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 76 focal events and 10 molecular subtypes across 522 patients, 397 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_2q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_2q31.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_3q26.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
amp_5p15.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_5p12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_6p12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_6q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_7p11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_7q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_8p11.23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_9p24.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_9p23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_9p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_9q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.
amp_11p13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_11q13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_12p13.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
amp_12q15 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_13q22.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_13q34 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_15q26.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_17q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_18p11.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_18q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_20q11.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_xq28 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_1p36.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_1q44 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_2q21.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_2q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_2q36.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_3p26.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p24.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_3p14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_3p12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_4p16.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4p15.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_4q35.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_5q12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_5q15 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_5q35.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_6p25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
del_7q31.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
del_7q36.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
del_8p23.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9q21.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_9q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_10p15.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_10p11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_11p15.5 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_12q24.33 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_13q12.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_13q14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_14q32.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_15q15.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_16q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q23.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p11.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_17q25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_19q13.43 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_21q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_xp22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_xp21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_xq21.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 76 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 397 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
del 1p36 21	95 (18%)	427	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.021 (0.0463)	0.00578 (0.015)	7e-05 (0.000277)	1e-05 (4.94e-05)	0.00709 (0.0176)	0.0405 (0.0807)	0.00355 (0.00992)	0.00681 (0.017)
amp 8q24 21	386 (74%)	136	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.00599 (0.0153)	0.447 (0.555)	1e-05 (4.94e-05)	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.00109 (0.00345)	0.00268 (0.00766)	0.0009 (0.00286)
del 4p15 2	208 (40%)	314	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.0248 (0.053)	0.336 (0.446)	0.00569 (0.0148)	1e-05 (4.94e-05)	0.00646 (0.0163)	0.0302 (0.0626)	0.00111 (0.00349)	0.00296 (0.00839)
amp 8q11 21	310 (59%)	212	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.0224 (0.0489)	0.635 (0.724)	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.00222 (0.00656)	0.00522 (0.0136)	0.0934 (0.161)	0.00434 (0.0117)
del 8p23 2	305 (58%)	217	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.122 (0.203)	0.322 (0.434)	1e-05 (4.94e-05)	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.00316 (0.00889)	0.0265 (0.0562)	5e-05 (0.000203)
del 1p13 2	133 (25%)	389	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.0108 (0.0256)	0.00712 (0.0176)	0.156 (0.251)	2e-05 (8.94e-05)	0.00081 (0.0026)	0.0001 (0.000382)	0.0769 (0.14)	0.628 (0.72)
del 3p26 2	348 (67%)	174	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.178 (0.276)	0.211 (0.316)	5e-05 (0.000203)	1e-05 (4.94e-05)	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.0534 (0.101)	0.0198 (0.0442)
del 3p24 1	368 (70%)	154	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.224 (0.329)	0.113 (0.19)	0.00126 (0.00394)	1e-05 (4.94e-05)	6e-05 (0.000241)	5e-05 (0.000203)	0.0142 (0.0326)	0.111 (0.188)
del 3p14 2	372 (71%)	150	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.359 (0.471)	0.175 (0.272)	0.00579 (0.015)	1e-05 (4.94e-05)	0.00144 (0.0044)	0.00041 (0.00141)	0.0319 (0.0655)	0.214 (0.318)
del 9p21 3	302 (58%)	220	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.152 (0.244)	0.361 (0.471)	4e-05 (0.000168)	1e-05 (4.94e-05)	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.277 (0.382)	0.0364 (0.0742)
del 10p11 21	163 (31%)	359	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.549 (0.645)	0.22 (0.324)	6e-05 (0.000241)	0.0221 (0.0485)	2e-05 (8.94e-05)	0.0111 (0.0261)	0.0386 (0.0774)	0.86 (0.89)
del 11p15 5	163 (31%)	359	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.769 (0.821)	0.282 (0.388)	0.00084 (0.00268)	0.0137 (0.0317)	2e-05 (8.94e-05)	0.0038 (0.0104)	0.336 (0.446)	0.0142 (0.0325)
del 11q23 1	246 (47%)	276	2e-05 (8.94e-05)	1e-05 (4.94e-05)	0.343 (0.452)	0.166 (0.261)	2e-05 (8.94e-05)	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.0132 (0.0304)	0.0446 (0.0871)	0.16 (0.255)
del 16q23 1	98 (19%)	424	0.00037 (0.00128)	1e-05 (4.94e-05)	0.789 (0.834)	0.455 (0.561)	1e-05 (4.94e-05)	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.0408 (0.0812)	0.273 (0.378)	0.00065 (0.00215)
del 17q25 3	71 (14%)	451	0.0144 (0.0328)	2e-05 (8.94e-05)	0.1 (0.172)	0.691 (0.766)	0.00266 (0.00763)	0.0831 (0.147)	0.00357 (0.00994)	0.0496 (0.0949)	0.028 (0.0592)	0.00597 (0.0153)
del 18q23	288 (55%)	234	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.181 (0.279)	0.246 (0.347)	1e-05 (4.94e-05)	1e-05 (4.94e-05)	2e-05 (8.94e-05)	1e-05 (4.94e-05)	0.0824 (0.146)	0.0169 (0.0382)
amp 2q11 2	107 (20%)	415	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.0416 (0.0821)	0.543 (0.642)	0.085 (0.149)	1e-05 (4.94e-05)	0.00065 (0.00215)	0.00068 (0.00223)	0.701 (0.771)	0.736 (0.792)
amp 2q31 2	112 (21%)	410	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.163 (0.259)	0.312 (0.423)	0.0412 (0.0816)	1e-05 (4.94e-05)	0.00442 (0.0118)	0.00667 (0.0168)	0.257 (0.358)	0.557 (0.654)
amp 7p11 2	222 (43%)	300	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.854 (0.887)	0.671 (0.754)	0.0238 (0.0513)	1e-05 (4.94e-05)	0.00022 (0.000789)	1e-05 (4.94e-05)	0.226 (0.329)	0.219 (0.323)
amp 9p24 1	126 (24%)	396	1e-05 (4.94e-05)	2e-05 (8.94e-05)	0.134 (0.22)	0.251 (0.352)	0.00075 (0.00243)	0.0143 (0.0326)	0.00385 (0.0105)	0.00129 (0.004)	0.263 (0.364)	0.326 (0.438)
amp 9p23	124 (24%)	398	1e-05 (4.94e-05)	0.00014 (0.000527)	0.387 (0.496)	0.425 (0.536)	0.00136 (0.0042)	0.0195 (0.0435)	0.00163 (0.00492)	0.00218 (0.00647)	0.331 (0.442)	0.534 (0.634)
amp 11q13 3	229 (44%)	293	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.797 (0.841)	0.733 (0.79)	1e-05 (4.94e-05)	0.0318 (0.0655)	0.0301 (0.0626)	0.0046 (0.0121)	0.381 (0.492)	0.201 (0.303)
amp 17q12	91 (17%)	431	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.698 (0.77)	0.722 (0.787)	0.00255 (0.00737)	3e-05 (0.000129)	0.0207 (0.0458)	4e-05 (0.000168)	0.705 (0.773)	0.224 (0.329)
amp 18p11 31	156 (30%)	366	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.211 (0.316)	0.516 (0.617)	0.00946 (0.0228)	1e-05 (4.94e-05)	0.0106 (0.0253)	0.0002 (0.000724)	0.95 (0.957)	0.222 (0.327)
amp 20q11 22	227 (43%)	295	1e-05 (4.94e-05)	3e-05 (0.000129)	0.0487 (0.0938)	0.832 (0.87)	0.0587 (0.11)	0.0287 (0.0603)	0.91 (0.924)	0.0236 (0.0511)	0.579 (0.672)	0.0173 (0.039)
del 1q44	48 (9%)	474	9e-05 (0.000349)	0.012 (0.0281)	0.8 (0.842)	0.91 (0.924)	0.00853 (0.0207)	0.0102 (0.0244)	0.00037 (0.00128)	0.0459 (0.0891)	0.242 (0.343)	0.486 (0.587)
del 3p12 1	343 (66%)	179	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.669 (0.753)	0.902 (0.92)	0.00161 (0.00487)	1e-05 (4.94e-05)	0.00014 (0.000527)	0.00047 (0.00159)	0.0808 (0.144)	0.482 (0.585)
del 4p16 3	205 (39%)	317	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.196 (0.297)	0.408 (0.518)	0.00246 (0.00716)	1e-05 (4.94e-05)	0.0641 (0.119)	0.0695 (0.128)	0.00814 (0.0199)	0.0412 (0.0816)
del 4q21 3	156 (30%)	366	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.732 (0.79)	0.0465 (0.0899)	0.146 (0.238)	2e-05 (8.94e-05)	0.259 (0.36)	0.0315 (0.065)	0.443 (0.552)	0.0296 (0.0619)
del 5q12 1	215 (41%)	307	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.00419 (0.0113)	0.361 (0.471)	0.0735 (0.135)	1e-05 (4.94e-05)	0.00264 (0.0076)	3e-05 (0.000129)	0.351 (0.461)	0.523 (0.623)
del 5q15	226 (43%)	296	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.0188 (0.0422)	0.431 (0.544)	0.311 (0.423)	1e-05 (4.94e-05)	0.0121 (0.0283)	2e-05 (8.94e-05)	0.651 (0.738)	0.78 (0.828)
del 5q35 3	199 (38%)	323	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.121 (0.202)	0.723 (0.787)	0.00702 (0.0174)	1e-05 (4.94e-05)	0.0377 (0.0763)	4e-05 (0.000168)	0.361 (0.471)	0.229 (0.332)
del 9p23	239 (46%)	283	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.124 (0.205)	0.113 (0.191)	0.00052 (0.00175)	1e-05 (4.94e-05)	1e-05 (4.94e-05)	9e-05 (0.000349)	0.485 (0.587)	0.979 (0.98)
del 10p15 3	170 (33%)	352	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.757 (0.812)	0.709 (0.776)	0.0008 (0.00258)	0.003 (0.00848)	0.00021 (0.000756)	0.0803 (0.144)	0.0276 (0.0585)	0.686 (0.764)
del 13q14 2	217 (42%)	305	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.214 (0.318)	0.566 (0.661)	3e-05 (0.000129)	7e-05 (0.000277)	0.0011 (0.00347)	0.216 (0.32)	0.91 (0.924)	0.0214 (0.0472)
del 14q32 32	75 (14%)	447	0.00129 (0.004)	1e-05 (4.94e-05)	0.0535 (0.101)	0.466 (0.568)	2e-05 (8.94e-05)	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.0289 (0.0605)	0.382 (0.492)	0.112 (0.189)
del 16q23 3	105 (20%)	417	0.00066 (0.00217)	1e-05 (4.94e-05)	0.42 (0.532)	0.233 (0.337)	1e-05 (4.94e-05)	1e-05 (4.94e-05)	5e-05 (0.000203)	0.165 (0.261)	0.379 (0.492)	0.0218 (0.0479)
del 19p13 3	175 (34%)	347	1e-05 (4.94e-05)	3e-05 (0.000129)	0.542 (0.642)	0.366 (0.476)	0.00073 (0.00237)	0.00069 (0.00225)	0.0466 (0.09)	0.0002 (0.000724)	0.536 (0.635)	0.252 (0.353)
del 21q22 3	208 (40%)	314	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.656 (0.739)	0.727 (0.789)	0.0459 (0.0891)	1e-05 (4.94e-05)	0.00028 (0.000985)	5e-05 (0.000203)	0.0842 (0.148)	0.19 (0.289)
del xq21 33	80 (15%)	442	3e-05 (0.000129)	1e-05 (4.94e-05)	0.585 (0.677)	0.128 (0.21)	0.00345 (0.00968)	0.00383 (0.0105)	0.00683 (0.017)	0.0123 (0.0288)	0.236 (0.339)	0.0778 (0.141)
amp 3q26 33	380 (73%)	142	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.0809 (0.144)	0.309 (0.422)	1e-05 (4.94e-05)	0.00023 (0.000821)	0.00057 (0.00191)	0.594 (0.685)	0.2 (0.302)	0.227 (0.33)
amp 7q21 3	169 (32%)	353	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.765 (0.818)	0.442 (0.552)	0.0128 (0.0297)	1e-05 (4.94e-05)	0.0827 (0.147)	0.00015 (0.000562)	0.242 (0.343)	0.935 (0.945)
amp 12p13 33	167 (32%)	355	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.251 (0.352)	0.524 (0.624)	0.00177 (0.0053)	9e-05 (0.000349)	0.0259 (0.0552)	0.0875 (0.152)	0.672 (0.754)	0.771 (0.822)
amp 18q11 2	106 (20%)	416	2e-05 (8.94e-05)	0.00033 (0.00116)	0.773 (0.823)	0.207 (0.311)	0.107 (0.182)	0.0126 (0.0293)	0.00799 (0.0196)	0.0287 (0.0603)	0.798 (0.841)	0.681 (0.76)
del 6p25 3	96 (18%)	426	0.00582 (0.015)	1e-05 (4.94e-05)	0.298 (0.409)	0.0107 (0.0254)	0.0036 (0.00999)	0.172 (0.269)	0.0373 (0.0756)	0.726 (0.789)	0.681 (0.76)	0.672 (0.754)
del 9q21 11	108 (21%)	414	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.703 (0.772)	0.237 (0.339)	0.0745 (0.136)	0.0228 (0.0497)	0.00234 (0.00684)	0.00061 (0.00203)	0.444 (0.553)	0.122 (0.203)
del 10q23 31	138 (26%)	384	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.237 (0.339)	0.98 (0.98)	0.00047 (0.00159)	0.00281 (0.008)	0.00035 (0.00122)	0.462 (0.565)	0.33 (0.441)	0.456 (0.561)
del 13q12 11	233 (45%)	289	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.162 (0.258)	0.24 (0.342)	0.0787 (0.142)	2e-05 (8.94e-05)	0.0199 (0.0443)	0.0308 (0.0638)	0.63 (0.721)	0.837 (0.873)
del xp22 2	157 (30%)	365	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.622 (0.714)	0.00247 (0.00716)	0.484 (0.586)	0.0173 (0.039)	0.00852 (0.0207)	0.158 (0.253)	0.867 (0.894)	0.891 (0.913)
amp 5p15 33	240 (46%)	282	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.517 (0.617)	0.83 (0.868)	0.00506 (0.0133)	0.687 (0.764)	0.695 (0.769)	0.0337 (0.0689)	0.573 (0.665)	0.636 (0.725)
amp 6p12 1	110 (21%)	412	1e-05 (4.94e-05)	2e-05 (8.94e-05)	0.499 (0.6)	0.951 (0.957)	0.112 (0.189)	0.0372 (0.0756)	0.562 (0.658)	0.0023 (0.00675)	0.402 (0.512)	0.237 (0.339)
amp 8p11 23	161 (31%)	361	1e-05 (4.94e-05)	0.0385 (0.0774)	0.949 (0.957)	0.874 (0.899)	0.241 (0.343)	0.17 (0.266)	0.0664 (0.123)	0.0109 (0.0258)	0.404 (0.514)	0.0453 (0.0883)
amp 9p13 3	139 (27%)	383	1e-05 (4.94e-05)	0.00389 (0.0106)	0.247 (0.348)	0.122 (0.203)	0.00027 (0.000954)	0.00144 (0.0044)	0.226 (0.329)	0.0595 (0.111)	0.758 (0.812)	0.454 (0.561)
amp 9q34 3	177 (34%)	345	1e-05 (4.94e-05)	0.00012 (0.000456)	0.652 (0.738)	0.0237 (0.0511)	0.38 (0.492)	0.00446 (0.0118)	0.225 (0.329)	0.0862 (0.151)	0.96 (0.965)	0.968 (0.972)
del 2q21 2	78 (15%)	444	0.0495 (0.0949)	0.0551 (0.104)	0.504 (0.605)	0.212 (0.317)	0.0063 (0.016)	0.0002 (0.000724)	0.0386 (0.0774)	0.259 (0.36)	0.311 (0.423)	0.171 (0.267)
del 2q22 1	121 (23%)	401	0.00468 (0.0123)	0.0001 (0.000382)	0.387 (0.496)	0.837 (0.873)	0.123 (0.204)	0.00972 (0.0233)	0.0811 (0.144)	0.00139 (0.00428)	0.89 (0.912)	0.572 (0.665)
del 2q36 2	157 (30%)	365	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.186 (0.285)	0.859 (0.89)	0.0088 (0.0213)	0.0659 (0.122)	0.0696 (0.128)	0.0248 (0.053)	0.103 (0.176)	0.0901 (0.156)
del 4q22 1	169 (32%)	353	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.477 (0.581)	0.0745 (0.136)	0.12 (0.201)	0.00024 (0.000852)	0.443 (0.552)	0.04 (0.08)	0.446 (0.554)	0.0871 (0.152)
del 4q35 2	213 (41%)	309	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.871 (0.897)	0.186 (0.285)	0.0807 (0.144)	0.00017 (0.000633)	0.235 (0.339)	0.00601 (0.0153)	0.147 (0.238)	0.164 (0.26)
del 14q11 2	75 (14%)	447	0.00365 (0.0101)	0.00672 (0.0169)	0.171 (0.267)	0.898 (0.919)	0.241 (0.342)	0.149 (0.242)	0.00447 (0.0118)	0.0326 (0.0668)	0.387 (0.496)	0.654 (0.738)
del 19q13 43	97 (19%)	425	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.214 (0.318)	0.587 (0.678)	0.338 (0.448)	5e-05 (0.000203)	0.0427 (0.0839)	0.0658 (0.122)	0.165 (0.261)	0.58 (0.672)
amp 5p12	205 (39%)	317	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.179 (0.276)	0.146 (0.238)	0.0502 (0.0959)	0.234 (0.338)	0.436 (0.548)	0.0162 (0.0367)	0.698 (0.77)	0.713 (0.778)
amp 6q12	96 (18%)	426	1e-05 (4.94e-05)	8e-05 (0.000315)	0.689 (0.766)	0.9 (0.919)	0.089 (0.155)	0.00612 (0.0156)	0.183 (0.281)	0.234 (0.338)	0.842 (0.876)	0.547 (0.645)
amp 11p13	102 (20%)	420	0.00223 (0.00657)	0.00049 (0.00166)	0.173 (0.269)	0.177 (0.274)	0.0839 (0.148)	0.565 (0.661)	0.632 (0.722)	0.492 (0.593)	0.905 (0.922)	0.0422 (0.083)
amp 12q15	103 (20%)	419	2e-05 (8.94e-05)	7e-05 (0.000277)	0.303 (0.415)	0.205 (0.309)	0.102 (0.175)	0.00167 (0.00502)	0.88 (0.904)	0.322 (0.434)	0.396 (0.506)	0.737 (0.792)
amp 13q34	106 (20%)	416	1e-05 (4.94e-05)	0.00047 (0.00159)	0.779 (0.828)	0.492 (0.593)	0.244 (0.344)	0.00402 (0.0109)	0.124 (0.205)	0.133 (0.217)	0.466 (0.568)	0.31 (0.423)
del 7q31 1	77 (15%)	445	0.00018 (0.000667)	0.342 (0.452)	0.73 (0.79)	0.381 (0.492)	0.00364 (0.0101)	0.548 (0.645)	0.00217 (0.00647)	0.176 (0.272)	0.187 (0.285)	0.398 (0.507)
del 7q36 1	132 (25%)	390	2e-05 (8.94e-05)	0.327 (0.439)	0.314 (0.426)	0.674 (0.754)	0.0429 (0.084)	0.805 (0.846)	0.00718 (0.0177)	0.331 (0.442)	0.517 (0.617)	0.29 (0.399)
del 9q34 3	79 (15%)	443	1e-05 (4.94e-05)	0.0002 (0.000724)	0.828 (0.868)	0.369 (0.48)	0.434 (0.546)	0.442 (0.552)	0.788 (0.834)	0.00958 (0.023)	0.452 (0.56)	0.26 (0.36)
del xp21 3	159 (30%)	363	1e-05 (4.94e-05)	4e-05 (0.000168)	0.787 (0.834)	0.0552 (0.104)	0.81 (0.85)	0.0233 (0.0505)	0.152 (0.245)	0.0848 (0.149)	0.712 (0.778)	0.457 (0.561)
amp 13q22 1	105 (20%)	417	1e-05 (4.94e-05)	1e-05 (4.94e-05)	0.384 (0.494)	0.157 (0.251)	0.65 (0.737)	0.0764 (0.139)	0.332 (0.442)	0.162 (0.258)	0.461 (0.565)	0.619 (0.712)
amp 15q26 3	105 (20%)	417	3e-05 (0.000129)	0.00443 (0.0118)	0.699 (0.77)	0.327 (0.439)	0.224 (0.329)	0.0757 (0.138)	0.549 (0.645)	0.051 (0.0969)	0.529 (0.629)	0.0794 (0.143)
amp xq28	150 (29%)	372	1e-05 (4.94e-05)	0.0001 (0.000382)	0.745 (0.8)	0.196 (0.297)	0.257 (0.358)	0.315 (0.427)	0.568 (0.662)	0.0946 (0.163)	0.694 (0.769)	0.605 (0.697)
del 12q24 33	63 (12%)	459	1e-05 (4.94e-05)	0.0002 (0.000724)	0.843 (0.877)	0.456 (0.561)	0.35 (0.461)	0.104 (0.178)	0.351 (0.461)	0.121 (0.202)	0.438 (0.55)	0.732 (0.79)
del 15q15 1	124 (24%)	398	1e-05 (4.94e-05)	0.0504 (0.096)	0.65 (0.737)	0.414 (0.525)	0.0248 (0.053)	0.0635 (0.119)	0.73 (0.79)	0.64 (0.728)	0.482 (0.585)	0.933 (0.944)
del 17p11 2	99 (19%)	423	1e-05 (4.94e-05)	0.00147 (0.00447)	0.858 (0.89)	0.973 (0.976)	0.193 (0.294)	0.1 (0.172)	0.14 (0.229)	0.126 (0.207)	0.867 (0.894)	0.933 (0.944)

