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

Pan-kidney cohort (KICH+KIRC+KIRP) (Primary solid tumor)

21 August 2015 | analyses__2015_08_21

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1XK8DSM

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 39 focal events and 12 molecular subtypes across 882 patients, 398 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q32.1 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_2q32.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3q26.32 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5q35.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7q31.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q24.22 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_10p14 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_17q25.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_xp22.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_xp11.4 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_xq11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_xq28 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.31 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p31.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1q43 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q37.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p26.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p21.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p14.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p12.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q34.3 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_5p15.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q22.31 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q26 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q26 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p23.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p23 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p21.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q21 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q23.1 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q12.13 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q14.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q31.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q23.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p13.3 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_xp22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 39 focal events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 398 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
amp 7q31 2	377 (43%)	505	0.034 (0.0409)	0.0445 (0.0528)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.0292 (0.0356)	0.00335 (0.00452)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)
del 3p26 3	489 (55%)	393	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)
del 3p21 2	503 (57%)	379	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)
del 3p14 1	408 (46%)	474	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.00045 (0.000677)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)
del 3p12 2	336 (38%)	546	2e-05 (3.43e-05)	0.00018 (0.00028)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.0494 (0.0581)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)
del 9p23	198 (22%)	684	0.01 (0.0128)	0.0216 (0.0268)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	2e-05 (3.43e-05)	8e-05 (0.00013)	2e-05 (3.43e-05)
del 9p21 3	209 (24%)	673	0.00363 (0.00485)	0.00762 (0.00982)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	2e-05 (3.43e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)
del 13q14 2	149 (17%)	733	0.0124 (0.0156)	0.0168 (0.0211)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.0307 (0.0374)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.00195 (0.00272)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)
del 14q31 1	279 (32%)	603	9e-05 (0.000145)	0.00031 (0.00048)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	2e-05 (3.43e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)
amp 3q26 32	193 (22%)	689	0.0332 (0.0402)	0.108 (0.123)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.038 (0.0452)	0.0009 (0.0013)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)
amp 5q35 1	376 (43%)	506	0.00103 (0.00148)	0.00187 (0.00261)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.149 (0.169)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)
amp 17q25 2	245 (28%)	637	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.32 (0.348)	0.0164 (0.0206)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)
amp xp22 2	126 (14%)	756	0.00228 (0.00314)	0.00224 (0.00309)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.323 (0.35)	0.00162 (0.00228)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)
amp xp11 4	134 (15%)	748	0.00159 (0.00225)	0.00422 (0.00559)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.495 (0.524)	0.00339 (0.00456)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)
amp xq11 2	135 (15%)	747	2e-05 (3.43e-05)	3e-05 (5.05e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.489 (0.519)	0.00295 (0.00401)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)
amp xq28	137 (16%)	745	0.00011 (0.000175)	0.00058 (0.000859)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.362 (0.39)	0.00038 (0.000579)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)
del 1p36 31	209 (24%)	673	0.00043 (0.000649)	0.00368 (0.00491)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.561 (0.588)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	2e-05 (3.43e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)
del 1p31 1	166 (19%)	716	0.00161 (0.00227)	0.0181 (0.0225)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.744 (0.759)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	3e-05 (5.05e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)
del 1q43	114 (13%)	768	0.0086 (0.011)	0.00749 (0.00972)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.984 (0.99)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)
del 2q37 3	111 (13%)	771	0.00017 (0.000265)	9e-05 (0.000145)	3e-05 (5.05e-05)	1e-05 (1.78e-05)	0.563 (0.588)	0.00013 (0.000206)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)
del 6q22 31	227 (26%)	655	0.00048 (0.000718)	0.00627 (0.00822)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.00497 (0.00655)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.768 (0.781)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)
del 6q26	233 (26%)	649	0.00053 (0.000787)	0.00761 (0.00982)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.00352 (0.00472)	2e-05 (3.43e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.572 (0.595)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)
del 6q26	234 (27%)	648	0.00049 (0.00073)	0.00721 (0.00943)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.00334 (0.00452)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.599 (0.62)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)
del 13q12 13	150 (17%)	732	0.028 (0.0343)	0.037 (0.0443)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.068 (0.0794)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.00072 (0.00105)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)
amp 8q24 22	125 (14%)	757	0.326 (0.354)	0.6 (0.62)	1e-05 (1.78e-05)	0.00183 (0.00256)	6e-05 (9.82e-05)	5e-05 (8.27e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.00104 (0.00149)	0.0238 (0.0293)	0.00034 (0.000523)	4e-05 (6.69e-05)
del 5p15 33	31 (4%)	851			0.0033 (0.00448)	1e-05 (1.78e-05)	0.0352 (0.0422)	0.0485 (0.0571)	5e-05 (8.27e-05)	1e-05 (1.78e-05)	4e-05 (6.69e-05)	1e-05 (1.78e-05)	0.00088 (0.00128)	5e-05 (8.27e-05)
amp 1q32 1	82 (9%)	800	0.549 (0.578)	0.695 (0.711)	1e-05 (1.78e-05)	0.0857 (0.099)	0.00066 (0.000971)	0.0102 (0.0129)	2e-05 (3.43e-05)	1e-05 (1.78e-05)	3e-05 (5.05e-05)	0.00036 (0.000552)	0.0307 (0.0374)	0.00066 (0.000971)
del 4q34 3	113 (13%)	769	0.561 (0.588)	0.318 (0.347)	1e-05 (1.78e-05)	0.00072 (0.00105)	0.0689 (0.0802)	0.00047 (0.000705)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.00213 (0.00295)	0.00451 (0.00596)	0.00014 (0.00022)	1e-05 (1.78e-05)
del 8p23 2	184 (21%)	698	0.6 (0.62)	0.605 (0.624)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.302 (0.33)	0.0075 (0.00972)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)
del 11q23 1	71 (8%)	811	0.0377 (0.0451)	0.0917 (0.105)	1e-05 (1.78e-05)	0.0893 (0.103)	0.289 (0.317)	0.00081 (0.00118)	3e-05 (5.05e-05)	1e-05 (1.78e-05)	0.0107 (0.0136)	0.00095 (0.00137)	1e-05 (1.78e-05)	1e-05 (1.78e-05)
del 18q22 2	155 (18%)	727	0.0878 (0.101)	0.228 (0.252)	1e-05 (1.78e-05)	0.031 (0.0376)	0.00039 (0.000593)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.00016 (0.00025)	0.852 (0.865)	0.00202 (0.00281)	1e-05 (1.78e-05)
del 19p13 3	43 (5%)	839	1 (1.00)	0.854 (0.866)	1e-05 (1.78e-05)	0.00034 (0.000523)	0.184 (0.205)	0.0181 (0.0225)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.00292 (0.00398)	1e-05 (1.78e-05)	0.00118 (0.00168)	6e-05 (9.82e-05)
del xp22 2	127 (14%)	755	0.0813 (0.0942)	0.108 (0.123)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.571 (0.595)	6e-05 (9.82e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)
amp 2q32 1	136 (15%)	746	0.607 (0.624)	0.371 (0.398)	1e-05 (1.78e-05)	0.00616 (0.0081)	0.521 (0.55)	0.00245 (0.00335)	0.00904 (0.0116)	1e-05 (1.78e-05)	0.361 (0.389)	7e-05 (0.000114)	0.0075 (0.00972)	0.00861 (0.011)
amp 19p13 2	98 (11%)	784	0.121 (0.138)	0.277 (0.304)	1e-05 (1.78e-05)	0.0407 (0.0483)	0.0503 (0.059)	0.00013 (0.000206)	0.0001 (0.00016)	1e-05 (1.78e-05)	0.00147 (0.00208)	7e-05 (0.000114)	0.0806 (0.0936)	0.00042 (0.000636)
del 10q23 31	164 (19%)	718	0.207 (0.231)	0.176 (0.197)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.488 (0.519)	0.00038 (0.000579)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.212 (0.235)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	1e-05 (1.78e-05)
del 11q21	61 (7%)	821	0.548 (0.578)	0.38 (0.407)	1e-05 (1.78e-05)	0.052 (0.0608)	0.608 (0.624)	0.0024 (0.00329)	1e-05 (1.78e-05)	1e-05 (1.78e-05)	0.0338 (0.0407)	0.00394 (0.00524)	0.00014 (0.00022)	2e-05 (3.43e-05)
amp 10p14	34 (4%)	848	0.15 (0.169)	0.478 (0.509)	1e-05 (1.78e-05)	0.0232 (0.0286)	0.0933 (0.107)	0.0472 (0.0558)	0.00138 (0.00196)	0.00069 (0.00101)	0.211 (0.234)	0.694 (0.711)	0.245 (0.27)	0.248 (0.273)
del 16q23 3	37 (4%)	845	0.868 (0.877)	0.915 (0.923)	0.017 (0.0213)	0.0113 (0.0143)	0.388 (0.415)	0.345 (0.373)	0.0243 (0.0298)	0.0001 (0.00016)	0.184 (0.205)	0.164 (0.184)	0.152 (0.171)	0.0219 (0.0271)

'amp_1q32.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S1. Gene #1: 'amp_1q32.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
AMP PEAK 1(1Q32.1) MUTATED	6	18	58
AMP PEAK 1(1Q32.1) WILD-TYPE	276	292	232

Figure S1. Get High-res Image Gene #1: 'amp_1q32.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q32.1' versus 'RPPA_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.00097

Table S2. Gene #1: 'amp_1q32.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
AMP PEAK 1(1Q32.1) MUTATED	20	12	8	31
AMP PEAK 1(1Q32.1) WILD-TYPE	162	169	179	166

Figure S2. Get High-res Image Gene #1: 'amp_1q32.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_1q32.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.013

Table S3. Gene #1: 'amp_1q32.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
AMP PEAK 1(1Q32.1) MUTATED	15	1	14	14	10	3	14
AMP PEAK 1(1Q32.1) WILD-TYPE	182	63	102	133	49	68	79

Figure S3. Get High-res Image Gene #1: 'amp_1q32.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_1q32.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.4e-05

Table S4. Gene #1: 'amp_1q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
AMP PEAK 1(1Q32.1) MUTATED	4	37	26	13
AMP PEAK 1(1Q32.1) WILD-TYPE	115	158	271	255

Figure S4. Get High-res Image Gene #1: 'amp_1q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q32.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S5. Gene #1: 'amp_1q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
AMP PEAK 1(1Q32.1) MUTATED	0	21	19	32	8	0
AMP PEAK 1(1Q32.1) WILD-TYPE	88	124	188	127	103	169

Figure S5. Get High-res Image Gene #1: 'amp_1q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q32.1' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 5.1e-05

Table S6. Gene #1: 'amp_1q32.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
AMP PEAK 1(1Q32.1) MUTATED	12	26	42
AMP PEAK 1(1Q32.1) WILD-TYPE	315	167	302

Figure S6. Get High-res Image Gene #1: 'amp_1q32.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q32.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.00055

Table S7. Gene #1: 'amp_1q32.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
AMP PEAK 1(1Q32.1) MUTATED	0	23	57
AMP PEAK 1(1Q32.1) WILD-TYPE	77	282	425

Figure S7. Get High-res Image Gene #1: 'amp_1q32.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q32.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0307 (Fisher's exact test), Q value = 0.037

Table S8. Gene #1: 'amp_1q32.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
AMP PEAK 1(1Q32.1) MUTATED	5	4	8	13
AMP PEAK 1(1Q32.1) WILD-TYPE	148	67	55	112

Figure S8. Get High-res Image Gene #1: 'amp_1q32.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_1q32.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.00097

Table S9. Gene #1: 'amp_1q32.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
AMP PEAK 1(1Q32.1) MUTATED	0	4	15	11	0
AMP PEAK 1(1Q32.1) WILD-TYPE	47	94	82	113	46

Figure S9. Get High-res Image Gene #1: 'amp_1q32.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_2q32.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S10. Gene #2: 'amp_2q32.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
AMP PEAK 2(2Q32.1) MUTATED	36	19	81
AMP PEAK 2(2Q32.1) WILD-TYPE	246	291	209

Figure S10. Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2q32.1' versus 'METHLYATION_CNMF'

P value = 0.00616 (Fisher's exact test), Q value = 0.0081

Table S11. Gene #2: 'amp_2q32.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
AMP PEAK 2(2Q32.1) MUTATED	9	48	42
AMP PEAK 2(2Q32.1) WILD-TYPE	119	255	179

Figure S11. Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2q32.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00245 (Fisher's exact test), Q value = 0.0034

Table S12. Gene #2: 'amp_2q32.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
AMP PEAK 2(2Q32.1) MUTATED	20	5	14	28	16	11	22
AMP PEAK 2(2Q32.1) WILD-TYPE	177	59	102	119	43	60	71

Figure S12. Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_2q32.1' versus 'MRNASEQ_CNMF'

P value = 0.00904 (Fisher's exact test), Q value = 0.012

Table S13. Gene #2: 'amp_2q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
AMP PEAK 2(2Q32.1) MUTATED	7	35	48	46
AMP PEAK 2(2Q32.1) WILD-TYPE	112	160	249	222

Figure S13. Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2q32.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S14. Gene #2: 'amp_2q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
AMP PEAK 2(2Q32.1) MUTATED	1	25	22	32	25	31
AMP PEAK 2(2Q32.1) WILD-TYPE	87	120	185	127	86	138

Figure S14. Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_2q32.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00011

Table S15. Gene #2: 'amp_2q32.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
AMP PEAK 2(2Q32.1) MUTATED	1	54	79
AMP PEAK 2(2Q32.1) WILD-TYPE	76	251	403

Figure S15. Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_2q32.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0075 (Fisher's exact test), Q value = 0.0097

Table S16. Gene #2: 'amp_2q32.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
AMP PEAK 2(2Q32.1) MUTATED	25	4	17	21
AMP PEAK 2(2Q32.1) WILD-TYPE	128	67	46	104

Figure S16. Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_2q32.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00861 (Fisher's exact test), Q value = 0.011

Table S17. Gene #2: 'amp_2q32.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
AMP PEAK 2(2Q32.1) MUTATED	5	18	23	20	1
AMP PEAK 2(2Q32.1) WILD-TYPE	42	80	74	104	45

Figure S17. Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.32' versus 'MRNA_CNMF'

P value = 0.0332 (Fisher's exact test), Q value = 0.04

Table S18. Gene #3: 'amp_3q26.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
AMP PEAK 3(3Q26.32) MUTATED	2	7	2	6
AMP PEAK 3(3Q26.32) WILD-TYPE	31	17	10	11

Figure S18. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S19. Gene #3: 'amp_3q26.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
AMP PEAK 3(3Q26.32) MUTATED	103	11	79
AMP PEAK 3(3Q26.32) WILD-TYPE	179	299	211

Figure S19. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S20. Gene #3: 'amp_3q26.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
AMP PEAK 3(3Q26.32) MUTATED	17	43	91
AMP PEAK 3(3Q26.32) WILD-TYPE	111	260	130

Figure S20. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.32' versus 'RPPA_CNMF'

P value = 0.038 (Fisher's exact test), Q value = 0.045

Table S21. Gene #3: 'amp_3q26.32' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
AMP PEAK 3(3Q26.32) MUTATED	30	33	40	55
AMP PEAK 3(3Q26.32) WILD-TYPE	152	148	147	142

