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

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

02 April 2015 | analyses__2015_04_02

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1HD7TPD

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 10 molecular subtypes across 882 patients, 341 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q32.1 cnv correlated to 'CN_CNMF', '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', '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', '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', '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', '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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_10p14 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_17q25.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', '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', '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', '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', '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', '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', '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', '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', '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', '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', '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', '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', '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', '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', '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', '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', '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', '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', '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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p23.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p23 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', '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', '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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q21 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q23.1 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q12.13 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', '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', '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', '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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', '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 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 341 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
amp 5q35 1	376 (43%)	506	0.00091 (0.00122)	0.00206 (0.00268)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)
amp 7q31 2	377 (43%)	505	0.0336 (0.0391)	0.0446 (0.0511)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)
amp 17q25 2	245 (28%)	637	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)
amp xp22 2	126 (14%)	756	0.00188 (0.00246)	0.00206 (0.00268)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)
amp xp11 4	134 (15%)	748	0.00151 (0.00199)	0.00448 (0.00565)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)
amp xq11 2	135 (15%)	747	3e-05 (4.61e-05)	2e-05 (3.12e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)
amp xq28	137 (16%)	745	0.00014 (0.000201)	0.00046 (0.000636)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)
del 1p36 31	209 (24%)	673	0.0004 (0.000555)	0.00357 (0.00452)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)
del 1p31 1	166 (19%)	716	0.00169 (0.00222)	0.018 (0.0215)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	2e-05 (3.12e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)
del 1q43	114 (13%)	768	0.00865 (0.0106)	0.0079 (0.00978)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)
del 2q37 3	111 (13%)	771	0.00013 (0.000187)	0.00018 (0.000255)	3e-05 (4.61e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)
del 3p26 3	489 (55%)	393	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)
del 3p21 2	503 (57%)	379	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)
del 3p14 1	408 (46%)	474	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)
del 3p12 2	336 (38%)	546	6e-05 (8.93e-05)	0.0002 (0.000283)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)
del 9p23	198 (22%)	684	0.0106 (0.0129)	0.0216 (0.0257)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	4e-05 (6.05e-05)	0.00025 (0.000352)
del 9p21 3	209 (24%)	673	0.00348 (0.00442)	0.00761 (0.00945)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	4e-05 (6.05e-05)
del 13q12 13	150 (17%)	732	0.0279 (0.0329)	0.0373 (0.0432)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	0.00075 (0.00102)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)
del 13q14 2	149 (17%)	733	0.0121 (0.0147)	0.0172 (0.0207)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	0.00211 (0.00272)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)
del 14q31 1	279 (32%)	603	7e-05 (0.000104)	0.00013 (0.000187)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)
amp 3q26 32	193 (22%)	689	0.0336 (0.0391)	0.11 (0.123)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)
del 6q22 31	227 (26%)	655	0.00034 (0.000474)	0.00672 (0.0084)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	0.772 (0.784)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)
del 6q26	233 (26%)	649	0.00052 (0.000712)	0.00796 (0.00982)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	0.569 (0.592)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)
del 6q26	234 (27%)	648	0.00051 (7e-04)	0.00759 (0.00945)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	0.605 (0.624)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)
amp 8q24 22	125 (14%)	757	0.324 (0.345)	0.599 (0.619)	1e-05 (1.6e-05)	0.00211 (0.00272)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	0.00077 (0.00105)	1e-05 (1.6e-05)	0.00028 (0.000391)	8e-05 (0.000118)
del 4q34 3	113 (13%)	769	0.566 (0.59)	0.318 (0.339)	1e-05 (1.6e-05)	0.00086 (0.00116)	2e-05 (3.12e-05)	1e-05 (1.6e-05)	0.00486 (0.00611)	1e-05 (1.6e-05)	0.00016 (0.000229)	1e-05 (1.6e-05)
del 5p15 33	31 (4%)	851			0.00324 (0.00413)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	4e-05 (6.05e-05)	6e-05 (8.93e-05)	0.00086 (0.00116)	0.00028 (0.000391)
del 8p23 2	184 (21%)	698	0.596 (0.619)	0.608 (0.624)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)
del 18q22 2	155 (18%)	727	0.0867 (0.0978)	0.228 (0.247)	1e-05 (1.6e-05)	0.032 (0.0375)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	8e-05 (0.000118)	0.00132 (0.00175)	0.00303 (0.00387)	3e-05 (4.61e-05)
del xp22 2	127 (14%)	755	0.0818 (0.0927)	0.107 (0.119)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)
amp 1q32 1	82 (9%)	800	0.551 (0.576)	0.695 (0.711)	1e-05 (1.6e-05)	0.0852 (0.0964)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	6e-05 (8.93e-05)	1e-05 (1.6e-05)	0.0304 (0.0357)	0.0001 (0.000146)
amp 2q32 1	136 (15%)	746	0.606 (0.624)	0.373 (0.396)	1e-05 (1.6e-05)	0.00665 (0.00834)	0.00897 (0.011)	1e-05 (1.6e-05)	0.408 (0.431)	0.00017 (0.000242)	0.0091 (0.0111)	0.0207 (0.0247)
amp 19p13 2	98 (11%)	784	0.119 (0.132)	0.28 (0.3)	1e-05 (1.6e-05)	0.0414 (0.0477)	0.0001 (0.000146)	1e-05 (1.6e-05)	0.00209 (0.00271)	6e-05 (8.93e-05)	0.072 (0.0819)	0.00092 (0.00123)
del 10q23 31	164 (19%)	718	0.21 (0.228)	0.176 (0.194)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	0.198 (0.217)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	1e-05 (1.6e-05)
del 11q23 1	71 (8%)	811	0.0395 (0.0456)	0.0904 (0.102)	1e-05 (1.6e-05)	0.0909 (0.102)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	0.00998 (0.0122)	0.739 (0.752)	2e-05 (3.12e-05)	2e-05 (3.12e-05)
del 19p13 3	43 (5%)	839	1 (1.00)	0.853 (0.864)	1e-05 (1.6e-05)	0.00048 (0.000661)	1e-05 (1.6e-05)	1e-05 (1.6e-05)	0.00266 (0.00341)	0.701 (0.716)	0.00121 (0.00161)	0.00011 (0.000159)
del 11q21	61 (7%)	821	0.548 (0.575)	0.379 (0.402)	2e-05 (3.12e-05)	0.0532 (0.0607)	3e-05 (4.61e-05)	1e-05 (1.6e-05)	0.0343 (0.0398)	0.255 (0.274)	9e-05 (0.000132)	1e-05 (1.6e-05)
del 16q23 3	37 (4%)	845	0.867 (0.876)	0.916 (0.923)	0.0166 (0.02)	0.0107 (0.013)	0.0246 (0.0291)	4e-05 (6.05e-05)	0.184 (0.202)	0.219 (0.237)	0.148 (0.164)	0.0449 (0.0513)
amp 10p14	34 (4%)	848	0.151 (0.166)	0.48 (0.505)	1e-05 (1.6e-05)	0.0227 (0.027)	0.00113 (0.0015)	0.00082 (0.00111)	0.199 (0.217)	0.445 (0.469)	0.24 (0.259)	0.204 (0.222)

'amp_1q32.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-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 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

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

'amp_1q32.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

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

'amp_1q32.1' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 8.9e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
AMP PEAK 1(1Q32.1) MUTATED	13	25	42
AMP PEAK 1(1Q32.1) WILD-TYPE	315	167	302

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

'amp_1q32.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
AMP PEAK 1(1Q32.1) MUTATED	0	79	1
AMP PEAK 1(1Q32.1) WILD-TYPE	77	502	205

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

'amp_1q32.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0304 (Fisher's exact test), Q value = 0.036

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
AMP PEAK 1(1Q32.1) MUTATED	5	4	8	13
AMP PEAK 1(1Q32.1) WILD-TYPE	148	66	55	112

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

'amp_1q32.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00015

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
AMP PEAK 1(1Q32.1) MUTATED	0	2	15	13	0
AMP PEAK 1(1Q32.1) WILD-TYPE	50	87	79	119	46

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

'amp_2q32.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S8. 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 S8. Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2q32.1' versus 'METHLYATION_CNMF'

P value = 0.00665 (Fisher's exact test), Q value = 0.0083

Table S9. 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 S9. Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2q32.1' versus 'MRNASEQ_CNMF'

P value = 0.00897 (Fisher's exact test), Q value = 0.011

Table S10. Gene #2: 'amp_2q32.1' versus Molecular Subtype #5: '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 S10. Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_2q32.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S11. Gene #2: 'amp_2q32.1' versus Molecular Subtype #6: '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 S11. Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_2q32.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00024

