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

Liver Hepatocellular Carcinoma

14 July 2016 | awg_lihc__2016_07_14

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 (2016): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1H994Q9

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 59 focal events and 10 molecular subtypes across 370 patients, 365 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1q42.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_2p24.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_2q33.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_3q26.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_4p14 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_5p15.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5q35.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
amp_6p25.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_6p21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_6q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_6q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_7q31.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_9q34.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_11q13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12q14.1 cnv correlated to 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_13q32.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_13q34 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_15q26.3 cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
amp_17q25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19p13.12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19q13.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20q13.13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_xq28 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.11 cnv correlated to '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 'MRNASEQ_CNMF'.
del_2q37.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4p16.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q24 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q35.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q27 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_8p23.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9q31.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q26.13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q14.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q25 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12p12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_12q24.33 cnv correlated to 'CN_CNMF'.
del_13q14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q23.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q32.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q26.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_16q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q21.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_19p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_22q12.1 cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.
del_22q13.32 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', and 'MRNASEQ_CNMF'.
del_xq26.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 59 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 365 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
del 3p13	73 (20%)	297	0.00356 (0.00938)	0.00173 (0.00523)	0.0361 (0.0618)	0.022 (0.041)	1e-05 (7.2e-05)	1e-05 (7.2e-05)	3e-05 (0.00017)	0.00299 (0.00824)	0.00036 (0.00138)	0.00301 (0.00826)
del 10q23 31	97 (26%)	273	1e-05 (7.2e-05)	2e-05 (0.00012)	0.00039 (0.00147)	0.00337 (0.009)	2e-05 (0.00012)	0.00156 (0.00487)	1e-05 (7.2e-05)	0.0001 (0.000472)	0.00031 (0.00124)	8e-05 (0.00039)
del 10q26 13	105 (28%)	265	1e-05 (7.2e-05)	0.00018 (0.000787)	0.00199 (0.00587)	0.0114 (0.024)	1e-05 (7.2e-05)	0.00052 (0.00187)	5e-05 (0.000261)	6e-05 (0.000305)	0.0168 (0.0334)	4e-05 (0.000219)