Figure S21. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_3q26.32' versus 'RPPA_CHIERARCHICAL'

P value = 9e-04 (Fisher's exact test), Q value = 0.0013

Table S22. Gene #3: 'amp_3q26.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
AMP PEAK 3(3Q26.32) MUTATED	35	11	38	25	18	20	11
AMP PEAK 3(3Q26.32) WILD-TYPE	162	53	78	122	41	51	82

Figure S22. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_3q26.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S23. Gene #3: 'amp_3q26.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
AMP PEAK 3(3Q26.32) MUTATED	13	53	25	102
AMP PEAK 3(3Q26.32) WILD-TYPE	106	142	272	166

Figure S23. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S24. Gene #3: 'amp_3q26.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
AMP PEAK 3(3Q26.32) MUTATED	10	31	18	45	11	78
AMP PEAK 3(3Q26.32) WILD-TYPE	78	114	189	114	100	91

Figure S24. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S25. Gene #3: 'amp_3q26.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
AMP PEAK 3(3Q26.32) MUTATED	110	37	43
AMP PEAK 3(3Q26.32) WILD-TYPE	217	156	301

Figure S25. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S26. Gene #3: 'amp_3q26.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
AMP PEAK 3(3Q26.32) MUTATED	9	110	71
AMP PEAK 3(3Q26.32) WILD-TYPE	68	195	411

Figure S26. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S27. Gene #3: 'amp_3q26.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
AMP PEAK 3(3Q26.32) MUTATED	61	5	15	12
AMP PEAK 3(3Q26.32) WILD-TYPE	92	66	48	113

Figure S27. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S28. Gene #3: 'amp_3q26.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
AMP PEAK 3(3Q26.32) MUTATED	14	44	22	9	4
AMP PEAK 3(3Q26.32) WILD-TYPE	33	54	75	115	42

Figure S28. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5q35.1' versus 'MRNA_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.0015

Table S29. Gene #4: 'amp_5q35.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
AMP PEAK 4(5Q35.1) MUTATED	20	15	3	2
AMP PEAK 4(5Q35.1) WILD-TYPE	13	9	9	15

Figure S29. Get High-res Image Gene #4: 'amp_5q35.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_5q35.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00187 (Fisher's exact test), Q value = 0.0026

Table S30. Gene #4: 'amp_5q35.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
AMP PEAK 4(5Q35.1) MUTATED	13	15	2	7	3
AMP PEAK 4(5Q35.1) WILD-TYPE	7	9	16	6	8

Figure S30. Get High-res Image Gene #4: 'amp_5q35.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_5q35.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S31. Gene #4: 'amp_5q35.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
AMP PEAK 4(5Q35.1) MUTATED	35	139	202
AMP PEAK 4(5Q35.1) WILD-TYPE	247	171	88

Figure S31. Get High-res Image Gene #4: 'amp_5q35.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5q35.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S32. Gene #4: 'amp_5q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
AMP PEAK 4(5Q35.1) MUTATED	17	197	23
AMP PEAK 4(5Q35.1) WILD-TYPE	111	106	198

Figure S32. Get High-res Image Gene #4: 'amp_5q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_5q35.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S33. Gene #4: 'amp_5q35.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
AMP PEAK 4(5Q35.1) MUTATED	83	8	45	87	43	30	41
AMP PEAK 4(5Q35.1) WILD-TYPE	114	56	71	60	16	41	52

Figure S33. Get High-res Image Gene #4: 'amp_5q35.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_5q35.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S34. Gene #4: 'amp_5q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
AMP PEAK 4(5Q35.1) MUTATED	16	121	203	34
AMP PEAK 4(5Q35.1) WILD-TYPE	103	74	94	234

Figure S34. Get High-res Image Gene #4: 'amp_5q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S35. Gene #4: 'amp_5q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
AMP PEAK 4(5Q35.1) MUTATED	11	30	145	110	68	10
AMP PEAK 4(5Q35.1) WILD-TYPE	77	115	62	49	43	159

Figure S35. Get High-res Image Gene #4: 'amp_5q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5q35.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S36. Gene #4: 'amp_5q35.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
AMP PEAK 4(5Q35.1) MUTATED	38	89	240
AMP PEAK 4(5Q35.1) WILD-TYPE	289	104	104

Figure S36. Get High-res Image Gene #4: 'amp_5q35.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_5q35.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S37. Gene #4: 'amp_5q35.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
AMP PEAK 4(5Q35.1) MUTATED	9	41	317
AMP PEAK 4(5Q35.1) WILD-TYPE	68	264	165

Figure S37. Get High-res Image Gene #4: 'amp_5q35.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_5q35.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S38. Gene #4: 'amp_5q35.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
AMP PEAK 4(5Q35.1) MUTATED	19	7	19	90
AMP PEAK 4(5Q35.1) WILD-TYPE	134	64	44	35

Figure S38. Get High-res Image Gene #4: 'amp_5q35.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_5q35.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S39. Gene #4: 'amp_5q35.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
AMP PEAK 4(5Q35.1) MUTATED	3	15	20	91	6
AMP PEAK 4(5Q35.1) WILD-TYPE	44	83	77	33	40

Figure S39. Get High-res Image Gene #4: 'amp_5q35.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q31.2' versus 'MRNA_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 0.041

Table S40. Gene #5: 'amp_7q31.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
AMP PEAK 5(7Q31.2) MUTATED	9	10	5	12
AMP PEAK 5(7Q31.2) WILD-TYPE	24	14	7	5

Figure S40. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_7q31.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0445 (Fisher's exact test), Q value = 0.053

Table S41. Gene #5: 'amp_7q31.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
AMP PEAK 5(7Q31.2) MUTATED	5	10	13	4	4
AMP PEAK 5(7Q31.2) WILD-TYPE	15	14	5	9	7

Figure S41. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S42. Gene #5: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
AMP PEAK 5(7Q31.2) MUTATED	194	42	141
AMP PEAK 5(7Q31.2) WILD-TYPE	88	268	149

Figure S42. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q31.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S43. Gene #5: 'amp_7q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
AMP PEAK 5(7Q31.2) MUTATED	42	85	155
AMP PEAK 5(7Q31.2) WILD-TYPE	86	218	66

Figure S43. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7q31.2' versus 'RPPA_CNMF'

P value = 0.0292 (Fisher's exact test), Q value = 0.036

Table S44. Gene #5: 'amp_7q31.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
AMP PEAK 5(7Q31.2) MUTATED	66	73	76	100
AMP PEAK 5(7Q31.2) WILD-TYPE	116	108	111	97

Figure S44. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_7q31.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00335 (Fisher's exact test), Q value = 0.0045

Table S45. Gene #5: 'amp_7q31.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
AMP PEAK 5(7Q31.2) MUTATED	95	24	58	44	28	34	32
AMP PEAK 5(7Q31.2) WILD-TYPE	102	40	58	103	31	37	61

Figure S45. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_7q31.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S46. Gene #5: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
AMP PEAK 5(7Q31.2) MUTATED	37	91	73	174
AMP PEAK 5(7Q31.2) WILD-TYPE	82	104	224	94

Figure S46. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S47. Gene #5: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
AMP PEAK 5(7Q31.2) MUTATED	30	44	61	70	26	144
AMP PEAK 5(7Q31.2) WILD-TYPE	58	101	146	89	85	25

Figure S47. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S48. Gene #5: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
AMP PEAK 5(7Q31.2) MUTATED	189	78	107
AMP PEAK 5(7Q31.2) WILD-TYPE	138	115	237

Figure S48. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S49. Gene #5: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
AMP PEAK 5(7Q31.2) MUTATED	29	194	151
AMP PEAK 5(7Q31.2) WILD-TYPE	48	111	331

Figure S49. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S50. Gene #5: 'amp_7q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
AMP PEAK 5(7Q31.2) MUTATED	110	24	29	37
AMP PEAK 5(7Q31.2) WILD-TYPE	43	47	34	88

Figure S50. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S51. Gene #5: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
AMP PEAK 5(7Q31.2) MUTATED	38	68	38	36	20
AMP PEAK 5(7Q31.2) WILD-TYPE	9	30	59	88	26

Figure S51. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S52. Gene #6: 'amp_8q24.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
AMP PEAK 6(8Q24.22) MUTATED	34	7	84
AMP PEAK 6(8Q24.22) WILD-TYPE	248	303	206

Figure S52. Get High-res Image Gene #6: 'amp_8q24.22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.22' versus 'METHLYATION_CNMF'

P value = 0.00183 (Fisher's exact test), Q value = 0.0026

Table S53. Gene #6: 'amp_8q24.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
AMP PEAK 6(8Q24.22) MUTATED	27	51	19
AMP PEAK 6(8Q24.22) WILD-TYPE	101	252	202

Figure S53. Get High-res Image Gene #6: 'amp_8q24.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.22' versus 'RPPA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 9.8e-05

Table S54. Gene #6: 'amp_8q24.22' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
AMP PEAK 6(8Q24.22) MUTATED	35	16	19	46
AMP PEAK 6(8Q24.22) WILD-TYPE	147	165	168	151

Figure S54. Get High-res Image Gene #6: 'amp_8q24.22' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_8q24.22' versus 'RPPA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 8.3e-05

Table S55. Gene #6: 'amp_8q24.22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
AMP PEAK 6(8Q24.22) MUTATED	25	7	35	13	16	8	12
AMP PEAK 6(8Q24.22) WILD-TYPE	172	57	81	134	43	63	81

Figure S55. Get High-res Image Gene #6: 'amp_8q24.22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_8q24.22' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S56. Gene #6: 'amp_8q24.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
AMP PEAK 6(8Q24.22) MUTATED	23	62	16	23
AMP PEAK 6(8Q24.22) WILD-TYPE	96	133	281	245

Figure S56. Get High-res Image Gene #6: 'amp_8q24.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S57. Gene #6: 'amp_8q24.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
AMP PEAK 6(8Q24.22) MUTATED	18	26	16	54	2	8
AMP PEAK 6(8Q24.22) WILD-TYPE	70	119	191	105	109	161

Figure S57. Get High-res Image Gene #6: 'amp_8q24.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.22' versus 'MIRSEQ_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.0015

Table S58. Gene #6: 'amp_8q24.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
AMP PEAK 6(8Q24.22) MUTATED	37	44	42
AMP PEAK 6(8Q24.22) WILD-TYPE	290	149	302

Figure S58. Get High-res Image Gene #6: 'amp_8q24.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0238 (Fisher's exact test), Q value = 0.029

Table S59. Gene #6: 'amp_8q24.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
AMP PEAK 6(8Q24.22) MUTATED	18	34	71
AMP PEAK 6(8Q24.22) WILD-TYPE	59	271	411

Figure S59. Get High-res Image Gene #6: 'amp_8q24.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.00052

Table S60. Gene #6: 'amp_8q24.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
AMP PEAK 6(8Q24.22) MUTATED	12	17	17	15
AMP PEAK 6(8Q24.22) WILD-TYPE	141	54	46	110

Figure S60. Get High-res Image Gene #6: 'amp_8q24.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 6.7e-05

Table S61. Gene #6: 'amp_8q24.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
AMP PEAK 6(8Q24.22) MUTATED	1	9	23	13	15
AMP PEAK 6(8Q24.22) WILD-TYPE	46	89	74	111	31

Figure S61. Get High-res Image Gene #6: 'amp_8q24.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10p14' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S62. Gene #7: 'amp_10p14' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
AMP PEAK 7(10P14) MUTATED	9	1	24
AMP PEAK 7(10P14) WILD-TYPE	273	309	266

Figure S62. Get High-res Image Gene #7: 'amp_10p14' versus Molecular Subtype #3: 'CN_CNMF'

'amp_10p14' versus 'METHLYATION_CNMF'

P value = 0.0232 (Fisher's exact test), Q value = 0.029

Table S63. Gene #7: 'amp_10p14' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
AMP PEAK 7(10P14) MUTATED	10	10	4
AMP PEAK 7(10P14) WILD-TYPE	118	293	217

Figure S63. Get High-res Image Gene #7: 'amp_10p14' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_10p14' versus 'RPPA_CHIERARCHICAL'

P value = 0.0472 (Fisher's exact test), Q value = 0.056

Table S64. Gene #7: 'amp_10p14' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
AMP PEAK 7(10P14) MUTATED	4	2	10	4	5	1	4
AMP PEAK 7(10P14) WILD-TYPE	193	62	106	143	54	70	89

Figure S64. Get High-res Image Gene #7: 'amp_10p14' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_10p14' versus 'MRNASEQ_CNMF'

P value = 0.00138 (Fisher's exact test), Q value = 0.002

Table S65. Gene #7: 'amp_10p14' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
AMP PEAK 7(10P14) MUTATED	6	16	4	8
AMP PEAK 7(10P14) WILD-TYPE	113	179	293	260

Figure S65. Get High-res Image Gene #7: 'amp_10p14' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_10p14' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00069 (Fisher's exact test), Q value = 0.001

Table S66. Gene #7: 'amp_10p14' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
AMP PEAK 7(10P14) MUTATED	4	10	4	13	0	3
AMP PEAK 7(10P14) WILD-TYPE	84	135	203	146	111	166

Figure S66. Get High-res Image Gene #7: 'amp_10p14' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q25.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S67. Gene #8: 'amp_17q25.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
AMP PEAK 8(17Q25.2) MUTATED	1	1	3	12
AMP PEAK 8(17Q25.2) WILD-TYPE	32	23	9	5

Figure S67. Get High-res Image Gene #8: 'amp_17q25.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q25.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S68. Gene #8: 'amp_17q25.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
AMP PEAK 8(17Q25.2) MUTATED	1	1	13	0	2
AMP PEAK 8(17Q25.2) WILD-TYPE	19	23	5	13	9

Figure S68. Get High-res Image Gene #8: 'amp_17q25.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S69. Gene #8: 'amp_17q25.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
AMP PEAK 8(17Q25.2) MUTATED	177	17	51
AMP PEAK 8(17Q25.2) WILD-TYPE	105	293	239

Figure S69. Get High-res Image Gene #8: 'amp_17q25.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q25.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S70. Gene #8: 'amp_17q25.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
AMP PEAK 8(17Q25.2) MUTATED	21	30	168
AMP PEAK 8(17Q25.2) WILD-TYPE	107	273	53

Figure S70. Get High-res Image Gene #8: 'amp_17q25.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q25.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 0.021

Table S71. Gene #8: 'amp_17q25.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
AMP PEAK 8(17Q25.2) MUTATED	53	23	29	27	11	26	18
AMP PEAK 8(17Q25.2) WILD-TYPE	144	41	87	120	48	45	75

Figure S71. Get High-res Image Gene #8: 'amp_17q25.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17q25.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S72. Gene #8: 'amp_17q25.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
AMP PEAK 8(17Q25.2) MUTATED	11	26	14	194
AMP PEAK 8(17Q25.2) WILD-TYPE	108	169	283	74

Figure S72. Get High-res Image Gene #8: 'amp_17q25.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S73. Gene #8: 'amp_17q25.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
AMP PEAK 8(17Q25.2) MUTATED	2	59	10	21	3	150
AMP PEAK 8(17Q25.2) WILD-TYPE	86	86	197	138	108	19

Figure S73. Get High-res Image Gene #8: 'amp_17q25.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q25.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S74. Gene #8: 'amp_17q25.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
AMP PEAK 8(17Q25.2) MUTATED	186	36	22
AMP PEAK 8(17Q25.2) WILD-TYPE	141	157	322