Table S12. Gene #2: 'amp_2q32.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
AMP PEAK 2(2Q32.1) MUTATED	1	97	36
AMP PEAK 2(2Q32.1) WILD-TYPE	76	484	170

Figure S12. Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_2q32.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0091 (Fisher's exact test), Q value = 0.011

Table S13. Gene #2: 'amp_2q32.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
AMP PEAK 2(2Q32.1) MUTATED	25	4	17	21
AMP PEAK 2(2Q32.1) WILD-TYPE	128	66	46	104

Figure S13. Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_2q32.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0207 (Fisher's exact test), Q value = 0.025

Table S14. Gene #2: 'amp_2q32.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
AMP PEAK 2(2Q32.1) MUTATED	6	17	20	23	1
AMP PEAK 2(2Q32.1) WILD-TYPE	44	72	74	109	45

Figure S14. Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.32' versus 'MRNA_CNMF'

P value = 0.0336 (Fisher's exact test), Q value = 0.039

Table S15. 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 S15. 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 = 1.6e-05

Table S16. 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 S16. 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 = 1.6e-05

Table S17. 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 S17. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S18. Gene #3: 'amp_3q26.32' versus Molecular Subtype #5: '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 S18. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3q26.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S19. Gene #3: 'amp_3q26.32' versus Molecular Subtype #6: '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 S19. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S20. Gene #3: 'amp_3q26.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
AMP PEAK 3(3Q26.32) MUTATED	110	37	43
AMP PEAK 3(3Q26.32) WILD-TYPE	218	155	301

Figure S20. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_3q26.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S21. Gene #3: 'amp_3q26.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
AMP PEAK 3(3Q26.32) MUTATED	9	94	87
AMP PEAK 3(3Q26.32) WILD-TYPE	68	487	119

Figure S21. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S22. Gene #3: 'amp_3q26.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
AMP PEAK 3(3Q26.32) MUTATED	60	5	15	12
AMP PEAK 3(3Q26.32) WILD-TYPE	93	65	48	113

Figure S22. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S23. Gene #3: 'amp_3q26.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
AMP PEAK 3(3Q26.32) MUTATED	16	39	19	14	4
AMP PEAK 3(3Q26.32) WILD-TYPE	34	50	75	118	42

Figure S23. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5q35.1' versus 'MRNA_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.0012

Table S24. 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 S24. Get High-res Image Gene #4: 'amp_5q35.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_5q35.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00206 (Fisher's exact test), Q value = 0.0027

Table S25. 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 S25. 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 = 1.6e-05

Table S26. 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 S26. 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 = 1.6e-05

Table S27. 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 S27. Get High-res Image Gene #4: 'amp_5q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_5q35.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S28. Gene #4: 'amp_5q35.1' versus Molecular Subtype #5: '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 S28. Get High-res Image Gene #4: 'amp_5q35.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S29. Gene #4: 'amp_5q35.1' versus Molecular Subtype #6: '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 S29. Get High-res Image Gene #4: 'amp_5q35.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5q35.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S30. Gene #4: 'amp_5q35.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
AMP PEAK 4(5Q35.1) MUTATED	38	89	240
AMP PEAK 4(5Q35.1) WILD-TYPE	290	103	104

Figure S30. Get High-res Image Gene #4: 'amp_5q35.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5q35.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S31. Gene #4: 'amp_5q35.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
AMP PEAK 4(5Q35.1) MUTATED	9	338	20
AMP PEAK 4(5Q35.1) WILD-TYPE	68	243	186

Figure S31. Get High-res Image Gene #4: 'amp_5q35.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5q35.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S32. Gene #4: 'amp_5q35.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
AMP PEAK 4(5Q35.1) MUTATED	19	7	19	90
AMP PEAK 4(5Q35.1) WILD-TYPE	134	63	44	35

Figure S32. Get High-res Image Gene #4: 'amp_5q35.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_5q35.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S33. Gene #4: 'amp_5q35.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
AMP PEAK 4(5Q35.1) MUTATED	3	14	15	97	6
AMP PEAK 4(5Q35.1) WILD-TYPE	47	75	79	35	40

Figure S33. Get High-res Image Gene #4: 'amp_5q35.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q31.2' versus 'MRNA_CNMF'

P value = 0.0336 (Fisher's exact test), Q value = 0.039

Table S34. 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 S34. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_7q31.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0446 (Fisher's exact test), Q value = 0.051

Table S35. 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 S35. 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 = 1.6e-05

Table S36. 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 S36. 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 = 1.6e-05

Table S37. 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 S37. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S38. Gene #5: 'amp_7q31.2' versus Molecular Subtype #5: '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 S38. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S39. Gene #5: 'amp_7q31.2' versus Molecular Subtype #6: '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 S39. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S40. Gene #5: 'amp_7q31.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
AMP PEAK 5(7Q31.2) MUTATED	189	78	107
AMP PEAK 5(7Q31.2) WILD-TYPE	139	114	237

Figure S40. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S41. Gene #5: 'amp_7q31.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
AMP PEAK 5(7Q31.2) MUTATED	29	194	151
AMP PEAK 5(7Q31.2) WILD-TYPE	48	387	55

Figure S41. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S42. Gene #5: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
AMP PEAK 5(7Q31.2) MUTATED	109	24	29	37
AMP PEAK 5(7Q31.2) WILD-TYPE	44	46	34	88

Figure S42. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S43. Gene #5: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
AMP PEAK 5(7Q31.2) MUTATED	41	62	35	41	20
AMP PEAK 5(7Q31.2) WILD-TYPE	9	27	59	91	26

Figure S43. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S44. 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 S44. Get High-res Image Gene #6: 'amp_8q24.22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.22' versus 'METHLYATION_CNMF'

P value = 0.00211 (Fisher's exact test), Q value = 0.0027

Table S45. 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 S45. Get High-res Image Gene #6: 'amp_8q24.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.22' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S46. Gene #6: 'amp_8q24.22' versus Molecular Subtype #5: '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 S46. Get High-res Image Gene #6: 'amp_8q24.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8q24.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S47. Gene #6: 'amp_8q24.22' versus Molecular Subtype #6: '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 S47. Get High-res Image Gene #6: 'amp_8q24.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.22' versus 'MIRSEQ_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.001

Table S48. Gene #6: 'amp_8q24.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
AMP PEAK 6(8Q24.22) MUTATED	37	44	42
AMP PEAK 6(8Q24.22) WILD-TYPE	291	148	302

Figure S48. Get High-res Image Gene #6: 'amp_8q24.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8q24.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S49. Gene #6: 'amp_8q24.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
AMP PEAK 6(8Q24.22) MUTATED	18	94	11
AMP PEAK 6(8Q24.22) WILD-TYPE	59	487	195

Figure S49. Get High-res Image Gene #6: 'amp_8q24.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.00039

Table S50. Gene #6: 'amp_8q24.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
AMP PEAK 6(8Q24.22) MUTATED	12	17	17	15
AMP PEAK 6(8Q24.22) WILD-TYPE	141	53	46	110

Figure S50. Get High-res Image Gene #6: 'amp_8q24.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00012

Table S51. Gene #6: 'amp_8q24.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
AMP PEAK 6(8Q24.22) MUTATED	1	8	20	17	15
AMP PEAK 6(8Q24.22) WILD-TYPE	49	81	74	115	31

Figure S51. Get High-res Image Gene #6: 'amp_8q24.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10p14' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S52. 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 S52. Get High-res Image Gene #7: 'amp_10p14' versus Molecular Subtype #3: 'CN_CNMF'

'amp_10p14' versus 'METHLYATION_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.027

Table S53. 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 S53. Get High-res Image Gene #7: 'amp_10p14' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_10p14' versus 'MRNASEQ_CNMF'

P value = 0.00113 (Fisher's exact test), Q value = 0.0015

Table S54. Gene #7: 'amp_10p14' versus Molecular Subtype #5: '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 S54. Get High-res Image Gene #7: 'amp_10p14' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_10p14' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00082 (Fisher's exact test), Q value = 0.0011

Table S55. Gene #7: 'amp_10p14' versus Molecular Subtype #6: '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 S55. Get High-res Image Gene #7: 'amp_10p14' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q25.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S56. 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 S56. 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 = 1.6e-05

Table S57. 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 S57. 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 = 1.6e-05

Table S58. 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 S58. 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 = 1.6e-05

