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

Stomach Adenocarcinoma (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1K64H1K

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 89 focal events and 10 molecular subtypes across 441 patients, 345 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p36.22 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
amp_1q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1q42.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_3q26.2 cnv correlated to 'CN_CNMF'.
amp_5p15.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_5p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_6p21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_6q21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_7p22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_7p11.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
amp_7q21.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
amp_7q22.1 cnv correlated to 'CN_CNMF'.
amp_8p23.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_9p24.1 cnv correlated to 'CN_CNMF'.
amp_9p13.2 cnv correlated to 'CN_CNMF'.
amp_9q34.3 cnv correlated to 'CN_CNMF'.
amp_10p11.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_10q22.2 cnv correlated to 'CN_CNMF'.
amp_10q26.13 cnv correlated to 'CN_CNMF'.
amp_11p13 cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_11p11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_11q13.3 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
amp_12p12.1 cnv correlated to 'CN_CNMF'.
amp_12q15 cnv correlated to 'CN_CNMF'.
amp_13q12.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_13q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_15q26.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_17q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_18q11.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_19p13.2 cnv correlated to 'CN_CNMF'.
amp_19q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_19q13.32 cnv correlated to 'CN_CNMF'.
amp_20q13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_xq27.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_1p36.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_1p13.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_1q44 cnv correlated to 'METHLYATION_CNMF'.
del_2q32.1 cnv correlated to 'CN_CNMF'.
del_2q33.3 cnv correlated to 'CN_CNMF'.
del_2q37.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_3p26.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_3p14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3q26.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_4p16.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_4q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_4q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_5q12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q23.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6p25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_6q14.1 cnv correlated to 'CN_CNMF'.
del_6q24.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_6q26 cnv correlated to 'CN_CNMF'.
del_7q31.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_7q36.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_8p23.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_9q21.11 cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_10p12.31 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
del_10q22.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_11p15.5 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', and 'MIRSEQ_CNMF'.
del_11q23.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_12p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_12q12 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_13q12.11 cnv correlated to 'CN_CNMF'.
del_14q23.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_14q32.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.
del_15q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q15.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_16q23.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
del_17p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_17p12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17q24.3 cnv correlated to 'CN_CNMF'.
del_18q12.2 cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_18q21.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
del_19p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19q13.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_21q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.
del_21q22.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_22q13.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_xp22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_xp21.1 cnv correlated to 'CN_CNMF'.
del_xq21.33 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 89 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, 345 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
amp 1q21 3	160 (36%)	281	1e-05 (0.0089)	1e-05 (0.0089)	0.0341 (1.00)	0.0278 (1.00)	1e-05 (0.0089)	1e-05 (0.0089)	1e-05 (0.0089)	1e-05 (0.0089)	1e-05 (0.0089)	0.00019 (0.111)
amp 6p21 1	124 (28%)	317	1e-05 (0.0089)	1e-05 (0.0089)	0.349 (1.00)	0.234 (1.00)	9e-05 (0.0547)	0.00011 (0.0664)	1e-05 (0.0089)	1e-05 (0.0089)	8e-05 (0.0491)	0.00039 (0.216)
del 5q12 1	170 (39%)	271	1e-05 (0.0089)	1e-05 (0.0089)	0.234 (1.00)	0.177 (1.00)	1e-05 (0.0089)	1e-05 (0.0089)	1e-05 (0.0089)	1e-05 (0.0089)	1e-05 (0.0089)	2e-05 (0.0137)
del 5q23 2	158 (36%)	283	1e-05 (0.0089)	1e-05 (0.0089)	0.135 (1.00)	0.0763 (1.00)	1e-05 (0.0089)	1e-05 (0.0089)	1e-05 (0.0089)	1e-05 (0.0089)	1e-05 (0.0089)	1e-05 (0.0089)
del 9p21 3	193 (44%)	248	1e-05 (0.0089)	1e-05 (0.0089)	6e-05 (0.0374)	3e-05 (0.0199)	1e-05 (0.0089)	1e-05 (0.0089)	1e-05 (0.0089)	1e-05 (0.0089)	0.0287 (1.00)	0.0307 (1.00)
del 19p13 3	162 (37%)	279	1e-05 (0.0089)	1e-05 (0.0089)	0.00368 (1.00)	0.00456 (1.00)	1e-05 (0.0089)	1e-05 (0.0089)	1e-05 (0.0089)	1e-05 (0.0089)	1e-05 (0.0089)	3e-05 (0.0199)
amp 1q42 3	150 (34%)	291	1e-05 (0.0089)	4e-05 (0.0257)	0.402 (1.00)	0.0954 (1.00)	1e-05 (0.0089)	4e-05 (0.0257)	1e-05 (0.0089)	1e-05 (0.0089)	3e-05 (0.0199)	0.161 (1.00)
amp 5p15 33	130 (29%)	311	1e-05 (0.0089)	1e-05 (0.0089)	0.127 (1.00)	0.985 (1.00)	1e-05 (0.0089)	2e-05 (0.0137)	1e-05 (0.0089)	1e-05 (0.0089)	0.00026 (0.148)	0.00069 (0.366)
amp 6q12	88 (20%)	353	1e-05 (0.0089)	1e-05 (0.0089)	0.0675 (1.00)	0.881 (1.00)	7e-05 (0.0433)	0.00044 (0.241)	5e-05 (0.0317)	1e-05 (0.0089)	2e-05 (0.0137)	0.0134 (1.00)
amp 13q22 1	181 (41%)	260	1e-05 (0.0089)	1e-05 (0.0089)	0.255 (1.00)	0.725 (1.00)	2e-05 (0.0137)	1e-05 (0.0089)	1e-05 (0.0089)	1e-05 (0.0089)	9e-05 (0.0547)	0.0344 (1.00)
amp 17q12	147 (33%)	294	1e-05 (0.0089)	1e-05 (0.0089)	0.792 (1.00)	0.0395 (1.00)	0.00015 (0.0888)	0.00024 (0.137)	1e-05 (0.0089)	6e-05 (0.0374)	0.00475 (1.00)	0.0003 (0.169)
amp 19q12	130 (29%)	311	1e-05 (0.0089)	1e-05 (0.0089)	0.00624 (1.00)	0.114 (1.00)	1e-05 (0.0089)	1e-05 (0.0089)	1e-05 (0.0089)	1e-05 (0.0089)	1e-05 (0.0089)	0.0479 (1.00)
amp 20q13 2	293 (66%)	148	1e-05 (0.0089)	1e-05 (0.0089)	0.00681 (1.00)	0.0123 (1.00)	1e-05 (0.0089)	1e-05 (0.0089)	1e-05 (0.0089)	1e-05 (0.0089)	8e-05 (0.0491)	0.0781 (1.00)
del 1p36 11	135 (31%)	306	1e-05 (0.0089)	1e-05 (0.0089)	0.159 (1.00)	0.00111 (0.566)	0.00024 (0.137)	1e-05 (0.0089)	2e-05 (0.0137)	2e-05 (0.0137)	2e-05 (0.0137)	0.00367 (1.00)
del 3p14 2	158 (36%)	283	1e-05 (0.0089)	2e-05 (0.0137)	0.409 (1.00)	0.374 (1.00)	0.00015 (0.0888)	0.00019 (0.111)	1e-05 (0.0089)	1e-05 (0.0089)	0.00485 (1.00)	0.00019 (0.111)
del 8p23 3	126 (29%)	315	1e-05 (0.0089)	1e-05 (0.0089)	0.0746 (1.00)	0.592 (1.00)	2e-05 (0.0137)	1e-05 (0.0089)	2e-05 (0.0137)	2e-05 (0.0137)	0.00887 (1.00)	0.00012 (0.0722)
del 10q23 31	116 (26%)	325	1e-05 (0.0089)	3e-05 (0.0199)	0.0628 (1.00)	0.00012 (0.0722)	1e-05 (0.0089)	1e-05 (0.0089)	1e-05 (0.0089)	1e-05 (0.0089)	0.00224 (1.00)	0.0503 (1.00)
del 15q11 2	120 (27%)	321	1e-05 (0.0089)	1e-05 (0.0089)	0.00167 (0.818)	0.267 (1.00)	1e-05 (0.0089)	2e-05 (0.0137)	0.0004 (0.221)	7e-05 (0.0433)	0.0295 (1.00)	0.00036 (0.201)
del 15q15 1	122 (28%)	319	1e-05 (0.0089)	1e-05 (0.0089)	0.00365 (1.00)	0.294 (1.00)	1e-05 (0.0089)	1e-05 (0.0089)	5e-05 (0.0317)	1e-05 (0.0089)	0.00577 (1.00)	0.00017 (0.0998)
del 16p13 3	93 (21%)	348	1e-05 (0.0089)	0.00034 (0.19)	0.701 (1.00)	0.818 (1.00)	1e-05 (0.0089)	1e-05 (0.0089)	1e-05 (0.0089)	1e-05 (0.0089)	1e-05 (0.0089)	0.0878 (1.00)
del 17p12	181 (41%)	260	1e-05 (0.0089)	1e-05 (0.0089)	0.396 (1.00)	0.0081 (1.00)	1e-05 (0.0089)	1e-05 (0.0089)	1e-05 (0.0089)	1e-05 (0.0089)	0.016 (1.00)	0.00013 (0.0779)
amp 11p11 2	92 (21%)	349	1e-05 (0.0089)	0.00029 (0.165)	0.692 (1.00)	0.168 (1.00)	3e-05 (0.0199)	0.00046 (0.251)	1e-05 (0.0089)	1e-05 (0.0089)	0.00042 (0.231)	0.00309 (1.00)
amp 13q12 3	170 (39%)	271	1e-05 (0.0089)	1e-05 (0.0089)	0.327 (1.00)	0.152 (1.00)	0.0172 (1.00)	3e-05 (0.0199)	5e-05 (0.0317)	3e-05 (0.0199)	0.00022 (0.127)	0.0617 (1.00)
del 3p26 1	143 (32%)	298	1e-05 (0.0089)	1e-05 (0.0089)	0.342 (1.00)	0.193 (1.00)	0.00669 (1.00)	5e-05 (0.0317)	3e-05 (0.0199)	1e-05 (0.0089)	0.00013 (0.0779)	0.00524 (1.00)
del 4p16 3	169 (38%)	272	1e-05 (0.0089)	0.00167 (0.818)	0.458 (1.00)	0.199 (1.00)	1e-05 (0.0089)	6e-05 (0.0374)	2e-05 (0.0137)	1e-05 (0.0089)	0.00033 (0.185)	0.0123 (1.00)
del 4q34 3	200 (45%)	241	1e-05 (0.0089)	1e-05 (0.0089)	0.0522 (1.00)	0.00866 (1.00)	3e-05 (0.0199)	2e-05 (0.0137)	1e-05 (0.0089)	1e-05 (0.0089)	0.0119 (1.00)	0.086 (1.00)
del 6p25 3	115 (26%)	326	1e-05 (0.0089)	0.00011 (0.0664)	0.138 (1.00)	0.823 (1.00)	9e-05 (0.0547)	3e-05 (0.0199)	5e-05 (0.0317)	1e-05 (0.0089)	0.111 (1.00)	0.0466 (1.00)
del 7q36 3	98 (22%)	343	1e-05 (0.0089)	1e-05 (0.0089)	0.383 (1.00)	0.0779 (1.00)	1e-05 (0.0089)	0.00033 (0.185)	1e-05 (0.0089)	1e-05 (0.0089)	0.00338 (1.00)	0.00871 (1.00)
del 14q23 3	136 (31%)	305	1e-05 (0.0089)	1e-05 (0.0089)	0.749 (1.00)	0.429 (1.00)	5e-05 (0.0317)	0.00027 (0.154)	1e-05 (0.0089)	1e-05 (0.0089)	0.0456 (1.00)	0.00262 (1.00)
