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

Lung Adenocarcinoma (Primary solid tumor)

16 April 2014 | analyses__2014_04_16

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1X928Z5

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 82 focal events and 12 molecular subtypes across 493 patients, 319 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p34.3 cnv correlated to 'CN_CNMF'.
amp_1p22.3 cnv correlated to 'CN_CNMF'.
amp_1q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_3q26.2 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_4q12 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
amp_5p15.33 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5p13.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
amp_5q35.1 cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_6p21.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_7p21.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7p11.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7q31.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_8p11.23 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_8p11.21 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_8q11.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_10p15.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_11q13.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12p12.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12q14.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12q15 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_13q33.3 cnv correlated to 'METHLYATION_CNMF'.
amp_14q13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_16p11.2 cnv correlated to 'CN_CNMF'.
amp_17q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_18q11.2 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19q12 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20p11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20q13.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_22q11.22 cnv correlated to 'CN_CNMF'.
amp_xq28 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_1p36.13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_1p13.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_2q22.1 cnv correlated to 'METHLYATION_CNMF'.
del_2q37.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_3p26.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_3p21.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_3q29 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
del_4p16.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_4q22.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_4q35.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q31.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q22.31 cnv correlated to 'METHLYATION_CNMF'.
del_6q26 cnv correlated to 'METHLYATION_CNMF'.
del_8p23.2 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p12 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_8p11.21 cnv correlated to 'CN_CNMF'.
del_9p21.3 cnv correlated to 'MRNASEQ_CNMF'.
del_9q21.11 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10p15.3 cnv correlated to 'CN_CNMF'.
del_10q26.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p15.5 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_11q23.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_11q25 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_12q12 cnv correlated to 'CN_CNMF'.
del_12q24.33 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_13q12.11 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_13q12.13 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_13q14.2 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_13q34 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_15q11.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_16q23.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_17p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_17p11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_18q21.32 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_18q23 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19q13.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_20p13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_21q11.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_22q13.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp22.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 82 focal events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 319 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
amp 8q11 1	224 (45%)	269	0.00472 (1.00)	0.0135 (1.00)	6.69e-22 (6.56e-19)	1.49e-06 (0.00122)	0.0271 (1.00)	0.0328 (1.00)	3.32e-08 (2.95e-05)	8.87e-06 (0.00683)	1.31e-06 (0.00107)	1.44e-05 (0.0109)	1.14e-05 (0.00873)	6.17e-06 (0.00483)
amp 14q13 3	222 (45%)	271	0.798 (1.00)	0.368 (1.00)	3.67e-14 (3.52e-11)	0.000127 (0.0877)	0.0321 (1.00)	0.0741 (1.00)	2.71e-16 (2.62e-13)	1e-06 (0.000835)	2.44e-08 (2.17e-05)	5.07e-09 (4.6e-06)	7.54e-05 (0.0533)	9.69e-06 (0.00744)
amp 20q13 33	237 (48%)	256	0.00559 (1.00)	0.0306 (1.00)	2.38e-08 (2.12e-05)	0.000282 (0.19)	0.00987 (1.00)	0.00327 (1.00)	2.01e-07 (0.000174)	0.000317 (0.213)	1.4e-05 (0.0106)	1.8e-08 (1.61e-05)	4.39e-05 (0.0318)	6.69e-05 (0.0474)
del 5q11 2	172 (35%)	321	0.26 (1.00)	0.233 (1.00)	4.98e-15 (4.8e-12)	0.000211 (0.144)	0.00504 (1.00)	0.00262 (1.00)	1.98e-06 (0.00161)	3.18e-12 (3.02e-09)	7.37e-10 (6.81e-07)	1.09e-06 (0.000903)	2.66e-07 (0.000228)	1.21e-09 (1.11e-06)
del 5q31 1	199 (40%)	294	0.0936 (1.00)	0.186 (1.00)	1.7e-14 (1.64e-11)	1.91e-05 (0.0143)	0.00896 (1.00)	0.000782 (0.498)	3.42e-07 (0.000292)	1.31e-12 (1.25e-09)	5.31e-10 (4.91e-07)	6.1e-08 (5.36e-05)	4.66e-06 (0.00372)	6.4e-08 (5.62e-05)
del 19p13 3	265 (54%)	228	0.572 (1.00)	0.595 (1.00)	7.85e-07 (0.000654)	2.9e-11 (2.73e-08)	0.196 (1.00)	0.276 (1.00)	7.58e-07 (0.000632)	1.89e-09 (1.72e-06)	1.35e-05 (0.0103)	5.77e-09 (5.23e-06)	0.000118 (0.0815)	8.02e-08 (7.03e-05)
del 19p13 2	260 (53%)	233	0.694 (1.00)	1 (1.00)	3.24e-07 (0.000277)	3.17e-12 (3.01e-09)	0.238 (1.00)	0.152 (1.00)	1.07e-06 (0.000888)	1.97e-08 (1.77e-05)	1.03e-05 (0.00787)	5.61e-08 (4.96e-05)	6.61e-05 (0.0469)	4.11e-07 (0.000349)
del 22q13 32	240 (49%)	253	0.0252 (1.00)	0.0285 (1.00)	1.3e-12 (1.24e-09)	4.7e-05 (0.034)	0.138 (1.00)	0.00464 (1.00)	2.61e-11 (2.47e-08)	4.26e-12 (4.03e-09)	2.54e-06 (0.00205)	1.04e-07 (9.02e-05)	1.15e-05 (0.00878)	1.55e-06 (0.00126)
amp 3q26 2	163 (33%)	330	0.000264 (0.178)	0.00332 (1.00)	6.69e-06 (0.00522)	0.0224 (1.00)	0.00938 (1.00)	0.00897 (1.00)	1.33e-10 (1.25e-07)	2.11e-10 (1.97e-07)	2.59e-06 (0.00209)	4.64e-07 (0.000393)	0.000396 (0.261)	3.02e-05 (0.0222)
amp 7p11 2	260 (53%)	233	0.959 (1.00)	0.684 (1.00)	2.87e-21 (2.8e-18)	0.00519 (1.00)	0.00108 (0.672)	0.00239 (1.00)	3.46e-11 (3.26e-08)	1.24e-11 (1.17e-08)	1.25e-07 (0.000109)	6.09e-05 (0.0434)	1.3e-05 (0.00986)	1.12e-06 (0.000925)
amp 8q24 21	310 (63%)	183	0.0343 (1.00)	0.0322 (1.00)	5.06e-18 (4.92e-15)	3.36e-08 (2.98e-05)	0.368 (1.00)	0.0663 (1.00)	3.81e-10 (3.53e-07)	5.74e-08 (5.06e-05)	5.64e-06 (0.00443)	0.000224 (0.152)	0.00113 (0.698)	0.000159 (0.109)
amp 11q13 3	165 (33%)	328	0.00676 (1.00)	0.00237 (1.00)	4.92e-16 (4.76e-13)	0.000393 (0.26)	0.0638 (1.00)	0.0911 (1.00)	3.62e-08 (3.21e-05)	4.04e-09 (3.68e-06)	7.3e-09 (6.6e-06)	7.46e-06 (0.00579)	4.48e-06 (0.00358)	5.23e-05 (0.0375)
amp 12p12 1	174 (35%)	319	0.198 (1.00)	0.033 (1.00)	2.73e-06 (0.00219)	0.0449 (1.00)	0.0412 (1.00)	0.158 (1.00)	7.47e-11 (7.01e-08)	1.7e-10 (1.59e-07)	7.09e-06 (0.00552)	1.51e-05 (0.0113)	2.07e-06 (0.00168)	5.17e-06 (0.0041)
amp 12q14 1	161 (33%)	332	0.406 (1.00)	0.302 (1.00)	5.86e-08 (5.16e-05)	0.00136 (0.824)	0.027 (1.00)	0.0402 (1.00)	5.27e-11 (4.96e-08)	3.26e-13 (3.12e-10)	1.97e-08 (1.76e-05)	4.41e-09 (4e-06)	4.18e-08 (3.7e-05)	2.72e-10 (2.54e-07)
amp 12q15	162 (33%)	331	0.221 (1.00)	0.103 (1.00)	5.89e-07 (0.000496)	0.00226 (1.00)	0.0412 (1.00)	0.0604 (1.00)	2.69e-11 (2.54e-08)	8.47e-12 (8.01e-09)	1.45e-08 (1.31e-05)	1.99e-08 (1.78e-05)	1.98e-08 (1.77e-05)	2.71e-08 (2.41e-05)
amp 17q12	219 (44%)	274	0.0901 (1.00)	0.0162 (1.00)	1.25e-12 (1.2e-09)	1.07e-05 (0.00817)	0.431 (1.00)	0.00859 (1.00)	6.09e-08 (5.36e-05)	1.4e-07 (0.000121)	4.29e-08 (3.8e-05)	5.62e-07 (0.000474)	0.00183 (1.00)	5.29e-06 (0.00418)
amp 19q12	133 (27%)	360	0.0514 (1.00)	0.0219 (1.00)	0.000866 (0.546)	6.69e-06 (0.00522)	0.26 (1.00)	0.485 (1.00)	0.000202 (0.138)	1.2e-06 (0.000985)	2.18e-05 (0.0162)	2.48e-07 (0.000214)	2.43e-05 (0.018)	2.51e-07 (0.000216)
amp 20p11 21	188 (38%)	305	0.0611 (1.00)	0.095 (1.00)	7.68e-06 (0.00596)	0.000228 (0.154)	0.369 (1.00)	0.227 (1.00)	4.9e-05 (0.0354)	4.8e-06 (0.00382)	0.000101 (0.0704)	2.61e-05 (0.0193)	0.000421 (0.276)	4.93e-05 (0.0356)
del 4q22 1	154 (31%)	339	0.000214 (0.146)	9.89e-05 (0.0692)	6.88e-07 (0.000575)	0.00139 (0.84)	0.315 (1.00)	0.125 (1.00)	2.27e-07 (0.000196)	5.83e-14 (5.6e-11)	5.26e-07 (0.000444)	3.11e-07 (0.000266)	0.000985 (0.616)	0.000424 (0.278)
del 4q35 1	182 (37%)	311	0.00204 (1.00)	0.00118 (0.722)	1.25e-09 (1.15e-06)	0.000648 (0.417)	0.0371 (1.00)	0.00109 (0.679)	2.37e-10 (2.21e-07)	2.81e-18 (2.73e-15)	4.34e-09 (3.94e-06)	3.98e-10 (3.69e-07)	7.38e-06 (0.00575)	1.49e-07 (0.000129)
amp 17q23 1	241 (49%)	252	0.0796 (1.00)	0.148 (1.00)	4.31e-13 (4.13e-10)	8.9e-08 (7.79e-05)	0.0919 (1.00)	0.00862 (1.00)	9.78e-08 (8.54e-05)	5.62e-10 (5.19e-07)	2.12e-07 (0.000183)	1.34e-05 (0.0102)	0.0125 (1.00)	0.000394 (0.26)
amp 18q11 2	99 (20%)	394	0.195 (1.00)	0.0151 (1.00)	0.000456 (0.297)	4.96e-06 (0.00395)	0.118 (1.00)	0.0149 (1.00)	4.95e-05 (0.0357)	2.95e-06 (0.00237)	0.000213 (0.145)	8.66e-07 (0.000721)	0.00524 (1.00)	4.93e-05 (0.0356)
del 8p23 2	241 (49%)	252	0.00526 (1.00)	0.0033 (1.00)	1.81e-22 (1.78e-19)	0.0985 (1.00)	0.00772 (1.00)	1.98e-05 (0.0148)	2.68e-07 (0.00023)	1.05e-06 (0.000873)	2.61e-05 (0.0193)	0.0183 (1.00)	0.000975 (0.612)	0.000105 (0.0728)
amp 7p21 1	270 (55%)	223	0.849 (1.00)	1 (1.00)	1.64e-23 (1.61e-20)	0.00162 (0.976)	0.00511 (1.00)	0.00769 (1.00)	1.12e-09 (1.03e-06)	4.49e-10 (4.15e-07)	3.6e-05 (0.0263)	0.00294 (1.00)	0.000862 (0.545)	0.000104 (0.0722)
amp 8p11 21	170 (34%)	323	0.253 (1.00)	0.124 (1.00)	1.13e-22 (1.11e-19)	0.00223 (1.00)	0.0147 (1.00)	0.0907 (1.00)	1.55e-09 (1.42e-06)	1.4e-06 (0.00115)	0.000769 (0.491)	9.25e-06 (0.00711)	0.000352 (0.236)	0.000449 (0.293)
amp 10p15 1	136 (28%)	357	0.023 (1.00)	0.0262 (1.00)	4.17e-06 (0.00333)	6.42e-05 (0.0457)	0.00256 (1.00)	0.00238 (1.00)	1.8e-05 (0.0135)	2.4e-08 (2.14e-05)	0.000473 (0.308)	1.41e-05 (0.0107)	0.00936 (1.00)	0.00183 (1.00)
del 4p16 3	126 (26%)	367	0.595 (1.00)	0.453 (1.00)	2.11e-06 (0.00171)	0.373 (1.00)	0.37 (1.00)	0.183 (1.00)	8.44e-06 (0.00652)	4.89e-07 (0.000414)	7.87e-06 (0.00609)	2.92e-06 (0.00235)	0.00514 (1.00)	0.000979 (0.614)
del 9q21 11	246 (50%)	247	0.0335 (1.00)	0.597 (1.00)	4.93e-07 (0.000416)	0.000982 (0.615)	0.274 (1.00)	0.0215 (1.00)	0.00293 (1.00)	1.03e-07 (8.97e-05)	0.00011 (0.0765)	6.52e-05 (0.0464)	0.0163 (1.00)	4.07e-05 (0.0296)
