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

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 32 focal events and 12 molecular subtypes across 882 patients, 329 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q32.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_2q32.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3q26.32 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5q35.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7q31.2 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q24.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_10p14 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_17q24.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_xq11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.31 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p31.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1q44 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q22.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q37.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p26.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p21.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p14.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p12.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5p15.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q26 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q26 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p23.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p23 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p21.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q13.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q31.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q23.3 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_19p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 32 focal events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 329 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
del 3p26 3	489 (55%)	393	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	2e-05 (3.32e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)
del 3p21 2	503 (57%)	379	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)
del 3p14 1	408 (46%)	474	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	0.00041 (0.000601)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)
del 3p12 2	336 (38%)	546	9e-05 (0.000139)	0.00021 (0.000314)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	0.0478 (0.056)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)
del 9p23	198 (22%)	684	0.0179 (0.0219)	0.0215 (0.0261)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	3e-05 (4.86e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	5e-05 (7.9e-05)
del 9p21 3	209 (24%)	673	0.00546 (0.00713)	0.00738 (0.00951)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)
del 13q13 2	149 (17%)	733	0.0235 (0.0285)	0.0177 (0.0217)	3e-05 (4.86e-05)	1e-05 (1.7e-05)	0.036 (0.0428)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	0.00308 (0.00415)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)
del 14q31 1	279 (32%)	603	3e-05 (4.86e-05)	0.00022 (0.000326)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)
amp 3q26 32	193 (22%)	689	0.0492 (0.0574)	0.111 (0.125)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	0.038 (0.0451)	0.0009 (0.00126)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)
amp 5q35 1	376 (43%)	506	0.00063 (0.000893)	0.002 (0.00274)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	0.15 (0.169)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)
amp 7q31 2	377 (43%)	505	0.0521 (0.0606)	0.0447 (0.0528)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	0.0302 (0.0362)	0.00336 (0.0045)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)
amp 17q24 3	243 (28%)	639	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	0.22 (0.245)	0.0159 (0.0197)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)
amp xq11 2	136 (15%)	746	4e-05 (6.37e-05)	2e-05 (3.32e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	0.609 (0.625)	0.00221 (0.00301)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)
del 1p36 31	209 (24%)	673	0.00157 (0.00216)	0.00352 (0.00469)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	0.558 (0.584)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	3e-05 (4.86e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)
del 1p31 1	166 (19%)	716	0.00396 (0.00523)	0.0176 (0.0217)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	0.743 (0.757)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)
del 1q44	116 (13%)	766	0.0146 (0.0183)	0.00787 (0.01)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	0.951 (0.958)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)
del 2q22 1	75 (9%)	807	0.00083 (0.00116)	0.00029 (0.000427)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	0.561 (0.586)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)
del 2q37 3	111 (13%)	771	0.00044 (0.00064)	7e-05 (0.00011)	0.00045 (0.000652)	1e-05 (1.7e-05)	0.564 (0.587)	0.00021 (0.000314)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	3e-05 (4.86e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)
del 6q26	233 (26%)	649	0.0014 (0.00194)	0.00805 (0.0102)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	0.0036 (0.00478)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	0.629 (0.644)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)
del 6q26	234 (27%)	648	0.00144 (0.00199)	0.00772 (0.00988)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	0.00327 (0.00439)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	0.571 (0.593)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)
amp 1q32 1	82 (9%)	800	0.6 (0.62)	0.696 (0.711)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	0.00061 (0.000871)	0.0102 (0.0129)	4e-05 (6.37e-05)	1e-05 (1.7e-05)	0.00014 (0.000212)	1e-05 (1.7e-05)	0.013 (0.0163)	1e-05 (1.7e-05)
amp 8q24 22	125 (14%)	757	0.423 (0.452)	0.6 (0.62)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	8e-05 (0.000125)	4e-05 (6.37e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	0.00493 (0.00646)	1e-05 (1.7e-05)	0.00019 (0.000286)	1e-05 (1.7e-05)
del 5p15 33	31 (4%)	851			0.0001 (0.000154)	0.00027 (0.000399)	0.0349 (0.0416)	0.0473 (0.0555)	3e-05 (4.86e-05)	1e-05 (1.7e-05)	0.00069 (0.000974)	1e-05 (1.7e-05)	0.00426 (0.0056)	0.00014 (0.000212)
del 4q34 3	113 (13%)	769	0.55 (0.577)	0.317 (0.345)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	0.0697 (0.0801)	0.00057 (0.000817)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	0.00617 (0.008)	1e-05 (1.7e-05)	0.00062 (0.000882)	5e-05 (7.9e-05)
del 8p23 2	184 (21%)	698	0.36 (0.39)	0.608 (0.625)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	0.303 (0.332)	0.00768 (0.00986)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)
del 11q23 1	71 (8%)	811	0.0558 (0.0646)	0.0897 (0.102)	0.00022 (0.000326)	1e-05 (1.7e-05)	0.289 (0.318)	0.00073 (0.00103)	2e-05 (3.32e-05)	1e-05 (1.7e-05)	0.0147 (0.0183)	2e-05 (3.32e-05)	1e-05 (1.7e-05)	2e-05 (3.32e-05)
del 19p13 3	43 (5%)	839	1 (1.00)	0.857 (0.871)	9e-05 (0.000139)	4e-05 (6.37e-05)	0.183 (0.205)	0.0186 (0.0228)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	0.00657 (0.00849)	0.0005 (0.000722)	9e-05 (0.000139)	0.0282 (0.0339)
del xp22 2	125 (14%)	757	0.0836 (0.0952)	0.0689 (0.0795)	0.00013 (0.000199)	1e-05 (1.7e-05)	0.453 (0.482)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)
del 10q23 31	164 (19%)	718	0.285 (0.314)	0.175 (0.196)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	0.488 (0.516)	0.00051 (0.000733)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	0.267 (0.296)	1e-05 (1.7e-05)	1e-05 (1.7e-05)	1e-05 (1.7e-05)
amp 2q32 1	136 (15%)	746	0.54 (0.569)	0.368 (0.398)	1e-05 (1.7e-05)	0.00017 (0.000257)	0.524 (0.553)	0.00251 (0.00339)	0.0192 (0.0234)	1e-05 (1.7e-05)	0.297 (0.326)	0.00042 (0.000613)	0.0771 (0.0881)	0.0141 (0.0176)
amp 10p14	34 (4%)	848	0.197 (0.22)	0.474 (0.503)	0.00216 (0.00295)	0.0251 (0.0304)	0.0939 (0.106)	0.046 (0.0542)	0.00223 (0.00303)	0.00139 (0.00193)	0.388 (0.415)	0.00588 (0.00765)	0.073 (0.0836)	0.373 (0.403)
del 16q23 3	37 (4%)	845	0.87 (0.882)	0.915 (0.925)	0.379 (0.408)	0.00378 (0.00501)	0.387 (0.415)	0.346 (0.376)	0.0328 (0.0393)	9e-05 (0.000139)	0.219 (0.244)	0.012 (0.0151)	0.0115 (0.0146)	0.0541 (0.0628)

'amp_1q32.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
AMP PEAK 1(1Q32.1) MUTATED	7	5	70
AMP PEAK 1(1Q32.1) WILD-TYPE	321	195	284

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

'amp_1q32.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S2. Gene #1: 'amp_1q32.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
AMP PEAK 1(1Q32.1) MUTATED	3	17	8	17	3
AMP PEAK 1(1Q32.1) WILD-TYPE	99	106	163	53	183

Figure S2. Get High-res Image Gene #1: 'amp_1q32.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q32.1' versus 'RPPA_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.00087

Table S3. Gene #1: 'amp_1q32.1' versus Molecular Subtype #5: 'RPPA_CNMF'

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

Figure S3. Get High-res Image Gene #1: 'amp_1q32.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_1q32.1' versus 'RPPA_CHIERARCHICAL'

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

Table S4. Gene #1: 'amp_1q32.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

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

Figure S4. Get High-res Image Gene #1: 'amp_1q32.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_1q32.1' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 6.4e-05

Table S5. Gene #1: 'amp_1q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
AMP PEAK 1(1Q32.1) MUTATED	5	36	25	14
AMP PEAK 1(1Q32.1) WILD-TYPE	117	163	260	259

Figure S5. Get High-res Image Gene #1: 'amp_1q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q32.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S6. Gene #1: 'amp_1q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
AMP PEAK 1(1Q32.1) MUTATED	0	9	16	12	24	8	8	3	0
AMP PEAK 1(1Q32.1) WILD-TYPE	88	52	132	72	97	30	103	56	169

Figure S6. Get High-res Image Gene #1: 'amp_1q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q32.1' versus 'MIRSEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00021

Table S7. Gene #1: 'amp_1q32.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
AMP PEAK 1(1Q32.1) MUTATED	15	24	41
AMP PEAK 1(1Q32.1) WILD-TYPE	327	170	287

Figure S7. Get High-res Image Gene #1: 'amp_1q32.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q32.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S8. Gene #1: 'amp_1q32.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
AMP PEAK 1(1Q32.1) MUTATED	0	60	19	1
AMP PEAK 1(1Q32.1) WILD-TYPE	76	287	214	207

Figure S8. Get High-res Image Gene #1: 'amp_1q32.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q32.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.016

Table S9. Gene #1: 'amp_1q32.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
AMP PEAK 1(1Q32.1) MUTATED	5	4	10	11
AMP PEAK 1(1Q32.1) WILD-TYPE	151	65	55	111

Figure S9. Get High-res Image Gene #1: 'amp_1q32.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_1q32.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S10. Gene #1: 'amp_1q32.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
AMP PEAK 1(1Q32.1) MUTATED	2	17	0	1	7	3	0
AMP PEAK 1(1Q32.1) WILD-TYPE	89	66	49	19	39	74	46

Figure S10. Get High-res Image Gene #1: 'amp_1q32.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_2q32.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S11. Gene #2: 'amp_2q32.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
AMP PEAK 2(2Q32.1) MUTATED	44	6	86
AMP PEAK 2(2Q32.1) WILD-TYPE	284	194	268

Figure S11. Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2q32.1' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00026

Table S12. Gene #2: 'amp_2q32.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
AMP PEAK 2(2Q32.1) MUTATED	5	14	26	20	34
AMP PEAK 2(2Q32.1) WILD-TYPE	97	109	145	50	152

Figure S12. Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2q32.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00251 (Fisher's exact test), Q value = 0.0034

Table S13. Gene #2: 'amp_2q32.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

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

Figure S13. Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_2q32.1' versus 'MRNASEQ_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.023

Table S14. Gene #2: 'amp_2q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
AMP PEAK 2(2Q32.1) MUTATED	8	34	47	47
AMP PEAK 2(2Q32.1) WILD-TYPE	114	165	238	226

Figure S14. Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2q32.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S15. Gene #2: 'amp_2q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
AMP PEAK 2(2Q32.1) MUTATED	1	11	20	14	27	5	25	2	31
AMP PEAK 2(2Q32.1) WILD-TYPE	87	50	128	70	94	33	86	57	138

Figure S15. Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_2q32.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.00061

Table S16. Gene #2: 'amp_2q32.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
AMP PEAK 2(2Q32.1) MUTATED	1	55	42	36
AMP PEAK 2(2Q32.1) WILD-TYPE	75	292	191	172

Figure S16. Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_2q32.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0141 (Fisher's exact test), Q value = 0.018

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
AMP PEAK 2(2Q32.1) MUTATED	18	20	5	2	10	11	1
AMP PEAK 2(2Q32.1) WILD-TYPE	73	63	44	18	36	66	45

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

'amp_3q26.32' versus 'MRNA_CNMF'

P value = 0.0492 (Fisher's exact test), Q value = 0.057

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
AMP PEAK 3(3Q26.32) MUTATED	2	7	2	6
AMP PEAK 3(3Q26.32) WILD-TYPE	29	18	11	11

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

'amp_3q26.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
AMP PEAK 3(3Q26.32) MUTATED	110	8	75
AMP PEAK 3(3Q26.32) WILD-TYPE	218	192	279

