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

Lung Squamous Cell Carcinoma (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1Z31XKZ

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 83 focal events and 12 molecular subtypes across 501 patients, 209 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q21.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_2p16.1 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_2q31.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_3q26.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5p15.33 cnv correlated to 'CN_CNMF'.
amp_5p12 cnv correlated to 'CN_CNMF'.
amp_6p12.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6q12 cnv correlated to 'CN_CNMF'.
amp_7p11.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
amp_7q21.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
amp_8p11.23 cnv correlated to 'CN_CNMF'.
amp_11q13.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_12p13.33 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
amp_12q15 cnv correlated to 'CN_CNMF'.
amp_15q26.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
amp_17q25.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_18p11.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_18q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19q12 cnv correlated to 'CN_CNMF'.
amp_19q13.2 cnv correlated to 'CN_CNMF'.
amp_20p12.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_20q11.21 cnv correlated to 'CN_CNMF'.
amp_22q11.21 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_1p36.11 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p13.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.
del_2q37.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p25.3 cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CHIERARCHICAL'.
del_3p13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p12.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_3p12.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_4p15.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q22.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_4q32.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q35.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_5q31.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_6p25.3 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_6q22.31 cnv correlated to 'CN_CNMF'.
del_6q26 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_7q36.3 cnv correlated to 'MRNASEQ_CNMF'.
del_8p23.2 cnv correlated to 'CN_CNMF'.
del_9p23 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_9p21.3 cnv correlated to 'CN_CNMF'.
del_9p21.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_9q21.11 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_10p15.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p15.5 cnv correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.
del_14q11.2 cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_16q23.1 cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17q11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_17q25.3 cnv correlated to 'CN_CNMF'.
del_19p13.3 cnv correlated to 'CN_CNMF'.
del_19q13.32 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_21q11.2 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
del_21q22.3 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
del_22q11.21 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
del_22q13.32 cnv correlated to 'MRNA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_xp22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp11.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xq22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 83 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, 209 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
del 1p36 11	228 (46%)	273	3e-05 (0.026)	1e-05 (0.00996)	1e-05 (0.00996)	1e-05 (0.00996)	0.0547 (1.00)	0.00352 (1.00)	1e-05 (0.00996)	1e-05 (0.00996)	1e-05 (0.00996)	1e-05 (0.00996)	1e-05 (0.00996)	1e-05 (0.00996)
del 1p13 1	221 (44%)	280	0.00015 (0.124)	3e-05 (0.026)	1e-05 (0.00996)	1e-05 (0.00996)	0.0241 (1.00)	0.207 (1.00)	1e-05 (0.00996)	1e-05 (0.00996)	1e-05 (0.00996)	1e-05 (0.00996)	0.00026 (0.208)	1e-05 (0.00996)
del 2q37 1	159 (32%)	342	0.00297 (1.00)	0.00059 (0.452)	1e-05 (0.00996)	1e-05 (0.00996)	0.385 (1.00)	0.189 (1.00)	1e-05 (0.00996)	2e-05 (0.0176)	1e-05 (0.00996)	3e-05 (0.026)	1e-05 (0.00996)	1e-05 (0.00996)
del 4p15 2	317 (63%)	184	0.00021 (0.171)	6e-05 (0.0511)	1e-05 (0.00996)	1e-05 (0.00996)	0.776 (1.00)	0.0631 (1.00)	0.00016 (0.132)	1e-05 (0.00996)	0.00225 (1.00)	0.0513 (1.00)	0.00011 (0.0923)	3e-05 (0.026)
del 9q21 11	251 (50%)	250	0.00024 (0.194)	5e-05 (0.0426)	1e-05 (0.00996)	1e-05 (0.00996)	0.556 (1.00)	0.145 (1.00)	1e-05 (0.00996)	1e-05 (0.00996)	1e-05 (0.00996)	1e-05 (0.00996)	0.0511 (1.00)	0.00906 (1.00)
amp 2p16 1	275 (55%)	226	0.00143 (1.00)	0.00028 (0.223)	1e-05 (0.00996)	2e-05 (0.0176)	0.95 (1.00)	0.672 (1.00)	1e-05 (0.00996)	2e-05 (0.0176)	0.00029 (0.23)	0.00067 (0.511)	0.0314 (1.00)	3e-05 (0.026)
amp 3q26 33	452 (90%)	49	0.00034 (0.267)	0.00055 (0.423)	1e-05 (0.00996)	1e-05 (0.00996)	0.264 (1.00)	0.0325 (1.00)	1e-05 (0.00996)	1e-05 (0.00996)	0.0001 (0.0842)	1e-05 (0.00996)	0.0187 (1.00)	7e-05 (0.0593)
amp 1q21 2	258 (51%)	243	0.039 (1.00)	0.101 (1.00)	1e-05 (0.00996)	2e-05 (0.0176)	0.18 (1.00)	0.0738 (1.00)	1e-05 (0.00996)	1e-05 (0.00996)	1e-05 (0.00996)	1e-05 (0.00996)	0.00112 (0.824)	0.00378 (1.00)
del 10p15 2	219 (44%)	282	0.262 (1.00)	0.467 (1.00)	1e-05 (0.00996)	1e-05 (0.00996)	0.146 (1.00)	0.142 (1.00)	1e-05 (0.00996)	0.00015 (0.124)	4e-05 (0.0343)	1e-05 (0.00996)	0.0241 (1.00)	0.01 (1.00)
del 10q23 31	268 (53%)	233	0.00323 (1.00)	0.00097 (0.723)	1e-05 (0.00996)	1e-05 (0.00996)	0.149 (1.00)	0.248 (1.00)	1e-05 (0.00996)	1e-05 (0.00996)	0.00118 (0.861)	4e-05 (0.0343)	0.0216 (1.00)	0.00019 (0.155)
del 17q11 2	132 (26%)	369	0.0001 (0.0842)	6e-05 (0.0511)	1e-05 (0.00996)	1e-05 (0.00996)	0.389 (1.00)	0.564 (1.00)	1e-05 (0.00996)	1e-05 (0.00996)	0.00416 (1.00)	0.00116 (0.849)	0.274 (1.00)	0.00043 (0.335)
del xp11 3	149 (30%)	352	0.0972 (1.00)	0.4 (1.00)	1e-05 (0.00996)	1e-05 (0.00996)	0.107 (1.00)	0.065 (1.00)	0.00016 (0.132)	0.00229 (1.00)	0.00012 (0.1)	0.00057 (0.438)	2e-05 (0.0176)	1e-05 (0.00996)
amp 7q21 2	264 (53%)	237	0.104 (1.00)	0.0154 (1.00)	1e-05 (0.00996)	1e-05 (0.00996)	0.0755 (1.00)	0.555 (1.00)	1e-05 (0.00996)	1e-05 (0.00996)	0.00022 (0.178)	0.00084 (0.634)	0.00175 (1.00)	0.00089 (0.667)
amp 17q25 1	236 (47%)	265	0.0088 (1.00)	0.136 (1.00)	1e-05 (0.00996)	1e-05 (0.00996)	0.404 (1.00)	0.523 (1.00)	1e-05 (0.00996)	1e-05 (0.00996)	0.00046 (0.357)	0.00467 (1.00)	0.00129 (0.939)	0.00024 (0.194)