Table S59. 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 S59. Get High-res Image Gene #8: 'amp_17q25.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q25.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S60. Gene #8: 'amp_17q25.2' versus Molecular Subtype #5: '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 S60. Get High-res Image Gene #8: 'amp_17q25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S61. Gene #8: 'amp_17q25.2' versus Molecular Subtype #6: '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 S61. Get High-res Image Gene #8: 'amp_17q25.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q25.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S62. Gene #8: 'amp_17q25.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
AMP PEAK 8(17Q25.2) MUTATED	187	35	22
AMP PEAK 8(17Q25.2) WILD-TYPE	141	157	322

Figure S62. Get High-res Image Gene #8: 'amp_17q25.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_17q25.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S63. Gene #8: 'amp_17q25.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
AMP PEAK 8(17Q25.2) MUTATED	1	82	161
AMP PEAK 8(17Q25.2) WILD-TYPE	76	499	45

Figure S63. Get High-res Image Gene #8: 'amp_17q25.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_17q25.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S64. Gene #8: 'amp_17q25.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
AMP PEAK 8(17Q25.2) MUTATED	119	7	30	5
AMP PEAK 8(17Q25.2) WILD-TYPE	34	63	33	120

Figure S64. Get High-res Image Gene #8: 'amp_17q25.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_17q25.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S65. Gene #8: 'amp_17q25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
AMP PEAK 8(17Q25.2) MUTATED	44	68	43	5	1
AMP PEAK 8(17Q25.2) WILD-TYPE	6	21	51	127	45

Figure S65. Get High-res Image Gene #8: 'amp_17q25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S66. 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 S66. Get High-res Image Gene #9: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.2' versus 'METHLYATION_CNMF'

P value = 0.0414 (Fisher's exact test), Q value = 0.048

Table S67. 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 S67. Get High-res Image Gene #9: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00015

Table S68. Gene #9: 'amp_19p13.2' versus Molecular Subtype #5: '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 S68. Get High-res Image Gene #9: 'amp_19p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S69. Gene #9: 'amp_19p13.2' versus Molecular Subtype #6: '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 S69. Get High-res Image Gene #9: 'amp_19p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'MIRSEQ_CNMF'

P value = 0.00209 (Fisher's exact test), Q value = 0.0027

Table S70. Gene #9: 'amp_19p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
AMP PEAK 9(19P13.2) MUTATED	51	11	35
AMP PEAK 9(19P13.2) WILD-TYPE	277	181	309

Figure S70. Get High-res Image Gene #9: 'amp_19p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_19p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 8.9e-05

Table S71. Gene #9: 'amp_19p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
AMP PEAK 9(19P13.2) MUTATED	22	50	25
AMP PEAK 9(19P13.2) WILD-TYPE	55	531	181

Figure S71. Get High-res Image Gene #9: 'amp_19p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00092 (Fisher's exact test), Q value = 0.0012

Table S72. Gene #9: 'amp_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
AMP PEAK 9(19P13.2) MUTATED	8	7	6	11	14
AMP PEAK 9(19P13.2) WILD-TYPE	42	82	88	121	32

Figure S72. Get High-res Image Gene #9: 'amp_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xp22.2' versus 'MRNA_CNMF'

P value = 0.00188 (Fisher's exact test), Q value = 0.0025

Table S73. 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 S73. Get High-res Image Gene #10: 'amp_xp22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_xp22.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00206 (Fisher's exact test), Q value = 0.0027

Table S74. 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 S74. 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 = 1.6e-05

Table S75. 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 S75. 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 = 1.6e-05

Table S76. 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 S76. Get High-res Image Gene #10: 'amp_xp22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xp22.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S77. Gene #10: 'amp_xp22.2' versus Molecular Subtype #5: '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 S77. Get High-res Image Gene #10: 'amp_xp22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_xp22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S78. Gene #10: 'amp_xp22.2' versus Molecular Subtype #6: '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 S78. Get High-res Image Gene #10: 'amp_xp22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_xp22.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S79. Gene #10: 'amp_xp22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
AMP PEAK 10(XP22.2) MUTATED	94	10	22
AMP PEAK 10(XP22.2) WILD-TYPE	234	182	322

Figure S79. Get High-res Image Gene #10: 'amp_xp22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_xp22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S80. Gene #10: 'amp_xp22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
AMP PEAK 10(XP22.2) MUTATED	7	38	81
AMP PEAK 10(XP22.2) WILD-TYPE	70	543	125

Figure S80. Get High-res Image Gene #10: 'amp_xp22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_xp22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S81. Gene #10: 'amp_xp22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
AMP PEAK 10(XP22.2) MUTATED	54	9	4	5
AMP PEAK 10(XP22.2) WILD-TYPE	99	61	59	120

Figure S81. Get High-res Image Gene #10: 'amp_xp22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_xp22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S82. Gene #10: 'amp_xp22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
AMP PEAK 10(XP22.2) MUTATED	18	32	12	4	6
AMP PEAK 10(XP22.2) WILD-TYPE	32	57	82	128	40

Figure S82. Get High-res Image Gene #10: 'amp_xp22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xp11.4' versus 'MRNA_CNMF'

P value = 0.00151 (Fisher's exact test), Q value = 0.002

Table S83. 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 S83. Get High-res Image Gene #11: 'amp_xp11.4' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_xp11.4' versus 'MRNA_CHIERARCHICAL'

P value = 0.00448 (Fisher's exact test), Q value = 0.0057

Table S84. 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 S84. 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 = 1.6e-05

Table S85. 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 S85. 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 = 1.6e-05

Table S86. 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 S86. Get High-res Image Gene #11: 'amp_xp11.4' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xp11.4' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S87. Gene #11: 'amp_xp11.4' versus Molecular Subtype #5: '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 S87. Get High-res Image Gene #11: 'amp_xp11.4' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_xp11.4' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S88. Gene #11: 'amp_xp11.4' versus Molecular Subtype #6: '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 S88. Get High-res Image Gene #11: 'amp_xp11.4' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.4' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S89. Gene #11: 'amp_xp11.4' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
AMP PEAK 11(XP11.4) MUTATED	100	10	23
AMP PEAK 11(XP11.4) WILD-TYPE	228	182	321

Figure S89. Get High-res Image Gene #11: 'amp_xp11.4' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_xp11.4' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S90. Gene #11: 'amp_xp11.4' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
AMP PEAK 11(XP11.4) MUTATED	7	38	88
AMP PEAK 11(XP11.4) WILD-TYPE	70	543	118

Figure S90. Get High-res Image Gene #11: 'amp_xp11.4' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_xp11.4' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S91. Gene #11: 'amp_xp11.4' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
AMP PEAK 11(XP11.4) MUTATED	56	8	4	6
AMP PEAK 11(XP11.4) WILD-TYPE	97	62	59	119

Figure S91. Get High-res Image Gene #11: 'amp_xp11.4' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_xp11.4' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S92. Gene #11: 'amp_xp11.4' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
AMP PEAK 11(XP11.4) MUTATED	19	34	10	5	6
AMP PEAK 11(XP11.4) WILD-TYPE	31	55	84	127	40

Figure S92. Get High-res Image Gene #11: 'amp_xp11.4' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xq11.2' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4.6e-05

Table S93. 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 S93. Get High-res Image Gene #12: 'amp_xq11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_xq11.2' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S94. 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 S94. 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 = 1.6e-05

Table S95. 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 S95. 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 = 1.6e-05

Table S96. 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 S96. Get High-res Image Gene #12: 'amp_xq11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xq11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S97. Gene #12: 'amp_xq11.2' versus Molecular Subtype #5: '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 S97. Get High-res Image Gene #12: 'amp_xq11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_xq11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S98. Gene #12: 'amp_xq11.2' versus Molecular Subtype #6: '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 S98. Get High-res Image Gene #12: 'amp_xq11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_xq11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S99. Gene #12: 'amp_xq11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
AMP PEAK 12(XQ11.2) MUTATED	105	12	17
AMP PEAK 12(XQ11.2) WILD-TYPE	223	180	327

Figure S99. Get High-res Image Gene #12: 'amp_xq11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_xq11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S100. Gene #12: 'amp_xq11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
AMP PEAK 12(XQ11.2) MUTATED	7	34	93
AMP PEAK 12(XQ11.2) WILD-TYPE	70	547	113

Figure S100. Get High-res Image Gene #12: 'amp_xq11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_xq11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S101. Gene #12: 'amp_xq11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
AMP PEAK 12(XQ11.2) MUTATED	59	9	3	5
AMP PEAK 12(XQ11.2) WILD-TYPE	94	61	60	120

Figure S101. Get High-res Image Gene #12: 'amp_xq11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_xq11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S102. Gene #12: 'amp_xq11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
AMP PEAK 12(XQ11.2) MUTATED	19	35	11	5	6
AMP PEAK 12(XQ11.2) WILD-TYPE	31	54	83	127	40