del 11p15 5	135 (27%)	358	0.268 (1.00)	0.0576 (1.00)	6.4e-07 (0.000536)	0.023 (1.00)	0.011 (1.00)	0.0358 (1.00)	0.000997 (0.622)	3.7e-08 (3.28e-05)	0.0001 (0.0701)	1.91e-05 (0.0143)	5.45e-06 (0.00429)	0.00107 (0.666)
del 19q13 33	187 (38%)	306	0.272 (1.00)	0.373 (1.00)	1.2e-08 (1.08e-05)	1.14e-06 (0.00094)	0.102 (1.00)	0.099 (1.00)	0.00184 (1.00)	0.000278 (0.188)	0.000211 (0.144)	4.73e-06 (0.00377)	0.0859 (1.00)	0.0008 (0.509)
del 21q11 2	167 (34%)	326	0.0604 (1.00)	0.0501 (1.00)	7.56e-07 (0.000631)	0.0138 (1.00)	0.0566 (1.00)	0.00219 (1.00)	1.39e-10 (1.3e-07)	1.03e-09 (9.52e-07)	1.45e-05 (0.011)	1.12e-07 (9.72e-05)	0.00118 (0.724)	0.000438 (0.286)
del 1p36 13	116 (24%)	377	0.795 (1.00)	0.441 (1.00)	0.000127 (0.0877)	9.93e-06 (0.00762)	0.754 (1.00)	0.691 (1.00)	9.05e-05 (0.0635)	1.14e-06 (0.000934)	0.0348 (1.00)	0.00474 (1.00)	0.0389 (1.00)	0.065 (1.00)
del 3p26 3	223 (45%)	270	0.0936 (1.00)	0.186 (1.00)	5.77e-06 (0.00453)	2.7e-05 (0.0198)	0.0721 (1.00)	0.00117 (0.714)	0.0632 (1.00)	3.1e-10 (2.88e-07)	3.81e-05 (0.0277)	0.0206 (1.00)	0.00417 (1.00)	0.00362 (1.00)
del 3p21 31	237 (48%)	256	0.132 (1.00)	0.454 (1.00)	1.6e-06 (0.0013)	1.67e-06 (0.00136)	0.0125 (1.00)	0.00122 (0.744)	0.0169 (1.00)	1.94e-12 (1.84e-09)	2.11e-05 (0.0157)	0.00398 (1.00)	0.00214 (1.00)	0.00191 (1.00)
del 8p12	215 (44%)	278	0.106 (1.00)	0.113 (1.00)	6.05e-20 (5.9e-17)	0.0406 (1.00)	0.0305 (1.00)	0.00129 (0.786)	2e-07 (0.000173)	1.05e-06 (0.000874)	0.000215 (0.146)	0.035 (1.00)	0.0011 (0.683)	0.000807 (0.513)
del 10q26 3	142 (29%)	351	0.62 (1.00)	0.235 (1.00)	1.82e-07 (0.000157)	0.0364 (1.00)	0.00517 (1.00)	0.00077 (0.491)	2.79e-05 (0.0205)	0.0172 (1.00)	0.00462 (1.00)	0.0019 (1.00)	1.65e-05 (0.0124)	0.000104 (0.0722)
del 13q12 11	282 (57%)	211	0.00113 (0.699)	0.0135 (1.00)	1.4e-20 (1.37e-17)	0.0206 (1.00)	0.000707 (0.454)	1.12e-06 (0.000925)	2.05e-09 (1.87e-06)	9.14e-08 (7.99e-05)	0.00225 (1.00)	0.00141 (0.85)	0.00331 (1.00)	0.0136 (1.00)
del 13q12 13	282 (57%)	211	0.00862 (1.00)	0.0225 (1.00)	3.01e-22 (2.96e-19)	0.0104 (1.00)	0.000707 (0.454)	3.86e-07 (0.000329)	6.3e-09 (5.7e-06)	6.23e-07 (0.000524)	0.00447 (1.00)	0.0012 (0.735)	0.00496 (1.00)	0.0181 (1.00)
del 13q14 2	271 (55%)	222	0.00862 (1.00)	0.0225 (1.00)	2.32e-21 (2.27e-18)	0.0885 (1.00)	0.000386 (0.256)	4.4e-07 (0.000373)	9.54e-10 (8.79e-07)	6.54e-08 (5.73e-05)	0.00209 (1.00)	0.000752 (0.482)	0.000848 (0.537)	0.0055 (1.00)
del 13q34	232 (47%)	261	0.0356 (1.00)	0.0451 (1.00)	3.58e-14 (3.44e-11)	0.0682 (1.00)	0.000584 (0.378)	1.71e-05 (0.0128)	5e-06 (0.00397)	3.82e-06 (0.00306)	0.0231 (1.00)	0.024 (1.00)	0.0457 (1.00)	0.389 (1.00)
del 15q11 2	253 (51%)	240	0.168 (1.00)	0.148 (1.00)	1.31e-10 (1.23e-07)	0.00597 (1.00)	0.0423 (1.00)	0.0351 (1.00)	5.61e-13 (5.36e-10)	2.24e-06 (0.00181)	3.38e-05 (0.0248)	0.00921 (1.00)	0.112 (1.00)	0.0272 (1.00)
del 17p13 3	265 (54%)	228	0.386 (1.00)	0.609 (1.00)	6.87e-18 (6.66e-15)	5.27e-05 (0.0378)	0.0624 (1.00)	0.00181 (1.00)	1.76e-06 (0.00143)	7.48e-06 (0.0058)	0.00697 (1.00)	0.069 (1.00)	0.0778 (1.00)	0.00527 (1.00)
del 17p11 2	216 (44%)	277	0.264 (1.00)	0.185 (1.00)	1.57e-16 (1.52e-13)	3.36e-07 (0.000287)	0.0108 (1.00)	0.00262 (1.00)	6.4e-06 (0.005)	5.17e-06 (0.0041)	0.022 (1.00)	0.0424 (1.00)	0.147 (1.00)	0.0155 (1.00)
del 20p13	126 (26%)	367	0.105 (1.00)	0.268 (1.00)	5.42e-06 (0.00427)	0.000145 (0.1)	0.00291 (1.00)	0.000968 (0.609)	2.45e-05 (0.0181)	8.62e-05 (0.0606)	0.97 (1.00)	0.976 (1.00)	0.266 (1.00)	1 (1.00)
amp 1q21 3	359 (73%)	134	0.362 (1.00)	0.465 (1.00)	3.93e-07 (0.000334)	7.4e-10 (6.82e-07)	0.345 (1.00)	0.447 (1.00)	0.00584 (1.00)	0.597 (1.00)	0.0078 (1.00)	3.63e-05 (0.0265)	0.0173 (1.00)	0.0127 (1.00)
amp 5p15 33	319 (65%)	174	0.878 (1.00)	0.901 (1.00)	1.25e-18 (1.22e-15)	0.423 (1.00)	0.0984 (1.00)	0.0274 (1.00)	5.91e-07 (0.000497)	0.00416 (1.00)	0.00332 (1.00)	0.00167 (1.00)	0.0192 (1.00)	0.00035 (0.235)
amp 5q35 1	123 (25%)	370	0.0862 (1.00)	0.453 (1.00)	0.0341 (1.00)	0.433 (1.00)	0.0173 (1.00)	0.0271 (1.00)	0.000359 (0.24)	3.73e-05 (0.0272)	0.00114 (0.699)	0.000365 (0.243)	0.00254 (1.00)	0.0011 (0.682)
amp 7q31 2	206 (42%)	287	0.482 (1.00)	0.388 (1.00)	3.36e-12 (3.18e-09)	0.023 (1.00)	0.358 (1.00)	0.123 (1.00)	2.68e-09 (2.44e-06)	7.41e-09 (6.69e-06)	0.000834 (0.529)	0.00381 (1.00)	0.00778 (1.00)	0.00416 (1.00)
amp 8p11 23	134 (27%)	359	0.294 (1.00)	0.107 (1.00)	3.34e-19 (3.26e-16)	0.000652 (0.419)	0.0622 (1.00)	0.0831 (1.00)	6.26e-07 (0.000525)	8.61e-06 (0.00664)	0.0364 (1.00)	0.0011 (0.683)	0.112 (1.00)	0.0368 (1.00)
amp xq28	149 (30%)	344	0.301 (1.00)	0.119 (1.00)	1.49e-12 (1.42e-09)	0.0105 (1.00)	0.193 (1.00)	0.0683 (1.00)	1.79e-05 (0.0134)	2.97e-06 (0.00238)	0.0139 (1.00)	0.259 (1.00)	0.00635 (1.00)	0.341 (1.00)
del 2q37 3	63 (13%)	430	0.703 (1.00)	0.206 (1.00)	1.3e-05 (0.00986)	5.82e-05 (0.0416)	0.0826 (1.00)	0.0433 (1.00)	0.0421 (1.00)	0.0287 (1.00)	0.00331 (1.00)	4.18e-05 (0.0304)	0.0105 (1.00)	0.00039 (0.258)
del 16q23 1	167 (34%)	326	0.0587 (1.00)	0.312 (1.00)	6.17e-06 (0.00483)	0.0029 (1.00)	0.0163 (1.00)	0.0476 (1.00)	3.87e-07 (0.00033)	6.01e-09 (5.44e-06)	0.0389 (1.00)	0.0494 (1.00)	0.0286 (1.00)	0.00171 (1.00)
del 18q21 32	241 (49%)	252	0.115 (1.00)	0.187 (1.00)	5.38e-13 (5.15e-10)	0.834 (1.00)	0.015 (1.00)	0.000642 (0.414)	2.19e-05 (0.0162)	0.000195 (0.134)	0.00693 (1.00)	0.369 (1.00)	0.263 (1.00)	0.097 (1.00)
del 18q23	238 (48%)	255	0.029 (1.00)	0.0914 (1.00)	4.65e-15 (4.49e-12)	0.52 (1.00)	0.00409 (1.00)	0.000391 (0.259)	2.18e-06 (0.00176)	3.55e-05 (0.026)	0.00293 (1.00)	0.328 (1.00)	0.104 (1.00)	0.072 (1.00)
del xp22 2	135 (27%)	358	0.691 (1.00)	0.896 (1.00)	1.29e-08 (1.16e-05)	0.064 (1.00)	0.0147 (1.00)	0.0335 (1.00)	0.000196 (0.135)	2.27e-05 (0.0168)	0.295 (1.00)	0.582 (1.00)	0.707 (1.00)	0.274 (1.00)
amp 4q12	93 (19%)	400	0.703 (1.00)	0.206 (1.00)	1.34e-09 (1.23e-06)	0.0107 (1.00)	0.123 (1.00)	0.0365 (1.00)	0.00435 (1.00)	9.15e-05 (0.064)	0.00552 (1.00)	0.028 (1.00)	0.0876 (1.00)	0.00269 (1.00)
amp 5p13 1	291 (59%)	202	0.263 (1.00)	0.897 (1.00)	4.12e-15 (3.98e-12)	0.116 (1.00)	0.544 (1.00)	0.205 (1.00)	5.04e-06 (0.004)	0.00219 (1.00)	0.000416 (0.273)	0.00171 (1.00)	0.00658 (1.00)	0.000453 (0.295)
amp 6p21 1	186 (38%)	307	0.675 (1.00)	0.206 (1.00)	1.08e-06 (0.000893)	2.24e-10 (2.09e-07)	0.08 (1.00)	0.865 (1.00)	0.00319 (1.00)	0.21 (1.00)	0.0168 (1.00)	0.0182 (1.00)	0.0725 (1.00)	0.0156 (1.00)
del 1p13 1	144 (29%)	349	0.618 (1.00)	0.631 (1.00)	2.64e-07 (0.000227)	0.00114 (0.699)	0.712 (1.00)	0.0757 (1.00)	7.66e-05 (0.054)	0.00767 (1.00)	0.262 (1.00)	0.000601 (0.389)	0.241 (1.00)	0.0215 (1.00)
del 3q29	133 (27%)	360	0.71 (1.00)	0.602 (1.00)	0.0554 (1.00)	9e-05 (0.0632)	0.217 (1.00)	0.00817 (1.00)	7.88e-05 (0.0555)	0.109 (1.00)	0.876 (1.00)	0.813 (1.00)	0.596 (1.00)	0.892 (1.00)
del 11q23 2	116 (24%)	377	0.433 (1.00)	0.453 (1.00)	1.05e-05 (0.00803)	0.00205 (1.00)	0.115 (1.00)	0.336 (1.00)	7.22e-05 (0.0511)	0.00256 (1.00)	0.00197 (1.00)	0.00825 (1.00)	0.0275 (1.00)	0.0797 (1.00)
del 11q25	112 (23%)	381	0.108 (1.00)	0.0799 (1.00)	0.000258 (0.175)	0.000569 (0.369)	0.0128 (1.00)	0.292 (1.00)	0.000365 (0.243)	0.019 (1.00)	0.154 (1.00)	0.0844 (1.00)	0.262 (1.00)	0.126 (1.00)
del 12q24 33	123 (25%)	370	0.063 (1.00)	0.0396 (1.00)	2.15e-05 (0.016)	0.215 (1.00)	0.0251 (1.00)	0.0233 (1.00)	4.97e-05 (0.0357)	0.00038 (0.252)	0.298 (1.00)	0.0125 (1.00)	0.186 (1.00)	0.119 (1.00)
amp 1p34 3	132 (27%)	361	0.553 (1.00)	0.384 (1.00)	2.23e-09 (2.04e-06)	0.967 (1.00)	0.254 (1.00)	0.044 (1.00)	0.0582 (1.00)	0.167 (1.00)	0.181 (1.00)	0.157 (1.00)	0.281 (1.00)	0.439 (1.00)
amp 1p22 3	133 (27%)	360	0.876 (1.00)	1 (1.00)	2.78e-10 (2.59e-07)	0.365 (1.00)	0.547 (1.00)	0.0861 (1.00)	0.0394 (1.00)	0.00423 (1.00)	0.082 (1.00)	0.0562 (1.00)	0.463 (1.00)	0.0395 (1.00)
amp 13q33 3	77 (16%)	416	0.463 (1.00)	0.453 (1.00)	0.0783 (1.00)	0.000334 (0.224)	0.754 (1.00)	0.953 (1.00)	0.499 (1.00)	0.12 (1.00)	0.141 (1.00)	0.092 (1.00)	0.27 (1.00)	0.0166 (1.00)
amp 16p11 2	159 (32%)	334	0.799 (1.00)	0.204 (1.00)	1.16e-06 (0.000949)	0.376 (1.00)	0.225 (1.00)	0.0356 (1.00)	0.326 (1.00)	0.0879 (1.00)	0.0202 (1.00)	0.00728 (1.00)	0.484 (1.00)	0.277 (1.00)
amp 22q11 22	87 (18%)	406	0.268 (1.00)	0.162 (1.00)	5.61e-06 (0.00441)	0.501 (1.00)	0.0405 (1.00)	0.0241 (1.00)	0.588 (1.00)	0.0527 (1.00)	0.0803 (1.00)	0.314 (1.00)	0.0472 (1.00)	0.0942 (1.00)
del 2q22 1	44 (9%)	449	0.869 (1.00)	0.78 (1.00)	0.00277 (1.00)	4.96e-05 (0.0357)	0.0303 (1.00)	0.332 (1.00)	0.0257 (1.00)	0.00382 (1.00)	0.0259 (1.00)	0.000614 (0.397)	0.199 (1.00)	0.00203 (1.00)
del 6q22 31	246 (50%)	247	0.54 (1.00)	0.179 (1.00)	0.0212 (1.00)	6.85e-07 (0.000573)	0.499 (1.00)	0.0743 (1.00)	0.0276 (1.00)	0.511 (1.00)	0.778 (1.00)	0.161 (1.00)	0.538 (1.00)	0.29 (1.00)
del 6q26	249 (51%)	244	0.368 (1.00)	0.263 (1.00)	0.00421 (1.00)	7.37e-05 (0.0521)	0.424 (1.00)	0.3 (1.00)	0.102 (1.00)	0.167 (1.00)	0.828 (1.00)	0.263 (1.00)	0.294 (1.00)	0.595 (1.00)
del 8p11 21	113 (23%)	380	0.795 (1.00)	0.504 (1.00)	2.18e-18 (2.12e-15)	0.216 (1.00)	0.391 (1.00)	0.23 (1.00)	0.0238 (1.00)	0.0672 (1.00)	0.301 (1.00)	0.614 (1.00)	0.256 (1.00)	0.475 (1.00)
del 9p21 3	278 (56%)	215	0.521 (1.00)	0.901 (1.00)	0.00358 (1.00)	0.306 (1.00)	0.217 (1.00)	0.167 (1.00)	8.44e-06 (0.00652)	0.00212 (1.00)	0.199 (1.00)	0.146 (1.00)	0.562 (1.00)	0.341 (1.00)
del 10p15 3	122 (25%)	371	1 (1.00)	0.854 (1.00)	5.61e-05 (0.0401)	0.114 (1.00)	0.513 (1.00)	0.251 (1.00)	0.00646 (1.00)	0.544 (1.00)	0.00229 (1.00)	0.00247 (1.00)	0.000403 (0.265)	0.0025 (1.00)
del 12q12	94 (19%)	399	0.597 (1.00)	0.644 (1.00)	0.000192 (0.132)	0.0464 (1.00)	0.0258 (1.00)	0.04 (1.00)	0.00906 (1.00)	0.0434 (1.00)	0.0694 (1.00)	0.0177 (1.00)	0.617 (1.00)	0.338 (1.00)
del 3q11 1	136 (28%)	357	0.609 (1.00)	0.602 (1.00)	0.18 (1.00)	0.00144 (0.87)	0.781 (1.00)	0.526 (1.00)	0.0996 (1.00)	0.0631 (1.00)	0.792 (1.00)	0.951 (1.00)	0.86 (1.00)	0.784 (1.00)
del 6q12	174 (35%)	319	0.488 (1.00)	0.52 (1.00)	0.096 (1.00)	0.0926 (1.00)	0.346 (1.00)	0.713 (1.00)	0.902 (1.00)	0.929 (1.00)	0.0283 (1.00)	0.0892 (1.00)	0.697 (1.00)	0.368 (1.00)
del 8q11 21	63 (13%)	430	1 (1.00)	1 (1.00)	0.0119 (1.00)	0.5 (1.00)	0.382 (1.00)	0.95 (1.00)	0.317 (1.00)	0.588 (1.00)	0.31 (1.00)	0.758 (1.00)	0.961 (1.00)	0.84 (1.00)
del 9p23	271 (55%)	222	0.521 (1.00)	0.901 (1.00)	0.0117 (1.00)	0.71 (1.00)	0.533 (1.00)	0.371 (1.00)	0.00444 (1.00)	0.000943 (0.594)	0.323 (1.00)	0.0982 (1.00)	0.491 (1.00)	0.273 (1.00)
del 12p13 2	134 (27%)	359	0.255 (1.00)	0.719 (1.00)	0.00139 (0.841)	0.00388 (1.00)	0.0215 (1.00)	0.0776 (1.00)	0.00859 (1.00)	0.066 (1.00)	0.796 (1.00)	0.987 (1.00)	0.445 (1.00)	0.611 (1.00)
del 14q32 33	144 (29%)	349	0.703 (1.00)	0.302 (1.00)	0.0566 (1.00)	0.203 (1.00)	0.0923 (1.00)	0.06 (1.00)	0.193 (1.00)	0.00598 (1.00)	0.132 (1.00)	0.0131 (1.00)	0.123 (1.00)	0.04 (1.00)
del 20q13 12	81 (16%)	412	0.17 (1.00)	0.874 (1.00)	0.595 (1.00)	0.168 (1.00)	0.126 (1.00)	0.583 (1.00)	0.17 (1.00)	0.696 (1.00)	0.181 (1.00)	0.174 (1.00)	0.0334 (1.00)	0.451 (1.00)