'amp_2q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S1. Gene #1: 'amp_2q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
AMP PEAK 1(2Q11.2) MUTATED	55	42	4	6
AMP PEAK 1(2Q11.2) WILD-TYPE	148	86	141	40

Figure S1. Get High-res Image Gene #1: 'amp_2q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S2. Gene #1: 'amp_2q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
AMP PEAK 1(2Q11.2) MUTATED	7	34	7	38	2	17	2
AMP PEAK 1(2Q11.2) WILD-TYPE	77	53	96	51	76	58	4

Figure S2. Get High-res Image Gene #1: 'amp_2q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_2q11.2' versus 'RPPA_CNMF'

P value = 0.0416 (Fisher's exact test), Q value = 0.082

Table S3. Gene #1: 'amp_2q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	29	31	29	67
AMP PEAK 1(2Q11.2) MUTATED	13	3	14	7	15
AMP PEAK 1(2Q11.2) WILD-TYPE	37	26	17	22	52

Figure S3. Get High-res Image Gene #1: 'amp_2q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_2q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S4. Gene #1: 'amp_2q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
AMP PEAK 1(2Q11.2) MUTATED	32	44	28	2
AMP PEAK 1(2Q11.2) WILD-TYPE	144	59	142	63

Figure S4. Get High-res Image Gene #1: 'amp_2q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_2q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.0021

Table S5. Gene #1: 'amp_2q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
AMP PEAK 1(2Q11.2) MUTATED	32	22	21	17	13
AMP PEAK 1(2Q11.2) WILD-TYPE	49	117	110	74	63

Figure S5. Get High-res Image Gene #1: 'amp_2q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_2q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00068 (Fisher's exact test), Q value = 0.0022

Table S6. Gene #1: 'amp_2q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
AMP PEAK 1(2Q11.2) MUTATED	35	44	26
AMP PEAK 1(2Q11.2) WILD-TYPE	155	98	160

Figure S6. Get High-res Image Gene #1: 'amp_2q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_2q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S7. Gene #2: 'amp_2q31.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
AMP PEAK 2(2Q31.2) MUTATED	56	46	6	4
AMP PEAK 2(2Q31.2) WILD-TYPE	147	82	139	42

Figure S7. Get High-res Image Gene #2: 'amp_2q31.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2q31.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S8. Gene #2: 'amp_2q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
AMP PEAK 2(2Q31.2) MUTATED	8	27	8	47	5	15	2
AMP PEAK 2(2Q31.2) WILD-TYPE	76	60	95	42	73	60	4

Figure S8. Get High-res Image Gene #2: 'amp_2q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_2q31.2' versus 'MRNASEQ_CNMF'

P value = 0.0412 (Fisher's exact test), Q value = 0.082

Table S9. Gene #2: 'amp_2q31.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
AMP PEAK 2(2Q31.2) MUTATED	33	14	43	22
AMP PEAK 2(2Q31.2) WILD-TYPE	102	99	128	73

Figure S9. Get High-res Image Gene #2: 'amp_2q31.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_2q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S10. Gene #2: 'amp_2q31.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
AMP PEAK 2(2Q31.2) MUTATED	35	41	32	4
AMP PEAK 2(2Q31.2) WILD-TYPE	141	62	138	61

Figure S10. Get High-res Image Gene #2: 'amp_2q31.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_2q31.2' versus 'MIRSEQ_CNMF'

P value = 0.00442 (Fisher's exact test), Q value = 0.012

Table S11. Gene #2: 'amp_2q31.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
AMP PEAK 2(2Q31.2) MUTATED	30	21	23	19	17
AMP PEAK 2(2Q31.2) WILD-TYPE	51	118	108	72	59

Figure S11. Get High-res Image Gene #2: 'amp_2q31.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_2q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00667 (Fisher's exact test), Q value = 0.017

Table S12. Gene #2: 'amp_2q31.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
AMP PEAK 2(2Q31.2) MUTATED	40	42	28
AMP PEAK 2(2Q31.2) WILD-TYPE	150	100	158

Figure S12. Get High-res Image Gene #2: 'amp_2q31.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S13. Gene #3: 'amp_3q26.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
AMP PEAK 3(3Q26.33) MUTATED	171	118	56	35
AMP PEAK 3(3Q26.33) WILD-TYPE	32	10	89	11

Figure S13. Get High-res Image Gene #3: 'amp_3q26.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S14. Gene #3: 'amp_3q26.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
AMP PEAK 3(3Q26.33) MUTATED	48	74	45	82	62	63	6
AMP PEAK 3(3Q26.33) WILD-TYPE	36	13	58	7	16	12	0

Figure S14. Get High-res Image Gene #3: 'amp_3q26.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q26.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S15. Gene #3: 'amp_3q26.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
AMP PEAK 3(3Q26.33) MUTATED	99	58	148	71
AMP PEAK 3(3Q26.33) WILD-TYPE	36	55	23	24

Figure S15. Get High-res Image Gene #3: 'amp_3q26.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3q26.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.00082

Table S16. Gene #3: 'amp_3q26.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
AMP PEAK 3(3Q26.33) MUTATED	130	89	107	50
AMP PEAK 3(3Q26.33) WILD-TYPE	46	14	63	15

Figure S16. Get High-res Image Gene #3: 'amp_3q26.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'MIRSEQ_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0019

Table S17. Gene #3: 'amp_3q26.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
AMP PEAK 3(3Q26.33) MUTATED	66	87	109	62	52
AMP PEAK 3(3Q26.33) WILD-TYPE	15	52	22	29	24

Figure S17. Get High-res Image Gene #3: 'amp_3q26.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S18. Gene #4: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
AMP PEAK 4(5P15.33) MUTATED	116	82	24	18
AMP PEAK 4(5P15.33) WILD-TYPE	87	46	121	28

Figure S18. Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S19. Gene #4: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
AMP PEAK 4(5P15.33) MUTATED	27	52	27	50	35	46	3
AMP PEAK 4(5P15.33) WILD-TYPE	57	35	76	39	43	29	3

Figure S19. Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 0.00506 (Fisher's exact test), Q value = 0.013

Table S20. Gene #4: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
AMP PEAK 4(5P15.33) MUTATED	74	37	82	46
AMP PEAK 4(5P15.33) WILD-TYPE	61	76	89	49

Figure S20. Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0337 (Fisher's exact test), Q value = 0.069

Table S21. Gene #4: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
AMP PEAK 4(5P15.33) MUTATED	86	77	74
AMP PEAK 4(5P15.33) WILD-TYPE	104	65	112

Figure S21. Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S22. Gene #5: 'amp_5p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
AMP PEAK 5(5P12) MUTATED	98	72	17	18
AMP PEAK 5(5P12) WILD-TYPE	105	56	128	28

Figure S22. Get High-res Image Gene #5: 'amp_5p12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S23. Gene #5: 'amp_5p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
AMP PEAK 5(5P12) MUTATED	21	47	25	40	28	41	3
AMP PEAK 5(5P12) WILD-TYPE	63	40	78	49	50	34	3

Figure S23. Get High-res Image Gene #5: 'amp_5p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0162 (Fisher's exact test), Q value = 0.037

Table S24. Gene #5: 'amp_5p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
AMP PEAK 5(5P12) MUTATED	74	68	60
AMP PEAK 5(5P12) WILD-TYPE	116	74	126

Figure S24. Get High-res Image Gene #5: 'amp_5p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S25. Gene #6: 'amp_6p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
AMP PEAK 6(6P12.1) MUTATED	59	30	9	12
AMP PEAK 6(6P12.1) WILD-TYPE	144	98	136	34

Figure S25. Get High-res Image Gene #6: 'amp_6p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p12.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S26. Gene #6: 'amp_6p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
AMP PEAK 6(6P12.1) MUTATED	9	27	15	24	7	26	2
AMP PEAK 6(6P12.1) WILD-TYPE	75	60	88	65	71	49	4

Figure S26. Get High-res Image Gene #6: 'amp_6p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0372 (Fisher's exact test), Q value = 0.076

Table S27. Gene #6: 'amp_6p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
AMP PEAK 6(6P12.1) MUTATED	39	28	35	6
AMP PEAK 6(6P12.1) WILD-TYPE	137	75	135	59

Figure S27. Get High-res Image Gene #6: 'amp_6p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0023 (Fisher's exact test), Q value = 0.0067

Table S28. Gene #6: 'amp_6p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
AMP PEAK 6(6P12.1) MUTATED	48	37	24
AMP PEAK 6(6P12.1) WILD-TYPE	142	105	162

Figure S28. Get High-res Image Gene #6: 'amp_6p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S29. Gene #7: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
AMP PEAK 7(6Q12) MUTATED	54	25	7	10
AMP PEAK 7(6Q12) WILD-TYPE	149	103	138	36

Figure S29. Get High-res Image Gene #7: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q12' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00032

Table S30. Gene #7: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
AMP PEAK 7(6Q12) MUTATED	9	20	14	24	4	23	2
AMP PEAK 7(6Q12) WILD-TYPE	75	67	89	65	74	52	4

Figure S30. Get High-res Image Gene #7: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00612 (Fisher's exact test), Q value = 0.016

Table S31. Gene #7: 'amp_6q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
AMP PEAK 7(6Q12) MUTATED	31	24	35	3
AMP PEAK 7(6Q12) WILD-TYPE	145	79	135	62

Figure S31. Get High-res Image Gene #7: 'amp_6q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S32. Gene #8: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
AMP PEAK 8(7P11.2) MUTATED	111	68	26	17
AMP PEAK 8(7P11.2) WILD-TYPE	92	60	119	29

Figure S32. Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S33. Gene #8: 'amp_7p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
AMP PEAK 8(7P11.2) MUTATED	30	48	41	54	6	40	3
AMP PEAK 8(7P11.2) WILD-TYPE	54	39	62	35	72	35	3

Figure S33. Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 0.0238 (Fisher's exact test), Q value = 0.051

Table S34. Gene #8: 'amp_7p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
AMP PEAK 8(7P11.2) MUTATED	71	47	60	41
AMP PEAK 8(7P11.2) WILD-TYPE	64	66	111	54

Figure S34. Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S35. Gene #8: 'amp_7p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
AMP PEAK 8(7P11.2) MUTATED	76	57	81	5
AMP PEAK 8(7P11.2) WILD-TYPE	100	46	89	60

Figure S35. Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00079

Table S36. Gene #8: 'amp_7p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
AMP PEAK 8(7P11.2) MUTATED	48	60	36	42	33
AMP PEAK 8(7P11.2) WILD-TYPE	33	79	95	49	43

Figure S36. Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S37. Gene #8: 'amp_7p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
AMP PEAK 8(7P11.2) MUTATED	84	83	52
AMP PEAK 8(7P11.2) WILD-TYPE	106	59	134

Figure S37. Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S38. Gene #9: 'amp_7q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
AMP PEAK 9(7Q21.3) MUTATED	88	55	17	9
AMP PEAK 9(7Q21.3) WILD-TYPE	115	73	128	37

Figure S38. Get High-res Image Gene #9: 'amp_7q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S39. Gene #9: 'amp_7q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
AMP PEAK 9(7Q21.3) MUTATED	14	39	24	60	9	22	1
AMP PEAK 9(7Q21.3) WILD-TYPE	70	48	79	29	69	53	5

Figure S39. Get High-res Image Gene #9: 'amp_7q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q21.3' versus 'MRNASEQ_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.03

