD-TYPE	132	17	30	7	37

Figure S280. Get High-res Image Gene #69: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.029

Table S281. Gene #69: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
DEL PEAK 36(16Q23.1) MUTATED	28	74	24
DEL PEAK 36(16Q23.1) WILD-TYPE	49	70	76

Figure S281. Get High-res Image Gene #69: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S282. Gene #70: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 37(17P12) MUTATED	13	21	40	3	64
DEL PEAK 37(17P12) WILD-TYPE	156	12	26	7	27

Figure S282. Get High-res Image Gene #70: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S283. Gene #70: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 37(17P12) MUTATED	36	66	23
DEL PEAK 37(17P12) WILD-TYPE	84	26	86

Figure S283. Get High-res Image Gene #70: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S284. Gene #70: 'del_17p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 37(17P12) MUTATED	15	10	19	12	42
DEL PEAK 37(17P12) WILD-TYPE	50	52	27	25	20

Figure S284. Get High-res Image Gene #70: 'del_17p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S285. Gene #70: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 37(17P12) MUTATED	14	2	7	25	17	30	3
DEL PEAK 37(17P12) WILD-TYPE	24	19	42	37	24	10	18

Figure S285. Get High-res Image Gene #70: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.023

Table S286. Gene #70: 'del_17p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
DEL PEAK 37(17P12) MUTATED	44	24	72
DEL PEAK 37(17P12) WILD-TYPE	75	84	69

Figure S286. Get High-res Image Gene #70: 'del_17p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S287. Gene #70: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
DEL PEAK 37(17P12) MUTATED	60	18	62
DEL PEAK 37(17P12) WILD-TYPE	119	65	44

Figure S287. Get High-res Image Gene #70: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S288. Gene #70: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
DEL PEAK 37(17P12) MUTATED	26	77	22
DEL PEAK 37(17P12) WILD-TYPE	51	67	78

Figure S288. Get High-res Image Gene #70: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S289. Gene #70: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
DEL PEAK 37(17P12) MUTATED	61	10	54
DEL PEAK 37(17P12) WILD-TYPE	116	52	28

Figure S289. Get High-res Image Gene #70: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S290. Gene #71: 'del_17q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 38(17Q24.3) MUTATED	7	9	16	3	33
DEL PEAK 38(17Q24.3) WILD-TYPE	162	24	50	7	58

Figure S290. Get High-res Image Gene #71: 'del_17q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q24.3' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.06

Table S291. Gene #71: 'del_17q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 38(17Q24.3) MUTATED	18	29	9
DEL PEAK 38(17Q24.3) WILD-TYPE	102	63	100

Figure S291. Get High-res Image Gene #71: 'del_17q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.2

Table S292. Gene #71: 'del_17q24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
DEL PEAK 38(17Q24.3) MUTATED	24	10	33
DEL PEAK 38(17Q24.3) WILD-TYPE	155	73	73

Figure S292. Get High-res Image Gene #71: 'del_17q24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S293. Gene #72: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 39(18Q21.2) MUTATED	34	23	46	2	64
DEL PEAK 39(18Q21.2) WILD-TYPE	135	10	20	8	27

Figure S293. Get High-res Image Gene #72: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.22

Table S294. Gene #72: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 39(18Q21.2) MUTATED	48	58	41
DEL PEAK 39(18Q21.2) WILD-TYPE	72	34	68

Figure S294. Get High-res Image Gene #72: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.16

Table S295. Gene #72: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 39(18Q21.2) MUTATED	26	19	23	11	41
DEL PEAK 39(18Q21.2) WILD-TYPE	39	43	23	26	21

Figure S295. Get High-res Image Gene #72: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.11

Table S296. Gene #72: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
DEL PEAK 39(18Q21.2) MUTATED	30	84	33
DEL PEAK 39(18Q21.2) WILD-TYPE	47	60	67

Figure S296. Get High-res Image Gene #72: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S297. Gene #73: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 40(19P13.3) MUTATED	7	13	35	4	68
DEL PEAK 40(19P13.3) WILD-TYPE	162	20	31	6	23

Figure S297. Get High-res Image Gene #73: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S298. Gene #73: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 40(19P13.3) MUTATED	26	63	22
DEL PEAK 40(19P13.3) WILD-TYPE	94	29	87

Figure S298. Get High-res Image Gene #73: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S299. Gene #73: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 40(19P13.3) MUTATED	13	4	13	8	47
DEL PEAK 40(19P13.3) WILD-TYPE	52	58	33	29	15