'amp_1p34.3' versus 'CN_CNMF'

P value = 2.23e-09 (Fisher's exact test), Q value = 2e-06

Table S1. Gene #1: 'amp_1p34.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 1(1P34.3) MUTATED	80	34	18
AMP PEAK 1(1P34.3) WILD-TYPE	106	182	73

Figure S1. Get High-res Image Gene #1: 'amp_1p34.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1p22.3' versus 'CN_CNMF'

P value = 2.78e-10 (Fisher's exact test), Q value = 2.6e-07

Table S2. Gene #2: 'amp_1p22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 2(1P22.3) MUTATED	81	31	21
AMP PEAK 2(1P22.3) WILD-TYPE	105	185	70

Figure S2. Get High-res Image Gene #2: 'amp_1p22.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q21.3' versus 'CN_CNMF'

P value = 3.93e-07 (Fisher's exact test), Q value = 0.00033

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 3(1Q21.3) MUTATED	150	131	78
AMP PEAK 3(1Q21.3) WILD-TYPE	36	85	13

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

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 7.4e-10 (Fisher's exact test), Q value = 6.8e-07

Table S4. Gene #3: 'amp_1q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
AMP PEAK 3(1Q21.3) MUTATED	124	110	83
AMP PEAK 3(1Q21.3) WILD-TYPE	17	30	67

Figure S4. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.63e-05 (Fisher's exact test), Q value = 0.027

Table S5. Gene #3: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 3(1Q21.3) MUTATED	31	203	121
AMP PEAK 3(1Q21.3) WILD-TYPE	20	46	67

Figure S5. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MRNA_CNMF'

P value = 0.000264 (Fisher's exact test), Q value = 0.18

Table S6. Gene #4: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	5	9	12	6
AMP PEAK 4(3Q26.2) MUTATED	0	6	0	4
AMP PEAK 4(3Q26.2) WILD-TYPE	5	3	12	2

Figure S6. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.2' versus 'CN_CNMF'

P value = 6.69e-06 (Fisher's exact test), Q value = 0.0052

Table S7. Gene #4: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 4(3Q26.2) MUTATED	74	47	42
AMP PEAK 4(3Q26.2) WILD-TYPE	112	169	49

Figure S7. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CNMF'

P value = 1.33e-10 (Chi-square test), Q value = 1.2e-07

Table S8. Gene #4: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 4(3Q26.2) MUTATED	56	7	32	50	17
AMP PEAK 4(3Q26.2) WILD-TYPE	82	105	44	56	37

Figure S8. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.11e-10 (Fisher's exact test), Q value = 2e-07

Table S9. Gene #4: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
AMP PEAK 4(3Q26.2) MUTATED	46	38	78
AMP PEAK 4(3Q26.2) WILD-TYPE	73	173	78

Figure S9. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_CNMF'

P value = 2.59e-06 (Fisher's exact test), Q value = 0.0021

Table S10. Gene #4: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 4(3Q26.2) MUTATED	38	102	21
AMP PEAK 4(3Q26.2) WILD-TYPE	141	129	57

Figure S10. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.64e-07 (Fisher's exact test), Q value = 0.00039

Table S11. Gene #4: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 4(3Q26.2) MUTATED	10	110	41
AMP PEAK 4(3Q26.2) WILD-TYPE	41	139	147

Figure S11. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.02e-05 (Fisher's exact test), Q value = 0.022

Table S12. Gene #4: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 4(3Q26.2) MUTATED	14	82	41
AMP PEAK 4(3Q26.2) WILD-TYPE	35	106	147

Figure S12. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q12' versus 'CN_CNMF'

P value = 1.34e-09 (Fisher's exact test), Q value = 1.2e-06

Table S13. Gene #5: 'amp_4q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 5(4Q12) MUTATED	62	19	12
AMP PEAK 5(4Q12) WILD-TYPE	124	197	79

Figure S13. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_4q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.15e-05 (Fisher's exact test), Q value = 0.064

Table S14. Gene #5: 'amp_4q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
AMP PEAK 5(4Q12) MUTATED	35	23	34
AMP PEAK 5(4Q12) WILD-TYPE	84	188	122

Figure S14. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1.25e-18 (Fisher's exact test), Q value = 1.2e-15

Table S15. Gene #6: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 6(5P15.33) MUTATED	163	99	57
AMP PEAK 6(5P15.33) WILD-TYPE	23	117	34

Figure S15. Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 5.91e-07 (Chi-square test), Q value = 5e-04

Table S16. Gene #6: 'amp_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 6(5P15.33) MUTATED	111	63	33	73	33
AMP PEAK 6(5P15.33) WILD-TYPE	27	49	43	33	21

Figure S16. Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.23

Table S17. Gene #6: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 6(5P15.33) MUTATED	30	142	106
AMP PEAK 6(5P15.33) WILD-TYPE	19	46	82

Figure S17. Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p13.1' versus 'CN_CNMF'

P value = 4.12e-15 (Fisher's exact test), Q value = 4e-12

Table S18. Gene #7: 'amp_5p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 7(5P13.1) MUTATED	148	87	56
AMP PEAK 7(5P13.1) WILD-TYPE	38	129	35

Figure S18. Get High-res Image Gene #7: 'amp_5p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p13.1' versus 'MRNASEQ_CNMF'

P value = 5.04e-06 (Chi-square test), Q value = 0.004

Table S19. Gene #7: 'amp_5p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 7(5P13.1) MUTATED	94	55	29	76	31
AMP PEAK 7(5P13.1) WILD-TYPE	44	57	47	30	23

Figure S19. Get High-res Image Gene #7: 'amp_5p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5q35.1' versus 'MRNASEQ_CNMF'

P value = 0.000359 (Chi-square test), Q value = 0.24

Table S20. Gene #8: 'amp_5q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 8(5Q35.1) MUTATED	34	42	8	20	16
AMP PEAK 8(5Q35.1) WILD-TYPE	104	70	68	86	38

Figure S20. Get High-res Image Gene #8: 'amp_5q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.73e-05 (Fisher's exact test), Q value = 0.027

Table S21. Gene #8: 'amp_5q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
AMP PEAK 8(5Q35.1) MUTATED	28	71	21
AMP PEAK 8(5Q35.1) WILD-TYPE	91	140	135

Figure S21. Get High-res Image Gene #8: 'amp_5q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5q35.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000365 (Fisher's exact test), Q value = 0.24

Table S22. Gene #8: 'amp_5q35.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 8(5Q35.1) MUTATED	18	44	61
AMP PEAK 8(5Q35.1) WILD-TYPE	33	205	127

Figure S22. Get High-res Image Gene #8: 'amp_5q35.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'CN_CNMF'

P value = 1.08e-06 (Fisher's exact test), Q value = 0.00089

Table S23. Gene #9: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 9(6P21.1) MUTATED	82	55	49
AMP PEAK 9(6P21.1) WILD-TYPE	104	161	42

Figure S23. Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p21.1' versus 'METHLYATION_CNMF'

P value = 2.24e-10 (Fisher's exact test), Q value = 2.1e-07

Table S24. Gene #9: 'amp_6p21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
AMP PEAK 9(6P21.1) MUTATED	78	59	28
AMP PEAK 9(6P21.1) WILD-TYPE	63	81	122

Figure S24. Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7p21.1' versus 'CN_CNMF'

P value = 1.64e-23 (Fisher's exact test), Q value = 1.6e-20

Table S25. Gene #10: 'amp_7p21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 10(7P21.1) MUTATED	155	80	35
AMP PEAK 10(7P21.1) WILD-TYPE	31	136	56

Figure S25. Get High-res Image Gene #10: 'amp_7p21.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7p21.1' versus 'MRNASEQ_CNMF'

P value = 1.12e-09 (Chi-square test), Q value = 1e-06

Table S26. Gene #10: 'amp_7p21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 10(7P21.1) MUTATED	108	43	36	49	29
AMP PEAK 10(7P21.1) WILD-TYPE	30	69	40	57	25

Figure S26. Get High-res Image Gene #10: 'amp_7p21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.49e-10 (Fisher's exact test), Q value = 4.2e-07

Table S27. Gene #10: 'amp_7p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
AMP PEAK 10(7P21.1) MUTATED	94	90	81
AMP PEAK 10(7P21.1) WILD-TYPE	25	121	75

Figure S27. Get High-res Image Gene #10: 'amp_7p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7p21.1' versus 'MIRSEQ_CNMF'

P value = 3.6e-05 (Fisher's exact test), Q value = 0.026

Table S28. Gene #10: 'amp_7p21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 10(7P21.1) MUTATED	76	136	55
AMP PEAK 10(7P21.1) WILD-TYPE	103	95	23

Figure S28. Get High-res Image Gene #10: 'amp_7p21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7p21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000104 (Fisher's exact test), Q value = 0.072

Table S29. Gene #10: 'amp_7p21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 10(7P21.1) MUTATED	37	110	83
AMP PEAK 10(7P21.1) WILD-TYPE	12	78	105

Figure S29. Get High-res Image Gene #10: 'amp_7p21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

P value = 2.87e-21 (Fisher's exact test), Q value = 2.8e-18

Table S30. Gene #11: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 11(7P11.2) MUTATED	149	76	35
AMP PEAK 11(7P11.2) WILD-TYPE	37	140	56

Figure S30. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 3.46e-11 (Chi-square test), Q value = 3.3e-08

Table S31. Gene #11: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 11(7P11.2) MUTATED	106	36	40	46	28
AMP PEAK 11(7P11.2) WILD-TYPE	32	76	36	60	26

Figure S31. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.24e-11 (Fisher's exact test), Q value = 1.2e-08

Table S32. Gene #11: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
AMP PEAK 11(7P11.2) MUTATED	93	81	82
AMP PEAK 11(7P11.2) WILD-TYPE	26	130	74

Figure S32. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 1.25e-07 (Fisher's exact test), Q value = 0.00011

Table S33. Gene #11: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 11(7P11.2) MUTATED	66	136	55
AMP PEAK 11(7P11.2) WILD-TYPE	113	95	23

Figure S33. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.09e-05 (Fisher's exact test), Q value = 0.043

Table S34. Gene #11: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 11(7P11.2) MUTATED	34	147	76
AMP PEAK 11(7P11.2) WILD-TYPE	17	102	112

Figure S34. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.3e-05 (Fisher's exact test), Q value = 0.0099

Table S35. Gene #11: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 11(7P11.2) MUTATED	58	113	51
AMP PEAK 11(7P11.2) WILD-TYPE	97	79	27

Figure S35. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.12e-06 (Fisher's exact test), Q value = 0.00092

Table S36. Gene #11: 'amp_7p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 11(7P11.2) MUTATED	36	113	73
AMP PEAK 11(7P11.2) WILD-TYPE	13	75	115

Figure S36. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q31.2' versus 'CN_CNMF'

P value = 3.36e-12 (Fisher's exact test), Q value = 3.2e-09

Table S37. Gene #12: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 12(7Q31.2) MUTATED	116	60	30
AMP PEAK 12(7Q31.2) WILD-TYPE	70	156	61

Figure S37. Get High-res Image Gene #12: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CNMF'

P value = 2.68e-09 (Chi-square test), Q value = 2.4e-06

Table S38. Gene #12: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 12(7Q31.2) MUTATED	86	24	33	36	23
AMP PEAK 12(7Q31.2) WILD-TYPE	52	88	43	70	31

Figure S38. Get High-res Image Gene #12: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.41e-09 (Fisher's exact test), Q value = 6.7e-06

Table S39. Gene #12: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
AMP PEAK 12(7Q31.2) MUTATED	77	64	61
AMP PEAK 12(7Q31.2) WILD-TYPE	42	147	95

Figure S39. Get High-res Image Gene #12: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.23' versus 'CN_CNMF'

P value = 3.34e-19 (Fisher's exact test), Q value = 3.3e-16

Table S40. Gene #13: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 13(8P11.23) MUTATED	34	38	62
AMP PEAK 13(8P11.23) WILD-TYPE	152	178	29

Figure S40. Get High-res Image Gene #13: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.23' versus 'MRNASEQ_CNMF'

P value = 6.26e-07 (Chi-square test), Q value = 0.00052

Table S41. Gene #13: 'amp_8p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 13(8P11.23) MUTATED	28	16	25	49	12
AMP PEAK 13(8P11.23) WILD-TYPE	110	96	51	57	42

Figure S41. Get High-res Image Gene #13: 'amp_8p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.61e-06 (Fisher's exact test), Q value = 0.0066

Table S42. Gene #13: 'amp_8p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
AMP PEAK 13(8P11.23) MUTATED	26	40	64
AMP PEAK 13(8P11.23) WILD-TYPE	93	171	92

Figure S42. Get High-res Image Gene #13: 'amp_8p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'CN_CNMF'

P value = 1.13e-22 (Fisher's exact test), Q value = 1.1e-19

Table S43. Gene #14: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 14(8P11.21) MUTATED	49	48	73
AMP PEAK 14(8P11.21) WILD-TYPE	137	168	18

Figure S43. Get High-res Image Gene #14: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CNMF'

P value = 1.55e-09 (Chi-square test), Q value = 1.4e-06

Table S44. Gene #14: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 14(8P11.21) MUTATED	44	19	25	63	14
AMP PEAK 14(8P11.21) WILD-TYPE	94	93	51	43	40

Figure S44. Get High-res Image Gene #14: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.4e-06 (Fisher's exact test), Q value = 0.0011

Table S45. Gene #14: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
AMP PEAK 14(8P11.21) MUTATED	41	48	76
AMP PEAK 14(8P11.21) WILD-TYPE	78	163	80

Figure S45. Get High-res Image Gene #14: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.25e-06 (Fisher's exact test), Q value = 0.0071

Table S46. Gene #14: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 14(8P11.21) MUTATED	17	110	42
AMP PEAK 14(8P11.21) WILD-TYPE	34	139	146

Figure S46. Get High-res Image Gene #14: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000352 (Fisher's exact test), Q value = 0.24

Table S47. Gene #14: 'amp_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 14(8P11.21) MUTATED	37	85	27
AMP PEAK 14(8P11.21) WILD-TYPE	118	107	51

Figure S47. Get High-res Image Gene #14: 'amp_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q11.1' versus 'CN_CNMF'

P value = 6.69e-22 (Fisher's exact test), Q value = 6.6e-19

Table S48. Gene #15: 'amp_8q11.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 15(8Q11.1) MUTATED	92	55	77
AMP PEAK 15(8Q11.1) WILD-TYPE	94	161	14

Figure S48. Get High-res Image Gene #15: 'amp_8q11.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q11.1' versus 'METHLYATION_CNMF'

P value = 1.49e-06 (Fisher's exact test), Q value = 0.0012

Table S49. Gene #15: 'amp_8q11.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
AMP PEAK 15(8Q11.1) MUTATED	78	75	43
AMP PEAK 15(8Q11.1) WILD-TYPE	63	65	107

Figure S49. Get High-res Image Gene #15: 'amp_8q11.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q11.1' versus 'MRNASEQ_CNMF'

P value = 3.32e-08 (Chi-square test), Q value = 2.9e-05

Table S50. Gene #15: 'amp_8q11.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 15(8Q11.1) MUTATED	67	28	32	71	21
AMP PEAK 15(8Q11.1) WILD-TYPE	71	84	44	35	33

Figure S50. Get High-res Image Gene #15: 'amp_8q11.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q11.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.87e-06 (Fisher's exact test), Q value = 0.0068

Table S51. Gene #15: 'amp_8q11.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
AMP PEAK 15(8Q11.1) MUTATED	59	70	90
AMP PEAK 15(8Q11.1) WILD-TYPE	60	141	66

Figure S51. Get High-res Image Gene #15: 'amp_8q11.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q11.1' versus 'MIRSEQ_CNMF'

P value = 1.31e-06 (Fisher's exact test), Q value = 0.0011

Table S52. Gene #15: 'amp_8q11.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 15(8Q11.1) MUTATED	55	130	37
AMP PEAK 15(8Q11.1) WILD-TYPE	124	101	41

Figure S52. Get High-res Image Gene #15: 'amp_8q11.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q11.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.44e-05 (Fisher's exact test), Q value = 0.011

Table S53. Gene #15: 'amp_8q11.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 15(8Q11.1) MUTATED	24	137	61
AMP PEAK 15(8Q11.1) WILD-TYPE	27	112	127

Figure S53. Get High-res Image Gene #15: 'amp_8q11.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q11.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.14e-05 (Fisher's exact test), Q value = 0.0087

Table S54. Gene #15: 'amp_8q11.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 15(8Q11.1) MUTATED	48	108	38
AMP PEAK 15(8Q11.1) WILD-TYPE	107	84	40

Figure S54. Get High-res Image Gene #15: 'amp_8q11.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q11.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.17e-06 (Fisher's exact test), Q value = 0.0048

Table S55. Gene #15: 'amp_8q11.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 15(8Q11.1) MUTATED	27	106	61
AMP PEAK 15(8Q11.1) WILD-TYPE	22	82	127

Figure S55. Get High-res Image Gene #15: 'amp_8q11.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 5.06e-18 (Fisher's exact test), Q value = 4.9e-15

Table S56. Gene #16: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 16(8Q24.21) MUTATED	136	92	82
AMP PEAK 16(8Q24.21) WILD-TYPE	50	124	9