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

'amp_3q26.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
AMP PEAK 3(3Q26.32) MUTATED	10	30	13	20	78
AMP PEAK 3(3Q26.32) WILD-TYPE	92	93	158	50	108

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

'amp_3q26.32' versus 'RPPA_CNMF'

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

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

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

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

'amp_3q26.32' versus 'RPPA_CHIERARCHICAL'

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

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

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

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

'amp_3q26.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
AMP PEAK 3(3Q26.32) MUTATED	13	53	24	103
AMP PEAK 3(3Q26.32) WILD-TYPE	109	146	261	170

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

'amp_3q26.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
AMP PEAK 3(3Q26.32) MUTATED	10	16	13	15	37	8	11	5	78
AMP PEAK 3(3Q26.32) WILD-TYPE	78	45	135	69	84	30	100	54	91

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

'amp_3q26.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
AMP PEAK 3(3Q26.32) MUTATED	112	37	41
AMP PEAK 3(3Q26.32) WILD-TYPE	230	157	287

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

'amp_3q26.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
AMP PEAK 3(3Q26.32) MUTATED	8	71	23	88
AMP PEAK 3(3Q26.32) WILD-TYPE	68	276	210	120

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

'amp_3q26.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
AMP PEAK 3(3Q26.32) MUTATED	61	5	15	12
AMP PEAK 3(3Q26.32) WILD-TYPE	95	64	50	110

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

'amp_3q26.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
AMP PEAK 3(3Q26.32) MUTATED	41	21	16	0	6	5	4
AMP PEAK 3(3Q26.32) WILD-TYPE	50	62	33	20	40	72	42

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

'amp_5q35.1' versus 'MRNA_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.00089

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
AMP PEAK 4(5Q35.1) MUTATED	19	16	3	2
AMP PEAK 4(5Q35.1) WILD-TYPE	12	9	10	15

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

'amp_5q35.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.002 (Fisher's exact test), Q value = 0.0027

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

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

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

'amp_5q35.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
AMP PEAK 4(5Q35.1) MUTATED	36	90	250
AMP PEAK 4(5Q35.1) WILD-TYPE	292	110	104

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

'amp_5q35.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
AMP PEAK 4(5Q35.1) MUTATED	10	60	113	40	14
AMP PEAK 4(5Q35.1) WILD-TYPE	92	63	58	30	172

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

'amp_5q35.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

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

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

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

'amp_5q35.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
AMP PEAK 4(5Q35.1) MUTATED	17	123	197	37
AMP PEAK 4(5Q35.1) WILD-TYPE	105	76	88	236

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

'amp_5q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
AMP PEAK 4(5Q35.1) MUTATED	11	10	108	20	81	29	68	37	10
AMP PEAK 4(5Q35.1) WILD-TYPE	77	51	40	64	40	9	43	22	159

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

'amp_5q35.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
AMP PEAK 4(5Q35.1) MUTATED	43	96	228
AMP PEAK 4(5Q35.1) WILD-TYPE	299	98	100

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

'amp_5q35.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
AMP PEAK 4(5Q35.1) MUTATED	9	176	162	20
AMP PEAK 4(5Q35.1) WILD-TYPE	67	171	71	188

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

'amp_5q35.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
AMP PEAK 4(5Q35.1) MUTATED	19	7	18	91
AMP PEAK 4(5Q35.1) WILD-TYPE	137	62	47	31

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

'amp_5q35.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
AMP PEAK 4(5Q35.1) MUTATED	15	22	2	0	33	57	6
AMP PEAK 4(5Q35.1) WILD-TYPE	76	61	47	20	13	20	40

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

'amp_7q31.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0447 (Fisher's exact test), Q value = 0.053

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

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

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

'amp_7q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S41. Gene #5: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
AMP PEAK 5(7Q31.2) MUTATED	206	20	151
AMP PEAK 5(7Q31.2) WILD-TYPE	122	180	203

Figure S41. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q31.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S42. Gene #5: 'amp_7q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
AMP PEAK 5(7Q31.2) MUTATED	30	45	40	31	136
AMP PEAK 5(7Q31.2) WILD-TYPE	72	78	131	39	50

Figure S42. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7q31.2' versus 'RPPA_CNMF'

P value = 0.0302 (Fisher's exact test), Q value = 0.036

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

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

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

'amp_7q31.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00336 (Fisher's exact test), Q value = 0.0045

Table S44. Gene #5: 'amp_7q31.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

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

Figure S44. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_7q31.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S45. Gene #5: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
AMP PEAK 5(7Q31.2) MUTATED	38	92	71	174
AMP PEAK 5(7Q31.2) WILD-TYPE	84	107	214	99

Figure S45. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S46. Gene #5: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
AMP PEAK 5(7Q31.2) MUTATED	30	22	45	22	55	15	26	16	144
AMP PEAK 5(7Q31.2) WILD-TYPE	58	39	103	62	66	23	85	43	25

Figure S46. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S47. Gene #5: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
AMP PEAK 5(7Q31.2) MUTATED	195	75	104
AMP PEAK 5(7Q31.2) WILD-TYPE	147	119	224

Figure S47. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S48. Gene #5: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
AMP PEAK 5(7Q31.2) MUTATED	29	127	65	153
AMP PEAK 5(7Q31.2) WILD-TYPE	47	220	168	55

Figure S48. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S49. Gene #5: 'amp_7q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
AMP PEAK 5(7Q31.2) MUTATED	111	23	28	38
AMP PEAK 5(7Q31.2) WILD-TYPE	45	46	37	84

Figure S49. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S50. Gene #5: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
AMP PEAK 5(7Q31.2) MUTATED	62	38	42	1	14	23	20
AMP PEAK 5(7Q31.2) WILD-TYPE	29	45	7	19	32	54	26

Figure S50. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S51. Gene #6: 'amp_8q24.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
AMP PEAK 6(8Q24.22) MUTATED	39	6	80
AMP PEAK 6(8Q24.22) WILD-TYPE	289	194	274

Figure S51. Get High-res Image Gene #6: 'amp_8q24.22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.22' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S52. Gene #6: 'amp_8q24.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
AMP PEAK 6(8Q24.22) MUTATED	21	29	8	28	11
AMP PEAK 6(8Q24.22) WILD-TYPE	81	94	163	42	175

Figure S52. Get High-res Image Gene #6: 'amp_8q24.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.22' versus 'RPPA_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00013

Table S53. Gene #6: 'amp_8q24.22' versus Molecular Subtype #5: 'RPPA_CNMF'

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

Figure S53. Get High-res Image Gene #6: 'amp_8q24.22' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_8q24.22' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 6.4e-05

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

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

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

'amp_8q24.22' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S55. Gene #6: 'amp_8q24.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
AMP PEAK 6(8Q24.22) MUTATED	23	63	14	24
AMP PEAK 6(8Q24.22) WILD-TYPE	99	136	271	249

Figure S55. Get High-res Image Gene #6: 'amp_8q24.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S56. Gene #6: 'amp_8q24.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
AMP PEAK 6(8Q24.22) MUTATED	18	12	11	14	50	4	2	5	8
AMP PEAK 6(8Q24.22) WILD-TYPE	70	49	137	70	71	34	109	54	161

Figure S56. Get High-res Image Gene #6: 'amp_8q24.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.22' versus 'MIRSEQ_CNMF'

P value = 0.00493 (Fisher's exact test), Q value = 0.0065

Table S57. Gene #6: 'amp_8q24.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
AMP PEAK 6(8Q24.22) MUTATED	40	42	41
AMP PEAK 6(8Q24.22) WILD-TYPE	302	152	287

Figure S57. Get High-res Image Gene #6: 'amp_8q24.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S58. Gene #6: 'amp_8q24.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
AMP PEAK 6(8Q24.22) MUTATED	18	81	13	11
AMP PEAK 6(8Q24.22) WILD-TYPE	58	266	220	197

Figure S58. Get High-res Image Gene #6: 'amp_8q24.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00029

Table S59. Gene #6: 'amp_8q24.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
AMP PEAK 6(8Q24.22) MUTATED	11	17	17	16
AMP PEAK 6(8Q24.22) WILD-TYPE	145	52	48	106

Figure S59. Get High-res Image Gene #6: 'amp_8q24.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S60. Gene #6: 'amp_8q24.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
AMP PEAK 6(8Q24.22) MUTATED	7	22	2	0	9	6	15
AMP PEAK 6(8Q24.22) WILD-TYPE	84	61	47	20	37	71	31

Figure S60. Get High-res Image Gene #6: 'amp_8q24.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10p14' versus 'CN_CNMF'

P value = 0.00216 (Fisher's exact test), Q value = 0.003

Table S61. Gene #7: 'amp_10p14' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
AMP PEAK 7(10P14) MUTATED	12	1	21
AMP PEAK 7(10P14) WILD-TYPE	316	199	333

Figure S61. Get High-res Image Gene #7: 'amp_10p14' versus Molecular Subtype #3: 'CN_CNMF'

'amp_10p14' versus 'METHLYATION_CNMF'

P value = 0.0251 (Fisher's exact test), Q value = 0.03

Table S62. Gene #7: 'amp_10p14' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
AMP PEAK 7(10P14) MUTATED	6	6	3	6	3
AMP PEAK 7(10P14) WILD-TYPE	96	117	168	64	183

Figure S62. Get High-res Image Gene #7: 'amp_10p14' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_10p14' versus 'RPPA_CHIERARCHICAL'

P value = 0.046 (Fisher's exact test), Q value = 0.054

Table S63. Gene #7: 'amp_10p14' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

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

Figure S63. Get High-res Image Gene #7: 'amp_10p14' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_10p14' versus 'MRNASEQ_CNMF'

P value = 0.00223 (Fisher's exact test), Q value = 0.003

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
AMP PEAK 7(10P14) MUTATED	6	16	4	8
AMP PEAK 7(10P14) WILD-TYPE	116	183	281	265

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

'amp_10p14' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00139 (Fisher's exact test), Q value = 0.0019

Table S65. Gene #7: 'amp_10p14' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
AMP PEAK 7(10P14) MUTATED	4	6	3	4	11	2	0	1	3
AMP PEAK 7(10P14) WILD-TYPE	84	55	145	80	110	36	111	58	166

Figure S65. Get High-res Image Gene #7: 'amp_10p14' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10p14' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00588 (Fisher's exact test), Q value = 0.0077

Table S66. Gene #7: 'amp_10p14' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
AMP PEAK 7(10P14) MUTATED	3	23	3	5
AMP PEAK 7(10P14) WILD-TYPE	73	324	230	203

Figure S66. Get High-res Image Gene #7: 'amp_10p14' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q24.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S67. Gene #8: 'amp_17q24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
AMP PEAK 8(17Q24.3) MUTATED	1	1	3	12
AMP PEAK 8(17Q24.3) WILD-TYPE	30	24	10	5

Figure S67. Get High-res Image Gene #8: 'amp_17q24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q24.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S68. Gene #8: 'amp_17q24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
AMP PEAK 8(17Q24.3) MUTATED	1	1	13	0	2
AMP PEAK 8(17Q24.3) WILD-TYPE	19	23	5	13	9

Figure S68. Get High-res Image Gene #8: 'amp_17q24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S69. Gene #8: 'amp_17q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
AMP PEAK 8(17Q24.3) MUTATED	191	4	48
AMP PEAK 8(17Q24.3) WILD-TYPE	137	196	306

Figure S69. Get High-res Image Gene #8: 'amp_17q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q24.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S70. Gene #8: 'amp_17q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
AMP PEAK 8(17Q24.3) MUTATED	10	29	11	20	147
AMP PEAK 8(17Q24.3) WILD-TYPE	92	94	160	50	39

Figure S70. Get High-res Image Gene #8: 'amp_17q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q24.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0159 (Fisher's exact test), Q value = 0.02

Table S71. Gene #8: 'amp_17q24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
AMP PEAK 8(17Q24.3) MUTATED	53	23	27	27	11	26	18
AMP PEAK 8(17Q24.3) WILD-TYPE	144	41	89	120	48	45	75