amp 18q11 2	151 (30%)	350	0.00036 (0.282)	0.0151 (1.00)	1e-05 (0.00996)	3e-05 (0.026)	0.254 (1.00)	0.746 (1.00)	1e-05 (0.00996)	6e-05 (0.0511)	0.0123 (1.00)	0.0028 (1.00)	0.0505 (1.00)	6e-05 (0.0511)
del 4q32 3	329 (66%)	172	0.0058 (1.00)	0.0187 (1.00)	1e-05 (0.00996)	6e-05 (0.0511)	0.0671 (1.00)	0.778 (1.00)	2e-05 (0.0176)	0.00028 (0.223)	0.00063 (0.481)	0.00246 (1.00)	0.0042 (1.00)	1e-05 (0.00996)
del xp21 1	152 (30%)	349	0.457 (1.00)	0.48 (1.00)	1e-05 (0.00996)	1e-05 (0.00996)	0.273 (1.00)	0.753 (1.00)	8e-05 (0.0676)	0.00095 (0.709)	0.00607 (1.00)	0.00129 (0.939)	2e-05 (0.0176)	1e-05 (0.00996)
amp 2q31 2	172 (34%)	329	0.0186 (1.00)	0.0229 (1.00)	1e-05 (0.00996)	1e-05 (0.00996)	0.725 (1.00)	0.639 (1.00)	1e-05 (0.00996)	1e-05 (0.00996)	0.00267 (1.00)	0.256 (1.00)	0.0033 (1.00)	0.00058 (0.445)
del 3p13	434 (87%)	67	0.255 (1.00)	0.353 (1.00)	1e-05 (0.00996)	0.00025 (0.201)	0.785 (1.00)	0.001 (0.741)	0.00073 (0.553)	0.00084 (0.634)	0.00253 (1.00)	1e-05 (0.00996)	0.00086 (0.647)	0.00025 (0.201)
del 4q35 2	331 (66%)	170	0.0686 (1.00)	0.202 (1.00)	1e-05 (0.00996)	1e-05 (0.00996)	0.362 (1.00)	0.862 (1.00)	1e-05 (0.00996)	0.0033 (1.00)	0.00041 (0.32)	0.00789 (1.00)	0.0486 (1.00)	1e-05 (0.00996)
del xp22 2	155 (31%)	346	0.713 (1.00)	0.524 (1.00)	2e-05 (0.0176)	0.00012 (0.1)	0.355 (1.00)	0.713 (1.00)	0.0118 (1.00)	0.00987 (1.00)	0.119 (1.00)	0.11 (1.00)	0.00022 (0.178)	8e-05 (0.0676)
del xq22 3	114 (23%)	387	0.0211 (1.00)	0.0102 (1.00)	1e-05 (0.00996)	2e-05 (0.0176)	0.87 (1.00)	0.889 (1.00)	0.00112 (0.824)	0.333 (1.00)	0.00591 (1.00)	0.00016 (0.132)	0.00812 (1.00)	0.00025 (0.201)
amp 18p11 32	179 (36%)	322	0.0429 (1.00)	0.00424 (1.00)	1e-05 (0.00996)	3e-05 (0.026)	0.503 (1.00)	0.979 (1.00)	0.0415 (1.00)	0.00132 (0.958)	0.0181 (1.00)	0.096 (1.00)	0.0754 (1.00)	0.00027 (0.215)
amp 22q11 21	256 (51%)	245	0.114 (1.00)	0.16 (1.00)	0.00016 (0.132)	0.00093 (0.696)	0.859 (1.00)	0.617 (1.00)	0.00013 (0.108)	0.00016 (0.132)	0.166 (1.00)	0.042 (1.00)	0.586 (1.00)	0.279 (1.00)
del 2q22 1	131 (26%)	370	0.321 (1.00)	0.336 (1.00)	1e-05 (0.00996)	0.00021 (0.171)	0.384 (1.00)	0.425 (1.00)	0.00223 (1.00)	0.0071 (1.00)	0.00021 (0.171)	0.00045 (0.35)	0.0188 (1.00)	0.0252 (1.00)
del 3p12 3	427 (85%)	74	0.277 (1.00)	0.228 (1.00)	1e-05 (0.00996)	0.0003 (0.237)	0.936 (1.00)	0.00178 (1.00)	0.00072 (0.546)	0.00475 (1.00)	0.0226 (1.00)	1e-05 (0.00996)	0.00055 (0.423)	0.00115 (0.843)
del 3p12 3	421 (84%)	80	0.229 (1.00)	0.398 (1.00)	1e-05 (0.00996)	0.00027 (0.215)	0.97 (1.00)	0.00648 (1.00)	0.00244 (1.00)	0.00769 (1.00)	0.0265 (1.00)	3e-05 (0.026)	0.00221 (1.00)	0.00252 (1.00)
del 5q12 1	369 (74%)	132	0.486 (1.00)	0.431 (1.00)	1e-05 (0.00996)	2e-05 (0.0176)	0.937 (1.00)	0.462 (1.00)	0.00195 (1.00)	0.00128 (0.933)	0.0109 (1.00)	1e-05 (0.00996)	0.064 (1.00)	0.00321 (1.00)
del 5q31 1	386 (77%)	115	0.158 (1.00)	0.276 (1.00)	1e-05 (0.00996)	1e-05 (0.00996)	0.369 (1.00)	0.522 (1.00)	0.0154 (1.00)	0.00717 (1.00)	0.00387 (1.00)	1e-05 (0.00996)	0.0802 (1.00)	0.00108 (0.799)
del 6p25 3	134 (27%)	367	0.456 (1.00)	0.285 (1.00)	0.00038 (0.298)	0.00011 (0.0923)	0.201 (1.00)	0.00669 (1.00)	1e-05 (0.00996)	1e-05 (0.00996)	0.138 (1.00)	0.00086 (0.647)	0.113 (1.00)	0.183 (1.00)
del 9p23	332 (66%)	169	0.0105 (1.00)	0.00188 (1.00)	1e-05 (0.00996)	0.0197 (1.00)	0.193 (1.00)	0.169 (1.00)	0.00012 (0.1)	0.00109 (0.806)	0.0109 (1.00)	0.00019 (0.155)	0.623 (1.00)	0.128 (1.00)
del 22q13 32	128 (26%)	373	0.00017 (0.14)	0.0132 (1.00)	0.224 (1.00)	0.0153 (1.00)	0.402 (1.00)	0.214 (1.00)	0.00012 (0.1)	1e-05 (0.00996)	0.271 (1.00)	0.00049 (0.379)	0.522 (1.00)	0.165 (1.00)
amp 6p12 1	166 (33%)	335	0.65 (1.00)	0.493 (1.00)	2e-05 (0.0176)	0.0526 (1.00)	0.927 (1.00)	0.544 (1.00)	0.0007 (0.532)	0.0628 (1.00)	0.572 (1.00)	0.117 (1.00)	0.213 (1.00)	0.00017 (0.14)
amp 7p11 2	256 (51%)	245	0.114 (1.00)	0.0298 (1.00)	1e-05 (0.00996)	0.00217 (1.00)	0.703 (1.00)	0.597 (1.00)	0.00197 (1.00)	2e-05 (0.0176)	0.155 (1.00)	0.0465 (1.00)	0.0453 (1.00)	0.33 (1.00)
amp 11q13 3	185 (37%)	316	0.0488 (1.00)	0.0338 (1.00)	3e-05 (0.026)	0.0003 (0.237)	0.261 (1.00)	0.337 (1.00)	0.03 (1.00)	0.0643 (1.00)	0.00143 (1.00)	0.00468 (1.00)	0.191 (1.00)	0.00284 (1.00)
amp 12p13 33	255 (51%)	246	0.00803 (1.00)	0.0219 (1.00)	1e-05 (0.00996)	0.00089 (0.667)	0.35 (1.00)	0.637 (1.00)	1e-05 (0.00996)	0.00176 (1.00)	0.134 (1.00)	0.00268 (1.00)	0.255 (1.00)	0.00592 (1.00)
amp 15q26 3	179 (36%)	322	0.362 (1.00)	0.05 (1.00)	1e-05 (0.00996)	0.00052 (0.401)	0.465 (1.00)	0.0271 (1.00)	9e-05 (0.0759)	0.003 (1.00)	0.0386 (1.00)	0.00638 (1.00)	0.0076 (1.00)	0.00424 (1.00)
amp 20p12 2	280 (56%)	221	0.00113 (0.829)	0.0022 (1.00)	1e-05 (0.00996)	0.00021 (0.171)	0.903 (1.00)	0.329 (1.00)	0.0171 (1.00)	0.0148 (1.00)	0.09 (1.00)	0.648 (1.00)	0.573 (1.00)	0.534 (1.00)
del 3p25 3	398 (79%)	103	0.385 (1.00)	0.201 (1.00)	0.00173 (1.00)	0.00098 (0.729)	0.882 (1.00)	0.228 (1.00)	0.00297 (1.00)	0.00026 (0.208)	0.00852 (1.00)	0.00019 (0.155)	0.015 (1.00)	0.0818 (1.00)
del 4q22 1	285 (57%)	216	0.00307 (1.00)	0.00486 (1.00)	1e-05 (0.00996)	0.00144 (1.00)	0.116 (1.00)	0.513 (1.00)	0.00013 (0.108)	0.0145 (1.00)	0.0163 (1.00)	0.00584 (1.00)	0.0567 (1.00)	0.0174 (1.00)
del 6q26	134 (27%)	367	0.042 (1.00)	0.00407 (1.00)	0.00016 (0.132)	0.0001 (0.0842)	0.921 (1.00)	0.657 (1.00)	0.00051 (0.394)	0.0055 (1.00)	0.0174 (1.00)	0.0731 (1.00)	0.033 (1.00)	0.104 (1.00)
del 9p21 1	326 (65%)	175	0.14 (1.00)	0.284 (1.00)	2e-05 (0.0176)	0.176 (1.00)	0.709 (1.00)	0.63 (1.00)	0.00032 (0.252)	0.00028 (0.223)	0.356 (1.00)	0.00912 (1.00)	0.156 (1.00)	0.359 (1.00)
del 11p15 5	245 (49%)	256	0.00038 (0.298)	0.0111 (1.00)	1e-05 (0.00996)	0.00459 (1.00)	0.00047 (0.364)	0.00026 (0.208)	0.00639 (1.00)	0.0817 (1.00)	0.00046 (0.357)	0.0888 (1.00)	0.733 (1.00)	0.00435 (1.00)
del 14q11 2	175 (35%)	326	0.0384 (1.00)	0.0339 (1.00)	0.536 (1.00)	0.99 (1.00)	0.26 (1.00)	0.166 (1.00)	0.00014 (0.116)	0.00023 (0.186)	0.0229 (1.00)	0.0102 (1.00)	0.00069 (0.525)	0.0327 (1.00)
del 19q13 32	149 (30%)	352	0.827 (1.00)	0.591 (1.00)	1e-05 (0.00996)	1e-05 (0.00996)	0.164 (1.00)	0.536 (1.00)	0.0146 (1.00)	0.00744 (1.00)	0.0377 (1.00)	0.503 (1.00)	0.0139 (1.00)	0.151 (1.00)
del 21q11 2	246 (49%)	255	0.564 (1.00)	0.562 (1.00)	4e-05 (0.0343)	0.149 (1.00)	0.982 (1.00)	0.728 (1.00)	0.0863 (1.00)	0.469 (1.00)	0.00075 (0.568)	0.00018 (0.147)	0.185 (1.00)	0.0152 (1.00)
del 21q22 3	281 (56%)	220	0.776 (1.00)	0.126 (1.00)	1e-05 (0.00996)	0.0429 (1.00)	0.511 (1.00)	0.0613 (1.00)	0.151 (1.00)	0.076 (1.00)	0.00987 (1.00)	0.0003 (0.237)	0.0143 (1.00)	0.0468 (1.00)
amp 5p15 33	387 (77%)	114	0.854 (1.00)	0.799 (1.00)	1e-05 (0.00996)	0.0335 (1.00)	0.405 (1.00)	0.371 (1.00)	0.491 (1.00)	0.0647 (1.00)	0.539 (1.00)	0.00578 (1.00)	0.478 (1.00)	0.28 (1.00)