Figure S56. Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 3.36e-08 (Fisher's exact test), Q value = 3e-05

Table S57. Gene #16: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
AMP PEAK 16(8Q24.21) MUTATED	97	106	66
AMP PEAK 16(8Q24.21) WILD-TYPE	44	34	84

Figure S57. Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 3.81e-10 (Chi-square test), Q value = 3.5e-07

Table S58. Gene #16: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 16(8Q24.21) MUTATED	103	49	39	86	26
AMP PEAK 16(8Q24.21) WILD-TYPE	35	63	37	20	28

Figure S58. Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.74e-08 (Fisher's exact test), Q value = 5.1e-05

Table S59. Gene #16: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
AMP PEAK 16(8Q24.21) MUTATED	89	101	113
AMP PEAK 16(8Q24.21) WILD-TYPE	30	110	43

Figure S59. Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 5.64e-06 (Fisher's exact test), Q value = 0.0044

Table S60. Gene #16: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 16(8Q24.21) MUTATED	88	168	51
AMP PEAK 16(8Q24.21) WILD-TYPE	91	63	27

Figure S60. Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000224 (Fisher's exact test), Q value = 0.15

Table S61. Gene #16: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 16(8Q24.21) MUTATED	30	178	99
AMP PEAK 16(8Q24.21) WILD-TYPE	21	71	89

Figure S61. Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000159 (Fisher's exact test), Q value = 0.11

Table S62. Gene #16: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 16(8Q24.21) MUTATED	32	136	97
AMP PEAK 16(8Q24.21) WILD-TYPE	17	52	91

Figure S62. Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10p15.1' versus 'CN_CNMF'

P value = 4.17e-06 (Fisher's exact test), Q value = 0.0033

Table S63. Gene #17: 'amp_10p15.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 17(10P15.1) MUTATED	60	37	39
AMP PEAK 17(10P15.1) WILD-TYPE	126	179	52

Figure S63. Get High-res Image Gene #17: 'amp_10p15.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_10p15.1' versus 'METHLYATION_CNMF'

P value = 6.42e-05 (Fisher's exact test), Q value = 0.046

Table S64. Gene #17: 'amp_10p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
AMP PEAK 17(10P15.1) MUTATED	48	47	22
AMP PEAK 17(10P15.1) WILD-TYPE	93	93	128

Figure S64. Get High-res Image Gene #17: 'amp_10p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_10p15.1' versus 'MRNASEQ_CNMF'

P value = 1.8e-05 (Chi-square test), Q value = 0.013

Table S65. Gene #17: 'amp_10p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 17(10P15.1) MUTATED	37	17	27	45	8
AMP PEAK 17(10P15.1) WILD-TYPE	101	95	49	61	46

Figure S65. Get High-res Image Gene #17: 'amp_10p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_10p15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.4e-08 (Fisher's exact test), Q value = 2.1e-05

Table S66. Gene #17: 'amp_10p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
AMP PEAK 17(10P15.1) MUTATED	33	33	68
AMP PEAK 17(10P15.1) WILD-TYPE	86	178	88

Figure S66. Get High-res Image Gene #17: 'amp_10p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10p15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.41e-05 (Fisher's exact test), Q value = 0.011

Table S67. Gene #17: 'amp_10p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 17(10P15.1) MUTATED	8	91	34
AMP PEAK 17(10P15.1) WILD-TYPE	43	158	154

Figure S67. Get High-res Image Gene #17: 'amp_10p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

P value = 4.92e-16 (Fisher's exact test), Q value = 4.8e-13

Table S68. Gene #18: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 18(11Q13.3) MUTATED	90	30	45
AMP PEAK 18(11Q13.3) WILD-TYPE	96	186	46

Figure S68. Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

P value = 3.62e-08 (Chi-square test), Q value = 3.2e-05

Table S69. Gene #18: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 18(11Q13.3) MUTATED	58	21	17	56	12
AMP PEAK 18(11Q13.3) WILD-TYPE	80	91	59	50	42

Figure S69. Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.04e-09 (Fisher's exact test), Q value = 3.7e-06

Table S70. Gene #18: 'amp_11q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
AMP PEAK 18(11Q13.3) MUTATED	50	40	74
AMP PEAK 18(11Q13.3) WILD-TYPE	69	171	82

Figure S70. Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

P value = 7.3e-09 (Fisher's exact test), Q value = 6.6e-06

Table S71. Gene #18: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 18(11Q13.3) MUTATED	31	105	26
AMP PEAK 18(11Q13.3) WILD-TYPE	148	126	52

Figure S71. Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.46e-06 (Fisher's exact test), Q value = 0.0058

Table S72. Gene #18: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 18(11Q13.3) MUTATED	17	106	39
AMP PEAK 18(11Q13.3) WILD-TYPE	34	143	149

Figure S72. Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.48e-06 (Fisher's exact test), Q value = 0.0036

Table S73. Gene #18: 'amp_11q13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 18(11Q13.3) MUTATED	29	83	28
AMP PEAK 18(11Q13.3) WILD-TYPE	126	109	50

Figure S73. Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.23e-05 (Fisher's exact test), Q value = 0.038

Table S74. Gene #18: 'amp_11q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 18(11Q13.3) MUTATED	19	80	41
AMP PEAK 18(11Q13.3) WILD-TYPE	30	108	147

Figure S74. Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p12.1' versus 'CN_CNMF'

P value = 2.73e-06 (Fisher's exact test), Q value = 0.0022

Table S75. Gene #19: 'amp_12p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 19(12P12.1) MUTATED	70	54	50
AMP PEAK 19(12P12.1) WILD-TYPE	116	162	41

Figure S75. Get High-res Image Gene #19: 'amp_12p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CNMF'

P value = 7.47e-11 (Chi-square test), Q value = 7e-08

Table S76. Gene #19: 'amp_12p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 19(12P12.1) MUTATED	55	10	38	53	16
AMP PEAK 19(12P12.1) WILD-TYPE	83	102	38	53	38

Figure S76. Get High-res Image Gene #19: 'amp_12p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.7e-10 (Fisher's exact test), Q value = 1.6e-07

Table S77. Gene #19: 'amp_12p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
AMP PEAK 19(12P12.1) MUTATED	45	43	84
AMP PEAK 19(12P12.1) WILD-TYPE	74	168	72

Figure S77. Get High-res Image Gene #19: 'amp_12p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_CNMF'

P value = 7.09e-06 (Fisher's exact test), Q value = 0.0055

Table S78. Gene #19: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 19(12P12.1) MUTATED	42	106	23
AMP PEAK 19(12P12.1) WILD-TYPE	137	125	55

Figure S78. Get High-res Image Gene #19: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.51e-05 (Fisher's exact test), Q value = 0.011

Table S79. Gene #19: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 19(12P12.1) MUTATED	13	112	46
AMP PEAK 19(12P12.1) WILD-TYPE	38	137	142

Figure S79. Get High-res Image Gene #19: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.07e-06 (Fisher's exact test), Q value = 0.0017

Table S80. Gene #19: 'amp_12p12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 19(12P12.1) MUTATED	31	88	28
AMP PEAK 19(12P12.1) WILD-TYPE	124	104	50

Figure S80. Get High-res Image Gene #19: 'amp_12p12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.17e-06 (Fisher's exact test), Q value = 0.0041

Table S81. Gene #19: 'amp_12p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 19(12P12.1) MUTATED	18	87	42
AMP PEAK 19(12P12.1) WILD-TYPE	31	101	146

Figure S81. Get High-res Image Gene #19: 'amp_12p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q14.1' versus 'CN_CNMF'

P value = 5.86e-08 (Fisher's exact test), Q value = 5.2e-05

Table S82. Gene #20: 'amp_12q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 20(12Q14.1) MUTATED	60	49	52
AMP PEAK 20(12Q14.1) WILD-TYPE	126	167	39

Figure S82. Get High-res Image Gene #20: 'amp_12q14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CNMF'

P value = 5.27e-11 (Chi-square test), Q value = 5e-08

Table S83. Gene #20: 'amp_12q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 20(12Q14.1) MUTATED	42	13	34	58	12
AMP PEAK 20(12Q14.1) WILD-TYPE	96	99	42	48	42

Figure S83. Get High-res Image Gene #20: 'amp_12q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.26e-13 (Fisher's exact test), Q value = 3.1e-10

Table S84. Gene #20: 'amp_12q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
AMP PEAK 20(12Q14.1) MUTATED	33	39	87
AMP PEAK 20(12Q14.1) WILD-TYPE	86	172	69

Figure S84. Get High-res Image Gene #20: 'amp_12q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'MIRSEQ_CNMF'

P value = 1.97e-08 (Fisher's exact test), Q value = 1.8e-05

Table S85. Gene #20: 'amp_12q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 20(12Q14.1) MUTATED	33	105	21
AMP PEAK 20(12Q14.1) WILD-TYPE	146	126	57

Figure S85. Get High-res Image Gene #20: 'amp_12q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.41e-09 (Fisher's exact test), Q value = 4e-06

Table S86. Gene #20: 'amp_12q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 20(12Q14.1) MUTATED	14	112	33
AMP PEAK 20(12Q14.1) WILD-TYPE	37	137	155

Figure S86. Get High-res Image Gene #20: 'amp_12q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.18e-08 (Fisher's exact test), Q value = 3.7e-05

Table S87. Gene #20: 'amp_12q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 20(12Q14.1) MUTATED	24	83	30
AMP PEAK 20(12Q14.1) WILD-TYPE	131	109	48

Figure S87. Get High-res Image Gene #20: 'amp_12q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.72e-10 (Fisher's exact test), Q value = 2.5e-07

Table S88. Gene #20: 'amp_12q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 20(12Q14.1) MUTATED	19	88	30
AMP PEAK 20(12Q14.1) WILD-TYPE	30	100	158

Figure S88. Get High-res Image Gene #20: 'amp_12q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

P value = 5.89e-07 (Fisher's exact test), Q value = 5e-04

Table S89. Gene #21: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 21(12Q15) MUTATED	59	52	51
AMP PEAK 21(12Q15) WILD-TYPE	127	164	40

Figure S89. Get High-res Image Gene #21: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q15' versus 'MRNASEQ_CNMF'

P value = 2.69e-11 (Chi-square test), Q value = 2.5e-08

Table S90. Gene #21: 'amp_12q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 21(12Q15) MUTATED	41	13	35	58	12
AMP PEAK 21(12Q15) WILD-TYPE	97	99	41	48	42

Figure S90. Get High-res Image Gene #21: 'amp_12q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.47e-12 (Fisher's exact test), Q value = 8e-09

Table S91. Gene #21: 'amp_12q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
AMP PEAK 21(12Q15) MUTATED	33	41	85
AMP PEAK 21(12Q15) WILD-TYPE	86	170	71

Figure S91. Get High-res Image Gene #21: 'amp_12q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_CNMF'

P value = 1.45e-08 (Fisher's exact test), Q value = 1.3e-05

Table S92. Gene #21: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 21(12Q15) MUTATED	33	106	22
AMP PEAK 21(12Q15) WILD-TYPE	146	125	56

Figure S92. Get High-res Image Gene #21: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q15' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.99e-08 (Fisher's exact test), Q value = 1.8e-05

Table S93. Gene #21: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 21(12Q15) MUTATED	16	111	34
AMP PEAK 21(12Q15) WILD-TYPE	35	138	154

Figure S93. Get High-res Image Gene #21: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.98e-08 (Fisher's exact test), Q value = 1.8e-05

Table S94. Gene #21: 'amp_12q15' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 21(12Q15) MUTATED	24	84	31
AMP PEAK 21(12Q15) WILD-TYPE	131	108	47

Figure S94. Get High-res Image Gene #21: 'amp_12q15' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12q15' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.71e-08 (Fisher's exact test), Q value = 2.4e-05

Table S95. Gene #21: 'amp_12q15' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 21(12Q15) MUTATED	19	86	34
AMP PEAK 21(12Q15) WILD-TYPE	30	102	154

Figure S95. Get High-res Image Gene #21: 'amp_12q15' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q33.3' versus 'METHLYATION_CNMF'

P value = 0.000334 (Fisher's exact test), Q value = 0.22

Table S96. Gene #22: 'amp_13q33.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
AMP PEAK 22(13Q33.3) MUTATED	36	16	14
AMP PEAK 22(13Q33.3) WILD-TYPE	105	124	136

Figure S96. Get High-res Image Gene #22: 'amp_13q33.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_14q13.3' versus 'CN_CNMF'

P value = 3.67e-14 (Fisher's exact test), Q value = 3.5e-11

Table S97. Gene #23: 'amp_14q13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 23(14Q13.3) MUTATED	101	57	64
AMP PEAK 23(14Q13.3) WILD-TYPE	85	159	27

Figure S97. Get High-res Image Gene #23: 'amp_14q13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_14q13.3' versus 'METHLYATION_CNMF'

P value = 0.000127 (Fisher's exact test), Q value = 0.088

Table S98. Gene #23: 'amp_14q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
AMP PEAK 23(14Q13.3) MUTATED	76	71	47
AMP PEAK 23(14Q13.3) WILD-TYPE	65	69	103

Figure S98. Get High-res Image Gene #23: 'amp_14q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_14q13.3' versus 'MRNASEQ_CNMF'

P value = 2.71e-16 (Chi-square test), Q value = 2.6e-13

Table S99. Gene #23: 'amp_14q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 23(14Q13.3) MUTATED	81	39	10	74	15
AMP PEAK 23(14Q13.3) WILD-TYPE	57	73	66	32	39

Figure S99. Get High-res Image Gene #23: 'amp_14q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_14q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-06 (Fisher's exact test), Q value = 0.00084

Table S100. Gene #23: 'amp_14q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
AMP PEAK 23(14Q13.3) MUTATED	69	67	83
AMP PEAK 23(14Q13.3) WILD-TYPE	50	144	73

Figure S100. Get High-res Image Gene #23: 'amp_14q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_14q13.3' versus 'MIRSEQ_CNMF'

P value = 2.44e-08 (Fisher's exact test), Q value = 2.2e-05

Table S101. Gene #23: 'amp_14q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 23(14Q13.3) MUTATED	50	131	38
AMP PEAK 23(14Q13.3) WILD-TYPE	129	100	40

Figure S101. Get High-res Image Gene #23: 'amp_14q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_14q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.07e-09 (Fisher's exact test), Q value = 4.6e-06

Table S102. Gene #23: 'amp_14q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 23(14Q13.3) MUTATED	26	141	52
AMP PEAK 23(14Q13.3) WILD-TYPE	25	108	136

Figure S102. Get High-res Image Gene #23: 'amp_14q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_14q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.54e-05 (Fisher's exact test), Q value = 0.053

Table S103. Gene #23: 'amp_14q13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 23(14Q13.3) MUTATED	48	100	42
AMP PEAK 23(14Q13.3) WILD-TYPE	107	92	36

Figure S103. Get High-res Image Gene #23: 'amp_14q13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_14q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.69e-06 (Fisher's exact test), Q value = 0.0074

Table S104. Gene #23: 'amp_14q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 23(14Q13.3) MUTATED	29	101	60
AMP PEAK 23(14Q13.3) WILD-TYPE	20	87	128

Figure S104. Get High-res Image Gene #23: 'amp_14q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_16p11.2' versus 'CN_CNMF'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.00095

Table S105. Gene #24: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 24(16P11.2) MUTATED	84	45	30
AMP PEAK 24(16P11.2) WILD-TYPE	102	171	61

Figure S105. Get High-res Image Gene #24: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'CN_CNMF'

P value = 1.25e-12 (Fisher's exact test), Q value = 1.2e-09

Table S106. Gene #25: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 25(17Q12) MUTATED	111	56	52
AMP PEAK 25(17Q12) WILD-TYPE	75	160	39

Figure S106. Get High-res Image Gene #25: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 1.07e-05 (Fisher's exact test), Q value = 0.0082

Table S107. Gene #25: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
AMP PEAK 25(17Q12) MUTATED	65	77	42
AMP PEAK 25(17Q12) WILD-TYPE	76	63	108

Figure S107. Get High-res Image Gene #25: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 6.09e-08 (Chi-square test), Q value = 5.4e-05

Table S108. Gene #25: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 25(17Q12) MUTATED	84	30	24	57	20
AMP PEAK 25(17Q12) WILD-TYPE	54	82	52	49	34

Figure S108. Get High-res Image Gene #25: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.4e-07 (Fisher's exact test), Q value = 0.00012

Table S109. Gene #25: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
AMP PEAK 25(17Q12) MUTATED	71	64	80
AMP PEAK 25(17Q12) WILD-TYPE	48	147	76

Figure S109. Get High-res Image Gene #25: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 4.29e-08 (Fisher's exact test), Q value = 3.8e-05

Table S110. Gene #25: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 25(17Q12) MUTATED	54	134	29
AMP PEAK 25(17Q12) WILD-TYPE	125	97	49