Figure S71. Get High-res Image Gene #8: 'amp_17q24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17q24.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S72. Gene #8: 'amp_17q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
AMP PEAK 8(17Q24.3) MUTATED	12	24	14	193
AMP PEAK 8(17Q24.3) WILD-TYPE	110	175	271	80

Figure S72. Get High-res Image Gene #8: 'amp_17q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S73. Gene #8: 'amp_17q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
AMP PEAK 8(17Q24.3) MUTATED	2	20	8	38	16	4	3	2	150
AMP PEAK 8(17Q24.3) WILD-TYPE	86	41	140	46	105	34	108	57	19

Figure S73. Get High-res Image Gene #8: 'amp_17q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q24.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S74. Gene #8: 'amp_17q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
AMP PEAK 8(17Q24.3) MUTATED	190	30	22
AMP PEAK 8(17Q24.3) WILD-TYPE	152	164	306

Figure S74. Get High-res Image Gene #8: 'amp_17q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S75. Gene #8: 'amp_17q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
AMP PEAK 8(17Q24.3) MUTATED	1	68	11	162
AMP PEAK 8(17Q24.3) WILD-TYPE	75	279	222	46

Figure S75. Get High-res Image Gene #8: 'amp_17q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S76. Gene #8: 'amp_17q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
AMP PEAK 8(17Q24.3) MUTATED	120	7	31	4
AMP PEAK 8(17Q24.3) WILD-TYPE	36	62	34	118

Figure S76. Get High-res Image Gene #8: 'amp_17q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S77. Gene #8: 'amp_17q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
AMP PEAK 8(17Q24.3) MUTATED	68	39	45	3	4	2	1
AMP PEAK 8(17Q24.3) WILD-TYPE	23	44	4	17	42	75	45

Figure S77. Get High-res Image Gene #8: 'amp_17q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xq11.2' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 6.4e-05

Table S78. Gene #9: 'amp_xq11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
AMP PEAK 9(XQ11.2) MUTATED	2	0	1	9
AMP PEAK 9(XQ11.2) WILD-TYPE	29	25	12	8

Figure S78. Get High-res Image Gene #9: 'amp_xq11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_xq11.2' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.3e-05

Table S79. Gene #9: 'amp_xq11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S79. Get High-res Image Gene #9: 'amp_xq11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_xq11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S80. Gene #9: 'amp_xq11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
AMP PEAK 9(XQ11.2) MUTATED	105	7	24
AMP PEAK 9(XQ11.2) WILD-TYPE	223	193	330

Figure S80. Get High-res Image Gene #9: 'amp_xq11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xq11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S81. Gene #9: 'amp_xq11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
AMP PEAK 9(XQ11.2) MUTATED	10	8	3	6	83
AMP PEAK 9(XQ11.2) WILD-TYPE	92	115	168	64	103

Figure S81. Get High-res Image Gene #9: 'amp_xq11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xq11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00221 (Fisher's exact test), Q value = 0.003

Table S82. Gene #9: 'amp_xq11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
AMP PEAK 9(XQ11.2) MUTATED	36	9	19	14	3	17	6
AMP PEAK 9(XQ11.2) WILD-TYPE	161	55	97	133	56	54	87

Figure S82. Get High-res Image Gene #9: 'amp_xq11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_xq11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S83. Gene #9: 'amp_xq11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
AMP PEAK 9(XQ11.2) MUTATED	13	14	11	98
AMP PEAK 9(XQ11.2) WILD-TYPE	109	185	274	175

Figure S83. Get High-res Image Gene #9: 'amp_xq11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xq11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S84. Gene #9: 'amp_xq11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
AMP PEAK 9(XQ11.2) MUTATED	9	6	3	10	11	1	6	2	88
AMP PEAK 9(XQ11.2) WILD-TYPE	79	55	145	74	110	37	105	57	81

Figure S84. Get High-res Image Gene #9: 'amp_xq11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xq11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S85. Gene #9: 'amp_xq11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
AMP PEAK 9(XQ11.2) MUTATED	108	11	16
AMP PEAK 9(XQ11.2) WILD-TYPE	234	183	312

Figure S85. Get High-res Image Gene #9: 'amp_xq11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_xq11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S86. Gene #9: 'amp_xq11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
AMP PEAK 9(XQ11.2) MUTATED	8	25	9	93
AMP PEAK 9(XQ11.2) WILD-TYPE	68	322	224	115

Figure S86. Get High-res Image Gene #9: 'amp_xq11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_xq11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S87. Gene #9: 'amp_xq11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
AMP PEAK 9(XQ11.2) MUTATED	60	9	3	5
AMP PEAK 9(XQ11.2) WILD-TYPE	96	60	62	117

Figure S87. Get High-res Image Gene #9: 'amp_xq11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_xq11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S88. Gene #9: 'amp_xq11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
AMP PEAK 9(XQ11.2) MUTATED	36	12	20	0	1	2	6
AMP PEAK 9(XQ11.2) WILD-TYPE	55	71	29	20	45	75	40

Figure S88. Get High-res Image Gene #9: 'amp_xq11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.31' versus 'MRNA_CNMF'

P value = 0.00157 (Fisher's exact test), Q value = 0.0022

Table S89. Gene #10: 'del_1p36.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
DEL PEAK 1(1P36.31) MUTATED	2	7	8	4
DEL PEAK 1(1P36.31) WILD-TYPE	29	18	5	13

Figure S89. Get High-res Image Gene #10: 'del_1p36.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.31' versus 'MRNA_CHIERARCHICAL'

P value = 0.00352 (Fisher's exact test), Q value = 0.0047

Table S90. Gene #10: 'del_1p36.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S90. Get High-res Image Gene #10: 'del_1p36.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p36.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S91. Gene #10: 'del_1p36.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
DEL PEAK 1(1P36.31) MUTATED	97	18	94
DEL PEAK 1(1P36.31) WILD-TYPE	231	182	260

Figure S91. Get High-res Image Gene #10: 'del_1p36.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S92. Gene #10: 'del_1p36.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
DEL PEAK 1(1P36.31) MUTATED	64	30	20	29	20
DEL PEAK 1(1P36.31) WILD-TYPE	38	93	151	41	166

Figure S92. Get High-res Image Gene #10: 'del_1p36.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.31' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S93. Gene #10: 'del_1p36.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

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

Figure S93. Get High-res Image Gene #10: 'del_1p36.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_1p36.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S94. Gene #10: 'del_1p36.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
DEL PEAK 1(1P36.31) MUTATED	72	54	32	51
DEL PEAK 1(1P36.31) WILD-TYPE	50	145	253	222

Figure S94. Get High-res Image Gene #10: 'del_1p36.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S95. Gene #10: 'del_1p36.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
DEL PEAK 1(1P36.31) MUTATED	70	21	19	28	33	11	9	9	9
DEL PEAK 1(1P36.31) WILD-TYPE	18	40	129	56	88	27	102	50	160

Figure S95. Get High-res Image Gene #10: 'del_1p36.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.31' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4.9e-05

Table S96. Gene #10: 'del_1p36.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
DEL PEAK 1(1P36.31) MUTATED	110	45	54
DEL PEAK 1(1P36.31) WILD-TYPE	232	149	274

Figure S96. Get High-res Image Gene #10: 'del_1p36.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S97. Gene #10: 'del_1p36.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
DEL PEAK 1(1P36.31) MUTATED	67	87	27	28
DEL PEAK 1(1P36.31) WILD-TYPE	9	260	206	180

Figure S97. Get High-res Image Gene #10: 'del_1p36.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S98. Gene #10: 'del_1p36.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
DEL PEAK 1(1P36.31) MUTATED	20	44	19	16
DEL PEAK 1(1P36.31) WILD-TYPE	136	25	46	106

Figure S98. Get High-res Image Gene #10: 'del_1p36.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S99. Gene #10: 'del_1p36.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
DEL PEAK 1(1P36.31) MUTATED	14	22	2	4	11	7	39
DEL PEAK 1(1P36.31) WILD-TYPE	77	61	47	16	35	70	7

Figure S99. Get High-res Image Gene #10: 'del_1p36.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p31.1' versus 'MRNA_CNMF'

P value = 0.00396 (Fisher's exact test), Q value = 0.0052

Table S100. Gene #11: 'del_1p31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
DEL PEAK 2(1P31.1) MUTATED	2	4	7	2
DEL PEAK 2(1P31.1) WILD-TYPE	29	21	6	15

Figure S100. Get High-res Image Gene #11: 'del_1p31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p31.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0176 (Fisher's exact test), Q value = 0.022

Table S101. Gene #11: 'del_1p31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S101. Get High-res Image Gene #11: 'del_1p31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S102. Gene #11: 'del_1p31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
DEL PEAK 2(1P31.1) MUTATED	87	15	64
DEL PEAK 2(1P31.1) WILD-TYPE	241	185	290

Figure S102. Get High-res Image Gene #11: 'del_1p31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p31.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S103. Gene #11: 'del_1p31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
DEL PEAK 2(1P31.1) MUTATED	62	18	15	22	14
DEL PEAK 2(1P31.1) WILD-TYPE	40	105	156	48	172

Figure S103. Get High-res Image Gene #11: 'del_1p31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p31.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S104. Gene #11: 'del_1p31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

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

Figure S104. Get High-res Image Gene #11: 'del_1p31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_1p31.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S105. Gene #11: 'del_1p31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
DEL PEAK 2(1P31.1) MUTATED	72	34	26	34
DEL PEAK 2(1P31.1) WILD-TYPE	50	165	259	239

Figure S105. Get High-res Image Gene #11: 'del_1p31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S106. Gene #11: 'del_1p31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
DEL PEAK 2(1P31.1) MUTATED	69	18	16	17	21	4	7	6	8
DEL PEAK 2(1P31.1) WILD-TYPE	19	43	132	67	100	34	104	53	161

Figure S106. Get High-res Image Gene #11: 'del_1p31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p31.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S107. Gene #11: 'del_1p31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
DEL PEAK 2(1P31.1) MUTATED	94	27	45
DEL PEAK 2(1P31.1) WILD-TYPE	248	167	283

Figure S107. Get High-res Image Gene #11: 'del_1p31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S108. Gene #11: 'del_1p31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
DEL PEAK 2(1P31.1) MUTATED	67	56	22	21
DEL PEAK 2(1P31.1) WILD-TYPE	9	291	211	187

Figure S108. Get High-res Image Gene #11: 'del_1p31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p31.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S109. Gene #11: 'del_1p31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
DEL PEAK 2(1P31.1) MUTATED	14	43	12	10
DEL PEAK 2(1P31.1) WILD-TYPE	142	26	53	112

Figure S109. Get High-res Image Gene #11: 'del_1p31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S110. Gene #11: 'del_1p31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
DEL PEAK 2(1P31.1) MUTATED	11	13	1	3	7	5	39
DEL PEAK 2(1P31.1) WILD-TYPE	80	70	48	17	39	72	7

Figure S110. Get High-res Image Gene #11: 'del_1p31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1q44' versus 'MRNA_CNMF'

P value = 0.0146 (Fisher's exact test), Q value = 0.018

Table S111. Gene #12: 'del_1q44' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
DEL PEAK 3(1Q44) MUTATED	2	1	5	1
DEL PEAK 3(1Q44) WILD-TYPE	29	24	8	16

Figure S111. Get High-res Image Gene #12: 'del_1q44' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1q44' versus 'MRNA_CHIERARCHICAL'

P value = 0.00787 (Fisher's exact test), Q value = 0.01

Table S112. Gene #12: 'del_1q44' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
DEL PEAK 3(1Q44) MUTATED	1	1	1	1	5
DEL PEAK 3(1Q44) WILD-TYPE	19	23	17	12	6

Figure S112. Get High-res Image Gene #12: 'del_1q44' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1q44' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S113. Gene #12: 'del_1q44' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
DEL PEAK 3(1Q44) MUTATED	80	12	24
DEL PEAK 3(1Q44) WILD-TYPE	248	188	330

Figure S113. Get High-res Image Gene #12: 'del_1q44' versus Molecular Subtype #3: 'CN_CNMF'