Figure S74. Get High-res Image Gene #8: 'amp_17q25.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q25.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S75. Gene #8: 'amp_17q25.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
AMP PEAK 8(17Q25.2) MUTATED	1	209	34
AMP PEAK 8(17Q25.2) WILD-TYPE	76	96	448

Figure S75. Get High-res Image Gene #8: 'amp_17q25.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q25.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S76. Gene #8: 'amp_17q25.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
AMP PEAK 8(17Q25.2) MUTATED	120	7	30	5
AMP PEAK 8(17Q25.2) WILD-TYPE	33	64	33	120

Figure S76. Get High-res Image Gene #8: 'amp_17q25.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q25.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S77. Gene #8: 'amp_17q25.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
AMP PEAK 8(17Q25.2) MUTATED	42	74	43	2	1
AMP PEAK 8(17Q25.2) WILD-TYPE	5	24	54	122	45

Figure S77. Get High-res Image Gene #8: 'amp_17q25.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S78. Gene #9: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
AMP PEAK 9(19P13.2) MUTATED	43	1	54
AMP PEAK 9(19P13.2) WILD-TYPE	239	309	236

Figure S78. Get High-res Image Gene #9: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.2' versus 'METHLYATION_CNMF'

P value = 0.0407 (Fisher's exact test), Q value = 0.048

Table S79. Gene #9: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
AMP PEAK 9(19P13.2) MUTATED	24	30	25
AMP PEAK 9(19P13.2) WILD-TYPE	104	273	196

Figure S79. Get High-res Image Gene #9: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00021

Table S80. Gene #9: 'amp_19p13.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
AMP PEAK 9(19P13.2) MUTATED	27	2	20	11	14	2	7
AMP PEAK 9(19P13.2) WILD-TYPE	170	62	96	136	45	69	86

Figure S80. Get High-res Image Gene #9: 'amp_19p13.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_19p13.2' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00016

Table S81. Gene #9: 'amp_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
AMP PEAK 9(19P13.2) MUTATED	25	27	17	29
AMP PEAK 9(19P13.2) WILD-TYPE	94	168	280	239

Figure S81. Get High-res Image Gene #9: 'amp_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S82. Gene #9: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
AMP PEAK 9(19P13.2) MUTATED	23	10	13	25	5	22
AMP PEAK 9(19P13.2) WILD-TYPE	65	135	194	134	106	147

Figure S82. Get High-res Image Gene #9: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'MIRSEQ_CNMF'

P value = 0.00147 (Fisher's exact test), Q value = 0.0021

Table S83. Gene #9: 'amp_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
AMP PEAK 9(19P13.2) MUTATED	51	11	35
AMP PEAK 9(19P13.2) WILD-TYPE	276	182	309

Figure S83. Get High-res Image Gene #9: 'amp_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00011

Table S84. Gene #9: 'amp_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
AMP PEAK 9(19P13.2) MUTATED	22	32	43
AMP PEAK 9(19P13.2) WILD-TYPE	55	273	439

Figure S84. Get High-res Image Gene #9: 'amp_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.00064

Table S85. Gene #9: 'amp_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
AMP PEAK 9(19P13.2) MUTATED	8	8	6	10	14
AMP PEAK 9(19P13.2) WILD-TYPE	39	90	91	114	32

Figure S85. Get High-res Image Gene #9: 'amp_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xp22.2' versus 'MRNA_CNMF'

P value = 0.00228 (Fisher's exact test), Q value = 0.0031

Table S86. Gene #10: 'amp_xp22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
AMP PEAK 10(XP22.2) MUTATED	2	2	1	8
AMP PEAK 10(XP22.2) WILD-TYPE	31	22	11	9

Figure S86. Get High-res Image Gene #10: 'amp_xp22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_xp22.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00224 (Fisher's exact test), Q value = 0.0031

Table S87. Gene #10: 'amp_xp22.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
AMP PEAK 10(XP22.2) MUTATED	0	2	8	2	1
AMP PEAK 10(XP22.2) WILD-TYPE	20	22	10	11	10

Figure S87. Get High-res Image Gene #10: 'amp_xp22.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_xp22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S88. Gene #10: 'amp_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
AMP PEAK 10(XP22.2) MUTATED	92	3	31
AMP PEAK 10(XP22.2) WILD-TYPE	190	307	259

Figure S88. Get High-res Image Gene #10: 'amp_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xp22.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S89. Gene #10: 'amp_xp22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
AMP PEAK 10(XP22.2) MUTATED	14	7	77
AMP PEAK 10(XP22.2) WILD-TYPE	114	296	144

Figure S89. Get High-res Image Gene #10: 'amp_xp22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xp22.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00162 (Fisher's exact test), Q value = 0.0023

Table S90. Gene #10: 'amp_xp22.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
AMP PEAK 10(XP22.2) MUTATED	32	9	18	11	7	17	4
AMP PEAK 10(XP22.2) WILD-TYPE	165	55	98	136	52	54	89

Figure S90. Get High-res Image Gene #10: 'amp_xp22.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_xp22.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S91. Gene #10: 'amp_xp22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
AMP PEAK 10(XP22.2) MUTATED	13	18	8	87
AMP PEAK 10(XP22.2) WILD-TYPE	106	177	289	181

Figure S91. Get High-res Image Gene #10: 'amp_xp22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xp22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S92. Gene #10: 'amp_xp22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
AMP PEAK 10(XP22.2) MUTATED	8	16	4	16	4	78
AMP PEAK 10(XP22.2) WILD-TYPE	80	129	203	143	107	91

Figure S92. Get High-res Image Gene #10: 'amp_xp22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xp22.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S93. Gene #10: 'amp_xp22.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
AMP PEAK 10(XP22.2) MUTATED	94	10	22
AMP PEAK 10(XP22.2) WILD-TYPE	233	183	322

Figure S93. Get High-res Image Gene #10: 'amp_xp22.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_xp22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S94. Gene #10: 'amp_xp22.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
AMP PEAK 10(XP22.2) MUTATED	7	93	26
AMP PEAK 10(XP22.2) WILD-TYPE	70	212	456

Figure S94. Get High-res Image Gene #10: 'amp_xp22.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_xp22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S95. Gene #10: 'amp_xp22.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
AMP PEAK 10(XP22.2) MUTATED	55	9	4	5
AMP PEAK 10(XP22.2) WILD-TYPE	98	62	59	120

Figure S95. Get High-res Image Gene #10: 'amp_xp22.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_xp22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S96. Gene #10: 'amp_xp22.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
AMP PEAK 10(XP22.2) MUTATED	16	37	10	4	6
AMP PEAK 10(XP22.2) WILD-TYPE	31	61	87	120	40

Figure S96. Get High-res Image Gene #10: 'amp_xp22.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xp11.4' versus 'MRNA_CNMF'

P value = 0.00159 (Fisher's exact test), Q value = 0.0022

Table S97. Gene #11: 'amp_xp11.4' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
AMP PEAK 11(XP11.4) MUTATED	3	1	1	8
AMP PEAK 11(XP11.4) WILD-TYPE	30	23	11	9

Figure S97. Get High-res Image Gene #11: 'amp_xp11.4' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_xp11.4' versus 'MRNA_CHIERARCHICAL'

P value = 0.00422 (Fisher's exact test), Q value = 0.0056

Table S98. Gene #11: 'amp_xp11.4' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
AMP PEAK 11(XP11.4) MUTATED	1	1	8	2	1
AMP PEAK 11(XP11.4) WILD-TYPE	19	23	10	11	10

Figure S98. Get High-res Image Gene #11: 'amp_xp11.4' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_xp11.4' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S99. Gene #11: 'amp_xp11.4' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
AMP PEAK 11(XP11.4) MUTATED	100	4	30
AMP PEAK 11(XP11.4) WILD-TYPE	182	306	260

Figure S99. Get High-res Image Gene #11: 'amp_xp11.4' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xp11.4' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S100. Gene #11: 'amp_xp11.4' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
AMP PEAK 11(XP11.4) MUTATED	14	11	84
AMP PEAK 11(XP11.4) WILD-TYPE	114	292	137

Figure S100. Get High-res Image Gene #11: 'amp_xp11.4' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xp11.4' versus 'RPPA_CHIERARCHICAL'

P value = 0.00339 (Fisher's exact test), Q value = 0.0046

Table S101. Gene #11: 'amp_xp11.4' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
AMP PEAK 11(XP11.4) MUTATED	34	9	19	12	6	17	5
AMP PEAK 11(XP11.4) WILD-TYPE	163	55	97	135	53	54	88

Figure S101. Get High-res Image Gene #11: 'amp_xp11.4' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_xp11.4' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S102. Gene #11: 'amp_xp11.4' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
AMP PEAK 11(XP11.4) MUTATED	11	21	8	94
AMP PEAK 11(XP11.4) WILD-TYPE	108	174	289	174

Figure S102. Get High-res Image Gene #11: 'amp_xp11.4' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xp11.4' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S103. Gene #11: 'amp_xp11.4' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
AMP PEAK 11(XP11.4) MUTATED	8	16	4	18	4	84
AMP PEAK 11(XP11.4) WILD-TYPE	80	129	203	141	107	85

Figure S103. Get High-res Image Gene #11: 'amp_xp11.4' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.4' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S104. Gene #11: 'amp_xp11.4' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
AMP PEAK 11(XP11.4) MUTATED	100	10	23
AMP PEAK 11(XP11.4) WILD-TYPE	227	183	321

Figure S104. Get High-res Image Gene #11: 'amp_xp11.4' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_xp11.4' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S105. Gene #11: 'amp_xp11.4' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
AMP PEAK 11(XP11.4) MUTATED	7	99	27
AMP PEAK 11(XP11.4) WILD-TYPE	70	206	455

Figure S105. Get High-res Image Gene #11: 'amp_xp11.4' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_xp11.4' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S106. Gene #11: 'amp_xp11.4' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
AMP PEAK 11(XP11.4) MUTATED	57	8	4	6
AMP PEAK 11(XP11.4) WILD-TYPE	96	63	59	119

Figure S106. Get High-res Image Gene #11: 'amp_xp11.4' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_xp11.4' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S107. Gene #11: 'amp_xp11.4' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
AMP PEAK 11(XP11.4) MUTATED	17	39	8	5	6
AMP PEAK 11(XP11.4) WILD-TYPE	30	59	89	119	40

Figure S107. Get High-res Image Gene #11: 'amp_xp11.4' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xq11.2' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.4e-05

Table S108. Gene #12: 'amp_xq11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
AMP PEAK 12(XQ11.2) MUTATED	2	0	1	9
AMP PEAK 12(XQ11.2) WILD-TYPE	31	24	11	8

Figure S108. Get High-res Image Gene #12: 'amp_xq11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_xq11.2' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 5.1e-05

Table S109. Gene #12: 'amp_xq11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
AMP PEAK 12(XQ11.2) MUTATED	0	0	9	2	1
AMP PEAK 12(XQ11.2) WILD-TYPE	20	24	9	11	10

Figure S109. Get High-res Image Gene #12: 'amp_xq11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_xq11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S110. Gene #12: 'amp_xq11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
AMP PEAK 12(XQ11.2) MUTATED	103	5	27
AMP PEAK 12(XQ11.2) WILD-TYPE	179	305	263

Figure S110. Get High-res Image Gene #12: 'amp_xq11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xq11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S111. Gene #12: 'amp_xq11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
AMP PEAK 12(XQ11.2) MUTATED	13	8	88
AMP PEAK 12(XQ11.2) WILD-TYPE	115	295	133

Figure S111. Get High-res Image Gene #12: 'amp_xq11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xq11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00295 (Fisher's exact test), Q value = 0.004

Table S112. Gene #12: 'amp_xq11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
AMP PEAK 12(XQ11.2) MUTATED	35	9	19	14	3	17	6
AMP PEAK 12(XQ11.2) WILD-TYPE	162	55	97	133	56	54	87

Figure S112. Get High-res Image Gene #12: 'amp_xq11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_xq11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S113. Gene #12: 'amp_xq11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
AMP PEAK 12(XQ11.2) MUTATED	11	15	11	98
AMP PEAK 12(XQ11.2) WILD-TYPE	108	180	286	170

Figure S113. Get High-res Image Gene #12: 'amp_xq11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xq11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S114. Gene #12: 'amp_xq11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
AMP PEAK 12(XQ11.2) MUTATED	8	16	5	12	6	88
AMP PEAK 12(XQ11.2) WILD-TYPE	80	129	202	147	105	81

Figure S114. Get High-res Image Gene #12: 'amp_xq11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xq11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S115. Gene #12: 'amp_xq11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
AMP PEAK 12(XQ11.2) MUTATED	105	12	17
AMP PEAK 12(XQ11.2) WILD-TYPE	222	181	327

Figure S115. Get High-res Image Gene #12: 'amp_xq11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_xq11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S116. Gene #12: 'amp_xq11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
AMP PEAK 12(XQ11.2) MUTATED	7	103	24
AMP PEAK 12(XQ11.2) WILD-TYPE	70	202	458

Figure S116. Get High-res Image Gene #12: 'amp_xq11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_xq11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S117. Gene #12: 'amp_xq11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
AMP PEAK 12(XQ11.2) MUTATED	60	9	3	5
AMP PEAK 12(XQ11.2) WILD-TYPE	93	62	60	120

Figure S117. Get High-res Image Gene #12: 'amp_xq11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_xq11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S118. Gene #12: 'amp_xq11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
AMP PEAK 12(XQ11.2) MUTATED	17	40	9	5	6
AMP PEAK 12(XQ11.2) WILD-TYPE	30	58	88	119	40

Figure S118. Get High-res Image Gene #12: 'amp_xq11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xq28' versus 'MRNA_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00018

Table S119. Gene #13: 'amp_xq28' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
AMP PEAK 13(XQ28) MUTATED	2	0	2	8
AMP PEAK 13(XQ28) WILD-TYPE	31	24	10	9

Figure S119. Get High-res Image Gene #13: 'amp_xq28' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_xq28' versus 'MRNA_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.00086

Table S120. Gene #13: 'amp_xq28' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
AMP PEAK 13(XQ28) MUTATED	1	0	8	1	2
AMP PEAK 13(XQ28) WILD-TYPE	19	24	10	12	9

Figure S120. Get High-res Image Gene #13: 'amp_xq28' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_xq28' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S121. Gene #13: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
AMP PEAK 13(XQ28) MUTATED	95	13	29
AMP PEAK 13(XQ28) WILD-TYPE	187	297	261

Figure S121. Get High-res Image Gene #13: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xq28' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S122. Gene #13: 'amp_xq28' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
AMP PEAK 13(XQ28) MUTATED	16	22	77
AMP PEAK 13(XQ28) WILD-TYPE	112	281	144

Figure S122. Get High-res Image Gene #13: 'amp_xq28' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xq28' versus 'RPPA_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.00058

Table S123. Gene #13: 'amp_xq28' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
AMP PEAK 13(XQ28) MUTATED	36	9	25	14	3	17	6
AMP PEAK 13(XQ28) WILD-TYPE	161	55	91	133	56	54	87

Figure S123. Get High-res Image Gene #13: 'amp_xq28' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_xq28' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S124. Gene #13: 'amp_xq28' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
AMP PEAK 13(XQ28) MUTATED	13	21	14	88
AMP PEAK 13(XQ28) WILD-TYPE	106	174	283	180