del 17p13 3	176 (40%)	265	1e-05 (0.0089)	1e-05 (0.0089)	0.555 (1.00)	0.0203 (1.00)	2e-05 (0.0137)	1e-05 (0.0089)	1e-05 (0.0089)	7e-05 (0.0433)	0.0612 (1.00)	0.00246 (1.00)
amp 5p13 1	126 (29%)	315	1e-05 (0.0089)	1e-05 (0.0089)	0.736 (1.00)	0.862 (1.00)	1e-05 (0.0089)	0.00062 (0.332)	4e-05 (0.0257)	1e-05 (0.0089)	0.0164 (1.00)	0.0303 (1.00)
amp 6q21	82 (19%)	359	1e-05 (0.0089)	0.00037 (0.206)	0.385 (1.00)	0.404 (1.00)	0.00154 (0.762)	0.00169 (0.825)	1e-05 (0.0089)	1e-05 (0.0089)	0.00018 (0.105)	0.00075 (0.392)
amp 7p22 1	229 (52%)	212	1e-05 (0.0089)	8e-05 (0.0491)	0.638 (1.00)	0.831 (1.00)	0.00012 (0.0722)	1e-05 (0.0089)	0.0043 (1.00)	5e-05 (0.0317)	0.0434 (1.00)	0.00215 (1.00)
del 9p23	195 (44%)	246	1e-05 (0.0089)	2e-05 (0.0137)	0.0278 (1.00)	0.00092 (0.475)	1e-05 (0.0089)	0.00185 (0.895)	1e-05 (0.0089)	0.00013 (0.0779)	0.151 (1.00)	0.00327 (1.00)
del 12p13 1	77 (17%)	364	1e-05 (0.0089)	1e-05 (0.0089)	0.54 (1.00)	0.418 (1.00)	6e-05 (0.0374)	3e-05 (0.0199)	0.00029 (0.165)	0.00329 (1.00)	0.204 (1.00)	0.0499 (1.00)
del 19q13 11	75 (17%)	366	1e-05 (0.0089)	1e-05 (0.0089)	0.0638 (1.00)	0.711 (1.00)	4e-05 (0.0257)	0.00071 (0.376)	1e-05 (0.0089)	1e-05 (0.0089)	0.00541 (1.00)	0.0089 (1.00)
del 22q13 31	161 (37%)	280	1e-05 (0.0089)	1e-05 (0.0089)	0.0498 (1.00)	0.00597 (1.00)	0.0014 (0.699)	0.0039 (1.00)	1e-05 (0.0089)	1e-05 (0.0089)	0.00013 (0.0779)	0.0142 (1.00)
amp 15q26 1	113 (26%)	328	1e-05 (0.0089)	0.00017 (0.0998)	0.15 (1.00)	0.237 (1.00)	3e-05 (0.0199)	3e-05 (0.0199)	0.00049 (0.266)	0.00046 (0.251)	0.00822 (1.00)	0.00118 (0.596)
del 3q26 31	47 (11%)	394	1e-05 (0.0089)	2e-05 (0.0137)	0.0367 (1.00)	0.0481 (1.00)	0.00048 (0.261)	5e-05 (0.0317)	5e-05 (0.0317)	0.00501 (1.00)	0.00416 (1.00)	0.076 (1.00)
del 10q22 3	79 (18%)	362	1e-05 (0.0089)	0.0028 (1.00)	0.847 (1.00)	0.088 (1.00)	0.0002 (0.116)	0.00065 (0.346)	4e-05 (0.0257)	5e-05 (0.0317)	0.0267 (1.00)	0.0561 (1.00)
del 11p15 5	97 (22%)	344	1e-05 (0.0089)	8e-05 (0.0491)	4e-05 (0.0257)	0.00512 (1.00)	0.00362 (1.00)	0.0313 (1.00)	9e-05 (0.0547)	0.00174 (0.846)	0.208 (1.00)	0.535 (1.00)
del 21q22 3	193 (44%)	248	1e-05 (0.0089)	0.0091 (1.00)	0.199 (1.00)	0.294 (1.00)	0.00559 (1.00)	0.00037 (0.206)	0.00022 (0.127)	0.00294 (1.00)	0.00029 (0.165)	0.0929 (1.00)
del xp22 2	85 (19%)	356	1e-05 (0.0089)	2e-05 (0.0137)	0.463 (1.00)	0.044 (1.00)	0.00021 (0.121)	0.00022 (0.127)	0.0511 (1.00)	0.00271 (1.00)	0.34 (1.00)	0.289 (1.00)
amp 8q24 21	309 (70%)	132	1e-05 (0.0089)	0.00057 (0.306)	0.382 (1.00)	0.378 (1.00)	0.00527 (1.00)	0.0108 (1.00)	2e-05 (0.0137)	1e-05 (0.0089)	0.00077 (0.402)	0.00456 (1.00)
amp 10p11 22	119 (27%)	322	1e-05 (0.0089)	3e-05 (0.0199)	0.145 (1.00)	0.521 (1.00)	0.00136 (0.68)	0.00886 (1.00)	0.00111 (0.566)	4e-05 (0.0257)	0.00281 (1.00)	0.0179 (1.00)
amp 11p13	88 (20%)	353	1e-05 (0.0089)	0.0168 (1.00)	0.646 (1.00)	0.118 (1.00)	0.00072 (0.38)	0.00567 (1.00)	4e-05 (0.0257)	0.00016 (0.0944)	0.0328 (1.00)	0.502 (1.00)
del 2q37 2	72 (16%)	369	1e-05 (0.0089)	1e-05 (0.0089)	0.327 (1.00)	0.241 (1.00)	0.00255 (1.00)	0.174 (1.00)	0.00116 (0.587)	3e-05 (0.0199)	0.217 (1.00)	0.0168 (1.00)
del 4q22 1	193 (44%)	248	1e-05 (0.0089)	0.00016 (0.0944)	0.108 (1.00)	0.267 (1.00)	0.00265 (1.00)	6e-05 (0.0374)	0.00103 (0.527)	0.00063 (0.336)	0.582 (1.00)	0.118 (1.00)
del 9q21 11	114 (26%)	327	1e-05 (0.0089)	0.00131 (0.658)	0.138 (1.00)	0.0562 (1.00)	0.00148 (0.736)	0.0363 (1.00)	3e-05 (0.0199)	1e-05 (0.0089)	0.0379 (1.00)	0.102 (1.00)
del 14q32 32	133 (30%)	308	1e-05 (0.0089)	0.00016 (0.0944)	0.767 (1.00)	0.59 (1.00)	0.00183 (0.888)	0.00056 (0.301)	0.00014 (0.083)	0.00714 (1.00)	0.257 (1.00)	0.0565 (1.00)
del 18q12 2	181 (41%)	260	1e-05 (0.0089)	0.00132 (0.661)	0.913 (1.00)	0.737 (1.00)	0.00476 (1.00)	0.0576 (1.00)	6e-05 (0.0374)	0.0004 (0.221)	0.00091 (0.47)	0.00805 (1.00)
del 18q21 2	204 (46%)	237	1e-05 (0.0089)	0.00074 (0.389)	0.665 (1.00)	0.45 (1.00)	0.00032 (0.18)	0.00429 (1.00)	5e-05 (0.0317)	0.00188 (0.906)	0.00108 (0.552)	0.00997 (1.00)
del 21q11 2	183 (41%)	258	1e-05 (0.0089)	0.00034 (0.19)	0.234 (1.00)	0.147 (1.00)	0.00257 (1.00)	0.00257 (1.00)	3e-05 (0.0199)	0.0009 (0.468)	0.00163 (0.8)	0.0926 (1.00)
amp 1p36 22	66 (15%)	375	1e-05 (0.0089)	0.0397 (1.00)	0.517 (1.00)	0.244 (1.00)	0.00018 (0.105)	0.12 (1.00)	0.011 (1.00)	0.00073 (0.385)	0.133 (1.00)	0.00884 (1.00)
amp 7p11 2	214 (49%)	227	1e-05 (0.0089)	0.00074 (0.389)	0.905 (1.00)	0.852 (1.00)	0.0424 (1.00)	0.0004 (0.221)	0.0317 (1.00)	0.0022 (1.00)	0.0968 (1.00)	0.00273 (1.00)
amp 7q21 2	204 (46%)	237	1e-05 (0.0089)	0.00263 (1.00)	0.215 (1.00)	0.773 (1.00)	0.458 (1.00)	2e-05 (0.0137)	0.0299 (1.00)	0.00161 (0.792)	0.101 (1.00)	0.00847 (1.00)
amp 8p23 1	177 (40%)	264	1e-05 (0.0089)	0.00022 (0.127)	0.584 (1.00)	0.601 (1.00)	0.0553 (1.00)	0.0177 (1.00)	0.143 (1.00)	0.0692 (1.00)	0.12 (1.00)	0.0546 (1.00)
amp 11q13 3	115 (26%)	326	1e-05 (0.0089)	0.00958 (1.00)	0.189 (1.00)	0.638 (1.00)	0.129 (1.00)	0.0371 (1.00)	3e-05 (0.0199)	0.00304 (1.00)	0.00157 (0.776)	0.0472 (1.00)
amp 18q11 2	140 (32%)	301	1e-05 (0.0089)	0.00038 (0.211)	0.29 (1.00)	0.288 (1.00)	0.0149 (1.00)	0.00385 (1.00)	0.00051 (0.275)	0.00114 (0.578)	0.368 (1.00)	0.315 (1.00)
amp xq27 3	86 (20%)	355	3e-05 (0.0199)	0.00695 (1.00)	0.373 (1.00)	0.943 (1.00)	0.467 (1.00)	8e-05 (0.0491)	0.0537 (1.00)	0.388 (1.00)	0.051 (1.00)	0.0151 (1.00)
del 1p13 2	94 (21%)	347	1e-05 (0.0089)	1e-05 (0.0089)	0.0794 (1.00)	0.065 (1.00)	0.00111 (0.566)	0.0009 (0.468)	0.00186 (0.898)	0.00689 (1.00)	0.139 (1.00)	0.0159 (1.00)
del 6q24 3	78 (18%)	363	1e-05 (0.0089)	0.0002 (0.116)	0.816 (1.00)	1 (1.00)	0.014 (1.00)	0.0228 (1.00)	0.247 (1.00)	0.0304 (1.00)	0.0146 (1.00)	0.0586 (1.00)
del 7q31 1	71 (16%)	370	1e-05 (0.0089)	1e-05 (0.0089)	0.715 (1.00)	0.5 (1.00)	0.00889 (1.00)	0.279 (1.00)	0.00074 (0.389)	0.0682 (1.00)	0.0662 (1.00)	0.126 (1.00)
del 10p12 31	67 (15%)	374	1e-05 (0.0089)	0.0076 (1.00)	0.206 (1.00)	0.413 (1.00)	0.173 (1.00)	0.5 (1.00)	3e-05 (0.0199)	0.0017 (0.828)	0.293 (1.00)	0.206 (1.00)
del 11q23 2	99 (22%)	342	1e-05 (0.0089)	0.0167 (1.00)	0.704 (1.00)	0.155 (1.00)	0.00096 (0.493)	0.00013 (0.0779)	0.196 (1.00)	0.072 (1.00)	0.0293 (1.00)	0.19 (1.00)
del 12q12	59 (13%)	382	1e-05 (0.0089)	8e-05 (0.0491)	0.921 (1.00)	0.933 (1.00)	0.0965 (1.00)	0.14 (1.00)	0.308 (1.00)	0.0399 (1.00)	0.796 (1.00)	0.693 (1.00)
del 16q23 1	182 (41%)	259	1e-05 (0.0089)	0.00233 (1.00)	0.469 (1.00)	0.169 (1.00)	0.00195 (0.936)	0.00855 (1.00)	0.00013 (0.0779)	0.00363 (1.00)	0.00878 (1.00)	0.0322 (1.00)
del xq21 33	56 (13%)	385	1e-05 (0.0089)	0.00033 (0.185)	0.815 (1.00)	0.0347 (1.00)	0.0088 (1.00)	0.0505 (1.00)	0.0132 (1.00)	0.0636 (1.00)	0.0961 (1.00)	0.0591 (1.00)
amp 3q26 2	164 (37%)	277	1e-05 (0.0089)	0.00831 (1.00)	0.858 (1.00)	0.00407 (1.00)	0.4 (1.00)	0.0107 (1.00)	0.00426 (1.00)	0.0168 (1.00)	0.0033 (1.00)	0.0139 (1.00)
amp 7q22 1	202 (46%)	239	1e-05 (0.0089)	0.017 (1.00)	0.228 (1.00)	0.887 (1.00)	0.767 (1.00)	0.0016 (0.789)	0.102 (1.00)	0.0301 (1.00)	0.145 (1.00)	0.0166 (1.00)
amp 9p24 1	65 (15%)	376	7e-05 (0.0433)	0.462 (1.00)	0.612 (1.00)	0.22 (1.00)	0.11 (1.00)	0.00541 (1.00)	0.033 (1.00)	0.33 (1.00)	0.0564 (1.00)	0.143 (1.00)
amp 9p13 2	91 (21%)	350	0.00044 (0.241)	0.587 (1.00)	0.377 (1.00)	0.328 (1.00)	0.0155 (1.00)	0.265 (1.00)	0.057 (1.00)	0.296 (1.00)	0.00236 (1.00)	0.183 (1.00)
amp 9q34 3	122 (28%)	319	3e-05 (0.0199)	0.176 (1.00)	0.721 (1.00)	0.47 (1.00)	0.0448 (1.00)	0.138 (1.00)	0.011 (1.00)	0.33 (1.00)	0.154 (1.00)	0.275 (1.00)
amp 10q22 2	88 (20%)	353	1e-05 (0.0089)	0.0233 (1.00)	0.0197 (1.00)	0.203 (1.00)	0.0162 (1.00)	0.0225 (1.00)	0.254 (1.00)	0.138 (1.00)	0.278 (1.00)	0.288 (1.00)
amp 10q26 13	88 (20%)	353	1e-05 (0.0089)	0.00392 (1.00)	0.0358 (1.00)	0.331 (1.00)	0.00565 (1.00)	0.03 (1.00)	0.199 (1.00)	0.203 (1.00)	0.82 (1.00)	0.586 (1.00)
amp 12p12 1	128 (29%)	313	1e-05 (0.0089)	0.0429 (1.00)	0.429 (1.00)	0.347 (1.00)	0.208 (1.00)	0.367 (1.00)	0.0368 (1.00)	0.136 (1.00)	0.609 (1.00)	0.0412 (1.00)
amp 12q15	109 (25%)	332	1e-05 (0.0089)	0.502 (1.00)	0.219 (1.00)	0.328 (1.00)	0.277 (1.00)	0.0742 (1.00)	0.136 (1.00)	0.171 (1.00)	0.0536 (1.00)	0.218 (1.00)
amp 19p13 2	47 (11%)	394	2e-05 (0.0137)	0.152 (1.00)	0.902 (1.00)	0.755 (1.00)	0.735 (1.00)	0.161 (1.00)	0.478 (1.00)	0.703 (1.00)	0.105 (1.00)	0.412 (1.00)
amp 19q13 32	111 (25%)	330	1e-05 (0.0089)	0.0591 (1.00)	0.384 (1.00)	0.474 (1.00)	0.00142 (0.707)	0.0845 (1.00)	0.00065 (0.346)	0.00476 (1.00)	0.00227 (1.00)	0.00849 (1.00)
del 1q44	26 (6%)	415	0.00231 (1.00)	0.00044 (0.241)	0.31 (1.00)	0.375 (1.00)	0.742 (1.00)	0.338 (1.00)	0.22 (1.00)	0.748 (1.00)	0.407 (1.00)	0.555 (1.00)
del 2q32 1	64 (15%)	377	0.00029 (0.165)	0.0333 (1.00)	0.49 (1.00)	0.0824 (1.00)	0.0899 (1.00)	0.241 (1.00)	0.0166 (1.00)	0.00063 (0.336)	0.219 (1.00)	0.0908 (1.00)
del 2q33 3	49 (11%)	392	0.00021 (0.121)	0.0261 (1.00)	0.399 (1.00)	0.645 (1.00)	0.177 (1.00)	0.807 (1.00)	0.0888 (1.00)	0.00947 (1.00)	0.155 (1.00)	0.0895 (1.00)
del 6q14 1	89 (20%)	352	1e-05 (0.0089)	0.0005 (0.27)	0.216 (1.00)	0.842 (1.00)	0.00054 (0.291)	0.00473 (1.00)	0.101 (1.00)	0.00097 (0.498)	0.107 (1.00)	0.188 (1.00)
del 6q26	102 (23%)	339	1e-05 (0.0089)	0.00295 (1.00)	0.791 (1.00)	0.702 (1.00)	0.0009 (0.468)	0.00234 (1.00)	0.0406 (1.00)	0.00737 (1.00)	0.00298 (1.00)	0.00188 (0.906)
del 13q12 11	63 (14%)	378	1e-05 (0.0089)	0.0697 (1.00)	0.427 (1.00)	0.367 (1.00)	0.0663 (1.00)	0.021 (1.00)	0.0754 (1.00)	0.277 (1.00)	0.988 (1.00)	0.371 (1.00)
del 17q24 3	76 (17%)	365	1e-05 (0.0089)	0.00083 (0.432)	0.178 (1.00)	0.265 (1.00)	0.0174 (1.00)	0.00545 (1.00)	0.00645 (1.00)	0.0415 (1.00)	0.233 (1.00)	0.561 (1.00)
del xp21 1	74 (17%)	367	1e-05 (0.0089)	0.00299 (1.00)	0.16 (1.00)	0.0324 (1.00)	0.00782 (1.00)	0.0601 (1.00)	0.131 (1.00)	0.243 (1.00)	0.486 (1.00)	0.619 (1.00)
del 1q44	30 (7%)	411	0.00055 (0.296)	0.00095 (0.489)	0.179 (1.00)	0.111 (1.00)	0.365 (1.00)	0.0267 (1.00)	0.00501 (1.00)	0.148 (1.00)	0.899 (1.00)	0.0166 (1.00)
del 20p12 1	39 (9%)	402	0.00118 (0.596)	0.00151 (0.749)	0.658 (1.00)	0.194 (1.00)	0.015 (1.00)	0.0843 (1.00)	0.00124 (0.624)	0.0552 (1.00)	0.663 (1.00)	0.0406 (1.00)