'del_1q44' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S114. Gene #12: 'del_1q44' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
DEL PEAK 3(1Q44) MUTATED	55	9	15	5	12
DEL PEAK 3(1Q44) WILD-TYPE	47	114	156	65	174

Figure S114. Get High-res Image Gene #12: 'del_1q44' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1q44' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S115. Gene #12: 'del_1q44' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 3(1Q44) MUTATED	30	13	35	10	6	3	6
DEL PEAK 3(1Q44) WILD-TYPE	167	51	81	137	53	68	87

Figure S115. Get High-res Image Gene #12: 'del_1q44' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_1q44' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S116. Gene #12: 'del_1q44' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
DEL PEAK 3(1Q44) MUTATED	64	14	20	18
DEL PEAK 3(1Q44) WILD-TYPE	58	185	265	255

Figure S116. Get High-res Image Gene #12: 'del_1q44' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1q44' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S117. Gene #12: 'del_1q44' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
DEL PEAK 3(1Q44) MUTATED	64	10	9	5	7	2	8	3	8
DEL PEAK 3(1Q44) WILD-TYPE	24	51	139	79	114	36	103	56	161

Figure S117. Get High-res Image Gene #12: 'del_1q44' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1q44' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S118. Gene #12: 'del_1q44' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
DEL PEAK 3(1Q44) MUTATED	76	15	25
DEL PEAK 3(1Q44) WILD-TYPE	266	179	303

Figure S118. Get High-res Image Gene #12: 'del_1q44' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1q44' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S119. Gene #12: 'del_1q44' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
DEL PEAK 3(1Q44) MUTATED	63	19	18	16
DEL PEAK 3(1Q44) WILD-TYPE	13	328	215	192

Figure S119. Get High-res Image Gene #12: 'del_1q44' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1q44' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S120. Gene #12: 'del_1q44' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
DEL PEAK 3(1Q44) MUTATED	10	38	6	9
DEL PEAK 3(1Q44) WILD-TYPE	146	31	59	113

Figure S120. Get High-res Image Gene #12: 'del_1q44' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1q44' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S121. Gene #12: 'del_1q44' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
DEL PEAK 3(1Q44) MUTATED	7	5	2	0	4	7	38
DEL PEAK 3(1Q44) WILD-TYPE	84	78	47	20	42	70	8

Figure S121. Get High-res Image Gene #12: 'del_1q44' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q22.1' versus 'MRNA_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.0012

Table S122. Gene #13: 'del_2q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
DEL PEAK 4(2Q22.1) MUTATED	0	1	5	1
DEL PEAK 4(2Q22.1) WILD-TYPE	31	24	8	16

Figure S122. Get High-res Image Gene #13: 'del_2q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_2q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.00043

Table S123. Gene #13: 'del_2q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
DEL PEAK 4(2Q22.1) MUTATED	0	1	1	0	5
DEL PEAK 4(2Q22.1) WILD-TYPE	20	23	17	13	6

Figure S123. Get High-res Image Gene #13: 'del_2q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_2q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S124. Gene #13: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
DEL PEAK 4(2Q22.1) MUTATED	57	8	10
DEL PEAK 4(2Q22.1) WILD-TYPE	271	192	344

Figure S124. Get High-res Image Gene #13: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S125. Gene #13: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
DEL PEAK 4(2Q22.1) MUTATED	53	6	1	3	2
DEL PEAK 4(2Q22.1) WILD-TYPE	49	117	170	67	184

Figure S125. Get High-res Image Gene #13: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q22.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S126. Gene #13: 'del_2q22.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 4(2Q22.1) MUTATED	15	13	26	4	3	3	2
DEL PEAK 4(2Q22.1) WILD-TYPE	182	51	90	143	56	68	91

Figure S126. Get High-res Image Gene #13: 'del_2q22.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S127. Gene #13: 'del_2q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
DEL PEAK 4(2Q22.1) MUTATED	59	7	0	9
DEL PEAK 4(2Q22.1) WILD-TYPE	63	192	285	264

Figure S127. Get High-res Image Gene #13: 'del_2q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S128. Gene #13: 'del_2q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
DEL PEAK 4(2Q22.1) MUTATED	58	5	1	7	4	0	0	0	0
DEL PEAK 4(2Q22.1) WILD-TYPE	30	56	147	77	117	38	111	59	169

Figure S128. Get High-res Image Gene #13: 'del_2q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S129. Gene #13: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
DEL PEAK 4(2Q22.1) MUTATED	66	3	6
DEL PEAK 4(2Q22.1) WILD-TYPE	276	191	322

Figure S129. Get High-res Image Gene #13: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S130. Gene #13: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
DEL PEAK 4(2Q22.1) MUTATED	57	14	0	4
DEL PEAK 4(2Q22.1) WILD-TYPE	19	333	233	204

Figure S130. Get High-res Image Gene #13: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S131. Gene #13: 'del_2q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
DEL PEAK 4(2Q22.1) MUTATED	4	37	4	0
DEL PEAK 4(2Q22.1) WILD-TYPE	152	32	61	122

Figure S131. Get High-res Image Gene #13: 'del_2q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_2q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S132. Gene #13: 'del_2q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
DEL PEAK 4(2Q22.1) MUTATED	3	4	1	1	1	0	35
DEL PEAK 4(2Q22.1) WILD-TYPE	88	79	48	19	45	77	11

Figure S132. Get High-res Image Gene #13: 'del_2q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q37.3' versus 'MRNA_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.00064

Table S133. Gene #14: 'del_2q37.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
DEL PEAK 5(2Q37.3) MUTATED	1	4	7	1
DEL PEAK 5(2Q37.3) WILD-TYPE	30	21	6	16

Figure S133. Get High-res Image Gene #14: 'del_2q37.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_2q37.3' versus 'MRNA_CHIERARCHICAL'

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

Table S134. Gene #14: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
DEL PEAK 5(2Q37.3) MUTATED	0	4	1	1	7
DEL PEAK 5(2Q37.3) WILD-TYPE	20	20	17	12	4

Figure S134. Get High-res Image Gene #14: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.00065

Table S135. Gene #14: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
DEL PEAK 5(2Q37.3) MUTATED	60	15	36
DEL PEAK 5(2Q37.3) WILD-TYPE	268	185	318

Figure S135. Get High-res Image Gene #14: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S136. Gene #14: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
DEL PEAK 5(2Q37.3) MUTATED	53	13	11	6	5
DEL PEAK 5(2Q37.3) WILD-TYPE	49	110	160	64	181

Figure S136. Get High-res Image Gene #14: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q37.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00031

Table S137. Gene #14: 'del_2q37.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

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

Figure S137. Get High-res Image Gene #14: 'del_2q37.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S138. Gene #14: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
DEL PEAK 5(2Q37.3) MUTATED	62	25	14	9
DEL PEAK 5(2Q37.3) WILD-TYPE	60	174	271	264

Figure S138. Get High-res Image Gene #14: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S139. Gene #14: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
DEL PEAK 5(2Q37.3) MUTATED	59	5	7	8	17	1	4	8	1
DEL PEAK 5(2Q37.3) WILD-TYPE	29	56	141	76	104	37	107	51	168

Figure S139. Get High-res Image Gene #14: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4.9e-05

Table S140. Gene #14: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
DEL PEAK 5(2Q37.3) MUTATED	67	17	25
DEL PEAK 5(2Q37.3) WILD-TYPE	275	177	303

Figure S140. Get High-res Image Gene #14: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S141. Gene #14: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
DEL PEAK 5(2Q37.3) MUTATED	58	33	12	6
DEL PEAK 5(2Q37.3) WILD-TYPE	18	314	221	202

Figure S141. Get High-res Image Gene #14: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S142. Gene #14: 'del_2q37.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
DEL PEAK 5(2Q37.3) MUTATED	6	38	6	7
DEL PEAK 5(2Q37.3) WILD-TYPE	150	31	59	115

Figure S142. Get High-res Image Gene #14: 'del_2q37.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_2q37.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S143. Gene #14: 'del_2q37.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
DEL PEAK 5(2Q37.3) MUTATED	6	7	0	1	3	4	36
DEL PEAK 5(2Q37.3) WILD-TYPE	85	76	49	19	43	73	10

Figure S143. Get High-res Image Gene #14: 'del_2q37.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p26.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S144. Gene #15: 'del_3p26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
DEL PEAK 6(3P26.3) MUTATED	30	24	4	0
DEL PEAK 6(3P26.3) WILD-TYPE	1	1	9	17

Figure S144. Get High-res Image Gene #15: 'del_3p26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p26.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S145. Gene #15: 'del_3p26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
DEL PEAK 6(3P26.3) MUTATED	20	23	1	12	2
DEL PEAK 6(3P26.3) WILD-TYPE	0	1	17	1	9

Figure S145. Get High-res Image Gene #15: 'del_3p26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S146. Gene #15: 'del_3p26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
DEL PEAK 6(3P26.3) MUTATED	13	149	327
DEL PEAK 6(3P26.3) WILD-TYPE	315	51	27

Figure S146. Get High-res Image Gene #15: 'del_3p26.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p26.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S147. Gene #15: 'del_3p26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
DEL PEAK 6(3P26.3) MUTATED	14	71	161	52	6
DEL PEAK 6(3P26.3) WILD-TYPE	88	52	10	18	180

Figure S147. Get High-res Image Gene #15: 'del_3p26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p26.3' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.3e-05

Table S148. Gene #15: 'del_3p26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
DEL PEAK 6(3P26.3) MUTATED	107	105	84	142
DEL PEAK 6(3P26.3) WILD-TYPE	75	76	103	55

Figure S148. Get High-res Image Gene #15: 'del_3p26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p26.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S149. Gene #15: 'del_3p26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 6(3P26.3) MUTATED	120	1	59	108	46	43	61
DEL PEAK 6(3P26.3) WILD-TYPE	77	63	57	39	13	28	32

Figure S149. Get High-res Image Gene #15: 'del_3p26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p26.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S150. Gene #15: 'del_3p26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
DEL PEAK 6(3P26.3) MUTATED	22	162	274	28
DEL PEAK 6(3P26.3) WILD-TYPE	100	37	11	245

Figure S150. Get High-res Image Gene #15: 'del_3p26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S151. Gene #15: 'del_3p26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
DEL PEAK 6(3P26.3) MUTATED	11	12	144	16	109	35	104	52	3
DEL PEAK 6(3P26.3) WILD-TYPE	77	49	4	68	12	3	7	7	166

Figure S151. Get High-res Image Gene #15: 'del_3p26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S152. Gene #15: 'del_3p26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
DEL PEAK 6(3P26.3) MUTATED	36	133	303
DEL PEAK 6(3P26.3) WILD-TYPE	306	61	25

Figure S152. Get High-res Image Gene #15: 'del_3p26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S153. Gene #15: 'del_3p26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
DEL PEAK 6(3P26.3) MUTATED	10	230	222	10
DEL PEAK 6(3P26.3) WILD-TYPE	66	117	11	198

Figure S153. Get High-res Image Gene #15: 'del_3p26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S154. Gene #15: 'del_3p26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
DEL PEAK 6(3P26.3) MUTATED	9	10	17	110
DEL PEAK 6(3P26.3) WILD-TYPE	147	59	48	12

Figure S154. Get High-res Image Gene #15: 'del_3p26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S155. Gene #15: 'del_3p26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
DEL PEAK 6(3P26.3) MUTATED	5	25	1	3	32	74	6
DEL PEAK 6(3P26.3) WILD-TYPE	86	58	48	17	14	3	40

Figure S155. Get High-res Image Gene #15: 'del_3p26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p21.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S156. Gene #16: 'del_3p21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
DEL PEAK 7(3P21.2) MUTATED	29	24	4	1
DEL PEAK 7(3P21.2) WILD-TYPE	2	1	9	16

Figure S156. Get High-res Image Gene #16: 'del_3p21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p21.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S157. Gene #16: 'del_3p21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
DEL PEAK 7(3P21.2) MUTATED	20	23	2	11	2
DEL PEAK 7(3P21.2) WILD-TYPE	0	1	16	2	9