Figure S124. Get High-res Image Gene #13: 'amp_xq28' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xq28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S125. Gene #13: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
AMP PEAK 13(XQ28) MUTATED	9	19	7	19	6	76
AMP PEAK 13(XQ28) WILD-TYPE	79	126	200	140	105	93

Figure S125. Get High-res Image Gene #13: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S126. Gene #13: 'amp_xq28' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
AMP PEAK 13(XQ28) MUTATED	96	18	22
AMP PEAK 13(XQ28) WILD-TYPE	231	175	322

Figure S126. Get High-res Image Gene #13: 'amp_xq28' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_xq28' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S127. Gene #13: 'amp_xq28' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
AMP PEAK 13(XQ28) MUTATED	8	94	34
AMP PEAK 13(XQ28) WILD-TYPE	69	211	448

Figure S127. Get High-res Image Gene #13: 'amp_xq28' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S128. Gene #13: 'amp_xq28' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
AMP PEAK 13(XQ28) MUTATED	53	10	5	10
AMP PEAK 13(XQ28) WILD-TYPE	100	61	58	115

Figure S128. Get High-res Image Gene #13: 'amp_xq28' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_xq28' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S129. Gene #13: 'amp_xq28' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
AMP PEAK 13(XQ28) MUTATED	18	34	11	9	6
AMP PEAK 13(XQ28) WILD-TYPE	29	64	86	115	40

Figure S129. Get High-res Image Gene #13: 'amp_xq28' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.31' versus 'MRNA_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.00065

Table S130. Gene #14: 'del_1p36.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
DEL PEAK 1(1P36.31) MUTATED	2	7	8	4
DEL PEAK 1(1P36.31) WILD-TYPE	31	17	4	13

Figure S130. Get High-res Image Gene #14: 'del_1p36.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.31' versus 'MRNA_CHIERARCHICAL'

P value = 0.00368 (Fisher's exact test), Q value = 0.0049

Table S131. Gene #14: 'del_1p36.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
DEL PEAK 1(1P36.31) MUTATED	1	7	5	1	7
DEL PEAK 1(1P36.31) WILD-TYPE	19	17	13	12	4

Figure S131. Get High-res Image Gene #14: 'del_1p36.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p36.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S132. Gene #14: 'del_1p36.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
DEL PEAK 1(1P36.31) MUTATED	86	24	99
DEL PEAK 1(1P36.31) WILD-TYPE	196	286	191

Figure S132. Get High-res Image Gene #14: 'del_1p36.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S133. Gene #14: 'del_1p36.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
DEL PEAK 1(1P36.31) MUTATED	73	58	32
DEL PEAK 1(1P36.31) WILD-TYPE	55	245	189

Figure S133. Get High-res Image Gene #14: 'del_1p36.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.31' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S134. Gene #14: 'del_1p36.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 1(1P36.31) MUTATED	41	21	46	18	25	11	22
DEL PEAK 1(1P36.31) WILD-TYPE	156	43	70	129	34	60	71

Figure S134. Get High-res Image Gene #14: 'del_1p36.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_1p36.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S135. Gene #14: 'del_1p36.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
DEL PEAK 1(1P36.31) MUTATED	73	54	34	48
DEL PEAK 1(1P36.31) WILD-TYPE	46	141	263	220

Figure S135. Get High-res Image Gene #14: 'del_1p36.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S136. Gene #14: 'del_1p36.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
DEL PEAK 1(1P36.31) MUTATED	70	49	28	44	9	9
DEL PEAK 1(1P36.31) WILD-TYPE	18	96	179	115	102	160

Figure S136. Get High-res Image Gene #14: 'del_1p36.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.31' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.4e-05

Table S137. Gene #14: 'del_1p36.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
DEL PEAK 1(1P36.31) MUTATED	106	47	56
DEL PEAK 1(1P36.31) WILD-TYPE	221	146	288

Figure S137. Get High-res Image Gene #14: 'del_1p36.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S138. Gene #14: 'del_1p36.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
DEL PEAK 1(1P36.31) MUTATED	68	60	81
DEL PEAK 1(1P36.31) WILD-TYPE	9	245	401

Figure S138. Get High-res Image Gene #14: 'del_1p36.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S139. Gene #14: 'del_1p36.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
DEL PEAK 1(1P36.31) MUTATED	19	43	17	20
DEL PEAK 1(1P36.31) WILD-TYPE	134	28	46	105

Figure S139. Get High-res Image Gene #14: 'del_1p36.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S140. Gene #14: 'del_1p36.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
DEL PEAK 1(1P36.31) MUTATED	2	14	28	16	39
DEL PEAK 1(1P36.31) WILD-TYPE	45	84	69	108	7

Figure S140. Get High-res Image Gene #14: 'del_1p36.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p31.1' versus 'MRNA_CNMF'

P value = 0.00161 (Fisher's exact test), Q value = 0.0023

Table S141. Gene #15: 'del_1p31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
DEL PEAK 2(1P31.1) MUTATED	2	4	7	2
DEL PEAK 2(1P31.1) WILD-TYPE	31	20	5	15

Figure S141. Get High-res Image Gene #15: 'del_1p31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p31.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0181 (Fisher's exact test), Q value = 0.022

Table S142. Gene #15: 'del_1p31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
DEL PEAK 2(1P31.1) MUTATED	1	4	3	1	6
DEL PEAK 2(1P31.1) WILD-TYPE	19	20	15	12	5

Figure S142. Get High-res Image Gene #15: 'del_1p31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S143. Gene #15: 'del_1p31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
DEL PEAK 2(1P31.1) MUTATED	79	12	75
DEL PEAK 2(1P31.1) WILD-TYPE	203	298	215

Figure S143. Get High-res Image Gene #15: 'del_1p31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p31.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S144. Gene #15: 'del_1p31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
DEL PEAK 2(1P31.1) MUTATED	69	41	21
DEL PEAK 2(1P31.1) WILD-TYPE	59	262	200

Figure S144. Get High-res Image Gene #15: 'del_1p31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p31.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S145. Gene #15: 'del_1p31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 2(1P31.1) MUTATED	37	19	42	16	15	6	13
DEL PEAK 2(1P31.1) WILD-TYPE	160	45	74	131	44	65	80

Figure S145. Get High-res Image Gene #15: 'del_1p31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_1p31.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S146. Gene #15: 'del_1p31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
DEL PEAK 2(1P31.1) MUTATED	73	34	28	31
DEL PEAK 2(1P31.1) WILD-TYPE	46	161	269	237

Figure S146. Get High-res Image Gene #15: 'del_1p31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S147. Gene #15: 'del_1p31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
DEL PEAK 2(1P31.1) MUTATED	69	35	22	25	7	8
DEL PEAK 2(1P31.1) WILD-TYPE	19	110	185	134	104	161

Figure S147. Get High-res Image Gene #15: 'del_1p31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p31.1' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 5.1e-05

Table S148. Gene #15: 'del_1p31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
DEL PEAK 2(1P31.1) MUTATED	91	29	46
DEL PEAK 2(1P31.1) WILD-TYPE	236	164	298

Figure S148. Get High-res Image Gene #15: 'del_1p31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S149. Gene #15: 'del_1p31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
DEL PEAK 2(1P31.1) MUTATED	68	44	54
DEL PEAK 2(1P31.1) WILD-TYPE	9	261	428

Figure S149. Get High-res Image Gene #15: 'del_1p31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p31.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S150. Gene #15: 'del_1p31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
DEL PEAK 2(1P31.1) MUTATED	13	41	12	13
DEL PEAK 2(1P31.1) WILD-TYPE	140	30	51	112

Figure S150. Get High-res Image Gene #15: 'del_1p31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S151. Gene #15: 'del_1p31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
DEL PEAK 2(1P31.1) MUTATED	1	11	19	9	39
DEL PEAK 2(1P31.1) WILD-TYPE	46	87	78	115	7

Figure S151. Get High-res Image Gene #15: 'del_1p31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1q43' versus 'MRNA_CNMF'

P value = 0.0086 (Fisher's exact test), Q value = 0.011

Table S152. Gene #16: 'del_1q43' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
DEL PEAK 3(1Q43) MUTATED	2	1	5	1
DEL PEAK 3(1Q43) WILD-TYPE	31	23	7	16

Figure S152. Get High-res Image Gene #16: 'del_1q43' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1q43' versus 'MRNA_CHIERARCHICAL'

P value = 0.00749 (Fisher's exact test), Q value = 0.0097

Table S153. Gene #16: 'del_1q43' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
DEL PEAK 3(1Q43) MUTATED	1	1	1	1	5
DEL PEAK 3(1Q43) WILD-TYPE	19	23	17	12	6

Figure S153. Get High-res Image Gene #16: 'del_1q43' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1q43' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S154. Gene #16: 'del_1q43' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
DEL PEAK 3(1Q43) MUTATED	75	4	35
DEL PEAK 3(1Q43) WILD-TYPE	207	306	255

Figure S154. Get High-res Image Gene #16: 'del_1q43' versus Molecular Subtype #3: 'CN_CNMF'

'del_1q43' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S155. Gene #16: 'del_1q43' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
DEL PEAK 3(1Q43) MUTATED	61	19	15
DEL PEAK 3(1Q43) WILD-TYPE	67	284	206

Figure S155. Get High-res Image Gene #16: 'del_1q43' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1q43' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S156. Gene #16: 'del_1q43' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 3(1Q43) MUTATED	30	13	34	10	6	3	5
DEL PEAK 3(1Q43) WILD-TYPE	167	51	82	137	53	68	88

Figure S156. Get High-res Image Gene #16: 'del_1q43' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_1q43' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S157. Gene #16: 'del_1q43' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
DEL PEAK 3(1Q43) MUTATED	64	13	19	18
DEL PEAK 3(1Q43) WILD-TYPE	55	182	278	250

Figure S157. Get High-res Image Gene #16: 'del_1q43' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1q43' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S158. Gene #16: 'del_1q43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
DEL PEAK 3(1Q43) MUTATED	64	15	12	8	7	8
DEL PEAK 3(1Q43) WILD-TYPE	24	130	195	151	104	161

Figure S158. Get High-res Image Gene #16: 'del_1q43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1q43' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S159. Gene #16: 'del_1q43' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
DEL PEAK 3(1Q43) MUTATED	74	16	24
DEL PEAK 3(1Q43) WILD-TYPE	253	177	320

Figure S159. Get High-res Image Gene #16: 'del_1q43' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1q43' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S160. Gene #16: 'del_1q43' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
DEL PEAK 3(1Q43) MUTATED	64	23	27
DEL PEAK 3(1Q43) WILD-TYPE	13	282	455

Figure S160. Get High-res Image Gene #16: 'del_1q43' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1q43' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S161. Gene #16: 'del_1q43' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
DEL PEAK 3(1Q43) MUTATED	9	38	7	9
DEL PEAK 3(1Q43) WILD-TYPE	144	33	56	116

Figure S161. Get High-res Image Gene #16: 'del_1q43' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1q43' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S162. Gene #16: 'del_1q43' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
DEL PEAK 3(1Q43) MUTATED	2	7	8	8	38
DEL PEAK 3(1Q43) WILD-TYPE	45	91	89	116	8

Figure S162. Get High-res Image Gene #16: 'del_1q43' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q37.3' versus 'MRNA_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00027

Table S163. Gene #17: 'del_2q37.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
DEL PEAK 4(2Q37.3) MUTATED	1	4	7	1
DEL PEAK 4(2Q37.3) WILD-TYPE	32	20	5	16

Figure S163. Get High-res Image Gene #17: 'del_2q37.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_2q37.3' versus 'MRNA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00014

Table S164. Gene #17: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
DEL PEAK 4(2Q37.3) MUTATED	0	4	1	1	7
DEL PEAK 4(2Q37.3) WILD-TYPE	20	20	17	12	4

Figure S164. Get High-res Image Gene #17: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 5.1e-05

Table S165. Gene #17: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
DEL PEAK 4(2Q37.3) MUTATED	54	20	37
DEL PEAK 4(2Q37.3) WILD-TYPE	228	290	253

Figure S165. Get High-res Image Gene #17: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S166. Gene #17: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
DEL PEAK 4(2Q37.3) MUTATED	56	26	6
DEL PEAK 4(2Q37.3) WILD-TYPE	72	277	215

Figure S166. Get High-res Image Gene #17: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q37.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00021

Table S167. Gene #17: 'del_2q37.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 4(2Q37.3) MUTATED	23	15	27	10	10	5	7
DEL PEAK 4(2Q37.3) WILD-TYPE	174	49	89	137	49	66	86

Figure S167. Get High-res Image Gene #17: 'del_2q37.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S168. Gene #17: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
DEL PEAK 4(2Q37.3) MUTATED	62	23	17	8
DEL PEAK 4(2Q37.3) WILD-TYPE	57	172	280	260

Figure S168. Get High-res Image Gene #17: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S169. Gene #17: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
DEL PEAK 4(2Q37.3) MUTATED	59	13	15	18	4	1
DEL PEAK 4(2Q37.3) WILD-TYPE	29	132	192	141	107	168

Figure S169. Get High-res Image Gene #17: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S170. Gene #17: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
DEL PEAK 4(2Q37.3) MUTATED	66	17	26
DEL PEAK 4(2Q37.3) WILD-TYPE	261	176	318

Figure S170. Get High-res Image Gene #17: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S171. Gene #17: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
DEL PEAK 4(2Q37.3) MUTATED	59	12	38
DEL PEAK 4(2Q37.3) WILD-TYPE	18	293	444

Figure S171. Get High-res Image Gene #17: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S172. Gene #17: 'del_2q37.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
DEL PEAK 4(2Q37.3) MUTATED	6	37	6	8
DEL PEAK 4(2Q37.3) WILD-TYPE	147	34	57	117

Figure S172. Get High-res Image Gene #17: 'del_2q37.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_2q37.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S173. Gene #17: 'del_2q37.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
DEL PEAK 4(2Q37.3) MUTATED	0	6	8	7	36
DEL PEAK 4(2Q37.3) WILD-TYPE	47	92	89	117	10

Figure S173. Get High-res Image Gene #17: 'del_2q37.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p26.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S174. Gene #18: 'del_3p26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
DEL PEAK 5(3P26.3) MUTATED	32	23	3	0
DEL PEAK 5(3P26.3) WILD-TYPE	1	1	9	17

Figure S174. Get High-res Image Gene #18: 'del_3p26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p26.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S175. Gene #18: 'del_3p26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
DEL PEAK 5(3P26.3) MUTATED	20	23	1	12	2
DEL PEAK 5(3P26.3) WILD-TYPE	0	1	17	1	9

Figure S175. Get High-res Image Gene #18: 'del_3p26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S176. Gene #18: 'del_3p26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
DEL PEAK 5(3P26.3) MUTATED	3	216	270
DEL PEAK 5(3P26.3) WILD-TYPE	279	94	20

Figure S176. Get High-res Image Gene #18: 'del_3p26.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p26.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S177. Gene #18: 'del_3p26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
DEL PEAK 5(3P26.3) MUTATED	17	273	14
DEL PEAK 5(3P26.3) WILD-TYPE	111	30	207

