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

Prostate Adenocarcinoma (Primary solid tumor)

28 January 2016 | analyses__2016_01_28

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 (2016): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1G1608M

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 63 focal events and 10 molecular subtypes across 492 patients, 419 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3q26.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_4p16.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.
amp_4q13.3 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_5q35.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7p14.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8p11.23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_9q33.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_11q13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_12q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_13q12.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_14q21.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_15q11.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_16q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_17p11.2 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q23.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_18q21.31 cnv correlated to 'CN_CNMF'.
amp_19q13.43 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_20q13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_xp22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_xq12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_xq21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_xq21.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_xq25 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_1p31.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1q23.1 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_1q42.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2p21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_2q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_3q29 cnv correlated to 'MRNASEQ_CNMF'.
del_4q28.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_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_5q13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6p25.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_6q14.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p23 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_11q22.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_11q23.2 cnv correlated to 'CN_CNMF'.
del_12p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12q24.32 cnv correlated to 'CN_CNMF'.
del_13q14.13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q24.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_17p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17q21.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_18q21.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19q13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_21q22.2 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_21q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 63 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, 419 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 8p11 23	67 (14%)	425	1e-05 (5.25e-05)	1e-05 (5.25e-05)	0.00037 (0.00112)	0.0108 (0.0205)	1e-05 (5.25e-05)	0.00039 (0.00118)	0.00097 (0.00257)	0.00131 (0.00324)	0.00017 (0.000561)	0.00053 (0.00155)
amp 8q22 1	157 (32%)	335	1e-05 (5.25e-05)	1e-05 (5.25e-05)	1e-05 (5.25e-05)	2e-05 (9e-05)	1e-05 (5.25e-05)	1e-05 (5.25e-05)	1e-05 (5.25e-05)	1e-05 (5.25e-05)	2e-05 (9e-05)	3e-05 (0.000129)
amp 8q24 21	152 (31%)	340	1e-05 (5.25e-05)	1e-05 (5.25e-05)	1e-05 (5.25e-05)	5e-05 (0.000198)	1e-05 (5.25e-05)	1e-05 (5.25e-05)	1e-05 (5.25e-05)	1e-05 (5.25e-05)	4e-05 (0.000161)	0.00056 (0.00162)
amp 12q23 1	36 (7%)	456	0.00096 (0.00255)	3e-05 (0.000129)	0.00515 (0.0107)	0.0123 (0.0231)	0.00205 (0.00484)	0.00757 (0.0149)	0.00655 (0.0131)	0.00013 (0.000445)	0.014 (0.0255)	0.0483 (0.0732)
del 2q22 1	92 (19%)	400	1e-05 (5.25e-05)	1e-05 (5.25e-05)	0.00194 (0.00463)	0.0477 (0.0726)	1e-05 (5.25e-05)	1e-05 (5.25e-05)	1e-05 (5.25e-05)	2e-05 (9e-05)	0.00094 (0.00255)	0.00107 (0.00281)
del 6q14 3	180 (37%)	312	1e-05 (5.25e-05)	1e-05 (5.25e-05)	0.00341 (0.00741)	8e-05 (0.000295)	1e-05 (5.25e-05)	1e-05 (5.25e-05)	1e-05 (5.25e-05)	2e-05 (9e-05)	0.0203 (0.0351)	0.00796 (0.0156)
del 13q22 1	176 (36%)	316	1e-05 (5.25e-05)	1e-05 (5.25e-05)	0.0245 (0.0409)	0.00012 (0.000418)	1e-05 (5.25e-05)	8e-05 (0.000295)	0.0182 (0.0318)	0.00148 (0.00359)	0.0008 (0.00224)	1e-05 (5.25e-05)
del 15q21 3	67 (14%)	425	1e-05 (5.25e-05)	2e-05 (9e-05)	0.00033 (0.00101)	0.0448 (0.0688)	7e-05 (0.000267)	1e-05 (5.25e-05)	0.00016 (0.000533)	3e-05 (0.000129)	0.00095 (0.00255)	8e-05 (0.000295)
del 17p13 1	163 (33%)	329	1e-05 (5.25e-05)	1e-05 (5.25e-05)	0.0235 (0.0397)	0.0286 (0.0469)	1e-05 (5.25e-05)	1e-05 (5.25e-05)	0.00013 (0.000445)	1e-05 (5.25e-05)	0.00502 (0.0105)	0.00222 (0.00509)
amp 1q22	40 (8%)	452	1e-05 (5.25e-05)	0.013 (0.024)	0.00289 (0.00646)	0.0423 (0.0659)	0.022 (0.0375)	0.00012 (0.000418)	0.00484 (0.0102)	0.00045 (0.00134)	0.143 (0.182)	0.0133 (0.0245)
amp 7p14 3	104 (21%)	388	1e-05 (5.25e-05)	1e-05 (5.25e-05)	0.00129 (0.00322)	0.316 (0.359)	1e-05 (5.25e-05)	3e-05 (0.000129)	0.00166 (0.00401)	0.00047 (0.0014)	0.00654 (0.0131)	0.00546 (0.0112)
amp 7q22 1	101 (21%)	391	1e-05 (5.25e-05)	1e-05 (5.25e-05)	0.00117 (0.003)	0.251 (0.294)	1e-05 (5.25e-05)	1e-05 (5.25e-05)	0.00066 (0.00188)	1e-05 (5.25e-05)	0.00124 (0.00314)	0.00064 (0.00183)
del 2q22 3	85 (17%)	407	1e-05 (5.25e-05)	1e-05 (5.25e-05)	0.00218 (0.00503)	0.107 (0.141)	1e-05 (5.25e-05)	1e-05 (5.25e-05)	1e-05 (5.25e-05)	2e-05 (9e-05)	0.00391 (0.00844)	0.00079 (0.00222)
del 8p21 3	294 (60%)	198	1e-05 (5.25e-05)	1e-05 (5.25e-05)	0.117 (0.151)	0.00139 (0.00341)	1e-05 (5.25e-05)	1e-05 (5.25e-05)	2e-05 (9e-05)	1e-05 (5.25e-05)	0.0112 (0.0211)	0.00852 (0.0167)
del 10q23 31	157 (32%)	335	1e-05 (5.25e-05)	1e-05 (5.25e-05)	0.00111 (0.00289)	0.22 (0.264)	1e-05 (5.25e-05)	1e-05 (5.25e-05)	9e-05 (0.000328)	1e-05 (5.25e-05)	0.0484 (0.0732)	0.00032 (0.000993)
del 12p13 1	124 (25%)	368	1e-05 (5.25e-05)	0.00091 (0.00249)	0.238 (0.282)	0.0238 (0.0402)	7e-05 (0.000267)	0.00393 (0.00845)	0.00011 (0.000389)	6e-05 (0.000233)	0.00035 (0.00107)	0.0162 (0.0286)
del 13q14 13	227 (46%)	265	1e-05 (5.25e-05)	1e-05 (5.25e-05)	0.101 (0.134)	0.0453 (0.0695)	0.00079 (0.00222)	6e-05 (0.000233)	0.00048 (0.00142)	0.00033 (0.00101)	1e-05 (5.25e-05)	0.00119 (0.00302)
del 18q21 31	131 (27%)	361	1e-05 (5.25e-05)	0.00013 (0.000445)	0.214 (0.259)	0.00219 (0.00504)	0.0001 (0.000358)	0.0124 (0.0231)	0.00014 (0.000477)	0.0182 (0.0318)	0.00279 (0.00626)	0.00011 (0.000389)
del 18q23	137 (28%)	355	1e-05 (5.25e-05)	0.00029 (0.000913)	0.623 (0.658)	0.0433 (0.0669)	0.00056 (0.00162)	0.0432 (0.0669)	0.00668 (0.0133)	0.00746 (0.0147)	0.00214 (0.00496)	0.00129 (0.00322)
amp 3q21 3	75 (15%)	417	1e-05 (5.25e-05)	4e-05 (0.000161)	0.0744 (0.106)	0.00521 (0.0107)	2e-05 (9e-05)	0.0001 (0.000358)	0.0565 (0.0833)	0.00032 (0.000993)	0.00597 (0.012)	0.00616 (0.0124)
amp 3q26 2	86 (17%)	406	1e-05 (5.25e-05)	0.00944 (0.0183)	0.152 (0.192)	0.0857 (0.117)	8e-05 (0.000295)	0.0147 (0.0267)	0.0334 (0.054)	0.00862 (0.0168)	0.0185 (0.0322)	5e-05 (0.000198)
amp 11q13 2	48 (10%)	444	1e-05 (5.25e-05)	0.00096 (0.00255)	0.0211 (0.0362)	0.11 (0.143)	0.00095 (0.00255)	0.00045 (0.00134)	0.0124 (0.0231)	0.00015 (0.000503)	0.00516 (0.0107)	0.0969 (0.13)
amp 20q13 2	45 (9%)	447	1e-05 (5.25e-05)	4e-05 (0.000161)	0.00454 (0.00957)	0.0279 (0.0461)	0.00024 (0.00076)	0.00135 (0.00332)	0.0458 (0.07)	7e-05 (0.000267)	0.0825 (0.114)	0.194 (0.237)
amp xq12	16 (3%)	476	2e-05 (9e-05)	4e-05 (0.000161)	0.0134 (0.0247)	0.0283 (0.0466)	8e-05 (0.000295)	0.00018 (0.000591)	0.0357 (0.0569)	0.00074 (0.0021)	0.619 (0.656)	0.427 (0.469)
del 1p22 1	58 (12%)	434	1e-05 (5.25e-05)	2e-05 (9e-05)	0.23 (0.275)	0.438 (0.481)	2e-05 (9e-05)	0.00015 (0.000503)	1e-05 (5.25e-05)	0.00317 (0.00703)	0.0353 (0.0564)	2e-05 (9e-05)
del 4q28 2	51 (10%)	441	1e-05 (5.25e-05)	1e-05 (5.25e-05)	0.336 (0.376)	0.0521 (0.0779)	1e-05 (5.25e-05)	2e-05 (9e-05)	0.00131 (0.00324)	0.0153 (0.0276)	0.00368 (0.00797)	0.00206 (0.00484)
del 5q11 2	105 (21%)	387	1e-05 (5.25e-05)	2e-05 (9e-05)	0.0738 (0.105)	0.478 (0.52)	1e-05 (5.25e-05)	6e-05 (0.000233)	2e-05 (9e-05)	1e-05 (5.25e-05)	0.0002 (0.000646)	9e-05 (0.000328)
del 5q13 2	99 (20%)	393	1e-05 (5.25e-05)	2e-05 (9e-05)	0.0581 (0.085)	0.687 (0.717)	1e-05 (5.25e-05)	0.00272 (0.00612)	1e-05 (5.25e-05)	1e-05 (5.25e-05)	0.00245 (0.00557)	4e-05 (0.000161)
del 5q21 1	109 (22%)	383	1e-05 (5.25e-05)	1e-05 (5.25e-05)	0.0859 (0.117)	0.171 (0.212)	1e-05 (5.25e-05)	1e-05 (5.25e-05)	1e-05 (5.25e-05)	0.00272 (0.00612)	0.00396 (0.00849)	0.00022 (7e-04)
del 11p11 2	34 (7%)	458	0.00012 (0.000418)	0.00512 (0.0106)	0.00142 (0.00345)	0.0959 (0.13)	3e-05 (0.000129)	0.0253 (0.0421)	0.0166 (0.0292)	0.024 (0.0404)	0.0282 (0.0466)	0.0755 (0.106)
del 16q22 3	191 (39%)	301	1e-05 (5.25e-05)	1e-05 (5.25e-05)	0.0841 (0.115)	0.299 (0.343)	1e-05 (5.25e-05)	0.00015 (0.000503)	1e-05 (5.25e-05)	1e-05 (5.25e-05)	2e-05 (9e-05)	0.0145 (0.0265)
del 1p31 3	60 (12%)	432	1e-05 (5.25e-05)	1e-05 (5.25e-05)	0.266 (0.308)	0.897 (0.905)	1e-05 (5.25e-05)	1e-05 (5.25e-05)	0.00085 (0.00236)	0.169 (0.211)	0.00327 (0.00715)	0.016 (0.0284)
del 16q24 1	213 (43%)	279	1e-05 (5.25e-05)	1e-05 (5.25e-05)	0.239 (0.282)	0.109 (0.143)	1e-05 (5.25e-05)	0.0059 (0.012)	1e-05 (5.25e-05)	1e-05 (5.25e-05)	0.00335 (0.0073)	0.191 (0.234)
amp 4q13 3	22 (4%)	470	0.0001 (0.000358)	0.125 (0.161)	0.0429 (0.0666)	0.039 (0.0613)	0.0155 (0.0278)	0.282 (0.325)	0.00955 (0.0185)	0.0658 (0.0953)	0.0464 (0.0707)	0.142 (0.18)
amp 5q35 3	28 (6%)	464	1e-05 (5.25e-05)	0.0003 (0.00094)	0.115 (0.149)	0.204 (0.248)	0.327 (0.368)	0.0422 (0.0658)	0.458 (0.5)	0.00101 (0.00266)	0.00318 (0.00703)	0.0444 (0.0684)
amp 9q33 3	62 (13%)	430	1e-05 (5.25e-05)	1e-05 (5.25e-05)	0.00428 (0.00911)	0.0707 (0.101)	3e-05 (0.000129)	0.0155 (0.0278)	0.0992 (0.133)	0.00093 (0.00254)	0.0812 (0.112)	0.0966 (0.13)
amp 13q12 11	25 (5%)	467	2e-05 (9e-05)	0.00119 (0.00302)	0.00325 (0.00713)	0.0013 (0.00324)	0.00206 (0.00484)	0.108 (0.142)	0.232 (0.276)	0.0321 (0.0519)	0.0793 (0.11)	0.27 (0.312)
amp 14q21 1	30 (6%)	462	1e-05 (5.25e-05)	0.0512 (0.0768)	0.321 (0.364)	0.816 (0.836)	4e-05 (0.000161)	0.036 (0.0573)	0.182 (0.224)	0.0107 (0.0205)	0.0161 (0.0286)	0.022 (0.0375)
amp xp22 2	27 (5%)	465	1e-05 (5.25e-05)	2e-05 (9e-05)	0.0936 (0.127)	0.0369 (0.0586)	0.00019 (0.00062)	0.0383 (0.0604)	0.0907 (0.123)	0.00746 (0.0147)	0.116 (0.151)	0.348 (0.389)
del 1q42 3	47 (10%)	445	0.00017 (0.000561)	1e-05 (5.25e-05)	0.307 (0.35)	0.307 (0.35)	0.0154 (0.0278)	0.0752 (0.106)	0.00207 (0.00485)	0.0312 (0.0507)	0.634 (0.668)	0.0159 (0.0283)
del 3p13	78 (16%)	414	0.00113 (0.00292)	1e-05 (5.25e-05)	0.0418 (0.0653)	0.209 (0.253)	1e-05 (5.25e-05)	1e-05 (5.25e-05)	0.132 (0.169)	0.0656 (0.0953)	0.00179 (0.00429)	0.0781 (0.109)
del 19q13 2	52 (11%)	440	1e-05 (5.25e-05)	0.00312 (0.00695)	0.589 (0.626)	0.418 (0.461)	0.00126 (0.00318)	0.0487 (0.0735)	0.00022 (7e-04)	0.00089 (0.00245)	0.0777 (0.109)	0.23 (0.275)
del 21q22 3	146 (30%)	346	4e-05 (0.000161)	1e-05 (5.25e-05)	0.0108 (0.0205)	0.363 (0.405)	1e-05 (5.25e-05)	1e-05 (5.25e-05)	0.0566 (0.0833)	1e-05 (5.25e-05)	0.922 (0.929)	0.057 (0.0836)
amp xq21 1	14 (3%)	478	0.00233 (0.00532)	0.0293 (0.048)	0.0775 (0.109)	0.0106 (0.0203)	0.0351 (0.0563)	0.00404 (0.00863)	0.415 (0.459)	0.236 (0.28)	0.566 (0.607)	0.88 (0.892)
amp xq21 31	13 (3%)	479	0.00112 (0.0029)	0.0128 (0.0238)	0.254 (0.297)	0.0278 (0.0461)	0.037 (0.0586)	0.00445 (0.00944)	0.408 (0.453)	0.189 (0.232)	0.846 (0.863)	0.423 (0.465)
amp xq25	19 (4%)	473	0.00214 (0.00496)	0.0157 (0.0279)	0.0133 (0.0245)	0.21 (0.254)	0.0493 (0.0741)	0.0242 (0.0405)	0.271 (0.312)	0.151 (0.191)	0.814 (0.835)	0.0839 (0.115)
del 1q23 1	28 (6%)	464	0.174 (0.215)	0.00323 (0.00711)	0.596 (0.632)	0.745 (0.773)	0.00579 (0.0118)	0.00084 (0.00234)	0.015 (0.0271)	0.054 (0.0805)	0.00944 (0.0183)	0.288 (0.332)
del 2p21	46 (9%)	446	0.0005 (0.00147)	4e-05 (0.000161)	0.407 (0.453)	0.578 (0.618)	0.00089 (0.00245)	0.0204 (0.0352)	0.00095 (0.00255)	0.0714 (0.102)	0.0642 (0.0934)	0.249 (0.293)
del 6p25 1	46 (9%)	446	1e-05 (5.25e-05)	0.00452 (0.00956)	0.0718 (0.103)	0.256 (0.298)	0.0338 (0.0544)	0.0118 (0.0224)	0.266 (0.308)	0.049 (0.0738)	0.144 (0.182)	0.742 (0.771)
del 9p23	45 (9%)	447	1e-05 (5.25e-05)	0.0601 (0.0877)	0.00492 (0.0103)	0.00545 (0.0112)	0.0972 (0.13)	0.00173 (0.00416)	0.0374 (0.059)	0.0804 (0.111)	0.394 (0.439)	0.102 (0.135)
del 17q21 31	96 (20%)	396	0.00548 (0.0112)	2e-05 (9e-05)	0.113 (0.147)	0.0348 (0.056)	3e-05 (0.000129)	0.0002 (0.000646)	0.0803 (0.111)	0.0543 (0.0807)	0.185 (0.228)	0.858 (0.871)
amp 4p16 3	20 (4%)	472	8e-05 (0.000295)	0.0172 (0.0302)	0.519 (0.56)	0.0215 (0.0368)	0.0303 (0.0495)	0.135 (0.173)	0.751 (0.779)	0.0755 (0.106)	0.765 (0.79)	0.626 (0.66)
amp 19q13 43	19 (4%)	473	1e-05 (5.25e-05)	0.0917 (0.124)	0.0687 (0.0988)	0.0661 (0.0955)	0.1 (0.134)	0.026 (0.0432)	0.0205 (0.0353)	0.0014 (0.00342)	0.157 (0.198)	0.0764 (0.108)
del 21q22 2	52 (11%)	440	0.322 (0.364)	0.00202 (0.0048)	0.17 (0.212)	0.797 (0.821)	0.00256 (0.0058)	0.00022 (7e-04)	0.0538 (0.0803)	0.041 (0.0642)	0.651 (0.684)	0.311 (0.354)
amp 16q11 2	30 (6%)	462	0.00037 (0.00112)	4e-05 (0.000161)	0.139 (0.178)	0.503 (0.545)	0.239 (0.282)	0.0574 (0.0842)	0.158 (0.198)	0.00109 (0.00285)	0.325 (0.367)	0.713 (0.744)
amp 17p11 2	22 (4%)	470	4e-05 (0.000161)	0.167 (0.21)	0.243 (0.287)	0.0184 (0.032)	0.161 (0.203)	0.393 (0.438)	0.217 (0.261)	0.0681 (0.0981)	0.802 (0.825)	0.0221 (0.0376)
amp 17q23 2	25 (5%)	467	0.00052 (0.00152)	0.00212 (0.00495)	0.097 (0.13)	0.29 (0.333)	0.13 (0.167)	0.232 (0.276)	0.22 (0.264)	0.0139 (0.0255)	0.417 (0.461)	0.448 (0.49)
amp 15q11 2	16 (3%)	476	0.00595 (0.012)	0.0241 (0.0404)	0.0566 (0.0833)	0.265 (0.307)	0.0545 (0.0807)	0.522 (0.562)	0.581 (0.619)	0.686 (0.717)	0.458 (0.5)	0.764 (0.79)
del 11q22 3	43 (9%)	449	0.0104 (0.02)	0.00986 (0.019)	0.553 (0.593)	0.114 (0.148)	0.106 (0.14)	0.104 (0.138)	0.123 (0.158)	0.783 (0.807)	0.513 (0.555)	0.168 (0.21)
amp 18q21 31	13 (3%)	479	0.00114 (0.00293)	0.0767 (0.108)	0.486 (0.528)	0.828 (0.845)	0.131 (0.168)	0.226 (0.27)	1 (1.00)	0.26 (0.302)	0.938 (0.942)	0.968 (0.971)
del 3q29	32 (7%)	460	0.828 (0.845)	0.107 (0.141)	0.316 (0.359)	0.659 (0.692)	0.0309 (0.0504)	0.0743 (0.106)	0.681 (0.714)	0.251 (0.294)	0.172 (0.213)	0.715 (0.745)
del 11q23 2	48 (10%)	444	0.0006 (0.00173)	0.191 (0.234)	0.334 (0.375)	0.101 (0.134)	0.85 (0.865)	0.924 (0.93)	0.173 (0.214)	0.465 (0.507)	0.507 (0.548)	0.59 (0.626)
del 12q24 32	43 (9%)	449	0.0129 (0.0239)	0.186 (0.228)	0.864 (0.877)	0.882 (0.892)	0.0861 (0.117)	0.569 (0.609)	0.198 (0.241)	0.553 (0.593)	0.33 (0.372)	0.991 (0.992)