'amp_1p36.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 1(1P36.22) MUTATED	38	6	4	16	2
AMP PEAK 1(1P36.22) WILD-TYPE	85	181	32	60	17

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

'amp_1p36.22' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.11

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

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

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

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 2(1Q21.3) MUTATED	85	16	13	36	10
AMP PEAK 2(1Q21.3) WILD-TYPE	38	171	23	40	9

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

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
AMP PEAK 2(1Q21.3) MUTATED	36	62	23
AMP PEAK 2(1Q21.3) WILD-TYPE	90	34	91

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

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

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

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

'amp_1q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

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

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

'amp_1q21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 2(1Q21.3) MUTATED	56	30	73
AMP PEAK 2(1Q21.3) WILD-TYPE	130	103	48

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

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 2(1Q21.3) MUTATED	34	41	20	64
AMP PEAK 2(1Q21.3) WILD-TYPE	45	134	59	43

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

'amp_1q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 2(1Q21.3) MUTATED	46	18	15	17	14	10
AMP PEAK 2(1Q21.3) WILD-TYPE	30	40	45	41	22	48

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

'amp_1q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.11

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
AMP PEAK 2(1Q21.3) MUTATED	78	11	31
AMP PEAK 2(1Q21.3) WILD-TYPE	123	62	41

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

'amp_1q42.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 3(1Q42.3) MUTATED	80	18	11	33	8
AMP PEAK 3(1Q42.3) WILD-TYPE	43	169	25	43	11

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

'amp_1q42.3' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.026

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
AMP PEAK 3(1Q42.3) MUTATED	32	51	27
AMP PEAK 3(1Q42.3) WILD-TYPE	94	45	87

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

'amp_1q42.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

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

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

'amp_1q42.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.026

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

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

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

'amp_1q42.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 3(1Q42.3) MUTATED	40	37	73
AMP PEAK 3(1Q42.3) WILD-TYPE	146	96	48

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

'amp_1q42.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 3(1Q42.3) MUTATED	30	32	24	64
AMP PEAK 3(1Q42.3) WILD-TYPE	49	143	55	43

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

'amp_1q42.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S17. Gene #3: 'amp_1q42.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 3(1Q42.3) MUTATED	43	12	16	17	16	11
AMP PEAK 3(1Q42.3) WILD-TYPE	33	46	44	41	20	47

Figure S17. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 4(3Q26.2) MUTATED	64	32	11	44	13
AMP PEAK 4(3Q26.2) WILD-TYPE	59	155	25	32	6

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

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 5(5P15.33) MUTATED	77	18	10	20	5
AMP PEAK 5(5P15.33) WILD-TYPE	46	169	26	56	14

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

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
AMP PEAK 5(5P15.33) MUTATED	20	52	25
AMP PEAK 5(5P15.33) WILD-TYPE	106	44	89

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

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

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

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

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

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

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

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

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 5(5P15.33) MUTATED	49	22	58
AMP PEAK 5(5P15.33) WILD-TYPE	137	111	63

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

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 5(5P15.33) MUTATED	17	41	15	56
AMP PEAK 5(5P15.33) WILD-TYPE	62	134	64	51

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

'amp_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.15

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 5(5P15.33) MUTATED	35	13	19	18	12	6
AMP PEAK 5(5P15.33) WILD-TYPE	41	45	41	40	24	52

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

'amp_5p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S26. Gene #6: 'amp_5p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 6(5P13.1) MUTATED	73	17	10	21	5
AMP PEAK 6(5P13.1) WILD-TYPE	50	170	26	55	14

Figure S26. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S27. Gene #6: 'amp_5p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
AMP PEAK 6(5P13.1) MUTATED	23	47	23
AMP PEAK 6(5P13.1) WILD-TYPE	103	49	91

Figure S27. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S28. Gene #6: 'amp_5p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

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

Figure S28. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p13.1' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.026

Table S29. Gene #6: 'amp_5p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 6(5P13.1) MUTATED	44	28	54
AMP PEAK 6(5P13.1) WILD-TYPE	142	105	67

Figure S29. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S30. Gene #6: 'amp_5p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 6(5P13.1) MUTATED	16	37	18	55
AMP PEAK 6(5P13.1) WILD-TYPE	63	138	61	52

Figure S30. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S31. Gene #7: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 7(6P21.1) MUTATED	79	8	5	25	7
AMP PEAK 7(6P21.1) WILD-TYPE	44	179	31	51	12

Figure S31. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S32. Gene #7: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
AMP PEAK 7(6P21.1) MUTATED	23	53	13
AMP PEAK 7(6P21.1) WILD-TYPE	103	43	101

Figure S32. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.055

Table S33. Gene #7: 'amp_6p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 7(6P21.1) MUTATED	10	10	10	11	30
AMP PEAK 7(6P21.1) WILD-TYPE	55	52	36	26	32

Figure S33. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.066

Table S34. Gene #7: 'amp_6p21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 7(6P21.1) MUTATED	10	1	5	17	15	20	3
AMP PEAK 7(6P21.1) WILD-TYPE	28	20	44	45	26	20	18

Figure S34. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 7(6P21.1) MUTATED	46	19	58
AMP PEAK 7(6P21.1) WILD-TYPE	140	114	63

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

'amp_6p21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S36. Gene #7: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 7(6P21.1) MUTATED	29	29	13	52
AMP PEAK 7(6P21.1) WILD-TYPE	50	146	66	55

Figure S36. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.049

Table S37. Gene #7: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 7(6P21.1) MUTATED	38	11	13	17	12	8
AMP PEAK 7(6P21.1) WILD-TYPE	38	47	47	41	24	50

Figure S37. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.22

Table S38. Gene #7: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
AMP PEAK 7(6P21.1) MUTATED	67	8	24
AMP PEAK 7(6P21.1) WILD-TYPE	134	65	48

Figure S38. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S39. Gene #8: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 8(6Q12) MUTATED	59	9	4	13	3
AMP PEAK 8(6Q12) WILD-TYPE	64	178	32	63	16

Figure S39. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S40. Gene #8: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
AMP PEAK 8(6Q12) MUTATED	16	36	10
AMP PEAK 8(6Q12) WILD-TYPE	110	60	104

Figure S40. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q12' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.043

Table S41. Gene #8: 'amp_6q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

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

Figure S41. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.24

Table S42. Gene #8: 'amp_6q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S42. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6q12' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.032

Table S43. Gene #8: 'amp_6q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 8(6Q12) MUTATED	30	15	42
AMP PEAK 8(6Q12) WILD-TYPE	156	118	79

Figure S43. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 8(6Q12) MUTATED	22	17	10	38
AMP PEAK 8(6Q12) WILD-TYPE	57	158	69	69

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

'amp_6q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S45. Gene #8: 'amp_6q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 8(6Q12) MUTATED	32	6	6	9	8	5
AMP PEAK 8(6Q12) WILD-TYPE	44	52	54	49	28	53

Figure S45. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_6q21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 9(6Q21) MUTATED	52	8	4	16	2
AMP PEAK 9(6Q21) WILD-TYPE	71	179	32	60	17

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

'amp_6q21' versus 'METHLYATION_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.21

Table S47. Gene #9: 'amp_6q21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
AMP PEAK 9(6Q21) MUTATED	16	29	12
AMP PEAK 9(6Q21) WILD-TYPE	110	67	102

Figure S47. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S48. Gene #9: 'amp_6q21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 9(6Q21) MUTATED	29	11	41
AMP PEAK 9(6Q21) WILD-TYPE	157	122	80

Figure S48. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6q21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S49. Gene #9: 'amp_6q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 9(6Q21) MUTATED	16	19	7	39
AMP PEAK 9(6Q21) WILD-TYPE	63	156	72	68

Figure S49. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6q21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.11

Table S50. Gene #9: 'amp_6q21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 9(6Q21) MUTATED	27	7	6	7	9	5
AMP PEAK 9(6Q21) WILD-TYPE	49	51	54	51	27	53

Figure S50. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7p22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 10(7P22.1) MUTATED	88	51	34	46	10
AMP PEAK 10(7P22.1) WILD-TYPE	35	136	2	30	9

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

'amp_7p22.1' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.049

Table S52. Gene #10: 'amp_7p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
AMP PEAK 10(7P22.1) MUTATED	63	66	44
AMP PEAK 10(7P22.1) WILD-TYPE	63	30	70

Figure S52. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p22.1' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.072

Table S53. Gene #10: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

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

Figure S53. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S54. Gene #10: 'amp_7p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 10(7P22.1) MUTATED	16	11	15	31	30	29	4
AMP PEAK 10(7P22.1) WILD-TYPE	22	10	34	31	11	11	17