Table S40. Gene #9: 'amp_7q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
AMP PEAK 9(7Q21.3) MUTATED	56	25	57	29
AMP PEAK 9(7Q21.3) WILD-TYPE	79	88	114	66

Figure S40. Get High-res Image Gene #9: 'amp_7q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S41. Gene #9: 'amp_7q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
AMP PEAK 9(7Q21.3) MUTATED	47	52	60	8
AMP PEAK 9(7Q21.3) WILD-TYPE	129	51	110	57

Figure S41. Get High-res Image Gene #9: 'amp_7q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00056

Table S42. Gene #9: 'amp_7q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
AMP PEAK 9(7Q21.3) MUTATED	56	65	45
AMP PEAK 9(7Q21.3) WILD-TYPE	134	77	141

Figure S42. Get High-res Image Gene #9: 'amp_7q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S43. Gene #10: 'amp_8p11.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
AMP PEAK 10(8P11.23) MUTATED	53	64	31	13
AMP PEAK 10(8P11.23) WILD-TYPE	150	64	114	33

Figure S43. Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p11.23' versus 'METHLYATION_CNMF'

P value = 0.0385 (Fisher's exact test), Q value = 0.077

Table S44. Gene #10: 'amp_8p11.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
AMP PEAK 10(8P11.23) MUTATED	20	34	24	35	26	22	0
AMP PEAK 10(8P11.23) WILD-TYPE	64	53	79	54	52	53	6

Figure S44. Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8p11.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.026

Table S45. Gene #10: 'amp_8p11.23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
AMP PEAK 10(8P11.23) MUTATED	47	57	55
AMP PEAK 10(8P11.23) WILD-TYPE	143	85	131

Figure S45. Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0453 (Fisher's exact test), Q value = 0.088

Table S46. Gene #10: 'amp_8p11.23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
AMP PEAK 10(8P11.23) MUTATED	40	34	69
AMP PEAK 10(8P11.23) WILD-TYPE	131	70	129

Figure S46. Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S47. Gene #11: 'amp_8q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
AMP PEAK 11(8Q11.21) MUTATED	154	66	57	33
AMP PEAK 11(8Q11.21) WILD-TYPE	49	62	88	13

Figure S47. Get High-res Image Gene #11: 'amp_8q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S48. Gene #11: 'amp_8q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
AMP PEAK 11(8Q11.21) MUTATED	53	48	63	51	29	62	4
AMP PEAK 11(8Q11.21) WILD-TYPE	31	39	40	38	49	13	2

Figure S48. Get High-res Image Gene #11: 'amp_8q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q11.21' versus 'RPPA_CNMF'

P value = 0.0224 (Fisher's exact test), Q value = 0.049

Table S49. Gene #11: 'amp_8q11.21' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	29	31	29	67
AMP PEAK 11(8Q11.21) MUTATED	26	11	15	19	47
AMP PEAK 11(8Q11.21) WILD-TYPE	24	18	16	10	20

Figure S49. Get High-res Image Gene #11: 'amp_8q11.21' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_8q11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S50. Gene #11: 'amp_8q11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
AMP PEAK 11(8Q11.21) MUTATED	89	70	75	71
AMP PEAK 11(8Q11.21) WILD-TYPE	46	43	96	24

Figure S50. Get High-res Image Gene #11: 'amp_8q11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S51. Gene #11: 'amp_8q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
AMP PEAK 11(8Q11.21) MUTATED	123	51	109	22
AMP PEAK 11(8Q11.21) WILD-TYPE	53	52	61	43

Figure S51. Get High-res Image Gene #11: 'amp_8q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q11.21' versus 'MIRSEQ_CNMF'

P value = 0.00222 (Fisher's exact test), Q value = 0.0066

Table S52. Gene #11: 'amp_8q11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
AMP PEAK 11(8Q11.21) MUTATED	54	89	58	58	49
AMP PEAK 11(8Q11.21) WILD-TYPE	27	50	73	33	27

Figure S52. Get High-res Image Gene #11: 'amp_8q11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00522 (Fisher's exact test), Q value = 0.014

Table S53. Gene #11: 'amp_8q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
AMP PEAK 11(8Q11.21) MUTATED	129	83	96
AMP PEAK 11(8Q11.21) WILD-TYPE	61	59	90

Figure S53. Get High-res Image Gene #11: 'amp_8q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00434 (Fisher's exact test), Q value = 0.012

Table S54. Gene #11: 'amp_8q11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
AMP PEAK 11(8Q11.21) MUTATED	116	63	101
AMP PEAK 11(8Q11.21) WILD-TYPE	55	41	97

Figure S54. Get High-res Image Gene #11: 'amp_8q11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S55. Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
AMP PEAK 12(8Q24.21) MUTATED	185	89	74	38
AMP PEAK 12(8Q24.21) WILD-TYPE	18	39	71	8

Figure S55. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S56. Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
AMP PEAK 12(8Q24.21) MUTATED	64	64	77	71	35	69	6
AMP PEAK 12(8Q24.21) WILD-TYPE	20	23	26	18	43	6	0

Figure S56. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'RPPA_CNMF'

P value = 0.00599 (Fisher's exact test), Q value = 0.015

Table S57. Gene #12: 'amp_8q24.21' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	29	31	29	67
AMP PEAK 12(8Q24.21) MUTATED	32	15	25	22	57
AMP PEAK 12(8Q24.21) WILD-TYPE	18	14	6	7	10

Figure S57. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S58. Gene #12: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
AMP PEAK 12(8Q24.21) MUTATED	114	85	100	81
AMP PEAK 12(8Q24.21) WILD-TYPE	21	28	71	14

Figure S58. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S59. Gene #12: 'amp_8q24.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
AMP PEAK 12(8Q24.21) MUTATED	142	75	136	27
AMP PEAK 12(8Q24.21) WILD-TYPE	34	28	34	38

Figure S59. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S60. Gene #12: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
AMP PEAK 12(8Q24.21) MUTATED	67	110	74	77	55
AMP PEAK 12(8Q24.21) WILD-TYPE	14	29	57	14	21

Figure S60. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00109 (Fisher's exact test), Q value = 0.0035

Table S61. Gene #12: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
AMP PEAK 12(8Q24.21) MUTATED	154	109	120
AMP PEAK 12(8Q24.21) WILD-TYPE	36	33	66

Figure S61. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00268 (Fisher's exact test), Q value = 0.0077

Table S62. Gene #12: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	189	143
AMP PEAK 12(8Q24.21) MUTATED	110	149	90
AMP PEAK 12(8Q24.21) WILD-TYPE	31	40	53

Figure S62. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-04 (Fisher's exact test), Q value = 0.0029

Table S63. Gene #12: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
AMP PEAK 12(8Q24.21) MUTATED	138	83	128
AMP PEAK 12(8Q24.21) WILD-TYPE	33	21	70

Figure S63. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9p24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S64. Gene #13: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
AMP PEAK 13(9P24.1) MUTATED	40	19	29	38
AMP PEAK 13(9P24.1) WILD-TYPE	163	109	116	8

Figure S64. Get High-res Image Gene #13: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p24.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S65. Gene #13: 'amp_9p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
AMP PEAK 13(9P24.1) MUTATED	15	9	45	19	20	17	1
AMP PEAK 13(9P24.1) WILD-TYPE	69	78	58	70	58	58	5

Figure S65. Get High-res Image Gene #13: 'amp_9p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9p24.1' versus 'MRNASEQ_CNMF'

P value = 0.00075 (Fisher's exact test), Q value = 0.0024

Table S66. Gene #13: 'amp_9p24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
AMP PEAK 13(9P24.1) MUTATED	31	42	27	22
AMP PEAK 13(9P24.1) WILD-TYPE	104	71	144	73

Figure S66. Get High-res Image Gene #13: 'amp_9p24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_9p24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.033

Table S67. Gene #13: 'amp_9p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
AMP PEAK 13(9P24.1) MUTATED	40	17	54	11
AMP PEAK 13(9P24.1) WILD-TYPE	136	86	116	54

Figure S67. Get High-res Image Gene #13: 'amp_9p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_9p24.1' versus 'MIRSEQ_CNMF'

P value = 0.00385 (Fisher's exact test), Q value = 0.01

Table S68. Gene #13: 'amp_9p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
AMP PEAK 13(9P24.1) MUTATED	9	44	32	27	14
AMP PEAK 13(9P24.1) WILD-TYPE	72	95	99	64	62

Figure S68. Get High-res Image Gene #13: 'amp_9p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_9p24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00129 (Fisher's exact test), Q value = 0.004

Table S69. Gene #13: 'amp_9p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
AMP PEAK 13(9P24.1) MUTATED	43	22	61
AMP PEAK 13(9P24.1) WILD-TYPE	147	120	125

Figure S69. Get High-res Image Gene #13: 'amp_9p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S70. Gene #14: 'amp_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
AMP PEAK 14(9P23) MUTATED	37	21	29	37
AMP PEAK 14(9P23) WILD-TYPE	166	107	116	9

Figure S70. Get High-res Image Gene #14: 'amp_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p23' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00053

Table S71. Gene #14: 'amp_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
AMP PEAK 14(9P23) MUTATED	16	9	43	19	19	17	1
AMP PEAK 14(9P23) WILD-TYPE	68	78	60	70	59	58	5

Figure S71. Get High-res Image Gene #14: 'amp_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9p23' versus 'MRNASEQ_CNMF'

P value = 0.00136 (Fisher's exact test), Q value = 0.0042

Table S72. Gene #14: 'amp_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
AMP PEAK 14(9P23) MUTATED	32	40	26	23
AMP PEAK 14(9P23) WILD-TYPE	103	73	145	72

Figure S72. Get High-res Image Gene #14: 'amp_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0195 (Fisher's exact test), Q value = 0.043

Table S73. Gene #14: 'amp_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
AMP PEAK 14(9P23) MUTATED	42	16	52	11
AMP PEAK 14(9P23) WILD-TYPE	134	87	118	54

Figure S73. Get High-res Image Gene #14: 'amp_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_9p23' versus 'MIRSEQ_CNMF'

P value = 0.00163 (Fisher's exact test), Q value = 0.0049

Table S74. Gene #14: 'amp_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
AMP PEAK 14(9P23) MUTATED	8	43	31	28	14
AMP PEAK 14(9P23) WILD-TYPE	73	96	100	63	62

Figure S74. Get High-res Image Gene #14: 'amp_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00218 (Fisher's exact test), Q value = 0.0065

Table S75. Gene #14: 'amp_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
AMP PEAK 14(9P23) MUTATED	45	21	58
AMP PEAK 14(9P23) WILD-TYPE	145	121	128

Figure S75. Get High-res Image Gene #14: 'amp_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_9p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S76. Gene #15: 'amp_9p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
AMP PEAK 15(9P13.3) MUTATED	48	29	29	33
AMP PEAK 15(9P13.3) WILD-TYPE	155	99	116	13

Figure S76. Get High-res Image Gene #15: 'amp_9p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p13.3' versus 'METHLYATION_CNMF'

P value = 0.00389 (Fisher's exact test), Q value = 0.011

Table S77. Gene #15: 'amp_9p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
AMP PEAK 15(9P13.3) MUTATED	19	17	44	24	14	19	2
AMP PEAK 15(9P13.3) WILD-TYPE	65	70	59	65	64	56	4

Figure S77. Get High-res Image Gene #15: 'amp_9p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.00095

Table S78. Gene #15: 'amp_9p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
AMP PEAK 15(9P13.3) MUTATED	30	43	30	33
AMP PEAK 15(9P13.3) WILD-TYPE	105	70	141	62

Figure S78. Get High-res Image Gene #15: 'amp_9p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_9p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00144 (Fisher's exact test), Q value = 0.0044

Table S79. Gene #15: 'amp_9p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
AMP PEAK 15(9P13.3) MUTATED	51	24	55	6
AMP PEAK 15(9P13.3) WILD-TYPE	125	79	115	59

Figure S79. Get High-res Image Gene #15: 'amp_9p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_9q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S80. Gene #16: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
AMP PEAK 16(9Q34.3) MUTATED	59	55	30	33
AMP PEAK 16(9Q34.3) WILD-TYPE	144	73	115	13

Figure S80. Get High-res Image Gene #16: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9q34.3' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00046

Table S81. Gene #16: 'amp_9q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
AMP PEAK 16(9Q34.3) MUTATED	20	23	51	37	22	19	5
AMP PEAK 16(9Q34.3) WILD-TYPE	64	64	52	52	56	56	1

Figure S81. Get High-res Image Gene #16: 'amp_9q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9q34.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0237 (Fisher's exact test), Q value = 0.051

Table S82. Gene #16: 'amp_9q34.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	76	82	48
AMP PEAK 16(9Q34.3) MUTATED	36	32	11
AMP PEAK 16(9Q34.3) WILD-TYPE	40	50	37

Figure S82. Get High-res Image Gene #16: 'amp_9q34.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_9q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00446 (Fisher's exact test), Q value = 0.012

Table S83. Gene #16: 'amp_9q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
AMP PEAK 16(9Q34.3) MUTATED	60	33	70	11
AMP PEAK 16(9Q34.3) WILD-TYPE	116	70	100	54

Figure S83. Get High-res Image Gene #16: 'amp_9q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11p13' versus 'CN_CNMF'

P value = 0.00223 (Fisher's exact test), Q value = 0.0066

Table S84. Gene #17: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
AMP PEAK 17(11P13) MUTATED	54	17	19	12
AMP PEAK 17(11P13) WILD-TYPE	149	111	126	34

Figure S84. Get High-res Image Gene #17: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11p13' versus 'METHLYATION_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0017

Table S85. Gene #17: 'amp_11p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
AMP PEAK 17(11P13) MUTATED	8	12	22	24	9	26	1
AMP PEAK 17(11P13) WILD-TYPE	76	75	81	65	69	49	5

Figure S85. Get High-res Image Gene #17: 'amp_11p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0422 (Fisher's exact test), Q value = 0.083

Table S86. Gene #17: 'amp_11p13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
AMP PEAK 17(11P13) MUTATED	32	29	31
AMP PEAK 17(11P13) WILD-TYPE	139	75	167

Figure S86. Get High-res Image Gene #17: 'amp_11p13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S87. Gene #18: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
AMP PEAK 18(11Q13.3) MUTATED	135	59	22	13
AMP PEAK 18(11Q13.3) WILD-TYPE	68	69	123	33

Figure S87. Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S88. Gene #18: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
AMP PEAK 18(11Q13.3) MUTATED	30	38	37	53	15	51	5
AMP PEAK 18(11Q13.3) WILD-TYPE	54	49	66	36	63	24	1

Figure S88. Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S89. Gene #18: 'amp_11q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
AMP PEAK 18(11Q13.3) MUTATED	84	45	54	44
AMP PEAK 18(11Q13.3) WILD-TYPE	51	68	117	51

Figure S89. Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0318 (Fisher's exact test), Q value = 0.065

Table S90. Gene #18: 'amp_11q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
AMP PEAK 18(11Q13.3) MUTATED	82	42	84	19
AMP PEAK 18(11Q13.3) WILD-TYPE	94	61	86	46

Figure S90. Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

P value = 0.0301 (Fisher's exact test), Q value = 0.063

Table S91. Gene #18: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
AMP PEAK 18(11Q13.3) MUTATED	42	67	45	45	28
AMP PEAK 18(11Q13.3) WILD-TYPE	39	72	86	46	48

Figure S91. Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0046 (Fisher's exact test), Q value = 0.012

Table S92. Gene #18: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
AMP PEAK 18(11Q13.3) MUTATED	91	72	64
AMP PEAK 18(11Q13.3) WILD-TYPE	99	70	122

Figure S92. Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_12p13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S93. Gene #19: 'amp_12p13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
AMP PEAK 19(12P13.33) MUTATED	77	62	12	16
AMP PEAK 19(12P13.33) WILD-TYPE	126	66	133	30

Figure S93. Get High-res Image Gene #19: 'amp_12p13.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p13.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S94. Gene #19: 'amp_12p13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
AMP PEAK 19(12P13.33) MUTATED	14	40	15	44	23	30	1
AMP PEAK 19(12P13.33) WILD-TYPE	70	47	88	45	55	45	5

Figure S94. Get High-res Image Gene #19: 'amp_12p13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12p13.33' versus 'MRNASEQ_CNMF'

P value = 0.00177 (Fisher's exact test), Q value = 0.0053

Table S95. Gene #19: 'amp_12p13.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
AMP PEAK 19(12P13.33) MUTATED	44	21	67	34
AMP PEAK 19(12P13.33) WILD-TYPE	91	92	104	61

Figure S95. Get High-res Image Gene #19: 'amp_12p13.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_12p13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00035