amp 5p12	354 (71%)	147	0.957 (1.00)	0.76 (1.00)	1e-05 (0.00996)	0.0106 (1.00)	0.219 (1.00)	0.935 (1.00)	0.365 (1.00)	0.901 (1.00)	0.709 (1.00)	0.0772 (1.00)	0.0638 (1.00)	0.71 (1.00)
amp 6q12	152 (30%)	349	0.937 (1.00)	0.729 (1.00)	2e-05 (0.0176)	0.00099 (0.736)	0.496 (1.00)	0.602 (1.00)	0.0011 (0.811)	0.0055 (1.00)	0.742 (1.00)	0.0227 (1.00)	0.0523 (1.00)	0.00669 (1.00)
amp 8p11 23	238 (48%)	263	0.0133 (1.00)	0.0923 (1.00)	0.00014 (0.116)	0.019 (1.00)	0.191 (1.00)	0.248 (1.00)	0.0597 (1.00)	0.0565 (1.00)	0.872 (1.00)	0.173 (1.00)	0.592 (1.00)	0.329 (1.00)
amp 12q15	178 (36%)	323	0.134 (1.00)	0.345 (1.00)	4e-05 (0.0343)	0.0154 (1.00)	0.767 (1.00)	0.438 (1.00)	0.00608 (1.00)	0.0105 (1.00)	0.358 (1.00)	0.644 (1.00)	0.0244 (1.00)	0.00359 (1.00)
amp 19q12	224 (45%)	277	0.371 (1.00)	0.648 (1.00)	1e-05 (0.00996)	0.00175 (1.00)	0.232 (1.00)	0.358 (1.00)	0.00296 (1.00)	0.0283 (1.00)	0.725 (1.00)	0.562 (1.00)	0.0077 (1.00)	0.00221 (1.00)
amp 19q13 2	234 (47%)	267	0.341 (1.00)	0.257 (1.00)	1e-05 (0.00996)	0.00296 (1.00)	0.371 (1.00)	0.49 (1.00)	0.00488 (1.00)	0.0806 (1.00)	0.796 (1.00)	0.503 (1.00)	0.0312 (1.00)	0.0134 (1.00)
amp 20q11 21	306 (61%)	195	0.812 (1.00)	0.505 (1.00)	1e-05 (0.00996)	0.00581 (1.00)	0.78 (1.00)	0.736 (1.00)	0.634 (1.00)	0.944 (1.00)	0.275 (1.00)	0.368 (1.00)	0.592 (1.00)	0.201 (1.00)
del 6q22 31	122 (24%)	379	0.0397 (1.00)	0.00342 (1.00)	0.00025 (0.201)	0.00191 (1.00)	0.478 (1.00)	0.511 (1.00)	0.00085 (0.64)	0.0173 (1.00)	0.263 (1.00)	0.209 (1.00)	0.198 (1.00)	0.371 (1.00)
del 7q36 3	104 (21%)	397	0.171 (1.00)	0.0479 (1.00)	0.00435 (1.00)	0.291 (1.00)	0.974 (1.00)	0.099 (1.00)	0.00024 (0.194)	0.00132 (0.958)	0.304 (1.00)	0.00447 (1.00)	0.773 (1.00)	0.0464 (1.00)
del 8p23 2	341 (68%)	160	0.591 (1.00)	0.706 (1.00)	2e-05 (0.0176)	0.0138 (1.00)	0.243 (1.00)	0.36 (1.00)	0.114 (1.00)	0.0929 (1.00)	0.318 (1.00)	0.0633 (1.00)	0.389 (1.00)	0.0421 (1.00)
del 9p21 3	388 (77%)	113	0.197 (1.00)	0.259 (1.00)	1e-05 (0.00996)	0.292 (1.00)	0.812 (1.00)	0.597 (1.00)	0.00059 (0.452)	0.0165 (1.00)	0.452 (1.00)	0.0117 (1.00)	0.379 (1.00)	0.0229 (1.00)
del 16q23 1	210 (42%)	291	0.93 (1.00)	0.113 (1.00)	0.0142 (1.00)	0.212 (1.00)	0.354 (1.00)	0.848 (1.00)	0.0691 (1.00)	0.0387 (1.00)	0.00669 (1.00)	0.445 (1.00)	0.00032 (0.252)	0.00029 (0.23)
del 17q25 3	102 (20%)	399	0.00429 (1.00)	0.0119 (1.00)	7e-05 (0.0593)	0.0306 (1.00)	0.623 (1.00)	0.994 (1.00)	0.00152 (1.00)	0.00135 (0.976)	0.645 (1.00)	0.0137 (1.00)	0.775 (1.00)	0.105 (1.00)
del 19p13 3	236 (47%)	265	0.449 (1.00)	0.233 (1.00)	4e-05 (0.0343)	0.78 (1.00)	0.0945 (1.00)	0.164 (1.00)	0.0657 (1.00)	0.0228 (1.00)	0.183 (1.00)	0.00093 (0.696)	0.794 (1.00)	0.0535 (1.00)
del 22q11 21	95 (19%)	406	0.0296 (1.00)	0.0967 (1.00)	0.142 (1.00)	0.0662 (1.00)	0.13 (1.00)	0.355 (1.00)	0.152 (1.00)	0.00018 (0.147)	0.732 (1.00)	0.402 (1.00)	0.258 (1.00)	0.144 (1.00)
amp 4q12	119 (24%)	382	0.882 (1.00)	0.882 (1.00)	0.00167 (1.00)	0.0694 (1.00)	0.295 (1.00)	0.132 (1.00)	0.0613 (1.00)	0.582 (1.00)	0.0337 (1.00)	0.35 (1.00)	0.394 (1.00)	0.0351 (1.00)
amp 8q24 21	352 (70%)	149	0.92 (1.00)	0.78 (1.00)	0.0205 (1.00)	0.335 (1.00)	0.824 (1.00)	0.57 (1.00)	0.814 (1.00)	0.551 (1.00)	0.279 (1.00)	0.257 (1.00)	0.846 (1.00)	0.898 (1.00)
amp 9p13 3	136 (27%)	365	0.123 (1.00)	0.716 (1.00)	0.00167 (1.00)	0.00202 (1.00)	0.0713 (1.00)	0.00296 (1.00)	0.0017 (1.00)	0.00149 (1.00)	0.00595 (1.00)	0.00319 (1.00)	0.0182 (1.00)	0.0122 (1.00)
amp 13q34	91 (18%)	410	0.982 (1.00)	0.833 (1.00)	0.382 (1.00)	0.713 (1.00)	0.871 (1.00)	0.215 (1.00)	0.744 (1.00)	0.105 (1.00)	0.0127 (1.00)	0.0347 (1.00)	0.969 (1.00)	0.465 (1.00)
amp 14q13 3	159 (32%)	342	0.357 (1.00)	0.0269 (1.00)	0.159 (1.00)	0.134 (1.00)	0.649 (1.00)	0.0789 (1.00)	0.102 (1.00)	0.00239 (1.00)	0.0184 (1.00)	0.11 (1.00)	0.749 (1.00)	0.843 (1.00)
amp 14q32 33	158 (32%)	343	0.0305 (1.00)	0.0153 (1.00)	0.00212 (1.00)	0.00109 (0.806)	0.0252 (1.00)	0.402 (1.00)	0.00078 (0.59)	0.00043 (0.335)	0.518 (1.00)	0.433 (1.00)	0.0549 (1.00)	0.127 (1.00)
amp xq28	124 (25%)	377	0.887 (1.00)	0.872 (1.00)	0.0108 (1.00)	0.0488 (1.00)	0.0349 (1.00)	0.0774 (1.00)	0.0478 (1.00)	0.306 (1.00)	0.203 (1.00)	0.165 (1.00)	0.0165 (1.00)	0.033 (1.00)
del 2p25 3	50 (10%)	451	0.122 (1.00)	0.459 (1.00)	0.0902 (1.00)	0.395 (1.00)	0.255 (1.00)	0.366 (1.00)	0.675 (1.00)	0.606 (1.00)	0.00769 (1.00)	0.365 (1.00)	0.0468 (1.00)	0.0295 (1.00)
del 3q11 1	79 (16%)	422	0.766 (1.00)	0.78 (1.00)	0.226 (1.00)	0.948 (1.00)	0.763 (1.00)	0.601 (1.00)	0.769 (1.00)	0.172 (1.00)	0.923 (1.00)	0.519 (1.00)	0.338 (1.00)	0.737 (1.00)
del 7q11 22	48 (10%)	453	0.801 (1.00)	0.701 (1.00)	0.00117 (0.855)	0.789 (1.00)	0.848 (1.00)	0.32 (1.00)	0.00202 (1.00)	0.00099 (0.736)	0.645 (1.00)	0.375 (1.00)	0.656 (1.00)	0.906 (1.00)
del 11q22 1	162 (32%)	339	0.559 (1.00)	0.256 (1.00)	0.00134 (0.97)	0.00063 (0.481)	0.15 (1.00)	0.964 (1.00)	0.014 (1.00)	0.0395 (1.00)	0.00443 (1.00)	0.0285 (1.00)	0.216 (1.00)	0.147 (1.00)
del 11q25	184 (37%)	317	0.801 (1.00)	0.706 (1.00)	0.00167 (1.00)	0.0505 (1.00)	0.174 (1.00)	0.689 (1.00)	0.0167 (1.00)	0.146 (1.00)	0.0318 (1.00)	0.149 (1.00)	0.378 (1.00)	0.125 (1.00)
del 12q24 31	86 (17%)	415	0.915 (1.00)	0.599 (1.00)	0.405 (1.00)	0.258 (1.00)	0.201 (1.00)	0.68 (1.00)	0.52 (1.00)	0.698 (1.00)	0.707 (1.00)	0.331 (1.00)	0.398 (1.00)	0.171 (1.00)
del 13q12 11	331 (66%)	170	0.105 (1.00)	0.568 (1.00)	0.00356 (1.00)	0.124 (1.00)	0.91 (1.00)	0.181 (1.00)	0.814 (1.00)	0.97 (1.00)	0.231 (1.00)	0.382 (1.00)	0.00428 (1.00)	0.00395 (1.00)
del 13q14 2	344 (69%)	157	0.119 (1.00)	0.1 (1.00)	0.00322 (1.00)	0.0207 (1.00)	0.707 (1.00)	0.73 (1.00)	0.431 (1.00)	0.574 (1.00)	0.073 (1.00)	0.147 (1.00)	0.0015 (1.00)	0.0198 (1.00)
del 15q11 2	167 (33%)	334	0.564 (1.00)	0.521 (1.00)	0.159 (1.00)	0.13 (1.00)	0.0889 (1.00)	0.0276 (1.00)	0.193 (1.00)	0.0608 (1.00)	0.0243 (1.00)	0.539 (1.00)	0.263 (1.00)	0.127 (1.00)
del 15q21 1	169 (34%)	332	0.453 (1.00)	0.761 (1.00)	0.0161 (1.00)	0.201 (1.00)	0.0885 (1.00)	0.00694 (1.00)	0.274 (1.00)	0.247 (1.00)	0.00305 (1.00)	0.0979 (1.00)	0.359 (1.00)	0.172 (1.00)
del 16p13 3	187 (37%)	314	0.257 (1.00)	0.445 (1.00)	0.00411 (1.00)	0.0496 (1.00)	0.208 (1.00)	0.259 (1.00)	0.514 (1.00)	0.917 (1.00)	0.174 (1.00)	0.633 (1.00)	0.0093 (1.00)	0.1 (1.00)
del 17p11 2	272 (54%)	229	0.243 (1.00)	0.113 (1.00)	0.00048 (0.372)	0.566 (1.00)	0.157 (1.00)	0.00841 (1.00)	0.127 (1.00)	0.016 (1.00)	0.309 (1.00)	0.0269 (1.00)	0.231 (1.00)	0.153 (1.00)
del 18q23	234 (47%)	267	0.6 (1.00)	0.172 (1.00)	0.0055 (1.00)	0.207 (1.00)	0.887 (1.00)	0.189 (1.00)	0.79 (1.00)	0.479 (1.00)	0.502 (1.00)	0.537 (1.00)	0.106 (1.00)	0.646 (1.00)