Figure S54. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7p22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.032

Table S55. Gene #10: 'amp_7p22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 10(7P22.1) MUTATED	46	79	30	73
AMP PEAK 10(7P22.1) WILD-TYPE	33	96	49	34

Figure S55. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S56. Gene #11: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 11(7P11.2) MUTATED	74	48	35	46	11
AMP PEAK 11(7P11.2) WILD-TYPE	49	139	1	30	8

Figure S56. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.22

Table S57. Gene #11: 'amp_7p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S57. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S58. Gene #12: 'amp_7q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 12(7Q21.2) MUTATED	63	50	36	43	12
AMP PEAK 12(7Q21.2) WILD-TYPE	60	137	0	33	7

Figure S58. Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S59. Gene #12: 'amp_7q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 12(7Q21.2) MUTATED	14	13	14	26	30	19	3
AMP PEAK 12(7Q21.2) WILD-TYPE	24	8	35	36	11	21	18

Figure S59. Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S60. Gene #13: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 13(7Q22.1) MUTATED	62	51	36	40	13
AMP PEAK 13(7Q22.1) WILD-TYPE	61	136	0	36	6

Figure S60. Get High-res Image Gene #13: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S61. Gene #14: 'amp_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 14(8P23.1) MUTATED	36	82	15	25	19
AMP PEAK 14(8P23.1) WILD-TYPE	87	105	21	51	0

Figure S61. Get High-res Image Gene #14: 'amp_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p23.1' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.13

Table S62. Gene #14: 'amp_8p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
AMP PEAK 14(8P23.1) MUTATED	67	29	35
AMP PEAK 14(8P23.1) WILD-TYPE	59	67	79

Figure S62. Get High-res Image Gene #14: 'amp_8p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S63. Gene #15: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 15(8Q24.21) MUTATED	111	107	24	49	18
AMP PEAK 15(8Q24.21) WILD-TYPE	12	80	12	27	1

Figure S63. Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S64. Gene #15: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 15(8Q24.21) MUTATED	130	75	103
AMP PEAK 15(8Q24.21) WILD-TYPE	56	58	18

Figure S64. Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S65. Gene #15: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 15(8Q24.21) MUTATED	64	106	47	91
AMP PEAK 15(8Q24.21) WILD-TYPE	15	69	32	16

Figure S65. Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_9p24.1' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.043

Table S66. Gene #16: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 16(9P24.1) MUTATED	30	29	3	1	2
AMP PEAK 16(9P24.1) WILD-TYPE	93	158	33	75	17

Figure S66. Get High-res Image Gene #16: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p13.2' versus 'CN_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.24

Table S67. Gene #17: 'amp_9p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 17(9P13.2) MUTATED	43	28	5	11	4
AMP PEAK 17(9P13.2) WILD-TYPE	80	159	31	65	15

Figure S67. Get High-res Image Gene #17: 'amp_9p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9q34.3' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S68. Gene #18: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 18(9Q34.3) MUTATED	52	31	13	19	7
AMP PEAK 18(9Q34.3) WILD-TYPE	71	156	23	57	12

Figure S68. Get High-res Image Gene #18: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10p11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S69. Gene #19: 'amp_10p11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 19(10P11.22) MUTATED	53	12	14	36	4
AMP PEAK 19(10P11.22) WILD-TYPE	70	175	22	40	15

Figure S69. Get High-res Image Gene #19: 'amp_10p11.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10p11.22' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S70. Gene #19: 'amp_10p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
AMP PEAK 19(10P11.22) MUTATED	26	44	20
AMP PEAK 19(10P11.22) WILD-TYPE	100	52	94

Figure S70. Get High-res Image Gene #19: 'amp_10p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_10p11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.026

Table S71. Gene #19: 'amp_10p11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 19(10P11.22) MUTATED	19	34	17	48
AMP PEAK 19(10P11.22) WILD-TYPE	60	141	62	59

Figure S71. Get High-res Image Gene #19: 'amp_10p11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_10q22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S72. Gene #20: 'amp_10q22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 20(10Q22.2) MUTATED	27	11	6	37	7
AMP PEAK 20(10Q22.2) WILD-TYPE	96	176	30	39	12

Figure S72. Get High-res Image Gene #20: 'amp_10q22.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10q26.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S73. Gene #21: 'amp_10q26.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 21(10Q26.13) MUTATED	31	14	8	30	5
AMP PEAK 21(10Q26.13) WILD-TYPE	92	173	28	46	14

Figure S73. Get High-res Image Gene #21: 'amp_10q26.13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S74. Gene #22: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 22(11P13) MUTATED	42	17	3	24	2
AMP PEAK 22(11P13) WILD-TYPE	81	170	33	52	17

Figure S74. Get High-res Image Gene #22: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11p13' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.026

Table S75. Gene #22: 'amp_11p13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 22(11P13) MUTATED	25	21	41
AMP PEAK 22(11P13) WILD-TYPE	161	112	80

Figure S75. Get High-res Image Gene #22: 'amp_11p13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_11p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.094

Table S76. Gene #22: 'amp_11p13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 22(11P13) MUTATED	11	25	13	38
AMP PEAK 22(11P13) WILD-TYPE	68	150	66	69

Figure S76. Get High-res Image Gene #22: 'amp_11p13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S77. Gene #23: 'amp_11p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 23(11P11.2) MUTATED	47	10	5	28	2
AMP PEAK 23(11P11.2) WILD-TYPE	76	177	31	48	17

Figure S77. Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11p11.2' versus 'METHLYATION_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.16

Table S78. Gene #23: 'amp_11p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
AMP PEAK 23(11P11.2) MUTATED	15	31	15
AMP PEAK 23(11P11.2) WILD-TYPE	111	65	99

Figure S78. Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11p11.2' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S79. Gene #23: 'amp_11p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 23(11P11.2) MUTATED	6	8	5	2	24
AMP PEAK 23(11P11.2) WILD-TYPE	59	54	41	35	38

Figure S79. Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_11p11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S80. Gene #23: 'amp_11p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 23(11P11.2) MUTATED	32	15	44
AMP PEAK 23(11P11.2) WILD-TYPE	154	118	77

Figure S80. Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_11p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S81. Gene #23: 'amp_11p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 23(11P11.2) MUTATED	14	29	7	41
AMP PEAK 23(11P11.2) WILD-TYPE	65	146	72	66

Figure S81. Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.23

Table S82. Gene #23: 'amp_11p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 23(11P11.2) MUTATED	26	16	5	7	9	6
AMP PEAK 23(11P11.2) WILD-TYPE	50	42	55	51	27	52

Figure S82. Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_11q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S83. Gene #24: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 24(11Q13.3) MUTATED	50	16	5	36	8
AMP PEAK 24(11Q13.3) WILD-TYPE	73	171	31	40	11

Figure S83. Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S84. Gene #24: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 24(11Q13.3) MUTATED	45	20	49
AMP PEAK 24(11Q13.3) WILD-TYPE	141	113	72

Figure S84. Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_12p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S85. Gene #25: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 25(12P12.1) MUTATED	39	26	13	42	8
AMP PEAK 25(12P12.1) WILD-TYPE	84	161	23	34	11

Figure S85. Get High-res Image Gene #25: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S86. Gene #26: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 26(12Q15) MUTATED	32	24	7	41	5
AMP PEAK 26(12Q15) WILD-TYPE	91	163	29	35	14

Figure S86. Get High-res Image Gene #26: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q12.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S87. Gene #27: 'amp_13q12.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 27(13Q12.3) MUTATED	79	35	27	19	10
AMP PEAK 27(13Q12.3) WILD-TYPE	44	152	9	57	9

Figure S87. Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q12.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S88. Gene #27: 'amp_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
AMP PEAK 27(13Q12.3) MUTATED	40	59	32
AMP PEAK 27(13Q12.3) WILD-TYPE	86	37	82

Figure S88. Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q12.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S89. Gene #27: 'amp_13q12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 27(13Q12.3) MUTATED	4	5	17	23	25	22	5
AMP PEAK 27(13Q12.3) WILD-TYPE	34	16	32	39	16	18	16

Figure S89. Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_13q12.3' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.032

Table S90. Gene #27: 'amp_13q12.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 27(13Q12.3) MUTATED	60	41	68
AMP PEAK 27(13Q12.3) WILD-TYPE	126	92	53

Figure S90. Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_13q12.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S91. Gene #27: 'amp_13q12.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 27(13Q12.3) MUTATED	36	48	25	60
AMP PEAK 27(13Q12.3) WILD-TYPE	43	127	54	47

Figure S91. Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_13q12.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.13

Table S92. Gene #27: 'amp_13q12.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 27(13Q12.3) MUTATED	40	16	20	21	21	12
AMP PEAK 27(13Q12.3) WILD-TYPE	36	42	40	37	15	46

Figure S92. Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_13q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S93. Gene #28: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 28(13Q22.1) MUTATED	89	40	25	20	7
AMP PEAK 28(13Q22.1) WILD-TYPE	34	147	11	56	12

Figure S93. Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S94. Gene #28: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
AMP PEAK 28(13Q22.1) MUTATED	38	59	34
AMP PEAK 28(13Q22.1) WILD-TYPE	88	37	80

Figure S94. Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S95. Gene #28: 'amp_13q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 28(13Q22.1) MUTATED	22	16	9	17	39
AMP PEAK 28(13Q22.1) WILD-TYPE	43	46	37	20	23

Figure S95. Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S96. Gene #28: 'amp_13q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 28(13Q22.1) MUTATED	7	6	15	18	24	28	5
AMP PEAK 28(13Q22.1) WILD-TYPE	31	15	34	44	17	12	16

Figure S96. Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S97. Gene #28: 'amp_13q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 28(13Q22.1) MUTATED	64	40	76
AMP PEAK 28(13Q22.1) WILD-TYPE	122	93	45

Figure S97. Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_13q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S98. Gene #28: 'amp_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 28(13Q22.1) MUTATED	37	50	25	68
AMP PEAK 28(13Q22.1) WILD-TYPE	42	125	54	39

Figure S98. Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.055

Table S99. Gene #28: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 28(13Q22.1) MUTATED	46	20	22	21	19	12
AMP PEAK 28(13Q22.1) WILD-TYPE	30	38	38	37	17	46

Figure S99. Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_15q26.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S100. Gene #29: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 29(15Q26.1) MUTATED	61	15	5	31	1
AMP PEAK 29(15Q26.1) WILD-TYPE	62	172	31	45	18

Figure S100. Get High-res Image Gene #29: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_15q26.1' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.1

Table S101. Gene #29: 'amp_15q26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
AMP PEAK 29(15Q26.1) MUTATED	25	40	19
AMP PEAK 29(15Q26.1) WILD-TYPE	101	56	95

Figure S101. Get High-res Image Gene #29: 'amp_15q26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_15q26.1' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S102. Gene #29: 'amp_15q26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 29(15Q26.1) MUTATED	13	4	10	10	28
AMP PEAK 29(15Q26.1) WILD-TYPE	52	58	36	27	34

Figure S102. Get High-res Image Gene #29: 'amp_15q26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_15q26.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S103. Gene #29: 'amp_15q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 29(15Q26.1) MUTATED	13	1	4	13	12	20	2
AMP PEAK 29(15Q26.1) WILD-TYPE	25	20	45	49	29	20	19

Figure S103. Get High-res Image Gene #29: 'amp_15q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S104. Gene #30: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 30(17Q12) MUTATED	82	21	14	23	7
AMP PEAK 30(17Q12) WILD-TYPE	41	166	22	53	12

Figure S104. Get High-res Image Gene #30: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S105. Gene #30: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
AMP PEAK 30(17Q12) MUTATED	32	54	20
AMP PEAK 30(17Q12) WILD-TYPE	94	42	94

Figure S105. Get High-res Image Gene #30: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.089

Table S106. Gene #30: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

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

Figure S106. Get High-res Image Gene #30: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.14

Table S107. Gene #30: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 30(17Q12) MUTATED	13	7	5	20	13	20	1
AMP PEAK 30(17Q12) WILD-TYPE	25	14	44	42	28	20	20

Figure S107. Get High-res Image Gene #30: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S108. Gene #30: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 30(17Q12) MUTATED	49	28	69
AMP PEAK 30(17Q12) WILD-TYPE	137	105	52

Figure S108. Get High-res Image Gene #30: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.037

Table S109. Gene #30: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 30(17Q12) MUTATED	19	55	17	55
AMP PEAK 30(17Q12) WILD-TYPE	60	120	62	52

Figure S109. Get High-res Image Gene #30: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.17

Table S110. Gene #30: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
AMP PEAK 30(17Q12) MUTATED	81	11	23
AMP PEAK 30(17Q12) WILD-TYPE	120	62	49

Figure S110. Get High-res Image Gene #30: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S111. Gene #31: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 31(18Q11.2) MUTATED	58	27	12	36	7
AMP PEAK 31(18Q11.2) WILD-TYPE	65	160	24	40	12