Figure S102. Get High-res Image Gene #12: 'amp_xq11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xq28' versus 'MRNA_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 2e-04

Table S103. 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 S103. Get High-res Image Gene #13: 'amp_xq28' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_xq28' versus 'MRNA_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.00064

Table S104. 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 S104. 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 = 1.6e-05

Table S105. 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 S105. 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 = 1.6e-05

Table S106. 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 S106. Get High-res Image Gene #13: 'amp_xq28' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xq28' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S107. Gene #13: 'amp_xq28' versus Molecular Subtype #5: '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 S107. Get High-res Image Gene #13: 'amp_xq28' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_xq28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S108. Gene #13: 'amp_xq28' versus Molecular Subtype #6: '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 S108. Get High-res Image Gene #13: 'amp_xq28' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S109. Gene #13: 'amp_xq28' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
AMP PEAK 13(XQ28) MUTATED	97	17	22
AMP PEAK 13(XQ28) WILD-TYPE	231	175	322

Figure S109. Get High-res Image Gene #13: 'amp_xq28' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_xq28' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S110. Gene #13: 'amp_xq28' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
AMP PEAK 13(XQ28) MUTATED	8	47	81
AMP PEAK 13(XQ28) WILD-TYPE	69	534	125

Figure S110. Get High-res Image Gene #13: 'amp_xq28' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S111. Gene #13: 'amp_xq28' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
AMP PEAK 13(XQ28) MUTATED	52	10	5	10
AMP PEAK 13(XQ28) WILD-TYPE	101	60	58	115

Figure S111. Get High-res Image Gene #13: 'amp_xq28' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_xq28' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S112. Gene #13: 'amp_xq28' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
AMP PEAK 13(XQ28) MUTATED	20	28	13	10	6
AMP PEAK 13(XQ28) WILD-TYPE	30	61	81	122	40

Figure S112. Get High-res Image Gene #13: 'amp_xq28' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.31' versus 'MRNA_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.00056

Table S113. 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 S113. Get High-res Image Gene #14: 'del_1p36.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.31' versus 'MRNA_CHIERARCHICAL'

P value = 0.00357 (Fisher's exact test), Q value = 0.0045

Table S114. 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 S114. 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 = 1.6e-05

Table S115. 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 S115. 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 = 1.6e-05

Table S116. 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 S116. Get High-res Image Gene #14: 'del_1p36.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S117. Gene #14: 'del_1p36.31' versus Molecular Subtype #5: '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 S117. Get High-res Image Gene #14: 'del_1p36.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p36.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S118. Gene #14: 'del_1p36.31' versus Molecular Subtype #6: '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 S118. Get High-res Image Gene #14: 'del_1p36.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S119. Gene #14: 'del_1p36.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
DEL PEAK 1(1P36.31) MUTATED	106	47	56
DEL PEAK 1(1P36.31) WILD-TYPE	222	145	288

Figure S119. Get High-res Image Gene #14: 'del_1p36.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p36.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S120. Gene #14: 'del_1p36.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
DEL PEAK 1(1P36.31) MUTATED	68	113	28
DEL PEAK 1(1P36.31) WILD-TYPE	9	468	178

Figure S120. Get High-res Image Gene #14: 'del_1p36.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S121. Gene #14: 'del_1p36.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
DEL PEAK 1(1P36.31) MUTATED	19	43	17	20
DEL PEAK 1(1P36.31) WILD-TYPE	134	27	46	105

Figure S121. Get High-res Image Gene #14: 'del_1p36.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p36.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S122. Gene #14: 'del_1p36.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
DEL PEAK 1(1P36.31) MUTATED	3	13	25	19	39
DEL PEAK 1(1P36.31) WILD-TYPE	47	76	69	113	7

Figure S122. Get High-res Image Gene #14: 'del_1p36.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p31.1' versus 'MRNA_CNMF'

P value = 0.00169 (Fisher's exact test), Q value = 0.0022

Table S123. 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 S123. Get High-res Image Gene #15: 'del_1p31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p31.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.018 (Fisher's exact test), Q value = 0.021

Table S124. 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 S124. 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 = 1.6e-05

Table S125. 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 S125. 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 = 1.6e-05

Table S126. 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 S126. Get High-res Image Gene #15: 'del_1p31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p31.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S127. Gene #15: 'del_1p31.1' versus Molecular Subtype #5: '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 S127. Get High-res Image Gene #15: 'del_1p31.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S128. Gene #15: 'del_1p31.1' versus Molecular Subtype #6: '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 S128. Get High-res Image Gene #15: 'del_1p31.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p31.1' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S129. Gene #15: 'del_1p31.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
DEL PEAK 2(1P31.1) MUTATED	91	29	46
DEL PEAK 2(1P31.1) WILD-TYPE	237	163	298

Figure S129. Get High-res Image Gene #15: 'del_1p31.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S130. Gene #15: 'del_1p31.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
DEL PEAK 2(1P31.1) MUTATED	68	77	21
DEL PEAK 2(1P31.1) WILD-TYPE	9	504	185

Figure S130. Get High-res Image Gene #15: 'del_1p31.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p31.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S131. Gene #15: 'del_1p31.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
DEL PEAK 2(1P31.1) MUTATED	13	41	12	13
DEL PEAK 2(1P31.1) WILD-TYPE	140	29	51	112

Figure S131. Get High-res Image Gene #15: 'del_1p31.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S132. Gene #15: 'del_1p31.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
DEL PEAK 2(1P31.1) MUTATED	2	10	17	11	39
DEL PEAK 2(1P31.1) WILD-TYPE	48	79	77	121	7

Figure S132. Get High-res Image Gene #15: 'del_1p31.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1q43' versus 'MRNA_CNMF'

P value = 0.00865 (Fisher's exact test), Q value = 0.011

Table S133. 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 S133. Get High-res Image Gene #16: 'del_1q43' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1q43' versus 'MRNA_CHIERARCHICAL'

P value = 0.0079 (Fisher's exact test), Q value = 0.0098

Table S134. 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 S134. 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 = 1.6e-05

Table S135. 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 S135. 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 = 1.6e-05

Table S136. 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 S136. Get High-res Image Gene #16: 'del_1q43' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1q43' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S137. Gene #16: 'del_1q43' versus Molecular Subtype #5: '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 S137. Get High-res Image Gene #16: 'del_1q43' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1q43' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S138. Gene #16: 'del_1q43' versus Molecular Subtype #6: '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 S138. Get High-res Image Gene #16: 'del_1q43' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1q43' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S139. Gene #16: 'del_1q43' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
DEL PEAK 3(1Q43) MUTATED	74	16	24
DEL PEAK 3(1Q43) WILD-TYPE	254	176	320

Figure S139. Get High-res Image Gene #16: 'del_1q43' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1q43' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S140. Gene #16: 'del_1q43' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
DEL PEAK 3(1Q43) MUTATED	64	34	16
DEL PEAK 3(1Q43) WILD-TYPE	13	547	190

Figure S140. Get High-res Image Gene #16: 'del_1q43' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1q43' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S141. Gene #16: 'del_1q43' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
DEL PEAK 3(1Q43) MUTATED	9	38	7	9
DEL PEAK 3(1Q43) WILD-TYPE	144	32	56	116

Figure S141. Get High-res Image Gene #16: 'del_1q43' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1q43' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S142. Gene #16: 'del_1q43' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
DEL PEAK 3(1Q43) MUTATED	3	6	6	10	38
DEL PEAK 3(1Q43) WILD-TYPE	47	83	88	122	8

Figure S142. Get High-res Image Gene #16: 'del_1q43' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q37.3' versus 'MRNA_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00019

Table S143. 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 S143. Get High-res Image Gene #17: 'del_2q37.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_2q37.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00026

Table S144. 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 S144. 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 = 4.6e-05

Table S145. 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 S145. 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 = 1.6e-05

Table S146. 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 S146. Get High-res Image Gene #17: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S147. Gene #17: 'del_2q37.3' versus Molecular Subtype #5: '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 S147. Get High-res Image Gene #17: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S148. Gene #17: 'del_2q37.3' versus Molecular Subtype #6: '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 S148. Get High-res Image Gene #17: 'del_2q37.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S149. Gene #17: 'del_2q37.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
DEL PEAK 4(2Q37.3) MUTATED	66	17	26
DEL PEAK 4(2Q37.3) WILD-TYPE	262	175	318

Figure S149. Get High-res Image Gene #17: 'del_2q37.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S150. Gene #17: 'del_2q37.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
DEL PEAK 4(2Q37.3) MUTATED	59	44	6
DEL PEAK 4(2Q37.3) WILD-TYPE	18	537	200