Table S96. Gene #19: 'amp_12p13.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
AMP PEAK 19(12P13.33) MUTATED	61	50	39	16
AMP PEAK 19(12P13.33) WILD-TYPE	115	53	131	49

Figure S96. Get High-res Image Gene #19: 'amp_12p13.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_12p13.33' versus 'MIRSEQ_CNMF'

P value = 0.0259 (Fisher's exact test), Q value = 0.055

Table S97. Gene #19: 'amp_12p13.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
AMP PEAK 19(12P13.33) MUTATED	32	34	52	29	19
AMP PEAK 19(12P13.33) WILD-TYPE	49	105	79	62	57

Figure S97. Get High-res Image Gene #19: 'amp_12p13.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_12q15' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S98. Gene #20: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
AMP PEAK 20(12Q15) MUTATED	46	37	10	10
AMP PEAK 20(12Q15) WILD-TYPE	157	91	135	36

Figure S98. Get High-res Image Gene #20: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00028

Table S99. Gene #20: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
AMP PEAK 20(12Q15) MUTATED	8	22	9	29	13	21	1
AMP PEAK 20(12Q15) WILD-TYPE	76	65	94	60	65	54	5

Figure S99. Get High-res Image Gene #20: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00167 (Fisher's exact test), Q value = 0.005

Table S100. Gene #20: 'amp_12q15' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
AMP PEAK 20(12Q15) MUTATED	35	34	25	8
AMP PEAK 20(12Q15) WILD-TYPE	141	69	145	57

Figure S100. Get High-res Image Gene #20: 'amp_12q15' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S101. Gene #21: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
AMP PEAK 21(13Q22.1) MUTATED	74	16	11	4
AMP PEAK 21(13Q22.1) WILD-TYPE	129	112	134	42

Figure S101. Get High-res Image Gene #21: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S102. Gene #21: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
AMP PEAK 21(13Q22.1) MUTATED	9	23	12	17	12	30	2
AMP PEAK 21(13Q22.1) WILD-TYPE	75	64	91	72	66	45	4

Figure S102. Get High-res Image Gene #21: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S103. Gene #22: 'amp_13q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
AMP PEAK 22(13Q34) MUTATED	71	14	13	8
AMP PEAK 22(13Q34) WILD-TYPE	132	114	132	38

Figure S103. Get High-res Image Gene #22: 'amp_13q34' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q34' versus 'METHLYATION_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0016

Table S104. Gene #22: 'amp_13q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
AMP PEAK 22(13Q34) MUTATED	12	20	14	19	10	30	1
AMP PEAK 22(13Q34) WILD-TYPE	72	67	89	70	68	45	5

Figure S104. Get High-res Image Gene #22: 'amp_13q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00402 (Fisher's exact test), Q value = 0.011

Table S105. Gene #22: 'amp_13q34' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
AMP PEAK 22(13Q34) MUTATED	46	22	33	4
AMP PEAK 22(13Q34) WILD-TYPE	130	81	137	61

Figure S105. Get High-res Image Gene #22: 'amp_13q34' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'CN_CNMF'

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

Table S106. Gene #23: 'amp_15q26.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
AMP PEAK 23(15Q26.3) MUTATED	54	33	13	5
AMP PEAK 23(15Q26.3) WILD-TYPE	149	95	132	41

Figure S106. Get High-res Image Gene #23: 'amp_15q26.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_15q26.3' versus 'METHLYATION_CNMF'

P value = 0.00443 (Fisher's exact test), Q value = 0.012

Table S107. Gene #23: 'amp_15q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
AMP PEAK 23(15Q26.3) MUTATED	9	21	19	26	8	20	2
AMP PEAK 23(15Q26.3) WILD-TYPE	75	66	84	63	70	55	4

Figure S107. Get High-res Image Gene #23: 'amp_15q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S108. Gene #24: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
AMP PEAK 24(17Q12) MUTATED	43	36	4	8
AMP PEAK 24(17Q12) WILD-TYPE	160	92	141	38

Figure S108. Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S109. Gene #24: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
AMP PEAK 24(17Q12) MUTATED	6	23	7	29	6	20	0
AMP PEAK 24(17Q12) WILD-TYPE	78	64	96	60	72	55	6

Figure S109. Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 0.00255 (Fisher's exact test), Q value = 0.0074

Table S110. Gene #24: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
AMP PEAK 24(17Q12) MUTATED	25	9	42	14
AMP PEAK 24(17Q12) WILD-TYPE	110	104	129	81

Figure S110. Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S111. Gene #24: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
AMP PEAK 24(17Q12) MUTATED	24	36	23	7
AMP PEAK 24(17Q12) WILD-TYPE	152	67	147	58

Figure S111. Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.046

Table S112. Gene #24: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
AMP PEAK 24(17Q12) MUTATED	24	22	17	18	9
AMP PEAK 24(17Q12) WILD-TYPE	57	117	114	73	67

Figure S112. Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00017

Table S113. Gene #24: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
AMP PEAK 24(17Q12) MUTATED	31	41	18
AMP PEAK 24(17Q12) WILD-TYPE	159	101	168

Figure S113. Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_18p11.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S114. Gene #25: 'amp_18p11.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
AMP PEAK 25(18P11.31) MUTATED	73	56	20	7
AMP PEAK 25(18P11.31) WILD-TYPE	130	72	125	39

Figure S114. Get High-res Image Gene #25: 'amp_18p11.31' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18p11.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S115. Gene #25: 'amp_18p11.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
AMP PEAK 25(18P11.31) MUTATED	9	50	15	33	21	26	2
AMP PEAK 25(18P11.31) WILD-TYPE	75	37	88	56	57	49	4

Figure S115. Get High-res Image Gene #25: 'amp_18p11.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_18p11.31' versus 'MRNASEQ_CNMF'

P value = 0.00946 (Fisher's exact test), Q value = 0.023

Table S116. Gene #25: 'amp_18p11.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
AMP PEAK 25(18P11.31) MUTATED	42	23	65	24
AMP PEAK 25(18P11.31) WILD-TYPE	93	90	106	71

Figure S116. Get High-res Image Gene #25: 'amp_18p11.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_18p11.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S117. Gene #25: 'amp_18p11.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
AMP PEAK 25(18P11.31) MUTATED	46	52	39	17
AMP PEAK 25(18P11.31) WILD-TYPE	130	51	131	48

Figure S117. Get High-res Image Gene #25: 'amp_18p11.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_18p11.31' versus 'MIRSEQ_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.025

Table S118. Gene #25: 'amp_18p11.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
AMP PEAK 25(18P11.31) MUTATED	36	38	40	27	14
AMP PEAK 25(18P11.31) WILD-TYPE	45	101	91	64	62

Figure S118. Get High-res Image Gene #25: 'amp_18p11.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_18p11.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00072

Table S119. Gene #25: 'amp_18p11.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
AMP PEAK 25(18P11.31) MUTATED	49	62	44
AMP PEAK 25(18P11.31) WILD-TYPE	141	80	142

Figure S119. Get High-res Image Gene #25: 'amp_18p11.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S120. Gene #26: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
AMP PEAK 26(18Q11.2) MUTATED	44	42	15	5
AMP PEAK 26(18Q11.2) WILD-TYPE	159	86	130	41

Figure S120. Get High-res Image Gene #26: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0012

Table S121. Gene #26: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
AMP PEAK 26(18Q11.2) MUTATED	7	27	12	26	17	15	2
AMP PEAK 26(18Q11.2) WILD-TYPE	77	60	91	63	61	60	4

Figure S121. Get High-res Image Gene #26: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0126 (Fisher's exact test), Q value = 0.029

Table S122. Gene #26: 'amp_18q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
AMP PEAK 26(18Q11.2) MUTATED	29	33	29	14
AMP PEAK 26(18Q11.2) WILD-TYPE	147	70	141	51

Figure S122. Get High-res Image Gene #26: 'amp_18q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00799 (Fisher's exact test), Q value = 0.02

Table S123. Gene #26: 'amp_18q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
AMP PEAK 26(18Q11.2) MUTATED	26	19	30	20	10
AMP PEAK 26(18Q11.2) WILD-TYPE	55	120	101	71	66

Figure S123. Get High-res Image Gene #26: 'amp_18q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0287 (Fisher's exact test), Q value = 0.06

Table S124. Gene #26: 'amp_18q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
AMP PEAK 26(18Q11.2) MUTATED	33	40	32
AMP PEAK 26(18Q11.2) WILD-TYPE	157	102	154

Figure S124. Get High-res Image Gene #26: 'amp_18q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20q11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S125. Gene #27: 'amp_20q11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
AMP PEAK 27(20Q11.22) MUTATED	115	55	35	22
AMP PEAK 27(20Q11.22) WILD-TYPE	88	73	110	24

Figure S125. Get High-res Image Gene #27: 'amp_20q11.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q11.22' versus 'METHLYATION_CNMF'

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

Table S126. Gene #27: 'amp_20q11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
AMP PEAK 27(20Q11.22) MUTATED	30	44	29	45	27	49	3
AMP PEAK 27(20Q11.22) WILD-TYPE	54	43	74	44	51	26	3

Figure S126. Get High-res Image Gene #27: 'amp_20q11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q11.22' versus 'RPPA_CNMF'

P value = 0.0487 (Fisher's exact test), Q value = 0.094

Table S127. Gene #27: 'amp_20q11.22' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	29	31	29	67
AMP PEAK 27(20Q11.22) MUTATED	22	19	14	15	22
AMP PEAK 27(20Q11.22) WILD-TYPE	28	10	17	14	45

Figure S127. Get High-res Image Gene #27: 'amp_20q11.22' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_20q11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0287 (Fisher's exact test), Q value = 0.06

Table S128. Gene #27: 'amp_20q11.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
AMP PEAK 27(20Q11.22) MUTATED	90	44	69	20
AMP PEAK 27(20Q11.22) WILD-TYPE	86	59	101	45

Figure S128. Get High-res Image Gene #27: 'amp_20q11.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0236 (Fisher's exact test), Q value = 0.051

Table S129. Gene #27: 'amp_20q11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
AMP PEAK 27(20Q11.22) MUTATED	96	61	68
AMP PEAK 27(20Q11.22) WILD-TYPE	94	81	118

Figure S129. Get High-res Image Gene #27: 'amp_20q11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20q11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0173 (Fisher's exact test), Q value = 0.039

Table S130. Gene #27: 'amp_20q11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
AMP PEAK 27(20Q11.22) MUTATED	84	49	70
AMP PEAK 27(20Q11.22) WILD-TYPE	87	55	128

Figure S130. Get High-res Image Gene #27: 'amp_20q11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xq28' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S131. Gene #28: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
AMP PEAK 28(XQ28) MUTATED	89	32	18	11
AMP PEAK 28(XQ28) WILD-TYPE	114	96	127	35

Figure S131. Get High-res Image Gene #28: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq28' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00038

Table S132. Gene #28: 'amp_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
AMP PEAK 28(XQ28) MUTATED	10	25	25	36	20	32	2
AMP PEAK 28(XQ28) WILD-TYPE	74	62	78	53	58	43	4

Figure S132. Get High-res Image Gene #28: 'amp_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S133. Gene #29: 'del_1p36.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 1(1P36.21) MUTATED	36	43	9	7
DEL PEAK 1(1P36.21) WILD-TYPE	167	85	136	39

Figure S133. Get High-res Image Gene #29: 'del_1p36.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S134. Gene #29: 'del_1p36.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 1(1P36.21) MUTATED	5	17	11	48	8	6	0
DEL PEAK 1(1P36.21) WILD-TYPE	79	70	92	41	70	69	6

Figure S134. Get High-res Image Gene #29: 'del_1p36.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.21' versus 'RPPA_CNMF'

P value = 0.021 (Fisher's exact test), Q value = 0.046

Table S135. Gene #29: 'del_1p36.21' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	29	31	29	67
DEL PEAK 1(1P36.21) MUTATED	9	6	14	3	13
DEL PEAK 1(1P36.21) WILD-TYPE	41	23	17	26	54

Figure S135. Get High-res Image Gene #29: 'del_1p36.21' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_1p36.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.00578 (Fisher's exact test), Q value = 0.015

Table S136. Gene #29: 'del_1p36.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	76	82	48
DEL PEAK 1(1P36.21) MUTATED	15	26	4
DEL PEAK 1(1P36.21) WILD-TYPE	61	56	44

Figure S136. Get High-res Image Gene #29: 'del_1p36.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_1p36.21' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00028

Table S137. Gene #29: 'del_1p36.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 1(1P36.21) MUTATED	25	8	48	13
DEL PEAK 1(1P36.21) WILD-TYPE	110	105	123	82

Figure S137. Get High-res Image Gene #29: 'del_1p36.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p36.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S138. Gene #29: 'del_1p36.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 1(1P36.21) MUTATED	27	43	17	7
DEL PEAK 1(1P36.21) WILD-TYPE	149	60	153	58

Figure S138. Get High-res Image Gene #29: 'del_1p36.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.21' versus 'MIRSEQ_CNMF'

P value = 0.00709 (Fisher's exact test), Q value = 0.018

Table S139. Gene #29: 'del_1p36.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 1(1P36.21) MUTATED	22	15	31	14	10
DEL PEAK 1(1P36.21) WILD-TYPE	59	124	100	77	66

Figure S139. Get High-res Image Gene #29: 'del_1p36.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p36.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0405 (Fisher's exact test), Q value = 0.081

Table S140. Gene #29: 'del_1p36.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 1(1P36.21) MUTATED	27	35	30
DEL PEAK 1(1P36.21) WILD-TYPE	163	107	156

Figure S140. Get High-res Image Gene #29: 'del_1p36.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00355 (Fisher's exact test), Q value = 0.0099

Table S141. Gene #29: 'del_1p36.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	189	143
DEL PEAK 1(1P36.21) MUTATED	23	22	37
DEL PEAK 1(1P36.21) WILD-TYPE	118	167	106

Figure S141. Get High-res Image Gene #29: 'del_1p36.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p36.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00681 (Fisher's exact test), Q value = 0.017

Table S142. Gene #29: 'del_1p36.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
DEL PEAK 1(1P36.21) MUTATED	24	11	47
DEL PEAK 1(1P36.21) WILD-TYPE	147	93	151

Figure S142. Get High-res Image Gene #29: 'del_1p36.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S143. Gene #30: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 2(1P13.2) MUTATED	67	46	7	13
DEL PEAK 2(1P13.2) WILD-TYPE	136	82	138	33

Figure S143. Get High-res Image Gene #30: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S144. Gene #30: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 2(1P13.2) MUTATED	13	27	15	55	6	14	3
DEL PEAK 2(1P13.2) WILD-TYPE	71	60	88	34	72	61	3

Figure S144. Get High-res Image Gene #30: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p13.2' versus 'RPPA_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.026

Table S145. Gene #30: 'del_1p13.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	29	31	29	67
DEL PEAK 2(1P13.2) MUTATED	7	6	15	9	23
DEL PEAK 2(1P13.2) WILD-TYPE	43	23	16	20	44

Figure S145. Get High-res Image Gene #30: 'del_1p13.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_1p13.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00712 (Fisher's exact test), Q value = 0.018

Table S146. Gene #30: 'del_1p13.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	76	82	48
DEL PEAK 2(1P13.2) MUTATED	17	34	9
DEL PEAK 2(1P13.2) WILD-TYPE	59	48	39

Figure S146. Get High-res Image Gene #30: 'del_1p13.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_1p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S147. Gene #30: 'del_1p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 2(1P13.2) MUTATED	43	45	37	6
DEL PEAK 2(1P13.2) WILD-TYPE	133	58	133	59

Figure S147. Get High-res Image Gene #30: 'del_1p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.2' versus 'MIRSEQ_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.0026

Table S148. Gene #30: 'del_1p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 2(1P13.2) MUTATED	34	27	39	16	15
DEL PEAK 2(1P13.2) WILD-TYPE	47	112	92	75	61

Figure S148. Get High-res Image Gene #30: 'del_1p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00038

Table S149. Gene #30: 'del_1p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 2(1P13.2) MUTATED	47	53	31
DEL PEAK 2(1P13.2) WILD-TYPE	143	89	155

Figure S149. Get High-res Image Gene #30: 'del_1p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1q44' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00035

Table S150. Gene #31: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 3(1Q44) MUTATED	28	7	4	9
DEL PEAK 3(1Q44) WILD-TYPE	175	121	141	37

Figure S150. Get High-res Image Gene #31: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q44' versus 'METHLYATION_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.028

Table S151. Gene #31: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 3(1Q44) MUTATED	8	6	12	7	1	14	0
DEL PEAK 3(1Q44) WILD-TYPE	76	81	91	82	77	61	6

Figure S151. Get High-res Image Gene #31: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1q44' versus 'MRNASEQ_CNMF'