Figure S177. Get High-res Image Gene #18: 'del_3p26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p26.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S178. Gene #18: 'del_3p26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
DEL PEAK 5(3P26.3) MUTATED	107	105	84	142
DEL PEAK 5(3P26.3) WILD-TYPE	75	76	103	55

Figure S178. Get High-res Image Gene #18: 'del_3p26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p26.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S179. Gene #18: 'del_3p26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 5(3P26.3) MUTATED	120	1	59	108	46	43	61
DEL PEAK 5(3P26.3) WILD-TYPE	77	63	57	39	13	28	32

Figure S179. Get High-res Image Gene #18: 'del_3p26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p26.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S180. Gene #18: 'del_3p26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
DEL PEAK 5(3P26.3) MUTATED	20	158	285	23
DEL PEAK 5(3P26.3) WILD-TYPE	99	37	12	245

Figure S180. Get High-res Image Gene #18: 'del_3p26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S181. Gene #18: 'del_3p26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
DEL PEAK 5(3P26.3) MUTATED	11	28	196	144	104	3
DEL PEAK 5(3P26.3) WILD-TYPE	77	117	11	15	7	166

Figure S181. Get High-res Image Gene #18: 'del_3p26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S182. Gene #18: 'del_3p26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
DEL PEAK 5(3P26.3) MUTATED	31	121	320
DEL PEAK 5(3P26.3) WILD-TYPE	296	72	24

Figure S182. Get High-res Image Gene #18: 'del_3p26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S183. Gene #18: 'del_3p26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
DEL PEAK 5(3P26.3) MUTATED	10	30	432
DEL PEAK 5(3P26.3) WILD-TYPE	67	275	50

Figure S183. Get High-res Image Gene #18: 'del_3p26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S184. Gene #18: 'del_3p26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
DEL PEAK 5(3P26.3) MUTATED	8	8	17	113
DEL PEAK 5(3P26.3) WILD-TYPE	145	63	46	12

Figure S184. Get High-res Image Gene #18: 'del_3p26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S185. Gene #18: 'del_3p26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
DEL PEAK 5(3P26.3) MUTATED	1	5	25	109	6
DEL PEAK 5(3P26.3) WILD-TYPE	46	93	72	15	40

Figure S185. Get High-res Image Gene #18: 'del_3p26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p21.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S186. Gene #19: 'del_3p21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
DEL PEAK 6(3P21.2) MUTATED	31	23	3	1
DEL PEAK 6(3P21.2) WILD-TYPE	2	1	9	16

Figure S186. Get High-res Image Gene #19: 'del_3p21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p21.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S187. Gene #19: 'del_3p21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
DEL PEAK 6(3P21.2) MUTATED	20	23	2	11	2
DEL PEAK 6(3P21.2) WILD-TYPE	0	1	16	2	9

Figure S187. Get High-res Image Gene #19: 'del_3p21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S188. Gene #19: 'del_3p21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
DEL PEAK 6(3P21.2) MUTATED	5	220	278
DEL PEAK 6(3P21.2) WILD-TYPE	277	90	12

Figure S188. Get High-res Image Gene #19: 'del_3p21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S189. Gene #19: 'del_3p21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
DEL PEAK 6(3P21.2) MUTATED	19	281	15
DEL PEAK 6(3P21.2) WILD-TYPE	109	22	206

Figure S189. Get High-res Image Gene #19: 'del_3p21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p21.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S190. Gene #19: 'del_3p21.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
DEL PEAK 6(3P21.2) MUTATED	111	109	85	146
DEL PEAK 6(3P21.2) WILD-TYPE	71	72	102	51

Figure S190. Get High-res Image Gene #19: 'del_3p21.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p21.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S191. Gene #19: 'del_3p21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 6(3P21.2) MUTATED	122	3	60	110	48	44	64
DEL PEAK 6(3P21.2) WILD-TYPE	75	61	56	37	11	27	29

Figure S191. Get High-res Image Gene #19: 'del_3p21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S192. Gene #19: 'del_3p21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
DEL PEAK 6(3P21.2) MUTATED	22	163	289	26
DEL PEAK 6(3P21.2) WILD-TYPE	97	32	8	242

Figure S192. Get High-res Image Gene #19: 'del_3p21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S193. Gene #19: 'del_3p21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
DEL PEAK 6(3P21.2) MUTATED	13	33	197	149	106	2
DEL PEAK 6(3P21.2) WILD-TYPE	75	112	10	10	5	167

Figure S193. Get High-res Image Gene #19: 'del_3p21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S194. Gene #19: 'del_3p21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
DEL PEAK 6(3P21.2) MUTATED	35	122	329
DEL PEAK 6(3P21.2) WILD-TYPE	292	71	15

Figure S194. Get High-res Image Gene #19: 'del_3p21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S195. Gene #19: 'del_3p21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
DEL PEAK 6(3P21.2) MUTATED	12	34	440
DEL PEAK 6(3P21.2) WILD-TYPE	65	271	42

Figure S195. Get High-res Image Gene #19: 'del_3p21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S196. Gene #19: 'del_3p21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
DEL PEAK 6(3P21.2) MUTATED	9	9	18	115
DEL PEAK 6(3P21.2) WILD-TYPE	144	62	45	10

Figure S196. Get High-res Image Gene #19: 'del_3p21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S197. Gene #19: 'del_3p21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
DEL PEAK 6(3P21.2) MUTATED	0	6	28	110	7
DEL PEAK 6(3P21.2) WILD-TYPE	47	92	69	14	39

Figure S197. Get High-res Image Gene #19: 'del_3p21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p14.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S198. Gene #20: 'del_3p14.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
DEL PEAK 7(3P14.1) MUTATED	22	20	3	0
DEL PEAK 7(3P14.1) WILD-TYPE	11	4	9	17

Figure S198. Get High-res Image Gene #20: 'del_3p14.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p14.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S199. Gene #20: 'del_3p14.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
DEL PEAK 7(3P14.1) MUTATED	15	20	1	7	2
DEL PEAK 7(3P14.1) WILD-TYPE	5	4	17	6	9

Figure S199. Get High-res Image Gene #20: 'del_3p14.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S200. Gene #20: 'del_3p14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
DEL PEAK 7(3P14.1) MUTATED	2	153	253
DEL PEAK 7(3P14.1) WILD-TYPE	280	157	37

Figure S200. Get High-res Image Gene #20: 'del_3p14.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p14.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S201. Gene #20: 'del_3p14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
DEL PEAK 7(3P14.1) MUTATED	18	230	14
DEL PEAK 7(3P14.1) WILD-TYPE	110	73	207

Figure S201. Get High-res Image Gene #20: 'del_3p14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p14.1' versus 'RPPA_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.00068

Table S202. Gene #20: 'del_3p14.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
DEL PEAK 7(3P14.1) MUTATED	89	88	70	117
DEL PEAK 7(3P14.1) WILD-TYPE	93	93	117	80

Figure S202. Get High-res Image Gene #20: 'del_3p14.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p14.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S203. Gene #20: 'del_3p14.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 7(3P14.1) MUTATED	100	3	47	85	39	37	53
DEL PEAK 7(3P14.1) WILD-TYPE	97	61	69	62	20	34	40

Figure S203. Get High-res Image Gene #20: 'del_3p14.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S204. Gene #20: 'del_3p14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
DEL PEAK 7(3P14.1) MUTATED	20	139	226	21
DEL PEAK 7(3P14.1) WILD-TYPE	99	56	71	247

Figure S204. Get High-res Image Gene #20: 'del_3p14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S205. Gene #20: 'del_3p14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
DEL PEAK 7(3P14.1) MUTATED	12	28	164	124	76	2
DEL PEAK 7(3P14.1) WILD-TYPE	76	117	43	35	35	167

Figure S205. Get High-res Image Gene #20: 'del_3p14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S206. Gene #20: 'del_3p14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
DEL PEAK 7(3P14.1) MUTATED	30	99	266
DEL PEAK 7(3P14.1) WILD-TYPE	297	94	78

Figure S206. Get High-res Image Gene #20: 'del_3p14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S207. Gene #20: 'del_3p14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
DEL PEAK 7(3P14.1) MUTATED	11	29	355
DEL PEAK 7(3P14.1) WILD-TYPE	66	276	127

Figure S207. Get High-res Image Gene #20: 'del_3p14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S208. Gene #20: 'del_3p14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
DEL PEAK 7(3P14.1) MUTATED	9	8	16	89
DEL PEAK 7(3P14.1) WILD-TYPE	144	63	47	36

Figure S208. Get High-res Image Gene #20: 'del_3p14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S209. Gene #20: 'del_3p14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
DEL PEAK 7(3P14.1) MUTATED	0	6	24	85	7
DEL PEAK 7(3P14.1) WILD-TYPE	47	92	73	39	39

Figure S209. Get High-res Image Gene #20: 'del_3p14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p12.2' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.4e-05

Table S210. Gene #21: 'del_3p12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
DEL PEAK 8(3P12.2) MUTATED	18	14	2	0
DEL PEAK 8(3P12.2) WILD-TYPE	15	10	10	17

Figure S210. Get High-res Image Gene #21: 'del_3p12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p12.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00028

Table S211. Gene #21: 'del_3p12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
DEL PEAK 8(3P12.2) MUTATED	12	14	1	6	1
DEL PEAK 8(3P12.2) WILD-TYPE	8	10	17	7	10

Figure S211. Get High-res Image Gene #21: 'del_3p12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S212. Gene #21: 'del_3p12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
DEL PEAK 8(3P12.2) MUTATED	2	106	228
DEL PEAK 8(3P12.2) WILD-TYPE	280	204	62

Figure S212. Get High-res Image Gene #21: 'del_3p12.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p12.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S213. Gene #21: 'del_3p12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
DEL PEAK 8(3P12.2) MUTATED	17	188	13
DEL PEAK 8(3P12.2) WILD-TYPE	111	115	208

Figure S213. Get High-res Image Gene #21: 'del_3p12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p12.2' versus 'RPPA_CNMF'

P value = 0.0494 (Fisher's exact test), Q value = 0.058

Table S214. Gene #21: 'del_3p12.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
DEL PEAK 8(3P12.2) MUTATED	73	74	62	93
DEL PEAK 8(3P12.2) WILD-TYPE	109	107	125	104

Figure S214. Get High-res Image Gene #21: 'del_3p12.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p12.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S215. Gene #21: 'del_3p12.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 8(3P12.2) MUTATED	79	2	43	64	37	32	45
DEL PEAK 8(3P12.2) WILD-TYPE	118	62	73	83	22	39	48

Figure S215. Get High-res Image Gene #21: 'del_3p12.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p12.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S216. Gene #21: 'del_3p12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
DEL PEAK 8(3P12.2) MUTATED	18	119	180	18
DEL PEAK 8(3P12.2) WILD-TYPE	101	76	117	250

Figure S216. Get High-res Image Gene #21: 'del_3p12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S217. Gene #21: 'del_3p12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
DEL PEAK 8(3P12.2) MUTATED	12	24	132	104	61	2
DEL PEAK 8(3P12.2) WILD-TYPE	76	121	75	55	50	167

Figure S217. Get High-res Image Gene #21: 'del_3p12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p12.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S218. Gene #21: 'del_3p12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
DEL PEAK 8(3P12.2) MUTATED	27	78	220
DEL PEAK 8(3P12.2) WILD-TYPE	300	115	124

Figure S218. Get High-res Image Gene #21: 'del_3p12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S219. Gene #21: 'del_3p12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
DEL PEAK 8(3P12.2) MUTATED	11	24	290
DEL PEAK 8(3P12.2) WILD-TYPE	66	281	192

Figure S219. Get High-res Image Gene #21: 'del_3p12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p12.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S220. Gene #21: 'del_3p12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
DEL PEAK 8(3P12.2) MUTATED	8	7	12	78
DEL PEAK 8(3P12.2) WILD-TYPE	145	64	51	47

Figure S220. Get High-res Image Gene #21: 'del_3p12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S221. Gene #21: 'del_3p12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
DEL PEAK 8(3P12.2) MUTATED	0	6	20	72	7
DEL PEAK 8(3P12.2) WILD-TYPE	47	92	77	52	39

Figure S221. Get High-res Image Gene #21: 'del_3p12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S222. Gene #22: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
DEL PEAK 9(4Q34.3) MUTATED	23	11	79
DEL PEAK 9(4Q34.3) WILD-TYPE	259	299	211

Figure S222. Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.001

Table S223. Gene #22: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
DEL PEAK 9(4Q34.3) MUTATED	17	54	15
DEL PEAK 9(4Q34.3) WILD-TYPE	111	249	206

Figure S223. Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q34.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 7e-04

Table S224. Gene #22: 'del_4q34.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 9(4Q34.3) MUTATED	24	4	27	11	14	6	16
DEL PEAK 9(4Q34.3) WILD-TYPE	173	60	89	136	45	65	77

Figure S224. Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S225. Gene #22: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
DEL PEAK 9(4Q34.3) MUTATED	8	48	33	24
DEL PEAK 9(4Q34.3) WILD-TYPE	111	147	264	244

Figure S225. Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S226. Gene #22: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
DEL PEAK 9(4Q34.3) MUTATED	2	36	25	37	11	2
DEL PEAK 9(4Q34.3) WILD-TYPE	86	109	182	122	100	167

Figure S226. Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CNMF'

P value = 0.00213 (Fisher's exact test), Q value = 0.0029

Table S227. Gene #22: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
DEL PEAK 9(4Q34.3) MUTATED	29	38	45
DEL PEAK 9(4Q34.3) WILD-TYPE	298	155	299

Figure S227. Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00451 (Fisher's exact test), Q value = 0.006

Table S228. Gene #22: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
DEL PEAK 9(4Q34.3) MUTATED	2	38	72
DEL PEAK 9(4Q34.3) WILD-TYPE	75	267	410

Figure S228. Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00022

Table S229. Gene #22: 'del_4q34.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
DEL PEAK 9(4Q34.3) MUTATED	10	5	18	18
DEL PEAK 9(4Q34.3) WILD-TYPE	143	66	45	107

Figure S229. Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S230. Gene #22: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
DEL PEAK 9(4Q34.3) MUTATED	0	7	26	16	2
DEL PEAK 9(4Q34.3) WILD-TYPE	47	91	71	108	44

Figure S230. Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5p15.33' versus 'CN_CNMF'

P value = 0.0033 (Fisher's exact test), Q value = 0.0045

Table S231. Gene #23: 'del_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
DEL PEAK 10(5P15.33) MUTATED	19	6	6
DEL PEAK 10(5P15.33) WILD-TYPE	263	304	284

Figure S231. Get High-res Image Gene #23: 'del_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_5p15.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S232. Gene #23: 'del_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
DEL PEAK 10(5P15.33) MUTATED	16	4	9
DEL PEAK 10(5P15.33) WILD-TYPE	112	299	212

Figure S232. Get High-res Image Gene #23: 'del_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5p15.33' versus 'RPPA_CNMF'

P value = 0.0352 (Fisher's exact test), Q value = 0.042

Table S233. Gene #23: 'del_5p15.33' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
DEL PEAK 10(5P15.33) MUTATED	12	8	2	6
DEL PEAK 10(5P15.33) WILD-TYPE	170	173	185	191

Figure S233. Get High-res Image Gene #23: 'del_5p15.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_5p15.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.0485 (Fisher's exact test), Q value = 0.057