'amp_1q22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
AMP PEAK 1(1Q22) MUTATED	5	0	3	32
AMP PEAK 1(1Q22) WILD-TYPE	103	91	95	163

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

'amp_1q22' versus 'METHLYATION_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.024

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
AMP PEAK 1(1Q22) MUTATED	6	10	13	11
AMP PEAK 1(1Q22) WILD-TYPE	155	127	111	59

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

'amp_1q22' versus 'RPPA_CNMF'

P value = 0.00289 (Fisher's exact test), Q value = 0.0065

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	51	44	51	58	38
AMP PEAK 1(1Q22) MUTATED	5	1	3	4	9	9
AMP PEAK 1(1Q22) WILD-TYPE	100	50	41	47	49	29

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

'amp_1q22' versus 'RPPA_CHIERARCHICAL'

P value = 0.0423 (Fisher's exact test), Q value = 0.066

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	74	113	92	68
AMP PEAK 1(1Q22) MUTATED	3	8	8	12
AMP PEAK 1(1Q22) WILD-TYPE	71	105	84	56

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

'amp_1q22' versus 'MRNASEQ_CNMF'

P value = 0.022 (Fisher's exact test), Q value = 0.037

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
AMP PEAK 1(1Q22) MUTATED	3	13	19	5
AMP PEAK 1(1Q22) WILD-TYPE	92	128	128	103

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

'amp_1q22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00042

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

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

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

'amp_1q22' versus 'MIRSEQ_CNMF'

P value = 0.00484 (Fisher's exact test), Q value = 0.01

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
AMP PEAK 1(1Q22) MUTATED	26	3	3	8
AMP PEAK 1(1Q22) WILD-TYPE	182	68	120	78

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

'amp_1q22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0013

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

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

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

'amp_1q22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0133 (Fisher's exact test), Q value = 0.024

Table S9. Gene #1: 'amp_1q22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
AMP PEAK 1(1Q22) MUTATED	2	15	4	1	4
AMP PEAK 1(1Q22) WILD-TYPE	73	71	65	22	61

Figure S9. Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S10. Gene #2: 'amp_3q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
AMP PEAK 2(3Q21.3) MUTATED	6	1	5	63
AMP PEAK 2(3Q21.3) WILD-TYPE	102	90	93	132

Figure S10. Get High-res Image Gene #2: 'amp_3q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q21.3' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
AMP PEAK 2(3Q21.3) MUTATED	12	25	16	22
AMP PEAK 2(3Q21.3) WILD-TYPE	149	112	108	48

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

'amp_3q21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00521 (Fisher's exact test), Q value = 0.011

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	74	113	92	68
AMP PEAK 2(3Q21.3) MUTATED	5	22	8	16
AMP PEAK 2(3Q21.3) WILD-TYPE	69	91	84	52

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

'amp_3q21.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
AMP PEAK 2(3Q21.3) MUTATED	7	19	41	8
AMP PEAK 2(3Q21.3) WILD-TYPE	88	122	106	100

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

'amp_3q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00036

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

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

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

'amp_3q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.00099

Table S15. Gene #2: 'amp_3q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S15. Get High-res Image Gene #2: 'amp_3q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00597 (Fisher's exact test), Q value = 0.012

Table S16. Gene #2: 'amp_3q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
AMP PEAK 2(3Q21.3) MUTATED	2	20	12	12
AMP PEAK 2(3Q21.3) WILD-TYPE	63	71	66	72

Figure S16. Get High-res Image Gene #2: 'amp_3q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_3q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00616 (Fisher's exact test), Q value = 0.012

Table S17. Gene #2: 'amp_3q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
AMP PEAK 2(3Q21.3) MUTATED	5	22	11	1	7
AMP PEAK 2(3Q21.3) WILD-TYPE	70	64	58	22	58

Figure S17. Get High-res Image Gene #2: 'amp_3q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S18. Gene #3: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
AMP PEAK 3(3Q26.2) MUTATED	8	3	8	67
AMP PEAK 3(3Q26.2) WILD-TYPE	100	88	90	128

Figure S18. Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 0.00944 (Fisher's exact test), Q value = 0.018

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
AMP PEAK 3(3Q26.2) MUTATED	20	24	20	22
AMP PEAK 3(3Q26.2) WILD-TYPE	141	113	104	48

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

'amp_3q26.2' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00029

Table S20. Gene #3: 'amp_3q26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
AMP PEAK 3(3Q26.2) MUTATED	8	23	43	12
AMP PEAK 3(3Q26.2) WILD-TYPE	87	118	104	96

Figure S20. Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0147 (Fisher's exact test), Q value = 0.027

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

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

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

'amp_3q26.2' versus 'MIRSEQ_CNMF'

P value = 0.0334 (Fisher's exact test), Q value = 0.054

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
AMP PEAK 3(3Q26.2) MUTATED	47	13	13	12
AMP PEAK 3(3Q26.2) WILD-TYPE	161	58	110	74

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

'amp_3q26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00862 (Fisher's exact test), Q value = 0.017

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

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

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

'amp_3q26.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.032

Table S24. Gene #3: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
AMP PEAK 3(3Q26.2) MUTATED	5	22	16	10
AMP PEAK 3(3Q26.2) WILD-TYPE	60	69	62	74

Figure S24. Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 2e-04

Table S25. Gene #3: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
AMP PEAK 3(3Q26.2) MUTATED	4	26	14	4	5
AMP PEAK 3(3Q26.2) WILD-TYPE	71	60	55	19	60

Figure S25. Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4p16.3' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00029

Table S26. Gene #4: 'amp_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
AMP PEAK 4(4P16.3) MUTATED	1	0	1	18
AMP PEAK 4(4P16.3) WILD-TYPE	107	91	97	177

Figure S26. Get High-res Image Gene #4: 'amp_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4p16.3' versus 'METHLYATION_CNMF'

P value = 0.0172 (Fisher's exact test), Q value = 0.03

Table S27. Gene #4: 'amp_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
AMP PEAK 4(4P16.3) MUTATED	2	7	4	7
AMP PEAK 4(4P16.3) WILD-TYPE	159	130	120	63

Figure S27. Get High-res Image Gene #4: 'amp_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_4p16.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0215 (Fisher's exact test), Q value = 0.037

Table S28. Gene #4: 'amp_4p16.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	74	113	92	68
AMP PEAK 4(4P16.3) MUTATED	3	1	3	7
AMP PEAK 4(4P16.3) WILD-TYPE	71	112	89	61

Figure S28. Get High-res Image Gene #4: 'amp_4p16.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_4p16.3' versus 'MRNASEQ_CNMF'

P value = 0.0303 (Fisher's exact test), Q value = 0.05

Table S29. Gene #4: 'amp_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
AMP PEAK 4(4P16.3) MUTATED	1	5	12	2
AMP PEAK 4(4P16.3) WILD-TYPE	94	136	135	106

Figure S29. Get High-res Image Gene #4: 'amp_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_4q13.3' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00036

Table S30. Gene #5: 'amp_4q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
AMP PEAK 5(4Q13.3) MUTATED	2	0	1	19
AMP PEAK 5(4Q13.3) WILD-TYPE	106	91	97	176

Figure S30. Get High-res Image Gene #5: 'amp_4q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4q13.3' versus 'RPPA_CNMF'

P value = 0.0429 (Fisher's exact test), Q value = 0.067

Table S31. Gene #5: 'amp_4q13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	51	44	51	58	38
AMP PEAK 5(4Q13.3) MUTATED	2	2	2	1	7	4
AMP PEAK 5(4Q13.3) WILD-TYPE	103	49	42	50	51	34

Figure S31. Get High-res Image Gene #5: 'amp_4q13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_4q13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.039 (Fisher's exact test), Q value = 0.061

Table S32. Gene #5: 'amp_4q13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	74	113	92	68
AMP PEAK 5(4Q13.3) MUTATED	1	8	2	7
AMP PEAK 5(4Q13.3) WILD-TYPE	73	105	90	61

Figure S32. Get High-res Image Gene #5: 'amp_4q13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_4q13.3' versus 'MRNASEQ_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 0.028

Table S33. Gene #5: 'amp_4q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
AMP PEAK 5(4Q13.3) MUTATED	0	6	12	4
AMP PEAK 5(4Q13.3) WILD-TYPE	95	135	135	104

Figure S33. Get High-res Image Gene #5: 'amp_4q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_4q13.3' versus 'MIRSEQ_CNMF'

P value = 0.00955 (Fisher's exact test), Q value = 0.018

Table S34. Gene #5: 'amp_4q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
AMP PEAK 5(4Q13.3) MUTATED	16	2	3	0
AMP PEAK 5(4Q13.3) WILD-TYPE	192	69	120	86

Figure S34. Get High-res Image Gene #5: 'amp_4q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_4q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0464 (Fisher's exact test), Q value = 0.071

Table S35. Gene #5: 'amp_4q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
AMP PEAK 5(4Q13.3) MUTATED	1	5	5	0
AMP PEAK 5(4Q13.3) WILD-TYPE	64	86	73	84

Figure S35. Get High-res Image Gene #5: 'amp_4q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_5q35.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S36. Gene #6: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
AMP PEAK 6(5Q35.3) MUTATED	4	0	1	23
AMP PEAK 6(5Q35.3) WILD-TYPE	104	91	97	172

Figure S36. Get High-res Image Gene #6: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q35.3' versus 'METHLYATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.00094

Table S37. Gene #6: 'amp_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
AMP PEAK 6(5Q35.3) MUTATED	3	7	6	12
AMP PEAK 6(5Q35.3) WILD-TYPE	158	130	118	58

Figure S37. Get High-res Image Gene #6: 'amp_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5q35.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0422 (Fisher's exact test), Q value = 0.066

Table S38. Gene #6: 'amp_5q35.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S38. Get High-res Image Gene #6: 'amp_5q35.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5q35.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00101 (Fisher's exact test), Q value = 0.0027

Table S39. Gene #6: 'amp_5q35.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S39. Get High-res Image Gene #6: 'amp_5q35.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5q35.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00318 (Fisher's exact test), Q value = 0.007

Table S40. Gene #6: 'amp_5q35.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
AMP PEAK 6(5Q35.3) MUTATED	0	11	6	2
AMP PEAK 6(5Q35.3) WILD-TYPE	65	80	72	82

Figure S40. Get High-res Image Gene #6: 'amp_5q35.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_5q35.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0444 (Fisher's exact test), Q value = 0.068

Table S41. Gene #6: 'amp_5q35.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
AMP PEAK 6(5Q35.3) MUTATED	4	11	3	0	1
AMP PEAK 6(5Q35.3) WILD-TYPE	71	75	66	23	64

Figure S41. Get High-res Image Gene #6: 'amp_5q35.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p14.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S42. Gene #7: 'amp_7p14.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
AMP PEAK 7(7P14.3) MUTATED	7	6	12	79
AMP PEAK 7(7P14.3) WILD-TYPE	101	85	86	116

Figure S42. Get High-res Image Gene #7: 'amp_7p14.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p14.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S43. Gene #7: 'amp_7p14.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
AMP PEAK 7(7P14.3) MUTATED	13	47	20	24
AMP PEAK 7(7P14.3) WILD-TYPE	148	90	104	46

Figure S43. Get High-res Image Gene #7: 'amp_7p14.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p14.3' versus 'RPPA_CNMF'

P value = 0.00129 (Fisher's exact test), Q value = 0.0032

Table S44. Gene #7: 'amp_7p14.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	51	44	51	58	38
AMP PEAK 7(7P14.3) MUTATED	18	13	10	4	24	8
AMP PEAK 7(7P14.3) WILD-TYPE	87	38	34	47	34	30

Figure S44. Get High-res Image Gene #7: 'amp_7p14.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_7p14.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S45. Gene #7: 'amp_7p14.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
AMP PEAK 7(7P14.3) MUTATED	14	21	60	9
AMP PEAK 7(7P14.3) WILD-TYPE	81	120	87	99

Figure S45. Get High-res Image Gene #7: 'amp_7p14.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p14.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00013

Table S46. Gene #7: 'amp_7p14.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S46. Get High-res Image Gene #7: 'amp_7p14.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7p14.3' versus 'MIRSEQ_CNMF'

P value = 0.00166 (Fisher's exact test), Q value = 0.004

Table S47. Gene #7: 'amp_7p14.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
AMP PEAK 7(7P14.3) MUTATED	56	17	12	18
AMP PEAK 7(7P14.3) WILD-TYPE	152	54	111	68

Figure S47. Get High-res Image Gene #7: 'amp_7p14.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7p14.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.0014

Table S48. Gene #7: 'amp_7p14.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S48. Get High-res Image Gene #7: 'amp_7p14.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7p14.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00654 (Fisher's exact test), Q value = 0.013

Table S49. Gene #7: 'amp_7p14.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
AMP PEAK 7(7P14.3) MUTATED	5	27	19	19
AMP PEAK 7(7P14.3) WILD-TYPE	60	64	59	65

Figure S49. Get High-res Image Gene #7: 'amp_7p14.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7p14.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00546 (Fisher's exact test), Q value = 0.011

Table S50. Gene #7: 'amp_7p14.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
AMP PEAK 7(7P14.3) MUTATED	9	29	18	2	12
AMP PEAK 7(7P14.3) WILD-TYPE	66	57	51	21	53

Figure S50. Get High-res Image Gene #7: 'amp_7p14.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S51. Gene #8: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
AMP PEAK 8(7Q22.1) MUTATED	7	6	11	77
AMP PEAK 8(7Q22.1) WILD-TYPE	101	85	87	118

Figure S51. Get High-res Image Gene #8: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S52. Gene #8: 'amp_7q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
AMP PEAK 8(7Q22.1) MUTATED	14	46	20	21
AMP PEAK 8(7Q22.1) WILD-TYPE	147	91	104	49