Figure S111. Get High-res Image Gene #31: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.21

Table S112. Gene #31: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
AMP PEAK 31(18Q11.2) MUTATED	30	46	30
AMP PEAK 31(18Q11.2) WILD-TYPE	96	50	84

Figure S112. Get High-res Image Gene #31: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S113. Gene #32: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 32(19P13.2) MUTATED	18	6	10	12	1
AMP PEAK 32(19P13.2) WILD-TYPE	105	181	26	64	18

Figure S113. Get High-res Image Gene #32: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S114. Gene #33: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 33(19Q12) MUTATED	79	17	10	23	1
AMP PEAK 33(19Q12) WILD-TYPE	44	170	26	53	18

Figure S114. Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S115. Gene #33: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
AMP PEAK 33(19Q12) MUTATED	22	50	30
AMP PEAK 33(19Q12) WILD-TYPE	104	46	84

Figure S115. Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S116. Gene #33: 'amp_19q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 33(19Q12) MUTATED	10	9	10	6	44
AMP PEAK 33(19Q12) WILD-TYPE	55	53	36	31	18

Figure S116. Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S117. Gene #33: 'amp_19q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 33(19Q12) MUTATED	10	5	6	15	11	29	3
AMP PEAK 33(19Q12) WILD-TYPE	28	16	43	47	30	11	18

Figure S117. Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S118. Gene #33: 'amp_19q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 33(19Q12) MUTATED	34	26	69
AMP PEAK 33(19Q12) WILD-TYPE	152	107	52

Figure S118. Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S119. Gene #33: 'amp_19q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 33(19Q12) MUTATED	18	27	17	67
AMP PEAK 33(19Q12) WILD-TYPE	61	148	62	40

Figure S119. Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S120. Gene #33: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 33(19Q12) MUTATED	43	9	15	12	13	12
AMP PEAK 33(19Q12) WILD-TYPE	33	49	45	46	23	46

Figure S120. Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_19q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S121. Gene #34: 'amp_19q13.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 34(19Q13.32) MUTATED	55	20	11	25	0
AMP PEAK 34(19Q13.32) WILD-TYPE	68	167	25	51	19

Figure S121. Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S122. Gene #35: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 35(20Q13.2) MUTATED	116	69	32	60	16
AMP PEAK 35(20Q13.2) WILD-TYPE	7	118	4	16	3

Figure S122. Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S123. Gene #35: 'amp_20q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
AMP PEAK 35(20Q13.2) MUTATED	67	87	67
AMP PEAK 35(20Q13.2) WILD-TYPE	59	9	47

Figure S123. Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S124. Gene #35: 'amp_20q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 35(20Q13.2) MUTATED	31	31	31	24	59
AMP PEAK 35(20Q13.2) WILD-TYPE	34	31	15	13	3

Figure S124. Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_20q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S125. Gene #35: 'amp_20q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 35(20Q13.2) MUTATED	23	19	19	43	31	38	3
AMP PEAK 35(20Q13.2) WILD-TYPE	15	2	30	19	10	2	18

Figure S125. Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S126. Gene #35: 'amp_20q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 35(20Q13.2) MUTATED	107	74	111
AMP PEAK 35(20Q13.2) WILD-TYPE	79	59	10

Figure S126. Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_20q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S127. Gene #35: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 35(20Q13.2) MUTATED	43	107	41	101
AMP PEAK 35(20Q13.2) WILD-TYPE	36	68	38	6

Figure S127. Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.049

Table S128. Gene #35: 'amp_20q13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 35(20Q13.2) MUTATED	65	30	38	36	26	29
AMP PEAK 35(20Q13.2) WILD-TYPE	11	28	22	22	10	29

Figure S128. Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_xq27.3' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S129. Gene #36: 'amp_xq27.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 36(XQ27.3) MUTATED	32	17	13	19	5
AMP PEAK 36(XQ27.3) WILD-TYPE	91	170	23	57	14

Figure S129. Get High-res Image Gene #36: 'amp_xq27.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq27.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.049

Table S130. Gene #36: 'amp_xq27.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 36(XQ27.3) MUTATED	8	4	3	10	19	3	2
AMP PEAK 36(XQ27.3) WILD-TYPE	30	17	46	52	22	37	19

Figure S130. Get High-res Image Gene #36: 'amp_xq27.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S131. Gene #37: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 1(1P36.11) MUTATED	73	12	5	39	6
DEL PEAK 1(1P36.11) WILD-TYPE	50	175	31	37	13

Figure S131. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S132. Gene #37: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 1(1P36.11) MUTATED	24	52	17
DEL PEAK 1(1P36.11) WILD-TYPE	102	44	97

Figure S132. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.14

Table S133. Gene #37: 'del_1p36.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

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

Figure S133. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S134. Gene #37: 'del_1p36.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S134. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S135. Gene #37: 'del_1p36.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 1(1P36.11) MUTATED	53	25	56
DEL PEAK 1(1P36.11) WILD-TYPE	133	108	65

Figure S135. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p36.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S136. Gene #37: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 1(1P36.11) MUTATED	21	45	13	55
DEL PEAK 1(1P36.11) WILD-TYPE	58	130	66	52

Figure S136. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S137. Gene #37: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 1(1P36.11) MUTATED	41	12	19	14	11	8
DEL PEAK 1(1P36.11) WILD-TYPE	35	46	41	44	25	50

Figure S137. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S138. Gene #38: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 2(1P13.2) MUTATED	57	7	7	19	4
DEL PEAK 2(1P13.2) WILD-TYPE	66	180	29	57	15

Figure S138. Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S139. Gene #38: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 2(1P13.2) MUTATED	23	38	9
DEL PEAK 2(1P13.2) WILD-TYPE	103	58	105

Figure S139. Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1q44' versus 'METHLYATION_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.24

Table S140. Gene #40: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 4(1Q44) MUTATED	7	15	2
DEL PEAK 4(1Q44) WILD-TYPE	119	81	112

Figure S140. Get High-res Image Gene #40: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q32.1' versus 'CN_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.16

Table S141. Gene #41: 'del_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 5(2Q32.1) MUTATED	28	12	7	15	2
DEL PEAK 5(2Q32.1) WILD-TYPE	95	175	29	61	17

Figure S141. Get High-res Image Gene #41: 'del_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q33.3' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.12

Table S142. Gene #42: 'del_2q33.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 6(2Q33.3) MUTATED	24	8	7	9	1
DEL PEAK 6(2Q33.3) WILD-TYPE	99	179	29	67	18

Figure S142. Get High-res Image Gene #42: 'del_2q33.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S143. Gene #43: 'del_2q37.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 7(2Q37.2) MUTATED	36	10	4	15	7
DEL PEAK 7(2Q37.2) WILD-TYPE	87	177	32	61	12

Figure S143. Get High-res Image Gene #43: 'del_2q37.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S144. Gene #43: 'del_2q37.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 7(2Q37.2) MUTATED	10	29	11
DEL PEAK 7(2Q37.2) WILD-TYPE	116	67	103

Figure S144. Get High-res Image Gene #43: 'del_2q37.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S145. Gene #43: 'del_2q37.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 7(2Q37.2) MUTATED	8	27	4	33
DEL PEAK 7(2Q37.2) WILD-TYPE	71	148	75	74

Figure S145. Get High-res Image Gene #43: 'del_2q37.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S146. Gene #44: 'del_3p26.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 8(3P26.1) MUTATED	65	19	16	36	7
DEL PEAK 8(3P26.1) WILD-TYPE	58	168	20	40	12

Figure S146. Get High-res Image Gene #44: 'del_3p26.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p26.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S147. Gene #44: 'del_3p26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 8(3P26.1) MUTATED	31	50	25
DEL PEAK 8(3P26.1) WILD-TYPE	95	46	89

Figure S147. Get High-res Image Gene #44: 'del_3p26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p26.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.032

Table S148. Gene #44: 'del_3p26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S148. Get High-res Image Gene #44: 'del_3p26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.1' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S149. Gene #44: 'del_3p26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 8(3P26.1) MUTATED	50	32	60
DEL PEAK 8(3P26.1) WILD-TYPE	136	101	61

Figure S149. Get High-res Image Gene #44: 'del_3p26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p26.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S150. Gene #44: 'del_3p26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 8(3P26.1) MUTATED	22	45	17	58
DEL PEAK 8(3P26.1) WILD-TYPE	57	130	62	49

Figure S150. Get High-res Image Gene #44: 'del_3p26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.078

Table S151. Gene #44: 'del_3p26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 8(3P26.1) MUTATED	40	18	14	13	16	11
DEL PEAK 8(3P26.1) WILD-TYPE	36	40	46	45	20	47

Figure S151. Get High-res Image Gene #44: 'del_3p26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S152. Gene #45: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 9(3P14.2) MUTATED	67	28	16	37	10
DEL PEAK 9(3P14.2) WILD-TYPE	56	159	20	39	9

Figure S152. Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S153. Gene #45: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 9(3P14.2) MUTATED	45	55	24
DEL PEAK 9(3P14.2) WILD-TYPE	81	41	90

Figure S153. Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p14.2' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.089

Table S154. Gene #45: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 9(3P14.2) MUTATED	16	10	15	13	34
DEL PEAK 9(3P14.2) WILD-TYPE	49	52	31	24	28

Figure S154. Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.11

Table S155. Gene #45: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 9(3P14.2) MUTATED	11	6	6	21	19	22	3
DEL PEAK 9(3P14.2) WILD-TYPE	27	15	43	41	22	18	18

Figure S155. Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S156. Gene #45: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 9(3P14.2) MUTATED	61	32	65
DEL PEAK 9(3P14.2) WILD-TYPE	125	101	56

Figure S156. Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S157. Gene #45: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 9(3P14.2) MUTATED	27	52	18	61
DEL PEAK 9(3P14.2) WILD-TYPE	52	123	61	46

Figure S157. Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.11

Table S158. Gene #45: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 9(3P14.2) MUTATED	84	12	29
DEL PEAK 9(3P14.2) WILD-TYPE	117	61	43

Figure S158. Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q26.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S159. Gene #46: 'del_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 10(3Q26.31) MUTATED	27	3	6	10	1
DEL PEAK 10(3Q26.31) WILD-TYPE	96	184	30	66	18

Figure S159. Get High-res Image Gene #46: 'del_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q26.31' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S160. Gene #46: 'del_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 10(3Q26.31) MUTATED	10	23	3
DEL PEAK 10(3Q26.31) WILD-TYPE	116	73	111

Figure S160. Get High-res Image Gene #46: 'del_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3q26.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.032

Table S161. Gene #46: 'del_3q26.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 10(3Q26.31) MUTATED	3	1	1	1	10	9	0
DEL PEAK 10(3Q26.31) WILD-TYPE	35	20	48	61	31	31	21

Figure S161. Get High-res Image Gene #46: 'del_3q26.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3q26.31' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.032

Table S162. Gene #46: 'del_3q26.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 10(3Q26.31) MUTATED	12	8	27
DEL PEAK 10(3Q26.31) WILD-TYPE	174	125	94

Figure S162. Get High-res Image Gene #46: 'del_3q26.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4p16.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S163. Gene #47: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 11(4P16.3) MUTATED	76	33	12	44	4
DEL PEAK 11(4P16.3) WILD-TYPE	47	154	24	32	15

Figure S163. Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4p16.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S164. Gene #47: 'del_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

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

Figure S164. Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.037

Table S165. Gene #47: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 11(4P16.3) MUTATED	10	4	18	18	17	28	3
DEL PEAK 11(4P16.3) WILD-TYPE	28	17	31	44	24	12	18

Figure S165. Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S166. Gene #47: 'del_4p16.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 11(4P16.3) MUTATED	53	49	67
DEL PEAK 11(4P16.3) WILD-TYPE	133	84	54

Figure S166. Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S167. Gene #47: 'del_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 11(4P16.3) MUTATED	23	49	27	70
DEL PEAK 11(4P16.3) WILD-TYPE	56	126	52	37

Figure S167. Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.19

Table S168. Gene #47: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 11(4P16.3) MUTATED	44	20	13	17	17	24
DEL PEAK 11(4P16.3) WILD-TYPE	32	38	47	41	19	34

Figure S168. Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S169. Gene #48: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 12(4Q22.1) MUTATED	83	30	17	55	8
DEL PEAK 12(4Q22.1) WILD-TYPE	40	157	19	21	11

Figure S169. Get High-res Image Gene #48: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.094

Table S170. Gene #48: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 12(4Q22.1) MUTATED	48	59	39
DEL PEAK 12(4Q22.1) WILD-TYPE	78	37	75

Figure S170. Get High-res Image Gene #48: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.037

Table S171. Gene #48: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 12(4Q22.1) MUTATED	16	4	16	23	25	27	3
DEL PEAK 12(4Q22.1) WILD-TYPE	22	17	33	39	16	13	18