Figure S299. Get High-res Image Gene #73: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S300. Gene #73: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 40(19P13.3) MUTATED	14	2	4	21	12	30	2
DEL PEAK 40(19P13.3) WILD-TYPE	24	19	45	41	29	10	19

Figure S300. Get High-res Image Gene #73: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S301. Gene #73: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
DEL PEAK 40(19P13.3) MUTATED	32	16	78
DEL PEAK 40(19P13.3) WILD-TYPE	87	92	63

Figure S301. Get High-res Image Gene #73: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S302. Gene #73: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
DEL PEAK 40(19P13.3) MUTATED	42	9	75
DEL PEAK 40(19P13.3) WILD-TYPE	137	74	31

Figure S302. Get High-res Image Gene #73: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S303. Gene #73: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
DEL PEAK 40(19P13.3) MUTATED	18	74	19
DEL PEAK 40(19P13.3) WILD-TYPE	59	70	81

Figure S303. Get High-res Image Gene #73: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S304. Gene #73: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
DEL PEAK 40(19P13.3) MUTATED	48	4	59
DEL PEAK 40(19P13.3) WILD-TYPE	129	58	23

Figure S304. Get High-res Image Gene #73: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S305. Gene #74: 'del_19q13.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 41(19Q13.11) MUTATED	4	5	15	4	29
DEL PEAK 41(19Q13.11) WILD-TYPE	165	28	51	6	62

Figure S305. Get High-res Image Gene #74: 'del_19q13.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S306. Gene #74: 'del_19q13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 41(19Q13.11) MUTATED	14	33	3
DEL PEAK 41(19Q13.11) WILD-TYPE	106	59	106

Figure S306. Get High-res Image Gene #74: 'del_19q13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19q13.11' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S307. Gene #74: 'del_19q13.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 41(19Q13.11) MUTATED	6	2	6	3	21
DEL PEAK 41(19Q13.11) WILD-TYPE	59	60	40	34	41

Figure S307. Get High-res Image Gene #74: 'del_19q13.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19q13.11' versus 'MIRSEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.12

Table S308. Gene #74: 'del_19q13.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
DEL PEAK 41(19Q13.11) MUTATED	15	7	35
DEL PEAK 41(19Q13.11) WILD-TYPE	104	101	106

Figure S308. Get High-res Image Gene #74: 'del_19q13.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19q13.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S309. Gene #74: 'del_19q13.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
DEL PEAK 41(19Q13.11) MUTATED	19	5	33
DEL PEAK 41(19Q13.11) WILD-TYPE	160	78	73

Figure S309. Get High-res Image Gene #74: 'del_19q13.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.14

Table S310. Gene #74: 'del_19q13.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
DEL PEAK 41(19Q13.11) MUTATED	9	35	6
DEL PEAK 41(19Q13.11) WILD-TYPE	68	109	94

Figure S310. Get High-res Image Gene #74: 'del_19q13.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19q13.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.034

Table S311. Gene #74: 'del_19q13.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
DEL PEAK 41(19Q13.11) MUTATED	22	3	25
DEL PEAK 41(19Q13.11) WILD-TYPE	155	59	57

Figure S311. Get High-res Image Gene #74: 'del_19q13.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S312. Gene #76: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 43(21Q11.2) MUTATED	27	18	40	7	48
DEL PEAK 43(21Q11.2) WILD-TYPE	142	15	26	3	43

Figure S312. Get High-res Image Gene #76: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.14

Table S313. Gene #76: 'del_21q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 43(21Q11.2) MUTATED	39	52	34
DEL PEAK 43(21Q11.2) WILD-TYPE	81	40	75

Figure S313. Get High-res Image Gene #76: 'del_21q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q11.2' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.034

Table S314. Gene #76: 'del_21q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
DEL PEAK 43(21Q11.2) MUTATED	36	30	74
DEL PEAK 43(21Q11.2) WILD-TYPE	83	78	67

Figure S314. Get High-res Image Gene #76: 'del_21q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_21q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.023

Table S315. Gene #76: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
DEL PEAK 43(21Q11.2) MUTATED	20	75	30
DEL PEAK 43(21Q11.2) WILD-TYPE	57	69	70

Figure S315. Get High-res Image Gene #76: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_21q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.16

Table S316. Gene #76: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
DEL PEAK 43(21Q11.2) MUTATED	61	17	47
DEL PEAK 43(21Q11.2) WILD-TYPE	116	45	35

Figure S316. Get High-res Image Gene #76: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q22.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S317. Gene #77: 'del_21q22.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 44(21Q22.13) MUTATED	30	17	46	7	52
DEL PEAK 44(21Q22.13) WILD-TYPE	139	16	20	3	39