Figure S150. Get High-res Image Gene #17: 'del_2q37.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S151. Gene #17: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
DEL PEAK 4(2Q37.3) MUTATED	6	37	6	8
DEL PEAK 4(2Q37.3) WILD-TYPE	147	33	57	117

Figure S151. Get High-res Image Gene #17: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_2q37.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S152. Gene #17: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
DEL PEAK 4(2Q37.3) MUTATED	0	6	7	8	36
DEL PEAK 4(2Q37.3) WILD-TYPE	50	83	87	124	10

Figure S152. Get High-res Image Gene #17: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p26.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S153. 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 S153. 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 = 1.6e-05

Table S154. 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 S154. 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 = 1.6e-05

Table S155. 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 S155. 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 = 1.6e-05

Table S156. 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 S156. Get High-res Image Gene #18: 'del_3p26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p26.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S157. Gene #18: 'del_3p26.3' versus Molecular Subtype #5: '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 S157. Get High-res Image Gene #18: 'del_3p26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S158. Gene #18: 'del_3p26.3' versus Molecular Subtype #6: '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 S158. Get High-res Image Gene #18: 'del_3p26.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S159. Gene #18: 'del_3p26.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
DEL PEAK 5(3P26.3) MUTATED	32	120	320
DEL PEAK 5(3P26.3) WILD-TYPE	296	72	24

Figure S159. Get High-res Image Gene #18: 'del_3p26.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S160. Gene #18: 'del_3p26.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
DEL PEAK 5(3P26.3) MUTATED	10	452	10
DEL PEAK 5(3P26.3) WILD-TYPE	67	129	196

Figure S160. Get High-res Image Gene #18: 'del_3p26.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S161. Gene #18: 'del_3p26.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
DEL PEAK 5(3P26.3) MUTATED	8	8	17	113
DEL PEAK 5(3P26.3) WILD-TYPE	145	62	46	12

Figure S161. Get High-res Image Gene #18: 'del_3p26.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S162. Gene #18: 'del_3p26.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
DEL PEAK 5(3P26.3) MUTATED	1	5	17	117	6
DEL PEAK 5(3P26.3) WILD-TYPE	49	84	77	15	40

Figure S162. Get High-res Image Gene #18: 'del_3p26.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p21.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S163. 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 S163. 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 = 1.6e-05

Table S164. 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 S164. 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 = 1.6e-05

Table S165. 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 S165. 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 = 1.6e-05

Table S166. 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 S166. Get High-res Image Gene #19: 'del_3p21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S167. Gene #19: 'del_3p21.2' versus Molecular Subtype #5: '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 S167. Get High-res Image Gene #19: 'del_3p21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S168. Gene #19: 'del_3p21.2' versus Molecular Subtype #6: '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 S168. Get High-res Image Gene #19: 'del_3p21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S169. Gene #19: 'del_3p21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
DEL PEAK 6(3P21.2) MUTATED	36	121	329
DEL PEAK 6(3P21.2) WILD-TYPE	292	71	15

Figure S169. Get High-res Image Gene #19: 'del_3p21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S170. Gene #19: 'del_3p21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
DEL PEAK 6(3P21.2) MUTATED	12	465	9
DEL PEAK 6(3P21.2) WILD-TYPE	65	116	197

Figure S170. Get High-res Image Gene #19: 'del_3p21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S171. Gene #19: 'del_3p21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
DEL PEAK 6(3P21.2) MUTATED	9	9	18	115
DEL PEAK 6(3P21.2) WILD-TYPE	144	61	45	10

Figure S171. Get High-res Image Gene #19: 'del_3p21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S172. Gene #19: 'del_3p21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
DEL PEAK 6(3P21.2) MUTATED	0	6	20	118	7
DEL PEAK 6(3P21.2) WILD-TYPE	50	83	74	14	39

Figure S172. Get High-res Image Gene #19: 'del_3p21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p14.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S173. 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 S173. 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 = 1.6e-05

Table S174. 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 S174. 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 = 1.6e-05

Table S175. 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 S175. 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 = 1.6e-05

Table S176. 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 S176. Get High-res Image Gene #20: 'del_3p14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S177. Gene #20: 'del_3p14.1' versus Molecular Subtype #5: '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 S177. Get High-res Image Gene #20: 'del_3p14.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S178. Gene #20: 'del_3p14.1' versus Molecular Subtype #6: '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 S178. Get High-res Image Gene #20: 'del_3p14.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S179. Gene #20: 'del_3p14.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
DEL PEAK 7(3P14.1) MUTATED	31	98	266
DEL PEAK 7(3P14.1) WILD-TYPE	297	94	78

Figure S179. Get High-res Image Gene #20: 'del_3p14.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S180. Gene #20: 'del_3p14.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
DEL PEAK 7(3P14.1) MUTATED	11	376	8
DEL PEAK 7(3P14.1) WILD-TYPE	66	205	198

Figure S180. Get High-res Image Gene #20: 'del_3p14.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S181. Gene #20: 'del_3p14.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
DEL PEAK 7(3P14.1) MUTATED	9	8	16	89
DEL PEAK 7(3P14.1) WILD-TYPE	144	62	47	36

Figure S181. Get High-res Image Gene #20: 'del_3p14.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S182. Gene #20: 'del_3p14.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
DEL PEAK 7(3P14.1) MUTATED	0	6	16	93	7
DEL PEAK 7(3P14.1) WILD-TYPE	50	83	78	39	39

Figure S182. Get High-res Image Gene #20: 'del_3p14.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p12.2' versus 'MRNA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 8.9e-05

Table S183. 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 S183. Get High-res Image Gene #21: 'del_3p12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p12.2' versus 'MRNA_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00028

Table S184. 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 S184. 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 = 1.6e-05

Table S185. 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 S185. 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 = 1.6e-05

Table S186. 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 S186. Get High-res Image Gene #21: 'del_3p12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p12.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S187. Gene #21: 'del_3p12.2' versus Molecular Subtype #5: '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 S187. Get High-res Image Gene #21: 'del_3p12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S188. Gene #21: 'del_3p12.2' versus Molecular Subtype #6: '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 S188. Get High-res Image Gene #21: 'del_3p12.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p12.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S189. Gene #21: 'del_3p12.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
DEL PEAK 8(3P12.2) MUTATED	27	78	220
DEL PEAK 8(3P12.2) WILD-TYPE	301	114	124

Figure S189. Get High-res Image Gene #21: 'del_3p12.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S190. Gene #21: 'del_3p12.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
DEL PEAK 8(3P12.2) MUTATED	11	306	8
DEL PEAK 8(3P12.2) WILD-TYPE	66	275	198

Figure S190. Get High-res Image Gene #21: 'del_3p12.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p12.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S191. Gene #21: 'del_3p12.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
DEL PEAK 8(3P12.2) MUTATED	8	7	12	78
DEL PEAK 8(3P12.2) WILD-TYPE	145	63	51	47

Figure S191. Get High-res Image Gene #21: 'del_3p12.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S192. Gene #21: 'del_3p12.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
DEL PEAK 8(3P12.2) MUTATED	0	6	14	78	7
DEL PEAK 8(3P12.2) WILD-TYPE	50	83	80	54	39

Figure S192. Get High-res Image Gene #21: 'del_3p12.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S193. 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 S193. Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 0.00086 (Fisher's exact test), Q value = 0.0012

Table S194. 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 S194. Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S195. Gene #22: 'del_4q34.3' versus Molecular Subtype #5: '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 S195. Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S196. Gene #22: 'del_4q34.3' versus Molecular Subtype #6: '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 S196. Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CNMF'

P value = 0.00486 (Fisher's exact test), Q value = 0.0061

Table S197. Gene #22: 'del_4q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
DEL PEAK 9(4Q34.3) MUTATED	30	37	45
DEL PEAK 9(4Q34.3) WILD-TYPE	298	155	299

Figure S197. Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S198. Gene #22: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
DEL PEAK 9(4Q34.3) MUTATED	2	98	12
DEL PEAK 9(4Q34.3) WILD-TYPE	75	483	194

Figure S198. Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00023

Table S199. Gene #22: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
DEL PEAK 9(4Q34.3) MUTATED	10	5	18	18
DEL PEAK 9(4Q34.3) WILD-TYPE	143	65	45	107

Figure S199. Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S200. Gene #22: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
DEL PEAK 9(4Q34.3) MUTATED	0	7	23	19	2
DEL PEAK 9(4Q34.3) WILD-TYPE	50	82	71	113	44

Figure S200. Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5p15.33' versus 'CN_CNMF'

P value = 0.00324 (Fisher's exact test), Q value = 0.0041

Table S201. 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 S201. 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 = 1.6e-05