Table S234. Gene #23: 'del_5p15.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 10(5P15.33) MUTATED	6	3	2	2	6	3	6
DEL PEAK 10(5P15.33) WILD-TYPE	191	61	114	145	53	68	87

Figure S234. Get High-res Image Gene #23: 'del_5p15.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_5p15.33' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 8.3e-05

Table S235. Gene #23: 'del_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
DEL PEAK 10(5P15.33) MUTATED	12	9	1	9
DEL PEAK 10(5P15.33) WILD-TYPE	107	186	296	259

Figure S235. Get High-res Image Gene #23: 'del_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S236. Gene #23: 'del_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
DEL PEAK 10(5P15.33) MUTATED	11	12	2	4	0	2
DEL PEAK 10(5P15.33) WILD-TYPE	77	133	205	155	111	167

Figure S236. Get High-res Image Gene #23: 'del_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5p15.33' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 6.7e-05

Table S237. Gene #23: 'del_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
DEL PEAK 10(5P15.33) MUTATED	21	8	2
DEL PEAK 10(5P15.33) WILD-TYPE	306	185	342

Figure S237. Get High-res Image Gene #23: 'del_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S238. Gene #23: 'del_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
DEL PEAK 10(5P15.33) MUTATED	11	13	7
DEL PEAK 10(5P15.33) WILD-TYPE	66	292	475

Figure S238. Get High-res Image Gene #23: 'del_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00088 (Fisher's exact test), Q value = 0.0013

Table S239. Gene #23: 'del_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
DEL PEAK 10(5P15.33) MUTATED	6	10	3	1
DEL PEAK 10(5P15.33) WILD-TYPE	147	61	60	124

Figure S239. Get High-res Image Gene #23: 'del_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 8.3e-05

Table S240. Gene #23: 'del_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
DEL PEAK 10(5P15.33) MUTATED	1	4	7	0	8
DEL PEAK 10(5P15.33) WILD-TYPE	46	94	90	124	38

Figure S240. Get High-res Image Gene #23: 'del_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q22.31' versus 'MRNA_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.00072

Table S241. Gene #24: 'del_6q22.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
DEL PEAK 11(6Q22.31) MUTATED	8	13	8	1
DEL PEAK 11(6Q22.31) WILD-TYPE	25	11	4	16

Figure S241. Get High-res Image Gene #24: 'del_6q22.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_6q22.31' versus 'MRNA_CHIERARCHICAL'

P value = 0.00627 (Fisher's exact test), Q value = 0.0082

Table S242. Gene #24: 'del_6q22.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
DEL PEAK 11(6Q22.31) MUTATED	5	13	2	3	7
DEL PEAK 11(6Q22.31) WILD-TYPE	15	11	16	10	4

Figure S242. Get High-res Image Gene #24: 'del_6q22.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_6q22.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S243. Gene #24: 'del_6q22.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
DEL PEAK 11(6Q22.31) MUTATED	66	3	158
DEL PEAK 11(6Q22.31) WILD-TYPE	216	307	132

Figure S243. Get High-res Image Gene #24: 'del_6q22.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q22.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S244. Gene #24: 'del_6q22.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
DEL PEAK 11(6Q22.31) MUTATED	66	74	18
DEL PEAK 11(6Q22.31) WILD-TYPE	62	229	203

Figure S244. Get High-res Image Gene #24: 'del_6q22.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q22.31' versus 'RPPA_CNMF'

P value = 0.00497 (Fisher's exact test), Q value = 0.0066

Table S245. Gene #24: 'del_6q22.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
DEL PEAK 11(6Q22.31) MUTATED	41	50	41	72
DEL PEAK 11(6Q22.31) WILD-TYPE	141	131	146	125

Figure S245. Get High-res Image Gene #24: 'del_6q22.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_6q22.31' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S246. Gene #24: 'del_6q22.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 11(6Q22.31) MUTATED	61	13	52	32	24	6	16
DEL PEAK 11(6Q22.31) WILD-TYPE	136	51	64	115	35	65	77

Figure S246. Get High-res Image Gene #24: 'del_6q22.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_6q22.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S247. Gene #24: 'del_6q22.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
DEL PEAK 11(6Q22.31) MUTATED	68	70	63	24
DEL PEAK 11(6Q22.31) WILD-TYPE	51	125	234	244

Figure S247. Get High-res Image Gene #24: 'del_6q22.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q22.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S248. Gene #24: 'del_6q22.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
DEL PEAK 11(6Q22.31) MUTATED	61	32	44	58	25	5
DEL PEAK 11(6Q22.31) WILD-TYPE	27	113	163	101	86	164

Figure S248. Get High-res Image Gene #24: 'del_6q22.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q22.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S249. Gene #24: 'del_6q22.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
DEL PEAK 11(6Q22.31) MUTATED	61	37	124
DEL PEAK 11(6Q22.31) WILD-TYPE	16	268	358

Figure S249. Get High-res Image Gene #24: 'del_6q22.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q22.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S250. Gene #24: 'del_6q22.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
DEL PEAK 11(6Q22.31) MUTATED	10	39	15	27
DEL PEAK 11(6Q22.31) WILD-TYPE	143	32	48	98

Figure S250. Get High-res Image Gene #24: 'del_6q22.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6q22.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S251. Gene #24: 'del_6q22.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
DEL PEAK 11(6Q22.31) MUTATED	2	7	20	25	37
DEL PEAK 11(6Q22.31) WILD-TYPE	45	91	77	99	9

Figure S251. Get High-res Image Gene #24: 'del_6q22.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q26' versus 'MRNA_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.00079

Table S252. Gene #25: 'del_6q26' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
DEL PEAK 12(6Q26) MUTATED	7	12	8	1
DEL PEAK 12(6Q26) WILD-TYPE	26	12	4	16

Figure S252. Get High-res Image Gene #25: 'del_6q26' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_6q26' versus 'MRNA_CHIERARCHICAL'

P value = 0.00761 (Fisher's exact test), Q value = 0.0098

Table S253. Gene #25: 'del_6q26' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
DEL PEAK 12(6Q26) MUTATED	4	12	2	3	7
DEL PEAK 12(6Q26) WILD-TYPE	16	12	16	10	4

Figure S253. Get High-res Image Gene #25: 'del_6q26' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S254. Gene #25: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
DEL PEAK 12(6Q26) MUTATED	65	3	165
DEL PEAK 12(6Q26) WILD-TYPE	217	307	125

Figure S254. Get High-res Image Gene #25: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S255. Gene #25: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
DEL PEAK 12(6Q26) MUTATED	64	76	21
DEL PEAK 12(6Q26) WILD-TYPE	64	227	200

Figure S255. Get High-res Image Gene #25: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q26' versus 'RPPA_CNMF'

P value = 0.00352 (Fisher's exact test), Q value = 0.0047

Table S256. Gene #25: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
DEL PEAK 12(6Q26) MUTATED	41	51	43	74
DEL PEAK 12(6Q26) WILD-TYPE	141	130	144	123

Figure S256. Get High-res Image Gene #25: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_6q26' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.4e-05

Table S257. Gene #25: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 12(6Q26) MUTATED	62	14	51	34	24	8	16
DEL PEAK 12(6Q26) WILD-TYPE	135	50	65	113	35	63	77

Figure S257. Get High-res Image Gene #25: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S258. Gene #25: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
DEL PEAK 12(6Q26) MUTATED	67	69	68	27
DEL PEAK 12(6Q26) WILD-TYPE	52	126	229	241

Figure S258. Get High-res Image Gene #25: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S259. Gene #25: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
DEL PEAK 12(6Q26) MUTATED	61	33	46	58	28	5
DEL PEAK 12(6Q26) WILD-TYPE	27	112	161	101	83	164

Figure S259. Get High-res Image Gene #25: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S260. Gene #25: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
DEL PEAK 12(6Q26) MUTATED	61	38	130
DEL PEAK 12(6Q26) WILD-TYPE	16	267	352

Figure S260. Get High-res Image Gene #25: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S261. Gene #25: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
DEL PEAK 12(6Q26) MUTATED	12	39	14	30
DEL PEAK 12(6Q26) WILD-TYPE	141	32	49	95

Figure S261. Get High-res Image Gene #25: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S262. Gene #25: 'del_6q26' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
DEL PEAK 12(6Q26) MUTATED	2	9	19	28	37
DEL PEAK 12(6Q26) WILD-TYPE	45	89	78	96	9

Figure S262. Get High-res Image Gene #25: 'del_6q26' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q26' versus 'MRNA_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.00073

Table S263. Gene #26: 'del_6q26' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
DEL PEAK 13(6Q26) MUTATED	7	12	8	1
DEL PEAK 13(6Q26) WILD-TYPE	26	12	4	16

Figure S263. Get High-res Image Gene #26: 'del_6q26' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_6q26' versus 'MRNA_CHIERARCHICAL'

P value = 0.00721 (Fisher's exact test), Q value = 0.0094

Table S264. Gene #26: 'del_6q26' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
DEL PEAK 13(6Q26) MUTATED	4	12	2	3	7
DEL PEAK 13(6Q26) WILD-TYPE	16	12	16	10	4

Figure S264. Get High-res Image Gene #26: 'del_6q26' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S265. Gene #26: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
DEL PEAK 13(6Q26) MUTATED	66	3	165
DEL PEAK 13(6Q26) WILD-TYPE	216	307	125

Figure S265. Get High-res Image Gene #26: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S266. Gene #26: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
DEL PEAK 13(6Q26) MUTATED	64	76	22
DEL PEAK 13(6Q26) WILD-TYPE	64	227	199

Figure S266. Get High-res Image Gene #26: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q26' versus 'RPPA_CNMF'

P value = 0.00334 (Fisher's exact test), Q value = 0.0045

Table S267. Gene #26: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
DEL PEAK 13(6Q26) MUTATED	41	51	43	74
DEL PEAK 13(6Q26) WILD-TYPE	141	130	144	123

Figure S267. Get High-res Image Gene #26: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_6q26' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S268. Gene #26: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 13(6Q26) MUTATED	61	14	51	34	25	8	16
DEL PEAK 13(6Q26) WILD-TYPE	136	50	65	113	34	63	77

Figure S268. Get High-res Image Gene #26: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S269. Gene #26: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
DEL PEAK 13(6Q26) MUTATED	67	70	67	28
DEL PEAK 13(6Q26) WILD-TYPE	52	125	230	240

Figure S269. Get High-res Image Gene #26: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S270. Gene #26: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
DEL PEAK 13(6Q26) MUTATED	61	33	46	58	28	6
DEL PEAK 13(6Q26) WILD-TYPE	27	112	161	101	83	163

Figure S270. Get High-res Image Gene #26: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S271. Gene #26: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
DEL PEAK 13(6Q26) MUTATED	61	39	130
DEL PEAK 13(6Q26) WILD-TYPE	16	266	352

Figure S271. Get High-res Image Gene #26: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S272. Gene #26: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
DEL PEAK 13(6Q26) MUTATED	12	39	14	30
DEL PEAK 13(6Q26) WILD-TYPE	141	32	49	95

Figure S272. Get High-res Image Gene #26: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S273. Gene #26: 'del_6q26' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
DEL PEAK 13(6Q26) MUTATED	2	9	19	28	37
DEL PEAK 13(6Q26) WILD-TYPE	45	89	78	96	9

Figure S273. Get High-res Image Gene #26: 'del_6q26' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S274. Gene #27: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
DEL PEAK 14(8P23.2) MUTATED	27	44	113
DEL PEAK 14(8P23.2) WILD-TYPE	255	266	177

Figure S274. Get High-res Image Gene #27: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S275. Gene #27: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
DEL PEAK 14(8P23.2) MUTATED	21	85	8
DEL PEAK 14(8P23.2) WILD-TYPE	107	218	213

Figure S275. Get High-res Image Gene #27: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0075 (Fisher's exact test), Q value = 0.0097

Table S276. Gene #27: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 14(8P23.2) MUTATED	37	8	29	27	21	11	28
DEL PEAK 14(8P23.2) WILD-TYPE	160	56	87	120	38	60	65

Figure S276. Get High-res Image Gene #27: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S277. Gene #27: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
DEL PEAK 14(8P23.2) MUTATED	21	73	75	14
DEL PEAK 14(8P23.2) WILD-TYPE	98	122	222	254

Figure S277. Get High-res Image Gene #27: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S278. Gene #27: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
DEL PEAK 14(8P23.2) MUTATED	17	16	59	62	25	4
DEL PEAK 14(8P23.2) WILD-TYPE	71	129	148	97	86	165

Figure S278. Get High-res Image Gene #27: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S279. Gene #27: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
DEL PEAK 14(8P23.2) MUTATED	31	53	97
DEL PEAK 14(8P23.2) WILD-TYPE	296	140	247

Figure S279. Get High-res Image Gene #27: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S280. Gene #27: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
DEL PEAK 14(8P23.2) MUTATED	16	22	143
DEL PEAK 14(8P23.2) WILD-TYPE	61	283	339

Figure S280. Get High-res Image Gene #27: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S281. Gene #27: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
DEL PEAK 14(8P23.2) MUTATED	6	10	8	36
DEL PEAK 14(8P23.2) WILD-TYPE	147	61	55	89

Figure S281. Get High-res Image Gene #27: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S282. Gene #27: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
DEL PEAK 14(8P23.2) MUTATED	1	5	11	36	7
DEL PEAK 14(8P23.2) WILD-TYPE	46	93	86	88	39

Figure S282. Get High-res Image Gene #27: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'MRNA_CNMF'

P value = 0.01 (Fisher's exact test), Q value = 0.013

Table S283. Gene #28: 'del_9p23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
DEL PEAK 15(9P23) MUTATED	5	12	1	3
DEL PEAK 15(9P23) WILD-TYPE	28	12	11	14

Figure S283. Get High-res Image Gene #28: 'del_9p23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p23' versus 'MRNA_CHIERARCHICAL'

P value = 0.0216 (Fisher's exact test), Q value = 0.027

Table S284. Gene #28: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
DEL PEAK 15(9P23) MUTATED	4	12	3	1	1
DEL PEAK 15(9P23) WILD-TYPE	16	12	15	12	10

Figure S284. Get High-res Image Gene #28: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S285. Gene #28: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
DEL PEAK 15(9P23) MUTATED	23	32	143
DEL PEAK 15(9P23) WILD-TYPE	259	278	147

Figure S285. Get High-res Image Gene #28: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S286. Gene #28: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
DEL PEAK 15(9P23) MUTATED	24	93	21
DEL PEAK 15(9P23) WILD-TYPE	104	210	200

Figure S286. Get High-res Image Gene #28: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p23' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S287. Gene #28: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
DEL PEAK 15(9P23) MUTATED	49	36	24	70
DEL PEAK 15(9P23) WILD-TYPE	133	145	163	127

Figure S287. Get High-res Image Gene #28: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p23' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S288. Gene #28: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 15(9P23) MUTATED	44	6	42	21	30	11	25
DEL PEAK 15(9P23) WILD-TYPE	153	58	74	126	29	60	68

Figure S288. Get High-res Image Gene #28: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S289. Gene #28: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
DEL PEAK 15(9P23) MUTATED	19	105	42	31
DEL PEAK 15(9P23) WILD-TYPE	100	90	255	237