Figure S52. Get High-res Image Gene #8: 'amp_7q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q22.1' versus 'RPPA_CNMF'

P value = 0.00117 (Fisher's exact test), Q value = 0.003

Table S53. Gene #8: 'amp_7q22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	51	44	51	58	38
AMP PEAK 8(7Q22.1) MUTATED	17	12	9	4	24	7
AMP PEAK 8(7Q22.1) WILD-TYPE	88	39	35	47	34	31

Figure S53. Get High-res Image Gene #8: 'amp_7q22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_7q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S54. Gene #8: 'amp_7q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
AMP PEAK 8(7Q22.1) MUTATED	14	18	61	8
AMP PEAK 8(7Q22.1) WILD-TYPE	81	123	86	100

Figure S54. Get High-res Image Gene #8: 'amp_7q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S55. Gene #8: 'amp_7q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S55. Get High-res Image Gene #8: 'amp_7q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q22.1' versus 'MIRSEQ_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0019

Table S56. Gene #8: 'amp_7q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
AMP PEAK 8(7Q22.1) MUTATED	55	18	11	16
AMP PEAK 8(7Q22.1) WILD-TYPE	153	53	112	70

Figure S56. Get High-res Image Gene #8: 'amp_7q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S57. Gene #8: 'amp_7q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S57. Get High-res Image Gene #8: 'amp_7q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00124 (Fisher's exact test), Q value = 0.0031

Table S58. Gene #8: 'amp_7q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
AMP PEAK 8(7Q22.1) MUTATED	4	27	21	17
AMP PEAK 8(7Q22.1) WILD-TYPE	61	64	57	67

Figure S58. Get High-res Image Gene #8: 'amp_7q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00064 (Fisher's exact test), Q value = 0.0018

Table S59. Gene #8: 'amp_7q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
AMP PEAK 8(7Q22.1) MUTATED	9	29	20	1	10
AMP PEAK 8(7Q22.1) WILD-TYPE	66	57	49	22	55

Figure S59. Get High-res Image Gene #8: 'amp_7q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S60. Gene #9: 'amp_8p11.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
AMP PEAK 9(8P11.23) MUTATED	1	6	3	57
AMP PEAK 9(8P11.23) WILD-TYPE	107	85	95	138

Figure S60. Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p11.23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S61. Gene #9: 'amp_8p11.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
AMP PEAK 9(8P11.23) MUTATED	7	29	10	21
AMP PEAK 9(8P11.23) WILD-TYPE	154	108	114	49

Figure S61. Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8p11.23' versus 'RPPA_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0011

Table S62. Gene #9: 'amp_8p11.23' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	51	44	51	58	38
AMP PEAK 9(8P11.23) MUTATED	6	7	4	5	17	10
AMP PEAK 9(8P11.23) WILD-TYPE	99	44	40	46	41	28

Figure S62. Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_8p11.23' versus 'RPPA_CHIERARCHICAL'

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

Table S63. Gene #9: 'amp_8p11.23' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	74	113	92	68
AMP PEAK 9(8P11.23) MUTATED	9	15	7	18
AMP PEAK 9(8P11.23) WILD-TYPE	65	98	85	50

Figure S63. Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_8p11.23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S64. Gene #9: 'amp_8p11.23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
AMP PEAK 9(8P11.23) MUTATED	8	10	42	7
AMP PEAK 9(8P11.23) WILD-TYPE	87	131	105	101

Figure S64. Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8p11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0012

Table S65. Gene #9: 'amp_8p11.23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S65. Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.23' versus 'MIRSEQ_CNMF'

P value = 0.00097 (Fisher's exact test), Q value = 0.0026

Table S66. Gene #9: 'amp_8p11.23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
AMP PEAK 9(8P11.23) MUTATED	41	9	6	10
AMP PEAK 9(8P11.23) WILD-TYPE	167	62	117	76

Figure S66. Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8p11.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00131 (Fisher's exact test), Q value = 0.0032

Table S67. Gene #9: 'amp_8p11.23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S67. Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00056

Table S68. Gene #9: 'amp_8p11.23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
AMP PEAK 9(8P11.23) MUTATED	2	25	8	10
AMP PEAK 9(8P11.23) WILD-TYPE	63	66	70	74

Figure S68. Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8p11.23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.0015

Table S69. Gene #9: 'amp_8p11.23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
AMP PEAK 9(8P11.23) MUTATED	5	25	8	1	6
AMP PEAK 9(8P11.23) WILD-TYPE	70	61	61	22	59

Figure S69. Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S70. Gene #10: 'amp_8q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
AMP PEAK 10(8Q22.1) MUTATED	16	8	8	125
AMP PEAK 10(8Q22.1) WILD-TYPE	92	83	90	70

Figure S70. Get High-res Image Gene #10: 'amp_8q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S71. Gene #10: 'amp_8q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
AMP PEAK 10(8Q22.1) MUTATED	21	61	38	37
AMP PEAK 10(8Q22.1) WILD-TYPE	140	76	86	33

Figure S71. Get High-res Image Gene #10: 'amp_8q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q22.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S72. Gene #10: 'amp_8q22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	51	44	51	58	38
AMP PEAK 10(8Q22.1) MUTATED	19	16	10	15	32	21
AMP PEAK 10(8Q22.1) WILD-TYPE	86	35	34	36	26	17

Figure S72. Get High-res Image Gene #10: 'amp_8q22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_8q22.1' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S73. Gene #10: 'amp_8q22.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	74	113	92	68
AMP PEAK 10(8Q22.1) MUTATED	14	33	27	39
AMP PEAK 10(8Q22.1) WILD-TYPE	60	80	65	29

Figure S73. Get High-res Image Gene #10: 'amp_8q22.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_8q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S74. Gene #10: 'amp_8q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
AMP PEAK 10(8Q22.1) MUTATED	17	39	77	24
AMP PEAK 10(8Q22.1) WILD-TYPE	78	102	70	84

Figure S74. Get High-res Image Gene #10: 'amp_8q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S75. Gene #10: 'amp_8q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S75. Get High-res Image Gene #10: 'amp_8q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q22.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S76. Gene #10: 'amp_8q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
AMP PEAK 10(8Q22.1) MUTATED	94	18	19	24
AMP PEAK 10(8Q22.1) WILD-TYPE	114	53	104	62

Figure S76. Get High-res Image Gene #10: 'amp_8q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S77. Gene #10: 'amp_8q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S77. Get High-res Image Gene #10: 'amp_8q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S78. Gene #10: 'amp_8q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
AMP PEAK 10(8Q22.1) MUTATED	9	47	20	25
AMP PEAK 10(8Q22.1) WILD-TYPE	56	44	58	59

Figure S78. Get High-res Image Gene #10: 'amp_8q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00013

Table S79. Gene #10: 'amp_8q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
AMP PEAK 10(8Q22.1) MUTATED	16	47	18	5	15
AMP PEAK 10(8Q22.1) WILD-TYPE	59	39	51	18	50

Figure S79. Get High-res Image Gene #10: 'amp_8q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S80. Gene #11: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
AMP PEAK 11(8Q24.21) MUTATED	16	9	7	120
AMP PEAK 11(8Q24.21) WILD-TYPE	92	82	91	75

Figure S80. Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S81. Gene #11: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
AMP PEAK 11(8Q24.21) MUTATED	21	58	36	37
AMP PEAK 11(8Q24.21) WILD-TYPE	140	79	88	33

Figure S81. Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S82. Gene #11: 'amp_8q24.21' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	51	44	51	58	38
AMP PEAK 11(8Q24.21) MUTATED	19	15	9	15	27	22
AMP PEAK 11(8Q24.21) WILD-TYPE	86	36	35	36	31	16

Figure S82. Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_8q24.21' versus 'RPPA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 2e-04

Table S83. Gene #11: 'amp_8q24.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	74	113	92	68
AMP PEAK 11(8Q24.21) MUTATED	14	30	26	37
AMP PEAK 11(8Q24.21) WILD-TYPE	60	83	66	31

Figure S83. Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S84. Gene #11: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
AMP PEAK 11(8Q24.21) MUTATED	17	36	78	21
AMP PEAK 11(8Q24.21) WILD-TYPE	78	105	69	87

Figure S84. Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S85. Gene #11: 'amp_8q24.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S85. Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S86. Gene #11: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
AMP PEAK 11(8Q24.21) MUTATED	91	19	17	23
AMP PEAK 11(8Q24.21) WILD-TYPE	117	52	106	63

Figure S86. Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S87. Gene #11: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S87. Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00016

Table S88. Gene #11: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
AMP PEAK 11(8Q24.21) MUTATED	9	45	20	24
AMP PEAK 11(8Q24.21) WILD-TYPE	56	46	58	60

Figure S88. Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0016

Table S89. Gene #11: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
AMP PEAK 11(8Q24.21) MUTATED	17	43	17	5	16
AMP PEAK 11(8Q24.21) WILD-TYPE	58	43	52	18	49

Figure S89. Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9q33.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S90. Gene #12: 'amp_9q33.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
AMP PEAK 12(9Q33.3) MUTATED	5	2	1	54
AMP PEAK 12(9Q33.3) WILD-TYPE	103	89	97	141

Figure S90. Get High-res Image Gene #12: 'amp_9q33.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9q33.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S91. Gene #12: 'amp_9q33.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
AMP PEAK 12(9Q33.3) MUTATED	12	9	18	23
AMP PEAK 12(9Q33.3) WILD-TYPE	149	128	106	47

Figure S91. Get High-res Image Gene #12: 'amp_9q33.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9q33.3' versus 'RPPA_CNMF'

P value = 0.00428 (Fisher's exact test), Q value = 0.0091

Table S92. Gene #12: 'amp_9q33.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	51	44	51	58	38
AMP PEAK 12(9Q33.3) MUTATED	6	8	5	3	10	11
AMP PEAK 12(9Q33.3) WILD-TYPE	99	43	39	48	48	27

Figure S92. Get High-res Image Gene #12: 'amp_9q33.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_9q33.3' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00013

Table S93. Gene #12: 'amp_9q33.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
AMP PEAK 12(9Q33.3) MUTATED	2	19	32	9
AMP PEAK 12(9Q33.3) WILD-TYPE	93	122	115	99

Figure S93. Get High-res Image Gene #12: 'amp_9q33.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_9q33.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0155 (Fisher's exact test), Q value = 0.028

Table S94. Gene #12: 'amp_9q33.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S94. Get High-res Image Gene #12: 'amp_9q33.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_9q33.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00093 (Fisher's exact test), Q value = 0.0025

Table S95. Gene #12: 'amp_9q33.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S95. Get High-res Image Gene #12: 'amp_9q33.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S96. Gene #13: 'amp_11q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
AMP PEAK 13(11Q13.2) MUTATED	4	0	2	42
AMP PEAK 13(11Q13.2) WILD-TYPE	104	91	96	153

Figure S96. Get High-res Image Gene #13: 'amp_11q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.2' versus 'METHLYATION_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.0026

Table S97. Gene #13: 'amp_11q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
AMP PEAK 13(11Q13.2) MUTATED	8	15	9	16
AMP PEAK 13(11Q13.2) WILD-TYPE	153	122	115	54

Figure S97. Get High-res Image Gene #13: 'amp_11q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11q13.2' versus 'RPPA_CNMF'

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

Table S98. Gene #13: 'amp_11q13.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	51	44	51	58	38
AMP PEAK 13(11Q13.2) MUTATED	6	6	2	3	13	4
AMP PEAK 13(11Q13.2) WILD-TYPE	99	45	42	48	45	34

Figure S98. Get High-res Image Gene #13: 'amp_11q13.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_11q13.2' versus 'MRNASEQ_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.0025

Table S99. Gene #13: 'amp_11q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
AMP PEAK 13(11Q13.2) MUTATED	4	9	27	8
AMP PEAK 13(11Q13.2) WILD-TYPE	91	132	120	100

Figure S99. Get High-res Image Gene #13: 'amp_11q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_11q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0013

Table S100. Gene #13: 'amp_11q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S100. Get High-res Image Gene #13: 'amp_11q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.2' versus 'MIRSEQ_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.023

Table S101. Gene #13: 'amp_11q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
AMP PEAK 13(11Q13.2) MUTATED	29	8	5	5
AMP PEAK 13(11Q13.2) WILD-TYPE	179	63	118	81

Figure S101. Get High-res Image Gene #13: 'amp_11q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_11q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 5e-04

Table S102. Gene #13: 'amp_11q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S102. Get High-res Image Gene #13: 'amp_11q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00516 (Fisher's exact test), Q value = 0.011

Table S103. Gene #13: 'amp_11q13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
AMP PEAK 13(11Q13.2) MUTATED	1	13	11	4
AMP PEAK 13(11Q13.2) WILD-TYPE	64	78	67	80

Figure S103. Get High-res Image Gene #13: 'amp_11q13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_12q23.1' versus 'CN_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.0026

Table S104. Gene #14: 'amp_12q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
AMP PEAK 14(12Q23.1) MUTATED	4	2	4	26
AMP PEAK 14(12Q23.1) WILD-TYPE	104	89	94	169

Figure S104. Get High-res Image Gene #14: 'amp_12q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q23.1' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00013

Table S105. Gene #14: 'amp_12q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
AMP PEAK 14(12Q23.1) MUTATED	7	10	3	16
AMP PEAK 14(12Q23.1) WILD-TYPE	154	127	121	54

Figure S105. Get High-res Image Gene #14: 'amp_12q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12q23.1' versus 'RPPA_CNMF'

P value = 0.00515 (Fisher's exact test), Q value = 0.011

Table S106. Gene #14: 'amp_12q23.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	51	44	51	58	38
AMP PEAK 14(12Q23.1) MUTATED	2	8	2	6	9	4
AMP PEAK 14(12Q23.1) WILD-TYPE	103	43	42	45	49	34

Figure S106. Get High-res Image Gene #14: 'amp_12q23.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_12q23.1' versus 'RPPA_CHIERARCHICAL'

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

Table S107. Gene #14: 'amp_12q23.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	74	113	92	68
AMP PEAK 14(12Q23.1) MUTATED	3	10	5	13
AMP PEAK 14(12Q23.1) WILD-TYPE	71	103	87	55

Figure S107. Get High-res Image Gene #14: 'amp_12q23.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_12q23.1' versus 'MRNASEQ_CNMF'

P value = 0.00205 (Fisher's exact test), Q value = 0.0048

Table S108. Gene #14: 'amp_12q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
AMP PEAK 14(12Q23.1) MUTATED	2	7	21	6
AMP PEAK 14(12Q23.1) WILD-TYPE	93	134	126	102

Figure S108. Get High-res Image Gene #14: 'amp_12q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_12q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00757 (Fisher's exact test), Q value = 0.015

Table S109. Gene #14: 'amp_12q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
AMP PEAK 14(12Q23.1) MUTATED	8	24	4
AMP PEAK 14(12Q23.1) WILD-TYPE	163	181	111

Figure S109. Get High-res Image Gene #14: 'amp_12q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_12q23.1' versus 'MIRSEQ_CNMF'

P value = 0.00655 (Fisher's exact test), Q value = 0.013

Table S110. Gene #14: 'amp_12q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
AMP PEAK 14(12Q23.1) MUTATED	23	6	5	1
AMP PEAK 14(12Q23.1) WILD-TYPE	185	65	118	85

Figure S110. Get High-res Image Gene #14: 'amp_12q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_12q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00045

Table S111. Gene #14: 'amp_12q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 14(12Q23.1) MUTATED	7	5	2	21	0
AMP PEAK 14(12Q23.1) WILD-TYPE	140	93	57	107	56

Figure S111. Get High-res Image Gene #14: 'amp_12q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_12q23.1' versus 'MIRSEQ_MATURE_CNMF'

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

Table S112. Gene #14: 'amp_12q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
AMP PEAK 14(12Q23.1) MUTATED	3	11	8	1
AMP PEAK 14(12Q23.1) WILD-TYPE	62	80	70	83

Figure S112. Get High-res Image Gene #14: 'amp_12q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_12q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0483 (Fisher's exact test), Q value = 0.073

Table S113. Gene #14: 'amp_12q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
AMP PEAK 14(12Q23.1) MUTATED	4	12	4	2	1
AMP PEAK 14(12Q23.1) WILD-TYPE	71	74	65	21	64

Figure S113. Get High-res Image Gene #14: 'amp_12q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q12.11' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S114. Gene #15: 'amp_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
AMP PEAK 15(13Q12.11) MUTATED	1	0	2	22
AMP PEAK 15(13Q12.11) WILD-TYPE	107	91	96	173

Figure S114. Get High-res Image Gene #15: 'amp_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q12.11' versus 'METHLYATION_CNMF'

P value = 0.00119 (Fisher's exact test), Q value = 0.003

Table S115. Gene #15: 'amp_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
AMP PEAK 15(13Q12.11) MUTATED	2	5	9	9
AMP PEAK 15(13Q12.11) WILD-TYPE	159	132	115	61

Figure S115. Get High-res Image Gene #15: 'amp_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q12.11' versus 'RPPA_CNMF'

P value = 0.00325 (Fisher's exact test), Q value = 0.0071

Table S116. Gene #15: 'amp_13q12.11' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	51	44	51	58	38
AMP PEAK 15(13Q12.11) MUTATED	2	2	0	3	5	7
AMP PEAK 15(13Q12.11) WILD-TYPE	103	49	44	48	53	31

Figure S116. Get High-res Image Gene #15: 'amp_13q12.11' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_13q12.11' versus 'RPPA_CHIERARCHICAL'

P value = 0.0013 (Fisher's exact test), Q value = 0.0032

Table S117. Gene #15: 'amp_13q12.11' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	74	113	92	68
AMP PEAK 15(13Q12.11) MUTATED	3	3	2	11
AMP PEAK 15(13Q12.11) WILD-TYPE	71	110	90	57