Figure S157. Get High-res Image Gene #16: 'del_3p21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S158. Gene #16: 'del_3p21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
DEL PEAK 7(3P21.2) MUTATED	15	151	337
DEL PEAK 7(3P21.2) WILD-TYPE	313	49	17

Figure S158. Get High-res Image Gene #16: 'del_3p21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S159. Gene #16: 'del_3p21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
DEL PEAK 7(3P21.2) MUTATED	16	75	163	56	5
DEL PEAK 7(3P21.2) WILD-TYPE	86	48	8	14	181

Figure S159. Get High-res Image Gene #16: 'del_3p21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p21.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S160. Gene #16: 'del_3p21.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
DEL PEAK 7(3P21.2) MUTATED	111	109	85	146
DEL PEAK 7(3P21.2) WILD-TYPE	71	72	102	51

Figure S160. Get High-res Image Gene #16: 'del_3p21.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p21.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S161. Gene #16: 'del_3p21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 7(3P21.2) MUTATED	122	3	60	110	48	44	64
DEL PEAK 7(3P21.2) WILD-TYPE	75	61	56	37	11	27	29

Figure S161. Get High-res Image Gene #16: 'del_3p21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S162. Gene #16: 'del_3p21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
DEL PEAK 7(3P21.2) MUTATED	24	167	278	31
DEL PEAK 7(3P21.2) WILD-TYPE	98	32	7	242

Figure S162. Get High-res Image Gene #16: 'del_3p21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S163. Gene #16: 'del_3p21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
DEL PEAK 7(3P21.2) MUTATED	13	13	146	20	112	37	106	51	2
DEL PEAK 7(3P21.2) WILD-TYPE	75	48	2	64	9	1	5	8	167

Figure S163. Get High-res Image Gene #16: 'del_3p21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S164. Gene #16: 'del_3p21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
DEL PEAK 7(3P21.2) MUTATED	40	134	312
DEL PEAK 7(3P21.2) WILD-TYPE	302	60	16

Figure S164. Get High-res Image Gene #16: 'del_3p21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S165. Gene #16: 'del_3p21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
DEL PEAK 7(3P21.2) MUTATED	12	238	227	9
DEL PEAK 7(3P21.2) WILD-TYPE	64	109	6	199

Figure S165. Get High-res Image Gene #16: 'del_3p21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S166. Gene #16: 'del_3p21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
DEL PEAK 7(3P21.2) MUTATED	9	11	18	113
DEL PEAK 7(3P21.2) WILD-TYPE	147	58	47	9

Figure S166. Get High-res Image Gene #16: 'del_3p21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S167. Gene #16: 'del_3p21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
DEL PEAK 7(3P21.2) MUTATED	6	28	0	4	31	75	7
DEL PEAK 7(3P21.2) WILD-TYPE	85	55	49	16	15	2	39

Figure S167. Get High-res Image Gene #16: 'del_3p21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p14.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S168. Gene #17: 'del_3p14.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
DEL PEAK 8(3P14.1) MUTATED	20	21	4	0
DEL PEAK 8(3P14.1) WILD-TYPE	11	4	9	17

Figure S168. Get High-res Image Gene #17: 'del_3p14.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p14.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S169. Gene #17: 'del_3p14.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
DEL PEAK 8(3P14.1) MUTATED	15	20	1	7	2
DEL PEAK 8(3P14.1) WILD-TYPE	5	4	17	6	9

Figure S169. Get High-res Image Gene #17: 'del_3p14.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S170. Gene #17: 'del_3p14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
DEL PEAK 8(3P14.1) MUTATED	7	99	302
DEL PEAK 8(3P14.1) WILD-TYPE	321	101	52

Figure S170. Get High-res Image Gene #17: 'del_3p14.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p14.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S171. Gene #17: 'del_3p14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
DEL PEAK 8(3P14.1) MUTATED	15	65	131	46	5
DEL PEAK 8(3P14.1) WILD-TYPE	87	58	40	24	181

Figure S171. Get High-res Image Gene #17: 'del_3p14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p14.1' versus 'RPPA_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 6e-04

Table S172. Gene #17: 'del_3p14.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
DEL PEAK 8(3P14.1) MUTATED	89	88	70	117
DEL PEAK 8(3P14.1) WILD-TYPE	93	93	117	80

Figure S172. Get High-res Image Gene #17: 'del_3p14.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p14.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S173. Gene #17: 'del_3p14.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 8(3P14.1) MUTATED	100	3	47	85	39	37	53
DEL PEAK 8(3P14.1) WILD-TYPE	97	61	69	62	20	34	40

Figure S173. Get High-res Image Gene #17: 'del_3p14.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S174. Gene #17: 'del_3p14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
DEL PEAK 8(3P14.1) MUTATED	22	142	217	25
DEL PEAK 8(3P14.1) WILD-TYPE	100	57	68	248

Figure S174. Get High-res Image Gene #17: 'del_3p14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S175. Gene #17: 'del_3p14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
DEL PEAK 8(3P14.1) MUTATED	12	13	117	15	96	28	76	47	2
DEL PEAK 8(3P14.1) WILD-TYPE	76	48	31	69	25	10	35	12	167

Figure S175. Get High-res Image Gene #17: 'del_3p14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S176. Gene #17: 'del_3p14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
DEL PEAK 8(3P14.1) MUTATED	35	105	255
DEL PEAK 8(3P14.1) WILD-TYPE	307	89	73

Figure S176. Get High-res Image Gene #17: 'del_3p14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S177. Gene #17: 'del_3p14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
DEL PEAK 8(3P14.1) MUTATED	11	200	176	8
DEL PEAK 8(3P14.1) WILD-TYPE	65	147	57	200

Figure S177. Get High-res Image Gene #17: 'del_3p14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S178. Gene #17: 'del_3p14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
DEL PEAK 8(3P14.1) MUTATED	9	10	16	87
DEL PEAK 8(3P14.1) WILD-TYPE	147	59	49	35

Figure S178. Get High-res Image Gene #17: 'del_3p14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S179. Gene #17: 'del_3p14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
DEL PEAK 8(3P14.1) MUTATED	6	25	0	2	26	56	7
DEL PEAK 8(3P14.1) WILD-TYPE	85	58	49	18	20	21	39

Figure S179. Get High-res Image Gene #17: 'del_3p14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p12.2' versus 'MRNA_CNMF'

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

Table S180. Gene #18: 'del_3p12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
DEL PEAK 9(3P12.2) MUTATED	17	14	3	0
DEL PEAK 9(3P12.2) WILD-TYPE	14	11	10	17

Figure S180. Get High-res Image Gene #18: 'del_3p12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p12.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00031

Table S181. Gene #18: 'del_3p12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
DEL PEAK 9(3P12.2) MUTATED	12	14	1	6	1
DEL PEAK 9(3P12.2) WILD-TYPE	8	10	17	7	10

Figure S181. Get High-res Image Gene #18: 'del_3p12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S182. Gene #18: 'del_3p12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
DEL PEAK 9(3P12.2) MUTATED	8	70	258
DEL PEAK 9(3P12.2) WILD-TYPE	320	130	96

Figure S182. Get High-res Image Gene #18: 'del_3p12.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p12.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S183. Gene #18: 'del_3p12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
DEL PEAK 9(3P12.2) MUTATED	14	54	106	39	5
DEL PEAK 9(3P12.2) WILD-TYPE	88	69	65	31	181

Figure S183. Get High-res Image Gene #18: 'del_3p12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p12.2' versus 'RPPA_CNMF'

P value = 0.0478 (Fisher's exact test), Q value = 0.056

Table S184. Gene #18: 'del_3p12.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
DEL PEAK 9(3P12.2) MUTATED	73	74	62	93
DEL PEAK 9(3P12.2) WILD-TYPE	109	107	125	104

Figure S184. Get High-res Image Gene #18: 'del_3p12.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p12.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S185. Gene #18: 'del_3p12.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 9(3P12.2) MUTATED	79	2	43	64	37	32	45
DEL PEAK 9(3P12.2) WILD-TYPE	118	62	73	83	22	39	48

Figure S185. Get High-res Image Gene #18: 'del_3p12.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p12.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S186. Gene #18: 'del_3p12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
DEL PEAK 9(3P12.2) MUTATED	21	122	171	21
DEL PEAK 9(3P12.2) WILD-TYPE	101	77	114	252

Figure S186. Get High-res Image Gene #18: 'del_3p12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S187. Gene #18: 'del_3p12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
DEL PEAK 9(3P12.2) MUTATED	12	11	93	13	81	23	61	39	2
DEL PEAK 9(3P12.2) WILD-TYPE	76	50	55	71	40	15	50	20	167

Figure S187. Get High-res Image Gene #18: 'del_3p12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p12.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S188. Gene #18: 'del_3p12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
DEL PEAK 9(3P12.2) MUTATED	31	84	210
DEL PEAK 9(3P12.2) WILD-TYPE	311	110	118

Figure S188. Get High-res Image Gene #18: 'del_3p12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S189. Gene #18: 'del_3p12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
DEL PEAK 9(3P12.2) MUTATED	11	170	136	8
DEL PEAK 9(3P12.2) WILD-TYPE	65	177	97	200

Figure S189. Get High-res Image Gene #18: 'del_3p12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p12.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S190. Gene #18: 'del_3p12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
DEL PEAK 9(3P12.2) MUTATED	8	8	12	77
DEL PEAK 9(3P12.2) WILD-TYPE	148	61	53	45

Figure S190. Get High-res Image Gene #18: 'del_3p12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S191. Gene #18: 'del_3p12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
DEL PEAK 9(3P12.2) MUTATED	6	21	0	1	22	48	7
DEL PEAK 9(3P12.2) WILD-TYPE	85	62	49	19	24	29	39

Figure S191. Get High-res Image Gene #18: 'del_3p12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S192. Gene #19: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
DEL PEAK 10(4Q34.3) MUTATED	26	10	77
DEL PEAK 10(4Q34.3) WILD-TYPE	302	190	277

Figure S192. Get High-res Image Gene #19: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S193. Gene #19: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
DEL PEAK 10(4Q34.3) MUTATED	6	21	21	30	8
DEL PEAK 10(4Q34.3) WILD-TYPE	96	102	150	40	178

Figure S193. Get High-res Image Gene #19: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q34.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00057 (Fisher's exact test), Q value = 0.00082

Table S194. Gene #19: 'del_4q34.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 10(4Q34.3) MUTATED	24	4	27	11	14	6	16
DEL PEAK 10(4Q34.3) WILD-TYPE	173	60	89	136	45	65	77

Figure S194. Get High-res Image Gene #19: 'del_4q34.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S195. Gene #19: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
DEL PEAK 10(4Q34.3) MUTATED	8	48	32	25
DEL PEAK 10(4Q34.3) WILD-TYPE	114	151	253	248

Figure S195. Get High-res Image Gene #19: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S196. Gene #19: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
DEL PEAK 10(4Q34.3) MUTATED	2	18	20	18	31	6	11	5	2
DEL PEAK 10(4Q34.3) WILD-TYPE	86	43	128	66	90	32	100	54	167

Figure S196. Get High-res Image Gene #19: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CNMF'

P value = 0.00617 (Fisher's exact test), Q value = 0.008

Table S197. Gene #19: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
DEL PEAK 10(4Q34.3) MUTATED	31	36	45
DEL PEAK 10(4Q34.3) WILD-TYPE	311	158	283

Figure S197. Get High-res Image Gene #19: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S198. Gene #19: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
DEL PEAK 10(4Q34.3) MUTATED	2	72	26	12
DEL PEAK 10(4Q34.3) WILD-TYPE	74	275	207	196

Figure S198. Get High-res Image Gene #19: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.00088

Table S199. Gene #19: 'del_4q34.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
DEL PEAK 10(4Q34.3) MUTATED	11	6	18	16
DEL PEAK 10(4Q34.3) WILD-TYPE	145	63	47	106

Figure S199. Get High-res Image Gene #19: 'del_4q34.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 7.9e-05