Figure S171. Get High-res Image Gene #48: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S172. Gene #49: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 13(4Q34.3) MUTATED	88	31	14	59	8
DEL PEAK 13(4Q34.3) WILD-TYPE	35	156	22	17	11

Figure S172. Get High-res Image Gene #49: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S173. Gene #49: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 13(4Q34.3) MUTATED	42	66	44
DEL PEAK 13(4Q34.3) WILD-TYPE	84	30	70

Figure S173. Get High-res Image Gene #49: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S174. Gene #49: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 13(4Q34.3) MUTATED	14	21	21	16	41
DEL PEAK 13(4Q34.3) WILD-TYPE	51	41	25	21	21

Figure S174. Get High-res Image Gene #49: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S175. Gene #49: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 13(4Q34.3) MUTATED	16	2	17	23	21	30	4
DEL PEAK 13(4Q34.3) WILD-TYPE	22	19	32	39	20	10	17

Figure S175. Get High-res Image Gene #49: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S176. Gene #49: 'del_4q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 13(4Q34.3) MUTATED	68	48	84
DEL PEAK 13(4Q34.3) WILD-TYPE	118	85	37

Figure S176. Get High-res Image Gene #49: 'del_4q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S177. Gene #49: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 13(4Q34.3) MUTATED	29	70	27	74
DEL PEAK 13(4Q34.3) WILD-TYPE	50	105	52	33

Figure S177. Get High-res Image Gene #49: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S178. Gene #50: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 14(5Q12.1) MUTATED	92	16	11	41	10
DEL PEAK 14(5Q12.1) WILD-TYPE	31	171	25	35	9

Figure S178. Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S179. Gene #50: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 14(5Q12.1) MUTATED	34	72	23
DEL PEAK 14(5Q12.1) WILD-TYPE	92	24	91

Figure S179. Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q12.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S180. Gene #50: 'del_5q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 14(5Q12.1) MUTATED	17	5	11	14	44
DEL PEAK 14(5Q12.1) WILD-TYPE	48	57	35	23	18

Figure S180. Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S181. Gene #50: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 14(5Q12.1) MUTATED	13	4	3	23	18	28	2
DEL PEAK 14(5Q12.1) WILD-TYPE	25	17	46	39	23	12	19

Figure S181. Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S182. Gene #50: 'del_5q12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 14(5Q12.1) MUTATED	60	27	83
DEL PEAK 14(5Q12.1) WILD-TYPE	126	106	38

Figure S182. Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S183. Gene #50: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 14(5Q12.1) MUTATED	26	55	11	78
DEL PEAK 14(5Q12.1) WILD-TYPE	53	120	68	29

Figure S183. Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S184. Gene #50: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 14(5Q12.1) MUTATED	52	22	22	19	15	11
DEL PEAK 14(5Q12.1) WILD-TYPE	24	36	38	39	21	47

Figure S184. Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5q12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S185. Gene #50: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 14(5Q12.1) MUTATED	100	14	27
DEL PEAK 14(5Q12.1) WILD-TYPE	101	59	45

Figure S185. Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S186. Gene #51: 'del_5q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 15(5Q23.2) MUTATED	90	12	11	35	10
DEL PEAK 15(5Q23.2) WILD-TYPE	33	175	25	41	9

Figure S186. Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S187. Gene #51: 'del_5q23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 15(5Q23.2) MUTATED	29	68	21
DEL PEAK 15(5Q23.2) WILD-TYPE	97	28	93

Figure S187. Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q23.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S188. Gene #51: 'del_5q23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 15(5Q23.2) MUTATED	15	3	10	12	43
DEL PEAK 15(5Q23.2) WILD-TYPE	50	59	36	25	19

Figure S188. Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S189. Gene #51: 'del_5q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 15(5Q23.2) MUTATED	7	5	2	21	18	28	2
DEL PEAK 15(5Q23.2) WILD-TYPE	31	16	47	41	23	12	19

Figure S189. Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q23.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S190. Gene #51: 'del_5q23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 15(5Q23.2) MUTATED	54	22	81
DEL PEAK 15(5Q23.2) WILD-TYPE	132	111	40

Figure S190. Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5q23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S191. Gene #51: 'del_5q23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 15(5Q23.2) MUTATED	22	54	10	71
DEL PEAK 15(5Q23.2) WILD-TYPE	57	121	69	36

Figure S191. Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S192. Gene #51: 'del_5q23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 15(5Q23.2) MUTATED	53	20	16	17	14	10
DEL PEAK 15(5Q23.2) WILD-TYPE	23	38	44	41	22	48

Figure S192. Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5q23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S193. Gene #51: 'del_5q23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 15(5Q23.2) MUTATED	93	12	25
DEL PEAK 15(5Q23.2) WILD-TYPE	108	61	47

Figure S193. Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S194. Gene #52: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 16(6P25.3) MUTATED	51	21	8	30	5
DEL PEAK 16(6P25.3) WILD-TYPE	72	166	28	46	14

Figure S194. Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.066

Table S195. Gene #52: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 16(6P25.3) MUTATED	30	41	19
DEL PEAK 16(6P25.3) WILD-TYPE	96	55	95

Figure S195. Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p25.3' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.055

Table S196. Gene #52: 'del_6p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 16(6P25.3) MUTATED	7	6	14	6	24
DEL PEAK 16(6P25.3) WILD-TYPE	58	56	32	31	38

Figure S196. Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S197. Gene #52: 'del_6p25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 16(6P25.3) MUTATED	10	0	4	15	9	18	1
DEL PEAK 16(6P25.3) WILD-TYPE	28	21	45	47	32	22	20

Figure S197. Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6p25.3' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.032

Table S198. Gene #52: 'del_6p25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 16(6P25.3) MUTATED	40	24	51
DEL PEAK 16(6P25.3) WILD-TYPE	146	109	70

Figure S198. Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S199. Gene #52: 'del_6p25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 16(6P25.3) MUTATED	12	47	10	46
DEL PEAK 16(6P25.3) WILD-TYPE	67	128	69	61

Figure S199. Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S200. Gene #53: 'del_6q14.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 17(6Q14.1) MUTATED	30	13	10	30	6
DEL PEAK 17(6Q14.1) WILD-TYPE	93	174	26	46	13

Figure S200. Get High-res Image Gene #53: 'del_6q14.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S201. Gene #54: 'del_6q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 18(6Q24.3) MUTATED	26	11	11	24	6
DEL PEAK 18(6Q24.3) WILD-TYPE	97	176	25	52	13

Figure S201. Get High-res Image Gene #54: 'del_6q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q24.3' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.12

Table S202. Gene #54: 'del_6q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 18(6Q24.3) MUTATED	12	29	15
DEL PEAK 18(6Q24.3) WILD-TYPE	114	67	99

Figure S202. Get High-res Image Gene #54: 'del_6q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S203. Gene #55: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 19(6Q26) MUTATED	36	21	12	29	4
DEL PEAK 19(6Q26) WILD-TYPE	87	166	24	47	15

Figure S203. Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S204. Gene #56: 'del_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 20(7Q31.1) MUTATED	33	10	1	23	4
DEL PEAK 20(7Q31.1) WILD-TYPE	90	177	35	53	15

Figure S204. Get High-res Image Gene #56: 'del_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q31.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S205. Gene #56: 'del_7q31.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 20(7Q31.1) MUTATED	19	27	5
DEL PEAK 20(7Q31.1) WILD-TYPE	107	69	109

Figure S205. Get High-res Image Gene #56: 'del_7q31.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q36.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S206. Gene #57: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 21(7Q36.3) MUTATED	50	8	1	31	8
DEL PEAK 21(7Q36.3) WILD-TYPE	73	179	35	45	11

Figure S206. Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q36.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S207. Gene #57: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 21(7Q36.3) MUTATED	22	38	14
DEL PEAK 21(7Q36.3) WILD-TYPE	104	58	100

Figure S207. Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q36.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S208. Gene #57: 'del_7q36.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 21(7Q36.3) MUTATED	7	8	8	3	27
DEL PEAK 21(7Q36.3) WILD-TYPE	58	54	38	34	35

Figure S208. Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_7q36.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.19

Table S209. Gene #57: 'del_7q36.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 21(7Q36.3) MUTATED	12	0	6	13	7	15	0
DEL PEAK 21(7Q36.3) WILD-TYPE	26	21	43	49	34	25	21

Figure S209. Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_7q36.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S210. Gene #57: 'del_7q36.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 21(7Q36.3) MUTATED	36	14	48
DEL PEAK 21(7Q36.3) WILD-TYPE	150	119	73

Figure S210. Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_7q36.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S211. Gene #57: 'del_7q36.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 21(7Q36.3) MUTATED	14	33	7	44
DEL PEAK 21(7Q36.3) WILD-TYPE	65	142	72	63

Figure S211. Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S212. Gene #58: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 22(8P23.3) MUTATED	61	16	16	33	0
DEL PEAK 22(8P23.3) WILD-TYPE	62	171	20	43	19

Figure S212. Get High-res Image Gene #58: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S213. Gene #58: 'del_8p23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 22(8P23.3) MUTATED	23	45	24
DEL PEAK 22(8P23.3) WILD-TYPE	103	51	90

Figure S213. Get High-res Image Gene #58: 'del_8p23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S214. Gene #58: 'del_8p23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 22(8P23.3) MUTATED	11	9	8	10	34
DEL PEAK 22(8P23.3) WILD-TYPE	54	53	38	27	28

Figure S214. Get High-res Image Gene #58: 'del_8p23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S215. Gene #58: 'del_8p23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 22(8P23.3) MUTATED	9	2	6	13	15	25	2
DEL PEAK 22(8P23.3) WILD-TYPE	29	19	43	49	26	15	19

Figure S215. Get High-res Image Gene #58: 'del_8p23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.3' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S216. Gene #58: 'del_8p23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 22(8P23.3) MUTATED	45	25	55
DEL PEAK 22(8P23.3) WILD-TYPE	141	108	66

Figure S216. Get High-res Image Gene #58: 'del_8p23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S217. Gene #58: 'del_8p23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 22(8P23.3) MUTATED	21	40	14	50
DEL PEAK 22(8P23.3) WILD-TYPE	58	135	65	57

Figure S217. Get High-res Image Gene #58: 'del_8p23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.072

Table S218. Gene #58: 'del_8p23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 22(8P23.3) MUTATED	74	8	19
DEL PEAK 22(8P23.3) WILD-TYPE	127	65	53

Figure S218. Get High-res Image Gene #58: 'del_8p23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S219. Gene #59: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 23(9P23) MUTATED	72	27	23	61	12
DEL PEAK 23(9P23) WILD-TYPE	51	160	13	15	7

Figure S219. Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S220. Gene #59: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 23(9P23) MUTATED	43	61	40
DEL PEAK 23(9P23) WILD-TYPE	83	35	74

Figure S220. Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S221. Gene #59: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 23(9P23) MUTATED	14	18	23	13	40
DEL PEAK 23(9P23) WILD-TYPE	51	44	23	24	22

Figure S221. Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S222. Gene #59: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 23(9P23) MUTATED	68	51	75
DEL PEAK 23(9P23) WILD-TYPE	118	82	46

Figure S222. Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.078

Table S223. Gene #59: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 23(9P23) MUTATED	27	72	28	67
DEL PEAK 23(9P23) WILD-TYPE	52	103	51	40

Figure S223. Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S224. Gene #60: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 24(9P21.3) MUTATED	73	29	21	59	11
DEL PEAK 24(9P21.3) WILD-TYPE	50	158	15	17	8

Figure S224. Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S225. Gene #60: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 24(9P21.3) MUTATED	40	65	40
DEL PEAK 24(9P21.3) WILD-TYPE	86	31	74

Figure S225. Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.037

Table S226. Gene #60: 'del_9p21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	90	91
DEL PEAK 24(9P21.3) MUTATED	17	41	47
DEL PEAK 24(9P21.3) WILD-TYPE	65	49	44

Figure S226. Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S227. Gene #60: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
DEL PEAK 24(9P21.3) MUTATED	8	45	10	42
DEL PEAK 24(9P21.3) WILD-TYPE	26	38	45	49

Figure S227. Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S228. Gene #60: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 24(9P21.3) MUTATED	9	18	23	15	43
DEL PEAK 24(9P21.3) WILD-TYPE	56	44	23	22	19

Figure S228. Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S229. Gene #60: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 24(9P21.3) MUTATED	19	1	11	30	18	27	2
DEL PEAK 24(9P21.3) WILD-TYPE	19	20	38	32	23	13	19

Figure S229. Get High-res Image Gene #60: '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 = 0.0089

Table S230. Gene #60: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 24(9P21.3) MUTATED	65	50	77
DEL PEAK 24(9P21.3) WILD-TYPE	121	83	44

Figure S230. Get High-res Image Gene #60: '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 = 0.0089

Table S231. Gene #60: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 24(9P21.3) MUTATED	25	71	27	69
DEL PEAK 24(9P21.3) WILD-TYPE	54	104	52	38

Figure S231. Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S232. Gene #61: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 25(9Q21.11) MUTATED	48	12	12	37	5
DEL PEAK 25(9Q21.11) WILD-TYPE	75	175	24	39	14