Figure S117. Get High-res Image Gene #15: 'amp_13q12.11' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_13q12.11' versus 'MRNASEQ_CNMF'

P value = 0.00206 (Fisher's exact test), Q value = 0.0048

Table S118. Gene #15: 'amp_13q12.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
AMP PEAK 15(13Q12.11) MUTATED	1	6	16	2
AMP PEAK 15(13Q12.11) WILD-TYPE	94	135	131	106

Figure S118. Get High-res Image Gene #15: 'amp_13q12.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_13q12.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0321 (Fisher's exact test), Q value = 0.052

Table S119. Gene #15: 'amp_13q12.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S119. Get High-res Image Gene #15: 'amp_13q12.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_14q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S120. Gene #16: 'amp_14q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
AMP PEAK 16(14Q21.1) MUTATED	1	0	3	26
AMP PEAK 16(14Q21.1) WILD-TYPE	107	91	95	169

Figure S120. Get High-res Image Gene #16: 'amp_14q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_14q21.1' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00016

Table S121. Gene #16: 'amp_14q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
AMP PEAK 16(14Q21.1) MUTATED	1	4	21	4
AMP PEAK 16(14Q21.1) WILD-TYPE	94	137	126	104

Figure S121. Get High-res Image Gene #16: 'amp_14q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_14q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.036 (Fisher's exact test), Q value = 0.057

Table S122. Gene #16: 'amp_14q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S122. Get High-res Image Gene #16: 'amp_14q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_14q21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0107 (Fisher's exact test), Q value = 0.02

Table S123. Gene #16: 'amp_14q21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S123. Get High-res Image Gene #16: 'amp_14q21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_14q21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.029

Table S124. Gene #16: 'amp_14q21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
AMP PEAK 16(14Q21.1) MUTATED	0	11	5	7
AMP PEAK 16(14Q21.1) WILD-TYPE	65	80	73	77

Figure S124. Get High-res Image Gene #16: 'amp_14q21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_14q21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.022 (Fisher's exact test), Q value = 0.037

Table S125. Gene #16: 'amp_14q21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
AMP PEAK 16(14Q21.1) MUTATED	2	13	5	0	3
AMP PEAK 16(14Q21.1) WILD-TYPE	73	73	64	23	62

Figure S125. Get High-res Image Gene #16: 'amp_14q21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_15q11.2' versus 'CN_CNMF'

P value = 0.00595 (Fisher's exact test), Q value = 0.012

Table S126. Gene #17: 'amp_15q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
AMP PEAK 17(15Q11.2) MUTATED	1	0	2	13
AMP PEAK 17(15Q11.2) WILD-TYPE	107	91	96	182

Figure S126. Get High-res Image Gene #17: 'amp_15q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_15q11.2' versus 'METHLYATION_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.04

Table S127. Gene #17: 'amp_15q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
AMP PEAK 17(15Q11.2) MUTATED	3	3	3	7
AMP PEAK 17(15Q11.2) WILD-TYPE	158	134	121	63

Figure S127. Get High-res Image Gene #17: 'amp_15q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_16q11.2' versus 'CN_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0011

Table S128. Gene #18: 'amp_16q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
AMP PEAK 18(16Q11.2) MUTATED	4	1	2	23
AMP PEAK 18(16Q11.2) WILD-TYPE	104	90	96	172

Figure S128. Get High-res Image Gene #18: 'amp_16q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_16q11.2' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00016

Table S129. Gene #18: 'amp_16q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
AMP PEAK 18(16Q11.2) MUTATED	3	6	6	15
AMP PEAK 18(16Q11.2) WILD-TYPE	158	131	118	55

Figure S129. Get High-res Image Gene #18: 'amp_16q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_16q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00109 (Fisher's exact test), Q value = 0.0028

Table S130. Gene #18: 'amp_16q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S130. Get High-res Image Gene #18: 'amp_16q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_17p11.2' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00016

Table S131. Gene #19: 'amp_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
AMP PEAK 19(17P11.2) MUTATED	2	1	0	19
AMP PEAK 19(17P11.2) WILD-TYPE	106	90	98	176

Figure S131. Get High-res Image Gene #19: 'amp_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0184 (Fisher's exact test), Q value = 0.032

Table S132. Gene #19: 'amp_17p11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	74	113	92	68
AMP PEAK 19(17P11.2) MUTATED	2	2	3	8
AMP PEAK 19(17P11.2) WILD-TYPE	72	111	89	60

Figure S132. Get High-res Image Gene #19: 'amp_17p11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_17p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0221 (Fisher's exact test), Q value = 0.038

Table S133. Gene #19: 'amp_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
AMP PEAK 19(17P11.2) MUTATED	0	8	1	1	3
AMP PEAK 19(17P11.2) WILD-TYPE	75	78	68	22	62

Figure S133. Get High-res Image Gene #19: 'amp_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q23.2' versus 'CN_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0015

Table S134. Gene #20: 'amp_17q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
AMP PEAK 20(17Q23.2) MUTATED	3	1	1	20
AMP PEAK 20(17Q23.2) WILD-TYPE	105	90	97	175

Figure S134. Get High-res Image Gene #20: 'amp_17q23.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q23.2' versus 'METHLYATION_CNMF'

P value = 0.00212 (Fisher's exact test), Q value = 0.0049

Table S135. Gene #20: 'amp_17q23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
AMP PEAK 20(17Q23.2) MUTATED	6	4	4	11
AMP PEAK 20(17Q23.2) WILD-TYPE	155	133	120	59

Figure S135. Get High-res Image Gene #20: 'amp_17q23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0139 (Fisher's exact test), Q value = 0.025

Table S136. Gene #20: 'amp_17q23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 20(17Q23.2) MUTATED	4	4	7	10	0
AMP PEAK 20(17Q23.2) WILD-TYPE	143	94	52	118	56

Figure S136. Get High-res Image Gene #20: 'amp_17q23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_18q21.31' versus 'CN_CNMF'

P value = 0.00114 (Fisher's exact test), Q value = 0.0029

Table S137. Gene #21: 'amp_18q21.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
AMP PEAK 21(18Q21.31) MUTATED	0	0	1	12
AMP PEAK 21(18Q21.31) WILD-TYPE	108	91	97	183

Figure S137. Get High-res Image Gene #21: 'amp_18q21.31' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q13.43' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S138. Gene #22: 'amp_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
AMP PEAK 22(19Q13.43) MUTATED	0	0	0	19
AMP PEAK 22(19Q13.43) WILD-TYPE	108	91	98	176

Figure S138. Get High-res Image Gene #22: 'amp_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q13.43' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.026 (Fisher's exact test), Q value = 0.043

Table S139. Gene #22: 'amp_19q13.43' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
AMP PEAK 22(19Q13.43) MUTATED	2	13	4
AMP PEAK 22(19Q13.43) WILD-TYPE	169	192	111

Figure S139. Get High-res Image Gene #22: 'amp_19q13.43' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19q13.43' versus 'MIRSEQ_CNMF'

P value = 0.0205 (Fisher's exact test), Q value = 0.035

Table S140. Gene #22: 'amp_19q13.43' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
AMP PEAK 22(19Q13.43) MUTATED	10	4	0	5
AMP PEAK 22(19Q13.43) WILD-TYPE	198	67	123	81

Figure S140. Get High-res Image Gene #22: 'amp_19q13.43' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_19q13.43' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0014 (Fisher's exact test), Q value = 0.0034

Table S141. Gene #22: 'amp_19q13.43' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 22(19Q13.43) MUTATED	0	5	1	11	2
AMP PEAK 22(19Q13.43) WILD-TYPE	147	93	58	117	54

Figure S141. Get High-res Image Gene #22: 'amp_19q13.43' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S142. Gene #23: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
AMP PEAK 23(20Q13.2) MUTATED	1	1	3	40
AMP PEAK 23(20Q13.2) WILD-TYPE	107	90	95	155

Figure S142. Get High-res Image Gene #23: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.2' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00016

Table S143. Gene #23: 'amp_20q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
AMP PEAK 23(20Q13.2) MUTATED	5	19	7	14
AMP PEAK 23(20Q13.2) WILD-TYPE	156	118	117	56

Figure S143. Get High-res Image Gene #23: 'amp_20q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q13.2' versus 'RPPA_CNMF'

P value = 0.00454 (Fisher's exact test), Q value = 0.0096

Table S144. Gene #23: 'amp_20q13.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	51	44	51	58	38
AMP PEAK 23(20Q13.2) MUTATED	7	2	5	1	13	3
AMP PEAK 23(20Q13.2) WILD-TYPE	98	49	39	50	45	35

Figure S144. Get High-res Image Gene #23: 'amp_20q13.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_20q13.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0279 (Fisher's exact test), Q value = 0.046

Table S145. Gene #23: 'amp_20q13.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	74	113	92	68
AMP PEAK 23(20Q13.2) MUTATED	4	11	4	12
AMP PEAK 23(20Q13.2) WILD-TYPE	70	102	88	56

Figure S145. Get High-res Image Gene #23: 'amp_20q13.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_20q13.2' versus 'MRNASEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00076

Table S146. Gene #23: 'amp_20q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
AMP PEAK 23(20Q13.2) MUTATED	4	9	27	5
AMP PEAK 23(20Q13.2) WILD-TYPE	91	132	120	103

Figure S146. Get High-res Image Gene #23: 'amp_20q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_20q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00135 (Fisher's exact test), Q value = 0.0033

Table S147. Gene #23: 'amp_20q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
AMP PEAK 23(20Q13.2) MUTATED	7	30	8
AMP PEAK 23(20Q13.2) WILD-TYPE	164	175	107

Figure S147. Get High-res Image Gene #23: 'amp_20q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_CNMF'

P value = 0.0458 (Fisher's exact test), Q value = 0.07

Table S148. Gene #23: 'amp_20q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
AMP PEAK 23(20Q13.2) MUTATED	27	5	5	8
AMP PEAK 23(20Q13.2) WILD-TYPE	181	66	118	78

Figure S148. Get High-res Image Gene #23: 'amp_20q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_20q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00027

Table S149. Gene #23: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S149. Get High-res Image Gene #23: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_xp22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S150. Gene #24: 'amp_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
AMP PEAK 24(XP22.2) MUTATED	4	0	0	23
AMP PEAK 24(XP22.2) WILD-TYPE	104	91	98	172

Figure S150. Get High-res Image Gene #24: 'amp_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp22.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S151. Gene #24: 'amp_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
AMP PEAK 24(XP22.2) MUTATED	3	6	4	14
AMP PEAK 24(XP22.2) WILD-TYPE	158	131	120	56

Figure S151. Get High-res Image Gene #24: 'amp_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xp22.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0369 (Fisher's exact test), Q value = 0.059

Table S152. Gene #24: 'amp_xp22.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	74	113	92	68
AMP PEAK 24(XP22.2) MUTATED	1	7	1	6
AMP PEAK 24(XP22.2) WILD-TYPE	73	106	91	62

Figure S152. Get High-res Image Gene #24: 'amp_xp22.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_xp22.2' versus 'MRNASEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00062

Table S153. Gene #24: 'amp_xp22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
AMP PEAK 24(XP22.2) MUTATED	0	5	18	4
AMP PEAK 24(XP22.2) WILD-TYPE	95	136	129	104

Figure S153. Get High-res Image Gene #24: 'amp_xp22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_xp22.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S154. Gene #24: 'amp_xp22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
AMP PEAK 24(XP22.2) MUTATED	4	17	6
AMP PEAK 24(XP22.2) WILD-TYPE	167	188	109

Figure S154. Get High-res Image Gene #24: 'amp_xp22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_xp22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00746 (Fisher's exact test), Q value = 0.015

Table S155. Gene #24: 'amp_xp22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 24(XP22.2) MUTATED	2	7	2	14	2
AMP PEAK 24(XP22.2) WILD-TYPE	145	91	57	114	54

Figure S155. Get High-res Image Gene #24: 'amp_xp22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_xq12' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S156. Gene #25: 'amp_xq12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
AMP PEAK 25(XQ12) MUTATED	0	0	0	16
AMP PEAK 25(XQ12) WILD-TYPE	108	91	98	179

Figure S156. Get High-res Image Gene #25: 'amp_xq12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq12' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00016

Table S157. Gene #25: 'amp_xq12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
AMP PEAK 25(XQ12) MUTATED	0	5	2	9
AMP PEAK 25(XQ12) WILD-TYPE	161	132	122	61

Figure S157. Get High-res Image Gene #25: 'amp_xq12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xq12' versus 'RPPA_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.025

Table S158. Gene #25: 'amp_xq12' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	51	44	51	58	38
AMP PEAK 25(XQ12) MUTATED	1	2	0	0	5	3
AMP PEAK 25(XQ12) WILD-TYPE	104	49	44	51	53	35

Figure S158. Get High-res Image Gene #25: 'amp_xq12' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_xq12' versus 'RPPA_CHIERARCHICAL'

P value = 0.0283 (Fisher's exact test), Q value = 0.047

Table S159. Gene #25: 'amp_xq12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	74	113	92	68
AMP PEAK 25(XQ12) MUTATED	1	5	0	5
AMP PEAK 25(XQ12) WILD-TYPE	73	108	92	63

Figure S159. Get High-res Image Gene #25: 'amp_xq12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_xq12' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00029

Table S160. Gene #25: 'amp_xq12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
AMP PEAK 25(XQ12) MUTATED	0	3	13	0
AMP PEAK 25(XQ12) WILD-TYPE	95	138	134	108

Figure S160. Get High-res Image Gene #25: 'amp_xq12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_xq12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00059

Table S161. Gene #25: 'amp_xq12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
AMP PEAK 25(XQ12) MUTATED	0	14	2
AMP PEAK 25(XQ12) WILD-TYPE	171	191	113

Figure S161. Get High-res Image Gene #25: 'amp_xq12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_xq12' versus 'MIRSEQ_CNMF'

P value = 0.0357 (Fisher's exact test), Q value = 0.057

Table S162. Gene #25: 'amp_xq12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
AMP PEAK 25(XQ12) MUTATED	11	2	0	3
AMP PEAK 25(XQ12) WILD-TYPE	197	69	123	83

Figure S162. Get High-res Image Gene #25: 'amp_xq12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_xq12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00074 (Fisher's exact test), Q value = 0.0021

Table S163. Gene #25: 'amp_xq12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 25(XQ12) MUTATED	0	5	0	10	1
AMP PEAK 25(XQ12) WILD-TYPE	147	93	59	118	55

Figure S163. Get High-res Image Gene #25: 'amp_xq12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_xq21.1' versus 'CN_CNMF'

P value = 0.00233 (Fisher's exact test), Q value = 0.0053

Table S164. Gene #26: 'amp_xq21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
AMP PEAK 26(XQ21.1) MUTATED	0	0	2	12
AMP PEAK 26(XQ21.1) WILD-TYPE	108	91	96	183

Figure S164. Get High-res Image Gene #26: 'amp_xq21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq21.1' versus 'METHLYATION_CNMF'

P value = 0.0293 (Fisher's exact test), Q value = 0.048

Table S165. Gene #26: 'amp_xq21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
AMP PEAK 26(XQ21.1) MUTATED	1	7	2	4
AMP PEAK 26(XQ21.1) WILD-TYPE	160	130	122	66

Figure S165. Get High-res Image Gene #26: 'amp_xq21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xq21.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0106 (Fisher's exact test), Q value = 0.02

Table S166. Gene #26: 'amp_xq21.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	74	113	92	68
AMP PEAK 26(XQ21.1) MUTATED	1	4	0	6
AMP PEAK 26(XQ21.1) WILD-TYPE	73	109	92	62

Figure S166. Get High-res Image Gene #26: 'amp_xq21.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_xq21.1' versus 'MRNASEQ_CNMF'

P value = 0.0351 (Fisher's exact test), Q value = 0.056

Table S167. Gene #26: 'amp_xq21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
AMP PEAK 26(XQ21.1) MUTATED	0	3	9	2
AMP PEAK 26(XQ21.1) WILD-TYPE	95	138	138	106

Figure S167. Get High-res Image Gene #26: 'amp_xq21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_xq21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00404 (Fisher's exact test), Q value = 0.0086

Table S168. Gene #26: 'amp_xq21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S168. Get High-res Image Gene #26: 'amp_xq21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_xq21.31' versus 'CN_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.0029

Table S169. Gene #27: 'amp_xq21.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
AMP PEAK 27(XQ21.31) MUTATED	0	0	1	12
AMP PEAK 27(XQ21.31) WILD-TYPE	108	91	97	183

Figure S169. Get High-res Image Gene #27: 'amp_xq21.31' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq21.31' versus 'METHLYATION_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.024

Table S170. Gene #27: 'amp_xq21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
AMP PEAK 27(XQ21.31) MUTATED	0	4	5	4
AMP PEAK 27(XQ21.31) WILD-TYPE	161	133	119	66

Figure S170. Get High-res Image Gene #27: 'amp_xq21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xq21.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0278 (Fisher's exact test), Q value = 0.046

Table S171. Gene #27: 'amp_xq21.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	74	113	92	68
AMP PEAK 27(XQ21.31) MUTATED	1	5	0	5
AMP PEAK 27(XQ21.31) WILD-TYPE	73	108	92	63

Figure S171. Get High-res Image Gene #27: 'amp_xq21.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_xq21.31' versus 'MRNASEQ_CNMF'

P value = 0.037 (Fisher's exact test), Q value = 0.059

Table S172. Gene #27: 'amp_xq21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
AMP PEAK 27(XQ21.31) MUTATED	1	4	8	0
AMP PEAK 27(XQ21.31) WILD-TYPE	94	137	139	108

Figure S172. Get High-res Image Gene #27: 'amp_xq21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_xq21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00445 (Fisher's exact test), Q value = 0.0094