Figure S289. Get High-res Image Gene #28: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S290. Gene #28: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
DEL PEAK 15(9P23) MUTATED	11	39	44	88	10	5
DEL PEAK 15(9P23) WILD-TYPE	77	106	163	71	101	164

Figure S290. Get High-res Image Gene #28: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S291. Gene #28: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
DEL PEAK 15(9P23) MUTATED	37	66	90
DEL PEAK 15(9P23) WILD-TYPE	290	127	254

Figure S291. Get High-res Image Gene #28: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.4e-05

Table S292. Gene #28: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
DEL PEAK 15(9P23) MUTATED	10	45	138
DEL PEAK 15(9P23) WILD-TYPE	67	260	344

Figure S292. Get High-res Image Gene #28: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00013

Table S293. Gene #28: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
DEL PEAK 15(9P23) MUTATED	12	12	21	27
DEL PEAK 15(9P23) WILD-TYPE	141	59	42	98

Figure S293. Get High-res Image Gene #28: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.4e-05

Table S294. Gene #28: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
DEL PEAK 15(9P23) MUTATED	2	8	32	24	6
DEL PEAK 15(9P23) WILD-TYPE	45	90	65	100	40

Figure S294. Get High-res Image Gene #28: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.3' versus 'MRNA_CNMF'

P value = 0.00363 (Fisher's exact test), Q value = 0.0049

Table S295. Gene #29: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
DEL PEAK 16(9P21.3) MUTATED	5	13	1	3
DEL PEAK 16(9P21.3) WILD-TYPE	28	11	11	14

Figure S295. Get High-res Image Gene #29: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p21.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00762 (Fisher's exact test), Q value = 0.0098

Table S296. Gene #29: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
DEL PEAK 16(9P21.3) MUTATED	4	13	3	1	1
DEL PEAK 16(9P21.3) WILD-TYPE	16	11	15	12	10

Figure S296. Get High-res Image Gene #29: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S297. Gene #29: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
DEL PEAK 16(9P21.3) MUTATED	27	34	148
DEL PEAK 16(9P21.3) WILD-TYPE	255	276	142

Figure S297. Get High-res Image Gene #29: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S298. Gene #29: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
DEL PEAK 16(9P21.3) MUTATED	29	94	22
DEL PEAK 16(9P21.3) WILD-TYPE	99	209	199

Figure S298. Get High-res Image Gene #29: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S299. Gene #29: 'del_9p21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
DEL PEAK 16(9P21.3) MUTATED	56	37	24	70
DEL PEAK 16(9P21.3) WILD-TYPE	126	144	163	127

Figure S299. Get High-res Image Gene #29: 'del_9p21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S300. Gene #29: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 16(9P21.3) MUTATED	41	6	46	23	30	12	29
DEL PEAK 16(9P21.3) WILD-TYPE	156	58	70	124	29	59	64

Figure S300. Get High-res Image Gene #29: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S301. Gene #29: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
DEL PEAK 16(9P21.3) MUTATED	20	113	43	32
DEL PEAK 16(9P21.3) WILD-TYPE	99	82	254	236

Figure S301. Get High-res Image Gene #29: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S302. Gene #29: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
DEL PEAK 16(9P21.3) MUTATED	11	45	45	92	10	5
DEL PEAK 16(9P21.3) WILD-TYPE	77	100	162	67	101	164

Figure S302. Get High-res Image Gene #29: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S303. Gene #29: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
DEL PEAK 16(9P21.3) MUTATED	39	75	89
DEL PEAK 16(9P21.3) WILD-TYPE	288	118	255

Figure S303. Get High-res Image Gene #29: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.4e-05

Table S304. Gene #29: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
DEL PEAK 16(9P21.3) MUTATED	10	50	143
DEL PEAK 16(9P21.3) WILD-TYPE	67	255	339

Figure S304. Get High-res Image Gene #29: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S305. Gene #29: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
DEL PEAK 16(9P21.3) MUTATED	11	12	24	29
DEL PEAK 16(9P21.3) WILD-TYPE	142	59	39	96

Figure S305. Get High-res Image Gene #29: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S306. Gene #29: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
DEL PEAK 16(9P21.3) MUTATED	2	7	36	25	6
DEL PEAK 16(9P21.3) WILD-TYPE	45	91	61	99	40

Figure S306. Get High-res Image Gene #29: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S307. Gene #30: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
DEL PEAK 17(10Q23.31) MUTATED	57	17	90
DEL PEAK 17(10Q23.31) WILD-TYPE	225	293	200

Figure S307. Get High-res Image Gene #30: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S308. Gene #30: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
DEL PEAK 17(10Q23.31) MUTATED	62	53	11
DEL PEAK 17(10Q23.31) WILD-TYPE	66	250	210

Figure S308. Get High-res Image Gene #30: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q23.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.00058

Table S309. Gene #30: 'del_10q23.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 17(10Q23.31) MUTATED	35	10	41	26	13	6	15
DEL PEAK 17(10Q23.31) WILD-TYPE	162	54	75	121	46	65	78

Figure S309. Get High-res Image Gene #30: 'del_10q23.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S310. Gene #30: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
DEL PEAK 17(10Q23.31) MUTATED	64	44	41	14
DEL PEAK 17(10Q23.31) WILD-TYPE	55	151	256	254

Figure S310. Get High-res Image Gene #30: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S311. Gene #30: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
DEL PEAK 17(10Q23.31) MUTATED	60	22	30	35	15	1
DEL PEAK 17(10Q23.31) WILD-TYPE	28	123	177	124	96	168

Figure S311. Get High-res Image Gene #30: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S312. Gene #30: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
DEL PEAK 17(10Q23.31) MUTATED	59	21	82
DEL PEAK 17(10Q23.31) WILD-TYPE	18	284	400

Figure S312. Get High-res Image Gene #30: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S313. Gene #30: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
DEL PEAK 17(10Q23.31) MUTATED	3	39	11	17
DEL PEAK 17(10Q23.31) WILD-TYPE	150	32	52	108

Figure S313. Get High-res Image Gene #30: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S314. Gene #30: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
DEL PEAK 17(10Q23.31) MUTATED	1	1	19	14	35
DEL PEAK 17(10Q23.31) WILD-TYPE	46	97	78	110	11

Figure S314. Get High-res Image Gene #30: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S315. Gene #31: 'del_11q21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
DEL PEAK 18(11Q21) MUTATED	20	5	36
DEL PEAK 18(11Q21) WILD-TYPE	262	305	254

Figure S315. Get High-res Image Gene #31: 'del_11q21' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q21' versus 'RPPA_CHIERARCHICAL'

P value = 0.0024 (Fisher's exact test), Q value = 0.0033

Table S316. Gene #31: 'del_11q21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 18(11Q21) MUTATED	8	4	16	5	9	3	9
DEL PEAK 18(11Q21) WILD-TYPE	189	60	100	142	50	68	84

Figure S316. Get High-res Image Gene #31: 'del_11q21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_11q21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S317. Gene #31: 'del_11q21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
DEL PEAK 18(11Q21) MUTATED	13	20	5	23
DEL PEAK 18(11Q21) WILD-TYPE	106	175	292	245

Figure S317. Get High-res Image Gene #31: 'del_11q21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S318. Gene #31: 'del_11q21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
DEL PEAK 18(11Q21) MUTATED	9	25	4	15	2	6
DEL PEAK 18(11Q21) WILD-TYPE	79	120	203	144	109	163

Figure S318. Get High-res Image Gene #31: 'del_11q21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q21' versus 'MIRSEQ_CNMF'

P value = 0.0338 (Fisher's exact test), Q value = 0.041

Table S319. Gene #31: 'del_11q21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
DEL PEAK 18(11Q21) MUTATED	29	17	15
DEL PEAK 18(11Q21) WILD-TYPE	298	176	329

Figure S319. Get High-res Image Gene #31: 'del_11q21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11q21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00394 (Fisher's exact test), Q value = 0.0052

Table S320. Gene #31: 'del_11q21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
DEL PEAK 18(11Q21) MUTATED	9	30	22
DEL PEAK 18(11Q21) WILD-TYPE	68	275	460

Figure S320. Get High-res Image Gene #31: 'del_11q21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11q21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00022

Table S321. Gene #31: 'del_11q21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
DEL PEAK 18(11Q21) MUTATED	9	9	13	3
DEL PEAK 18(11Q21) WILD-TYPE	144	62	50	122

Figure S321. Get High-res Image Gene #31: 'del_11q21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11q21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.4e-05

Table S322. Gene #31: 'del_11q21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
DEL PEAK 18(11Q21) MUTATED	1	6	18	1	8
DEL PEAK 18(11Q21) WILD-TYPE	46	92	79	123	38

Figure S322. Get High-res Image Gene #31: 'del_11q21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q23.1' versus 'MRNA_CNMF'

P value = 0.0377 (Fisher's exact test), Q value = 0.045

Table S323. Gene #32: 'del_11q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
DEL PEAK 19(11Q23.1) MUTATED	0	2	2	0
DEL PEAK 19(11Q23.1) WILD-TYPE	33	22	10	17

Figure S323. Get High-res Image Gene #32: 'del_11q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S324. Gene #32: 'del_11q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
DEL PEAK 19(11Q23.1) MUTATED	22	7	42
DEL PEAK 19(11Q23.1) WILD-TYPE	260	303	248

Figure S324. Get High-res Image Gene #32: 'del_11q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00081 (Fisher's exact test), Q value = 0.0012

Table S325. Gene #32: 'del_11q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 19(11Q23.1) MUTATED	10	5	19	6	10	3	10
DEL PEAK 19(11Q23.1) WILD-TYPE	187	59	97	141	49	68	83

Figure S325. Get High-res Image Gene #32: 'del_11q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_11q23.1' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 5.1e-05

Table S326. Gene #32: 'del_11q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
DEL PEAK 19(11Q23.1) MUTATED	13	25	6	27
DEL PEAK 19(11Q23.1) WILD-TYPE	106	170	291	241

Figure S326. Get High-res Image Gene #32: 'del_11q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S327. Gene #32: 'del_11q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
DEL PEAK 19(11Q23.1) MUTATED	8	30	7	18	1	7
DEL PEAK 19(11Q23.1) WILD-TYPE	80	115	200	141	110	162

Figure S327. Get High-res Image Gene #32: 'del_11q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.1' versus 'MIRSEQ_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.014

Table S328. Gene #32: 'del_11q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
DEL PEAK 19(11Q23.1) MUTATED	32	22	17
DEL PEAK 19(11Q23.1) WILD-TYPE	295	171	327

Figure S328. Get High-res Image Gene #32: 'del_11q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00095 (Fisher's exact test), Q value = 0.0014

Table S329. Gene #32: 'del_11q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
DEL PEAK 19(11Q23.1) MUTATED	8	38	25
DEL PEAK 19(11Q23.1) WILD-TYPE	69	267	457

Figure S329. Get High-res Image Gene #32: 'del_11q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S330. Gene #32: 'del_11q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
DEL PEAK 19(11Q23.1) MUTATED	9	8	17	4
DEL PEAK 19(11Q23.1) WILD-TYPE	144	63	46	121

Figure S330. Get High-res Image Gene #32: 'del_11q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S331. Gene #32: 'del_11q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
DEL PEAK 19(11Q23.1) MUTATED	1	6	22	2	7
DEL PEAK 19(11Q23.1) WILD-TYPE	46	92	75	122	39

Figure S331. Get High-res Image Gene #32: 'del_11q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q12.13' versus 'MRNA_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.034

Table S332. Gene #33: 'del_13q12.13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
DEL PEAK 20(13Q12.13) MUTATED	1	6	3	1
DEL PEAK 20(13Q12.13) WILD-TYPE	32	18	9	16

Figure S332. Get High-res Image Gene #33: 'del_13q12.13' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q12.13' versus 'MRNA_CHIERARCHICAL'

P value = 0.037 (Fisher's exact test), Q value = 0.044

Table S333. Gene #33: 'del_13q12.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
DEL PEAK 20(13Q12.13) MUTATED	0	6	1	1	3
DEL PEAK 20(13Q12.13) WILD-TYPE	20	18	17	12	8

Figure S333. Get High-res Image Gene #33: 'del_13q12.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q12.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S334. Gene #33: 'del_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
DEL PEAK 20(13Q12.13) MUTATED	62	12	76
DEL PEAK 20(13Q12.13) WILD-TYPE	220	298	214

Figure S334. Get High-res Image Gene #33: 'del_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q12.13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S335. Gene #33: 'del_13q12.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
DEL PEAK 20(13Q12.13) MUTATED	62	46	11
DEL PEAK 20(13Q12.13) WILD-TYPE	66	257	210

Figure S335. Get High-res Image Gene #33: 'del_13q12.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q12.13' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S336. Gene #33: 'del_13q12.13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 20(13Q12.13) MUTATED	26	11	42	13	17	7	19
DEL PEAK 20(13Q12.13) WILD-TYPE	171	53	74	134	42	64	74

Figure S336. Get High-res Image Gene #33: 'del_13q12.13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_13q12.13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S337. Gene #33: 'del_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
DEL PEAK 20(13Q12.13) MUTATED	56	57	21	16
DEL PEAK 20(13Q12.13) WILD-TYPE	63	138	276	252

Figure S337. Get High-res Image Gene #33: 'del_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q12.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S338. Gene #33: 'del_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
DEL PEAK 20(13Q12.13) MUTATED	52	28	11	47	10	2
DEL PEAK 20(13Q12.13) WILD-TYPE	36	117	196	112	101	167

Figure S338. Get High-res Image Gene #33: 'del_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q12.13' versus 'MIRSEQ_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.001

Table S339. Gene #33: 'del_13q12.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
DEL PEAK 20(13Q12.13) MUTATED	67	42	39
DEL PEAK 20(13Q12.13) WILD-TYPE	260	151	305

Figure S339. Get High-res Image Gene #33: 'del_13q12.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q12.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S340. Gene #33: 'del_13q12.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
DEL PEAK 20(13Q12.13) MUTATED	51	33	64
DEL PEAK 20(13Q12.13) WILD-TYPE	26	272	418

Figure S340. Get High-res Image Gene #33: 'del_13q12.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q12.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S341. Gene #33: 'del_13q12.13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
DEL PEAK 20(13Q12.13) MUTATED	7	33	19	13
DEL PEAK 20(13Q12.13) WILD-TYPE	146	38	44	112

Figure S341. Get High-res Image Gene #33: 'del_13q12.13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_13q12.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S342. Gene #33: 'del_13q12.13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
DEL PEAK 20(13Q12.13) MUTATED	1	3	25	12	31
DEL PEAK 20(13Q12.13) WILD-TYPE	46	95	72	112	15

Figure S342. Get High-res Image Gene #33: 'del_13q12.13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q14.2' versus 'MRNA_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.016

Table S343. Gene #34: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
DEL PEAK 21(13Q14.2) MUTATED	1	7	3	1
DEL PEAK 21(13Q14.2) WILD-TYPE	32	17	9	16

Figure S343. Get High-res Image Gene #34: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q14.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.021

Table S344. Gene #34: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
DEL PEAK 21(13Q14.2) MUTATED	0	7	1	1	3
DEL PEAK 21(13Q14.2) WILD-TYPE	20	17	17	12	8

Figure S344. Get High-res Image Gene #34: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S345. Gene #34: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
DEL PEAK 21(13Q14.2) MUTATED	62	11	76
DEL PEAK 21(13Q14.2) WILD-TYPE	220	299	214