Table S202. 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 S202. Get High-res Image Gene #23: 'del_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5p15.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S203. Gene #23: 'del_5p15.33' versus Molecular Subtype #5: '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 S203. Get High-res Image Gene #23: 'del_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S204. Gene #23: 'del_5p15.33' versus Molecular Subtype #6: '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 S204. Get High-res Image Gene #23: 'del_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5p15.33' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 6e-05

Table S205. Gene #23: 'del_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
DEL PEAK 10(5P15.33) MUTATED	21	8	2
DEL PEAK 10(5P15.33) WILD-TYPE	307	184	342

Figure S205. Get High-res Image Gene #23: 'del_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 8.9e-05

Table S206. Gene #23: 'del_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
DEL PEAK 10(5P15.33) MUTATED	11	14	6
DEL PEAK 10(5P15.33) WILD-TYPE	66	567	200

Figure S206. Get High-res Image Gene #23: 'del_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00086 (Fisher's exact test), Q value = 0.0012

Table S207. Gene #23: 'del_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
DEL PEAK 10(5P15.33) MUTATED	6	10	3	1
DEL PEAK 10(5P15.33) WILD-TYPE	147	60	60	124

Figure S207. Get High-res Image Gene #23: 'del_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.00039

Table S208. Gene #23: 'del_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
DEL PEAK 10(5P15.33) MUTATED	1	3	7	1	8
DEL PEAK 10(5P15.33) WILD-TYPE	49	86	87	131	38

Figure S208. Get High-res Image Gene #23: 'del_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q22.31' versus 'MRNA_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.00047

Table S209. 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 S209. Get High-res Image Gene #24: 'del_6q22.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_6q22.31' versus 'MRNA_CHIERARCHICAL'

P value = 0.00672 (Fisher's exact test), Q value = 0.0084

Table S210. 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 S210. 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 = 1.6e-05

Table S211. 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 S211. 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 = 1.6e-05

Table S212. 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 S212. Get High-res Image Gene #24: 'del_6q22.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q22.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S213. Gene #24: 'del_6q22.31' versus Molecular Subtype #5: '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 S213. Get High-res Image Gene #24: 'del_6q22.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q22.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S214. Gene #24: 'del_6q22.31' versus Molecular Subtype #6: '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 S214. Get High-res Image Gene #24: 'del_6q22.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q22.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S215. Gene #24: 'del_6q22.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
DEL PEAK 11(6Q22.31) MUTATED	61	142	19
DEL PEAK 11(6Q22.31) WILD-TYPE	16	439	187

Figure S215. Get High-res Image Gene #24: 'del_6q22.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q22.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S216. Gene #24: 'del_6q22.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
DEL PEAK 11(6Q22.31) MUTATED	10	39	15	27
DEL PEAK 11(6Q22.31) WILD-TYPE	143	31	48	98

Figure S216. Get High-res Image Gene #24: 'del_6q22.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6q22.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S217. Gene #24: 'del_6q22.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
DEL PEAK 11(6Q22.31) MUTATED	2	7	17	28	37
DEL PEAK 11(6Q22.31) WILD-TYPE	48	82	77	104	9

Figure S217. Get High-res Image Gene #24: 'del_6q22.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q26' versus 'MRNA_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.00071

Table S218. 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 S218. Get High-res Image Gene #25: 'del_6q26' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_6q26' versus 'MRNA_CHIERARCHICAL'

P value = 0.00796 (Fisher's exact test), Q value = 0.0098

Table S219. 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 S219. 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 = 1.6e-05

Table S220. 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 S220. 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 = 1.6e-05

Table S221. 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 S221. Get High-res Image Gene #25: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S222. Gene #25: 'del_6q26' versus Molecular Subtype #5: '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 S222. Get High-res Image Gene #25: 'del_6q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S223. Gene #25: 'del_6q26' versus Molecular Subtype #6: '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 S223. Get High-res Image Gene #25: 'del_6q26' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S224. Gene #25: 'del_6q26' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
DEL PEAK 12(6Q26) MUTATED	61	148	20
DEL PEAK 12(6Q26) WILD-TYPE	16	433	186

Figure S224. Get High-res Image Gene #25: 'del_6q26' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S225. Gene #25: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
DEL PEAK 12(6Q26) MUTATED	12	39	14	30
DEL PEAK 12(6Q26) WILD-TYPE	141	31	49	95

Figure S225. Get High-res Image Gene #25: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S226. Gene #25: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
DEL PEAK 12(6Q26) MUTATED	2	9	16	31	37
DEL PEAK 12(6Q26) WILD-TYPE	48	80	78	101	9

Figure S226. Get High-res Image Gene #25: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q26' versus 'MRNA_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 7e-04

Table S227. 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 S227. Get High-res Image Gene #26: 'del_6q26' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_6q26' versus 'MRNA_CHIERARCHICAL'

P value = 0.00759 (Fisher's exact test), Q value = 0.0095

Table S228. 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 S228. 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 = 1.6e-05

Table S229. 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 S229. 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 = 1.6e-05

Table S230. 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 S230. Get High-res Image Gene #26: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S231. Gene #26: 'del_6q26' versus Molecular Subtype #5: '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 S231. Get High-res Image Gene #26: 'del_6q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S232. Gene #26: 'del_6q26' versus Molecular Subtype #6: '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 S232. Get High-res Image Gene #26: 'del_6q26' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S233. Gene #26: 'del_6q26' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
DEL PEAK 13(6Q26) MUTATED	61	148	21
DEL PEAK 13(6Q26) WILD-TYPE	16	433	185

Figure S233. Get High-res Image Gene #26: 'del_6q26' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S234. Gene #26: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
DEL PEAK 13(6Q26) MUTATED	12	39	14	30
DEL PEAK 13(6Q26) WILD-TYPE	141	31	49	95

Figure S234. Get High-res Image Gene #26: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S235. Gene #26: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
DEL PEAK 13(6Q26) MUTATED	2	9	16	31	37
DEL PEAK 13(6Q26) WILD-TYPE	48	80	78	101	9

Figure S235. Get High-res Image Gene #26: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S236. 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 S236. 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 = 1.6e-05

Table S237. 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 S237. Get High-res Image Gene #27: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S238. Gene #27: 'del_8p23.2' versus Molecular Subtype #5: '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 S238. Get High-res Image Gene #27: 'del_8p23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S239. Gene #27: 'del_8p23.2' versus Molecular Subtype #6: '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 S239. Get High-res Image Gene #27: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S240. Gene #27: 'del_8p23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
DEL PEAK 14(8P23.2) MUTATED	31	53	97
DEL PEAK 14(8P23.2) WILD-TYPE	297	139	247

Figure S240. Get High-res Image Gene #27: 'del_8p23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S241. Gene #27: 'del_8p23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
DEL PEAK 14(8P23.2) MUTATED	16	158	7
DEL PEAK 14(8P23.2) WILD-TYPE	61	423	199

Figure S241. Get High-res Image Gene #27: 'del_8p23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S242. Gene #27: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
DEL PEAK 14(8P23.2) MUTATED	7	9	8	36
DEL PEAK 14(8P23.2) WILD-TYPE	146	61	55	89

Figure S242. Get High-res Image Gene #27: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S243. Gene #27: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
DEL PEAK 14(8P23.2) MUTATED	1	4	10	38	7
DEL PEAK 14(8P23.2) WILD-TYPE	49	85	84	94	39

Figure S243. Get High-res Image Gene #27: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'MRNA_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.013

Table S244. 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 S244. 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 = 0.026

Table S245. 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 S245. 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 = 1.6e-05

Table S246. 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 S246. 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 = 1.6e-05

Table S247. 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 S247. Get High-res Image Gene #28: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S248. Gene #28: 'del_9p23' versus Molecular Subtype #5: '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 S248. Get High-res Image Gene #28: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S249. Gene #28: 'del_9p23' versus Molecular Subtype #6: '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 S249. Get High-res Image Gene #28: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S250. Gene #28: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
DEL PEAK 15(9P23) MUTATED	38	65	90
DEL PEAK 15(9P23) WILD-TYPE	290	127	254

Figure S250. Get High-res Image Gene #28: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S251. Gene #28: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
DEL PEAK 15(9P23) MUTATED	10	167	16
DEL PEAK 15(9P23) WILD-TYPE	67	414	190

Figure S251. Get High-res Image Gene #28: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 6e-05

Table S252. Gene #28: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
DEL PEAK 15(9P23) MUTATED	12	12	21	27
DEL PEAK 15(9P23) WILD-TYPE	141	58	42	98

Figure S252. Get High-res Image Gene #28: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.00035