Table S173. Gene #27: 'amp_xq21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
AMP PEAK 27(XQ21.31) MUTATED	0	10	3
AMP PEAK 27(XQ21.31) WILD-TYPE	171	195	112

Figure S173. Get High-res Image Gene #27: 'amp_xq21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_xq25' versus 'CN_CNMF'

P value = 0.00214 (Fisher's exact test), Q value = 0.005

Table S174. Gene #28: 'amp_xq25' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
AMP PEAK 28(XQ25) MUTATED	1	0	3	15
AMP PEAK 28(XQ25) WILD-TYPE	107	91	95	180

Figure S174. Get High-res Image Gene #28: 'amp_xq25' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq25' versus 'METHLYATION_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.028

Table S175. Gene #28: 'amp_xq25' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
AMP PEAK 28(XQ25) MUTATED	3	7	2	7
AMP PEAK 28(XQ25) WILD-TYPE	158	130	122	63

Figure S175. Get High-res Image Gene #28: 'amp_xq25' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xq25' versus 'RPPA_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.024

Table S176. Gene #28: 'amp_xq25' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	51	44	51	58	38
AMP PEAK 28(XQ25) MUTATED	2	1	0	1	7	3
AMP PEAK 28(XQ25) WILD-TYPE	103	50	44	50	51	35

Figure S176. Get High-res Image Gene #28: 'amp_xq25' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_xq25' versus 'MRNASEQ_CNMF'

P value = 0.0493 (Fisher's exact test), Q value = 0.074

Table S177. Gene #28: 'amp_xq25' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
AMP PEAK 28(XQ25) MUTATED	2	5	11	1
AMP PEAK 28(XQ25) WILD-TYPE	93	136	136	107

Figure S177. Get High-res Image Gene #28: 'amp_xq25' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_xq25' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0242 (Fisher's exact test), Q value = 0.04

Table S178. Gene #28: 'amp_xq25' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
AMP PEAK 28(XQ25) MUTATED	3	14	2
AMP PEAK 28(XQ25) WILD-TYPE	168	191	113

Figure S178. Get High-res Image Gene #28: 'amp_xq25' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p31.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S179. Gene #29: 'del_1p31.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 1(1P31.3) MUTATED	5	0	13	42
DEL PEAK 1(1P31.3) WILD-TYPE	103	91	85	153

Figure S179. Get High-res Image Gene #29: 'del_1p31.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p31.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S180. Gene #29: 'del_1p31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 1(1P31.3) MUTATED	3	15	29	13
DEL PEAK 1(1P31.3) WILD-TYPE	158	122	95	57

Figure S180. Get High-res Image Gene #29: 'del_1p31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p31.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S181. Gene #29: 'del_1p31.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 1(1P31.3) MUTATED	4	32	20	4
DEL PEAK 1(1P31.3) WILD-TYPE	91	109	127	104

Figure S181. Get High-res Image Gene #29: 'del_1p31.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p31.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S182. Gene #29: 'del_1p31.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S182. Get High-res Image Gene #29: 'del_1p31.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p31.3' versus 'MIRSEQ_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.0024

Table S183. Gene #29: 'del_1p31.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
DEL PEAK 1(1P31.3) MUTATED	33	7	4	15
DEL PEAK 1(1P31.3) WILD-TYPE	175	64	119	71

Figure S183. Get High-res Image Gene #29: 'del_1p31.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p31.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00327 (Fisher's exact test), Q value = 0.0072

Table S184. Gene #29: 'del_1p31.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
DEL PEAK 1(1P31.3) MUTATED	2	21	11	12
DEL PEAK 1(1P31.3) WILD-TYPE	63	70	67	72

Figure S184. Get High-res Image Gene #29: 'del_1p31.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p31.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.016 (Fisher's exact test), Q value = 0.028

Table S185. Gene #29: 'del_1p31.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
DEL PEAK 1(1P31.3) MUTATED	4	20	12	2	8
DEL PEAK 1(1P31.3) WILD-TYPE	71	66	57	21	57

Figure S185. Get High-res Image Gene #29: 'del_1p31.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S186. Gene #30: 'del_1p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 2(1P22.1) MUTATED	4	0	11	43
DEL PEAK 2(1P22.1) WILD-TYPE	104	91	87	152

Figure S186. Get High-res Image Gene #30: 'del_1p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p22.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S187. Gene #30: 'del_1p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 2(1P22.1) MUTATED	4	23	20	11
DEL PEAK 2(1P22.1) WILD-TYPE	157	114	104	59

Figure S187. Get High-res Image Gene #30: 'del_1p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p22.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S188. Gene #30: 'del_1p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 2(1P22.1) MUTATED	2	23	27	6
DEL PEAK 2(1P22.1) WILD-TYPE	93	118	120	102

Figure S188. Get High-res Image Gene #30: 'del_1p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 5e-04

Table S189. Gene #30: 'del_1p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S189. Get High-res Image Gene #30: 'del_1p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p22.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S190. Gene #30: 'del_1p22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
DEL PEAK 2(1P22.1) MUTATED	41	5	2	9
DEL PEAK 2(1P22.1) WILD-TYPE	167	66	121	77

Figure S190. Get High-res Image Gene #30: 'del_1p22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00317 (Fisher's exact test), Q value = 0.007

Table S191. Gene #30: 'del_1p22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S191. Get High-res Image Gene #30: 'del_1p22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0353 (Fisher's exact test), Q value = 0.056

Table S192. Gene #30: 'del_1p22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
DEL PEAK 2(1P22.1) MUTATED	3	18	8	12
DEL PEAK 2(1P22.1) WILD-TYPE	62	73	70	72

Figure S192. Get High-res Image Gene #30: 'del_1p22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S193. Gene #30: 'del_1p22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
DEL PEAK 2(1P22.1) MUTATED	1	24	8	0	8
DEL PEAK 2(1P22.1) WILD-TYPE	74	62	61	23	57

Figure S193. Get High-res Image Gene #30: 'del_1p22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1q23.1' versus 'METHLYATION_CNMF'

P value = 0.00323 (Fisher's exact test), Q value = 0.0071

Table S194. Gene #31: 'del_1q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 3(1Q23.1) MUTATED	3	16	5	4
DEL PEAK 3(1Q23.1) WILD-TYPE	158	121	119	66

Figure S194. Get High-res Image Gene #31: 'del_1q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1q23.1' versus 'MRNASEQ_CNMF'

P value = 0.00579 (Fisher's exact test), Q value = 0.012

Table S195. Gene #31: 'del_1q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 3(1Q23.1) MUTATED	5	6	16	1
DEL PEAK 3(1Q23.1) WILD-TYPE	90	135	131	107

Figure S195. Get High-res Image Gene #31: 'del_1q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00084 (Fisher's exact test), Q value = 0.0023

Table S196. Gene #31: 'del_1q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S196. Get High-res Image Gene #31: 'del_1q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1q23.1' versus 'MIRSEQ_CNMF'

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

Table S197. Gene #31: 'del_1q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
DEL PEAK 3(1Q23.1) MUTATED	15	4	1	8
DEL PEAK 3(1Q23.1) WILD-TYPE	193	67	122	78

Figure S197. Get High-res Image Gene #31: 'del_1q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00944 (Fisher's exact test), Q value = 0.018

Table S198. Gene #31: 'del_1q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
DEL PEAK 3(1Q23.1) MUTATED	0	11	3	6
DEL PEAK 3(1Q23.1) WILD-TYPE	65	80	75	78

Figure S198. Get High-res Image Gene #31: 'del_1q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1q42.3' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00056

Table S199. Gene #32: 'del_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 4(1Q42.3) MUTATED	5	1	14	27
DEL PEAK 4(1Q42.3) WILD-TYPE	103	90	84	168

Figure S199. Get High-res Image Gene #32: 'del_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q42.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S200. Gene #32: 'del_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 4(1Q42.3) MUTATED	5	28	12	2
DEL PEAK 4(1Q42.3) WILD-TYPE	156	109	112	68

Figure S200. Get High-res Image Gene #32: 'del_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1q42.3' versus 'MRNASEQ_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.028

Table S201. Gene #32: 'del_1q42.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 4(1Q42.3) MUTATED	5	8	23	11
DEL PEAK 4(1Q42.3) WILD-TYPE	90	133	124	97

Figure S201. Get High-res Image Gene #32: 'del_1q42.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1q42.3' versus 'MIRSEQ_CNMF'

P value = 0.00207 (Fisher's exact test), Q value = 0.0048

Table S202. Gene #32: 'del_1q42.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
DEL PEAK 4(1Q42.3) MUTATED	30	7	3	7
DEL PEAK 4(1Q42.3) WILD-TYPE	178	64	120	79

Figure S202. Get High-res Image Gene #32: 'del_1q42.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1q42.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0312 (Fisher's exact test), Q value = 0.051

Table S203. Gene #32: 'del_1q42.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S203. Get High-res Image Gene #32: 'del_1q42.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1q42.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0159 (Fisher's exact test), Q value = 0.028

Table S204. Gene #32: 'del_1q42.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
DEL PEAK 4(1Q42.3) MUTATED	2	16	7	1	7
DEL PEAK 4(1Q42.3) WILD-TYPE	73	70	62	22	58

Figure S204. Get High-res Image Gene #32: 'del_1q42.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2p21' versus 'CN_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0015

Table S205. Gene #33: 'del_2p21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 5(2P21) MUTATED	8	1	7	30
DEL PEAK 5(2P21) WILD-TYPE	100	90	91	165

Figure S205. Get High-res Image Gene #33: 'del_2p21' versus Molecular Subtype #1: 'CN_CNMF'

'del_2p21' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00016

Table S206. Gene #33: 'del_2p21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 5(2P21) MUTATED	3	13	20	10
DEL PEAK 5(2P21) WILD-TYPE	158	124	104	60

Figure S206. Get High-res Image Gene #33: 'del_2p21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2p21' versus 'MRNASEQ_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.0024

Table S207. Gene #33: 'del_2p21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 5(2P21) MUTATED	2	21	18	5
DEL PEAK 5(2P21) WILD-TYPE	93	120	129	103

Figure S207. Get High-res Image Gene #33: 'del_2p21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2p21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0204 (Fisher's exact test), Q value = 0.035

Table S208. Gene #33: 'del_2p21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S208. Get High-res Image Gene #33: 'del_2p21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2p21' versus 'MIRSEQ_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.0025

Table S209. Gene #33: 'del_2p21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
DEL PEAK 5(2P21) MUTATED	31	2	5	5
DEL PEAK 5(2P21) WILD-TYPE	177	69	118	81

Figure S209. Get High-res Image Gene #33: 'del_2p21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S210. Gene #34: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 6(2Q22.1) MUTATED	4	1	21	66
DEL PEAK 6(2Q22.1) WILD-TYPE	104	90	77	129

Figure S210. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S211. Gene #34: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 6(2Q22.1) MUTATED	8	53	15	16
DEL PEAK 6(2Q22.1) WILD-TYPE	153	84	109	54

Figure S211. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.1' versus 'RPPA_CNMF'

P value = 0.00194 (Fisher's exact test), Q value = 0.0046

Table S212. Gene #34: 'del_2q22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	51	44	51	58	38
DEL PEAK 6(2Q22.1) MUTATED	12	11	9	5	21	4
DEL PEAK 6(2Q22.1) WILD-TYPE	93	40	35	46	37	34

Figure S212. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_2q22.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0477 (Fisher's exact test), Q value = 0.073

Table S213. Gene #34: 'del_2q22.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	74	113	92	68
DEL PEAK 6(2Q22.1) MUTATED	9	17	16	20
DEL PEAK 6(2Q22.1) WILD-TYPE	65	96	76	48

Figure S213. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S214. Gene #34: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 6(2Q22.1) MUTATED	8	20	56	8
DEL PEAK 6(2Q22.1) WILD-TYPE	87	121	91	100

Figure S214. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S215. Gene #34: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S215. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S216. Gene #34: 'del_2q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
DEL PEAK 6(2Q22.1) MUTATED	58	9	6	19
DEL PEAK 6(2Q22.1) WILD-TYPE	150	62	117	67

Figure S216. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S217. Gene #34: 'del_2q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S217. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00094 (Fisher's exact test), Q value = 0.0025

Table S218. Gene #34: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
DEL PEAK 6(2Q22.1) MUTATED	4	27	11	19
DEL PEAK 6(2Q22.1) WILD-TYPE	61	64	67	65

Figure S218. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_2q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00107 (Fisher's exact test), Q value = 0.0028

Table S219. Gene #34: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
DEL PEAK 6(2Q22.1) MUTATED	8	29	12	1	11
DEL PEAK 6(2Q22.1) WILD-TYPE	67	57	57	22	54

Figure S219. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S220. Gene #35: 'del_2q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 7(2Q22.3) MUTATED	7	1	17	60
DEL PEAK 7(2Q22.3) WILD-TYPE	101	90	81	135

Figure S220. Get High-res Image Gene #35: 'del_2q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S221. Gene #35: 'del_2q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 7(2Q22.3) MUTATED	8	47	16	14
DEL PEAK 7(2Q22.3) WILD-TYPE	153	90	108	56

Figure S221. Get High-res Image Gene #35: 'del_2q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.3' versus 'RPPA_CNMF'

P value = 0.00218 (Fisher's exact test), Q value = 0.005

Table S222. Gene #35: 'del_2q22.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	51	44	51	58	38
DEL PEAK 7(2Q22.3) MUTATED	9	12	6	3	17	5
DEL PEAK 7(2Q22.3) WILD-TYPE	96	39	38	48	41	33

Figure S222. Get High-res Image Gene #35: 'del_2q22.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_2q22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S223. Gene #35: 'del_2q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 7(2Q22.3) MUTATED	10	18	50	7
DEL PEAK 7(2Q22.3) WILD-TYPE	85	123	97	101

Figure S223. Get High-res Image Gene #35: 'del_2q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S224. Gene #35: 'del_2q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 7(2Q22.3) MUTATED	12	56	17
DEL PEAK 7(2Q22.3) WILD-TYPE	159	149	98

Figure S224. Get High-res Image Gene #35: 'del_2q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S225. Gene #35: 'del_2q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
DEL PEAK 7(2Q22.3) MUTATED	50	9	5	21
DEL PEAK 7(2Q22.3) WILD-TYPE	158	62	118	65

Figure S225. Get High-res Image Gene #35: 'del_2q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S226. Gene #35: 'del_2q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 7(2Q22.3) MUTATED	14	15	4	36	16
DEL PEAK 7(2Q22.3) WILD-TYPE	133	83	55	92	40

Figure S226. Get High-res Image Gene #35: 'del_2q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00391 (Fisher's exact test), Q value = 0.0084

Table S227. Gene #35: 'del_2q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
DEL PEAK 7(2Q22.3) MUTATED	4	24	10	18
DEL PEAK 7(2Q22.3) WILD-TYPE	61	67	68	66

Figure S227. Get High-res Image Gene #35: 'del_2q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_2q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.0022

Table S228. Gene #35: 'del_2q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
DEL PEAK 7(2Q22.3) MUTATED	7	26	11	0	12
DEL PEAK 7(2Q22.3) WILD-TYPE	68	60	58	23	53

Figure S228. Get High-res Image Gene #35: 'del_2q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p13' versus 'CN_CNMF'

P value = 0.00113 (Fisher's exact test), Q value = 0.0029

Table S229. Gene #36: 'del_3p13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 8(3P13) MUTATED	30	8	17	23
DEL PEAK 8(3P13) WILD-TYPE	78	83	81	172

Figure S229. Get High-res Image Gene #36: 'del_3p13' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S230. Gene #36: 'del_3p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 8(3P13) MUTATED	18	10	42	8
DEL PEAK 8(3P13) WILD-TYPE	143	127	82	62

Figure S230. Get High-res Image Gene #36: 'del_3p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p13' versus 'RPPA_CNMF'

P value = 0.0418 (Fisher's exact test), Q value = 0.065

Table S231. Gene #36: 'del_3p13' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	51	44	51	58	38
DEL PEAK 8(3P13) MUTATED	16	5	3	15	6	5
DEL PEAK 8(3P13) WILD-TYPE	89	46	41	36	52	33

Figure S231. Get High-res Image Gene #36: 'del_3p13' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_3p13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S232. Gene #36: 'del_3p13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 8(3P13) MUTATED	8	47	12	11
DEL PEAK 8(3P13) WILD-TYPE	87	94	135	97

Figure S232. Get High-res Image Gene #36: 'del_3p13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S233. Gene #36: 'del_3p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 8(3P13) MUTATED	20	19	39
DEL PEAK 8(3P13) WILD-TYPE	151	186	76

Figure S233. Get High-res Image Gene #36: 'del_3p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00179 (Fisher's exact test), Q value = 0.0043

Table S234. Gene #36: 'del_3p13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
DEL PEAK 8(3P13) MUTATED	14	19	7	4
DEL PEAK 8(3P13) WILD-TYPE	51	72	71	80

Figure S234. Get High-res Image Gene #36: 'del_3p13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3q29' versus 'MRNASEQ_CNMF'

P value = 0.0309 (Fisher's exact test), Q value = 0.05

Table S235. Gene #37: 'del_3q29' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 9(3Q29) MUTATED	4	17	7	4
DEL PEAK 9(3Q29) WILD-TYPE	91	124	140	104

Figure S235. Get High-res Image Gene #37: 'del_3q29' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q28.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S236. Gene #38: 'del_4q28.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 10(4Q28.2) MUTATED	3	0	7	41
DEL PEAK 10(4Q28.2) WILD-TYPE	105	91	91	154

Figure S236. Get High-res Image Gene #38: 'del_4q28.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q28.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S237. Gene #38: 'del_4q28.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 10(4Q28.2) MUTATED	3	29	9	10
DEL PEAK 10(4Q28.2) WILD-TYPE	158	108	115	60