Table S200. Gene #19: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
DEL PEAK 10(4Q34.3) MUTATED	7	20	0	2	11	9	2
DEL PEAK 10(4Q34.3) WILD-TYPE	84	63	49	18	35	68	44

Figure S200. Get High-res Image Gene #19: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5p15.33' versus 'CN_CNMF'

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

Table S201. Gene #20: 'del_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
DEL PEAK 11(5P15.33) MUTATED	22	6	3
DEL PEAK 11(5P15.33) WILD-TYPE	306	194	351

Figure S201. Get High-res Image Gene #20: 'del_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_5p15.33' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 4e-04

Table S202. Gene #20: 'del_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
DEL PEAK 11(5P15.33) MUTATED	13	4	1	3	8
DEL PEAK 11(5P15.33) WILD-TYPE	89	119	170	67	178

Figure S202. Get High-res Image Gene #20: 'del_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5p15.33' versus 'RPPA_CNMF'

P value = 0.0349 (Fisher's exact test), Q value = 0.042

Table S203. Gene #20: 'del_5p15.33' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
DEL PEAK 11(5P15.33) MUTATED	12	8	2	6
DEL PEAK 11(5P15.33) WILD-TYPE	170	173	185	191

Figure S203. Get High-res Image Gene #20: 'del_5p15.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_5p15.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.0473 (Fisher's exact test), Q value = 0.056

Table S204. Gene #20: 'del_5p15.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 11(5P15.33) MUTATED	6	3	2	2	6	3	6
DEL PEAK 11(5P15.33) WILD-TYPE	191	61	114	145	53	68	87

Figure S204. Get High-res Image Gene #20: 'del_5p15.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_5p15.33' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4.9e-05

Table S205. Gene #20: 'del_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
DEL PEAK 11(5P15.33) MUTATED	12	9	1	9
DEL PEAK 11(5P15.33) WILD-TYPE	110	190	284	264

Figure S205. Get High-res Image Gene #20: 'del_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S206. Gene #20: 'del_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
DEL PEAK 11(5P15.33) MUTATED	11	7	1	5	4	0	0	1	2
DEL PEAK 11(5P15.33) WILD-TYPE	77	54	147	79	117	38	111	58	167

Figure S206. Get High-res Image Gene #20: 'del_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5p15.33' versus 'MIRSEQ_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.00097

Table S207. Gene #20: 'del_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
DEL PEAK 11(5P15.33) MUTATED	21	7	3
DEL PEAK 11(5P15.33) WILD-TYPE	321	187	325

Figure S207. Get High-res Image Gene #20: 'del_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S208. Gene #20: 'del_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
DEL PEAK 11(5P15.33) MUTATED	11	14	0	6
DEL PEAK 11(5P15.33) WILD-TYPE	65	333	233	202

Figure S208. Get High-res Image Gene #20: 'del_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00426 (Fisher's exact test), Q value = 0.0056

Table S209. Gene #20: 'del_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
DEL PEAK 11(5P15.33) MUTATED	6	8	5	1
DEL PEAK 11(5P15.33) WILD-TYPE	150	61	60	121

Figure S209. Get High-res Image Gene #20: 'del_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00021

Table S210. Gene #20: 'del_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
DEL PEAK 11(5P15.33) MUTATED	3	8	1	0	0	0	8
DEL PEAK 11(5P15.33) WILD-TYPE	88	75	48	20	46	77	38

Figure S210. Get High-res Image Gene #20: 'del_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q26' versus 'MRNA_CNMF'

P value = 0.0014 (Fisher's exact test), Q value = 0.0019

Table S211. Gene #21: 'del_6q26' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
DEL PEAK 12(6Q26) MUTATED	7	12	8	1
DEL PEAK 12(6Q26) WILD-TYPE	24	13	5	16

Figure S211. Get High-res Image Gene #21: 'del_6q26' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_6q26' versus 'MRNA_CHIERARCHICAL'

P value = 0.00805 (Fisher's exact test), Q value = 0.01

Table S212. Gene #21: 'del_6q26' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
DEL PEAK 12(6Q26) MUTATED	4	12	2	3	7
DEL PEAK 12(6Q26) WILD-TYPE	16	12	16	10	4

Figure S212. Get High-res Image Gene #21: 'del_6q26' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S213. Gene #21: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
DEL PEAK 12(6Q26) MUTATED	78	11	144
DEL PEAK 12(6Q26) WILD-TYPE	250	189	210

Figure S213. Get High-res Image Gene #21: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S214. Gene #21: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
DEL PEAK 12(6Q26) MUTATED	58	29	33	29	12
DEL PEAK 12(6Q26) WILD-TYPE	44	94	138	41	174

Figure S214. Get High-res Image Gene #21: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q26' versus 'RPPA_CNMF'

P value = 0.0036 (Fisher's exact test), Q value = 0.0048

Table S215. Gene #21: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
DEL PEAK 12(6Q26) MUTATED	41	51	43	74
DEL PEAK 12(6Q26) WILD-TYPE	141	130	144	123

Figure S215. Get High-res Image Gene #21: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_6q26' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S216. Gene #21: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 12(6Q26) MUTATED	62	14	51	34	24	8	16
DEL PEAK 12(6Q26) WILD-TYPE	135	50	65	113	35	63	77

Figure S216. Get High-res Image Gene #21: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S217. Gene #21: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
DEL PEAK 12(6Q26) MUTATED	67	70	65	29
DEL PEAK 12(6Q26) WILD-TYPE	55	129	220	244

Figure S217. Get High-res Image Gene #21: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S218. Gene #21: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
DEL PEAK 12(6Q26) MUTATED	61	18	30	15	49	9	28	16	5
DEL PEAK 12(6Q26) WILD-TYPE	27	43	118	69	72	29	83	43	164

Figure S218. Get High-res Image Gene #21: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S219. Gene #21: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
DEL PEAK 12(6Q26) MUTATED	60	97	52	20
DEL PEAK 12(6Q26) WILD-TYPE	16	250	181	188

Figure S219. Get High-res Image Gene #21: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S220. Gene #21: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
DEL PEAK 12(6Q26) MUTATED	12	39	15	29
DEL PEAK 12(6Q26) WILD-TYPE	144	30	50	93

Figure S220. Get High-res Image Gene #21: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S221. Gene #21: 'del_6q26' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
DEL PEAK 12(6Q26) MUTATED	9	16	2	0	15	16	37
DEL PEAK 12(6Q26) WILD-TYPE	82	67	47	20	31	61	9

Figure S221. Get High-res Image Gene #21: 'del_6q26' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q26' versus 'MRNA_CNMF'

P value = 0.00144 (Fisher's exact test), Q value = 0.002

Table S222. Gene #22: 'del_6q26' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
DEL PEAK 13(6Q26) MUTATED	7	12	8	1
DEL PEAK 13(6Q26) WILD-TYPE	24	13	5	16

Figure S222. Get High-res Image Gene #22: 'del_6q26' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_6q26' versus 'MRNA_CHIERARCHICAL'

P value = 0.00772 (Fisher's exact test), Q value = 0.0099

Table S223. Gene #22: 'del_6q26' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
DEL PEAK 13(6Q26) MUTATED	4	12	2	3	7
DEL PEAK 13(6Q26) WILD-TYPE	16	12	16	10	4

Figure S223. Get High-res Image Gene #22: 'del_6q26' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S224. Gene #22: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
DEL PEAK 13(6Q26) MUTATED	79	10	145
DEL PEAK 13(6Q26) WILD-TYPE	249	190	209

Figure S224. Get High-res Image Gene #22: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S225. Gene #22: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
DEL PEAK 13(6Q26) MUTATED	58	30	32	29	13
DEL PEAK 13(6Q26) WILD-TYPE	44	93	139	41	173

Figure S225. Get High-res Image Gene #22: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q26' versus 'RPPA_CNMF'

P value = 0.00327 (Fisher's exact test), Q value = 0.0044

Table S226. Gene #22: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
DEL PEAK 13(6Q26) MUTATED	41	51	43	74
DEL PEAK 13(6Q26) WILD-TYPE	141	130	144	123

Figure S226. Get High-res Image Gene #22: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_6q26' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S227. Gene #22: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 13(6Q26) MUTATED	61	14	51	34	25	8	16
DEL PEAK 13(6Q26) WILD-TYPE	136	50	65	113	34	63	77

Figure S227. Get High-res Image Gene #22: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S228. Gene #22: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
DEL PEAK 13(6Q26) MUTATED	67	71	64	30
DEL PEAK 13(6Q26) WILD-TYPE	55	128	221	243

Figure S228. Get High-res Image Gene #22: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S229. Gene #22: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
DEL PEAK 13(6Q26) MUTATED	61	18	30	15	50	8	28	16	6
DEL PEAK 13(6Q26) WILD-TYPE	27	43	118	69	71	30	83	43	163

Figure S229. Get High-res Image Gene #22: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S230. Gene #22: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
DEL PEAK 13(6Q26) MUTATED	60	97	52	21
DEL PEAK 13(6Q26) WILD-TYPE	16	250	181	187

Figure S230. Get High-res Image Gene #22: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S231. Gene #22: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
DEL PEAK 13(6Q26) MUTATED	12	39	15	29
DEL PEAK 13(6Q26) WILD-TYPE	144	30	50	93

Figure S231. Get High-res Image Gene #22: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S232. Gene #22: 'del_6q26' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
DEL PEAK 13(6Q26) MUTATED	9	16	2	0	15	16	37
DEL PEAK 13(6Q26) WILD-TYPE	82	67	47	20	31	61	9

Figure S232. Get High-res Image Gene #22: 'del_6q26' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S233. Gene #23: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
DEL PEAK 14(8P23.2) MUTATED	31	28	125
DEL PEAK 14(8P23.2) WILD-TYPE	297	172	229

Figure S233. Get High-res Image Gene #23: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S234. Gene #23: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
DEL PEAK 14(8P23.2) MUTATED	16	30	39	22	7
DEL PEAK 14(8P23.2) WILD-TYPE	86	93	132	48	179

Figure S234. Get High-res Image Gene #23: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00768 (Fisher's exact test), Q value = 0.0099

Table S235. Gene #23: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 14(8P23.2) MUTATED	37	8	29	27	21	11	28
DEL PEAK 14(8P23.2) WILD-TYPE	160	56	87	120	38	60	65

Figure S235. Get High-res Image Gene #23: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S236. Gene #23: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
DEL PEAK 14(8P23.2) MUTATED	22	76	70	15
DEL PEAK 14(8P23.2) WILD-TYPE	100	123	215	258

Figure S236. Get High-res Image Gene #23: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S237. Gene #23: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
DEL PEAK 14(8P23.2) MUTATED	17	11	39	5	56	6	25	20	4
DEL PEAK 14(8P23.2) WILD-TYPE	71	50	109	79	65	32	86	39	165

Figure S237. Get High-res Image Gene #23: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S238. Gene #23: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
DEL PEAK 14(8P23.2) MUTATED	33	55	93
DEL PEAK 14(8P23.2) WILD-TYPE	309	139	235

Figure S238. Get High-res Image Gene #23: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S239. Gene #23: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
DEL PEAK 14(8P23.2) MUTATED	15	107	52	7
DEL PEAK 14(8P23.2) WILD-TYPE	61	240	181	201

Figure S239. Get High-res Image Gene #23: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S240. Gene #23: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
DEL PEAK 14(8P23.2) MUTATED	5	10	10	35
DEL PEAK 14(8P23.2) WILD-TYPE	151	59	55	87

Figure S240. Get High-res Image Gene #23: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S241. Gene #23: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
DEL PEAK 14(8P23.2) MUTATED	4	10	1	2	17	19	7
DEL PEAK 14(8P23.2) WILD-TYPE	87	73	48	18	29	58	39

Figure S241. Get High-res Image Gene #23: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'MRNA_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.022

Table S242. Gene #24: 'del_9p23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
DEL PEAK 15(9P23) MUTATED	5	12	1	3
DEL PEAK 15(9P23) WILD-TYPE	26	13	12	14

Figure S242. Get High-res Image Gene #24: 'del_9p23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p23' versus 'MRNA_CHIERARCHICAL'