'amp_1q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S1. Gene #1: 'amp_1q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
AMP PEAK 1(1Q21.2) MUTATED	73	122	63
AMP PEAK 1(1Q21.2) WILD-TYPE	109	44	90

Figure S1. Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q21.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S2. Gene #1: 'amp_1q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
AMP PEAK 1(1Q21.2) MUTATED	50	78	51
AMP PEAK 1(1Q21.2) WILD-TYPE	92	36	49

Figure S2. Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S3. Gene #1: 'amp_1q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	113	152	154	79
AMP PEAK 1(1Q21.2) MUTATED	44	106	80	27
AMP PEAK 1(1Q21.2) WILD-TYPE	69	46	74	52

Figure S3. Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S4. Gene #1: 'amp_1q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
AMP PEAK 1(1Q21.2) MUTATED	63	123	71
AMP PEAK 1(1Q21.2) WILD-TYPE	115	66	60

Figure S4. Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S5. Gene #1: 'amp_1q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	121	134	121	62	37
AMP PEAK 1(1Q21.2) MUTATED	66	81	41	43	13
AMP PEAK 1(1Q21.2) WILD-TYPE	55	53	80	19	24

Figure S5. Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S6. Gene #1: 'amp_1q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
AMP PEAK 1(1Q21.2) MUTATED	64	67	89	24
AMP PEAK 1(1Q21.2) WILD-TYPE	25	51	110	45

Figure S6. Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_2p16.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.22

Table S7. Gene #2: 'amp_2p16.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
AMP PEAK 2(2P16.1) MUTATED	24	42	19
AMP PEAK 2(2P16.1) WILD-TYPE	23	14	32

Figure S7. Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_2p16.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S8. Gene #2: 'amp_2p16.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
AMP PEAK 2(2P16.1) MUTATED	67	126	82
AMP PEAK 2(2P16.1) WILD-TYPE	115	40	71

Figure S8. Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2p16.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S9. Gene #2: 'amp_2p16.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
AMP PEAK 2(2P16.1) MUTATED	61	85	54
AMP PEAK 2(2P16.1) WILD-TYPE	81	29	46

Figure S9. Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2p16.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S10. Gene #2: 'amp_2p16.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	113	152	154	79
AMP PEAK 2(2P16.1) MUTATED	47	113	87	26
AMP PEAK 2(2P16.1) WILD-TYPE	66	39	67	53

Figure S10. Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2p16.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S11. Gene #2: 'amp_2p16.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
AMP PEAK 2(2P16.1) MUTATED	82	131	60
AMP PEAK 2(2P16.1) WILD-TYPE	96	58	71

Figure S11. Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_2p16.1' versus 'MIRSEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.23

Table S12. Gene #2: 'amp_2p16.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	121	134	121	62	37
AMP PEAK 2(2P16.1) MUTATED	65	93	50	33	22
AMP PEAK 2(2P16.1) WILD-TYPE	56	41	71	29	15

Figure S12. Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_2p16.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.026

Table S13. Gene #2: 'amp_2p16.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	151	144
AMP PEAK 2(2P16.1) MUTATED	22	104	60
AMP PEAK 2(2P16.1) WILD-TYPE	17	47	84

Figure S13. Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_2q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S14. Gene #3: 'amp_2q31.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
AMP PEAK 3(2Q31.2) MUTATED	38	80	54
AMP PEAK 3(2Q31.2) WILD-TYPE	144	86	99

Figure S14. Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2q31.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S15. Gene #3: 'amp_2q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
AMP PEAK 3(2Q31.2) MUTATED	36	62	29
AMP PEAK 3(2Q31.2) WILD-TYPE	106	52	71

Figure S15. Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2q31.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S16. Gene #3: 'amp_2q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	113	152	154	79
AMP PEAK 3(2Q31.2) MUTATED	28	78	48	17
AMP PEAK 3(2Q31.2) WILD-TYPE	85	74	106	62

Figure S16. Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S17. Gene #3: 'amp_2q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
AMP PEAK 3(2Q31.2) MUTATED	42	91	38
AMP PEAK 3(2Q31.2) WILD-TYPE	136	98	93

Figure S17. Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S18. Gene #4: 'amp_3q26.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
AMP PEAK 4(3Q26.33) MUTATED	141	165	146
AMP PEAK 4(3Q26.33) WILD-TYPE	41	1	7

Figure S18. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S19. Gene #4: 'amp_3q26.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
AMP PEAK 4(3Q26.33) MUTATED	112	114	94
AMP PEAK 4(3Q26.33) WILD-TYPE	30	0	6

Figure S19. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S20. Gene #4: 'amp_3q26.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	113	152	154	79
AMP PEAK 4(3Q26.33) MUTATED	107	152	132	58
AMP PEAK 4(3Q26.33) WILD-TYPE	6	0	22	21

Figure S20. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S21. Gene #4: 'amp_3q26.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
AMP PEAK 4(3Q26.33) MUTATED	163	188	98
AMP PEAK 4(3Q26.33) WILD-TYPE	15	1	33

Figure S21. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'MIRSEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.084

Table S22. Gene #4: 'amp_3q26.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	121	134	121	62	37
AMP PEAK 4(3Q26.33) MUTATED	108	130	97	59	35
AMP PEAK 4(3Q26.33) WILD-TYPE	13	4	24	3	2

Figure S22. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S23. Gene #4: 'amp_3q26.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
AMP PEAK 4(3Q26.33) MUTATED	89	108	189	43
AMP PEAK 4(3Q26.33) WILD-TYPE	0	10	10	26

Figure S23. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.059

Table S24. Gene #4: 'amp_3q26.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	151	144
AMP PEAK 4(3Q26.33) MUTATED	36	146	118
AMP PEAK 4(3Q26.33) WILD-TYPE	3	5	26

Figure S24. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S25. Gene #6: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
AMP PEAK 6(5P15.33) MUTATED	126	121	140
AMP PEAK 6(5P15.33) WILD-TYPE	56	45	13

Figure S25. Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S26. Gene #7: 'amp_5p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
AMP PEAK 7(5P12) MUTATED	106	118	130
AMP PEAK 7(5P12) WILD-TYPE	76	48	23

Figure S26. Get High-res Image Gene #7: 'amp_5p12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p12.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S27. Gene #8: 'amp_6p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
AMP PEAK 8(6P12.1) MUTATED	36	72	58
AMP PEAK 8(6P12.1) WILD-TYPE	146	94	95

Figure S27. Get High-res Image Gene #8: 'amp_6p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.14

Table S28. Gene #8: 'amp_6p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	151	144
AMP PEAK 8(6P12.1) MUTATED	13	67	31
AMP PEAK 8(6P12.1) WILD-TYPE	26	84	113

Figure S28. Get High-res Image Gene #8: 'amp_6p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q12' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S29. Gene #9: 'amp_6q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
AMP PEAK 9(6Q12) MUTATED	33	64	55
AMP PEAK 9(6Q12) WILD-TYPE	149	102	98

Figure S29. Get High-res Image Gene #9: 'amp_6q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S30. Gene #10: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
AMP PEAK 10(7P11.2) MUTATED	73	109	74
AMP PEAK 10(7P11.2) WILD-TYPE	109	57	79

Figure S30. Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S31. Gene #10: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
AMP PEAK 10(7P11.2) MUTATED	78	122	54
AMP PEAK 10(7P11.2) WILD-TYPE	100	67	77

Figure S31. Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S32. Gene #11: 'amp_7q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
AMP PEAK 11(7Q21.2) MUTATED	59	122	83
AMP PEAK 11(7Q21.2) WILD-TYPE	123	44	70

Figure S32. Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S33. Gene #11: 'amp_7q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
AMP PEAK 11(7Q21.2) MUTATED	49	76	55
AMP PEAK 11(7Q21.2) WILD-TYPE	93	38	45

Figure S33. Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7q21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S34. Gene #11: 'amp_7q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	113	152	154	79
AMP PEAK 11(7Q21.2) MUTATED	55	108	69	30
AMP PEAK 11(7Q21.2) WILD-TYPE	58	44	85	49

Figure S34. Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S35. Gene #11: 'amp_7q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
AMP PEAK 11(7Q21.2) MUTATED	74	130	58
AMP PEAK 11(7Q21.2) WILD-TYPE	104	59	73

Figure S35. Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'MIRSEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.18

Table S36. Gene #11: 'amp_7q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	121	134	121	62	37
AMP PEAK 11(7Q21.2) MUTATED	71	86	45	35	17
AMP PEAK 11(7Q21.2) WILD-TYPE	50	48	76	27	20

Figure S36. Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8p11.23' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.12

Table S37. Gene #12: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
AMP PEAK 12(8P11.23) MUTATED	73	71	94
AMP PEAK 12(8P11.23) WILD-TYPE	109	95	59

Figure S37. Get High-res Image Gene #12: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q13.3' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.026

Table S38. Gene #15: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
AMP PEAK 15(11Q13.3) MUTATED	46	62	77
AMP PEAK 15(11Q13.3) WILD-TYPE	136	104	76

Figure S38. Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.24

Table S39. Gene #15: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
AMP PEAK 15(11Q13.3) MUTATED	40	41	54
AMP PEAK 15(11Q13.3) WILD-TYPE	102	73	46

Figure S39. Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12p13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S40. Gene #16: 'amp_12p13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
AMP PEAK 16(12P13.33) MUTATED	63	110	82
AMP PEAK 16(12P13.33) WILD-TYPE	119	56	71