Figure S237. Get High-res Image Gene #38: 'del_4q28.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q28.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S238. Gene #38: 'del_4q28.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 10(4Q28.2) MUTATED	4	9	35	3
DEL PEAK 10(4Q28.2) WILD-TYPE	91	132	112	105

Figure S238. Get High-res Image Gene #38: 'del_4q28.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q28.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S239. Gene #38: 'del_4q28.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 10(4Q28.2) MUTATED	5	37	9
DEL PEAK 10(4Q28.2) WILD-TYPE	166	168	106

Figure S239. Get High-res Image Gene #38: 'del_4q28.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q28.2' versus 'MIRSEQ_CNMF'

P value = 0.00131 (Fisher's exact test), Q value = 0.0032

Table S240. Gene #38: 'del_4q28.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
DEL PEAK 10(4Q28.2) MUTATED	32	4	4	10
DEL PEAK 10(4Q28.2) WILD-TYPE	176	67	119	76

Figure S240. Get High-res Image Gene #38: 'del_4q28.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q28.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0153 (Fisher's exact test), Q value = 0.028

Table S241. Gene #38: 'del_4q28.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 10(4Q28.2) MUTATED	11	8	3	24	4
DEL PEAK 10(4Q28.2) WILD-TYPE	136	90	56	104	52

Figure S241. Get High-res Image Gene #38: 'del_4q28.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q28.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00368 (Fisher's exact test), Q value = 0.008

Table S242. Gene #38: 'del_4q28.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
DEL PEAK 10(4Q28.2) MUTATED	0	13	6	10
DEL PEAK 10(4Q28.2) WILD-TYPE	65	78	72	74

Figure S242. Get High-res Image Gene #38: 'del_4q28.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q28.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00206 (Fisher's exact test), Q value = 0.0048

Table S243. Gene #38: 'del_4q28.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
DEL PEAK 10(4Q28.2) MUTATED	2	17	6	0	4
DEL PEAK 10(4Q28.2) WILD-TYPE	73	69	63	23	61

Figure S243. Get High-res Image Gene #38: 'del_4q28.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S244. Gene #39: 'del_5q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 11(5Q11.2) MUTATED	12	2	13	78
DEL PEAK 11(5Q11.2) WILD-TYPE	96	89	85	117

Figure S244. Get High-res Image Gene #39: 'del_5q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q11.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S245. Gene #39: 'del_5q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 11(5Q11.2) MUTATED	13	39	31	22
DEL PEAK 11(5Q11.2) WILD-TYPE	148	98	93	48

Figure S245. Get High-res Image Gene #39: '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 = 5.2e-05

Table S246. Gene #39: 'del_5q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 11(5Q11.2) MUTATED	5	31	53	16
DEL PEAK 11(5Q11.2) WILD-TYPE	90	110	94	92

Figure S246. Get High-res Image Gene #39: 'del_5q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00023

Table S247. Gene #39: 'del_5q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 11(5Q11.2) MUTATED	18	57	30
DEL PEAK 11(5Q11.2) WILD-TYPE	153	148	85

Figure S247. Get High-res Image Gene #39: 'del_5q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S248. Gene #39: 'del_5q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
DEL PEAK 11(5Q11.2) MUTATED	67	8	16	13
DEL PEAK 11(5Q11.2) WILD-TYPE	141	63	107	73

Figure S248. Get High-res Image Gene #39: '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 = 5.2e-05

Table S249. Gene #39: 'del_5q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 11(5Q11.2) MUTATED	21	9	16	47	11
DEL PEAK 11(5Q11.2) WILD-TYPE	126	89	43	81	45

Figure S249. Get High-res Image Gene #39: 'del_5q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.00065

Table S250. Gene #39: 'del_5q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
DEL PEAK 11(5Q11.2) MUTATED	6	34	12	19
DEL PEAK 11(5Q11.2) WILD-TYPE	59	57	66	65

Figure S250. Get High-res Image Gene #39: 'del_5q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00033

Table S251. Gene #39: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
DEL PEAK 11(5Q11.2) MUTATED	10	36	12	2	11
DEL PEAK 11(5Q11.2) WILD-TYPE	65	50	57	21	54

Figure S251. Get High-res Image Gene #39: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S252. Gene #40: 'del_5q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 12(5Q13.2) MUTATED	12	1	12	74
DEL PEAK 12(5Q13.2) WILD-TYPE	96	90	86	121

Figure S252. Get High-res Image Gene #40: 'del_5q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q13.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S253. Gene #40: 'del_5q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 12(5Q13.2) MUTATED	12	40	24	23
DEL PEAK 12(5Q13.2) WILD-TYPE	149	97	100	47

Figure S253. Get High-res Image Gene #40: 'del_5q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S254. Gene #40: 'del_5q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 12(5Q13.2) MUTATED	2	27	53	17
DEL PEAK 12(5Q13.2) WILD-TYPE	93	114	94	91

Figure S254. Get High-res Image Gene #40: 'del_5q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00272 (Fisher's exact test), Q value = 0.0061

Table S255. Gene #40: 'del_5q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 12(5Q13.2) MUTATED	21	54	24
DEL PEAK 12(5Q13.2) WILD-TYPE	150	151	91

Figure S255. Get High-res Image Gene #40: 'del_5q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q13.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S256. Gene #40: 'del_5q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
DEL PEAK 12(5Q13.2) MUTATED	65	4	20	9
DEL PEAK 12(5Q13.2) WILD-TYPE	143	67	103	77

Figure S256. Get High-res Image Gene #40: 'del_5q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S257. Gene #40: 'del_5q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 12(5Q13.2) MUTATED	27	7	14	44	6
DEL PEAK 12(5Q13.2) WILD-TYPE	120	91	45	84	50

Figure S257. Get High-res Image Gene #40: 'del_5q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00245 (Fisher's exact test), Q value = 0.0056

Table S258. Gene #40: 'del_5q13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
DEL PEAK 12(5Q13.2) MUTATED	6	30	13	15
DEL PEAK 12(5Q13.2) WILD-TYPE	59	61	65	69

Figure S258. Get High-res Image Gene #40: 'del_5q13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00016

Table S259. Gene #40: 'del_5q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
DEL PEAK 12(5Q13.2) MUTATED	12	34	9	4	5
DEL PEAK 12(5Q13.2) WILD-TYPE	63	52	60	19	60

Figure S259. Get High-res Image Gene #40: 'del_5q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S260. Gene #41: 'del_5q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 13(5Q21.1) MUTATED	5	1	26	77
DEL PEAK 13(5Q21.1) WILD-TYPE	103	90	72	118

Figure S260. Get High-res Image Gene #41: 'del_5q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S261. Gene #41: 'del_5q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 13(5Q21.1) MUTATED	12	60	21	16
DEL PEAK 13(5Q21.1) WILD-TYPE	149	77	103	54

Figure S261. Get High-res Image Gene #41: 'del_5q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q21.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S262. Gene #41: 'del_5q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 13(5Q21.1) MUTATED	9	18	70	12
DEL PEAK 13(5Q21.1) WILD-TYPE	86	123	77	96

Figure S262. Get High-res Image Gene #41: 'del_5q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S263. Gene #41: 'del_5q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 13(5Q21.1) MUTATED	17	72	20
DEL PEAK 13(5Q21.1) WILD-TYPE	154	133	95

Figure S263. Get High-res Image Gene #41: 'del_5q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q21.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S264. Gene #41: 'del_5q21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
DEL PEAK 13(5Q21.1) MUTATED	69	6	15	18
DEL PEAK 13(5Q21.1) WILD-TYPE	139	65	108	68

Figure S264. Get High-res Image Gene #41: 'del_5q21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5q21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00272 (Fisher's exact test), Q value = 0.0061

Table S265. Gene #41: 'del_5q21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 13(5Q21.1) MUTATED	26	14	14	44	10
DEL PEAK 13(5Q21.1) WILD-TYPE	121	84	45	84	46

Figure S265. Get High-res Image Gene #41: 'del_5q21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00396 (Fisher's exact test), Q value = 0.0085

Table S266. Gene #41: 'del_5q21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
DEL PEAK 13(5Q21.1) MUTATED	7	25	10	25
DEL PEAK 13(5Q21.1) WILD-TYPE	58	66	68	59

Figure S266. Get High-res Image Gene #41: 'del_5q21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5q21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 7e-04

Table S267. Gene #41: 'del_5q21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
DEL PEAK 13(5Q21.1) MUTATED	8	33	13	2	11
DEL PEAK 13(5Q21.1) WILD-TYPE	67	53	56	21	54

Figure S267. Get High-res Image Gene #41: 'del_5q21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p25.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S268. Gene #42: 'del_6p25.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 14(6P25.1) MUTATED	10	0	6	30
DEL PEAK 14(6P25.1) WILD-TYPE	98	91	92	165

Figure S268. Get High-res Image Gene #42: 'del_6p25.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.1' versus 'METHLYATION_CNMF'

P value = 0.00452 (Fisher's exact test), Q value = 0.0096

Table S269. Gene #42: 'del_6p25.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 14(6P25.1) MUTATED	7	11	15	13
DEL PEAK 14(6P25.1) WILD-TYPE	154	126	109	57

Figure S269. Get High-res Image Gene #42: 'del_6p25.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p25.1' versus 'MRNASEQ_CNMF'

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

Table S270. Gene #42: 'del_6p25.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 14(6P25.1) MUTATED	3	20	14	9
DEL PEAK 14(6P25.1) WILD-TYPE	92	121	133	99

Figure S270. Get High-res Image Gene #42: 'del_6p25.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6p25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0118 (Fisher's exact test), Q value = 0.022

Table S271. Gene #42: 'del_6p25.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 14(6P25.1) MUTATED	10	17	19
DEL PEAK 14(6P25.1) WILD-TYPE	161	188	96

Figure S271. Get High-res Image Gene #42: 'del_6p25.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6p25.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.049 (Fisher's exact test), Q value = 0.074

Table S272. Gene #42: 'del_6p25.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 14(6P25.1) MUTATED	9	5	8	19	5
DEL PEAK 14(6P25.1) WILD-TYPE	138	93	51	109	51

Figure S272. Get High-res Image Gene #42: 'del_6p25.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q14.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S273. Gene #43: 'del_6q14.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 15(6Q14.3) MUTATED	8	4	62	106
DEL PEAK 15(6Q14.3) WILD-TYPE	100	87	36	89

Figure S273. Get High-res Image Gene #43: 'del_6q14.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q14.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S274. Gene #43: 'del_6q14.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 15(6Q14.3) MUTATED	23	101	27	29
DEL PEAK 15(6Q14.3) WILD-TYPE	138	36	97	41

Figure S274. Get High-res Image Gene #43: 'del_6q14.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q14.3' versus 'RPPA_CNMF'

P value = 0.00341 (Fisher's exact test), Q value = 0.0074

Table S275. Gene #43: 'del_6q14.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	51	44	51	58	38
DEL PEAK 15(6Q14.3) MUTATED	26	19	13	20	33	15
DEL PEAK 15(6Q14.3) WILD-TYPE	79	32	31	31	25	23

Figure S275. Get High-res Image Gene #43: 'del_6q14.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_6q14.3' versus 'RPPA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00029

Table S276. Gene #43: 'del_6q14.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	74	113	92	68
DEL PEAK 15(6Q14.3) MUTATED	19	43	24	40
DEL PEAK 15(6Q14.3) WILD-TYPE	55	70	68	28

Figure S276. Get High-res Image Gene #43: 'del_6q14.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_6q14.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S277. Gene #43: 'del_6q14.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 15(6Q14.3) MUTATED	25	33	93	29
DEL PEAK 15(6Q14.3) WILD-TYPE	70	108	54	79

Figure S277. Get High-res Image Gene #43: 'del_6q14.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q14.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S278. Gene #43: 'del_6q14.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 15(6Q14.3) MUTATED	33	117	30
DEL PEAK 15(6Q14.3) WILD-TYPE	138	88	85

Figure S278. Get High-res Image Gene #43: 'del_6q14.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q14.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S279. Gene #43: 'del_6q14.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
DEL PEAK 15(6Q14.3) MUTATED	106	20	20	33
DEL PEAK 15(6Q14.3) WILD-TYPE	102	51	103	53

Figure S279. Get High-res Image Gene #43: 'del_6q14.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6q14.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S280. Gene #43: 'del_6q14.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 15(6Q14.3) MUTATED	38	35	14	68	24
DEL PEAK 15(6Q14.3) WILD-TYPE	109	63	45	60	32

Figure S280. Get High-res Image Gene #43: 'del_6q14.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q14.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0203 (Fisher's exact test), Q value = 0.035

Table S281. Gene #43: 'del_6q14.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
DEL PEAK 15(6Q14.3) MUTATED	14	40	23	32
DEL PEAK 15(6Q14.3) WILD-TYPE	51	51	55	52

Figure S281. Get High-res Image Gene #43: 'del_6q14.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6q14.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00796 (Fisher's exact test), Q value = 0.016

Table S282. Gene #43: 'del_6q14.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
DEL PEAK 15(6Q14.3) MUTATED	20	41	25	3	20
DEL PEAK 15(6Q14.3) WILD-TYPE	55	45	44	20	45

Figure S282. Get High-res Image Gene #43: 'del_6q14.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S283. Gene #44: 'del_8p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 16(8P21.3) MUTATED	81	14	53	146
DEL PEAK 16(8P21.3) WILD-TYPE	27	77	45	49

Figure S283. Get High-res Image Gene #44: 'del_8p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S284. Gene #44: 'del_8p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 16(8P21.3) MUTATED	61	84	93	56
DEL PEAK 16(8P21.3) WILD-TYPE	100	53	31	14

Figure S284. Get High-res Image Gene #44: 'del_8p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00139 (Fisher's exact test), Q value = 0.0034

Table S285. Gene #44: 'del_8p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	74	113	92	68
DEL PEAK 16(8P21.3) MUTATED	32	72	55	51
DEL PEAK 16(8P21.3) WILD-TYPE	42	41	37	17

Figure S285. Get High-res Image Gene #44: 'del_8p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_8p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S286. Gene #44: 'del_8p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 16(8P21.3) MUTATED	36	110	95	53
DEL PEAK 16(8P21.3) WILD-TYPE	59	31	52	55

Figure S286. Get High-res Image Gene #44: 'del_8p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S287. Gene #44: 'del_8p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 16(8P21.3) MUTATED	77	128	89
DEL PEAK 16(8P21.3) WILD-TYPE	94	77	26

Figure S287. Get High-res Image Gene #44: 'del_8p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p21.3' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S288. Gene #44: 'del_8p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
DEL PEAK 16(8P21.3) MUTATED	149	31	59	53
DEL PEAK 16(8P21.3) WILD-TYPE	59	40	64	33

Figure S288. Get High-res Image Gene #44: 'del_8p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S289. Gene #44: 'del_8p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 16(8P21.3) MUTATED	67	50	42	97	36
DEL PEAK 16(8P21.3) WILD-TYPE	80	48	17	31	20

Figure S289. Get High-res Image Gene #44: 'del_8p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.021

Table S290. Gene #44: 'del_8p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
DEL PEAK 16(8P21.3) MUTATED	27	61	40	50
DEL PEAK 16(8P21.3) WILD-TYPE	38	30	38	34

Figure S290. Get High-res Image Gene #44: 'del_8p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00852 (Fisher's exact test), Q value = 0.017

Table S291. Gene #44: 'del_8p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
DEL PEAK 16(8P21.3) MUTATED	29	57	39	13	40
DEL PEAK 16(8P21.3) WILD-TYPE	46	29	30	10	25

Figure S291. Get High-res Image Gene #44: 'del_8p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S292. Gene #45: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 17(9P23) MUTATED	3	2	6	34
DEL PEAK 17(9P23) WILD-TYPE	105	89	92	161

Figure S292. Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'RPPA_CNMF'

P value = 0.00492 (Fisher's exact test), Q value = 0.01

Table S293. Gene #45: 'del_9p23' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	51	44	51	58	38
DEL PEAK 17(9P23) MUTATED	2	6	3	8	5	7
DEL PEAK 17(9P23) WILD-TYPE	103	45	41	43	53	31

Figure S293. Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_9p23' versus 'RPPA_CHIERARCHICAL'

P value = 0.00545 (Fisher's exact test), Q value = 0.011

Table S294. Gene #45: 'del_9p23' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	74	113	92	68
DEL PEAK 17(9P23) MUTATED	2	11	5	13
DEL PEAK 17(9P23) WILD-TYPE	72	102	87	55

Figure S294. Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00173 (Fisher's exact test), Q value = 0.0042

Table S295. Gene #45: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 17(9P23) MUTATED	7	19	19
DEL PEAK 17(9P23) WILD-TYPE	164	186	96

Figure S295. Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 0.0374 (Fisher's exact test), Q value = 0.059

Table S296. Gene #45: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
DEL PEAK 17(9P23) MUTATED	27	3	6	8
DEL PEAK 17(9P23) WILD-TYPE	181	68	117	78

Figure S296. Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S297. Gene #46: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 18(10Q23.31) MUTATED	45	1	23	88
DEL PEAK 18(10Q23.31) WILD-TYPE	63	90	75	107

Figure S297. Get High-res Image Gene #46: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S298. Gene #46: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 18(10Q23.31) MUTATED	28	29	64	36
DEL PEAK 18(10Q23.31) WILD-TYPE	133	108	60	34

Figure S298. Get High-res Image Gene #46: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'RPPA_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0029

Table S299. Gene #46: 'del_10q23.31' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	51	44	51	58	38
DEL PEAK 18(10Q23.31) MUTATED	25	26	18	16	13	19
DEL PEAK 18(10Q23.31) WILD-TYPE	80	25	26	35	45	19