Figure S232. Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q21.11' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S233. Gene #61: 'del_9q21.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 25(9Q21.11) MUTATED	34	29	51
DEL PEAK 25(9Q21.11) WILD-TYPE	152	104	70

Figure S233. Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9q21.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S234. Gene #61: 'del_9q21.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 25(9Q21.11) MUTATED	13	34	17	50
DEL PEAK 25(9Q21.11) WILD-TYPE	66	141	62	57

Figure S234. Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10p12.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S235. Gene #62: 'del_10p12.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 26(10P12.31) MUTATED	34	11	3	12	7
DEL PEAK 26(10P12.31) WILD-TYPE	89	176	33	64	12

Figure S235. Get High-res Image Gene #62: 'del_10p12.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p12.31' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S236. Gene #62: 'del_10p12.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 26(10P12.31) MUTATED	23	10	34
DEL PEAK 26(10P12.31) WILD-TYPE	163	123	87

Figure S236. Get High-res Image Gene #62: 'del_10p12.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S237. Gene #63: 'del_10q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 27(10Q22.3) MUTATED	46	8	11	8	6
DEL PEAK 27(10Q22.3) WILD-TYPE	77	179	25	68	13

Figure S237. Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q22.3' versus 'MRNASEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.12

Table S238. Gene #63: 'del_10q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 27(10Q22.3) MUTATED	8	2	4	8	19
DEL PEAK 27(10Q22.3) WILD-TYPE	57	60	42	29	43

Figure S238. Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q22.3' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.026

Table S239. Gene #63: 'del_10q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 27(10Q22.3) MUTATED	34	10	35
DEL PEAK 27(10Q22.3) WILD-TYPE	152	123	86

Figure S239. Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.032

Table S240. Gene #63: 'del_10q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 27(10Q22.3) MUTATED	18	21	6	34
DEL PEAK 27(10Q22.3) WILD-TYPE	61	154	73	73

Figure S240. Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S241. Gene #64: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 28(10Q23.31) MUTATED	66	13	11	18	8
DEL PEAK 28(10Q23.31) WILD-TYPE	57	174	25	58	11

Figure S241. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S242. Gene #64: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 28(10Q23.31) MUTATED	22	41	17
DEL PEAK 28(10Q23.31) WILD-TYPE	104	55	97

Figure S242. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.072

Table S243. Gene #64: 'del_10q23.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
DEL PEAK 28(10Q23.31) MUTATED	7	34	8	13
DEL PEAK 28(10Q23.31) WILD-TYPE	27	49	47	78

Figure S243. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S244. Gene #64: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 28(10Q23.31) MUTATED	8	4	9	12	28
DEL PEAK 28(10Q23.31) WILD-TYPE	57	58	37	25	34

Figure S244. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S245. Gene #64: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 28(10Q23.31) MUTATED	2	3	4	16	18	17	1
DEL PEAK 28(10Q23.31) WILD-TYPE	36	18	45	46	23	23	20

Figure S245. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S246. Gene #64: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 28(10Q23.31) MUTATED	51	17	48
DEL PEAK 28(10Q23.31) WILD-TYPE	135	116	73

Figure S246. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S247. Gene #64: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 28(10Q23.31) MUTATED	21	39	9	47
DEL PEAK 28(10Q23.31) WILD-TYPE	58	136	70	60

Figure S247. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S248. Gene #65: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 29(11P15.5) MUTATED	51	10	8	27	1
DEL PEAK 29(11P15.5) WILD-TYPE	72	177	28	49	18

Figure S248. Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.049

Table S249. Gene #65: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 29(11P15.5) MUTATED	18	34	15
DEL PEAK 29(11P15.5) WILD-TYPE	108	62	99

Figure S249. Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.5' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.026

Table S250. Gene #65: 'del_11p15.5' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	90	91
DEL PEAK 29(11P15.5) MUTATED	7	15	33
DEL PEAK 29(11P15.5) WILD-TYPE	75	75	58

Figure S250. Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.055

Table S251. Gene #65: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 29(11P15.5) MUTATED	33	20	44
DEL PEAK 29(11P15.5) WILD-TYPE	153	113	77

Figure S251. Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11q23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S252. Gene #66: 'del_11q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 30(11Q23.2) MUTATED	42	18	7	28	4
DEL PEAK 30(11Q23.2) WILD-TYPE	81	169	29	48	15

Figure S252. Get High-res Image Gene #66: 'del_11q23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.078

Table S253. Gene #66: 'del_11q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 30(11Q23.2) MUTATED	4	1	7	24	7	12	0
DEL PEAK 30(11Q23.2) WILD-TYPE	34	20	42	38	34	28	21

Figure S253. Get High-res Image Gene #66: 'del_11q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S254. Gene #67: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 31(12P13.1) MUTATED	46	6	6	12	7
DEL PEAK 31(12P13.1) WILD-TYPE	77	181	30	64	12

Figure S254. Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S255. Gene #67: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 31(12P13.1) MUTATED	10	36	7
DEL PEAK 31(12P13.1) WILD-TYPE	116	60	107

Figure S255. Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12p13.1' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.037

Table S256. Gene #67: 'del_12p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 31(12P13.1) MUTATED	4	5	5	4	23
DEL PEAK 31(12P13.1) WILD-TYPE	61	57	41	33	39

Figure S256. Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S257. Gene #67: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 31(12P13.1) MUTATED	7	0	3	8	6	17	0
DEL PEAK 31(12P13.1) WILD-TYPE	31	21	46	54	35	23	21

Figure S257. Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.16

Table S258. Gene #67: 'del_12p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 31(12P13.1) MUTATED	29	13	35
DEL PEAK 31(12P13.1) WILD-TYPE	157	120	86

Figure S258. Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_12q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S259. Gene #68: 'del_12q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 32(12Q12) MUTATED	34	5	5	12	3
DEL PEAK 32(12Q12) WILD-TYPE	89	182	31	64	16

Figure S259. Get High-res Image Gene #68: 'del_12q12' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q12' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.049

Table S260. Gene #68: 'del_12q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 32(12Q12) MUTATED	9	25	8
DEL PEAK 32(12Q12) WILD-TYPE	117	71	106

Figure S260. Get High-res Image Gene #68: 'del_12q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q12.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S261. Gene #69: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 33(13Q12.11) MUTATED	25	9	3	23	3
DEL PEAK 33(13Q12.11) WILD-TYPE	98	178	33	53	16

Figure S261. Get High-res Image Gene #69: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S262. Gene #70: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 34(14Q23.3) MUTATED	61	19	6	43	7
DEL PEAK 34(14Q23.3) WILD-TYPE	62	168	30	33	12

Figure S262. Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q23.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S263. Gene #70: 'del_14q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 34(14Q23.3) MUTATED	27	49	25
DEL PEAK 34(14Q23.3) WILD-TYPE	99	47	89

Figure S263. Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q23.3' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.032

Table S264. Gene #70: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 34(14Q23.3) MUTATED	11	14	13	6	33
DEL PEAK 34(14Q23.3) WILD-TYPE	54	48	33	31	29

Figure S264. Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.15

Table S265. Gene #70: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 34(14Q23.3) MUTATED	9	5	10	15	10	25	3
DEL PEAK 34(14Q23.3) WILD-TYPE	29	16	39	47	31	15	18

Figure S265. Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q23.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S266. Gene #70: 'del_14q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 34(14Q23.3) MUTATED	48	27	61
DEL PEAK 34(14Q23.3) WILD-TYPE	138	106	60

Figure S266. Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_14q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S267. Gene #70: 'del_14q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 34(14Q23.3) MUTATED	16	47	16	57
DEL PEAK 34(14Q23.3) WILD-TYPE	63	128	63	50

Figure S267. Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_14q32.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S268. Gene #71: 'del_14q32.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 35(14Q32.32) MUTATED	55	20	4	48	6
DEL PEAK 35(14Q32.32) WILD-TYPE	68	167	32	28	13

Figure S268. Get High-res Image Gene #71: 'del_14q32.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.32' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.094

Table S269. Gene #71: 'del_14q32.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 35(14Q32.32) MUTATED	29	45	25
DEL PEAK 35(14Q32.32) WILD-TYPE	97	51	89

Figure S269. Get High-res Image Gene #71: 'del_14q32.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q32.32' versus 'MIRSEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.083

Table S270. Gene #71: 'del_14q32.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 35(14Q32.32) MUTATED	49	29	55
DEL PEAK 35(14Q32.32) WILD-TYPE	137	104	66

Figure S270. Get High-res Image Gene #71: 'del_14q32.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_15q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S271. Gene #72: 'del_15q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 36(15Q11.2) MUTATED	61	16	10	27	6
DEL PEAK 36(15Q11.2) WILD-TYPE	62	171	26	49	13

Figure S271. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S272. Gene #72: 'del_15q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 36(15Q11.2) MUTATED	25	45	23
DEL PEAK 36(15Q11.2) WILD-TYPE	101	51	91

Figure S272. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S273. Gene #72: 'del_15q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 36(15Q11.2) MUTATED	9	3	15	8	31
DEL PEAK 36(15Q11.2) WILD-TYPE	56	59	31	29	31

Figure S273. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S274. Gene #72: 'del_15q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 36(15Q11.2) MUTATED	8	3	2	19	16	17	1
DEL PEAK 36(15Q11.2) WILD-TYPE	30	18	47	43	25	23	20

Figure S274. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.22

Table S275. Gene #72: 'del_15q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 36(15Q11.2) MUTATED	49	23	48
DEL PEAK 36(15Q11.2) WILD-TYPE	137	110	73

Figure S275. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_15q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.043

Table S276. Gene #72: 'del_15q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 36(15Q11.2) MUTATED	18	44	11	47
DEL PEAK 36(15Q11.2) WILD-TYPE	61	131	68	60

Figure S276. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.2

Table S277. Gene #72: 'del_15q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 36(15Q11.2) MUTATED	69	8	19
DEL PEAK 36(15Q11.2) WILD-TYPE	132	65	53

Figure S277. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S278. Gene #73: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 37(15Q15.1) MUTATED	63	15	9	29	6
DEL PEAK 37(15Q15.1) WILD-TYPE	60	172	27	47	13

Figure S278. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q15.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S279. Gene #73: 'del_15q15.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 37(15Q15.1) MUTATED	24	46	21
DEL PEAK 37(15Q15.1) WILD-TYPE	102	50	93

Figure S279. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q15.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S280. Gene #73: 'del_15q15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 37(15Q15.1) MUTATED	11	3	16	7	31
DEL PEAK 37(15Q15.1) WILD-TYPE	54	59	30	30	31

Figure S280. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S281. Gene #73: 'del_15q15.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 37(15Q15.1) MUTATED	10	4	1	19	14	19	1
DEL PEAK 37(15Q15.1) WILD-TYPE	28	17	48	43	27	21	20

Figure S281. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.032

Table S282. Gene #73: 'del_15q15.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 37(15Q15.1) MUTATED	49	22	51
DEL PEAK 37(15Q15.1) WILD-TYPE	137	111	70

Figure S282. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_15q15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S283. Gene #73: 'del_15q15.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 37(15Q15.1) MUTATED	18	46	10	48
DEL PEAK 37(15Q15.1) WILD-TYPE	61	129	69	59

Figure S283. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.1

Table S284. Gene #73: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 37(15Q15.1) MUTATED	67	7	20
DEL PEAK 37(15Q15.1) WILD-TYPE	134	66	52

Figure S284. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S285. Gene #74: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 38(16P13.3) MUTATED	54	10	3	24	2
DEL PEAK 38(16P13.3) WILD-TYPE	69	177	33	52	17

Figure S285. Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16p13.3' versus 'METHLYATION_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.19

Table S286. Gene #74: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 38(16P13.3) MUTATED	19	34	17
DEL PEAK 38(16P13.3) WILD-TYPE	107	62	97

Figure S286. Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S287. Gene #74: 'del_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 38(16P13.3) MUTATED	8	6	4	3	29
DEL PEAK 38(16P13.3) WILD-TYPE	57	56	42	34	33

Figure S287. Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S288. Gene #74: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 38(16P13.3) MUTATED	8	0	4	7	6	22	3
DEL PEAK 38(16P13.3) WILD-TYPE	30	21	45	55	35	18	18

Figure S288. Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S289. Gene #74: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 38(16P13.3) MUTATED	26	14	53
DEL PEAK 38(16P13.3) WILD-TYPE	160	119	68

Figure S289. Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S290. Gene #74: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 38(16P13.3) MUTATED	7	30	9	47
DEL PEAK 38(16P13.3) WILD-TYPE	72	145	70	60

Figure S290. Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S291. Gene #74: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 38(16P13.3) MUTATED	34	10	5	7	13	5
DEL PEAK 38(16P13.3) WILD-TYPE	42	48	55	51	23	53

Figure S291. Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S292. Gene #75: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 39(16Q23.1) MUTATED	74	43	13	44	8
DEL PEAK 39(16Q23.1) WILD-TYPE	49	144	23	32	11