Figure S40. Get High-res Image Gene #16: 'amp_12p13.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12p13.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S41. Gene #16: 'amp_12p13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	113	152	154	79
AMP PEAK 16(12P13.33) MUTATED	37	98	90	28
AMP PEAK 16(12P13.33) WILD-TYPE	76	54	64	51

Figure S41. Get High-res Image Gene #16: 'amp_12p13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q15' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.034

Table S42. Gene #17: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
AMP PEAK 17(12Q15) MUTATED	46	80	52
AMP PEAK 17(12Q15) WILD-TYPE	136	86	101

Figure S42. Get High-res Image Gene #17: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

'amp_15q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S43. Gene #21: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
AMP PEAK 21(15Q26.3) MUTATED	41	82	56
AMP PEAK 21(15Q26.3) WILD-TYPE	141	84	97

Figure S43. Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.076

Table S44. Gene #21: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	113	152	154	79
AMP PEAK 21(15Q26.3) MUTATED	28	76	49	23
AMP PEAK 21(15Q26.3) WILD-TYPE	85	76	105	56

Figure S44. Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q25.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S45. Gene #22: 'amp_17q25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
AMP PEAK 22(17Q25.1) MUTATED	54	112	70
AMP PEAK 22(17Q25.1) WILD-TYPE	128	54	83

Figure S45. Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q25.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S46. Gene #22: 'amp_17q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
AMP PEAK 22(17Q25.1) MUTATED	40	72	52
AMP PEAK 22(17Q25.1) WILD-TYPE	102	42	48

Figure S46. Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q25.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S47. Gene #22: 'amp_17q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	113	152	154	79
AMP PEAK 22(17Q25.1) MUTATED	41	97	70	26
AMP PEAK 22(17Q25.1) WILD-TYPE	72	55	84	53

Figure S47. Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S48. Gene #22: 'amp_17q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
AMP PEAK 22(17Q25.1) MUTATED	67	115	52
AMP PEAK 22(17Q25.1) WILD-TYPE	111	74	79

Figure S48. Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q25.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.19

Table S49. Gene #22: 'amp_17q25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	151	144
AMP PEAK 22(17Q25.1) MUTATED	14	88	52
AMP PEAK 22(17Q25.1) WILD-TYPE	25	63	92

Figure S49. Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18p11.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S50. Gene #23: 'amp_18p11.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
AMP PEAK 23(18P11.32) MUTATED	38	81	60
AMP PEAK 23(18P11.32) WILD-TYPE	144	85	93

Figure S50. Get High-res Image Gene #23: 'amp_18p11.32' versus Molecular Subtype #3: 'CN_CNMF'

'amp_18p11.32' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.026

Table S51. Gene #23: 'amp_18p11.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
AMP PEAK 23(18P11.32) MUTATED	31	51	46
AMP PEAK 23(18P11.32) WILD-TYPE	111	63	54

Figure S51. Get High-res Image Gene #23: 'amp_18p11.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_18p11.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.22

Table S52. Gene #23: 'amp_18p11.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	151	144
AMP PEAK 23(18P11.32) MUTATED	11	71	36
AMP PEAK 23(18P11.32) WILD-TYPE	28	80	108

Figure S52. Get High-res Image Gene #23: 'amp_18p11.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S53. Gene #24: 'amp_18q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
AMP PEAK 24(18Q11.2) MUTATED	30	76	45
AMP PEAK 24(18Q11.2) WILD-TYPE	152	90	108

Figure S53. Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.026

Table S54. Gene #24: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
AMP PEAK 24(18Q11.2) MUTATED	24	49	31
AMP PEAK 24(18Q11.2) WILD-TYPE	118	65	69

Figure S54. Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S55. Gene #24: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	113	152	154	79
AMP PEAK 24(18Q11.2) MUTATED	26	64	51	9
AMP PEAK 24(18Q11.2) WILD-TYPE	87	88	103	70

Figure S55. Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.051

Table S56. Gene #24: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
AMP PEAK 24(18Q11.2) MUTATED	35	77	38
AMP PEAK 24(18Q11.2) WILD-TYPE	143	112	93

Figure S56. Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.051

Table S57. Gene #24: 'amp_18q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	151	144
AMP PEAK 24(18Q11.2) MUTATED	7	61	26
AMP PEAK 24(18Q11.2) WILD-TYPE	32	90	118

Figure S57. Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S58. Gene #25: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
AMP PEAK 25(19Q12) MUTATED	56	106	62
AMP PEAK 25(19Q12) WILD-TYPE	126	60	91

Figure S58. Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S59. Gene #26: 'amp_19q13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
AMP PEAK 26(19Q13.2) MUTATED	60	107	67
AMP PEAK 26(19Q13.2) WILD-TYPE	122	59	86

Figure S59. Get High-res Image Gene #26: 'amp_19q13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S60. Gene #27: 'amp_20p12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
AMP PEAK 27(20P12.2) MUTATED	70	119	91
AMP PEAK 27(20P12.2) WILD-TYPE	112	47	62

Figure S60. Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p12.2' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.17

Table S61. Gene #27: 'amp_20p12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
AMP PEAK 27(20P12.2) MUTATED	67	82	54
AMP PEAK 27(20P12.2) WILD-TYPE	75	32	46

Figure S61. Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S62. Gene #28: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
AMP PEAK 28(20Q11.21) MUTATED	82	114	110
AMP PEAK 28(20Q11.21) WILD-TYPE	100	52	43

Figure S62. Get High-res Image Gene #28: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_22q11.21' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.13

Table S63. Gene #29: 'amp_22q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
AMP PEAK 29(22Q11.21) MUTATED	71	100	85
AMP PEAK 29(22Q11.21) WILD-TYPE	111	66	68

Figure S63. Get High-res Image Gene #29: 'amp_22q11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_22q11.21' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.11

Table S64. Gene #29: 'amp_22q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	113	152	154	79
AMP PEAK 29(22Q11.21) MUTATED	55	100	68	31
AMP PEAK 29(22Q11.21) WILD-TYPE	58	52	86	48

Figure S64. Get High-res Image Gene #29: 'amp_22q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_22q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.13

Table S65. Gene #29: 'amp_22q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
AMP PEAK 29(22Q11.21) MUTATED	97	110	47
AMP PEAK 29(22Q11.21) WILD-TYPE	81	79	84

Figure S65. Get High-res Image Gene #29: 'amp_22q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.026

Table S66. Gene #31: 'del_1p36.11' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	52	32	28
DEL PEAK 1(1P36.11) MUTATED	12	39	13	10
DEL PEAK 1(1P36.11) WILD-TYPE	30	13	19	18

Figure S66. Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.11' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S67. Gene #31: 'del_1p36.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
DEL PEAK 1(1P36.11) MUTATED	14	43	17
DEL PEAK 1(1P36.11) WILD-TYPE	33	13	34

Figure S67. Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p36.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S68. Gene #31: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 1(1P36.11) MUTATED	45	138	45
DEL PEAK 1(1P36.11) WILD-TYPE	137	28	108

Figure S68. Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S69. Gene #31: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 1(1P36.11) MUTATED	26	89	40
DEL PEAK 1(1P36.11) WILD-TYPE	116	25	60

Figure S69. Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S70. Gene #31: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	113	152	154	79
DEL PEAK 1(1P36.11) MUTATED	32	120	52	23
DEL PEAK 1(1P36.11) WILD-TYPE	81	32	102	56

Figure S70. Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S71. Gene #31: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 1(1P36.11) MUTATED	46	140	41
DEL PEAK 1(1P36.11) WILD-TYPE	132	49	90

Figure S71. Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S72. Gene #31: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	121	134	121	62	37
DEL PEAK 1(1P36.11) MUTATED	57	74	31	43	11
DEL PEAK 1(1P36.11) WILD-TYPE	64	60	90	19	26

Figure S72. Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S73. Gene #31: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 1(1P36.11) MUTATED	66	52	83	15
DEL PEAK 1(1P36.11) WILD-TYPE	23	66	116	54

Figure S73. Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S74. Gene #31: 'del_1p36.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	129	116
DEL PEAK 1(1P36.11) MUTATED	21	56	67
DEL PEAK 1(1P36.11) WILD-TYPE	68	73	49

Figure S74. Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S75. Gene #31: 'del_1p36.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	151	144
DEL PEAK 1(1P36.11) MUTATED	9	90	45
DEL PEAK 1(1P36.11) WILD-TYPE	30	61	99

Figure S75. Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p13.1' versus 'MRNA_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.12

Table S76. Gene #32: 'del_1p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	52	32	28
DEL PEAK 2(1P13.1) MUTATED	17	37	9	9
DEL PEAK 2(1P13.1) WILD-TYPE	25	15	23	19

Figure S76. Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p13.1' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.026

Table S77. Gene #32: 'del_1p13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
DEL PEAK 2(1P13.1) MUTATED	19	39	14
DEL PEAK 2(1P13.1) WILD-TYPE	28	17	37

Figure S77. Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S78. Gene #32: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 2(1P13.1) MUTATED	47	124	50
DEL PEAK 2(1P13.1) WILD-TYPE	135	42	103

Figure S78. Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S79. Gene #32: 'del_1p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 2(1P13.1) MUTATED	36	79	37
DEL PEAK 2(1P13.1) WILD-TYPE	106	35	63

Figure S79. Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S80. Gene #32: 'del_1p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	113	152	154	79
DEL PEAK 2(1P13.1) MUTATED	34	107	55	24
DEL PEAK 2(1P13.1) WILD-TYPE	79	45	99	55

Figure S80. Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S81. Gene #32: 'del_1p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 2(1P13.1) MUTATED	48	125	47
DEL PEAK 2(1P13.1) WILD-TYPE	130	64	84

Figure S81. Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S82. Gene #32: 'del_1p13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	121	134	121	62	37
DEL PEAK 2(1P13.1) MUTATED	51	70	28	44	17
DEL PEAK 2(1P13.1) WILD-TYPE	70	64	93	18	20

Figure S82. Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S83. Gene #32: 'del_1p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 2(1P13.1) MUTATED	62	53	79	16
DEL PEAK 2(1P13.1) WILD-TYPE	27	65	120	53

Figure S83. Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.21

Table S84. Gene #32: 'del_1p13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	129	116
DEL PEAK 2(1P13.1) MUTATED	23	57	62
DEL PEAK 2(1P13.1) WILD-TYPE	66	72	54