P value = 0.0215 (Fisher's exact test), Q value = 0.026

Table S243. Gene #24: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
DEL PEAK 15(9P23) MUTATED	4	12	3	1	1
DEL PEAK 15(9P23) WILD-TYPE	16	12	15	12	10

Figure S243. Get High-res Image Gene #24: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S244. Gene #24: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
DEL PEAK 15(9P23) MUTATED	34	13	151
DEL PEAK 15(9P23) WILD-TYPE	294	187	203

Figure S244. Get High-res Image Gene #24: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S245. Gene #24: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
DEL PEAK 15(9P23) MUTATED	16	46	23	44	9
DEL PEAK 15(9P23) WILD-TYPE	86	77	148	26	177

Figure S245. Get High-res Image Gene #24: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p23' versus 'RPPA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4.9e-05

Table S246. Gene #24: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
DEL PEAK 15(9P23) MUTATED	49	36	24	70
DEL PEAK 15(9P23) WILD-TYPE	133	145	163	127

Figure S246. Get High-res Image Gene #24: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p23' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S247. Gene #24: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 15(9P23) MUTATED	44	6	42	21	30	11	25
DEL PEAK 15(9P23) WILD-TYPE	153	58	74	126	29	60	68

Figure S247. Get High-res Image Gene #24: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S248. Gene #24: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
DEL PEAK 15(9P23) MUTATED	19	107	37	34
DEL PEAK 15(9P23) WILD-TYPE	103	92	248	239

Figure S248. Get High-res Image Gene #24: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S249. Gene #24: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
DEL PEAK 15(9P23) MUTATED	11	24	24	15	76	12	10	20	5
DEL PEAK 15(9P23) WILD-TYPE	77	37	124	69	45	26	101	39	164

Figure S249. Get High-res Image Gene #24: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S250. Gene #24: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
DEL PEAK 15(9P23) MUTATED	40	65	88
DEL PEAK 15(9P23) WILD-TYPE	302	129	240

Figure S250. Get High-res Image Gene #24: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S251. Gene #24: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
DEL PEAK 15(9P23) MUTATED	10	135	32	16
DEL PEAK 15(9P23) WILD-TYPE	66	212	201	192

Figure S251. Get High-res Image Gene #24: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S252. Gene #24: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
DEL PEAK 15(9P23) MUTATED	11	10	24	27
DEL PEAK 15(9P23) WILD-TYPE	145	59	41	95

Figure S252. Get High-res Image Gene #24: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 7.9e-05

Table S253. Gene #24: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
DEL PEAK 15(9P23) MUTATED	8	26	2	4	15	11	6
DEL PEAK 15(9P23) WILD-TYPE	83	57	47	16	31	66	40

Figure S253. Get High-res Image Gene #24: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.3' versus 'MRNA_CNMF'

P value = 0.00546 (Fisher's exact test), Q value = 0.0071

Table S254. Gene #25: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
DEL PEAK 16(9P21.3) MUTATED	5	13	1	3
DEL PEAK 16(9P21.3) WILD-TYPE	26	12	12	14

Figure S254. Get High-res Image Gene #25: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p21.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00738 (Fisher's exact test), Q value = 0.0095

Table S255. Gene #25: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
DEL PEAK 16(9P21.3) MUTATED	4	13	3	1	1
DEL PEAK 16(9P21.3) WILD-TYPE	16	11	15	12	10

Figure S255. Get High-res Image Gene #25: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S256. Gene #25: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
DEL PEAK 16(9P21.3) MUTATED	38	14	157
DEL PEAK 16(9P21.3) WILD-TYPE	290	186	197

Figure S256. Get High-res Image Gene #25: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S257. Gene #25: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
DEL PEAK 16(9P21.3) MUTATED	18	52	24	42	9
DEL PEAK 16(9P21.3) WILD-TYPE	84	71	147	28	177

Figure S257. Get High-res Image Gene #25: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S258. Gene #25: 'del_9p21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
DEL PEAK 16(9P21.3) MUTATED	56	37	24	70
DEL PEAK 16(9P21.3) WILD-TYPE	126	144	163	127

Figure S258. Get High-res Image Gene #25: 'del_9p21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S259. Gene #25: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 16(9P21.3) MUTATED	41	6	46	23	30	12	29
DEL PEAK 16(9P21.3) WILD-TYPE	156	58	70	124	29	59	64

Figure S259. Get High-res Image Gene #25: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S260. Gene #25: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
DEL PEAK 16(9P21.3) MUTATED	20	115	38	35
DEL PEAK 16(9P21.3) WILD-TYPE	102	84	247	238

Figure S260. Get High-res Image Gene #25: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S261. Gene #25: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
DEL PEAK 16(9P21.3) MUTATED	11	30	25	15	79	13	10	20	5
DEL PEAK 16(9P21.3) WILD-TYPE	77	31	123	69	42	25	101	39	164

Figure S261. Get High-res Image Gene #25: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S262. Gene #25: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
DEL PEAK 16(9P21.3) MUTATED	43	73	87
DEL PEAK 16(9P21.3) WILD-TYPE	299	121	241

Figure S262. Get High-res Image Gene #25: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S263. Gene #25: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
DEL PEAK 16(9P21.3) MUTATED	10	144	32	17
DEL PEAK 16(9P21.3) WILD-TYPE	66	203	201	191

Figure S263. Get High-res Image Gene #25: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S264. Gene #25: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
DEL PEAK 16(9P21.3) MUTATED	10	10	27	29
DEL PEAK 16(9P21.3) WILD-TYPE	146	59	38	93

Figure S264. Get High-res Image Gene #25: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S265. Gene #25: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
DEL PEAK 16(9P21.3) MUTATED	7	30	2	4	17	10	6
DEL PEAK 16(9P21.3) WILD-TYPE	84	53	47	16	29	67	40

Figure S265. Get High-res Image Gene #25: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S266. Gene #26: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
DEL PEAK 17(10Q23.31) MUTATED	62	16	86
DEL PEAK 17(10Q23.31) WILD-TYPE	266	184	268

Figure S266. Get High-res Image Gene #26: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S267. Gene #26: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
DEL PEAK 17(10Q23.31) MUTATED	57	22	23	20	4
DEL PEAK 17(10Q23.31) WILD-TYPE	45	101	148	50	182

Figure S267. Get High-res Image Gene #26: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q23.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.00073

Table S268. Gene #26: 'del_10q23.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 17(10Q23.31) MUTATED	35	10	41	26	13	6	15
DEL PEAK 17(10Q23.31) WILD-TYPE	162	54	75	121	46	65	78

Figure S268. Get High-res Image Gene #26: 'del_10q23.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S269. Gene #26: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
DEL PEAK 17(10Q23.31) MUTATED	64	45	40	14
DEL PEAK 17(10Q23.31) WILD-TYPE	58	154	245	259

Figure S269. Get High-res Image Gene #26: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S270. Gene #26: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
DEL PEAK 17(10Q23.31) MUTATED	60	9	24	13	32	3	15	6	1
DEL PEAK 17(10Q23.31) WILD-TYPE	28	52	124	71	89	35	96	53	168

Figure S270. Get High-res Image Gene #26: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S271. Gene #26: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
DEL PEAK 17(10Q23.31) MUTATED	58	69	29	6
DEL PEAK 17(10Q23.31) WILD-TYPE	18	278	204	202

Figure S271. Get High-res Image Gene #26: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S272. Gene #26: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
DEL PEAK 17(10Q23.31) MUTATED	3	40	12	15
DEL PEAK 17(10Q23.31) WILD-TYPE	153	29	53	107

Figure S272. Get High-res Image Gene #26: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S273. Gene #26: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
DEL PEAK 17(10Q23.31) MUTATED	1	12	1	3	9	9	35
DEL PEAK 17(10Q23.31) WILD-TYPE	90	71	48	17	37	68	11

Figure S273. Get High-res Image Gene #26: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q23.1' versus 'CN_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00033

Table S274. Gene #27: 'del_11q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
DEL PEAK 18(11Q23.1) MUTATED	28	4	39
DEL PEAK 18(11Q23.1) WILD-TYPE	300	196	315

Figure S274. Get High-res Image Gene #27: 'del_11q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S275. Gene #27: 'del_11q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
DEL PEAK 18(11Q23.1) MUTATED	10	20	5	18	8
DEL PEAK 18(11Q23.1) WILD-TYPE	92	103	166	52	178

Figure S275. Get High-res Image Gene #27: 'del_11q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00073 (Fisher's exact test), Q value = 0.001

Table S276. Gene #27: 'del_11q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 18(11Q23.1) MUTATED	10	5	19	6	10	3	10
DEL PEAK 18(11Q23.1) WILD-TYPE	187	59	97	141	49	68	83

Figure S276. Get High-res Image Gene #27: 'del_11q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_11q23.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.3e-05

Table S277. Gene #27: 'del_11q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
DEL PEAK 18(11Q23.1) MUTATED	13	24	6	28
DEL PEAK 18(11Q23.1) WILD-TYPE	109	175	279	245

Figure S277. Get High-res Image Gene #27: 'del_11q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S278. Gene #27: 'del_11q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
DEL PEAK 18(11Q23.1) MUTATED	8	16	4	14	17	1	1	3	7
DEL PEAK 18(11Q23.1) WILD-TYPE	80	45	144	70	104	37	110	56	162

Figure S278. Get High-res Image Gene #27: 'del_11q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.1' versus 'MIRSEQ_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.018

Table S279. Gene #27: 'del_11q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
DEL PEAK 18(11Q23.1) MUTATED	34	21	16
DEL PEAK 18(11Q23.1) WILD-TYPE	308	173	312

Figure S279. Get High-res Image Gene #27: 'del_11q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.3e-05

Table S280. Gene #27: 'del_11q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
DEL PEAK 18(11Q23.1) MUTATED	8	43	4	16
DEL PEAK 18(11Q23.1) WILD-TYPE	68	304	229	192

Figure S280. Get High-res Image Gene #27: 'del_11q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S281. Gene #27: 'del_11q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
DEL PEAK 18(11Q23.1) MUTATED	9	9	18	2
DEL PEAK 18(11Q23.1) WILD-TYPE	147	60	47	120

Figure S281. Get High-res Image Gene #27: 'del_11q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.3e-05

Table S282. Gene #27: 'del_11q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
DEL PEAK 18(11Q23.1) MUTATED	6	19	1	0	4	1	7
DEL PEAK 18(11Q23.1) WILD-TYPE	85	64	48	20	42	76	39

Figure S282. Get High-res Image Gene #27: 'del_11q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q13.2' versus 'MRNA_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 0.029

Table S283. Gene #28: 'del_13q13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
DEL PEAK 19(13Q13.2) MUTATED	1	7	3	1
DEL PEAK 19(13Q13.2) WILD-TYPE	30	18	10	16

Figure S283. Get High-res Image Gene #28: 'del_13q13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q13.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0177 (Fisher's exact test), Q value = 0.022

Table S284. Gene #28: 'del_13q13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
DEL PEAK 19(13Q13.2) MUTATED	0	7	1	1	3
DEL PEAK 19(13Q13.2) WILD-TYPE	20	17	17	12	8

Figure S284. Get High-res Image Gene #28: 'del_13q13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q13.2' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4.9e-05

Table S285. Gene #28: 'del_13q13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
DEL PEAK 19(13Q13.2) MUTATED	69	13	67
DEL PEAK 19(13Q13.2) WILD-TYPE	259	187	287

Figure S285. Get High-res Image Gene #28: 'del_13q13.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S286. Gene #28: 'del_13q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
DEL PEAK 19(13Q13.2) MUTATED	51	29	10	20	7
DEL PEAK 19(13Q13.2) WILD-TYPE	51	94	161	50	179

Figure S286. Get High-res Image Gene #28: 'del_13q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q13.2' versus 'RPPA_CNMF'

P value = 0.036 (Fisher's exact test), Q value = 0.043

Table S287. Gene #28: 'del_13q13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
DEL PEAK 19(13Q13.2) MUTATED	42	25	26	41
DEL PEAK 19(13Q13.2) WILD-TYPE	140	156	161	156