Figure S110. Get High-res Image Gene #25: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.62e-07 (Fisher's exact test), Q value = 0.00047

Table S111. Gene #25: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 25(17Q12) MUTATED	17	140	60
AMP PEAK 25(17Q12) WILD-TYPE	34	109	128

Figure S111. Get High-res Image Gene #25: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.29e-06 (Fisher's exact test), Q value = 0.0042

Table S112. Gene #25: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 25(17Q12) MUTATED	20	105	58
AMP PEAK 25(17Q12) WILD-TYPE	29	83	130

Figure S112. Get High-res Image Gene #25: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q23.1' versus 'CN_CNMF'

P value = 4.31e-13 (Fisher's exact test), Q value = 4.1e-10

Table S113. Gene #26: 'amp_17q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 26(17Q23.1) MUTATED	123	65	53
AMP PEAK 26(17Q23.1) WILD-TYPE	63	151	38

Figure S113. Get High-res Image Gene #26: 'amp_17q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q23.1' versus 'METHLYATION_CNMF'

P value = 8.9e-08 (Fisher's exact test), Q value = 7.8e-05

Table S114. Gene #26: 'amp_17q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
AMP PEAK 26(17Q23.1) MUTATED	64	92	49
AMP PEAK 26(17Q23.1) WILD-TYPE	77	48	101

Figure S114. Get High-res Image Gene #26: 'amp_17q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q23.1' versus 'MRNASEQ_CNMF'

P value = 9.78e-08 (Chi-square test), Q value = 8.5e-05

Table S115. Gene #26: 'amp_17q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 26(17Q23.1) MUTATED	95	37	30	54	21
AMP PEAK 26(17Q23.1) WILD-TYPE	43	75	46	52	33

Figure S115. Get High-res Image Gene #26: 'amp_17q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.62e-10 (Fisher's exact test), Q value = 5.2e-07

Table S116. Gene #26: 'amp_17q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
AMP PEAK 26(17Q23.1) MUTATED	82	70	85
AMP PEAK 26(17Q23.1) WILD-TYPE	37	141	71

Figure S116. Get High-res Image Gene #26: 'amp_17q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q23.1' versus 'MIRSEQ_CNMF'

P value = 2.12e-07 (Fisher's exact test), Q value = 0.00018

Table S117. Gene #26: 'amp_17q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 26(17Q23.1) MUTATED	63	143	33
AMP PEAK 26(17Q23.1) WILD-TYPE	116	88	45

Figure S117. Get High-res Image Gene #26: 'amp_17q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.34e-05 (Fisher's exact test), Q value = 0.01

Table S118. Gene #26: 'amp_17q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 26(17Q23.1) MUTATED	19	148	72
AMP PEAK 26(17Q23.1) WILD-TYPE	32	101	116

Figure S118. Get High-res Image Gene #26: 'amp_17q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 4.96e-06 (Fisher's exact test), Q value = 0.0039

Table S119. Gene #27: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
AMP PEAK 27(18Q11.2) MUTATED	47	27	15
AMP PEAK 27(18Q11.2) WILD-TYPE	94	113	135

Figure S119. Get High-res Image Gene #27: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CNMF'

P value = 4.95e-05 (Chi-square test), Q value = 0.036

Table S120. Gene #27: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 27(18Q11.2) MUTATED	24	12	19	37	6
AMP PEAK 27(18Q11.2) WILD-TYPE	114	100	57	69	48

Figure S120. Get High-res Image Gene #27: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.95e-06 (Fisher's exact test), Q value = 0.0024

Table S121. Gene #27: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
AMP PEAK 27(18Q11.2) MUTATED	21	25	52
AMP PEAK 27(18Q11.2) WILD-TYPE	98	186	104

Figure S121. Get High-res Image Gene #27: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_CNMF'

P value = 0.000213 (Fisher's exact test), Q value = 0.15

Table S122. Gene #27: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 27(18Q11.2) MUTATED	20	63	15
AMP PEAK 27(18Q11.2) WILD-TYPE	159	168	63

Figure S122. Get High-res Image Gene #27: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.66e-07 (Fisher's exact test), Q value = 0.00072

Table S123. Gene #27: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 27(18Q11.2) MUTATED	4	73	21
AMP PEAK 27(18Q11.2) WILD-TYPE	47	176	167

Figure S123. Get High-res Image Gene #27: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.93e-05 (Fisher's exact test), Q value = 0.036

Table S124. Gene #27: 'amp_18q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 27(18Q11.2) MUTATED	7	58	24
AMP PEAK 27(18Q11.2) WILD-TYPE	42	130	164

Figure S124. Get High-res Image Gene #27: 'amp_18q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 6.69e-06 (Fisher's exact test), Q value = 0.0052

Table S125. Gene #28: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
AMP PEAK 28(19Q12) MUTATED	61	28	31
AMP PEAK 28(19Q12) WILD-TYPE	80	112	119

Figure S125. Get High-res Image Gene #28: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 0.000202 (Chi-square test), Q value = 0.14

Table S126. Gene #28: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 28(19Q12) MUTATED	38	17	28	40	8
AMP PEAK 28(19Q12) WILD-TYPE	100	95	48	66	46

Figure S126. Get High-res Image Gene #28: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.2e-06 (Fisher's exact test), Q value = 0.00098

Table S127. Gene #28: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
AMP PEAK 28(19Q12) MUTATED	34	34	63
AMP PEAK 28(19Q12) WILD-TYPE	85	177	93

Figure S127. Get High-res Image Gene #28: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 2.18e-05 (Fisher's exact test), Q value = 0.016

Table S128. Gene #28: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 28(19Q12) MUTATED	30	85	18
AMP PEAK 28(19Q12) WILD-TYPE	149	146	60

Figure S128. Get High-res Image Gene #28: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.48e-07 (Fisher's exact test), Q value = 0.00021

Table S129. Gene #28: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 28(19Q12) MUTATED	5	94	34
AMP PEAK 28(19Q12) WILD-TYPE	46	155	154

Figure S129. Get High-res Image Gene #28: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.43e-05 (Fisher's exact test), Q value = 0.018

Table S130. Gene #28: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 28(19Q12) MUTATED	28	75	16
AMP PEAK 28(19Q12) WILD-TYPE	127	117	62

Figure S130. Get High-res Image Gene #28: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.51e-07 (Fisher's exact test), Q value = 0.00022

Table S131. Gene #28: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 28(19Q12) MUTATED	7	78	34
AMP PEAK 28(19Q12) WILD-TYPE	42	110	154

Figure S131. Get High-res Image Gene #28: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20p11.21' versus 'CN_CNMF'

P value = 7.68e-06 (Fisher's exact test), Q value = 0.006

Table S132. Gene #29: 'amp_20p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 29(20P11.21) MUTATED	73	62	53
AMP PEAK 29(20P11.21) WILD-TYPE	113	154	38

Figure S132. Get High-res Image Gene #29: 'amp_20p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p11.21' versus 'METHLYATION_CNMF'

P value = 0.000228 (Fisher's exact test), Q value = 0.15

Table S133. Gene #29: 'amp_20p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
AMP PEAK 29(20P11.21) MUTATED	72	45	44
AMP PEAK 29(20P11.21) WILD-TYPE	69	95	106

Figure S133. Get High-res Image Gene #29: 'amp_20p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20p11.21' versus 'MRNASEQ_CNMF'

P value = 4.9e-05 (Chi-square test), Q value = 0.035

Table S134. Gene #29: 'amp_20p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 29(20P11.21) MUTATED	47	34	25	62	16
AMP PEAK 29(20P11.21) WILD-TYPE	91	78	51	44	38

Figure S134. Get High-res Image Gene #29: 'amp_20p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.8e-06 (Fisher's exact test), Q value = 0.0038

Table S135. Gene #29: 'amp_20p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
AMP PEAK 29(20P11.21) MUTATED	42	59	83
AMP PEAK 29(20P11.21) WILD-TYPE	77	152	73

Figure S135. Get High-res Image Gene #29: 'amp_20p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20p11.21' versus 'MIRSEQ_CNMF'

P value = 0.000101 (Fisher's exact test), Q value = 0.07

Table S136. Gene #29: 'amp_20p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 29(20P11.21) MUTATED	47	108	31
AMP PEAK 29(20P11.21) WILD-TYPE	132	123	47

Figure S136. Get High-res Image Gene #29: 'amp_20p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.61e-05 (Fisher's exact test), Q value = 0.019

Table S137. Gene #29: 'amp_20p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 29(20P11.21) MUTATED	23	115	48
AMP PEAK 29(20P11.21) WILD-TYPE	28	134	140

Figure S137. Get High-res Image Gene #29: 'amp_20p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.93e-05 (Fisher's exact test), Q value = 0.036

Table S138. Gene #29: 'amp_20p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 29(20P11.21) MUTATED	21	91	50
AMP PEAK 29(20P11.21) WILD-TYPE	28	97	138

Figure S138. Get High-res Image Gene #29: 'amp_20p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.33' versus 'CN_CNMF'

P value = 2.38e-08 (Fisher's exact test), Q value = 2.1e-05

Table S139. Gene #30: 'amp_20q13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 30(20Q13.33) MUTATED	103	73	61
AMP PEAK 30(20Q13.33) WILD-TYPE	83	143	30

Figure S139. Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.33' versus 'METHLYATION_CNMF'

P value = 0.000282 (Fisher's exact test), Q value = 0.19

Table S140. Gene #30: 'amp_20q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
AMP PEAK 30(20Q13.33) MUTATED	83	68	53
AMP PEAK 30(20Q13.33) WILD-TYPE	58	72	97

Figure S140. Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CNMF'

P value = 2.01e-07 (Chi-square test), Q value = 0.00017

Table S141. Gene #30: 'amp_20q13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 30(20Q13.33) MUTATED	71	41	27	75	19
AMP PEAK 30(20Q13.33) WILD-TYPE	67	71	49	31	35

Figure S141. Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000317 (Fisher's exact test), Q value = 0.21

Table S142. Gene #30: 'amp_20q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
AMP PEAK 30(20Q13.33) MUTATED	62	80	91
AMP PEAK 30(20Q13.33) WILD-TYPE	57	131	65

Figure S142. Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_CNMF'

P value = 1.4e-05 (Fisher's exact test), Q value = 0.011

Table S143. Gene #30: 'amp_20q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 30(20Q13.33) MUTATED	63	135	35
AMP PEAK 30(20Q13.33) WILD-TYPE	116	96	43

Figure S143. Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.8e-08 (Fisher's exact test), Q value = 1.6e-05

Table S144. Gene #30: 'amp_20q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 30(20Q13.33) MUTATED	29	146	58
AMP PEAK 30(20Q13.33) WILD-TYPE	22	103	130

Figure S144. Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.39e-05 (Fisher's exact test), Q value = 0.032

Table S145. Gene #30: 'amp_20q13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 30(20Q13.33) MUTATED	54	113	36
AMP PEAK 30(20Q13.33) WILD-TYPE	101	79	42

Figure S145. Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.69e-05 (Fisher's exact test), Q value = 0.047

Table S146. Gene #30: 'amp_20q13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 30(20Q13.33) MUTATED	25	110	68
AMP PEAK 30(20Q13.33) WILD-TYPE	24	78	120

Figure S146. Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_22q11.22' versus 'CN_CNMF'

P value = 5.61e-06 (Fisher's exact test), Q value = 0.0044

Table S147. Gene #31: 'amp_22q11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 31(22Q11.22) MUTATED	52	20	15
AMP PEAK 31(22Q11.22) WILD-TYPE	134	196	76

Figure S147. Get High-res Image Gene #31: 'amp_22q11.22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xq28' versus 'CN_CNMF'

P value = 1.49e-12 (Fisher's exact test), Q value = 1.4e-09

Table S148. Gene #32: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
AMP PEAK 32(XQ28) MUTATED	91	33	25
AMP PEAK 32(XQ28) WILD-TYPE	95	183	66

Figure S148. Get High-res Image Gene #32: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xq28' versus 'MRNASEQ_CNMF'

P value = 1.79e-05 (Chi-square test), Q value = 0.013

Table S149. Gene #32: 'amp_xq28' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
AMP PEAK 32(XQ28) MUTATED	65	23	17	32	12
AMP PEAK 32(XQ28) WILD-TYPE	73	89	59	74	42

Figure S149. Get High-res Image Gene #32: 'amp_xq28' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xq28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.97e-06 (Fisher's exact test), Q value = 0.0024

Table S150. Gene #32: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
AMP PEAK 32(XQ28) MUTATED	56	43	50
AMP PEAK 32(XQ28) WILD-TYPE	63	168	106

Figure S150. Get High-res Image Gene #32: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.13' versus 'CN_CNMF'

P value = 0.000127 (Fisher's exact test), Q value = 0.088

Table S151. Gene #33: 'del_1p36.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 1(1P36.13) MUTATED	32	47	37
DEL PEAK 1(1P36.13) WILD-TYPE	154	169	54

Figure S151. Get High-res Image Gene #33: 'del_1p36.13' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.13' versus 'METHLYATION_CNMF'

P value = 9.93e-06 (Fisher's exact test), Q value = 0.0076

Table S152. Gene #33: 'del_1p36.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 1(1P36.13) MUTATED	47	35	16
DEL PEAK 1(1P36.13) WILD-TYPE	94	105	134

Figure S152. Get High-res Image Gene #33: 'del_1p36.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.13' versus 'MRNASEQ_CNMF'

P value = 9.05e-05 (Chi-square test), Q value = 0.063

Table S153. Gene #33: 'del_1p36.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 1(1P36.13) MUTATED	31	15	23	38	5
DEL PEAK 1(1P36.13) WILD-TYPE	107	97	53	68	49

Figure S153. Get High-res Image Gene #33: 'del_1p36.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.14e-06 (Fisher's exact test), Q value = 0.00093

Table S154. Gene #33: 'del_1p36.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
DEL PEAK 1(1P36.13) MUTATED	29	27	56
DEL PEAK 1(1P36.13) WILD-TYPE	90	184	100

Figure S154. Get High-res Image Gene #33: 'del_1p36.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.1' versus 'CN_CNMF'

P value = 2.64e-07 (Fisher's exact test), Q value = 0.00023

Table S155. Gene #34: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 2(1P13.1) MUTATED	44	51	49
DEL PEAK 2(1P13.1) WILD-TYPE	142	165	42

Figure S155. Get High-res Image Gene #34: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p13.1' versus 'MRNASEQ_CNMF'

P value = 7.66e-05 (Chi-square test), Q value = 0.054

Table S156. Gene #34: 'del_1p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 2(1P13.1) MUTATED	33	25	23	50	10
DEL PEAK 2(1P13.1) WILD-TYPE	105	87	53	56	44

Figure S156. Get High-res Image Gene #34: 'del_1p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 4.96e-05 (Fisher's exact test), Q value = 0.036

Table S157. Gene #35: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 3(2Q22.1) MUTATED	23	12	3
DEL PEAK 3(2Q22.1) WILD-TYPE	118	128	147

Figure S157. Get High-res Image Gene #35: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q37.3' versus 'CN_CNMF'

P value = 1.3e-05 (Fisher's exact test), Q value = 0.0099

Table S158. Gene #36: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 4(2Q37.3) MUTATED	36	11	16
DEL PEAK 4(2Q37.3) WILD-TYPE	150	205	75

Figure S158. Get High-res Image Gene #36: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 5.82e-05 (Fisher's exact test), Q value = 0.042

Table S159. Gene #36: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 4(2Q37.3) MUTATED	25	22	5
DEL PEAK 4(2Q37.3) WILD-TYPE	116	118	145

Figure S159. Get High-res Image Gene #36: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.18e-05 (Fisher's exact test), Q value = 0.03

Table S160. Gene #36: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
DEL PEAK 4(2Q37.3) MUTATED	5	48	10
DEL PEAK 4(2Q37.3) WILD-TYPE	46	201	178

Figure S160. Get High-res Image Gene #36: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.3' versus 'CN_CNMF'

P value = 5.77e-06 (Fisher's exact test), Q value = 0.0045

Table S161. Gene #37: 'del_3p26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 5(3P26.3) MUTATED	96	72	55
DEL PEAK 5(3P26.3) WILD-TYPE	90	144	36

Figure S161. Get High-res Image Gene #37: 'del_3p26.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p26.3' versus 'METHLYATION_CNMF'

P value = 2.7e-05 (Fisher's exact test), Q value = 0.02

Table S162. Gene #37: 'del_3p26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 5(3P26.3) MUTATED	86	54	55
DEL PEAK 5(3P26.3) WILD-TYPE	55	86	95

Figure S162. Get High-res Image Gene #37: 'del_3p26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.1e-10 (Fisher's exact test), Q value = 2.9e-07

Table S163. Gene #37: 'del_3p26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
DEL PEAK 5(3P26.3) MUTATED	48	69	104
DEL PEAK 5(3P26.3) WILD-TYPE	71	142	52

Figure S163. Get High-res Image Gene #37: 'del_3p26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.3' versus 'MIRSEQ_CNMF'