P value = 0.00853 (Fisher's exact test), Q value = 0.021

Table S152. Gene #31: 'del_1q44' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 3(1Q44) MUTATED	14	16	6	10
DEL PEAK 3(1Q44) WILD-TYPE	121	97	165	85

Figure S152. Get High-res Image Gene #31: 'del_1q44' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1q44' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.024

Table S153. Gene #31: 'del_1q44' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 3(1Q44) MUTATED	25	8	12	1
DEL PEAK 3(1Q44) WILD-TYPE	151	95	158	64

Figure S153. Get High-res Image Gene #31: 'del_1q44' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1q44' versus 'MIRSEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0013

Table S154. Gene #31: 'del_1q44' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 3(1Q44) MUTATED	4	23	3	7	10
DEL PEAK 3(1Q44) WILD-TYPE	77	116	128	84	66

Figure S154. Get High-res Image Gene #31: 'del_1q44' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1q44' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0459 (Fisher's exact test), Q value = 0.089

Table S155. Gene #31: 'del_1q44' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 3(1Q44) MUTATED	25	11	11
DEL PEAK 3(1Q44) WILD-TYPE	165	131	175

Figure S155. Get High-res Image Gene #31: 'del_1q44' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q21.2' versus 'CN_CNMF'

P value = 0.0495 (Fisher's exact test), Q value = 0.095

Table S156. Gene #32: 'del_2q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 4(2Q21.2) MUTATED	35	15	16	12
DEL PEAK 4(2Q21.2) WILD-TYPE	168	113	129	34

Figure S156. Get High-res Image Gene #32: 'del_2q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q21.2' versus 'MRNASEQ_CNMF'

P value = 0.0063 (Fisher's exact test), Q value = 0.016

Table S157. Gene #32: 'del_2q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 4(2Q21.2) MUTATED	29	21	17	8
DEL PEAK 4(2Q21.2) WILD-TYPE	106	92	154	87

Figure S157. Get High-res Image Gene #32: 'del_2q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00072

Table S158. Gene #32: 'del_2q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 4(2Q21.2) MUTATED	24	6	40	5
DEL PEAK 4(2Q21.2) WILD-TYPE	152	97	130	60

Figure S158. Get High-res Image Gene #32: 'del_2q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q21.2' versus 'MIRSEQ_CNMF'

P value = 0.0386 (Fisher's exact test), Q value = 0.077

Table S159. Gene #32: 'del_2q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 4(2Q21.2) MUTATED	17	28	16	10	6
DEL PEAK 4(2Q21.2) WILD-TYPE	64	111	115	81	70

Figure S159. Get High-res Image Gene #32: 'del_2q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'CN_CNMF'

P value = 0.00468 (Fisher's exact test), Q value = 0.012

Table S160. Gene #33: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 5(2Q22.1) MUTATED	55	33	19	14
DEL PEAK 5(2Q22.1) WILD-TYPE	148	95	126	32

Figure S160. Get High-res Image Gene #33: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00038

Table S161. Gene #33: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 5(2Q22.1) MUTATED	10	18	24	39	11	18	1
DEL PEAK 5(2Q22.1) WILD-TYPE	74	69	79	50	67	57	5

Figure S161. Get High-res Image Gene #33: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00972 (Fisher's exact test), Q value = 0.023

Table S162. Gene #33: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 5(2Q22.1) MUTATED	34	30	47	7
DEL PEAK 5(2Q22.1) WILD-TYPE	142	73	123	58

Figure S162. Get High-res Image Gene #33: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00139 (Fisher's exact test), Q value = 0.0043

Table S163. Gene #33: 'del_2q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 5(2Q22.1) MUTATED	39	49	33
DEL PEAK 5(2Q22.1) WILD-TYPE	151	93	153

Figure S163. Get High-res Image Gene #33: 'del_2q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q36.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S164. Gene #34: 'del_2q36.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 6(2Q36.2) MUTATED	62	58	17	20
DEL PEAK 6(2Q36.2) WILD-TYPE	141	70	128	26

Figure S164. Get High-res Image Gene #34: 'del_2q36.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q36.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S165. Gene #34: 'del_2q36.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 6(2Q36.2) MUTATED	8	28	25	48	24	21	3
DEL PEAK 6(2Q36.2) WILD-TYPE	76	59	78	41	54	54	3

Figure S165. Get High-res Image Gene #34: 'del_2q36.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q36.2' versus 'MRNASEQ_CNMF'

P value = 0.0088 (Fisher's exact test), Q value = 0.021

Table S166. Gene #34: 'del_2q36.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 6(2Q36.2) MUTATED	49	25	60	20
DEL PEAK 6(2Q36.2) WILD-TYPE	86	88	111	75

Figure S166. Get High-res Image Gene #34: 'del_2q36.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q36.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0248 (Fisher's exact test), Q value = 0.053

Table S167. Gene #34: 'del_2q36.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 6(2Q36.2) MUTATED	49	55	50
DEL PEAK 6(2Q36.2) WILD-TYPE	141	87	136

Figure S167. Get High-res Image Gene #34: 'del_2q36.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S168. Gene #35: 'del_3p26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 7(3P26.2) MUTATED	190	96	30	32
DEL PEAK 7(3P26.2) WILD-TYPE	13	32	115	14

Figure S168. Get High-res Image Gene #35: 'del_3p26.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p26.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S169. Gene #35: 'del_3p26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 7(3P26.2) MUTATED	50	73	55	76	19	69	6
DEL PEAK 7(3P26.2) WILD-TYPE	34	14	48	13	59	6	0

Figure S169. Get High-res Image Gene #35: 'del_3p26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p26.2' versus 'MRNASEQ_CNMF'

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

Table S170. Gene #35: 'del_3p26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 7(3P26.2) MUTATED	103	64	100	76
DEL PEAK 7(3P26.2) WILD-TYPE	32	49	71	19

Figure S170. Get High-res Image Gene #35: 'del_3p26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S171. Gene #35: 'del_3p26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 7(3P26.2) MUTATED	134	83	107	19
DEL PEAK 7(3P26.2) WILD-TYPE	42	20	63	46

Figure S171. Get High-res Image Gene #35: 'del_3p26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S172. Gene #35: 'del_3p26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 7(3P26.2) MUTATED	68	85	67	68	58
DEL PEAK 7(3P26.2) WILD-TYPE	13	54	64	23	18

Figure S172. Get High-res Image Gene #35: 'del_3p26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S173. Gene #35: 'del_3p26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 7(3P26.2) MUTATED	144	106	96
DEL PEAK 7(3P26.2) WILD-TYPE	46	36	90

Figure S173. Get High-res Image Gene #35: 'del_3p26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0198 (Fisher's exact test), Q value = 0.044

Table S174. Gene #35: 'del_3p26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
DEL PEAK 7(3P26.2) MUTATED	127	68	120
DEL PEAK 7(3P26.2) WILD-TYPE	44	36	78

Figure S174. Get High-res Image Gene #35: 'del_3p26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S175. Gene #36: 'del_3p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 8(3P24.1) MUTATED	191	107	36	34
DEL PEAK 8(3P24.1) WILD-TYPE	12	21	109	12

Figure S175. Get High-res Image Gene #36: 'del_3p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p24.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S176. Gene #36: 'del_3p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 8(3P24.1) MUTATED	50	78	56	80	29	69	6
DEL PEAK 8(3P24.1) WILD-TYPE	34	9	47	9	49	6	0

Figure S176. Get High-res Image Gene #36: 'del_3p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p24.1' versus 'MRNASEQ_CNMF'

P value = 0.00126 (Fisher's exact test), Q value = 0.0039

Table S177. Gene #36: 'del_3p24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 8(3P24.1) MUTATED	105	66	116	76
DEL PEAK 8(3P24.1) WILD-TYPE	30	47	55	19

Figure S177. Get High-res Image Gene #36: 'del_3p24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S178. Gene #36: 'del_3p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 8(3P24.1) MUTATED	137	91	108	27
DEL PEAK 8(3P24.1) WILD-TYPE	39	12	62	38

Figure S178. Get High-res Image Gene #36: 'del_3p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p24.1' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00024

Table S179. Gene #36: 'del_3p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 8(3P24.1) MUTATED	70	87	78	70	60
DEL PEAK 8(3P24.1) WILD-TYPE	11	52	53	21	16

Figure S179. Get High-res Image Gene #36: 'del_3p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p24.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S180. Gene #36: 'del_3p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 8(3P24.1) MUTATED	147	110	108
DEL PEAK 8(3P24.1) WILD-TYPE	43	32	78

Figure S180. Get High-res Image Gene #36: 'del_3p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.033

Table S181. Gene #36: 'del_3p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	189	143
DEL PEAK 8(3P24.1) MUTATED	109	119	104
DEL PEAK 8(3P24.1) WILD-TYPE	32	70	39

Figure S181. Get High-res Image Gene #36: 'del_3p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S182. Gene #37: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 9(3P14.2) MUTATED	190	110	36	36
DEL PEAK 9(3P14.2) WILD-TYPE	13	18	109	10

Figure S182. Get High-res Image Gene #37: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S183. Gene #37: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 9(3P14.2) MUTATED	50	79	54	82	34	67	6
DEL PEAK 9(3P14.2) WILD-TYPE	34	8	49	7	44	8	0

Figure S183. Get High-res Image Gene #37: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p14.2' versus 'MRNASEQ_CNMF'

P value = 0.00579 (Fisher's exact test), Q value = 0.015

Table S184. Gene #37: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 9(3P14.2) MUTATED	105	67	121	74
DEL PEAK 9(3P14.2) WILD-TYPE	30	46	50	21

Figure S184. Get High-res Image Gene #37: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S185. Gene #37: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 9(3P14.2) MUTATED	135	93	108	31
DEL PEAK 9(3P14.2) WILD-TYPE	41	10	62	34

Figure S185. Get High-res Image Gene #37: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_CNMF'

P value = 0.00144 (Fisher's exact test), Q value = 0.0044

Table S186. Gene #37: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 9(3P14.2) MUTATED	70	92	82	68	57
DEL PEAK 9(3P14.2) WILD-TYPE	11	47	49	23	19

Figure S186. Get High-res Image Gene #37: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0014

Table S187. Gene #37: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 9(3P14.2) MUTATED	145	111	113
DEL PEAK 9(3P14.2) WILD-TYPE	45	31	73

Figure S187. Get High-res Image Gene #37: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0319 (Fisher's exact test), Q value = 0.065

Table S188. Gene #37: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	189	143
DEL PEAK 9(3P14.2) MUTATED	106	121	108
DEL PEAK 9(3P14.2) WILD-TYPE	35	68	35

Figure S188. Get High-res Image Gene #37: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S189. Gene #38: 'del_3p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 10(3P12.1) MUTATED	180	104	28	31
DEL PEAK 10(3P12.1) WILD-TYPE	23	24	117	15

Figure S189. Get High-res Image Gene #38: 'del_3p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S190. Gene #38: 'del_3p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 10(3P12.1) MUTATED	46	75	51	82	24	60	5
DEL PEAK 10(3P12.1) WILD-TYPE	38	12	52	7	54	15	1

Figure S190. Get High-res Image Gene #38: 'del_3p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p12.1' versus 'MRNASEQ_CNMF'

P value = 0.00161 (Fisher's exact test), Q value = 0.0049

Table S191. Gene #38: 'del_3p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 10(3P12.1) MUTATED	101	60	109	69
DEL PEAK 10(3P12.1) WILD-TYPE	34	53	62	26

Figure S191. Get High-res Image Gene #38: 'del_3p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S192. Gene #38: 'del_3p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 10(3P12.1) MUTATED	124	88	104	23
DEL PEAK 10(3P12.1) WILD-TYPE	52	15	66	42

Figure S192. Get High-res Image Gene #38: 'del_3p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p12.1' versus 'MIRSEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00053

Table S193. Gene #38: 'del_3p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 10(3P12.1) MUTATED	68	83	72	63	54
DEL PEAK 10(3P12.1) WILD-TYPE	13	56	59	28	22

Figure S193. Get High-res Image Gene #38: 'del_3p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.0016

Table S194. Gene #38: 'del_3p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 10(3P12.1) MUTATED	130	107	103
DEL PEAK 10(3P12.1) WILD-TYPE	60	35	83

Figure S194. Get High-res Image Gene #38: 'del_3p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S195. Gene #39: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 11(4P16.3) MUTATED	95	84	10	16
DEL PEAK 11(4P16.3) WILD-TYPE	108	44	135	30

Figure S195. Get High-res Image Gene #39: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4p16.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S196. Gene #39: 'del_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 11(4P16.3) MUTATED	20	47	26	61	20	26	5
DEL PEAK 11(4P16.3) WILD-TYPE	64	40	77	28	58	49	1

Figure S196. Get High-res Image Gene #39: 'del_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4p16.3' versus 'MRNASEQ_CNMF'

P value = 0.00246 (Fisher's exact test), Q value = 0.0072

Table S197. Gene #39: 'del_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 11(4P16.3) MUTATED	61	30	79	32
DEL PEAK 11(4P16.3) WILD-TYPE	74	83	92	63

Figure S197. Get High-res Image Gene #39: 'del_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S198. Gene #39: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 11(4P16.3) MUTATED	72	63	51	16
DEL PEAK 11(4P16.3) WILD-TYPE	104	40	119	49

Figure S198. Get High-res Image Gene #39: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00814 (Fisher's exact test), Q value = 0.02

Table S199. Gene #39: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	189	143
DEL PEAK 11(4P16.3) MUTATED	60	57	65
DEL PEAK 11(4P16.3) WILD-TYPE	81	132	78

Figure S199. Get High-res Image Gene #39: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0412 (Fisher's exact test), Q value = 0.082

Table S200. Gene #39: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
DEL PEAK 11(4P16.3) MUTATED	71	29	82
DEL PEAK 11(4P16.3) WILD-TYPE	100	75	116

Figure S200. Get High-res Image Gene #39: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4p15.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S201. Gene #40: 'del_4p15.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 12(4P15.2) MUTATED	95	86	10	17
DEL PEAK 12(4P15.2) WILD-TYPE	108	42	135	29

Figure S201. Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_4p15.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S202. Gene #40: 'del_4p15.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 12(4P15.2) MUTATED	22	47	25	65	21	23	5
DEL PEAK 12(4P15.2) WILD-TYPE	62	40	78	24	57	52	1

Figure S202. Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4p15.2' versus 'RPPA_CNMF'

P value = 0.0248 (Fisher's exact test), Q value = 0.053

Table S203. Gene #40: 'del_4p15.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	29	31	29	67
DEL PEAK 12(4P15.2) MUTATED	26	13	20	9	23
DEL PEAK 12(4P15.2) WILD-TYPE	24	16	11	20	44

Figure S203. Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_4p15.2' versus 'MRNASEQ_CNMF'

P value = 0.00569 (Fisher's exact test), Q value = 0.015

Table S204. Gene #40: 'del_4p15.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 12(4P15.2) MUTATED	58	30	80	37
DEL PEAK 12(4P15.2) WILD-TYPE	77	83	91	58

Figure S204. Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4p15.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S205. Gene #40: 'del_4p15.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 12(4P15.2) MUTATED	74	64	49	18
DEL PEAK 12(4P15.2) WILD-TYPE	102	39	121	47

Figure S205. Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4p15.2' versus 'MIRSEQ_CNMF'

P value = 0.00646 (Fisher's exact test), Q value = 0.016

Table S206. Gene #40: 'del_4p15.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 12(4P15.2) MUTATED	43	41	57	32	33
DEL PEAK 12(4P15.2) WILD-TYPE	38	98	74	59	43

Figure S206. Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4p15.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0302 (Fisher's exact test), Q value = 0.063

Table S207. Gene #40: 'del_4p15.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 12(4P15.2) MUTATED	76	68	62
DEL PEAK 12(4P15.2) WILD-TYPE	114	74	124

Figure S207. Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4p15.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0035

Table S208. Gene #40: 'del_4p15.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	189	143
DEL PEAK 12(4P15.2) MUTATED	64	55	66
DEL PEAK 12(4P15.2) WILD-TYPE	77	134	77

Figure S208. Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4p15.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00296 (Fisher's exact test), Q value = 0.0084

Table S209. Gene #40: 'del_4p15.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
DEL PEAK 12(4P15.2) MUTATED	76	26	83
DEL PEAK 12(4P15.2) WILD-TYPE	95	78	115

Figure S209. Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S210. Gene #41: 'del_4q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 13(4Q21.3) MUTATED	67	61	12	16
DEL PEAK 13(4Q21.3) WILD-TYPE	136	67	133	30

Figure S210. Get High-res Image Gene #41: 'del_4q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S211. Gene #41: 'del_4q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 13(4Q21.3) MUTATED	15	32	19	48	17	23	2
DEL PEAK 13(4Q21.3) WILD-TYPE	69	55	84	41	61	52	4