Figure S84. Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S85. Gene #32: 'del_1p13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	151	144
DEL PEAK 2(1P13.1) MUTATED	10	88	44
DEL PEAK 2(1P13.1) WILD-TYPE	29	63	100

Figure S85. Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S86. Gene #34: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 4(2Q22.1) MUTATED	26	64	41
DEL PEAK 4(2Q22.1) WILD-TYPE	156	102	112

Figure S86. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.17

Table S87. Gene #34: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 4(2Q22.1) MUTATED	19	39	27
DEL PEAK 4(2Q22.1) WILD-TYPE	123	75	73

Figure S87. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q22.1' versus 'MIRSEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.17

Table S88. Gene #34: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	121	134	121	62	37
DEL PEAK 4(2Q22.1) MUTATED	37	48	16	20	6
DEL PEAK 4(2Q22.1) WILD-TYPE	84	86	105	42	31

Figure S88. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q37.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S89. Gene #35: 'del_2q37.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 5(2Q37.1) MUTATED	33	85	41
DEL PEAK 5(2Q37.1) WILD-TYPE	149	81	112

Figure S89. Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q37.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S90. Gene #35: 'del_2q37.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 5(2Q37.1) MUTATED	25	55	36
DEL PEAK 5(2Q37.1) WILD-TYPE	117	59	64

Figure S90. Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q37.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S91. Gene #35: 'del_2q37.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	113	152	154	79
DEL PEAK 5(2Q37.1) MUTATED	33	72	43	10
DEL PEAK 5(2Q37.1) WILD-TYPE	80	80	111	69

Figure S91. Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q37.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S92. Gene #35: 'del_2q37.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 5(2Q37.1) MUTATED	38	88	32
DEL PEAK 5(2Q37.1) WILD-TYPE	140	101	99

Figure S92. Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S93. Gene #35: 'del_2q37.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	121	134	121	62	37
DEL PEAK 5(2Q37.1) MUTATED	38	70	17	21	7
DEL PEAK 5(2Q37.1) WILD-TYPE	83	64	104	41	30

Figure S93. Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q37.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.026

Table S94. Gene #35: 'del_2q37.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 5(2Q37.1) MUTATED	34	54	56	9
DEL PEAK 5(2Q37.1) WILD-TYPE	55	64	143	60

Figure S94. Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S95. Gene #35: 'del_2q37.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	129	116
DEL PEAK 5(2Q37.1) MUTATED	11	45	50
DEL PEAK 5(2Q37.1) WILD-TYPE	78	84	66

Figure S95. Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_2q37.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S96. Gene #35: 'del_2q37.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	151	144
DEL PEAK 5(2Q37.1) MUTATED	4	69	33
DEL PEAK 5(2Q37.1) WILD-TYPE	35	82	111

Figure S96. Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.21

Table S97. Gene #36: 'del_3p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 6(3P25.3) MUTATED	141	165	90
DEL PEAK 6(3P25.3) WILD-TYPE	37	24	41

Figure S97. Get High-res Image Gene #36: 'del_3p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.16

Table S98. Gene #36: 'del_3p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 6(3P25.3) MUTATED	76	94	166	40
DEL PEAK 6(3P25.3) WILD-TYPE	13	24	33	29

Figure S98. Get High-res Image Gene #36: 'del_3p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S99. Gene #37: 'del_3p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 7(3P13) MUTATED	136	157	141
DEL PEAK 7(3P13) WILD-TYPE	46	9	12

Figure S99. Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p13' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.2

Table S100. Gene #37: 'del_3p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 7(3P13) MUTATED	110	107	91
DEL PEAK 7(3P13) WILD-TYPE	32	7	9

Figure S100. Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S101. Gene #37: 'del_3p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 7(3P13) MUTATED	79	104	185	43
DEL PEAK 7(3P13) WILD-TYPE	10	14	14	26

Figure S101. Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.2

Table S102. Gene #37: 'del_3p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	151	144
DEL PEAK 7(3P13) MUTATED	34	143	114
DEL PEAK 7(3P13) WILD-TYPE	5	8	30

Figure S102. Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p12.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S103. Gene #38: 'del_3p12.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 8(3P12.3) MUTATED	134	156	137
DEL PEAK 8(3P12.3) WILD-TYPE	48	10	16

Figure S103. Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p12.3' versus 'METHLYATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.24

Table S104. Gene #38: 'del_3p12.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 8(3P12.3) MUTATED	107	106	89
DEL PEAK 8(3P12.3) WILD-TYPE	35	8	11

Figure S104. Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p12.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S105. Gene #38: 'del_3p12.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 8(3P12.3) MUTATED	79	103	180	42
DEL PEAK 8(3P12.3) WILD-TYPE	10	15	19	27

Figure S105. Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p12.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S106. Gene #39: 'del_3p12.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 9(3P12.3) MUTATED	133	153	135
DEL PEAK 9(3P12.3) WILD-TYPE	49	13	18

Figure S106. Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p12.3' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.22

Table S107. Gene #39: 'del_3p12.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 9(3P12.3) MUTATED	106	106	86
DEL PEAK 9(3P12.3) WILD-TYPE	36	8	14

Figure S107. Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p12.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.026

Table S108. Gene #39: 'del_3p12.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 9(3P12.3) MUTATED	79	101	176	42
DEL PEAK 9(3P12.3) WILD-TYPE	10	17	23	27

Figure S108. Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4p15.2' versus 'MRNA_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.17

Table S109. Gene #41: 'del_4p15.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	52	32	28
DEL PEAK 11(4P15.2) MUTATED	31	41	12	13
DEL PEAK 11(4P15.2) WILD-TYPE	11	11	20	15

Figure S109. Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4p15.2' versus 'MRNA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.051

Table S110. Gene #41: 'del_4p15.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
DEL PEAK 11(4P15.2) MUTATED	34	44	19
DEL PEAK 11(4P15.2) WILD-TYPE	13	12	32

Figure S110. Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4p15.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S111. Gene #41: 'del_4p15.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 11(4P15.2) MUTATED	88	136	93
DEL PEAK 11(4P15.2) WILD-TYPE	94	30	60

Figure S111. Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p15.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S112. Gene #41: 'del_4p15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 11(4P15.2) MUTATED	66	87	69
DEL PEAK 11(4P15.2) WILD-TYPE	76	27	31

Figure S112. Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p15.2' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.13

Table S113. Gene #41: 'del_4p15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	113	152	154	79
DEL PEAK 11(4P15.2) MUTATED	74	116	83	43
DEL PEAK 11(4P15.2) WILD-TYPE	39	36	71	36

Figure S113. Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p15.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S114. Gene #41: 'del_4p15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 11(4P15.2) MUTATED	106	147	63
DEL PEAK 11(4P15.2) WILD-TYPE	72	42	68

Figure S114. Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p15.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.092

Table S115. Gene #41: 'del_4p15.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	129	116
DEL PEAK 11(4P15.2) MUTATED	43	80	89
DEL PEAK 11(4P15.2) WILD-TYPE	46	49	27

Figure S115. Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4p15.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.026

Table S116. Gene #41: 'del_4p15.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	151	144
DEL PEAK 11(4P15.2) MUTATED	19	116	77
DEL PEAK 11(4P15.2) WILD-TYPE	20	35	67

Figure S116. Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S117. Gene #42: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 12(4Q22.1) MUTATED	82	123	80
DEL PEAK 12(4Q22.1) WILD-TYPE	100	43	73

Figure S117. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.11

Table S118. Gene #42: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	113	152	154	79
DEL PEAK 12(4Q22.1) MUTATED	61	107	82	33
DEL PEAK 12(4Q22.1) WILD-TYPE	52	45	72	46

Figure S118. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q32.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S119. Gene #43: 'del_4q32.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 13(4Q32.3) MUTATED	95	141	93
DEL PEAK 13(4Q32.3) WILD-TYPE	87	25	60

Figure S119. Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q32.3' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.051

Table S120. Gene #43: 'del_4q32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 13(4Q32.3) MUTATED	74	88	70
DEL PEAK 13(4Q32.3) WILD-TYPE	68	26	30

Figure S120. Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q32.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S121. Gene #43: 'del_4q32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	113	152	154	79
DEL PEAK 13(4Q32.3) MUTATED	72	122	94	39
DEL PEAK 13(4Q32.3) WILD-TYPE	41	30	60	40

Figure S121. Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q32.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.22

Table S122. Gene #43: 'del_4q32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 13(4Q32.3) MUTATED	110	144	73
DEL PEAK 13(4Q32.3) WILD-TYPE	68	45	58

Figure S122. Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q32.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S123. Gene #43: 'del_4q32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	151	144
DEL PEAK 13(4Q32.3) MUTATED	27	120	71
DEL PEAK 13(4Q32.3) WILD-TYPE	12	31	73

Figure S123. Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q35.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S124. Gene #44: 'del_4q35.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 14(4Q35.2) MUTATED	98	140	93
DEL PEAK 14(4Q35.2) WILD-TYPE	84	26	60

Figure S124. Get High-res Image Gene #44: 'del_4q35.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q35.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S125. Gene #44: 'del_4q35.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 14(4Q35.2) MUTATED	74	90	67
DEL PEAK 14(4Q35.2) WILD-TYPE	68	24	33

Figure S125. Get High-res Image Gene #44: 'del_4q35.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q35.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S126. Gene #44: 'del_4q35.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	113	152	154	79
DEL PEAK 14(4Q35.2) MUTATED	70	122	98	39
DEL PEAK 14(4Q35.2) WILD-TYPE	43	30	56	40

Figure S126. Get High-res Image Gene #44: 'del_4q35.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q35.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S127. Gene #44: 'del_4q35.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	151	144
DEL PEAK 14(4Q35.2) MUTATED	28	117	73
DEL PEAK 14(4Q35.2) WILD-TYPE	11	34	71

Figure S127. Get High-res Image Gene #44: 'del_4q35.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S128. Gene #45: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 15(5Q12.1) MUTATED	99	136	134
DEL PEAK 15(5Q12.1) WILD-TYPE	83	30	19

Figure S128. Get High-res Image Gene #45: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S129. Gene #45: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 15(5Q12.1) MUTATED	84	93	83
DEL PEAK 15(5Q12.1) WILD-TYPE	58	21	17