Table S253. Gene #28: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
DEL PEAK 15(9P23) MUTATED	2	8	26	30	6
DEL PEAK 15(9P23) WILD-TYPE	48	81	68	102	40

Figure S253. Get High-res Image Gene #28: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.3' versus 'MRNA_CNMF'

P value = 0.00348 (Fisher's exact test), Q value = 0.0044

Table S254. 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 S254. Get High-res Image Gene #29: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p21.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00761 (Fisher's exact test), Q value = 0.0095

Table S255. 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 S255. 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 = 1.6e-05

Table S256. 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 S256. 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 = 1.6e-05

Table S257. 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 S257. Get High-res Image Gene #29: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S258. Gene #29: 'del_9p21.3' versus Molecular Subtype #5: '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 S258. Get High-res Image Gene #29: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S259. Gene #29: 'del_9p21.3' versus Molecular Subtype #6: '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 S259. Get High-res Image Gene #29: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S260. Gene #29: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
DEL PEAK 16(9P21.3) MUTATED	40	74	89
DEL PEAK 16(9P21.3) WILD-TYPE	288	118	255

Figure S260. Get High-res Image Gene #29: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S261. Gene #29: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
DEL PEAK 16(9P21.3) MUTATED	10	176	17
DEL PEAK 16(9P21.3) WILD-TYPE	67	405	189

Figure S261. Get High-res Image Gene #29: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S262. Gene #29: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
DEL PEAK 16(9P21.3) MUTATED	11	12	24	29
DEL PEAK 16(9P21.3) WILD-TYPE	142	58	39	96

Figure S262. Get High-res Image Gene #29: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 6e-05

Table S263. Gene #29: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
DEL PEAK 16(9P21.3) MUTATED	2	7	29	32	6
DEL PEAK 16(9P21.3) WILD-TYPE	48	82	65	100	40

Figure S263. Get High-res Image Gene #29: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S264. 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 S264. 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 = 1.6e-05

Table S265. 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 S265. Get High-res Image Gene #30: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S266. Gene #30: 'del_10q23.31' versus Molecular Subtype #5: '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 S266. Get High-res Image Gene #30: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S267. Gene #30: 'del_10q23.31' versus Molecular Subtype #6: '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 S267. Get High-res Image Gene #30: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S268. Gene #30: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
DEL PEAK 17(10Q23.31) MUTATED	59	97	6
DEL PEAK 17(10Q23.31) WILD-TYPE	18	484	200

Figure S268. Get High-res Image Gene #30: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S269. Gene #30: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
DEL PEAK 17(10Q23.31) MUTATED	3	39	11	17
DEL PEAK 17(10Q23.31) WILD-TYPE	150	31	52	108

Figure S269. Get High-res Image Gene #30: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S270. Gene #30: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
DEL PEAK 17(10Q23.31) MUTATED	1	1	17	16	35
DEL PEAK 17(10Q23.31) WILD-TYPE	49	88	77	116	11

Figure S270. Get High-res Image Gene #30: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q21' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S271. 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 S271. Get High-res Image Gene #31: 'del_11q21' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q21' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4.6e-05

Table S272. Gene #31: 'del_11q21' versus Molecular Subtype #5: '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 S272. Get High-res Image Gene #31: 'del_11q21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S273. Gene #31: 'del_11q21' versus Molecular Subtype #6: '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 S273. Get High-res Image Gene #31: 'del_11q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q21' versus 'MIRSEQ_CNMF'

P value = 0.0343 (Fisher's exact test), Q value = 0.04

Table S274. Gene #31: 'del_11q21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
DEL PEAK 18(11Q21) MUTATED	29	17	15
DEL PEAK 18(11Q21) WILD-TYPE	299	175	329

Figure S274. Get High-res Image Gene #31: 'del_11q21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11q21' versus 'MIRSEQ_MATURE_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00013

Table S275. Gene #31: 'del_11q21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
DEL PEAK 18(11Q21) MUTATED	9	9	13	3
DEL PEAK 18(11Q21) WILD-TYPE	144	61	50	122

Figure S275. Get High-res Image Gene #31: 'del_11q21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S276. Gene #31: 'del_11q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
DEL PEAK 18(11Q21) MUTATED	1	6	17	2	8
DEL PEAK 18(11Q21) WILD-TYPE	49	83	77	130	38

Figure S276. Get High-res Image Gene #31: 'del_11q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q23.1' versus 'MRNA_CNMF'

P value = 0.0395 (Fisher's exact test), Q value = 0.046

Table S277. 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 S277. 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 = 1.6e-05

Table S278. 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 S278. Get High-res Image Gene #32: 'del_11q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S279. Gene #32: 'del_11q23.1' versus Molecular Subtype #5: '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 S279. Get High-res Image Gene #32: 'del_11q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S280. Gene #32: 'del_11q23.1' versus Molecular Subtype #6: '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 S280. Get High-res Image Gene #32: 'del_11q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.1' versus 'MIRSEQ_CNMF'

P value = 0.00998 (Fisher's exact test), Q value = 0.012

Table S281. Gene #32: 'del_11q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
DEL PEAK 19(11Q23.1) MUTATED	32	22	17
DEL PEAK 19(11Q23.1) WILD-TYPE	296	170	327

Figure S281. Get High-res Image Gene #32: 'del_11q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S282. Gene #32: 'del_11q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
DEL PEAK 19(11Q23.1) MUTATED	9	8	17	4
DEL PEAK 19(11Q23.1) WILD-TYPE	144	62	46	121

Figure S282. Get High-res Image Gene #32: 'del_11q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S283. Gene #32: 'del_11q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
DEL PEAK 19(11Q23.1) MUTATED	1	6	21	3	7
DEL PEAK 19(11Q23.1) WILD-TYPE	49	83	73	129	39

Figure S283. Get High-res Image Gene #32: 'del_11q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q12.13' versus 'MRNA_CNMF'

P value = 0.0279 (Fisher's exact test), Q value = 0.033

Table S284. 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 S284. Get High-res Image Gene #33: 'del_13q12.13' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q12.13' versus 'MRNA_CHIERARCHICAL'

P value = 0.0373 (Fisher's exact test), Q value = 0.043

Table S285. 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 S285. 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 = 1.6e-05

Table S286. 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 S286. 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 = 1.6e-05

Table S287. 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 S287. Get High-res Image Gene #33: 'del_13q12.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q12.13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S288. Gene #33: 'del_13q12.13' versus Molecular Subtype #5: '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 S288. Get High-res Image Gene #33: 'del_13q12.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q12.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S289. Gene #33: 'del_13q12.13' versus Molecular Subtype #6: '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 S289. Get High-res Image Gene #33: 'del_13q12.13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q12.13' versus 'MIRSEQ_CNMF'

P value = 0.00075 (Fisher's exact test), Q value = 0.001

Table S290. Gene #33: 'del_13q12.13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
DEL PEAK 20(13Q12.13) MUTATED	67	42	39
DEL PEAK 20(13Q12.13) WILD-TYPE	261	150	305

Figure S290. Get High-res Image Gene #33: 'del_13q12.13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_13q12.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S291. Gene #33: 'del_13q12.13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
DEL PEAK 20(13Q12.13) MUTATED	51	87	10
DEL PEAK 20(13Q12.13) WILD-TYPE	26	494	196

Figure S291. Get High-res Image Gene #33: 'del_13q12.13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q12.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S292. Gene #33: 'del_13q12.13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
DEL PEAK 20(13Q12.13) MUTATED	7	33	19	13
DEL PEAK 20(13Q12.13) WILD-TYPE	146	37	44	112

Figure S292. Get High-res Image Gene #33: 'del_13q12.13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_13q12.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S293. Gene #33: 'del_13q12.13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
DEL PEAK 20(13Q12.13) MUTATED	1	3	22	15	31
DEL PEAK 20(13Q12.13) WILD-TYPE	49	86	72	117	15

Figure S293. Get High-res Image Gene #33: 'del_13q12.13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q14.2' versus 'MRNA_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.015

Table S294. 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 S294. Get High-res Image Gene #34: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q14.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0172 (Fisher's exact test), Q value = 0.021

Table S295. 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 S295. 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 = 1.6e-05

Table S296. 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 S296. 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 = 1.6e-05

Table S297. 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 S297. Get High-res Image Gene #34: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S298. Gene #34: 'del_13q14.2' versus Molecular Subtype #5: '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 S298. Get High-res Image Gene #34: 'del_13q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S299. Gene #34: 'del_13q14.2' versus Molecular Subtype #6: '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 S299. Get High-res Image Gene #34: 'del_13q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 0.00211 (Fisher's exact test), Q value = 0.0027