P value = 3.81e-05 (Fisher's exact test), Q value = 0.028

Table S164. Gene #37: 'del_3p26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 5(3P26.3) MUTATED	57	118	44
DEL PEAK 5(3P26.3) WILD-TYPE	122	113	34

Figure S164. Get High-res Image Gene #37: 'del_3p26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p21.31' versus 'CN_CNMF'

P value = 1.6e-06 (Fisher's exact test), Q value = 0.0013

Table S165. Gene #38: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 6(3P21.31) MUTATED	101	77	59
DEL PEAK 6(3P21.31) WILD-TYPE	85	139	32

Figure S165. Get High-res Image Gene #38: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p21.31' versus 'METHLYATION_CNMF'

P value = 1.67e-06 (Fisher's exact test), Q value = 0.0014

Table S166. Gene #38: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 6(3P21.31) MUTATED	93	57	58
DEL PEAK 6(3P21.31) WILD-TYPE	48	83	92

Figure S166. Get High-res Image Gene #38: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.94e-12 (Fisher's exact test), Q value = 1.8e-09

Table S167. Gene #38: 'del_3p21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
DEL PEAK 6(3P21.31) MUTATED	55	68	110
DEL PEAK 6(3P21.31) WILD-TYPE	64	143	46

Figure S167. Get High-res Image Gene #38: 'del_3p21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_CNMF'

P value = 2.11e-05 (Fisher's exact test), Q value = 0.016

Table S168. Gene #38: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 6(3P21.31) MUTATED	61	127	45
DEL PEAK 6(3P21.31) WILD-TYPE	118	104	33

Figure S168. Get High-res Image Gene #38: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3q29' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.063

Table S169. Gene #40: 'del_3q29' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 8(3Q29) MUTATED	55	42	25
DEL PEAK 8(3Q29) WILD-TYPE	86	98	125

Figure S169. Get High-res Image Gene #40: 'del_3q29' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3q29' versus 'MRNASEQ_CNMF'

P value = 7.88e-05 (Chi-square test), Q value = 0.055

Table S170. Gene #40: 'del_3q29' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 8(3Q29) MUTATED	22	40	13	41	15
DEL PEAK 8(3Q29) WILD-TYPE	116	72	63	65	39

Figure S170. Get High-res Image Gene #40: 'del_3q29' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p16.3' versus 'CN_CNMF'

P value = 2.11e-06 (Fisher's exact test), Q value = 0.0017

Table S171. Gene #41: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 9(4P16.3) MUTATED	49	36	41
DEL PEAK 9(4P16.3) WILD-TYPE	137	180	50

Figure S171. Get High-res Image Gene #41: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.3' versus 'MRNASEQ_CNMF'

P value = 8.44e-06 (Chi-square test), Q value = 0.0065

Table S172. Gene #41: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 9(4P16.3) MUTATED	35	12	20	45	13
DEL PEAK 9(4P16.3) WILD-TYPE	103	100	56	61	41

Figure S172. Get High-res Image Gene #41: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.89e-07 (Fisher's exact test), Q value = 0.00041

Table S173. Gene #41: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
DEL PEAK 9(4P16.3) MUTATED	27	34	64
DEL PEAK 9(4P16.3) WILD-TYPE	92	177	92

Figure S173. Get High-res Image Gene #41: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_CNMF'

P value = 7.87e-06 (Fisher's exact test), Q value = 0.0061

Table S174. Gene #41: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 9(4P16.3) MUTATED	25	80	20
DEL PEAK 9(4P16.3) WILD-TYPE	154	151	58

Figure S174. Get High-res Image Gene #41: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.92e-06 (Fisher's exact test), Q value = 0.0024

Table S175. Gene #41: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
DEL PEAK 9(4P16.3) MUTATED	8	88	29
DEL PEAK 9(4P16.3) WILD-TYPE	43	161	159

Figure S175. Get High-res Image Gene #41: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MRNA_CNMF'

P value = 0.000214 (Fisher's exact test), Q value = 0.15

Table S176. Gene #42: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	5	9	12	6
DEL PEAK 10(4Q22.1) MUTATED	3	1	0	5
DEL PEAK 10(4Q22.1) WILD-TYPE	2	8	12	1

Figure S176. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 9.89e-05 (Fisher's exact test), Q value = 0.069

Table S177. Gene #42: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	13	12
DEL PEAK 10(4Q22.1) MUTATED	6	0	3
DEL PEAK 10(4Q22.1) WILD-TYPE	1	13	9

Figure S177. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 6.88e-07 (Fisher's exact test), Q value = 0.00058

Table S178. Gene #42: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 10(4Q22.1) MUTATED	64	44	46
DEL PEAK 10(4Q22.1) WILD-TYPE	122	172	45

Figure S178. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 2.27e-07 (Chi-square test), Q value = 2e-04

Table S179. Gene #42: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 10(4Q22.1) MUTATED	40	15	31	52	14
DEL PEAK 10(4Q22.1) WILD-TYPE	98	97	45	54	40

Figure S179. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.83e-14 (Fisher's exact test), Q value = 5.6e-11

Table S180. Gene #42: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
DEL PEAK 10(4Q22.1) MUTATED	29	37	86
DEL PEAK 10(4Q22.1) WILD-TYPE	90	174	70

Figure S180. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_CNMF'

P value = 5.26e-07 (Fisher's exact test), Q value = 0.00044

Table S181. Gene #42: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 10(4Q22.1) MUTATED	31	96	26
DEL PEAK 10(4Q22.1) WILD-TYPE	148	135	52

Figure S181. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.11e-07 (Fisher's exact test), Q value = 0.00027

Table S182. Gene #42: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
DEL PEAK 10(4Q22.1) MUTATED	14	105	34
DEL PEAK 10(4Q22.1) WILD-TYPE	37	144	154

Figure S182. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q35.1' versus 'CN_CNMF'

P value = 1.25e-09 (Fisher's exact test), Q value = 1.1e-06

Table S183. Gene #43: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 11(4Q35.1) MUTATED	75	51	56
DEL PEAK 11(4Q35.1) WILD-TYPE	111	165	35

Figure S183. Get High-res Image Gene #43: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q35.1' versus 'MRNASEQ_CNMF'

P value = 2.37e-10 (Chi-square test), Q value = 2.2e-07

Table S184. Gene #43: 'del_4q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 11(4Q35.1) MUTATED	45	18	37	63	16
DEL PEAK 11(4Q35.1) WILD-TYPE	93	94	39	43	38

Figure S184. Get High-res Image Gene #43: 'del_4q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.81e-18 (Fisher's exact test), Q value = 2.7e-15

Table S185. Gene #43: 'del_4q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
DEL PEAK 11(4Q35.1) MUTATED	32	45	102
DEL PEAK 11(4Q35.1) WILD-TYPE	87	166	54

Figure S185. Get High-res Image Gene #43: 'del_4q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MIRSEQ_CNMF'

P value = 4.34e-09 (Fisher's exact test), Q value = 3.9e-06

Table S186. Gene #43: 'del_4q35.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 11(4Q35.1) MUTATED	40	118	23
DEL PEAK 11(4Q35.1) WILD-TYPE	139	113	55

Figure S186. Get High-res Image Gene #43: 'del_4q35.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q35.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.98e-10 (Fisher's exact test), Q value = 3.7e-07

Table S187. Gene #43: 'del_4q35.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
DEL PEAK 11(4Q35.1) MUTATED	13	127	41
DEL PEAK 11(4Q35.1) WILD-TYPE	38	122	147

Figure S187. Get High-res Image Gene #43: 'del_4q35.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.38e-06 (Fisher's exact test), Q value = 0.0057

Table S188. Gene #43: 'del_4q35.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
DEL PEAK 11(4Q35.1) MUTATED	40	95	22
DEL PEAK 11(4Q35.1) WILD-TYPE	115	97	56

Figure S188. Get High-res Image Gene #43: 'del_4q35.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q35.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.49e-07 (Fisher's exact test), Q value = 0.00013

Table S189. Gene #43: 'del_4q35.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
DEL PEAK 11(4Q35.1) MUTATED	14	97	46
DEL PEAK 11(4Q35.1) WILD-TYPE	35	91	142

Figure S189. Get High-res Image Gene #43: 'del_4q35.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q11.2' versus 'CN_CNMF'

P value = 4.98e-15 (Fisher's exact test), Q value = 4.8e-12

Table S190. Gene #44: 'del_5q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 12(5Q11.2) MUTATED	95	34	43
DEL PEAK 12(5Q11.2) WILD-TYPE	91	182	48

Figure S190. Get High-res Image Gene #44: 'del_5q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q11.2' versus 'METHLYATION_CNMF'

P value = 0.000211 (Fisher's exact test), Q value = 0.14

Table S191. Gene #44: 'del_5q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 12(5Q11.2) MUTATED	64	47	34
DEL PEAK 12(5Q11.2) WILD-TYPE	77	93	116

Figure S191. Get High-res Image Gene #44: 'del_5q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q11.2' versus 'MRNASEQ_CNMF'

P value = 1.98e-06 (Chi-square test), Q value = 0.0016

Table S192. Gene #44: 'del_5q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 12(5Q11.2) MUTATED	57	19	29	52	12
DEL PEAK 12(5Q11.2) WILD-TYPE	81	93	47	54	42

Figure S192. Get High-res Image Gene #44: 'del_5q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.18e-12 (Fisher's exact test), Q value = 3e-09

Table S193. Gene #44: 'del_5q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
DEL PEAK 12(5Q11.2) MUTATED	45	39	85
DEL PEAK 12(5Q11.2) WILD-TYPE	74	172	71

Figure S193. Get High-res Image Gene #44: 'del_5q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_CNMF'

P value = 7.37e-10 (Fisher's exact test), Q value = 6.8e-07

Table S194. Gene #44: 'del_5q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 12(5Q11.2) MUTATED	33	112	24
DEL PEAK 12(5Q11.2) WILD-TYPE	146	119	54

Figure S194. Get High-res Image Gene #44: 'del_5q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.09e-06 (Fisher's exact test), Q value = 9e-04

Table S195. Gene #44: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
DEL PEAK 12(5Q11.2) MUTATED	15	113	41
DEL PEAK 12(5Q11.2) WILD-TYPE	36	136	147

Figure S195. Get High-res Image Gene #44: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.66e-07 (Fisher's exact test), Q value = 0.00023

Table S196. Gene #44: 'del_5q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
DEL PEAK 12(5Q11.2) MUTATED	30	90	23
DEL PEAK 12(5Q11.2) WILD-TYPE	125	102	55

Figure S196. Get High-res Image Gene #44: 'del_5q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.21e-09 (Fisher's exact test), Q value = 1.1e-06

Table S197. Gene #44: 'del_5q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
DEL PEAK 12(5Q11.2) MUTATED	12	94	37
DEL PEAK 12(5Q11.2) WILD-TYPE	37	94	151

Figure S197. Get High-res Image Gene #44: 'del_5q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q31.1' versus 'CN_CNMF'

P value = 1.7e-14 (Fisher's exact test), Q value = 1.6e-11

Table S198. Gene #45: 'del_5q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 13(5Q31.1) MUTATED	102	45	52
DEL PEAK 13(5Q31.1) WILD-TYPE	84	171	39

Figure S198. Get High-res Image Gene #45: 'del_5q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q31.1' versus 'METHLYATION_CNMF'

P value = 1.91e-05 (Fisher's exact test), Q value = 0.014

Table S199. Gene #45: 'del_5q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 13(5Q31.1) MUTATED	71	63	38
DEL PEAK 13(5Q31.1) WILD-TYPE	70	77	112

Figure S199. Get High-res Image Gene #45: 'del_5q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q31.1' versus 'MRNASEQ_CNMF'

P value = 3.42e-07 (Chi-square test), Q value = 0.00029

Table S200. Gene #45: 'del_5q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 13(5Q31.1) MUTATED	66	23	33	59	15
DEL PEAK 13(5Q31.1) WILD-TYPE	72	89	43	47	39

Figure S200. Get High-res Image Gene #45: 'del_5q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.31e-12 (Fisher's exact test), Q value = 1.3e-09

Table S201. Gene #45: 'del_5q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
DEL PEAK 13(5Q31.1) MUTATED	52	49	95
DEL PEAK 13(5Q31.1) WILD-TYPE	67	162	61

Figure S201. Get High-res Image Gene #45: 'del_5q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q31.1' versus 'MIRSEQ_CNMF'

P value = 5.31e-10 (Fisher's exact test), Q value = 4.9e-07

Table S202. Gene #45: 'del_5q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 13(5Q31.1) MUTATED	43	127	26
DEL PEAK 13(5Q31.1) WILD-TYPE	136	104	52

Figure S202. Get High-res Image Gene #45: 'del_5q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.1e-08 (Fisher's exact test), Q value = 5.4e-05

Table S203. Gene #45: 'del_5q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
DEL PEAK 13(5Q31.1) MUTATED	15	131	50
DEL PEAK 13(5Q31.1) WILD-TYPE	36	118	138

Figure S203. Get High-res Image Gene #45: 'del_5q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q31.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.66e-06 (Fisher's exact test), Q value = 0.0037

Table S204. Gene #45: 'del_5q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
DEL PEAK 13(5Q31.1) MUTATED	42	101	27
DEL PEAK 13(5Q31.1) WILD-TYPE	113	91	51

Figure S204. Get High-res Image Gene #45: 'del_5q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.4e-08 (Fisher's exact test), Q value = 5.6e-05

Table S205. Gene #45: 'del_5q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
DEL PEAK 13(5Q31.1) MUTATED	14	104	52
DEL PEAK 13(5Q31.1) WILD-TYPE	35	84	136

Figure S205. Get High-res Image Gene #45: 'del_5q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q22.31' versus 'METHLYATION_CNMF'

P value = 6.85e-07 (Fisher's exact test), Q value = 0.00057

Table S206. Gene #47: 'del_6q22.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 15(6Q22.31) MUTATED	73	93	53
DEL PEAK 15(6Q22.31) WILD-TYPE	68	47	97

Figure S206. Get High-res Image Gene #47: 'del_6q22.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 7.37e-05 (Fisher's exact test), Q value = 0.052

Table S207. Gene #48: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 16(6Q26) MUTATED	78	84	54
DEL PEAK 16(6Q26) WILD-TYPE	63	56	96

Figure S207. Get High-res Image Gene #48: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.2' versus 'CN_CNMF'

P value = 1.81e-22 (Fisher's exact test), Q value = 1.8e-19

Table S208. Gene #49: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 17(8P23.2) MUTATED	141	58	42
DEL PEAK 17(8P23.2) WILD-TYPE	45	158	49

Figure S208. Get High-res Image Gene #49: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'RPPA_CHIERARCHICAL'

P value = 1.98e-05 (Fisher's exact test), Q value = 0.015

Table S209. Gene #49: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	106	70	59
DEL PEAK 17(8P23.2) MUTATED	68	20	29
DEL PEAK 17(8P23.2) WILD-TYPE	38	50	30

Figure S209. Get High-res Image Gene #49: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 2.68e-07 (Chi-square test), Q value = 0.00023

Table S210. Gene #49: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 17(8P23.2) MUTATED	96	39	32	50	21
DEL PEAK 17(8P23.2) WILD-TYPE	42	73	44	56	33

Figure S210. Get High-res Image Gene #49: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.05e-06 (Fisher's exact test), Q value = 0.00087

Table S211. Gene #49: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
DEL PEAK 17(8P23.2) MUTATED	80	79	79
DEL PEAK 17(8P23.2) WILD-TYPE	39	132	77

Figure S211. Get High-res Image Gene #49: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 2.61e-05 (Fisher's exact test), Q value = 0.019

Table S212. Gene #49: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 17(8P23.2) MUTATED	63	130	45
DEL PEAK 17(8P23.2) WILD-TYPE	116	101	33

Figure S212. Get High-res Image Gene #49: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000105 (Fisher's exact test), Q value = 0.073

Table S213. Gene #49: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
DEL PEAK 17(8P23.2) MUTATED	20	112	72
DEL PEAK 17(8P23.2) WILD-TYPE	29	76	116

Figure S213. Get High-res Image Gene #49: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p12' versus 'CN_CNMF'

P value = 6.05e-20 (Fisher's exact test), Q value = 5.9e-17

Table S214. Gene #50: 'del_8p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 18(8P12) MUTATED	129	51	35
DEL PEAK 18(8P12) WILD-TYPE	57	165	56

Figure S214. Get High-res Image Gene #50: 'del_8p12' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p12' versus 'MRNASEQ_CNMF'

P value = 2e-07 (Chi-square test), Q value = 0.00017

Table S215. Gene #50: 'del_8p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 18(8P12) MUTATED	89	35	29	44	16
DEL PEAK 18(8P12) WILD-TYPE	49	77	47	62	38

Figure S215. Get High-res Image Gene #50: 'del_8p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.05e-06 (Fisher's exact test), Q value = 0.00087