Figure S299. Get High-res Image Gene #46: 'del_10q23.31' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S300. Gene #46: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 18(10Q23.31) MUTATED	6	91	40	20
DEL PEAK 18(10Q23.31) WILD-TYPE	89	50	107	88

Figure S300. Get High-res Image Gene #46: '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 = 5.2e-05

Table S301. Gene #46: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 18(10Q23.31) MUTATED	33	47	77
DEL PEAK 18(10Q23.31) WILD-TYPE	138	158	38

Figure S301. Get High-res Image Gene #46: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00033

Table S302. Gene #46: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
DEL PEAK 18(10Q23.31) MUTATED	79	9	32	35
DEL PEAK 18(10Q23.31) WILD-TYPE	129	62	91	51

Figure S302. Get High-res Image Gene #46: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S303. Gene #46: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 18(10Q23.31) MUTATED	41	12	25	57	20
DEL PEAK 18(10Q23.31) WILD-TYPE	106	86	34	71	36

Figure S303. Get High-res Image Gene #46: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0484 (Fisher's exact test), Q value = 0.073

Table S304. Gene #46: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
DEL PEAK 18(10Q23.31) MUTATED	15	36	24	36
DEL PEAK 18(10Q23.31) WILD-TYPE	50	55	54	48

Figure S304. Get High-res Image Gene #46: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.00099

Table S305. Gene #46: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
DEL PEAK 18(10Q23.31) MUTATED	13	43	21	9	25
DEL PEAK 18(10Q23.31) WILD-TYPE	62	43	48	14	40

Figure S305. Get High-res Image Gene #46: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p11.2' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00042

Table S306. Gene #47: 'del_11p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 19(11P11.2) MUTATED	2	1	6	25
DEL PEAK 19(11P11.2) WILD-TYPE	106	90	92	170

Figure S306. Get High-res Image Gene #47: 'del_11p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p11.2' versus 'METHLYATION_CNMF'

P value = 0.00512 (Fisher's exact test), Q value = 0.011

Table S307. Gene #47: 'del_11p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 19(11P11.2) MUTATED	5	17	5	7
DEL PEAK 19(11P11.2) WILD-TYPE	156	120	119	63

Figure S307. Get High-res Image Gene #47: 'del_11p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p11.2' versus 'RPPA_CNMF'

P value = 0.00142 (Fisher's exact test), Q value = 0.0035

Table S308. Gene #47: 'del_11p11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	51	44	51	58	38
DEL PEAK 19(11P11.2) MUTATED	2	5	1	1	10	4
DEL PEAK 19(11P11.2) WILD-TYPE	103	46	43	50	48	34

Figure S308. Get High-res Image Gene #47: 'del_11p11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_11p11.2' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00013

Table S309. Gene #47: 'del_11p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 19(11P11.2) MUTATED	0	6	22	6
DEL PEAK 19(11P11.2) WILD-TYPE	95	135	125	102

Figure S309. Get High-res Image Gene #47: 'del_11p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11p11.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S310. Gene #47: 'del_11p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 19(11P11.2) MUTATED	7	22	5
DEL PEAK 19(11P11.2) WILD-TYPE	164	183	110

Figure S310. Get High-res Image Gene #47: 'del_11p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11p11.2' versus 'MIRSEQ_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.029

Table S311. Gene #47: 'del_11p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
DEL PEAK 19(11P11.2) MUTATED	23	3	3	5
DEL PEAK 19(11P11.2) WILD-TYPE	185	68	120	81

Figure S311. Get High-res Image Gene #47: 'del_11p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.024 (Fisher's exact test), Q value = 0.04

Table S312. Gene #47: 'del_11p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 19(11P11.2) MUTATED	5	7	2	17	3
DEL PEAK 19(11P11.2) WILD-TYPE	142	91	57	111	53

Figure S312. Get High-res Image Gene #47: 'del_11p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0282 (Fisher's exact test), Q value = 0.047

Table S313. Gene #47: 'del_11p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
DEL PEAK 19(11P11.2) MUTATED	0	10	5	5
DEL PEAK 19(11P11.2) WILD-TYPE	65	81	73	79

Figure S313. Get High-res Image Gene #47: 'del_11p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q22.3' versus 'CN_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.02

Table S314. Gene #48: 'del_11q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 20(11Q22.3) MUTATED	8	3	5	27
DEL PEAK 20(11Q22.3) WILD-TYPE	100	88	93	168

Figure S314. Get High-res Image Gene #48: 'del_11q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q22.3' versus 'METHLYATION_CNMF'

P value = 0.00986 (Fisher's exact test), Q value = 0.019

Table S315. Gene #48: 'del_11q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 20(11Q22.3) MUTATED	10	14	6	13
DEL PEAK 20(11Q22.3) WILD-TYPE	151	123	118	57

Figure S315. Get High-res Image Gene #48: 'del_11q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q23.2' versus 'CN_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0017

Table S316. Gene #49: 'del_11q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 21(11Q23.2) MUTATED	13	1	6	28
DEL PEAK 21(11Q23.2) WILD-TYPE	95	90	92	167

Figure S316. Get High-res Image Gene #49: 'del_11q23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S317. Gene #50: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 22(12P13.1) MUTATED	28	3	22	71
DEL PEAK 22(12P13.1) WILD-TYPE	80	88	76	124

Figure S317. Get High-res Image Gene #50: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.0025

Table S318. Gene #50: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 22(12P13.1) MUTATED	23	42	39	20
DEL PEAK 22(12P13.1) WILD-TYPE	138	95	85	50

Figure S318. Get High-res Image Gene #50: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12p13.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0238 (Fisher's exact test), Q value = 0.04

Table S319. Gene #50: 'del_12p13.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	74	113	92	68
DEL PEAK 22(12P13.1) MUTATED	13	29	21	27
DEL PEAK 22(12P13.1) WILD-TYPE	61	84	71	41

Figure S319. Get High-res Image Gene #50: 'del_12p13.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_12p13.1' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00027

Table S320. Gene #50: 'del_12p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 22(12P13.1) MUTATED	10	51	42	21
DEL PEAK 22(12P13.1) WILD-TYPE	85	90	105	87

Figure S320. Get High-res Image Gene #50: 'del_12p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00393 (Fisher's exact test), Q value = 0.0085

Table S321. Gene #50: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 22(12P13.1) MUTATED	31	52	41
DEL PEAK 22(12P13.1) WILD-TYPE	140	153	74

Figure S321. Get High-res Image Gene #50: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00039

Table S322. Gene #50: 'del_12p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
DEL PEAK 22(12P13.1) MUTATED	70	9	19	23
DEL PEAK 22(12P13.1) WILD-TYPE	138	62	104	63

Figure S322. Get High-res Image Gene #50: 'del_12p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_12p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00023

Table S323. Gene #50: 'del_12p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 22(12P13.1) MUTATED	31	10	18	47	15
DEL PEAK 22(12P13.1) WILD-TYPE	116	88	41	81	41

Figure S323. Get High-res Image Gene #50: 'del_12p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0011

Table S324. Gene #50: 'del_12p13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
DEL PEAK 22(12P13.1) MUTATED	6	35	19	19
DEL PEAK 22(12P13.1) WILD-TYPE	59	56	59	65

Figure S324. Get High-res Image Gene #50: 'del_12p13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_12p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0162 (Fisher's exact test), Q value = 0.029

Table S325. Gene #50: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
DEL PEAK 22(12P13.1) MUTATED	17	33	15	3	11
DEL PEAK 22(12P13.1) WILD-TYPE	58	53	54	20	54

Figure S325. Get High-res Image Gene #50: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q24.32' versus 'CN_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.024

Table S326. Gene #51: 'del_12q24.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 23(12Q24.32) MUTATED	7	3	6	27
DEL PEAK 23(12Q24.32) WILD-TYPE	101	88	92	168

Figure S326. Get High-res Image Gene #51: 'del_12q24.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S327. Gene #52: 'del_13q14.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 24(13Q14.13) MUTATED	30	10	49	138
DEL PEAK 24(13Q14.13) WILD-TYPE	78	81	49	57

Figure S327. Get High-res Image Gene #52: 'del_13q14.13' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S328. Gene #52: 'del_13q14.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 24(13Q14.13) MUTATED	42	83	57	45
DEL PEAK 24(13Q14.13) WILD-TYPE	119	54	67	25

Figure S328. Get High-res Image Gene #52: 'del_13q14.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q14.13' versus 'RPPA_CHIERARCHICAL'

P value = 0.0453 (Fisher's exact test), Q value = 0.069

Table S329. Gene #52: 'del_13q14.13' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	74	113	92	68
DEL PEAK 24(13Q14.13) MUTATED	31	53	34	40
DEL PEAK 24(13Q14.13) WILD-TYPE	43	60	58	28

Figure S329. Get High-res Image Gene #52: 'del_13q14.13' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_13q14.13' versus 'MRNASEQ_CNMF'

P value = 0.00079 (Fisher's exact test), Q value = 0.0022

Table S330. Gene #52: 'del_13q14.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 24(13Q14.13) MUTATED	31	76	79	41
DEL PEAK 24(13Q14.13) WILD-TYPE	64	65	68	67

Figure S330. Get High-res Image Gene #52: 'del_13q14.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q14.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00023

Table S331. Gene #52: 'del_13q14.13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 24(13Q14.13) MUTATED	56	105	66
DEL PEAK 24(13Q14.13) WILD-TYPE	115	100	49

Figure S331. Get High-res Image Gene #52: 'del_13q14.13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.13' versus 'MIRSEQ_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.0014

Table S332. Gene #52: 'del_13q14.13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
DEL PEAK 24(13Q14.13) MUTATED	114	28	40	44
DEL PEAK 24(13Q14.13) WILD-TYPE	94	43	83	42

Figure S332. Get High-res Image Gene #52: 'del_13q14.13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_13q14.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.001

Table S333. Gene #52: 'del_13q14.13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 24(13Q14.13) MUTATED	55	37	25	78	31
DEL PEAK 24(13Q14.13) WILD-TYPE	92	61	34	50	25

Figure S333. Get High-res Image Gene #52: 'del_13q14.13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S334. Gene #52: 'del_13q14.13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
DEL PEAK 24(13Q14.13) MUTATED	17	57	27	51
DEL PEAK 24(13Q14.13) WILD-TYPE	48	34	51	33

Figure S334. Get High-res Image Gene #52: 'del_13q14.13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_13q14.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00119 (Fisher's exact test), Q value = 0.003

Table S335. Gene #52: 'del_13q14.13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
DEL PEAK 24(13Q14.13) MUTATED	25	56	29	10	32
DEL PEAK 24(13Q14.13) WILD-TYPE	50	30	40	13	33

Figure S335. Get High-res Image Gene #52: 'del_13q14.13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S336. Gene #53: 'del_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 25(13Q22.1) MUTATED	20	4	33	119
DEL PEAK 25(13Q22.1) WILD-TYPE	88	87	65	76

Figure S336. Get High-res Image Gene #53: 'del_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S337. Gene #53: 'del_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 25(13Q22.1) MUTATED	34	59	46	37
DEL PEAK 25(13Q22.1) WILD-TYPE	127	78	78	33

Figure S337. Get High-res Image Gene #53: 'del_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q22.1' versus 'RPPA_CNMF'

P value = 0.0245 (Fisher's exact test), Q value = 0.041

Table S338. Gene #53: 'del_13q22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	51	44	51	58	38
DEL PEAK 25(13Q22.1) MUTATED	30	19	15	13	26	21
DEL PEAK 25(13Q22.1) WILD-TYPE	75	32	29	38	32	17

Figure S338. Get High-res Image Gene #53: 'del_13q22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_13q22.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00042

Table S339. Gene #53: 'del_13q22.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	74	113	92	68
DEL PEAK 25(13Q22.1) MUTATED	19	40	25	40
DEL PEAK 25(13Q22.1) WILD-TYPE	55	73	67	28

Figure S339. Get High-res Image Gene #53: 'del_13q22.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_13q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S340. Gene #53: 'del_13q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 25(13Q22.1) MUTATED	18	63	70	25
DEL PEAK 25(13Q22.1) WILD-TYPE	77	78	77	83

Figure S340. Get High-res Image Gene #53: 'del_13q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00029

Table S341. Gene #53: 'del_13q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 25(13Q22.1) MUTATED	40	86	50
DEL PEAK 25(13Q22.1) WILD-TYPE	131	119	65

Figure S341. Get High-res Image Gene #53: 'del_13q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q22.1' versus 'MIRSEQ_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.032

Table S342. Gene #53: 'del_13q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
DEL PEAK 25(13Q22.1) MUTATED	87	23	31	33
DEL PEAK 25(13Q22.1) WILD-TYPE	121	48	92	53

Figure S342. Get High-res Image Gene #53: 'del_13q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_13q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00148 (Fisher's exact test), Q value = 0.0036

Table S343. Gene #53: 'del_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 25(13Q22.1) MUTATED	42	27	19	64	22
DEL PEAK 25(13Q22.1) WILD-TYPE	105	71	40	64	34

Figure S343. Get High-res Image Gene #53: 'del_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0022

Table S344. Gene #53: 'del_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
DEL PEAK 25(13Q22.1) MUTATED	13	42	24	40
DEL PEAK 25(13Q22.1) WILD-TYPE	52	49	54	44

Figure S344. Get High-res Image Gene #53: 'del_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_13q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S345. Gene #53: 'del_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
DEL PEAK 25(13Q22.1) MUTATED	16	51	23	6	23
DEL PEAK 25(13Q22.1) WILD-TYPE	59	35	46	17	42

Figure S345. Get High-res Image Gene #53: 'del_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S346. Gene #54: 'del_15q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 26(15Q21.3) MUTATED	11	1	4	51
DEL PEAK 26(15Q21.3) WILD-TYPE	97	90	94	144

Figure S346. Get High-res Image Gene #54: 'del_15q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q21.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S347. Gene #54: 'del_15q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 26(15Q21.3) MUTATED	5	20	25	17
DEL PEAK 26(15Q21.3) WILD-TYPE	156	117	99	53

Figure S347. Get High-res Image Gene #54: 'del_15q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q21.3' versus 'RPPA_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.001

Table S348. Gene #54: 'del_15q21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	51	44	51	58	38
DEL PEAK 26(15Q21.3) MUTATED	5	13	7	2	6	9
DEL PEAK 26(15Q21.3) WILD-TYPE	100	38	37	49	52	29

Figure S348. Get High-res Image Gene #54: 'del_15q21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_15q21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0448 (Fisher's exact test), Q value = 0.069

Table S349. Gene #54: 'del_15q21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	74	113	92	68
DEL PEAK 26(15Q21.3) MUTATED	3	18	10	11
DEL PEAK 26(15Q21.3) WILD-TYPE	71	95	82	57

Figure S349. Get High-res Image Gene #54: 'del_15q21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_15q21.3' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00027

Table S350. Gene #54: 'del_15q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 26(15Q21.3) MUTATED	7	25	31	4
DEL PEAK 26(15Q21.3) WILD-TYPE	88	116	116	104

Figure S350. Get High-res Image Gene #54: 'del_15q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S351. Gene #54: 'del_15q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 26(15Q21.3) MUTATED	7	37	23
DEL PEAK 26(15Q21.3) WILD-TYPE	164	168	92

Figure S351. Get High-res Image Gene #54: 'del_15q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q21.3' versus 'MIRSEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00053

Table S352. Gene #54: 'del_15q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
DEL PEAK 26(15Q21.3) MUTATED	39	8	4	14
DEL PEAK 26(15Q21.3) WILD-TYPE	169	63	119	72

Figure S352. Get High-res Image Gene #54: 'del_15q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_15q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00013

Table S353. Gene #54: 'del_15q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 26(15Q21.3) MUTATED	7	8	10	28	12
DEL PEAK 26(15Q21.3) WILD-TYPE	140	90	49	100	44

Figure S353. Get High-res Image Gene #54: 'del_15q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.0025

Table S354. Gene #54: 'del_15q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
DEL PEAK 26(15Q21.3) MUTATED	1	20	10	13
DEL PEAK 26(15Q21.3) WILD-TYPE	64	71	68	71

Figure S354. Get High-res Image Gene #54: 'del_15q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_15q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00029

Table S355. Gene #54: 'del_15q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
DEL PEAK 26(15Q21.3) MUTATED	2	24	9	1	8
DEL PEAK 26(15Q21.3) WILD-TYPE	73	62	60	22	57

Figure S355. Get High-res Image Gene #54: 'del_15q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S356. Gene #55: 'del_16q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 27(16Q22.3) MUTATED	60	3	14	114
DEL PEAK 27(16Q22.3) WILD-TYPE	48	88	84	81

Figure S356. Get High-res Image Gene #55: 'del_16q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S357. Gene #55: 'del_16q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 27(16Q22.3) MUTATED	31	53	63	44
DEL PEAK 27(16Q22.3) WILD-TYPE	130	84	61	26

Figure S357. Get High-res Image Gene #55: 'del_16q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S358. Gene #55: 'del_16q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 27(16Q22.3) MUTATED	16	81	66	28
DEL PEAK 27(16Q22.3) WILD-TYPE	79	60	81	80

Figure S358. Get High-res Image Gene #55: 'del_16q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 5e-04

Table S359. Gene #55: 'del_16q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 27(16Q22.3) MUTATED	51	77	63
DEL PEAK 27(16Q22.3) WILD-TYPE	120	128	52

Figure S359. Get High-res Image Gene #55: 'del_16q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q22.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S360. Gene #55: 'del_16q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
DEL PEAK 27(16Q22.3) MUTATED	111	13	33	32
DEL PEAK 27(16Q22.3) WILD-TYPE	97	58	90	54

Figure S360. Get High-res Image Gene #55: 'del_16q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S361. Gene #55: 'del_16q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 27(16Q22.3) MUTATED	44	22	28	78	17
DEL PEAK 27(16Q22.3) WILD-TYPE	103	76	31	50	39