Figure S345. Get High-res Image Gene #34: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S346. Gene #34: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
DEL PEAK 21(13Q14.2) MUTATED	62	45	10
DEL PEAK 21(13Q14.2) WILD-TYPE	66	258	211

Figure S346. Get High-res Image Gene #34: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'RPPA_CNMF'

P value = 0.0307 (Fisher's exact test), Q value = 0.037

Table S347. Gene #34: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
DEL PEAK 21(13Q14.2) MUTATED	42	25	26	42
DEL PEAK 21(13Q14.2) WILD-TYPE	140	156	161	155

Figure S347. Get High-res Image Gene #34: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q14.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S348. Gene #34: 'del_13q14.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 21(13Q14.2) MUTATED	27	10	41	12	18	7	20
DEL PEAK 21(13Q14.2) WILD-TYPE	170	54	75	135	41	64	73

Figure S348. Get High-res Image Gene #34: 'del_13q14.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S349. Gene #34: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
DEL PEAK 21(13Q14.2) MUTATED	55	58	21	15
DEL PEAK 21(13Q14.2) WILD-TYPE	64	137	276	253

Figure S349. Get High-res Image Gene #34: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S350. Gene #34: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
DEL PEAK 21(13Q14.2) MUTATED	51	28	10	47	11	2
DEL PEAK 21(13Q14.2) WILD-TYPE	37	117	197	112	100	167

Figure S350. Get High-res Image Gene #34: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 0.00195 (Fisher's exact test), Q value = 0.0027

Table S351. Gene #34: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
DEL PEAK 21(13Q14.2) MUTATED	66	41	40
DEL PEAK 21(13Q14.2) WILD-TYPE	261	152	304

Figure S351. Get High-res Image Gene #34: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S352. Gene #34: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
DEL PEAK 21(13Q14.2) MUTATED	50	33	64
DEL PEAK 21(13Q14.2) WILD-TYPE	27	272	418

Figure S352. Get High-res Image Gene #34: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S353. Gene #34: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
DEL PEAK 21(13Q14.2) MUTATED	6	33	18	12
DEL PEAK 21(13Q14.2) WILD-TYPE	147	38	45	113

Figure S353. Get High-res Image Gene #34: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S354. Gene #34: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
DEL PEAK 21(13Q14.2) MUTATED	1	3	23	11	31
DEL PEAK 21(13Q14.2) WILD-TYPE	46	95	74	113	15

Figure S354. Get High-res Image Gene #34: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q31.1' versus 'MRNA_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00014

Table S355. Gene #35: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
DEL PEAK 22(14Q31.1) MUTATED	10	19	2	4
DEL PEAK 22(14Q31.1) WILD-TYPE	23	5	10	13

Figure S355. Get High-res Image Gene #35: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q31.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.00048

Table S356. Gene #35: 'del_14q31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
DEL PEAK 22(14Q31.1) MUTATED	5	19	4	5	2
DEL PEAK 22(14Q31.1) WILD-TYPE	15	5	14	8	9

Figure S356. Get High-res Image Gene #35: 'del_14q31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S357. Gene #35: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
DEL PEAK 22(14Q31.1) MUTATED	35	82	162
DEL PEAK 22(14Q31.1) WILD-TYPE	247	228	128

Figure S357. Get High-res Image Gene #35: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q31.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S358. Gene #35: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
DEL PEAK 22(14Q31.1) MUTATED	15	138	27
DEL PEAK 22(14Q31.1) WILD-TYPE	113	165	194

Figure S358. Get High-res Image Gene #35: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q31.1' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.4e-05

Table S359. Gene #35: 'del_14q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
DEL PEAK 22(14Q31.1) MUTATED	62	61	34	88
DEL PEAK 22(14Q31.1) WILD-TYPE	120	120	153	109

Figure S359. Get High-res Image Gene #35: 'del_14q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_14q31.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S360. Gene #35: 'del_14q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 22(14Q31.1) MUTATED	65	3	46	43	32	18	38
DEL PEAK 22(14Q31.1) WILD-TYPE	132	61	70	104	27	53	55

Figure S360. Get High-res Image Gene #35: 'del_14q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_14q31.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S361. Gene #35: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
DEL PEAK 22(14Q31.1) MUTATED	11	120	103	42
DEL PEAK 22(14Q31.1) WILD-TYPE	108	75	194	226

Figure S361. Get High-res Image Gene #35: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S362. Gene #35: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
DEL PEAK 22(14Q31.1) MUTATED	5	40	77	110	33	11
DEL PEAK 22(14Q31.1) WILD-TYPE	83	105	130	49	78	158

Figure S362. Get High-res Image Gene #35: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q31.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S363. Gene #35: 'del_14q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
DEL PEAK 22(14Q31.1) MUTATED	42	79	152
DEL PEAK 22(14Q31.1) WILD-TYPE	285	114	192

Figure S363. Get High-res Image Gene #35: 'del_14q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_14q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S364. Gene #35: 'del_14q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
DEL PEAK 22(14Q31.1) MUTATED	4	52	217
DEL PEAK 22(14Q31.1) WILD-TYPE	73	253	265

Figure S364. Get High-res Image Gene #35: 'del_14q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q31.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S365. Gene #35: 'del_14q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
DEL PEAK 22(14Q31.1) MUTATED	15	5	23	50
DEL PEAK 22(14Q31.1) WILD-TYPE	138	66	40	75

Figure S365. Get High-res Image Gene #35: 'del_14q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_14q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S366. Gene #35: 'del_14q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
DEL PEAK 22(14Q31.1) MUTATED	4	9	31	47	2
DEL PEAK 22(14Q31.1) WILD-TYPE	43	89	66	77	44

Figure S366. Get High-res Image Gene #35: 'del_14q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.3' versus 'CN_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 0.021

Table S367. Gene #36: 'del_16q23.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
DEL PEAK 23(16Q23.3) MUTATED	10	7	20
DEL PEAK 23(16Q23.3) WILD-TYPE	272	303	270

Figure S367. Get High-res Image Gene #36: 'del_16q23.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_16q23.3' versus 'METHLYATION_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.014

Table S368. Gene #36: 'del_16q23.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
DEL PEAK 23(16Q23.3) MUTATED	12	12	5
DEL PEAK 23(16Q23.3) WILD-TYPE	116	291	216

Figure S368. Get High-res Image Gene #36: 'del_16q23.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16q23.3' versus 'MRNASEQ_CNMF'

P value = 0.0243 (Fisher's exact test), Q value = 0.03

Table S369. Gene #36: 'del_16q23.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
DEL PEAK 23(16Q23.3) MUTATED	8	14	8	7
DEL PEAK 23(16Q23.3) WILD-TYPE	111	181	289	261

Figure S369. Get High-res Image Gene #36: 'del_16q23.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00016

Table S370. Gene #36: 'del_16q23.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
DEL PEAK 23(16Q23.3) MUTATED	5	14	5	10	3	0
DEL PEAK 23(16Q23.3) WILD-TYPE	83	131	202	149	108	169

Figure S370. Get High-res Image Gene #36: 'del_16q23.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0219 (Fisher's exact test), Q value = 0.027

Table S371. Gene #36: 'del_16q23.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
DEL PEAK 23(16Q23.3) MUTATED	0	3	11	5	4
DEL PEAK 23(16Q23.3) WILD-TYPE	47	95	86	119	42

Figure S371. Get High-res Image Gene #36: 'del_16q23.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S372. Gene #37: 'del_18q22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
DEL PEAK 24(18Q22.2) MUTATED	38	27	90
DEL PEAK 24(18Q22.2) WILD-TYPE	244	283	200

Figure S372. Get High-res Image Gene #37: 'del_18q22.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q22.2' versus 'METHLYATION_CNMF'

P value = 0.031 (Fisher's exact test), Q value = 0.038

Table S373. Gene #37: 'del_18q22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
DEL PEAK 24(18Q22.2) MUTATED	24	63	27
DEL PEAK 24(18Q22.2) WILD-TYPE	104	240	194

Figure S373. Get High-res Image Gene #37: 'del_18q22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q22.2' versus 'RPPA_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.00059

Table S374. Gene #37: 'del_18q22.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
DEL PEAK 24(18Q22.2) MUTATED	41	18	28	49
DEL PEAK 24(18Q22.2) WILD-TYPE	141	163	159	148

Figure S374. Get High-res Image Gene #37: 'del_18q22.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_18q22.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S375. Gene #37: 'del_18q22.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 24(18Q22.2) MUTATED	20	8	39	16	24	8	21
DEL PEAK 24(18Q22.2) WILD-TYPE	177	56	77	131	35	63	72

Figure S375. Get High-res Image Gene #37: 'del_18q22.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_18q22.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S376. Gene #37: 'del_18q22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
DEL PEAK 24(18Q22.2) MUTATED	15	79	19	41
DEL PEAK 24(18Q22.2) WILD-TYPE	104	116	278	227

Figure S376. Get High-res Image Gene #37: 'del_18q22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S377. Gene #37: 'del_18q22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
DEL PEAK 24(18Q22.2) MUTATED	12	45	18	62	8	9
DEL PEAK 24(18Q22.2) WILD-TYPE	76	100	189	97	103	160

Figure S377. Get High-res Image Gene #37: 'del_18q22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q22.2' versus 'MIRSEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00025

Table S378. Gene #37: 'del_18q22.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
DEL PEAK 24(18Q22.2) MUTATED	46	55	54
DEL PEAK 24(18Q22.2) WILD-TYPE	281	138	290

Figure S378. Get High-res Image Gene #37: 'del_18q22.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18q22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00202 (Fisher's exact test), Q value = 0.0028

Table S379. Gene #37: 'del_18q22.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
DEL PEAK 24(18Q22.2) MUTATED	20	14	20	13
DEL PEAK 24(18Q22.2) WILD-TYPE	133	57	43	112

Figure S379. Get High-res Image Gene #37: 'del_18q22.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S380. Gene #37: 'del_18q22.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
DEL PEAK 24(18Q22.2) MUTATED	1	14	33	11	8
DEL PEAK 24(18Q22.2) WILD-TYPE	46	84	64	113	38

Figure S380. Get High-res Image Gene #37: 'del_18q22.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S381. Gene #38: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
DEL PEAK 25(19P13.3) MUTATED	15	1	27
DEL PEAK 25(19P13.3) WILD-TYPE	267	309	263

Figure S381. Get High-res Image Gene #38: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.00052

Table S382. Gene #38: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
DEL PEAK 25(19P13.3) MUTATED	9	6	21
DEL PEAK 25(19P13.3) WILD-TYPE	119	297	200

Figure S382. Get High-res Image Gene #38: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0181 (Fisher's exact test), Q value = 0.022

Table S383. Gene #38: 'del_19p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 25(19P13.3) MUTATED	6	1	13	3	2	3	6
DEL PEAK 25(19P13.3) WILD-TYPE	191	63	103	144	57	68	87

Figure S383. Get High-res Image Gene #38: 'del_19p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S384. Gene #38: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
DEL PEAK 25(19P13.3) MUTATED	3	15	2	23
DEL PEAK 25(19P13.3) WILD-TYPE	116	180	295	245

Figure S384. Get High-res Image Gene #38: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S385. Gene #38: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
DEL PEAK 25(19P13.3) MUTATED	2	22	1	9	1	8
DEL PEAK 25(19P13.3) WILD-TYPE	86	123	206	150	110	161

Figure S385. Get High-res Image Gene #38: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 0.00292 (Fisher's exact test), Q value = 0.004

Table S386. Gene #38: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
DEL PEAK 25(19P13.3) MUTATED	23	13	7
DEL PEAK 25(19P13.3) WILD-TYPE	304	180	337

Figure S386. Get High-res Image Gene #38: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S387. Gene #38: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
DEL PEAK 25(19P13.3) MUTATED	2	30	11
DEL PEAK 25(19P13.3) WILD-TYPE	75	275	471

Figure S387. Get High-res Image Gene #38: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00118 (Fisher's exact test), Q value = 0.0017

Table S388. Gene #38: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
DEL PEAK 25(19P13.3) MUTATED	12	2	11	3
DEL PEAK 25(19P13.3) WILD-TYPE	141	69	52	122

Figure S388. Get High-res Image Gene #38: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 9.8e-05

Table S389. Gene #38: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
DEL PEAK 25(19P13.3) MUTATED	1	8	16	1	2
DEL PEAK 25(19P13.3) WILD-TYPE	46	90	81	123	44

Figure S389. Get High-res Image Gene #38: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S390. Gene #39: 'del_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
DEL PEAK 26(XP22.2) MUTATED	67	11	49
DEL PEAK 26(XP22.2) WILD-TYPE	215	299	241

Figure S390. Get High-res Image Gene #39: 'del_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_xp22.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S391. Gene #39: 'del_xp22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
DEL PEAK 26(XP22.2) MUTATED	55	34	16
DEL PEAK 26(XP22.2) WILD-TYPE	73	269	205

Figure S391. Get High-res Image Gene #39: 'del_xp22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xp22.2' versus 'RPPA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 9.8e-05

Table S392. Gene #39: 'del_xp22.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 26(XP22.2) MUTATED	33	9	31	12	4	3	16
DEL PEAK 26(XP22.2) WILD-TYPE	164	55	85	135	55	68	77

Figure S392. Get High-res Image Gene #39: 'del_xp22.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_xp22.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S393. Gene #39: 'del_xp22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
DEL PEAK 26(XP22.2) MUTATED	53	21	26	27
DEL PEAK 26(XP22.2) WILD-TYPE	66	174	271	241

Figure S393. Get High-res Image Gene #39: 'del_xp22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_xp22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S394. Gene #39: 'del_xp22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
DEL PEAK 26(XP22.2) MUTATED	50	30	19	15	7	6
DEL PEAK 26(XP22.2) WILD-TYPE	38	115	188	144	104	163

Figure S394. Get High-res Image Gene #39: 'del_xp22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_xp22.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S395. Gene #39: 'del_xp22.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	327	193	344
DEL PEAK 26(XP22.2) MUTATED	73	22	31
DEL PEAK 26(XP22.2) WILD-TYPE	254	171	313

Figure S395. Get High-res Image Gene #39: 'del_xp22.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_xp22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S396. Gene #39: 'del_xp22.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	305	482
DEL PEAK 26(XP22.2) MUTATED	49	35	42
DEL PEAK 26(XP22.2) WILD-TYPE	28	270	440

Figure S396. Get High-res Image Gene #39: 'del_xp22.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_xp22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S397. Gene #39: 'del_xp22.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	71	63	125
DEL PEAK 26(XP22.2) MUTATED	9	34	9	11
DEL PEAK 26(XP22.2) WILD-TYPE	144	37	54	114

Figure S397. Get High-res Image Gene #39: 'del_xp22.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_xp22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.8e-05

Table S398. Gene #39: 'del_xp22.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	98	97	124	46
DEL PEAK 26(XP22.2) MUTATED	0	6	21	7	29
DEL PEAK 26(XP22.2) WILD-TYPE	47	92	76	117	17

Figure S398. Get High-res Image Gene #39: 'del_xp22.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIPAN-TP/19782223/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIPAN-TP/20125873/KIPAN-TP.transferedmergedcluster.txt
Number of patients = 882
Number of significantly focal cnvs = 39
Number of molecular subtypes = 12
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

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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