Figure S317. Get High-res Image Gene #77: 'del_21q22.13' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q22.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.18

Table S318. Gene #77: 'del_21q22.13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 44(21Q22.13) MUTATED	19	2	16	20	17	24	3
DEL PEAK 44(21Q22.13) WILD-TYPE	19	19	33	42	24	16	18

Figure S318. Get High-res Image Gene #77: 'del_21q22.13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_21q22.13' versus 'MIRSEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.12

Table S319. Gene #77: 'del_21q22.13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
DEL PEAK 44(21Q22.13) MUTATED	41	34	77
DEL PEAK 44(21Q22.13) WILD-TYPE	78	74	64

Figure S319. Get High-res Image Gene #77: 'del_21q22.13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_21q22.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.023

Table S320. Gene #77: 'del_21q22.13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
DEL PEAK 44(21Q22.13) MUTATED	24	79	31
DEL PEAK 44(21Q22.13) WILD-TYPE	53	65	69

Figure S320. Get High-res Image Gene #77: 'del_21q22.13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S321. Gene #78: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 45(22Q13.31) MUTATED	17	10	42	6	54
DEL PEAK 45(22Q13.31) WILD-TYPE	152	23	24	4	37

Figure S321. Get High-res Image Gene #78: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S322. Gene #78: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 45(22Q13.31) MUTATED	35	55	22
DEL PEAK 45(22Q13.31) WILD-TYPE	85	37	87

Figure S322. Get High-res Image Gene #78: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.31' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S323. Gene #78: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
DEL PEAK 45(22Q13.31) MUTATED	31	27	70
DEL PEAK 45(22Q13.31) WILD-TYPE	88	81	71

Figure S323. Get High-res Image Gene #78: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S324. Gene #78: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
DEL PEAK 45(22Q13.31) MUTATED	48	19	61
DEL PEAK 45(22Q13.31) WILD-TYPE	131	64	45

Figure S324. Get High-res Image Gene #78: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S325. Gene #78: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
DEL PEAK 45(22Q13.31) MUTATED	55	11	46
DEL PEAK 45(22Q13.31) WILD-TYPE	122	51	36

Figure S325. Get High-res Image Gene #78: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S326. Gene #79: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 46(XP22.2) MUTATED	6	6	21	3	31
DEL PEAK 46(XP22.2) WILD-TYPE	163	27	45	7	60

Figure S326. Get High-res Image Gene #79: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp22.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S327. Gene #79: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 46(XP22.2) MUTATED	17	34	10
DEL PEAK 46(XP22.2) WILD-TYPE	103	58	99

Figure S327. Get High-res Image Gene #79: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp22.2' versus 'MRNASEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.1

Table S328. Gene #79: 'del_xp22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 46(XP22.2) MUTATED	3	8	8	10	21
DEL PEAK 46(XP22.2) WILD-TYPE	62	54	38	27	41

Figure S328. Get High-res Image Gene #79: 'del_xp22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.12

Table S329. Gene #79: 'del_xp22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 46(XP22.2) MUTATED	11	0	5	10	15	9	0
DEL PEAK 46(XP22.2) WILD-TYPE	27	21	44	52	26	31	21

Figure S329. Get High-res Image Gene #79: 'del_xp22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.086

Table S330. Gene #79: 'del_xp22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
DEL PEAK 46(XP22.2) MUTATED	27	6	29
DEL PEAK 46(XP22.2) WILD-TYPE	150	56	53

Figure S330. Get High-res Image Gene #79: 'del_xp22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S331. Gene #80: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 47(XP21.1) MUTATED	6	8	21	2	27
DEL PEAK 47(XP21.1) WILD-TYPE	163	25	45	8	64

Figure S331. Get High-res Image Gene #80: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq21.33' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S332. Gene #81: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
DEL PEAK 48(XQ21.33) MUTATED	6	6	14	0	20
DEL PEAK 48(XQ21.33) WILD-TYPE	163	27	52	10	71

Figure S332. Get High-res Image Gene #81: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq21.33' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.11

Table S333. Gene #81: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
DEL PEAK 48(XQ21.33) MUTATED	12	21	5
DEL PEAK 48(XQ21.33) WILD-TYPE	108	71	104

Figure S333. Get High-res Image Gene #81: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = STAD-TP.transferedmergedcluster.txt
Number of patients = 369
Number of significantly focal cnvs = 81
Number of molecular subtypes = 10
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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