Figure S211. Get High-res Image Gene #41: 'del_4q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0465 (Fisher's exact test), Q value = 0.09

Table S212. Gene #41: 'del_4q21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	76	82	48
DEL PEAK 13(4Q21.3) MUTATED	21	32	9
DEL PEAK 13(4Q21.3) WILD-TYPE	55	50	39

Figure S212. Get High-res Image Gene #41: 'del_4q21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_4q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S213. Gene #41: 'del_4q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 13(4Q21.3) MUTATED	63	44	30	15
DEL PEAK 13(4Q21.3) WILD-TYPE	113	59	140	50

Figure S213. Get High-res Image Gene #41: 'del_4q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0315 (Fisher's exact test), Q value = 0.065

Table S214. Gene #41: 'del_4q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 13(4Q21.3) MUTATED	63	48	42
DEL PEAK 13(4Q21.3) WILD-TYPE	127	94	144

Figure S214. Get High-res Image Gene #41: 'del_4q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0296 (Fisher's exact test), Q value = 0.062

Table S215. Gene #41: 'del_4q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
DEL PEAK 13(4Q21.3) MUTATED	59	21	64
DEL PEAK 13(4Q21.3) WILD-TYPE	112	83	134

Figure S215. Get High-res Image Gene #41: 'del_4q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S216. Gene #42: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 14(4Q22.1) MUTATED	75	66	11	17
DEL PEAK 14(4Q22.1) WILD-TYPE	128	62	134	29

Figure S216. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S217. Gene #42: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 14(4Q22.1) MUTATED	12	34	22	58	18	23	2
DEL PEAK 14(4Q22.1) WILD-TYPE	72	53	81	31	60	52	4

Figure S217. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.00085

Table S218. Gene #42: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 14(4Q22.1) MUTATED	63	48	40	15
DEL PEAK 14(4Q22.1) WILD-TYPE	113	55	130	50

Figure S218. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.04 (Fisher's exact test), Q value = 0.08

Table S219. Gene #42: 'del_4q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 14(4Q22.1) MUTATED	66	53	47
DEL PEAK 14(4Q22.1) WILD-TYPE	124	89	139

Figure S219. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q35.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S220. Gene #43: 'del_4q35.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 15(4Q35.2) MUTATED	102	70	16	25
DEL PEAK 15(4Q35.2) WILD-TYPE	101	58	129	21

Figure S220. Get High-res Image Gene #43: 'del_4q35.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q35.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S221. Gene #43: 'del_4q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 15(4Q35.2) MUTATED	24	43	34	55	20	35	2
DEL PEAK 15(4Q35.2) WILD-TYPE	60	44	69	34	58	40	4

Figure S221. Get High-res Image Gene #43: 'del_4q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q35.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00063

Table S222. Gene #43: 'del_4q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 15(4Q35.2) MUTATED	79	55	59	15
DEL PEAK 15(4Q35.2) WILD-TYPE	97	48	111	50

Figure S222. Get High-res Image Gene #43: 'del_4q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00601 (Fisher's exact test), Q value = 0.015

Table S223. Gene #43: 'del_4q35.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 15(4Q35.2) MUTATED	84	68	59
DEL PEAK 15(4Q35.2) WILD-TYPE	106	74	127

Figure S223. Get High-res Image Gene #43: 'del_4q35.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S224. Gene #44: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 16(5Q12.1) MUTATED	112	86	8	9
DEL PEAK 16(5Q12.1) WILD-TYPE	91	42	137	37

Figure S224. Get High-res Image Gene #44: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S225. Gene #44: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 16(5Q12.1) MUTATED	16	56	22	62	10	46	3
DEL PEAK 16(5Q12.1) WILD-TYPE	68	31	81	27	68	29	3

Figure S225. Get High-res Image Gene #44: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q12.1' versus 'RPPA_CNMF'

P value = 0.00419 (Fisher's exact test), Q value = 0.011

Table S226. Gene #44: 'del_5q12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	29	31	29	67
DEL PEAK 16(5Q12.1) MUTATED	19	7	22	12	33
DEL PEAK 16(5Q12.1) WILD-TYPE	31	22	9	17	34

Figure S226. Get High-res Image Gene #44: 'del_5q12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S227. Gene #44: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 16(5Q12.1) MUTATED	81	70	48	14
DEL PEAK 16(5Q12.1) WILD-TYPE	95	33	122	51

Figure S227. Get High-res Image Gene #44: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_CNMF'

P value = 0.00264 (Fisher's exact test), Q value = 0.0076

Table S228. Gene #44: 'del_5q12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 16(5Q12.1) MUTATED	49	52	44	36	31
DEL PEAK 16(5Q12.1) WILD-TYPE	32	87	87	55	45

Figure S228. Get High-res Image Gene #44: 'del_5q12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S229. Gene #44: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 16(5Q12.1) MUTATED	84	75	53
DEL PEAK 16(5Q12.1) WILD-TYPE	106	67	133

Figure S229. Get High-res Image Gene #44: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S230. Gene #45: 'del_5q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 17(5Q15) MUTATED	114	89	13	10
DEL PEAK 17(5Q15) WILD-TYPE	89	39	132	36

Figure S230. Get High-res Image Gene #45: 'del_5q15' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q15' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S231. Gene #45: 'del_5q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 17(5Q15) MUTATED	17	59	24	64	12	46	4
DEL PEAK 17(5Q15) WILD-TYPE	67	28	79	25	66	29	2

Figure S231. Get High-res Image Gene #45: 'del_5q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q15' versus 'RPPA_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.042

Table S232. Gene #45: 'del_5q15' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	29	31	29	67
DEL PEAK 17(5Q15) MUTATED	19	9	22	12	30
DEL PEAK 17(5Q15) WILD-TYPE	31	20	9	17	37

Figure S232. Get High-res Image Gene #45: 'del_5q15' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_5q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S233. Gene #45: 'del_5q15' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 17(5Q15) MUTATED	82	71	54	16
DEL PEAK 17(5Q15) WILD-TYPE	94	32	116	49

Figure S233. Get High-res Image Gene #45: 'del_5q15' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q15' versus 'MIRSEQ_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.028

Table S234. Gene #45: 'del_5q15' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 17(5Q15) MUTATED	49	56	49	40	29
DEL PEAK 17(5Q15) WILD-TYPE	32	83	82	51	47

Figure S234. Get High-res Image Gene #45: 'del_5q15' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5q15' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S235. Gene #45: 'del_5q15' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 17(5Q15) MUTATED	86	80	57
DEL PEAK 17(5Q15) WILD-TYPE	104	62	129

Figure S235. Get High-res Image Gene #45: 'del_5q15' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q35.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S236. Gene #46: 'del_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 18(5Q35.3) MUTATED	94	87	7	11
DEL PEAK 18(5Q35.3) WILD-TYPE	109	41	138	35

Figure S236. Get High-res Image Gene #46: 'del_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q35.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S237. Gene #46: 'del_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 18(5Q35.3) MUTATED	17	63	15	49	11	39	5
DEL PEAK 18(5Q35.3) WILD-TYPE	67	24	88	40	67	36	1

Figure S237. Get High-res Image Gene #46: 'del_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q35.3' versus 'MRNASEQ_CNMF'

P value = 0.00702 (Fisher's exact test), Q value = 0.017

Table S238. Gene #46: 'del_5q35.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 18(5Q35.3) MUTATED	48	31	81	38
DEL PEAK 18(5Q35.3) WILD-TYPE	87	82	90	57

Figure S238. Get High-res Image Gene #46: 'del_5q35.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q35.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S239. Gene #46: 'del_5q35.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 18(5Q35.3) MUTATED	76	69	39	14
DEL PEAK 18(5Q35.3) WILD-TYPE	100	34	131	51

Figure S239. Get High-res Image Gene #46: 'del_5q35.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q35.3' versus 'MIRSEQ_CNMF'

P value = 0.0377 (Fisher's exact test), Q value = 0.076

Table S240. Gene #46: 'del_5q35.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 18(5Q35.3) MUTATED	43	51	42	31	29
DEL PEAK 18(5Q35.3) WILD-TYPE	38	88	89	60	47

Figure S240. Get High-res Image Gene #46: 'del_5q35.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5q35.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00017

Table S241. Gene #46: 'del_5q35.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 18(5Q35.3) MUTATED	79	70	47
DEL PEAK 18(5Q35.3) WILD-TYPE	111	72	139

Figure S241. Get High-res Image Gene #46: 'del_5q35.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

P value = 0.00582 (Fisher's exact test), Q value = 0.015

Table S242. Gene #47: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 19(6P25.3) MUTATED	41	32	14	9
DEL PEAK 19(6P25.3) WILD-TYPE	162	96	131	37

Figure S242. Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S243. Gene #47: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 19(6P25.3) MUTATED	11	13	9	37	11	13	2
DEL PEAK 19(6P25.3) WILD-TYPE	73	74	94	52	67	62	4

Figure S243. Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p25.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0107 (Fisher's exact test), Q value = 0.025

Table S244. Gene #47: 'del_6p25.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	76	82	48
DEL PEAK 19(6P25.3) MUTATED	15	25	4
DEL PEAK 19(6P25.3) WILD-TYPE	61	57	44

Figure S244. Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_6p25.3' versus 'MRNASEQ_CNMF'

P value = 0.0036 (Fisher's exact test), Q value = 0.01

Table S245. Gene #47: 'del_6p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 19(6P25.3) MUTATED	29	9	32	24
DEL PEAK 19(6P25.3) WILD-TYPE	106	104	139	71

Figure S245. Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6p25.3' versus 'MIRSEQ_CNMF'

P value = 0.0373 (Fisher's exact test), Q value = 0.076

Table S246. Gene #47: 'del_6p25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 19(6P25.3) MUTATED	13	18	32	13	20
DEL PEAK 19(6P25.3) WILD-TYPE	68	121	99	78	56

Figure S246. Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_7q31.1' versus 'CN_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00067

Table S247. Gene #48: 'del_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 20(7Q31.1) MUTATED	42	17	8	10
DEL PEAK 20(7Q31.1) WILD-TYPE	161	111	137	36

Figure S247. Get High-res Image Gene #48: 'del_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q31.1' versus 'MRNASEQ_CNMF'

P value = 0.00364 (Fisher's exact test), Q value = 0.01

Table S248. Gene #48: 'del_7q31.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 20(7Q31.1) MUTATED	33	17	17	10
DEL PEAK 20(7Q31.1) WILD-TYPE	102	96	154	85

Figure S248. Get High-res Image Gene #48: 'del_7q31.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_7q31.1' versus 'MIRSEQ_CNMF'

P value = 0.00217 (Fisher's exact test), Q value = 0.0065

Table S249. Gene #48: 'del_7q31.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 20(7Q31.1) MUTATED	22	26	13	10	6
DEL PEAK 20(7Q31.1) WILD-TYPE	59	113	118	81	70

Figure S249. Get High-res Image Gene #48: 'del_7q31.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_7q36.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S250. Gene #49: 'del_7q36.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 21(7Q36.1) MUTATED	71	29	18	14
DEL PEAK 21(7Q36.1) WILD-TYPE	132	99	127	32

Figure S250. Get High-res Image Gene #49: 'del_7q36.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q36.1' versus 'MRNASEQ_CNMF'

P value = 0.0429 (Fisher's exact test), Q value = 0.084

Table S251. Gene #49: 'del_7q36.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 21(7Q36.1) MUTATED	46	21	41	23
DEL PEAK 21(7Q36.1) WILD-TYPE	89	92	130	72

Figure S251. Get High-res Image Gene #49: 'del_7q36.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_7q36.1' versus 'MIRSEQ_CNMF'

P value = 0.00718 (Fisher's exact test), Q value = 0.018

Table S252. Gene #49: 'del_7q36.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 21(7Q36.1) MUTATED	30	37	26	14	23
DEL PEAK 21(7Q36.1) WILD-TYPE	51	102	105	77	53

Figure S252. Get High-res Image Gene #49: 'del_7q36.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S253. Gene #50: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 22(8P23.2) MUTATED	169	59	49	28
DEL PEAK 22(8P23.2) WILD-TYPE	34	69	96	18

Figure S253. Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S254. Gene #50: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 22(8P23.2) MUTATED	49	47	68	63	16	56	6
DEL PEAK 22(8P23.2) WILD-TYPE	35	40	35	26	62	19	0

Figure S254. Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S255. Gene #50: 'del_8p23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 22(8P23.2) MUTATED	101	67	67	65
DEL PEAK 22(8P23.2) WILD-TYPE	34	46	104	30

Figure S255. Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S256. Gene #50: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 22(8P23.2) MUTATED	115	62	112	11
DEL PEAK 22(8P23.2) WILD-TYPE	61	41	58	54

Figure S256. Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S257. Gene #50: 'del_8p23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 22(8P23.2) MUTATED	53	93	46	64	47
DEL PEAK 22(8P23.2) WILD-TYPE	28	46	85	27	29

Figure S257. Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00316 (Fisher's exact test), Q value = 0.0089

Table S258. Gene #50: 'del_8p23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 22(8P23.2) MUTATED	125	87	91
DEL PEAK 22(8P23.2) WILD-TYPE	65	55	95

Figure S258. Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0265 (Fisher's exact test), Q value = 0.056

Table S259. Gene #50: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	189	143
DEL PEAK 22(8P23.2) MUTATED	92	113	71
DEL PEAK 22(8P23.2) WILD-TYPE	49	76	72

Figure S259. Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S260. Gene #50: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
DEL PEAK 22(8P23.2) MUTATED	114	70	92
DEL PEAK 22(8P23.2) WILD-TYPE	57	34	106

Figure S260. Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S261. Gene #51: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 23(9P23) MUTATED	132	76	29	2
DEL PEAK 23(9P23) WILD-TYPE	71	52	116	44

Figure S261. Get High-res Image Gene #51: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S262. Gene #51: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 23(9P23) MUTATED	28	64	35	63	9	37	3
DEL PEAK 23(9P23) WILD-TYPE	56	23	68	26	69	38	3

Figure S262. Get High-res Image Gene #51: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0017

Table S263. Gene #51: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 23(9P23) MUTATED	82	40	75	40
DEL PEAK 23(9P23) WILD-TYPE	53	73	96	55

Figure S263. Get High-res Image Gene #51: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S264. Gene #51: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 23(9P23) MUTATED	77	68	80	12
DEL PEAK 23(9P23) WILD-TYPE	99	35	90	53

Figure S264. Get High-res Image Gene #51: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S265. Gene #51: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 23(9P23) MUTATED	57	64	42	38	35
DEL PEAK 23(9P23) WILD-TYPE	24	75	89	53	41

Figure S265. Get High-res Image Gene #51: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00035

Table S266. Gene #51: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 23(9P23) MUTATED	85	85	66
DEL PEAK 23(9P23) WILD-TYPE	105	57	120

Figure S266. Get High-res Image Gene #51: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S267. Gene #52: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 24(9P21.3) MUTATED	148	90	53	11
DEL PEAK 24(9P21.3) WILD-TYPE	55	38	92	35

Figure S267. Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S268. Gene #52: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 24(9P21.3) MUTATED	43	73	54	67	11	49	5
DEL PEAK 24(9P21.3) WILD-TYPE	41	14	49	22	67	26	1

Figure S268. Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00017

Table S269. Gene #52: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 24(9P21.3) MUTATED	100	64	80	56
DEL PEAK 24(9P21.3) WILD-TYPE	35	49	91	39

Figure S269. Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S270. Gene #52: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 24(9P21.3) MUTATED	103	75	107	15
DEL PEAK 24(9P21.3) WILD-TYPE	73	28	63	50

Figure S270. Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S271. Gene #52: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 24(9P21.3) MUTATED	67	79	53	54	47
DEL PEAK 24(9P21.3) WILD-TYPE	14	60	78	37	29

Figure S271. Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S272. Gene #52: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 24(9P21.3) MUTATED	113	108	79
DEL PEAK 24(9P21.3) WILD-TYPE	77	34	107

Figure S272. Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0364 (Fisher's exact test), Q value = 0.074

Table S273. Gene #52: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
DEL PEAK 24(9P21.3) MUTATED	99	70	103
DEL PEAK 24(9P21.3) WILD-TYPE	72	34	95

Figure S273. Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q21.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S274. Gene #53: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 25(9Q21.11) MUTATED	70	27	10	1
DEL PEAK 25(9Q21.11) WILD-TYPE	133	101	135	45

Figure S274. Get High-res Image Gene #53: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q21.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S275. Gene #53: 'del_9q21.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 25(9Q21.11) MUTATED	13	32	10	27	4	19	3
DEL PEAK 25(9Q21.11) WILD-TYPE	71	55	93	62	74	56	3