Figure S361. Get High-res Image Gene #55: 'del_16q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S362. Gene #55: 'del_16q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
DEL PEAK 27(16Q22.3) MUTATED	11	51	22	30
DEL PEAK 27(16Q22.3) WILD-TYPE	54	40	56	54

Figure S362. Get High-res Image Gene #55: 'del_16q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0145 (Fisher's exact test), Q value = 0.026

Table S363. Gene #55: 'del_16q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
DEL PEAK 27(16Q22.3) MUTATED	23	43	21	4	23
DEL PEAK 27(16Q22.3) WILD-TYPE	52	43	48	19	42

Figure S363. Get High-res Image Gene #55: 'del_16q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S364. Gene #56: 'del_16q24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 28(16Q24.1) MUTATED	71	4	13	125
DEL PEAK 28(16Q24.1) WILD-TYPE	37	87	85	70

Figure S364. Get High-res Image Gene #56: 'del_16q24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q24.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S365. Gene #56: 'del_16q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 28(16Q24.1) MUTATED	39	54	67	53
DEL PEAK 28(16Q24.1) WILD-TYPE	122	83	57	17

Figure S365. Get High-res Image Gene #56: 'del_16q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q24.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S366. Gene #56: 'del_16q24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 28(16Q24.1) MUTATED	18	88	72	35
DEL PEAK 28(16Q24.1) WILD-TYPE	77	53	75	73

Figure S366. Get High-res Image Gene #56: 'del_16q24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0059 (Fisher's exact test), Q value = 0.012

Table S367. Gene #56: 'del_16q24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 28(16Q24.1) MUTATED	63	86	64
DEL PEAK 28(16Q24.1) WILD-TYPE	108	119	51

Figure S367. Get High-res Image Gene #56: 'del_16q24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q24.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S368. Gene #56: 'del_16q24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
DEL PEAK 28(16Q24.1) MUTATED	116	17	42	35
DEL PEAK 28(16Q24.1) WILD-TYPE	92	54	81	51

Figure S368. Get High-res Image Gene #56: 'del_16q24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S369. Gene #56: 'del_16q24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 28(16Q24.1) MUTATED	50	25	32	86	17
DEL PEAK 28(16Q24.1) WILD-TYPE	97	73	27	42	39

Figure S369. Get High-res Image Gene #56: 'del_16q24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00335 (Fisher's exact test), Q value = 0.0073

Table S370. Gene #56: 'del_16q24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
DEL PEAK 28(16Q24.1) MUTATED	17	50	29	33
DEL PEAK 28(16Q24.1) WILD-TYPE	48	41	49	51

Figure S370. Get High-res Image Gene #56: 'del_16q24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S371. Gene #57: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 29(17P13.1) MUTATED	45	4	12	102
DEL PEAK 29(17P13.1) WILD-TYPE	63	87	86	93

Figure S371. Get High-res Image Gene #57: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S372. Gene #57: 'del_17p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 29(17P13.1) MUTATED	30	24	67	42
DEL PEAK 29(17P13.1) WILD-TYPE	131	113	57	28

Figure S372. Get High-res Image Gene #57: 'del_17p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p13.1' versus 'RPPA_CNMF'

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

Table S373. Gene #57: 'del_17p13.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	51	44	51	58	38
DEL PEAK 29(17P13.1) MUTATED	29	16	11	21	16	21
DEL PEAK 29(17P13.1) WILD-TYPE	76	35	33	30	42	17

Figure S373. Get High-res Image Gene #57: 'del_17p13.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_17p13.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0286 (Fisher's exact test), Q value = 0.047

Table S374. Gene #57: 'del_17p13.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	74	113	92	68
DEL PEAK 29(17P13.1) MUTATED	22	33	26	33
DEL PEAK 29(17P13.1) WILD-TYPE	52	80	66	35

Figure S374. Get High-res Image Gene #57: 'del_17p13.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_17p13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S375. Gene #57: 'del_17p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 29(17P13.1) MUTATED	13	76	50	24
DEL PEAK 29(17P13.1) WILD-TYPE	82	65	97	84

Figure S375. Get High-res Image Gene #57: 'del_17p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S376. Gene #57: 'del_17p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 29(17P13.1) MUTATED	38	54	71
DEL PEAK 29(17P13.1) WILD-TYPE	133	151	44

Figure S376. Get High-res Image Gene #57: 'del_17p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.1' versus 'MIRSEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00045

Table S377. Gene #57: 'del_17p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
DEL PEAK 29(17P13.1) MUTATED	91	14	31	25
DEL PEAK 29(17P13.1) WILD-TYPE	117	57	92	61

Figure S377. Get High-res Image Gene #57: 'del_17p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S378. Gene #57: 'del_17p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 29(17P13.1) MUTATED	36	15	34	60	16
DEL PEAK 29(17P13.1) WILD-TYPE	111	83	25	68	40

Figure S378. Get High-res Image Gene #57: 'del_17p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00502 (Fisher's exact test), Q value = 0.01

Table S379. Gene #57: 'del_17p13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
DEL PEAK 29(17P13.1) MUTATED	15	44	22	32
DEL PEAK 29(17P13.1) WILD-TYPE	50	47	56	52

Figure S379. Get High-res Image Gene #57: 'del_17p13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00222 (Fisher's exact test), Q value = 0.0051

Table S380. Gene #57: 'del_17p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
DEL PEAK 29(17P13.1) MUTATED	20	46	19	8	20
DEL PEAK 29(17P13.1) WILD-TYPE	55	40	50	15	45

Figure S380. Get High-res Image Gene #57: 'del_17p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q21.31' versus 'CN_CNMF'

P value = 0.00548 (Fisher's exact test), Q value = 0.011

Table S381. Gene #58: 'del_17q21.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 30(17Q21.31) MUTATED	27	10	12	47
DEL PEAK 30(17Q21.31) WILD-TYPE	81	81	86	148

Figure S381. Get High-res Image Gene #58: 'del_17q21.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q21.31' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S382. Gene #58: 'del_17q21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 30(17Q21.31) MUTATED	24	13	43	16
DEL PEAK 30(17Q21.31) WILD-TYPE	137	124	81	54

Figure S382. Get High-res Image Gene #58: 'del_17q21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q21.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0348 (Fisher's exact test), Q value = 0.056

Table S383. Gene #58: 'del_17q21.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	74	113	92	68
DEL PEAK 30(17Q21.31) MUTATED	20	28	12	9
DEL PEAK 30(17Q21.31) WILD-TYPE	54	85	80	59

Figure S383. Get High-res Image Gene #58: 'del_17q21.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_17q21.31' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00013

Table S384. Gene #58: 'del_17q21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 30(17Q21.31) MUTATED	13	48	18	17
DEL PEAK 30(17Q21.31) WILD-TYPE	82	93	129	91

Figure S384. Get High-res Image Gene #58: 'del_17q21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17q21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00065

Table S385. Gene #58: 'del_17q21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 30(17Q21.31) MUTATED	33	26	37
DEL PEAK 30(17Q21.31) WILD-TYPE	138	179	78

Figure S385. Get High-res Image Gene #58: 'del_17q21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S386. Gene #59: 'del_18q21.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 31(18Q21.31) MUTATED	28	3	8	92
DEL PEAK 31(18Q21.31) WILD-TYPE	80	88	90	103

Figure S386. Get High-res Image Gene #59: 'del_18q21.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q21.31' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00045

Table S387. Gene #59: 'del_18q21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 31(18Q21.31) MUTATED	23	42	44	22
DEL PEAK 31(18Q21.31) WILD-TYPE	138	95	80	48

Figure S387. Get High-res Image Gene #59: 'del_18q21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q21.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00219 (Fisher's exact test), Q value = 0.005

Table S388. Gene #59: 'del_18q21.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	74	113	92	68
DEL PEAK 31(18Q21.31) MUTATED	14	28	16	29
DEL PEAK 31(18Q21.31) WILD-TYPE	60	85	76	39

Figure S388. Get High-res Image Gene #59: 'del_18q21.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_18q21.31' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00036

Table S389. Gene #59: 'del_18q21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 31(18Q21.31) MUTATED	18	40	57	16
DEL PEAK 31(18Q21.31) WILD-TYPE	77	101	90	92

Figure S389. Get High-res Image Gene #59: 'del_18q21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0124 (Fisher's exact test), Q value = 0.023

Table S390. Gene #59: 'del_18q21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 31(18Q21.31) MUTATED	32	63	36
DEL PEAK 31(18Q21.31) WILD-TYPE	139	142	79

Figure S390. Get High-res Image Gene #59: 'del_18q21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.31' versus 'MIRSEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00048

Table S391. Gene #59: 'del_18q21.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
DEL PEAK 31(18Q21.31) MUTATED	74	14	18	23
DEL PEAK 31(18Q21.31) WILD-TYPE	134	57	105	63

Figure S391. Get High-res Image Gene #59: 'del_18q21.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0182 (Fisher's exact test), Q value = 0.032

Table S392. Gene #59: 'del_18q21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 31(18Q21.31) MUTATED	29	20	20	45	15
DEL PEAK 31(18Q21.31) WILD-TYPE	118	78	39	83	41

Figure S392. Get High-res Image Gene #59: 'del_18q21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00279 (Fisher's exact test), Q value = 0.0063

Table S393. Gene #59: 'del_18q21.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
DEL PEAK 31(18Q21.31) MUTATED	8	35	19	24
DEL PEAK 31(18Q21.31) WILD-TYPE	57	56	59	60

Figure S393. Get High-res Image Gene #59: 'del_18q21.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_18q21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00039

Table S394. Gene #59: 'del_18q21.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
DEL PEAK 31(18Q21.31) MUTATED	11	40	16	3	16
DEL PEAK 31(18Q21.31) WILD-TYPE	64	46	53	20	49

Figure S394. Get High-res Image Gene #59: 'del_18q21.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S395. Gene #60: 'del_18q23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 32(18Q23) MUTATED	32	4	6	95
DEL PEAK 32(18Q23) WILD-TYPE	76	87	92	100

Figure S395. Get High-res Image Gene #60: 'del_18q23' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q23' versus 'METHLYATION_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.00091

Table S396. Gene #60: 'del_18q23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 32(18Q23) MUTATED	27	38	46	26
DEL PEAK 32(18Q23) WILD-TYPE	134	99	78	44

Figure S396. Get High-res Image Gene #60: 'del_18q23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q23' versus 'RPPA_CHIERARCHICAL'

P value = 0.0433 (Fisher's exact test), Q value = 0.067

Table S397. Gene #60: 'del_18q23' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	74	113	92	68
DEL PEAK 32(18Q23) MUTATED	18	31	18	27
DEL PEAK 32(18Q23) WILD-TYPE	56	82	74	41

Figure S397. Get High-res Image Gene #60: 'del_18q23' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_18q23' versus 'MRNASEQ_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0016

Table S398. Gene #60: 'del_18q23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 32(18Q23) MUTATED	18	45	55	19
DEL PEAK 32(18Q23) WILD-TYPE	77	96	92	89

Figure S398. Get High-res Image Gene #60: 'del_18q23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0432 (Fisher's exact test), Q value = 0.067

Table S399. Gene #60: 'del_18q23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 32(18Q23) MUTATED	37	60	40
DEL PEAK 32(18Q23) WILD-TYPE	134	145	75

Figure S399. Get High-res Image Gene #60: 'del_18q23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_CNMF'

P value = 0.00668 (Fisher's exact test), Q value = 0.013

Table S400. Gene #60: 'del_18q23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
DEL PEAK 32(18Q23) MUTATED	71	14	23	27
DEL PEAK 32(18Q23) WILD-TYPE	137	57	100	59

Figure S400. Get High-res Image Gene #60: 'del_18q23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00746 (Fisher's exact test), Q value = 0.015

Table S401. Gene #60: 'del_18q23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 32(18Q23) MUTATED	29	21	22	46	17
DEL PEAK 32(18Q23) WILD-TYPE	118	77	37	82	39

Figure S401. Get High-res Image Gene #60: 'del_18q23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00214 (Fisher's exact test), Q value = 0.005

Table S402. Gene #60: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	91	78	84
DEL PEAK 32(18Q23) MUTATED	9	36	18	28
DEL PEAK 32(18Q23) WILD-TYPE	56	55	60	56

Figure S402. Get High-res Image Gene #60: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_18q23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00129 (Fisher's exact test), Q value = 0.0032

Table S403. Gene #60: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	86	69	23	65
DEL PEAK 32(18Q23) MUTATED	12	38	17	4	20
DEL PEAK 32(18Q23) WILD-TYPE	63	48	52	19	45

Figure S403. Get High-res Image Gene #60: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S404. Gene #61: 'del_19q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 33(19Q13.2) MUTATED	6	0	7	39
DEL PEAK 33(19Q13.2) WILD-TYPE	102	91	91	156

Figure S404. Get High-res Image Gene #61: 'del_19q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.2' versus 'METHLYATION_CNMF'

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

Table S405. Gene #61: 'del_19q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 33(19Q13.2) MUTATED	7	14	21	10
DEL PEAK 33(19Q13.2) WILD-TYPE	154	123	103	60

Figure S405. Get High-res Image Gene #61: 'del_19q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19q13.2' versus 'MRNASEQ_CNMF'

P value = 0.00126 (Fisher's exact test), Q value = 0.0032

Table S406. Gene #61: 'del_19q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 33(19Q13.2) MUTATED	4	15	27	6
DEL PEAK 33(19Q13.2) WILD-TYPE	91	126	120	102

Figure S406. Get High-res Image Gene #61: 'del_19q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0487 (Fisher's exact test), Q value = 0.074

Table S407. Gene #61: 'del_19q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 33(19Q13.2) MUTATED	11	29	12
DEL PEAK 33(19Q13.2) WILD-TYPE	160	176	103

Figure S407. Get High-res Image Gene #61: 'del_19q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.2' versus 'MIRSEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 7e-04

Table S408. Gene #61: 'del_19q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	71	123	86
DEL PEAK 33(19Q13.2) MUTATED	34	4	3	9
DEL PEAK 33(19Q13.2) WILD-TYPE	174	67	120	77

Figure S408. Get High-res Image Gene #61: 'del_19q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00089 (Fisher's exact test), Q value = 0.0024

Table S409. Gene #61: 'del_19q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 33(19Q13.2) MUTATED	6	7	13	19	5
DEL PEAK 33(19Q13.2) WILD-TYPE	141	91	46	109	51

Figure S409. Get High-res Image Gene #61: 'del_19q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_21q22.2' versus 'METHLYATION_CNMF'

P value = 0.00202 (Fisher's exact test), Q value = 0.0048

Table S410. Gene #62: 'del_21q22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 34(21Q22.2) MUTATED	14	6	23	9
DEL PEAK 34(21Q22.2) WILD-TYPE	147	131	101	61

Figure S410. Get High-res Image Gene #62: 'del_21q22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q22.2' versus 'MRNASEQ_CNMF'

P value = 0.00256 (Fisher's exact test), Q value = 0.0058

Table S411. Gene #62: 'del_21q22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 34(21Q22.2) MUTATED	7	27	12	6
DEL PEAK 34(21Q22.2) WILD-TYPE	88	114	135	102

Figure S411. Get High-res Image Gene #62: 'del_21q22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_21q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 7e-04

Table S412. Gene #62: 'del_21q22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 34(21Q22.2) MUTATED	12	15	25
DEL PEAK 34(21Q22.2) WILD-TYPE	159	190	90

Figure S412. Get High-res Image Gene #62: 'del_21q22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_21q22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.041 (Fisher's exact test), Q value = 0.064

Table S413. Gene #62: 'del_21q22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 34(21Q22.2) MUTATED	11	7	13	15	5
DEL PEAK 34(21Q22.2) WILD-TYPE	136	91	46	113	51

Figure S413. Get High-res Image Gene #62: 'del_21q22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_21q22.3' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00016

Table S414. Gene #63: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	91	98	195
DEL PEAK 35(21Q22.3) MUTATED	50	15	26	55
DEL PEAK 35(21Q22.3) WILD-TYPE	58	76	72	140

Figure S414. Get High-res Image Gene #63: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S415. Gene #63: 'del_21q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	137	124	70
DEL PEAK 35(21Q22.3) MUTATED	37	8	74	27
DEL PEAK 35(21Q22.3) WILD-TYPE	124	129	50	43

Figure S415. Get High-res Image Gene #63: 'del_21q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q22.3' versus 'RPPA_CNMF'

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

Table S416. Gene #63: 'del_21q22.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	51	44	51	58	38
DEL PEAK 35(21Q22.3) MUTATED	27	17	13	23	10	17
DEL PEAK 35(21Q22.3) WILD-TYPE	78	34	31	28	48	21

Figure S416. Get High-res Image Gene #63: 'del_21q22.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_21q22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S417. Gene #63: 'del_21q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	95	141	147	108
DEL PEAK 35(21Q22.3) MUTATED	9	100	18	19
DEL PEAK 35(21Q22.3) WILD-TYPE	86	41	129	89

Figure S417. Get High-res Image Gene #63: 'del_21q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_21q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S418. Gene #63: 'del_21q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	205	115
DEL PEAK 35(21Q22.3) MUTATED	43	21	82
DEL PEAK 35(21Q22.3) WILD-TYPE	128	184	33

Figure S418. Get High-res Image Gene #63: 'del_21q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_21q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S419. Gene #63: 'del_21q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 35(21Q22.3) MUTATED	44	15	33	38	14
DEL PEAK 35(21Q22.3) WILD-TYPE	103	83	26	90	42

Figure S419. Get High-res Image Gene #63: 'del_21q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PRAD-TP/22533739/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PRAD-TP/22553796/PRAD-TP.transferedmergedcluster.txt
Number of patients = 492
Number of significantly focal cnvs = 63
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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