Table S300. Gene #34: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
DEL PEAK 21(13Q14.2) MUTATED	66	41	40
DEL PEAK 21(13Q14.2) WILD-TYPE	262	151	304

Figure S300. Get High-res Image Gene #34: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S301. Gene #34: 'del_13q14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
DEL PEAK 21(13Q14.2) MUTATED	50	86	11
DEL PEAK 21(13Q14.2) WILD-TYPE	27	495	195

Figure S301. Get High-res Image Gene #34: 'del_13q14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S302. Gene #34: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
DEL PEAK 21(13Q14.2) MUTATED	6	33	18	12
DEL PEAK 21(13Q14.2) WILD-TYPE	147	37	45	113

Figure S302. Get High-res Image Gene #34: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S303. Gene #34: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
DEL PEAK 21(13Q14.2) MUTATED	1	3	20	14	31
DEL PEAK 21(13Q14.2) WILD-TYPE	49	86	74	118	15

Figure S303. Get High-res Image Gene #34: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q31.1' versus 'MRNA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 1e-04

Table S304. 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 S304. Get High-res Image Gene #35: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q31.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00019

Table S305. 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 S305. 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 = 1.6e-05

Table S306. 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 S306. 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 = 1.6e-05

Table S307. 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 S307. Get High-res Image Gene #35: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q31.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S308. Gene #35: 'del_14q31.1' versus Molecular Subtype #5: '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 S308. Get High-res Image Gene #35: 'del_14q31.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S309. Gene #35: 'del_14q31.1' versus Molecular Subtype #6: '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 S309. Get High-res Image Gene #35: 'del_14q31.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q31.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S310. Gene #35: 'del_14q31.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
DEL PEAK 22(14Q31.1) MUTATED	43	78	152
DEL PEAK 22(14Q31.1) WILD-TYPE	285	114	192

Figure S310. Get High-res Image Gene #35: 'del_14q31.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_14q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S311. Gene #35: 'del_14q31.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
DEL PEAK 22(14Q31.1) MUTATED	4	248	21
DEL PEAK 22(14Q31.1) WILD-TYPE	73	333	185

Figure S311. Get High-res Image Gene #35: 'del_14q31.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_14q31.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S312. Gene #35: 'del_14q31.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
DEL PEAK 22(14Q31.1) MUTATED	15	5	23	50
DEL PEAK 22(14Q31.1) WILD-TYPE	138	65	40	75

Figure S312. Get High-res Image Gene #35: 'del_14q31.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_14q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S313. Gene #35: 'del_14q31.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
DEL PEAK 22(14Q31.1) MUTATED	5	8	23	55	2
DEL PEAK 22(14Q31.1) WILD-TYPE	45	81	71	77	44

Figure S313. Get High-res Image Gene #35: 'del_14q31.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.3' versus 'CN_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.02

Table S314. 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 S314. Get High-res Image Gene #36: 'del_16q23.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_16q23.3' versus 'METHLYATION_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.013

Table S315. 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 S315. Get High-res Image Gene #36: 'del_16q23.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16q23.3' versus 'MRNASEQ_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 0.029

Table S316. Gene #36: 'del_16q23.3' versus Molecular Subtype #5: '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 S316. Get High-res Image Gene #36: 'del_16q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 6e-05

Table S317. Gene #36: 'del_16q23.3' versus Molecular Subtype #6: '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 S317. Get High-res Image Gene #36: 'del_16q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0449 (Fisher's exact test), Q value = 0.051

Table S318. Gene #36: 'del_16q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
DEL PEAK 23(16Q23.3) MUTATED	0	3	10	6	4
DEL PEAK 23(16Q23.3) WILD-TYPE	50	86	84	126	42

Figure S318. Get High-res Image Gene #36: 'del_16q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S319. 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 S319. Get High-res Image Gene #37: 'del_18q22.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q22.2' versus 'METHLYATION_CNMF'

P value = 0.032 (Fisher's exact test), Q value = 0.037

Table S320. 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 S320. Get High-res Image Gene #37: 'del_18q22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q22.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S321. Gene #37: 'del_18q22.2' versus Molecular Subtype #5: '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 S321. Get High-res Image Gene #37: 'del_18q22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S322. Gene #37: 'del_18q22.2' versus Molecular Subtype #6: '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 S322. Get High-res Image Gene #37: 'del_18q22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q22.2' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00012

Table S323. Gene #37: 'del_18q22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
DEL PEAK 24(18Q22.2) MUTATED	46	55	54
DEL PEAK 24(18Q22.2) WILD-TYPE	282	137	290

Figure S323. Get High-res Image Gene #37: 'del_18q22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00132 (Fisher's exact test), Q value = 0.0017

Table S324. Gene #37: 'del_18q22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
DEL PEAK 24(18Q22.2) MUTATED	12	122	21
DEL PEAK 24(18Q22.2) WILD-TYPE	65	459	185

Figure S324. Get High-res Image Gene #37: 'del_18q22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00303 (Fisher's exact test), Q value = 0.0039

Table S325. Gene #37: 'del_18q22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
DEL PEAK 24(18Q22.2) MUTATED	21	13	20	13
DEL PEAK 24(18Q22.2) WILD-TYPE	132	57	43	112

Figure S325. Get High-res Image Gene #37: 'del_18q22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_18q22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 4.6e-05

Table S326. Gene #37: 'del_18q22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
DEL PEAK 24(18Q22.2) MUTATED	1	13	30	15	8
DEL PEAK 24(18Q22.2) WILD-TYPE	49	76	64	117	38

Figure S326. Get High-res Image Gene #37: 'del_18q22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S327. 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 S327. Get High-res Image Gene #38: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.00066

Table S328. 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 S328. Get High-res Image Gene #38: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S329. Gene #38: 'del_19p13.3' versus Molecular Subtype #5: '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 S329. Get High-res Image Gene #38: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S330. Gene #38: 'del_19p13.3' versus Molecular Subtype #6: '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 S330. Get High-res Image Gene #38: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 0.00266 (Fisher's exact test), Q value = 0.0034

Table S331. Gene #38: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
DEL PEAK 25(19P13.3) MUTATED	23	13	7
DEL PEAK 25(19P13.3) WILD-TYPE	305	179	337

Figure S331. Get High-res Image Gene #38: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00121 (Fisher's exact test), Q value = 0.0016

Table S332. Gene #38: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
DEL PEAK 25(19P13.3) MUTATED	12	2	11	3
DEL PEAK 25(19P13.3) WILD-TYPE	141	68	52	122

Figure S332. Get High-res Image Gene #38: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00016

Table S333. Gene #38: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
DEL PEAK 25(19P13.3) MUTATED	1	7	16	2	2
DEL PEAK 25(19P13.3) WILD-TYPE	49	82	78	130	44

Figure S333. Get High-res Image Gene #38: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S334. 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 S334. 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 = 1.6e-05

Table S335. 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 S335. Get High-res Image Gene #39: 'del_xp22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xp22.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S336. Gene #39: 'del_xp22.2' versus Molecular Subtype #5: '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 S336. Get High-res Image Gene #39: 'del_xp22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S337. Gene #39: 'del_xp22.2' versus Molecular Subtype #6: '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 S337. Get High-res Image Gene #39: 'del_xp22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp22.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S338. Gene #39: 'del_xp22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
DEL PEAK 26(XP22.2) MUTATED	74	21	31
DEL PEAK 26(XP22.2) WILD-TYPE	254	171	313

Figure S338. Get High-res Image Gene #39: 'del_xp22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xp22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S339. Gene #39: 'del_xp22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
DEL PEAK 26(XP22.2) MUTATED	49	62	15
DEL PEAK 26(XP22.2) WILD-TYPE	28	519	191

Figure S339. Get High-res Image Gene #39: 'del_xp22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xp22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S340. Gene #39: 'del_xp22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
DEL PEAK 26(XP22.2) MUTATED	9	34	9	11
DEL PEAK 26(XP22.2) WILD-TYPE	144	36	54	114

Figure S340. Get High-res Image Gene #39: 'del_xp22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xp22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S341. Gene #39: 'del_xp22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
DEL PEAK 26(XP22.2) MUTATED	0	5	19	10	29
DEL PEAK 26(XP22.2) WILD-TYPE	50	84	75	122	17

Figure S341. Get High-res Image Gene #39: 'del_xp22.2' versus Molecular Subtype #10: '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/15087107/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIPAN-TP/15165233/KIPAN-TP.transferedmergedcluster.txt
Number of patients = 882
Number of significantly focal cnvs = 39
Number of molecular subtypes = 10
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

Made with Nozzle