Figure S129. Get High-res Image Gene #45: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S130. Gene #45: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 15(5Q12.1) MUTATED	66	82	167	38
DEL PEAK 15(5Q12.1) WILD-TYPE	23	36	32	31

Figure S130. Get High-res Image Gene #45: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S131. Gene #46: 'del_5q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 16(5Q31.1) MUTATED	110	138	138
DEL PEAK 16(5Q31.1) WILD-TYPE	72	28	15

Figure S131. Get High-res Image Gene #46: 'del_5q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q31.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S132. Gene #46: 'del_5q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 16(5Q31.1) MUTATED	91	95	90
DEL PEAK 16(5Q31.1) WILD-TYPE	51	19	10

Figure S132. Get High-res Image Gene #46: 'del_5q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S133. Gene #46: 'del_5q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 16(5Q31.1) MUTATED	69	90	171	38
DEL PEAK 16(5Q31.1) WILD-TYPE	20	28	28	31

Figure S133. Get High-res Image Gene #46: 'del_5q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.092

Table S134. Gene #47: 'del_6p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 17(6P25.3) MUTATED	26	48	26
DEL PEAK 17(6P25.3) WILD-TYPE	116	66	74

Figure S134. Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6p25.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S135. Gene #47: 'del_6p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	113	152	154	79
DEL PEAK 17(6P25.3) MUTATED	30	63	23	17
DEL PEAK 17(6P25.3) WILD-TYPE	83	89	131	62

Figure S135. Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S136. Gene #47: 'del_6p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 17(6P25.3) MUTATED	37	78	18
DEL PEAK 17(6P25.3) WILD-TYPE	141	111	113

Figure S136. Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q22.31' versus 'CN_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.2

Table S137. Gene #48: 'del_6q22.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 18(6Q22.31) MUTATED	32	59	31
DEL PEAK 18(6Q22.31) WILD-TYPE	150	107	122

Figure S137. Get High-res Image Gene #48: 'del_6q22.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q26' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.13

Table S138. Gene #49: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 19(6Q26) MUTATED	35	64	35
DEL PEAK 19(6Q26) WILD-TYPE	147	102	118

Figure S138. Get High-res Image Gene #49: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.084

Table S139. Gene #49: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 19(6Q26) MUTATED	27	48	23
DEL PEAK 19(6Q26) WILD-TYPE	115	66	77

Figure S139. Get High-res Image Gene #49: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_7q36.3' versus 'MRNASEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.19

Table S140. Gene #51: 'del_7q36.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	113	152	154	79
DEL PEAK 21(7Q36.3) MUTATED	28	18	47	11
DEL PEAK 21(7Q36.3) WILD-TYPE	85	134	107	68

Figure S140. Get High-res Image Gene #51: 'del_7q36.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S141. Gene #52: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 22(8P23.2) MUTATED	101	120	120
DEL PEAK 22(8P23.2) WILD-TYPE	81	46	33

Figure S141. Get High-res Image Gene #52: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S142. Gene #53: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 23(9P23) MUTATED	102	101	129
DEL PEAK 23(9P23) WILD-TYPE	80	65	24

Figure S142. Get High-res Image Gene #53: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.1

Table S143. Gene #53: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	113	152	154	79
DEL PEAK 23(9P23) MUTATED	89	87	110	43
DEL PEAK 23(9P23) WILD-TYPE	24	65	44	36

Figure S143. Get High-res Image Gene #53: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.16

Table S144. Gene #53: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 23(9P23) MUTATED	50	81	151	35
DEL PEAK 23(9P23) WILD-TYPE	39	37	48	34

Figure S144. Get High-res Image Gene #53: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S145. Gene #54: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 24(9P21.3) MUTATED	121	130	137
DEL PEAK 24(9P21.3) WILD-TYPE	61	36	16

Figure S145. Get High-res Image Gene #54: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S146. Gene #55: 'del_9p21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 25(9P21.1) MUTATED	106	97	123
DEL PEAK 25(9P21.1) WILD-TYPE	76	69	30

Figure S146. Get High-res Image Gene #55: 'del_9p21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.22

Table S147. Gene #55: 'del_9p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 25(9P21.1) MUTATED	135	106	82
DEL PEAK 25(9P21.1) WILD-TYPE	43	83	49

Figure S147. Get High-res Image Gene #55: 'del_9p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MRNA_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.19

Table S148. Gene #56: 'del_9q21.11' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	52	32	28
DEL PEAK 26(9Q21.11) MUTATED	28	13	19	15
DEL PEAK 26(9Q21.11) WILD-TYPE	14	39	13	13

Figure S148. Get High-res Image Gene #56: 'del_9q21.11' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9q21.11' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.043

Table S149. Gene #56: 'del_9q21.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
DEL PEAK 26(9Q21.11) MUTATED	31	14	30
DEL PEAK 26(9Q21.11) WILD-TYPE	16	42	21

Figure S149. Get High-res Image Gene #56: 'del_9q21.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9q21.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S150. Gene #56: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 26(9Q21.11) MUTATED	88	53	110
DEL PEAK 26(9Q21.11) WILD-TYPE	94	113	43

Figure S150. Get High-res Image Gene #56: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_9q21.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S151. Gene #56: 'del_9q21.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 26(9Q21.11) MUTATED	84	31	66
DEL PEAK 26(9Q21.11) WILD-TYPE	58	83	34

Figure S151. Get High-res Image Gene #56: 'del_9q21.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q21.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S152. Gene #56: 'del_9q21.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	113	152	154	79
DEL PEAK 26(9Q21.11) MUTATED	73	36	100	40
DEL PEAK 26(9Q21.11) WILD-TYPE	40	116	54	39

Figure S152. Get High-res Image Gene #56: 'del_9q21.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9q21.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S153. Gene #56: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 26(9Q21.11) MUTATED	125	46	78
DEL PEAK 26(9Q21.11) WILD-TYPE	53	143	53

Figure S153. Get High-res Image Gene #56: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S154. Gene #56: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	121	134	121	62	37
DEL PEAK 26(9Q21.11) MUTATED	58	62	71	17	29
DEL PEAK 26(9Q21.11) WILD-TYPE	63	72	50	45	8

Figure S154. Get High-res Image Gene #56: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9q21.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S155. Gene #56: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 26(9Q21.11) MUTATED	23	54	129	31
DEL PEAK 26(9Q21.11) WILD-TYPE	66	64	70	38

Figure S155. Get High-res Image Gene #56: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S156. Gene #57: 'del_10p15.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 27(10P15.2) MUTATED	58	94	67
DEL PEAK 27(10P15.2) WILD-TYPE	124	72	86

Figure S156. Get High-res Image Gene #57: 'del_10p15.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_10p15.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S157. Gene #57: 'del_10p15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 27(10P15.2) MUTATED	45	82	32
DEL PEAK 27(10P15.2) WILD-TYPE	97	32	68

Figure S157. Get High-res Image Gene #57: 'del_10p15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10p15.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S158. Gene #57: 'del_10p15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	113	152	154	79
DEL PEAK 27(10P15.2) MUTATED	39	94	60	25
DEL PEAK 27(10P15.2) WILD-TYPE	74	58	94	54

Figure S158. Get High-res Image Gene #57: 'del_10p15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10p15.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.12

Table S159. Gene #57: 'del_10p15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 27(10P15.2) MUTATED	66	106	46
DEL PEAK 27(10P15.2) WILD-TYPE	112	83	85

Figure S159. Get High-res Image Gene #57: 'del_10p15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.2' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.034

Table S160. Gene #57: 'del_10p15.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	121	134	121	62	37
DEL PEAK 27(10P15.2) MUTATED	53	64	35	40	20
DEL PEAK 27(10P15.2) WILD-TYPE	68	70	86	22	17

Figure S160. Get High-res Image Gene #57: 'del_10p15.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10p15.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S161. Gene #57: 'del_10p15.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 27(10P15.2) MUTATED	63	42	91	16
DEL PEAK 27(10P15.2) WILD-TYPE	26	76	108	53

Figure S161. Get High-res Image Gene #57: 'del_10p15.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S162. Gene #58: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 28(10Q23.31) MUTATED	74	119	75
DEL PEAK 28(10Q23.31) WILD-TYPE	108	47	78

Figure S162. Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S163. Gene #58: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 28(10Q23.31) MUTATED	52	84	53
DEL PEAK 28(10Q23.31) WILD-TYPE	90	30	47

Figure S163. Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S164. Gene #58: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	113	152	154	79
DEL PEAK 28(10Q23.31) MUTATED	49	114	69	35
DEL PEAK 28(10Q23.31) WILD-TYPE	64	38	85	44

Figure S164. Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S165. Gene #58: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 28(10Q23.31) MUTATED	78	135	54
DEL PEAK 28(10Q23.31) WILD-TYPE	100	54	77

Figure S165. Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.034

Table S166. Gene #58: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 28(10Q23.31) MUTATED	64	51	112	27
DEL PEAK 28(10Q23.31) WILD-TYPE	25	67	87	42

Figure S166. Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.16

Table S167. Gene #58: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	151	144
DEL PEAK 28(10Q23.31) MUTATED	20	99	60
DEL PEAK 28(10Q23.31) WILD-TYPE	19	52	84

Figure S167. Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S168. Gene #59: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 29(11P15.5) MUTATED	63	80	102
DEL PEAK 29(11P15.5) WILD-TYPE	119	86	51

Figure S168. Get High-res Image Gene #59: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'del_11p15.5' versus 'RPPA_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.21

Table S169. Gene #59: 'del_11p15.5' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	41	52	47
DEL PEAK 29(11P15.5) MUTATED	28	15	38	16
DEL PEAK 29(11P15.5) WILD-TYPE	26	26	14	31

Figure S169. Get High-res Image Gene #59: 'del_11p15.5' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_14q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.12

Table S170. Gene #65: 'del_14q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	113	152	154	79
DEL PEAK 35(14Q11.2) MUTATED	25	57	71	20
DEL PEAK 35(14Q11.2) WILD-TYPE	88	95	83	59

Figure S170. Get High-res Image Gene #65: 'del_14q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.19

Table S171. Gene #65: 'del_14q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 35(14Q11.2) MUTATED	43	69	61
DEL PEAK 35(14Q11.2) WILD-TYPE	135	120	70

Figure S171. Get High-res Image Gene #65: 'del_14q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.23