Figure S275. Get High-res Image Gene #53: 'del_9q21.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9q21.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0228 (Fisher's exact test), Q value = 0.05

Table S276. Gene #53: 'del_9q21.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 25(9Q21.11) MUTATED	33	28	40	6
DEL PEAK 25(9Q21.11) WILD-TYPE	143	75	130	59

Figure S276. Get High-res Image Gene #53: 'del_9q21.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_CNMF'

P value = 0.00234 (Fisher's exact test), Q value = 0.0068

Table S277. Gene #53: 'del_9q21.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 25(9Q21.11) MUTATED	30	29	19	17	11
DEL PEAK 25(9Q21.11) WILD-TYPE	51	110	112	74	65

Figure S277. Get High-res Image Gene #53: 'del_9q21.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9q21.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.002

Table S278. Gene #53: 'del_9q21.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 25(9Q21.11) MUTATED	33	45	28
DEL PEAK 25(9Q21.11) WILD-TYPE	157	97	158

Figure S278. Get High-res Image Gene #53: 'del_9q21.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S279. Gene #54: 'del_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 26(9Q34.3) MUTATED	49	16	13	1
DEL PEAK 26(9Q34.3) WILD-TYPE	154	112	132	45

Figure S279. Get High-res Image Gene #54: 'del_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q34.3' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.00072

Table S280. Gene #54: 'del_9q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 26(9Q34.3) MUTATED	6	25	8	15	7	17	1
DEL PEAK 26(9Q34.3) WILD-TYPE	78	62	95	74	71	58	5

Figure S280. Get High-res Image Gene #54: 'del_9q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00958 (Fisher's exact test), Q value = 0.023

Table S281. Gene #54: 'del_9q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 26(9Q34.3) MUTATED	28	32	19
DEL PEAK 26(9Q34.3) WILD-TYPE	162	110	167

Figure S281. Get High-res Image Gene #54: 'del_9q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S282. Gene #55: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 27(10P15.3) MUTATED	98	36	17	19
DEL PEAK 27(10P15.3) WILD-TYPE	105	92	128	27

Figure S282. Get High-res Image Gene #55: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S283. Gene #55: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 27(10P15.3) MUTATED	18	27	35	43	10	34	3
DEL PEAK 27(10P15.3) WILD-TYPE	66	60	68	46	68	41	3

Figure S283. Get High-res Image Gene #55: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0026

Table S284. Gene #55: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 27(10P15.3) MUTATED	61	28	44	35
DEL PEAK 27(10P15.3) WILD-TYPE	74	85	127	60

Figure S284. Get High-res Image Gene #55: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.003 (Fisher's exact test), Q value = 0.0085

Table S285. Gene #55: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 27(10P15.3) MUTATED	66	33	60	9
DEL PEAK 27(10P15.3) WILD-TYPE	110	70	110	56

Figure S285. Get High-res Image Gene #55: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00076

Table S286. Gene #55: 'del_10p15.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 27(10P15.3) MUTATED	38	34	33	41	22
DEL PEAK 27(10P15.3) WILD-TYPE	43	105	98	50	54

Figure S286. Get High-res Image Gene #55: 'del_10p15.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10p15.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0276 (Fisher's exact test), Q value = 0.059

Table S287. Gene #55: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	189	143
DEL PEAK 27(10P15.3) MUTATED	57	50	48
DEL PEAK 27(10P15.3) WILD-TYPE	84	139	95

Figure S287. Get High-res Image Gene #55: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S288. Gene #56: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 28(10P11.21) MUTATED	98	38	12	15
DEL PEAK 28(10P11.21) WILD-TYPE	105	90	133	31

Figure S288. Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S289. Gene #56: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 28(10P11.21) MUTATED	14	28	29	42	12	35	3
DEL PEAK 28(10P11.21) WILD-TYPE	70	59	74	47	66	40	3

Figure S289. Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p11.21' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00024

Table S290. Gene #56: 'del_10p11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 28(10P11.21) MUTATED	64	24	45	28
DEL PEAK 28(10P11.21) WILD-TYPE	71	89	126	67

Figure S290. Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0221 (Fisher's exact test), Q value = 0.048

Table S291. Gene #56: 'del_10p11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 28(10P11.21) MUTATED	60	35	56	10
DEL PEAK 28(10P11.21) WILD-TYPE	116	68	114	55

Figure S291. Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10p11.21' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S292. Gene #56: 'del_10p11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 28(10P11.21) MUTATED	41	33	32	38	17
DEL PEAK 28(10P11.21) WILD-TYPE	40	106	99	53	59

Figure S292. Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0111 (Fisher's exact test), Q value = 0.026

Table S293. Gene #56: 'del_10p11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 28(10P11.21) MUTATED	62	55	44
DEL PEAK 28(10P11.21) WILD-TYPE	128	87	142

Figure S293. Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0386 (Fisher's exact test), Q value = 0.077

Table S294. Gene #56: 'del_10p11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	189	143
DEL PEAK 28(10P11.21) MUTATED	49	48	54
DEL PEAK 28(10P11.21) WILD-TYPE	92	141	89

Figure S294. Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S295. Gene #57: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 29(10Q23.31) MUTATED	60	50	18	10
DEL PEAK 29(10Q23.31) WILD-TYPE	143	78	127	36

Figure S295. Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S296. Gene #57: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 29(10Q23.31) MUTATED	8	29	12	38	24	24	3
DEL PEAK 29(10Q23.31) WILD-TYPE	76	58	91	51	54	51	3

Figure S296. Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0016

Table S297. Gene #57: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 29(10Q23.31) MUTATED	35	17	63	21
DEL PEAK 29(10Q23.31) WILD-TYPE	100	96	108	74

Figure S297. Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00281 (Fisher's exact test), Q value = 0.008

Table S298. Gene #57: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 29(10Q23.31) MUTATED	45	39	31	21
DEL PEAK 29(10Q23.31) WILD-TYPE	131	64	139	44

Figure S298. Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0012

Table S299. Gene #57: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 29(10Q23.31) MUTATED	29	25	47	23	11
DEL PEAK 29(10Q23.31) WILD-TYPE	52	114	84	68	65

Figure S299. Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S300. Gene #58: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 30(11P15.5) MUTATED	69	70	17	7
DEL PEAK 30(11P15.5) WILD-TYPE	134	58	128	39

Figure S300. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S301. Gene #58: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 30(11P15.5) MUTATED	19	31	14	53	26	19	1
DEL PEAK 30(11P15.5) WILD-TYPE	65	56	89	36	52	56	5

Figure S301. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.0027

Table S302. Gene #58: 'del_11p15.5' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 30(11P15.5) MUTATED	50	21	66	24
DEL PEAK 30(11P15.5) WILD-TYPE	85	92	105	71

Figure S302. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 0.032

Table S303. Gene #58: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 30(11P15.5) MUTATED	42	43	52	24
DEL PEAK 30(11P15.5) WILD-TYPE	134	60	118	41

Figure S303. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S304. Gene #58: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 30(11P15.5) MUTATED	35	22	53	32	21
DEL PEAK 30(11P15.5) WILD-TYPE	46	117	78	59	55

Figure S304. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0038 (Fisher's exact test), Q value = 0.01

Table S305. Gene #58: 'del_11p15.5' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 30(11P15.5) MUTATED	46	59	58
DEL PEAK 30(11P15.5) WILD-TYPE	144	83	128

Figure S305. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0142 (Fisher's exact test), Q value = 0.033

Table S306. Gene #58: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
DEL PEAK 30(11P15.5) MUTATED	40	32	74
DEL PEAK 30(11P15.5) WILD-TYPE	131	72	124

Figure S306. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q23.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S307. Gene #59: 'del_11q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 31(11Q23.1) MUTATED	108	75	43	20
DEL PEAK 31(11Q23.1) WILD-TYPE	95	53	102	26

Figure S307. Get High-res Image Gene #59: 'del_11q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S308. Gene #59: 'del_11q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 31(11Q23.1) MUTATED	27	35	27	48	65	41	3
DEL PEAK 31(11Q23.1) WILD-TYPE	57	52	76	41	13	34	3

Figure S308. Get High-res Image Gene #59: 'del_11q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q23.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S309. Gene #59: 'del_11q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 31(11Q23.1) MUTATED	69	33	102	38
DEL PEAK 31(11Q23.1) WILD-TYPE	66	80	69	57

Figure S309. Get High-res Image Gene #59: 'del_11q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S310. Gene #59: 'del_11q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 31(11Q23.1) MUTATED	74	42	71	55
DEL PEAK 31(11Q23.1) WILD-TYPE	102	61	99	10

Figure S310. Get High-res Image Gene #59: 'del_11q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S311. Gene #59: 'del_11q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 31(11Q23.1) MUTATED	36	49	88	38	34
DEL PEAK 31(11Q23.1) WILD-TYPE	45	90	43	53	42

Figure S311. Get High-res Image Gene #59: 'del_11q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0132 (Fisher's exact test), Q value = 0.03

Table S312. Gene #59: 'del_11q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 31(11Q23.1) MUTATED	80	61	104
DEL PEAK 31(11Q23.1) WILD-TYPE	110	81	82

Figure S312. Get High-res Image Gene #59: 'del_11q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0446 (Fisher's exact test), Q value = 0.087

Table S313. Gene #59: 'del_11q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	189	143
DEL PEAK 31(11Q23.1) MUTATED	66	77	78
DEL PEAK 31(11Q23.1) WILD-TYPE	75	112	65

Figure S313. Get High-res Image Gene #59: 'del_11q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_12q24.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S314. Gene #60: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 32(12Q24.33) MUTATED	41	18	1	3
DEL PEAK 32(12Q24.33) WILD-TYPE	162	110	144	43

Figure S314. Get High-res Image Gene #60: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q24.33' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.00072

Table S315. Gene #60: 'del_12q24.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 32(12Q24.33) MUTATED	5	14	6	23	4	10	1
DEL PEAK 32(12Q24.33) WILD-TYPE	79	73	97	66	74	65	5

Figure S315. Get High-res Image Gene #60: 'del_12q24.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q12.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S316. Gene #61: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 33(13Q12.11) MUTATED	100	94	19	20
DEL PEAK 33(13Q12.11) WILD-TYPE	103	34	126	26

Figure S316. Get High-res Image Gene #61: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q12.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S317. Gene #61: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 33(13Q12.11) MUTATED	21	58	28	58	25	41	2
DEL PEAK 33(13Q12.11) WILD-TYPE	63	29	75	31	53	34	4

Figure S317. Get High-res Image Gene #61: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q12.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S318. Gene #61: 'del_13q12.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 33(13Q12.11) MUTATED	83	66	62	19
DEL PEAK 33(13Q12.11) WILD-TYPE	93	37	108	46

Figure S318. Get High-res Image Gene #61: 'del_13q12.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q12.11' versus 'MIRSEQ_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.044

Table S319. Gene #61: 'del_13q12.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 33(13Q12.11) MUTATED	50	59	54	35	34
DEL PEAK 33(13Q12.11) WILD-TYPE	31	80	77	56	42

Figure S319. Get High-res Image Gene #61: 'del_13q12.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_13q12.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0308 (Fisher's exact test), Q value = 0.064

Table S320. Gene #61: 'del_13q12.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 33(13Q12.11) MUTATED	86	75	71
DEL PEAK 33(13Q12.11) WILD-TYPE	104	67	115

Figure S320. Get High-res Image Gene #61: 'del_13q12.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S321. Gene #62: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 34(13Q14.2) MUTATED	71	95	32	19
DEL PEAK 34(13Q14.2) WILD-TYPE	132	33	113	27

Figure S321. Get High-res Image Gene #62: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S322. Gene #62: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 34(13Q14.2) MUTATED	17	50	23	49	44	32	2
DEL PEAK 34(13Q14.2) WILD-TYPE	67	37	80	40	34	43	4

Figure S322. Get High-res Image Gene #62: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

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

Table S323. Gene #62: 'del_13q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 34(13Q14.2) MUTATED	58	31	94	32
DEL PEAK 34(13Q14.2) WILD-TYPE	77	82	77	63

Figure S323. Get High-res Image Gene #62: 'del_13q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00028

Table S324. Gene #62: 'del_13q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 34(13Q14.2) MUTATED	70	55	52	38
DEL PEAK 34(13Q14.2) WILD-TYPE	106	48	118	27

Figure S324. Get High-res Image Gene #62: 'del_13q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 0.0011 (Fisher's exact test), Q value = 0.0035

Table S325. Gene #62: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 34(13Q14.2) MUTATED	42	46	70	32	26
DEL PEAK 34(13Q14.2) WILD-TYPE	39	93	61	59	50

Figure S325. Get High-res Image Gene #62: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0214 (Fisher's exact test), Q value = 0.047

Table S326. Gene #62: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
DEL PEAK 34(13Q14.2) MUTATED	60	41	97
DEL PEAK 34(13Q14.2) WILD-TYPE	111	63	101

Figure S326. Get High-res Image Gene #62: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q11.2' versus 'CN_CNMF'

P value = 0.00365 (Fisher's exact test), Q value = 0.01

Table S327. Gene #63: 'del_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 35(14Q11.2) MUTATED	36	25	12	2
DEL PEAK 35(14Q11.2) WILD-TYPE	167	103	133	44

Figure S327. Get High-res Image Gene #63: 'del_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q11.2' versus 'METHLYATION_CNMF'

P value = 0.00672 (Fisher's exact test), Q value = 0.017

Table S328. Gene #63: 'del_14q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 35(14Q11.2) MUTATED	5	21	16	18	9	6	0
DEL PEAK 35(14Q11.2) WILD-TYPE	79	66	87	71	69	69	6

Figure S328. Get High-res Image Gene #63: 'del_14q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00447 (Fisher's exact test), Q value = 0.012

Table S329. Gene #63: 'del_14q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 35(14Q11.2) MUTATED	21	17	20	10	4
DEL PEAK 35(14Q11.2) WILD-TYPE	60	122	111	81	72

Figure S329. Get High-res Image Gene #63: 'del_14q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_14q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0326 (Fisher's exact test), Q value = 0.067

Table S330. Gene #63: 'del_14q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 35(14Q11.2) MUTATED	20	29	23
DEL PEAK 35(14Q11.2) WILD-TYPE	170	113	163

Figure S330. Get High-res Image Gene #63: 'del_14q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_14q32.32' versus 'CN_CNMF'

P value = 0.00129 (Fisher's exact test), Q value = 0.004

Table S331. Gene #64: 'del_14q32.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 36(14Q32.32) MUTATED	15	28	25	7
DEL PEAK 36(14Q32.32) WILD-TYPE	188	100	120	39

Figure S331. Get High-res Image Gene #64: 'del_14q32.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S332. Gene #64: 'del_14q32.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 36(14Q32.32) MUTATED	3	14	5	17	32	4	0
DEL PEAK 36(14Q32.32) WILD-TYPE	81	73	98	72	46	71	6

Figure S332. Get High-res Image Gene #64: 'del_14q32.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q32.32' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S333. Gene #64: 'del_14q32.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 36(14Q32.32) MUTATED	12	7	43	11
DEL PEAK 36(14Q32.32) WILD-TYPE	123	106	128	84

Figure S333. Get High-res Image Gene #64: 'del_14q32.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q32.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S334. Gene #64: 'del_14q32.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 36(14Q32.32) MUTATED	21	15	9	28
DEL PEAK 36(14Q32.32) WILD-TYPE	155	88	161	37

Figure S334. Get High-res Image Gene #64: 'del_14q32.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S335. Gene #64: 'del_14q32.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 36(14Q32.32) MUTATED	11	7	42	5	9
DEL PEAK 36(14Q32.32) WILD-TYPE	70	132	89	86	67

Figure S335. Get High-res Image Gene #64: 'del_14q32.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_14q32.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0289 (Fisher's exact test), Q value = 0.061

Table S336. Gene #64: 'del_14q32.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 36(14Q32.32) MUTATED	21	16	37
DEL PEAK 36(14Q32.32) WILD-TYPE	169	126	149

Figure S336. Get High-res Image Gene #64: 'del_14q32.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S337. Gene #65: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 37(15Q15.1) MUTATED	66	26	11	21
DEL PEAK 37(15Q15.1) WILD-TYPE	137	102	134	25

Figure S337. Get High-res Image Gene #65: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q15.1' versus 'MRNASEQ_CNMF'

P value = 0.0248 (Fisher's exact test), Q value = 0.053

Table S338. Gene #65: 'del_15q15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 37(15Q15.1) MUTATED	39	16	42	27
DEL PEAK 37(15Q15.1) WILD-TYPE	96	97	129	68

Figure S338. Get High-res Image Gene #65: 'del_15q15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0013