Figure S292. Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.078

Table S293. Gene #75: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 39(16Q23.1) MUTATED	74	40	68
DEL PEAK 39(16Q23.1) WILD-TYPE	112	93	53

Figure S293. Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S294. Gene #76: 'del_17p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 40(17P13.3) MUTATED	80	18	17	52	9
DEL PEAK 40(17P13.3) WILD-TYPE	43	169	19	24	10

Figure S294. Get High-res Image Gene #76: 'del_17p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S295. Gene #76: 'del_17p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 40(17P13.3) MUTATED	38	65	28
DEL PEAK 40(17P13.3) WILD-TYPE	88	31	86

Figure S295. Get High-res Image Gene #76: 'del_17p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p13.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S296. Gene #76: 'del_17p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 40(17P13.3) MUTATED	14	13	18	13	38
DEL PEAK 40(17P13.3) WILD-TYPE	51	49	28	24	24

Figure S296. Get High-res Image Gene #76: 'del_17p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S297. Gene #76: 'del_17p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 40(17P13.3) MUTATED	15	2	10	23	17	27	2
DEL PEAK 40(17P13.3) WILD-TYPE	23	19	39	39	24	13	19

Figure S297. Get High-res Image Gene #76: 'del_17p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S298. Gene #76: 'del_17p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 40(17P13.3) MUTATED	68	36	71
DEL PEAK 40(17P13.3) WILD-TYPE	118	97	50

Figure S298. Get High-res Image Gene #76: 'del_17p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.043

Table S299. Gene #76: 'del_17p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 40(17P13.3) MUTATED	26	68	20	61
DEL PEAK 40(17P13.3) WILD-TYPE	53	107	59	46

Figure S299. Get High-res Image Gene #76: 'del_17p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S300. Gene #77: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 41(17P12) MUTATED	88	17	17	52	7
DEL PEAK 41(17P12) WILD-TYPE	35	170	19	24	12

Figure S300. Get High-res Image Gene #77: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S301. Gene #77: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 41(17P12) MUTATED	38	70	25
DEL PEAK 41(17P12) WILD-TYPE	88	26	89

Figure S301. Get High-res Image Gene #77: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S302. Gene #77: 'del_17p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 41(17P12) MUTATED	15	10	19	12	42
DEL PEAK 41(17P12) WILD-TYPE	50	52	27	25	20

Figure S302. Get High-res Image Gene #77: 'del_17p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S303. Gene #77: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 41(17P12) MUTATED	14	2	7	25	17	30	3
DEL PEAK 41(17P12) WILD-TYPE	24	19	42	37	24	10	18

Figure S303. Get High-res Image Gene #77: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S304. Gene #77: 'del_17p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 41(17P12) MUTATED	72	31	77
DEL PEAK 41(17P12) WILD-TYPE	114	102	44

Figure S304. Get High-res Image Gene #77: 'del_17p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S305. Gene #77: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 41(17P12) MUTATED	28	67	17	68
DEL PEAK 41(17P12) WILD-TYPE	51	108	62	39

Figure S305. Get High-res Image Gene #77: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.078

Table S306. Gene #77: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 41(17P12) MUTATED	97	15	31
DEL PEAK 41(17P12) WILD-TYPE	104	58	41

Figure S306. Get High-res Image Gene #77: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S307. Gene #78: 'del_17q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 42(17Q24.3) MUTATED	35	10	6	19	6
DEL PEAK 42(17Q24.3) WILD-TYPE	88	177	30	57	13

Figure S307. Get High-res Image Gene #78: 'del_17q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S308. Gene #79: 'del_18q12.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 43(18Q12.2) MUTATED	82	29	20	46	4
DEL PEAK 43(18Q12.2) WILD-TYPE	41	158	16	30	15

Figure S308. Get High-res Image Gene #79: 'del_18q12.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q12.2' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.037

Table S309. Gene #79: 'del_18q12.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 43(18Q12.2) MUTATED	68	43	70
DEL PEAK 43(18Q12.2) WILD-TYPE	118	90	51

Figure S309. Get High-res Image Gene #79: 'del_18q12.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.22

Table S310. Gene #79: 'del_18q12.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 43(18Q12.2) MUTATED	25	69	25	62
DEL PEAK 43(18Q12.2) WILD-TYPE	54	106	54	45

Figure S310. Get High-res Image Gene #79: 'del_18q12.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S311. Gene #80: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 44(18Q21.2) MUTATED	89	35	25	51	4
DEL PEAK 44(18Q21.2) WILD-TYPE	34	152	11	25	15

Figure S311. Get High-res Image Gene #80: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.18

Table S312. Gene #80: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 44(18Q21.2) MUTATED	26	19	23	11	41
DEL PEAK 44(18Q21.2) WILD-TYPE	39	43	23	26	21

Figure S312. Get High-res Image Gene #80: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.032

Table S313. Gene #80: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 44(18Q21.2) MUTATED	80	48	76
DEL PEAK 44(18Q21.2) WILD-TYPE	106	85	45

Figure S313. Get High-res Image Gene #80: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S314. Gene #81: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 45(19P13.3) MUTATED	92	9	12	42	7
DEL PEAK 45(19P13.3) WILD-TYPE	31	178	24	34	12

Figure S314. Get High-res Image Gene #81: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S315. Gene #81: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 45(19P13.3) MUTATED	28	67	24
DEL PEAK 45(19P13.3) WILD-TYPE	98	29	90

Figure S315. Get High-res Image Gene #81: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S316. Gene #81: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 45(19P13.3) MUTATED	13	4	13	8	47
DEL PEAK 45(19P13.3) WILD-TYPE	52	58	33	29	15

Figure S316. Get High-res Image Gene #81: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S317. Gene #81: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 45(19P13.3) MUTATED	14	2	4	21	12	30	2
DEL PEAK 45(19P13.3) WILD-TYPE	24	19	45	41	29	10	19

Figure S317. Get High-res Image Gene #81: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S318. Gene #81: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 45(19P13.3) MUTATED	53	23	85
DEL PEAK 45(19P13.3) WILD-TYPE	133	110	36

Figure S318. Get High-res Image Gene #81: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S319. Gene #81: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 45(19P13.3) MUTATED	20	49	7	85
DEL PEAK 45(19P13.3) WILD-TYPE	59	126	72	22

Figure S319. Get High-res Image Gene #81: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S320. Gene #81: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 45(19P13.3) MUTATED	50	17	17	20	18	7
DEL PEAK 45(19P13.3) WILD-TYPE	26	41	43	38	18	51

Figure S320. Get High-res Image Gene #81: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S321. Gene #81: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 45(19P13.3) MUTATED	91	10	28
DEL PEAK 45(19P13.3) WILD-TYPE	110	63	44

Figure S321. Get High-res Image Gene #81: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S322. Gene #82: 'del_19q13.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 46(19Q13.11) MUTATED	41	5	6	16	7
DEL PEAK 46(19Q13.11) WILD-TYPE	82	182	30	60	12

Figure S322. Get High-res Image Gene #82: 'del_19q13.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S323. Gene #82: 'del_19q13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 46(19Q13.11) MUTATED	14	36	3
DEL PEAK 46(19Q13.11) WILD-TYPE	112	60	111

Figure S323. Get High-res Image Gene #82: 'del_19q13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19q13.11' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.026

Table S324. Gene #82: 'del_19q13.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 46(19Q13.11) MUTATED	6	2	6	3	21
DEL PEAK 46(19Q13.11) WILD-TYPE	59	60	40	34	41

Figure S324. Get High-res Image Gene #82: 'del_19q13.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19q13.11' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S325. Gene #82: 'del_19q13.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 46(19Q13.11) MUTATED	26	8	41
DEL PEAK 46(19Q13.11) WILD-TYPE	160	125	80

Figure S325. Get High-res Image Gene #82: 'del_19q13.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19q13.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S326. Gene #82: 'del_19q13.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 46(19Q13.11) MUTATED	12	16	5	42
DEL PEAK 46(19Q13.11) WILD-TYPE	67	159	74	65

Figure S326. Get High-res Image Gene #82: 'del_19q13.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_21q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S327. Gene #84: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 48(21Q11.2) MUTATED	75	35	16	46	11
DEL PEAK 48(21Q11.2) WILD-TYPE	48	152	20	30	8

Figure S327. Get High-res Image Gene #84: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.19

Table S328. Gene #84: 'del_21q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 48(21Q11.2) MUTATED	43	55	37
DEL PEAK 48(21Q11.2) WILD-TYPE	83	41	77

Figure S328. Get High-res Image Gene #84: 'del_21q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q11.2' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S329. Gene #84: 'del_21q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 48(21Q11.2) MUTATED	68	43	72
DEL PEAK 48(21Q11.2) WILD-TYPE	118	90	49

Figure S329. Get High-res Image Gene #84: 'del_21q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_21q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S330. Gene #85: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 49(21Q22.3) MUTATED	73	39	17	53	11
DEL PEAK 49(21Q22.3) WILD-TYPE	50	148	19	23	8

Figure S330. Get High-res Image Gene #85: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.21

Table S331. Gene #85: 'del_21q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 49(21Q22.3) MUTATED	19	2	14	21	17	23	3
DEL PEAK 49(21Q22.3) WILD-TYPE	19	19	35	41	24	17	18

Figure S331. Get High-res Image Gene #85: 'del_21q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_21q22.3' versus 'MIRSEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.13

Table S332. Gene #85: 'del_21q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 49(21Q22.3) MUTATED	78	44	71
DEL PEAK 49(21Q22.3) WILD-TYPE	108	89	50

Figure S332. Get High-res Image Gene #85: 'del_21q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_21q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.16

Table S333. Gene #85: 'del_21q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 49(21Q22.3) MUTATED	42	32	21	21	24	16
DEL PEAK 49(21Q22.3) WILD-TYPE	34	26	39	37	12	42

Figure S333. Get High-res Image Gene #85: 'del_21q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S334. Gene #86: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 50(22Q13.31) MUTATED	73	21	11	47	9
DEL PEAK 50(22Q13.31) WILD-TYPE	50	166	25	29	10

Figure S334. Get High-res Image Gene #86: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S335. Gene #86: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 50(22Q13.31) MUTATED	36	58	26
DEL PEAK 50(22Q13.31) WILD-TYPE	90	38	88

Figure S335. Get High-res Image Gene #86: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S336. Gene #86: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 50(22Q13.31) MUTATED	56	34	70
DEL PEAK 50(22Q13.31) WILD-TYPE	130	99	51

Figure S336. Get High-res Image Gene #86: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S337. Gene #86: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 50(22Q13.31) MUTATED	24	54	18	64
DEL PEAK 50(22Q13.31) WILD-TYPE	55	121	61	43

Figure S337. Get High-res Image Gene #86: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.078

Table S338. Gene #86: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 50(22Q13.31) MUTATED	41	22	22	12	19	13
DEL PEAK 50(22Q13.31) WILD-TYPE	35	36	38	46	17	45

Figure S338. Get High-res Image Gene #86: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xp22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S339. Gene #87: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 51(XP22.2) MUTATED	42	11	4	24	4
DEL PEAK 51(XP22.2) WILD-TYPE	81	176	32	52	15

Figure S339. Get High-res Image Gene #87: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp22.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S340. Gene #87: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 51(XP22.2) MUTATED	19	37	11
DEL PEAK 51(XP22.2) WILD-TYPE	107	59	103

Figure S340. Get High-res Image Gene #87: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp22.2' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.12

Table S341. Gene #87: 'del_xp22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 51(XP22.2) MUTATED	3	8	9	10	21
DEL PEAK 51(XP22.2) WILD-TYPE	62	54	37	27	41

Figure S341. Get High-res Image Gene #87: 'del_xp22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.13

Table S342. Gene #87: 'del_xp22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 51(XP22.2) MUTATED	11	0	5	11	15	9	0
DEL PEAK 51(XP22.2) WILD-TYPE	27	21	44	51	26	31	21

Figure S342. Get High-res Image Gene #87: 'del_xp22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S343. Gene #88: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 52(XP21.1) MUTATED	35	8	7	21	3
DEL PEAK 52(XP21.1) WILD-TYPE	88	179	29	55	16

Figure S343. Get High-res Image Gene #88: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq21.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S344. Gene #89: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 53(XQ21.33) MUTATED	27	6	5	17	1
DEL PEAK 53(XQ21.33) WILD-TYPE	96	181	31	59	18

Figure S344. Get High-res Image Gene #89: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq21.33' versus 'METHLYATION_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.19

Table S345. Gene #89: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
DEL PEAK 53(XQ21.33) MUTATED	13	21	5
DEL PEAK 53(XQ21.33) WILD-TYPE	113	75	109

Figure S345. Get High-res Image Gene #89: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = STAD-TP.transferedmergedcluster.txt
Number of patients = 441
Number of significantly focal cnvs = 89
Number of molecular subtypes = 10
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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