Table S172. Gene #69: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	151	144
DEL PEAK 39(16Q23.1) MUTATED	10	81	50
DEL PEAK 39(16Q23.1) WILD-TYPE	29	70	94

Figure S172. Get High-res Image Gene #69: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q11.2' versus 'MRNA_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.084

Table S173. Gene #71: 'del_17q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	52	32	28
DEL PEAK 41(17Q11.2) MUTATED	21	5	11	6
DEL PEAK 41(17Q11.2) WILD-TYPE	21	47	21	22

Figure S173. Get High-res Image Gene #71: 'del_17q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.051

Table S174. Gene #71: 'del_17q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
DEL PEAK 41(17Q11.2) MUTATED	21	5	17
DEL PEAK 41(17Q11.2) WILD-TYPE	26	51	34

Figure S174. Get High-res Image Gene #71: 'del_17q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S175. Gene #71: 'del_17q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 41(17Q11.2) MUTATED	50	17	65
DEL PEAK 41(17Q11.2) WILD-TYPE	132	149	88

Figure S175. Get High-res Image Gene #71: 'del_17q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_17q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S176. Gene #71: 'del_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 41(17Q11.2) MUTATED	47	11	30
DEL PEAK 41(17Q11.2) WILD-TYPE	95	103	70

Figure S176. Get High-res Image Gene #71: 'del_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S177. Gene #71: 'del_17q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	113	152	154	79
DEL PEAK 41(17Q11.2) MUTATED	43	13	50	25
DEL PEAK 41(17Q11.2) WILD-TYPE	70	139	104	54

Figure S177. Get High-res Image Gene #71: 'del_17q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S178. Gene #71: 'del_17q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 41(17Q11.2) MUTATED	74	19	38
DEL PEAK 41(17Q11.2) WILD-TYPE	104	170	93

Figure S178. Get High-res Image Gene #71: 'del_17q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17q25.3' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.059

Table S179. Gene #72: 'del_17q25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 42(17Q25.3) MUTATED	37	18	47
DEL PEAK 42(17Q25.3) WILD-TYPE	145	148	106

Figure S179. Get High-res Image Gene #72: 'del_17q25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.3' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.034

Table S180. Gene #74: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 44(19P13.3) MUTATED	67	76	93
DEL PEAK 44(19P13.3) WILD-TYPE	115	90	60

Figure S180. Get High-res Image Gene #74: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S181. Gene #75: 'del_19q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 45(19Q13.32) MUTATED	32	73	44
DEL PEAK 45(19Q13.32) WILD-TYPE	150	93	109

Figure S181. Get High-res Image Gene #75: 'del_19q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q13.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S182. Gene #75: 'del_19q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 45(19Q13.32) MUTATED	21	43	37
DEL PEAK 45(19Q13.32) WILD-TYPE	121	71	63

Figure S182. Get High-res Image Gene #75: 'del_19q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_21q11.2' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.034

Table S183. Gene #76: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 46(21Q11.2) MUTATED	66	92	88
DEL PEAK 46(21Q11.2) WILD-TYPE	116	74	65

Figure S183. Get High-res Image Gene #76: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.15

Table S184. Gene #76: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 46(21Q11.2) MUTATED	42	66	109	18
DEL PEAK 46(21Q11.2) WILD-TYPE	47	52	90	51

Figure S184. Get High-res Image Gene #76: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_21q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S185. Gene #77: 'del_21q22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 47(21Q22.3) MUTATED	71	110	100
DEL PEAK 47(21Q22.3) WILD-TYPE	111	56	53

Figure S185. Get High-res Image Gene #77: 'del_21q22.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.24

Table S186. Gene #77: 'del_21q22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 47(21Q22.3) MUTATED	55	70	121	23
DEL PEAK 47(21Q22.3) WILD-TYPE	34	48	78	46

Figure S186. Get High-res Image Gene #77: 'del_21q22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_22q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.15

Table S187. Gene #78: 'del_22q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 48(22Q11.21) MUTATED	23	31	41
DEL PEAK 48(22Q11.21) WILD-TYPE	155	158	90

Figure S187. Get High-res Image Gene #78: 'del_22q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MRNA_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.14

Table S188. Gene #79: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	52	32	28
DEL PEAK 49(22Q13.32) MUTATED	8	8	8	17
DEL PEAK 49(22Q13.32) WILD-TYPE	34	44	24	11

Figure S188. Get High-res Image Gene #79: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.1

Table S189. Gene #79: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	113	152	154	79
DEL PEAK 49(22Q13.32) MUTATED	29	23	59	17
DEL PEAK 49(22Q13.32) WILD-TYPE	84	129	95	62

Figure S189. Get High-res Image Gene #79: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S190. Gene #79: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 49(22Q13.32) MUTATED	39	30	59
DEL PEAK 49(22Q13.32) WILD-TYPE	139	159	72

Figure S190. Get High-res Image Gene #79: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_xp22.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S191. Gene #80: 'del_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 50(XP22.2) MUTATED	35	69	51
DEL PEAK 50(XP22.2) WILD-TYPE	147	97	102

Figure S191. Get High-res Image Gene #80: 'del_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_xp22.2' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.1

Table S192. Gene #80: 'del_xp22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 50(XP22.2) MUTATED	26	45	39
DEL PEAK 50(XP22.2) WILD-TYPE	116	69	61

Figure S192. Get High-res Image Gene #80: 'del_xp22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xp22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.18

Table S193. Gene #80: 'del_xp22.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	129	116
DEL PEAK 50(XP22.2) MUTATED	15	39	50
DEL PEAK 50(XP22.2) WILD-TYPE	74	90	66

Figure S193. Get High-res Image Gene #80: 'del_xp22.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_xp22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.068

Table S194. Gene #80: 'del_xp22.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	151	144
DEL PEAK 50(XP22.2) MUTATED	8	66	30
DEL PEAK 50(XP22.2) WILD-TYPE	31	85	114

Figure S194. Get High-res Image Gene #80: 'del_xp22.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S195. Gene #81: 'del_xp21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 51(XP21.1) MUTATED	30	73	49
DEL PEAK 51(XP21.1) WILD-TYPE	152	93	104

Figure S195. Get High-res Image Gene #81: 'del_xp21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S196. Gene #81: 'del_xp21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 51(XP21.1) MUTATED	21	47	39
DEL PEAK 51(XP21.1) WILD-TYPE	121	67	61

Figure S196. Get High-res Image Gene #81: 'del_xp21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xp21.1' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.068

Table S197. Gene #81: 'del_xp21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	113	152	154	79
DEL PEAK 51(XP21.1) MUTATED	35	66	34	15
DEL PEAK 51(XP21.1) WILD-TYPE	78	86	120	64

Figure S197. Get High-res Image Gene #81: 'del_xp21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_xp21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S198. Gene #81: 'del_xp21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	129	116
DEL PEAK 51(XP21.1) MUTATED	10	43	47
DEL PEAK 51(XP21.1) WILD-TYPE	79	86	69

Figure S198. Get High-res Image Gene #81: 'del_xp21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_xp21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S199. Gene #81: 'del_xp21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	151	144
DEL PEAK 51(XP21.1) MUTATED	6	67	27
DEL PEAK 51(XP21.1) WILD-TYPE	33	84	117

Figure S199. Get High-res Image Gene #81: 'del_xp21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp11.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S200. Gene #82: 'del_xp11.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 52(XP11.3) MUTATED	30	73	46
DEL PEAK 52(XP11.3) WILD-TYPE	152	93	107

Figure S200. Get High-res Image Gene #82: 'del_xp11.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_xp11.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S201. Gene #82: 'del_xp11.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 52(XP11.3) MUTATED	20	48	36
DEL PEAK 52(XP11.3) WILD-TYPE	122	66	64

Figure S201. Get High-res Image Gene #82: 'del_xp11.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xp11.3' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.13

Table S202. Gene #82: 'del_xp11.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	113	152	154	79
DEL PEAK 52(XP11.3) MUTATED	31	65	39	13
DEL PEAK 52(XP11.3) WILD-TYPE	82	87	115	66

Figure S202. Get High-res Image Gene #82: 'del_xp11.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_xp11.3' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.1

Table S203. Gene #82: 'del_xp11.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	121	134	121	62	37
DEL PEAK 52(XP11.3) MUTATED	36	50	18	26	13
DEL PEAK 52(XP11.3) WILD-TYPE	85	84	103	36	24

Figure S203. Get High-res Image Gene #82: 'del_xp11.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_xp11.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S204. Gene #82: 'del_xp11.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	129	116
DEL PEAK 52(XP11.3) MUTATED	10	40	47
DEL PEAK 52(XP11.3) WILD-TYPE	79	89	69

Figure S204. Get High-res Image Gene #82: 'del_xp11.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_xp11.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S205. Gene #82: 'del_xp11.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	151	144
DEL PEAK 52(XP11.3) MUTATED	7	64	26
DEL PEAK 52(XP11.3) WILD-TYPE	32	87	118

Figure S205. Get High-res Image Gene #82: 'del_xp11.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xq22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S206. Gene #83: 'del_xq22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	166	153
DEL PEAK 53(XQ22.3) MUTATED	19	37	58
DEL PEAK 53(XQ22.3) WILD-TYPE	163	129	95

Figure S206. Get High-res Image Gene #83: 'del_xq22.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_xq22.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S207. Gene #83: 'del_xq22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 53(XQ22.3) MUTATED	13	25	37
DEL PEAK 53(XQ22.3) WILD-TYPE	129	89	63

Figure S207. Get High-res Image Gene #83: 'del_xq22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xq22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.13

Table S208. Gene #83: 'del_xq22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 53(XQ22.3) MUTATED	20	33	54	3
DEL PEAK 53(XQ22.3) WILD-TYPE	69	85	145	66

Figure S208. Get High-res Image Gene #83: 'del_xq22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_xq22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.2

Table S209. Gene #83: 'del_xq22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	151	144
DEL PEAK 53(XQ22.3) MUTATED	10	46	17
DEL PEAK 53(XQ22.3) WILD-TYPE	29	105	127

Figure S209. Get High-res Image Gene #83: 'del_xq22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = LUSC-TP.transferedmergedcluster.txt
Number of patients = 501
Number of significantly focal cnvs = 83
Number of molecular subtypes = 12
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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