Table S216. Gene #50: 'del_8p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
DEL PEAK 18(8P12) MUTATED	75	70	68
DEL PEAK 18(8P12) WILD-TYPE	44	141	88

Figure S216. Get High-res Image Gene #50: 'del_8p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p12' versus 'MIRSEQ_CNMF'

P value = 0.000215 (Fisher's exact test), Q value = 0.15

Table S217. Gene #50: 'del_8p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 18(8P12) MUTATED	57	120	35
DEL PEAK 18(8P12) WILD-TYPE	122	111	43

Figure S217. Get High-res Image Gene #50: 'del_8p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p11.21' versus 'CN_CNMF'

P value = 2.18e-18 (Fisher's exact test), Q value = 2.1e-15

Table S218. Gene #51: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 19(8P11.21) MUTATED	82	28	3
DEL PEAK 19(8P11.21) WILD-TYPE	104	188	88

Figure S218. Get High-res Image Gene #51: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 8.44e-06 (Chi-square test), Q value = 0.0065

Table S219. Gene #54: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 22(9P21.3) MUTATED	73	60	64	51	27
DEL PEAK 22(9P21.3) WILD-TYPE	65	52	12	55	27

Figure S219. Get High-res Image Gene #54: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9q21.11' versus 'CN_CNMF'

P value = 4.93e-07 (Fisher's exact test), Q value = 0.00042

Table S220. Gene #55: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 23(9Q21.11) MUTATED	100	82	64
DEL PEAK 23(9Q21.11) WILD-TYPE	86	134	27

Figure S220. Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_9q21.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.03e-07 (Fisher's exact test), Q value = 9e-05

Table S221. Gene #55: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
DEL PEAK 23(9Q21.11) MUTATED	53	84	107
DEL PEAK 23(9Q21.11) WILD-TYPE	66	127	49

Figure S221. Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.077

Table S222. Gene #55: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 23(9Q21.11) MUTATED	67	128	48
DEL PEAK 23(9Q21.11) WILD-TYPE	112	103	30

Figure S222. Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9q21.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.52e-05 (Fisher's exact test), Q value = 0.046

Table S223. Gene #55: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
DEL PEAK 23(9Q21.11) MUTATED	22	148	73
DEL PEAK 23(9Q21.11) WILD-TYPE	29	101	115

Figure S223. Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.07e-05 (Fisher's exact test), Q value = 0.03

Table S224. Gene #55: 'del_9q21.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
DEL PEAK 23(9Q21.11) MUTATED	26	113	70
DEL PEAK 23(9Q21.11) WILD-TYPE	23	75	118

Figure S224. Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 5.61e-05 (Fisher's exact test), Q value = 0.04

Table S225. Gene #56: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 24(10P15.3) MUTATED	62	33	27
DEL PEAK 24(10P15.3) WILD-TYPE	124	183	64

Figure S225. Get High-res Image Gene #56: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q26.3' versus 'CN_CNMF'

P value = 1.82e-07 (Fisher's exact test), Q value = 0.00016

Table S226. Gene #57: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 25(10Q26.3) MUTATED	77	36	29
DEL PEAK 25(10Q26.3) WILD-TYPE	109	180	62

Figure S226. Get High-res Image Gene #57: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 2.79e-05 (Chi-square test), Q value = 0.021

Table S227. Gene #57: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 25(10Q26.3) MUTATED	59	19	13	34	16
DEL PEAK 25(10Q26.3) WILD-TYPE	79	93	63	72	38

Figure S227. Get High-res Image Gene #57: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.65e-05 (Fisher's exact test), Q value = 0.012

Table S228. Gene #57: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
DEL PEAK 25(10Q26.3) MUTATED	25	61	34
DEL PEAK 25(10Q26.3) WILD-TYPE	130	131	44

Figure S228. Get High-res Image Gene #57: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000104 (Fisher's exact test), Q value = 0.072

Table S229. Gene #57: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
DEL PEAK 25(10Q26.3) MUTATED	20	66	34
DEL PEAK 25(10Q26.3) WILD-TYPE	29	122	154

Figure S229. Get High-res Image Gene #57: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 6.4e-07 (Fisher's exact test), Q value = 0.00054

Table S230. Gene #58: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 26(11P15.5) MUTATED	72	34	29
DEL PEAK 26(11P15.5) WILD-TYPE	114	182	62

Figure S230. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.7e-08 (Fisher's exact test), Q value = 3.3e-05

Table S231. Gene #58: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
DEL PEAK 26(11P15.5) MUTATED	35	31	65
DEL PEAK 26(11P15.5) WILD-TYPE	84	180	91

Figure S231. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.07

Table S232. Gene #58: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 26(11P15.5) MUTATED	33	84	16
DEL PEAK 26(11P15.5) WILD-TYPE	146	147	62

Figure S232. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.91e-05 (Fisher's exact test), Q value = 0.014

Table S233. Gene #58: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
DEL PEAK 26(11P15.5) MUTATED	5	89	39
DEL PEAK 26(11P15.5) WILD-TYPE	46	160	149

Figure S233. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.45e-06 (Fisher's exact test), Q value = 0.0043

Table S234. Gene #58: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
DEL PEAK 26(11P15.5) MUTATED	27	75	14
DEL PEAK 26(11P15.5) WILD-TYPE	128	117	64

Figure S234. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11q23.2' versus 'CN_CNMF'

P value = 1.05e-05 (Fisher's exact test), Q value = 0.008

Table S235. Gene #59: 'del_11q23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 27(11Q23.2) MUTATED	41	36	39
DEL PEAK 27(11Q23.2) WILD-TYPE	145	180	52

Figure S235. Get High-res Image Gene #59: 'del_11q23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q23.2' versus 'MRNASEQ_CNMF'

P value = 7.22e-05 (Chi-square test), Q value = 0.051

Table S236. Gene #59: 'del_11q23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 27(11Q23.2) MUTATED	26	13	25	38	10
DEL PEAK 27(11Q23.2) WILD-TYPE	112	99	51	68	44

Figure S236. Get High-res Image Gene #59: 'del_11q23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q25' versus 'CN_CNMF'

P value = 0.000258 (Fisher's exact test), Q value = 0.17

Table S237. Gene #60: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 28(11Q25) MUTATED	44	34	34
DEL PEAK 28(11Q25) WILD-TYPE	142	182	57

Figure S237. Get High-res Image Gene #60: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q25' versus 'MRNASEQ_CNMF'

P value = 0.000365 (Chi-square test), Q value = 0.24

Table S238. Gene #60: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 28(11Q25) MUTATED	24	14	26	34	10
DEL PEAK 28(11Q25) WILD-TYPE	114	98	50	72	44

Figure S238. Get High-res Image Gene #60: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12q12' versus 'CN_CNMF'

P value = 0.000192 (Fisher's exact test), Q value = 0.13

Table S239. Gene #62: 'del_12q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 30(12Q12) MUTATED	53	31	10
DEL PEAK 30(12Q12) WILD-TYPE	133	185	81

Figure S239. Get High-res Image Gene #62: 'del_12q12' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q24.33' versus 'CN_CNMF'

P value = 2.15e-05 (Fisher's exact test), Q value = 0.016

Table S240. Gene #63: 'del_12q24.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 31(12Q24.33) MUTATED	64	50	9
DEL PEAK 31(12Q24.33) WILD-TYPE	122	166	82

Figure S240. Get High-res Image Gene #63: 'del_12q24.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q24.33' versus 'MRNASEQ_CNMF'

P value = 4.97e-05 (Chi-square test), Q value = 0.036

Table S241. Gene #63: 'del_12q24.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 31(12Q24.33) MUTATED	46	35	7	16	18
DEL PEAK 31(12Q24.33) WILD-TYPE	92	77	69	90	36

Figure S241. Get High-res Image Gene #63: 'del_12q24.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q12.11' versus 'CN_CNMF'

P value = 1.4e-20 (Fisher's exact test), Q value = 1.4e-17

Table S242. Gene #64: 'del_13q12.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 32(13Q12.11) MUTATED	142	72	68
DEL PEAK 32(13Q12.11) WILD-TYPE	44	144	23

Figure S242. Get High-res Image Gene #64: 'del_13q12.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q12.11' versus 'RPPA_CHIERARCHICAL'

P value = 1.12e-06 (Fisher's exact test), Q value = 0.00092

Table S243. Gene #64: 'del_13q12.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	106	70	59
DEL PEAK 32(13Q12.11) MUTATED	77	23	33
DEL PEAK 32(13Q12.11) WILD-TYPE	29	47	26

Figure S243. Get High-res Image Gene #64: 'del_13q12.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_13q12.11' versus 'MRNASEQ_CNMF'

P value = 2.05e-09 (Chi-square test), Q value = 1.9e-06

Table S244. Gene #64: 'del_13q12.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 32(13Q12.11) MUTATED	100	45	30	76	27
DEL PEAK 32(13Q12.11) WILD-TYPE	38	67	46	30	27

Figure S244. Get High-res Image Gene #64: 'del_13q12.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q12.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.14e-08 (Fisher's exact test), Q value = 8e-05

Table S245. Gene #64: 'del_13q12.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
DEL PEAK 32(13Q12.11) MUTATED	83	90	105
DEL PEAK 32(13Q12.11) WILD-TYPE	36	121	51

Figure S245. Get High-res Image Gene #64: 'del_13q12.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q12.13' versus 'CN_CNMF'

P value = 3.01e-22 (Fisher's exact test), Q value = 3e-19

Table S246. Gene #65: 'del_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 33(13Q12.13) MUTATED	144	70	68
DEL PEAK 33(13Q12.13) WILD-TYPE	42	146	23

Figure S246. Get High-res Image Gene #65: 'del_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q12.13' versus 'RPPA_CHIERARCHICAL'

P value = 3.86e-07 (Fisher's exact test), Q value = 0.00033

Table S247. Gene #65: 'del_13q12.13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	106	70	59
DEL PEAK 33(13Q12.13) MUTATED	77	22	34
DEL PEAK 33(13Q12.13) WILD-TYPE	29	48	25

Figure S247. Get High-res Image Gene #65: 'del_13q12.13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_13q12.13' versus 'MRNASEQ_CNMF'

P value = 6.3e-09 (Chi-square test), Q value = 5.7e-06

Table S248. Gene #65: 'del_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 33(13Q12.13) MUTATED	99	47	29	76	27
DEL PEAK 33(13Q12.13) WILD-TYPE	39	65	47	30	27

Figure S248. Get High-res Image Gene #65: 'del_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q12.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.23e-07 (Fisher's exact test), Q value = 0.00052

Table S249. Gene #65: 'del_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
DEL PEAK 33(13Q12.13) MUTATED	83	92	103
DEL PEAK 33(13Q12.13) WILD-TYPE	36	119	53

Figure S249. Get High-res Image Gene #65: 'del_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 2.32e-21 (Fisher's exact test), Q value = 2.3e-18

Table S250. Gene #66: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 34(13Q14.2) MUTATED	139	66	66
DEL PEAK 34(13Q14.2) WILD-TYPE	47	150	25

Figure S250. Get High-res Image Gene #66: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'RPPA_CHIERARCHICAL'

P value = 4.4e-07 (Fisher's exact test), Q value = 0.00037

Table S251. Gene #66: 'del_13q14.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	106	70	59
DEL PEAK 34(13Q14.2) MUTATED	72	19	34
DEL PEAK 34(13Q14.2) WILD-TYPE	34	51	25

Figure S251. Get High-res Image Gene #66: 'del_13q14.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 9.54e-10 (Chi-square test), Q value = 8.8e-07

Table S252. Gene #66: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 34(13Q14.2) MUTATED	98	43	28	74	25
DEL PEAK 34(13Q14.2) WILD-TYPE	40	69	48	32	29

Figure S252. Get High-res Image Gene #66: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.54e-08 (Fisher's exact test), Q value = 5.7e-05

Table S253. Gene #66: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
DEL PEAK 34(13Q14.2) MUTATED	84	86	98
DEL PEAK 34(13Q14.2) WILD-TYPE	35	125	58

Figure S253. Get High-res Image Gene #66: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q34' versus 'CN_CNMF'

P value = 3.58e-14 (Fisher's exact test), Q value = 3.4e-11

Table S254. Gene #67: 'del_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 35(13Q34) MUTATED	114	59	59
DEL PEAK 35(13Q34) WILD-TYPE	72	157	32

Figure S254. Get High-res Image Gene #67: 'del_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q34' versus 'RPPA_CHIERARCHICAL'

P value = 1.71e-05 (Fisher's exact test), Q value = 0.013

Table S255. Gene #67: 'del_13q34' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	106	70	59
DEL PEAK 35(13Q34) MUTATED	58	15	31
DEL PEAK 35(13Q34) WILD-TYPE	48	55	28

Figure S255. Get High-res Image Gene #67: 'del_13q34' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_13q34' versus 'MRNASEQ_CNMF'

P value = 5e-06 (Chi-square test), Q value = 0.004

Table S256. Gene #67: 'del_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 35(13Q34) MUTATED	80	38	25	65	22
DEL PEAK 35(13Q34) WILD-TYPE	58	74	51	41	32

Figure S256. Get High-res Image Gene #67: 'del_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.82e-06 (Fisher's exact test), Q value = 0.0031

Table S257. Gene #67: 'del_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
DEL PEAK 35(13Q34) MUTATED	71	73	86
DEL PEAK 35(13Q34) WILD-TYPE	48	138	70

Figure S257. Get High-res Image Gene #67: 'del_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q11.2' versus 'CN_CNMF'

P value = 1.31e-10 (Fisher's exact test), Q value = 1.2e-07

Table S258. Gene #69: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 37(15Q11.2) MUTATED	122	74	57
DEL PEAK 37(15Q11.2) WILD-TYPE	64	142	34

Figure S258. Get High-res Image Gene #69: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q11.2' versus 'MRNASEQ_CNMF'

P value = 5.61e-13 (Chi-square test), Q value = 5.4e-10

Table S259. Gene #69: 'del_15q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 37(15Q11.2) MUTATED	96	43	15	68	26
DEL PEAK 37(15Q11.2) WILD-TYPE	42	69	61	38	28

Figure S259. Get High-res Image Gene #69: 'del_15q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.24e-06 (Fisher's exact test), Q value = 0.0018

Table S260. Gene #69: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
DEL PEAK 37(15Q11.2) MUTATED	83	86	79
DEL PEAK 37(15Q11.2) WILD-TYPE	36	125	77

Figure S260. Get High-res Image Gene #69: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_CNMF'

P value = 3.38e-05 (Fisher's exact test), Q value = 0.025

Table S261. Gene #69: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 37(15Q11.2) MUTATED	68	136	47
DEL PEAK 37(15Q11.2) WILD-TYPE	111	95	31

Figure S261. Get High-res Image Gene #69: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 6.17e-06 (Fisher's exact test), Q value = 0.0048

Table S262. Gene #70: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 38(16Q23.1) MUTATED	81	48	38
DEL PEAK 38(16Q23.1) WILD-TYPE	105	168	53

Figure S262. Get High-res Image Gene #70: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 3.87e-07 (Chi-square test), Q value = 0.00033

Table S263. Gene #70: 'del_16q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 38(16Q23.1) MUTATED	69	19	26	40	11
DEL PEAK 38(16Q23.1) WILD-TYPE	69	93	50	66	43

Figure S263. Get High-res Image Gene #70: 'del_16q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.01e-09 (Fisher's exact test), Q value = 5.4e-06

Table S264. Gene #70: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
DEL PEAK 38(16Q23.1) MUTATED	63	43	59
DEL PEAK 38(16Q23.1) WILD-TYPE	56	168	97

Figure S264. Get High-res Image Gene #70: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.3' versus 'CN_CNMF'

P value = 6.87e-18 (Fisher's exact test), Q value = 6.7e-15

Table S265. Gene #71: 'del_17p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 39(17P13.3) MUTATED	142	71	52
DEL PEAK 39(17P13.3) WILD-TYPE	44	145	39

Figure S265. Get High-res Image Gene #71: 'del_17p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p13.3' versus 'METHLYATION_CNMF'

P value = 5.27e-05 (Fisher's exact test), Q value = 0.038

Table S266. Gene #71: 'del_17p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 39(17P13.3) MUTATED	73	94	62
DEL PEAK 39(17P13.3) WILD-TYPE	68	46	88

Figure S266. Get High-res Image Gene #71: 'del_17p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p13.3' versus 'MRNASEQ_CNMF'

P value = 1.76e-06 (Chi-square test), Q value = 0.0014

Table S267. Gene #71: 'del_17p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 39(17P13.3) MUTATED	98	42	36	61	24
DEL PEAK 39(17P13.3) WILD-TYPE	40	70	40	45	30

Figure S267. Get High-res Image Gene #71: 'del_17p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.48e-06 (Fisher's exact test), Q value = 0.0058

Table S268. Gene #71: 'del_17p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
DEL PEAK 39(17P13.3) MUTATED	84	91	86
DEL PEAK 39(17P13.3) WILD-TYPE	35	120	70