Table S339. Gene #66: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 38(16Q23.1) MUTATED	27	36	20	15
DEL PEAK 38(16Q23.1) WILD-TYPE	176	92	125	31

Figure S339. Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S340. Gene #66: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 38(16Q23.1) MUTATED	5	17	10	30	27	8	1
DEL PEAK 38(16Q23.1) WILD-TYPE	79	70	93	59	51	67	5

Figure S340. Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S341. Gene #66: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 38(16Q23.1) MUTATED	17	8	60	13
DEL PEAK 38(16Q23.1) WILD-TYPE	118	105	111	82

Figure S341. Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S342. Gene #66: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 38(16Q23.1) MUTATED	24	31	17	26
DEL PEAK 38(16Q23.1) WILD-TYPE	152	72	153	39

Figure S342. Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S343. Gene #66: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 38(16Q23.1) MUTATED	14	13	46	12	12
DEL PEAK 38(16Q23.1) WILD-TYPE	67	126	85	79	64

Figure S343. Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0408 (Fisher's exact test), Q value = 0.081

Table S344. Gene #66: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 38(16Q23.1) MUTATED	25	30	42
DEL PEAK 38(16Q23.1) WILD-TYPE	165	112	144

Figure S344. Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00065 (Fisher's exact test), Q value = 0.0021

Table S345. Gene #66: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
DEL PEAK 38(16Q23.1) MUTATED	23	12	53
DEL PEAK 38(16Q23.1) WILD-TYPE	148	92	145

Figure S345. Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.3' versus 'CN_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0022

Table S346. Gene #67: 'del_16q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 39(16Q23.3) MUTATED	30	37	22	16
DEL PEAK 39(16Q23.3) WILD-TYPE	173	91	123	30

Figure S346. Get High-res Image Gene #67: 'del_16q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S347. Gene #67: 'del_16q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 39(16Q23.3) MUTATED	6	16	16	32	27	7	1
DEL PEAK 39(16Q23.3) WILD-TYPE	78	71	87	57	51	68	5

Figure S347. Get High-res Image Gene #67: 'del_16q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S348. Gene #67: 'del_16q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 39(16Q23.3) MUTATED	17	13	60	14
DEL PEAK 39(16Q23.3) WILD-TYPE	118	100	111	81

Figure S348. Get High-res Image Gene #67: 'del_16q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S349. Gene #67: 'del_16q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 39(16Q23.3) MUTATED	27	31	19	27
DEL PEAK 39(16Q23.3) WILD-TYPE	149	72	151	38

Figure S349. Get High-res Image Gene #67: 'del_16q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.3' versus 'MIRSEQ_CNMF'

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

Table S350. Gene #67: 'del_16q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 39(16Q23.3) MUTATED	15	16	47	13	13
DEL PEAK 39(16Q23.3) WILD-TYPE	66	123	84	78	63

Figure S350. Get High-res Image Gene #67: 'del_16q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 0.048

Table S351. Gene #67: 'del_16q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
DEL PEAK 39(16Q23.3) MUTATED	29	14	51
DEL PEAK 39(16Q23.3) WILD-TYPE	142	90	147

Figure S351. Get High-res Image Gene #67: 'del_16q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S352. Gene #68: 'del_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 40(17P11.2) MUTATED	49	36	5	9
DEL PEAK 40(17P11.2) WILD-TYPE	154	92	140	37

Figure S352. Get High-res Image Gene #68: 'del_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p11.2' versus 'METHLYATION_CNMF'

P value = 0.00147 (Fisher's exact test), Q value = 0.0045

Table S353. Gene #68: 'del_17p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 40(17P11.2) MUTATED	9	24	11	25	13	14	3
DEL PEAK 40(17P11.2) WILD-TYPE	75	63	92	64	65	61	3

Figure S353. Get High-res Image Gene #68: 'del_17p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q25.3' versus 'CN_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.033

Table S354. Gene #69: 'del_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 41(17Q25.3) MUTATED	31	25	10	5
DEL PEAK 41(17Q25.3) WILD-TYPE	172	103	135	41

Figure S354. Get High-res Image Gene #69: 'del_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q25.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S355. Gene #69: 'del_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 41(17Q25.3) MUTATED	3	10	7	22	19	8	2
DEL PEAK 41(17Q25.3) WILD-TYPE	81	77	96	67	59	67	4

Figure S355. Get High-res Image Gene #69: 'del_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q25.3' versus 'MRNASEQ_CNMF'

P value = 0.00266 (Fisher's exact test), Q value = 0.0076

Table S356. Gene #69: 'del_17q25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 41(17Q25.3) MUTATED	23	8	32	6
DEL PEAK 41(17Q25.3) WILD-TYPE	112	105	139	89

Figure S356. Get High-res Image Gene #69: 'del_17q25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17q25.3' versus 'MIRSEQ_CNMF'

P value = 0.00357 (Fisher's exact test), Q value = 0.0099

Table S357. Gene #69: 'del_17q25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 41(17Q25.3) MUTATED	13	11	30	10	6
DEL PEAK 41(17Q25.3) WILD-TYPE	68	128	101	81	70

Figure S357. Get High-res Image Gene #69: 'del_17q25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17q25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0496 (Fisher's exact test), Q value = 0.095

Table S358. Gene #69: 'del_17q25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 41(17Q25.3) MUTATED	17	25	28
DEL PEAK 41(17Q25.3) WILD-TYPE	173	117	158

Figure S358. Get High-res Image Gene #69: 'del_17q25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17q25.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.059

Table S359. Gene #69: 'del_17q25.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	189	143
DEL PEAK 41(17Q25.3) MUTATED	11	31	25
DEL PEAK 41(17Q25.3) WILD-TYPE	130	158	118

Figure S359. Get High-res Image Gene #69: 'del_17q25.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17q25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00597 (Fisher's exact test), Q value = 0.015

Table S360. Gene #69: 'del_17q25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
DEL PEAK 41(17Q25.3) MUTATED	14	14	39
DEL PEAK 41(17Q25.3) WILD-TYPE	157	90	159

Figure S360. Get High-res Image Gene #69: 'del_17q25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S361. Gene #70: 'del_18q23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 42(18Q23) MUTATED	155	78	28	27
DEL PEAK 42(18Q23) WILD-TYPE	48	50	117	19

Figure S361. Get High-res Image Gene #70: 'del_18q23' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S362. Gene #70: 'del_18q23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 42(18Q23) MUTATED	44	63	44	67	9	58	3
DEL PEAK 42(18Q23) WILD-TYPE	40	24	59	22	69	17	3

Figure S362. Get High-res Image Gene #70: 'del_18q23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S363. Gene #70: 'del_18q23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 42(18Q23) MUTATED	94	56	73	61
DEL PEAK 42(18Q23) WILD-TYPE	41	57	98	34

Figure S363. Get High-res Image Gene #70: 'del_18q23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S364. Gene #70: 'del_18q23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 42(18Q23) MUTATED	110	70	95	9
DEL PEAK 42(18Q23) WILD-TYPE	66	33	75	56

Figure S364. Get High-res Image Gene #70: 'del_18q23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S365. Gene #70: 'del_18q23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 42(18Q23) MUTATED	58	79	48	54	47
DEL PEAK 42(18Q23) WILD-TYPE	23	60	83	37	29

Figure S365. Get High-res Image Gene #70: 'del_18q23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S366. Gene #70: 'del_18q23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 42(18Q23) MUTATED	119	92	75
DEL PEAK 42(18Q23) WILD-TYPE	71	50	111

Figure S366. Get High-res Image Gene #70: 'del_18q23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0169 (Fisher's exact test), Q value = 0.038

Table S367. Gene #70: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
DEL PEAK 42(18Q23) MUTATED	106	62	95
DEL PEAK 42(18Q23) WILD-TYPE	65	42	103

Figure S367. Get High-res Image Gene #70: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S368. Gene #71: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 43(19P13.3) MUTATED	96	43	18	18
DEL PEAK 43(19P13.3) WILD-TYPE	107	85	127	28

Figure S368. Get High-res Image Gene #71: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

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

Table S369. Gene #71: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 43(19P13.3) MUTATED	18	31	34	40	14	38	0
DEL PEAK 43(19P13.3) WILD-TYPE	66	56	69	49	64	37	6

Figure S369. Get High-res Image Gene #71: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.0024

Table S370. Gene #71: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 43(19P13.3) MUTATED	61	29	45	38
DEL PEAK 43(19P13.3) WILD-TYPE	74	84	126	57

Figure S370. Get High-res Image Gene #71: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00069 (Fisher's exact test), Q value = 0.0023

Table S371. Gene #71: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 43(19P13.3) MUTATED	71	39	54	9
DEL PEAK 43(19P13.3) WILD-TYPE	105	64	116	56

Figure S371. Get High-res Image Gene #71: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 0.0466 (Fisher's exact test), Q value = 0.09

Table S372. Gene #71: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 43(19P13.3) MUTATED	35	50	31	30	26
DEL PEAK 43(19P13.3) WILD-TYPE	46	89	100	61	50

Figure S372. Get High-res Image Gene #71: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00072

Table S373. Gene #71: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 43(19P13.3) MUTATED	72	59	41
DEL PEAK 43(19P13.3) WILD-TYPE	118	83	145

Figure S373. Get High-res Image Gene #71: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.43' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S374. Gene #72: 'del_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 44(19Q13.43) MUTATED	54	33	2	8
DEL PEAK 44(19Q13.43) WILD-TYPE	149	95	143	38

Figure S374. Get High-res Image Gene #72: 'del_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.43' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S375. Gene #72: 'del_19q13.43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 44(19Q13.43) MUTATED	8	21	11	29	5	22	1
DEL PEAK 44(19Q13.43) WILD-TYPE	76	66	92	60	73	53	5

Figure S375. Get High-res Image Gene #72: 'del_19q13.43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19q13.43' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S376. Gene #72: 'del_19q13.43' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 44(19Q13.43) MUTATED	34	34	23	4
DEL PEAK 44(19Q13.43) WILD-TYPE	142	69	147	61

Figure S376. Get High-res Image Gene #72: 'del_19q13.43' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.43' versus 'MIRSEQ_CNMF'

P value = 0.0427 (Fisher's exact test), Q value = 0.084

Table S377. Gene #72: 'del_19q13.43' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 44(19Q13.43) MUTATED	25	25	20	15	10
DEL PEAK 44(19Q13.43) WILD-TYPE	56	114	111	76	66

Figure S377. Get High-res Image Gene #72: 'del_19q13.43' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_21q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S378. Gene #73: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 45(21Q22.3) MUTATED	113	59	11	25
DEL PEAK 45(21Q22.3) WILD-TYPE	90	69	134	21

Figure S378. Get High-res Image Gene #73: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S379. Gene #73: 'del_21q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 45(21Q22.3) MUTATED	24	39	34	50	12	47	2
DEL PEAK 45(21Q22.3) WILD-TYPE	60	48	69	39	66	28	4

Figure S379. Get High-res Image Gene #73: 'del_21q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q22.3' versus 'MRNASEQ_CNMF'

P value = 0.0459 (Fisher's exact test), Q value = 0.089

Table S380. Gene #73: 'del_21q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 45(21Q22.3) MUTATED	65	39	59	42
DEL PEAK 45(21Q22.3) WILD-TYPE	70	74	112	53

Figure S380. Get High-res Image Gene #73: 'del_21q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_21q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S381. Gene #73: 'del_21q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 45(21Q22.3) MUTATED	89	46	59	11
DEL PEAK 45(21Q22.3) WILD-TYPE	87	57	111	54

Figure S381. Get High-res Image Gene #73: 'del_21q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_21q22.3' versus 'MIRSEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.00099

Table S382. Gene #73: 'del_21q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 45(21Q22.3) MUTATED	45	58	35	32	37
DEL PEAK 45(21Q22.3) WILD-TYPE	36	81	96	59	39

Figure S382. Get High-res Image Gene #73: 'del_21q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_21q22.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S383. Gene #73: 'del_21q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 45(21Q22.3) MUTATED	88	68	51
DEL PEAK 45(21Q22.3) WILD-TYPE	102	74	135

Figure S383. Get High-res Image Gene #73: 'del_21q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xp22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S384. Gene #74: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 46(XP22.2) MUTATED	85	46	16	10
DEL PEAK 46(XP22.2) WILD-TYPE	118	82	129	36

Figure S384. Get High-res Image Gene #74: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp22.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S385. Gene #74: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 46(XP22.2) MUTATED	14	28	20	50	17	27	1
DEL PEAK 46(XP22.2) WILD-TYPE	70	59	83	39	61	48	5

Figure S385. Get High-res Image Gene #74: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp22.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00247 (Fisher's exact test), Q value = 0.0072

Table S386. Gene #74: 'del_xp22.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	76	82	48
DEL PEAK 46(XP22.2) MUTATED	19	39	11
DEL PEAK 46(XP22.2) WILD-TYPE	57	43	37

Figure S386. Get High-res Image Gene #74: 'del_xp22.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_xp22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0173 (Fisher's exact test), Q value = 0.039

Table S387. Gene #74: 'del_xp22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 46(XP22.2) MUTATED	60	40	38	18
DEL PEAK 46(XP22.2) WILD-TYPE	116	63	132	47

Figure S387. Get High-res Image Gene #74: 'del_xp22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp22.2' versus 'MIRSEQ_CNMF'

P value = 0.00852 (Fisher's exact test), Q value = 0.021

Table S388. Gene #74: 'del_xp22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 46(XP22.2) MUTATED	35	29	44	24	22
DEL PEAK 46(XP22.2) WILD-TYPE	46	110	87	67	54

Figure S388. Get High-res Image Gene #74: 'del_xp22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xp21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S389. Gene #75: 'del_xp21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 47(XP21.3) MUTATED	90	43	17	9
DEL PEAK 47(XP21.3) WILD-TYPE	113	85	128	37

Figure S389. Get High-res Image Gene #75: 'del_xp21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp21.3' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00017

Table S390. Gene #75: 'del_xp21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 47(XP21.3) MUTATED	16	30	24	44	15	29	1
DEL PEAK 47(XP21.3) WILD-TYPE	68	57	79	45	63	46	5

Figure S390. Get High-res Image Gene #75: 'del_xp21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0233 (Fisher's exact test), Q value = 0.051

Table S391. Gene #75: 'del_xp21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 47(XP21.3) MUTATED	62	39	40	16
DEL PEAK 47(XP21.3) WILD-TYPE	114	64	130	49

Figure S391. Get High-res Image Gene #75: 'del_xp21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xq21.33' versus 'CN_CNMF'

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

Table S392. Gene #76: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
DEL PEAK 48(XQ21.33) MUTATED	39	30	8	3
DEL PEAK 48(XQ21.33) WILD-TYPE	164	98	137	43

Figure S392. Get High-res Image Gene #76: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq21.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S393. Gene #76: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
DEL PEAK 48(XQ21.33) MUTATED	4	16	5	30	11	13	1
DEL PEAK 48(XQ21.33) WILD-TYPE	80	71	98	59	67	62	5

Figure S393. Get High-res Image Gene #76: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq21.33' versus 'MRNASEQ_CNMF'

P value = 0.00345 (Fisher's exact test), Q value = 0.0097

Table S394. Gene #76: 'del_xq21.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
DEL PEAK 48(XQ21.33) MUTATED	26	12	35	6
DEL PEAK 48(XQ21.33) WILD-TYPE	109	101	136	89

Figure S394. Get High-res Image Gene #76: 'del_xq21.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xq21.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00383 (Fisher's exact test), Q value = 0.01

Table S395. Gene #76: 'del_xq21.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
DEL PEAK 48(XQ21.33) MUTATED	17	26	23	13
DEL PEAK 48(XQ21.33) WILD-TYPE	159	77	147	52

Figure S395. Get High-res Image Gene #76: 'del_xq21.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xq21.33' versus 'MIRSEQ_CNMF'

P value = 0.00683 (Fisher's exact test), Q value = 0.017

Table S396. Gene #76: 'del_xq21.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
DEL PEAK 48(XQ21.33) MUTATED	21	16	26	9	7
DEL PEAK 48(XQ21.33) WILD-TYPE	60	123	105	82	69

Figure S396. Get High-res Image Gene #76: 'del_xq21.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xq21.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0123 (Fisher's exact test), Q value = 0.029

Table S397. Gene #76: 'del_xq21.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
DEL PEAK 48(XQ21.33) MUTATED	18	29	32
DEL PEAK 48(XQ21.33) WILD-TYPE	172	113	154

Figure S397. Get High-res Image Gene #76: 'del_xq21.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/HNSC-TP/22508724/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/HNSC-TP/22541004/HNSC-TP.transferedmergedcluster.txt
Number of patients = 522
Number of significantly focal cnvs = 76
Number of molecular subtypes = 10
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

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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