Figure S287. Get High-res Image Gene #28: 'del_13q13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q13.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S288. Gene #28: 'del_13q13.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 19(13Q13.2) MUTATED	26	10	41	12	18	7	20
DEL PEAK 19(13Q13.2) WILD-TYPE	171	54	75	135	41	64	73

Figure S288. Get High-res Image Gene #28: 'del_13q13.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_13q13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S289. Gene #28: 'del_13q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
DEL PEAK 19(13Q13.2) MUTATED	56	57	20	16
DEL PEAK 19(13Q13.2) WILD-TYPE	66	142	265	257

Figure S289. Get High-res Image Gene #28: 'del_13q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S290. Gene #28: 'del_13q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
DEL PEAK 19(13Q13.2) MUTATED	52	19	6	9	39	8	11	3	2
DEL PEAK 19(13Q13.2) WILD-TYPE	36	42	142	75	82	30	100	56	167

Figure S290. Get High-res Image Gene #28: 'del_13q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q13.2' versus 'MIRSEQ_CNMF'

P value = 0.00308 (Fisher's exact test), Q value = 0.0041

Table S291. Gene #28: 'del_13q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
DEL PEAK 19(13Q13.2) MUTATED	69	40	38
DEL PEAK 19(13Q13.2) WILD-TYPE	273	154	290

Figure S291. Get High-res Image Gene #28: 'del_13q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S292. Gene #28: 'del_13q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
DEL PEAK 19(13Q13.2) MUTATED	50	69	17	11
DEL PEAK 19(13Q13.2) WILD-TYPE	26	278	216	197

Figure S292. Get High-res Image Gene #28: 'del_13q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S293. Gene #28: 'del_13q13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
DEL PEAK 19(13Q13.2) MUTATED	6	33	19	11
DEL PEAK 19(13Q13.2) WILD-TYPE	150	36	46	111

Figure S293. Get High-res Image Gene #28: 'del_13q13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_13q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S294. Gene #28: 'del_13q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
DEL PEAK 19(13Q13.2) MUTATED	3	20	1	1	9	4	31
DEL PEAK 19(13Q13.2) WILD-TYPE	88	63	48	19	37	73	15

Figure S294. Get High-res Image Gene #28: 'del_13q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q31.1' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4.9e-05

Table S295. Gene #29: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
DEL PEAK 20(14Q31.1) MUTATED	9	20	2	4
DEL PEAK 20(14Q31.1) WILD-TYPE	22	5	11	13

Figure S295. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q31.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.00033

Table S296. Gene #29: 'del_14q31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
DEL PEAK 20(14Q31.1) MUTATED	5	19	4	5	2
DEL PEAK 20(14Q31.1) WILD-TYPE	15	5	14	8	9

Figure S296. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S297. Gene #29: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
DEL PEAK 20(14Q31.1) MUTATED	44	33	202
DEL PEAK 20(14Q31.1) WILD-TYPE	284	167	152

Figure S297. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q31.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S298. Gene #29: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
DEL PEAK 20(14Q31.1) MUTATED	5	57	60	42	16
DEL PEAK 20(14Q31.1) WILD-TYPE	97	66	111	28	170

Figure S298. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q31.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S299. Gene #29: 'del_14q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
DEL PEAK 20(14Q31.1) MUTATED	62	61	34	88
DEL PEAK 20(14Q31.1) WILD-TYPE	120	120	153	109

Figure S299. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_14q31.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S300. Gene #29: 'del_14q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 20(14Q31.1) MUTATED	65	3	46	43	32	18	38
DEL PEAK 20(14Q31.1) WILD-TYPE	132	61	70	104	27	53	55

Figure S300. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_14q31.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S301. Gene #29: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
DEL PEAK 20(14Q31.1) MUTATED	12	121	97	46
DEL PEAK 20(14Q31.1) WILD-TYPE	110	78	188	227

Figure S301. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S302. Gene #29: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
DEL PEAK 20(14Q31.1) MUTATED	5	22	50	18	76	34	33	27	11
DEL PEAK 20(14Q31.1) WILD-TYPE	83	39	98	66	45	4	78	32	158

Figure S302. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q31.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S303. Gene #29: 'del_14q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
DEL PEAK 20(14Q31.1) MUTATED	47	80	146
DEL PEAK 20(14Q31.1) WILD-TYPE	295	114	182

Figure S303. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_14q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S304. Gene #29: 'del_14q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
DEL PEAK 20(14Q31.1) MUTATED	4	165	83	21
DEL PEAK 20(14Q31.1) WILD-TYPE	72	182	150	187

Figure S304. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q31.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S305. Gene #29: 'del_14q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
DEL PEAK 20(14Q31.1) MUTATED	17	5	22	49
DEL PEAK 20(14Q31.1) WILD-TYPE	139	64	43	73

Figure S305. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_14q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S306. Gene #29: 'del_14q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
DEL PEAK 20(14Q31.1) MUTATED	9	32	4	3	15	28	2
DEL PEAK 20(14Q31.1) WILD-TYPE	82	51	45	17	31	49	44

Figure S306. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.3' versus 'METHLYATION_CNMF'

P value = 0.00378 (Fisher's exact test), Q value = 0.005

Table S307. Gene #30: 'del_16q23.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
DEL PEAK 21(16Q23.3) MUTATED	7	8	5	7	2
DEL PEAK 21(16Q23.3) WILD-TYPE	95	115	166	63	184

Figure S307. Get High-res Image Gene #30: 'del_16q23.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16q23.3' versus 'MRNASEQ_CNMF'

P value = 0.0328 (Fisher's exact test), Q value = 0.039

Table S308. Gene #30: 'del_16q23.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
DEL PEAK 21(16Q23.3) MUTATED	9	13	8	7
DEL PEAK 21(16Q23.3) WILD-TYPE	113	186	277	266

Figure S308. Get High-res Image Gene #30: 'del_16q23.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16q23.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S309. Gene #30: 'del_16q23.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
DEL PEAK 21(16Q23.3) MUTATED	5	8	5	6	9	1	3	0	0
DEL PEAK 21(16Q23.3) WILD-TYPE	83	53	143	78	112	37	108	59	169

Figure S309. Get High-res Image Gene #30: 'del_16q23.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.015

Table S310. Gene #30: 'del_16q23.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
DEL PEAK 21(16Q23.3) MUTATED	5	22	4	5
DEL PEAK 21(16Q23.3) WILD-TYPE	71	325	229	203

Figure S310. Get High-res Image Gene #30: 'del_16q23.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.015

Table S311. Gene #30: 'del_16q23.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
DEL PEAK 21(16Q23.3) MUTATED	3	7	7	6
DEL PEAK 21(16Q23.3) WILD-TYPE	153	62	58	116

Figure S311. Get High-res Image Gene #30: 'del_16q23.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'CN_CNMF'

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

Table S312. Gene #31: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
DEL PEAK 22(19P13.3) MUTATED	17	0	26
DEL PEAK 22(19P13.3) WILD-TYPE	311	200	328

Figure S312. Get High-res Image Gene #31: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 6.4e-05

Table S313. Gene #31: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
DEL PEAK 22(19P13.3) MUTATED	4	9	1	12	10
DEL PEAK 22(19P13.3) WILD-TYPE	98	114	170	58	176

Figure S313. Get High-res Image Gene #31: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0186 (Fisher's exact test), Q value = 0.023

Table S314. Gene #31: 'del_19p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 22(19P13.3) MUTATED	6	1	13	3	2	3	6
DEL PEAK 22(19P13.3) WILD-TYPE	191	63	103	144	57	68	87

Figure S314. Get High-res Image Gene #31: 'del_19p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S315. Gene #31: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
DEL PEAK 22(19P13.3) MUTATED	3	14	2	24
DEL PEAK 22(19P13.3) WILD-TYPE	119	185	283	249

Figure S315. Get High-res Image Gene #31: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S316. Gene #31: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
DEL PEAK 22(19P13.3) MUTATED	2	10	1	12	9	0	1	0	8
DEL PEAK 22(19P13.3) WILD-TYPE	86	51	147	72	112	38	110	59	161

Figure S316. Get High-res Image Gene #31: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 0.00657 (Fisher's exact test), Q value = 0.0085

Table S317. Gene #31: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
DEL PEAK 22(19P13.3) MUTATED	24	12	7
DEL PEAK 22(19P13.3) WILD-TYPE	318	182	321

Figure S317. Get High-res Image Gene #31: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.00072

Table S318. Gene #31: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
DEL PEAK 22(19P13.3) MUTATED	2	27	2	12
DEL PEAK 22(19P13.3) WILD-TYPE	74	320	231	196

Figure S318. Get High-res Image Gene #31: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

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

Table S319. Gene #31: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
DEL PEAK 22(19P13.3) MUTATED	11	2	13	2
DEL PEAK 22(19P13.3) WILD-TYPE	145	67	52	120

Figure S319. Get High-res Image Gene #31: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0282 (Fisher's exact test), Q value = 0.034

Table S320. Gene #31: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
DEL PEAK 22(19P13.3) MUTATED	7	12	1	1	4	1	2
DEL PEAK 22(19P13.3) WILD-TYPE	84	71	48	19	42	76	44

Figure S320. Get High-res Image Gene #31: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp22.2' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 2e-04

Table S321. Gene #32: 'del_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
DEL PEAK 23(XP22.2) MUTATED	65	14	46
DEL PEAK 23(XP22.2) WILD-TYPE	263	186	308

Figure S321. Get High-res Image Gene #32: 'del_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_xp22.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S322. Gene #32: 'del_xp22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
DEL PEAK 23(XP22.2) MUTATED	48	12	16	19	10
DEL PEAK 23(XP22.2) WILD-TYPE	54	111	155	51	176

Figure S322. Get High-res Image Gene #32: 'del_xp22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xp22.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S323. Gene #32: 'del_xp22.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
DEL PEAK 23(XP22.2) MUTATED	33	9	31	12	3	3	15
DEL PEAK 23(XP22.2) WILD-TYPE	164	55	85	135	56	68	78

Figure S323. Get High-res Image Gene #32: 'del_xp22.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_xp22.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S324. Gene #32: 'del_xp22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
DEL PEAK 23(XP22.2) MUTATED	53	21	24	27
DEL PEAK 23(XP22.2) WILD-TYPE	69	178	261	246

Figure S324. Get High-res Image Gene #32: 'del_xp22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_xp22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S325. Gene #32: 'del_xp22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
DEL PEAK 23(XP22.2) MUTATED	50	14	11	16	10	5	7	7	5
DEL PEAK 23(XP22.2) WILD-TYPE	38	47	137	68	111	33	104	52	164

Figure S325. Get High-res Image Gene #32: 'del_xp22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_xp22.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S326. Gene #32: 'del_xp22.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
DEL PEAK 23(XP22.2) MUTATED	76	19	29
DEL PEAK 23(XP22.2) WILD-TYPE	266	175	299

Figure S326. Get High-res Image Gene #32: 'del_xp22.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_xp22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S327. Gene #32: 'del_xp22.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
DEL PEAK 23(XP22.2) MUTATED	48	45	17	14
DEL PEAK 23(XP22.2) WILD-TYPE	28	302	216	194

Figure S327. Get High-res Image Gene #32: 'del_xp22.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_xp22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S328. Gene #32: 'del_xp22.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
DEL PEAK 23(XP22.2) MUTATED	8	34	12	9
DEL PEAK 23(XP22.2) WILD-TYPE	148	35	53	113

Figure S328. Get High-res Image Gene #32: 'del_xp22.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_xp22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S329. Gene #32: 'del_xp22.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
DEL PEAK 23(XP22.2) MUTATED	5	19	0	3	4	3	29
DEL PEAK 23(XP22.2) WILD-TYPE	86	64	49	17	42	74	17

Figure S329. Get High-res Image Gene #32: 'del_xp22.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIPAN-TP/22533781/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIPAN-TP/22570984/KIPAN-TP.transferedmergedcluster.txt
Number of patients = 882
Number of significantly focal cnvs = 32
Number of molecular subtypes = 12
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

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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