Figure S268. Get High-res Image Gene #71: 'del_17p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p11.2' versus 'CN_CNMF'

P value = 1.57e-16 (Fisher's exact test), Q value = 1.5e-13

Table S269. Gene #72: 'del_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 40(17P11.2) MUTATED	119	50	47
DEL PEAK 40(17P11.2) WILD-TYPE	67	166	44

Figure S269. Get High-res Image Gene #72: 'del_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p11.2' versus 'METHLYATION_CNMF'

P value = 3.36e-07 (Fisher's exact test), Q value = 0.00029

Table S270. Gene #72: 'del_17p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 40(17P11.2) MUTATED	52	86	47
DEL PEAK 40(17P11.2) WILD-TYPE	89	54	103

Figure S270. Get High-res Image Gene #72: 'del_17p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p11.2' versus 'MRNASEQ_CNMF'

P value = 6.4e-06 (Chi-square test), Q value = 0.005

Table S271. Gene #72: 'del_17p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 40(17P11.2) MUTATED	84	32	32	48	18
DEL PEAK 40(17P11.2) WILD-TYPE	54	80	44	58	36

Figure S271. Get High-res Image Gene #72: 'del_17p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.17e-06 (Fisher's exact test), Q value = 0.0041

Table S272. Gene #72: 'del_17p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
DEL PEAK 40(17P11.2) MUTATED	74	72	68
DEL PEAK 40(17P11.2) WILD-TYPE	45	139	88

Figure S272. Get High-res Image Gene #72: 'del_17p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.32' versus 'CN_CNMF'

P value = 5.38e-13 (Fisher's exact test), Q value = 5.1e-10

Table S273. Gene #73: 'del_18q21.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 41(18Q21.32) MUTATED	131	77	33
DEL PEAK 41(18Q21.32) WILD-TYPE	55	139	58

Figure S273. Get High-res Image Gene #73: 'del_18q21.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q21.32' versus 'MRNASEQ_CNMF'

P value = 2.19e-05 (Chi-square test), Q value = 0.016

Table S274. Gene #73: 'del_18q21.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 41(18Q21.32) MUTATED	91	42	40	42	23
DEL PEAK 41(18Q21.32) WILD-TYPE	47	70	36	64	31

Figure S274. Get High-res Image Gene #73: 'del_18q21.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q21.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000195 (Fisher's exact test), Q value = 0.13

Table S275. Gene #73: 'del_18q21.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
DEL PEAK 41(18Q21.32) MUTATED	77	87	74
DEL PEAK 41(18Q21.32) WILD-TYPE	42	124	82

Figure S275. Get High-res Image Gene #73: 'del_18q21.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q23' versus 'CN_CNMF'

P value = 4.65e-15 (Fisher's exact test), Q value = 4.5e-12

Table S276. Gene #74: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 42(18Q23) MUTATED	133	75	30
DEL PEAK 42(18Q23) WILD-TYPE	53	141	61

Figure S276. Get High-res Image Gene #74: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q23' versus 'MRNASEQ_CNMF'

P value = 2.18e-06 (Chi-square test), Q value = 0.0018

Table S277. Gene #74: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 42(18Q23) MUTATED	92	42	40	38	23
DEL PEAK 42(18Q23) WILD-TYPE	46	70	36	68	31

Figure S277. Get High-res Image Gene #74: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.55e-05 (Fisher's exact test), Q value = 0.026

Table S278. Gene #74: 'del_18q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
DEL PEAK 42(18Q23) MUTATED	78	84	73
DEL PEAK 42(18Q23) WILD-TYPE	41	127	83

Figure S278. Get High-res Image Gene #74: 'del_18q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 7.85e-07 (Fisher's exact test), Q value = 0.00065

Table S279. Gene #75: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 43(19P13.3) MUTATED	105	92	68
DEL PEAK 43(19P13.3) WILD-TYPE	81	124	23

Figure S279. Get High-res Image Gene #75: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 2.9e-11 (Fisher's exact test), Q value = 2.7e-08

Table S280. Gene #75: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 43(19P13.3) MUTATED	108	64	58
DEL PEAK 43(19P13.3) WILD-TYPE	33	76	92

Figure S280. Get High-res Image Gene #75: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 7.58e-07 (Chi-square test), Q value = 0.00063

Table S281. Gene #75: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 43(19P13.3) MUTATED	70	49	50	76	17
DEL PEAK 43(19P13.3) WILD-TYPE	68	63	26	30	37

Figure S281. Get High-res Image Gene #75: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.89e-09 (Fisher's exact test), Q value = 1.7e-06

Table S282. Gene #75: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
DEL PEAK 43(19P13.3) MUTATED	55	91	116
DEL PEAK 43(19P13.3) WILD-TYPE	64	120	40

Figure S282. Get High-res Image Gene #75: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 1.35e-05 (Fisher's exact test), Q value = 0.01

Table S283. Gene #75: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 43(19P13.3) MUTATED	78	149	33
DEL PEAK 43(19P13.3) WILD-TYPE	101	82	45

Figure S283. Get High-res Image Gene #75: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.77e-09 (Fisher's exact test), Q value = 5.2e-06

Table S284. Gene #75: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
DEL PEAK 43(19P13.3) MUTATED	17	166	77
DEL PEAK 43(19P13.3) WILD-TYPE	34	83	111

Figure S284. Get High-res Image Gene #75: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000118 (Fisher's exact test), Q value = 0.082

Table S285. Gene #75: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
DEL PEAK 43(19P13.3) MUTATED	71	125	33
DEL PEAK 43(19P13.3) WILD-TYPE	84	67	45

Figure S285. Get High-res Image Gene #75: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.02e-08 (Fisher's exact test), Q value = 7e-05

Table S286. Gene #75: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
DEL PEAK 43(19P13.3) MUTATED	18	130	81
DEL PEAK 43(19P13.3) WILD-TYPE	31	58	107

Figure S286. Get High-res Image Gene #75: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.2' versus 'CN_CNMF'

P value = 3.24e-07 (Fisher's exact test), Q value = 0.00028

Table S287. Gene #76: 'del_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 44(19P13.2) MUTATED	107	87	66
DEL PEAK 44(19P13.2) WILD-TYPE	79	129	25

Figure S287. Get High-res Image Gene #76: 'del_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.2' versus 'METHLYATION_CNMF'

P value = 3.17e-12 (Fisher's exact test), Q value = 3e-09

Table S288. Gene #76: 'del_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 44(19P13.2) MUTATED	107	67	52
DEL PEAK 44(19P13.2) WILD-TYPE	34	73	98

Figure S288. Get High-res Image Gene #76: 'del_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p13.2' versus 'MRNASEQ_CNMF'

P value = 1.07e-06 (Chi-square test), Q value = 0.00089

Table S289. Gene #76: 'del_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 44(19P13.2) MUTATED	71	47	45	77	17
DEL PEAK 44(19P13.2) WILD-TYPE	67	65	31	29	37

Figure S289. Get High-res Image Gene #76: 'del_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.97e-08 (Fisher's exact test), Q value = 1.8e-05

Table S290. Gene #76: 'del_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
DEL PEAK 44(19P13.2) MUTATED	58	87	112
DEL PEAK 44(19P13.2) WILD-TYPE	61	124	44

Figure S290. Get High-res Image Gene #76: 'del_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.2' versus 'MIRSEQ_CNMF'

P value = 1.03e-05 (Fisher's exact test), Q value = 0.0079

Table S291. Gene #76: 'del_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 44(19P13.2) MUTATED	76	147	32
DEL PEAK 44(19P13.2) WILD-TYPE	103	84	46

Figure S291. Get High-res Image Gene #76: 'del_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.61e-08 (Fisher's exact test), Q value = 5e-05

Table S292. Gene #76: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
DEL PEAK 44(19P13.2) MUTATED	16	161	78
DEL PEAK 44(19P13.2) WILD-TYPE	35	88	110

Figure S292. Get High-res Image Gene #76: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.61e-05 (Fisher's exact test), Q value = 0.047

Table S293. Gene #76: 'del_19p13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
DEL PEAK 44(19P13.2) MUTATED	68	124	33
DEL PEAK 44(19P13.2) WILD-TYPE	87	68	45

Figure S293. Get High-res Image Gene #76: 'del_19p13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.11e-07 (Fisher's exact test), Q value = 0.00035

Table S294. Gene #76: 'del_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
DEL PEAK 44(19P13.2) MUTATED	19	127	79
DEL PEAK 44(19P13.2) WILD-TYPE	30	61	109

Figure S294. Get High-res Image Gene #76: 'del_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.33' versus 'CN_CNMF'

P value = 1.2e-08 (Fisher's exact test), Q value = 1.1e-05

Table S295. Gene #77: 'del_19q13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 45(19Q13.33) MUTATED	97	51	39
DEL PEAK 45(19Q13.33) WILD-TYPE	89	165	52

Figure S295. Get High-res Image Gene #77: 'del_19q13.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q13.33' versus 'METHLYATION_CNMF'

P value = 1.14e-06 (Fisher's exact test), Q value = 0.00094

Table S296. Gene #77: 'del_19q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 45(19Q13.33) MUTATED	69	56	31
DEL PEAK 45(19Q13.33) WILD-TYPE	72	84	119

Figure S296. Get High-res Image Gene #77: 'del_19q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000278 (Fisher's exact test), Q value = 0.19

Table S297. Gene #77: 'del_19q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
DEL PEAK 45(19Q13.33) MUTATED	55	59	71
DEL PEAK 45(19Q13.33) WILD-TYPE	64	152	85

Figure S297. Get High-res Image Gene #77: 'del_19q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.33' versus 'MIRSEQ_CNMF'

P value = 0.000211 (Fisher's exact test), Q value = 0.14

Table S298. Gene #77: 'del_19q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 45(19Q13.33) MUTATED	47	106	30
DEL PEAK 45(19Q13.33) WILD-TYPE	132	125	48

Figure S298. Get High-res Image Gene #77: 'del_19q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19q13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.73e-06 (Fisher's exact test), Q value = 0.0038

Table S299. Gene #77: 'del_19q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
DEL PEAK 45(19Q13.33) MUTATED	17	119	47
DEL PEAK 45(19Q13.33) WILD-TYPE	34	130	141

Figure S299. Get High-res Image Gene #77: 'del_19q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_20p13' versus 'CN_CNMF'

P value = 5.42e-06 (Fisher's exact test), Q value = 0.0043

Table S300. Gene #78: 'del_20p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 46(20P13) MUTATED	71	39	16
DEL PEAK 46(20P13) WILD-TYPE	115	177	75

Figure S300. Get High-res Image Gene #78: 'del_20p13' versus Molecular Subtype #3: 'CN_CNMF'

'del_20p13' versus 'METHLYATION_CNMF'

P value = 0.000145 (Fisher's exact test), Q value = 0.1

Table S301. Gene #78: 'del_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 46(20P13) MUTATED	25	54	32
DEL PEAK 46(20P13) WILD-TYPE	116	86	118

Figure S301. Get High-res Image Gene #78: 'del_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_20p13' versus 'MRNASEQ_CNMF'

P value = 2.45e-05 (Chi-square test), Q value = 0.018

Table S302. Gene #78: 'del_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 46(20P13) MUTATED	56	23	21	14	12
DEL PEAK 46(20P13) WILD-TYPE	82	89	55	92	42

Figure S302. Get High-res Image Gene #78: 'del_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_20p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.62e-05 (Fisher's exact test), Q value = 0.061

Table S303. Gene #78: 'del_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
DEL PEAK 46(20P13) MUTATED	49	41	36
DEL PEAK 46(20P13) WILD-TYPE	70	170	120

Figure S303. Get High-res Image Gene #78: 'del_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_21q11.2' versus 'CN_CNMF'

P value = 7.56e-07 (Fisher's exact test), Q value = 0.00063

Table S304. Gene #80: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 48(21Q11.2) MUTATED	54	60	53
DEL PEAK 48(21Q11.2) WILD-TYPE	132	156	38

Figure S304. Get High-res Image Gene #80: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q11.2' versus 'MRNASEQ_CNMF'

P value = 1.39e-10 (Chi-square test), Q value = 1.3e-07

Table S305. Gene #80: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 48(21Q11.2) MUTATED	49	13	30	59	12
DEL PEAK 48(21Q11.2) WILD-TYPE	89	99	46	47	42

Figure S305. Get High-res Image Gene #80: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_21q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.03e-09 (Fisher's exact test), Q value = 9.5e-07

Table S306. Gene #80: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
DEL PEAK 48(21Q11.2) MUTATED	40	42	81
DEL PEAK 48(21Q11.2) WILD-TYPE	79	169	75

Figure S306. Get High-res Image Gene #80: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_CNMF'

P value = 1.45e-05 (Fisher's exact test), Q value = 0.011

Table S307. Gene #80: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 48(21Q11.2) MUTATED	41	102	21
DEL PEAK 48(21Q11.2) WILD-TYPE	138	129	57

Figure S307. Get High-res Image Gene #80: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_21q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.12e-07 (Fisher's exact test), Q value = 9.7e-05

Table S308. Gene #80: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
DEL PEAK 48(21Q11.2) MUTATED	10	113	41
DEL PEAK 48(21Q11.2) WILD-TYPE	41	136	147

Figure S308. Get High-res Image Gene #80: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 1.3e-12 (Fisher's exact test), Q value = 1.2e-09

Table S309. Gene #81: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 49(22Q13.32) MUTATED	110	66	64
DEL PEAK 49(22Q13.32) WILD-TYPE	76	150	27

Figure S309. Get High-res Image Gene #81: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.32' versus 'METHLYATION_CNMF'

P value = 4.7e-05 (Fisher's exact test), Q value = 0.034

Table S310. Gene #81: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 49(22Q13.32) MUTATED	74	84	52
DEL PEAK 49(22Q13.32) WILD-TYPE	67	56	98

Figure S310. Get High-res Image Gene #81: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 2.61e-11 (Chi-square test), Q value = 2.5e-08

Table S311. Gene #81: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 49(22Q13.32) MUTATED	80	33	36	74	12
DEL PEAK 49(22Q13.32) WILD-TYPE	58	79	40	32	42

Figure S311. Get High-res Image Gene #81: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.26e-12 (Fisher's exact test), Q value = 4e-09

Table S312. Gene #81: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
DEL PEAK 49(22Q13.32) MUTATED	67	64	104
DEL PEAK 49(22Q13.32) WILD-TYPE	52	147	52

Figure S312. Get High-res Image Gene #81: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_CNMF'

P value = 2.54e-06 (Fisher's exact test), Q value = 0.002

Table S313. Gene #81: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 49(22Q13.32) MUTATED	62	138	37
DEL PEAK 49(22Q13.32) WILD-TYPE	117	93	41

Figure S313. Get High-res Image Gene #81: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_22q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.04e-07 (Fisher's exact test), Q value = 9e-05

Table S314. Gene #81: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
DEL PEAK 49(22Q13.32) MUTATED	17	152	68
DEL PEAK 49(22Q13.32) WILD-TYPE	34	97	120

Figure S314. Get High-res Image Gene #81: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.15e-05 (Fisher's exact test), Q value = 0.0088

Table S315. Gene #81: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
DEL PEAK 49(22Q13.32) MUTATED	59	117	29
DEL PEAK 49(22Q13.32) WILD-TYPE	96	75	49

Figure S315. Get High-res Image Gene #81: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_22q13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.55e-06 (Fisher's exact test), Q value = 0.0013

Table S316. Gene #81: 'del_22q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
DEL PEAK 49(22Q13.32) MUTATED	19	117	69
DEL PEAK 49(22Q13.32) WILD-TYPE	30	71	119

Figure S316. Get High-res Image Gene #81: 'del_22q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp22.2' versus 'CN_CNMF'

P value = 1.29e-08 (Fisher's exact test), Q value = 1.2e-05

Table S317. Gene #82: 'del_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
DEL PEAK 50(XP22.2) MUTATED	79	34	22
DEL PEAK 50(XP22.2) WILD-TYPE	107	182	69

Figure S317. Get High-res Image Gene #82: 'del_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_xp22.2' versus 'MRNASEQ_CNMF'

P value = 0.000196 (Chi-square test), Q value = 0.13

Table S318. Gene #82: 'del_xp22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
DEL PEAK 50(XP22.2) MUTATED	58	28	13	25	10
DEL PEAK 50(XP22.2) WILD-TYPE	80	84	63	81	44

Figure S318. Get High-res Image Gene #82: 'del_xp22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_xp22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.27e-05 (Fisher's exact test), Q value = 0.017

Table S319. Gene #82: 'del_xp22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
DEL PEAK 50(XP22.2) MUTATED	53	46	35
DEL PEAK 50(XP22.2) WILD-TYPE	66	165	121

Figure S319. Get High-res Image Gene #82: 'del_xp22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = LUAD-TP.transferedmergedcluster.txt
Number of patients = 493
Number of significantly focal cnvs = 82
Number of molecular subtypes = 12
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[3] 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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