del 13q14 2	179 (48%)	191	1e-05 (7.2e-05)	0.00318 (0.00865)	0.0343 (0.0594)	0.044 (0.0729)	1e-05 (7.2e-05)	1e-05 (7.2e-05)	2e-05 (0.00012)	5e-05 (0.000261)	0.0104 (0.0226)	1e-05 (7.2e-05)
del 14q23 3	131 (35%)	239	1e-05 (7.2e-05)	0.0009 (0.00292)	0.00275 (0.00776)	0.00378 (0.00978)	1e-05 (7.2e-05)	0.00064 (0.00222)	0.00721 (0.0166)	0.00593 (0.0143)	7e-05 (0.000347)	0.00765 (0.0175)
del 16q23 1	162 (44%)	208	1e-05 (7.2e-05)	1e-05 (7.2e-05)	0.00084 (0.00277)	0.00059 (0.00207)	1e-05 (7.2e-05)	1e-05 (7.2e-05)	2e-05 (0.00012)	1e-05 (7.2e-05)	1e-05 (7.2e-05)	0.00041 (0.00153)
del 17p13 1	226 (61%)	144	1e-05 (7.2e-05)	0.00067 (0.00227)	0.0182 (0.0358)	0.00168 (0.00514)	1e-05 (7.2e-05)	0.00233 (0.00674)	1e-05 (7.2e-05)	5e-05 (0.000261)	2e-05 (0.00012)	1e-05 (7.2e-05)
amp 1q21 3	271 (73%)	99	1e-05 (7.2e-05)	1e-05 (7.2e-05)	0.0667 (0.103)	0.0211 (0.0398)	0.00018 (0.000787)	6e-05 (0.000305)	0.00694 (0.0161)	0.00018 (0.000787)	0.0044 (0.0111)	0.0164 (0.0328)
amp 17q25 3	145 (39%)	225	1e-05 (7.2e-05)	0.00633 (0.0149)	0.0134 (0.0276)	0.0304 (0.0533)	0.00025 (0.00102)	0.0804 (0.119)	0.0199 (0.0379)	0.00595 (0.0143)	0.0249 (0.0457)	0.00361 (0.00947)
amp 20q13 13	124 (34%)	246	2e-05 (0.00012)	0.0017 (0.00517)	0.378 (0.434)	0.0162 (0.0324)	0.00462 (0.0115)	0.00036 (0.00138)	0.0491 (0.0794)	0.0149 (0.0302)	3e-05 (0.00017)	0.0169 (0.0334)
del 4q21 3	171 (46%)	199	1e-05 (7.2e-05)	1e-05 (7.2e-05)	0.0193 (0.037)	0.26 (0.317)	1e-05 (7.2e-05)	2e-05 (0.00012)	0.00023 (0.000969)	2e-05 (0.00012)	1e-05 (7.2e-05)	1e-05 (7.2e-05)
del 4q24	173 (47%)	197	1e-05 (7.2e-05)	1e-05 (7.2e-05)	0.0383 (0.0647)	0.281 (0.339)	1e-05 (7.2e-05)	1e-05 (7.2e-05)	0.00012 (0.00054)	1e-05 (7.2e-05)	1e-05 (7.2e-05)	1e-05 (7.2e-05)
del 4q35 1	172 (46%)	198	1e-05 (7.2e-05)	1e-05 (7.2e-05)	0.0329 (0.0571)	0.44 (0.498)	1e-05 (7.2e-05)	5e-05 (0.000261)	0.00141 (0.00442)	4e-05 (0.000219)	1e-05 (7.2e-05)	1e-05 (7.2e-05)
del 14q32 33	133 (36%)	237	1e-05 (7.2e-05)	0.00012 (0.00054)	0.0142 (0.029)	0.107 (0.152)	0.00013 (0.000581)	0.00024 (0.000997)	0.00428 (0.0109)	0.0103 (0.0223)	0.00057 (0.00203)	0.00614 (0.0147)
amp 4p14	54 (15%)	316	0.00859 (0.0194)	0.00323 (0.00874)	0.0122 (0.0256)	0.0627 (0.0971)	2e-05 (0.00012)	0.00044 (0.00162)	0.028 (0.0499)	0.0136 (0.0279)	0.00093 (0.003)	0.0528 (0.0846)
amp 8q24 21	231 (62%)	139	1e-05 (7.2e-05)	0.00033 (0.00131)	0.172 (0.227)	0.246 (0.306)	1e-05 (7.2e-05)	1e-05 (7.2e-05)	0.0215 (0.0404)	3e-05 (0.00017)	1e-05 (7.2e-05)	0.0002 (0.000868)
amp 13q32 3	67 (18%)	303	1e-05 (7.2e-05)	0.015 (0.0303)	0.328 (0.387)	0.0364 (0.062)	0.00258 (0.00735)	0.0109 (0.0233)	0.0124 (0.0259)	0.289 (0.347)	0.00051 (0.00186)	0.00335 (0.00898)
amp 19p13 12	69 (19%)	301	0.00042 (0.00156)	1e-05 (7.2e-05)	0.271 (0.33)	0.0716 (0.109)	3e-05 (0.00017)	0.00066 (0.00226)	0.0154 (0.0311)	0.00039 (0.00147)	7e-05 (0.000347)	3e-05 (0.00017)
amp 19q13 11	91 (25%)	279	0.00038 (0.00145)	1e-05 (7.2e-05)	0.0668 (0.103)	0.0299 (0.0525)	6e-05 (0.000305)	0.00021 (0.000904)	0.0605 (0.0951)	0.00024 (0.000997)	0.0001 (0.000472)	0.00012 (0.00054)
del 1p36 31	162 (44%)	208	1e-05 (7.2e-05)	1e-05 (7.2e-05)	0.0687 (0.105)	0.108 (0.153)	1e-05 (7.2e-05)	1e-05 (7.2e-05)	0.00066 (0.00226)	0.00079 (0.00262)	8e-05 (0.00039)	0.00034 (0.00134)
del 1p36 11	142 (38%)	228	1e-05 (7.2e-05)	1e-05 (7.2e-05)	0.0881 (0.128)	0.335 (0.393)	1e-05 (7.2e-05)	1e-05 (7.2e-05)	2e-05 (0.00012)	1e-05 (7.2e-05)	1e-05 (7.2e-05)	1e-05 (7.2e-05)
del 9p21 3	150 (41%)	220	1e-05 (7.2e-05)	2e-05 (0.00012)	0.286 (0.343)	0.251 (0.308)	2e-05 (0.00012)	2e-05 (0.00012)	0.00069 (0.00233)	0.00031 (0.00124)	0.00025 (0.00102)	1e-05 (7.2e-05)
del 9q31 3	119 (32%)	251	1e-05 (7.2e-05)	0.00101 (0.00324)	0.34 (0.398)	0.4 (0.456)	9e-05 (0.000435)	3e-05 (0.00017)	0.0268 (0.0486)	0.0029 (0.0081)	0.00088 (0.00287)	2e-05 (0.00012)
del 15q26 3	79 (21%)	291	1e-05 (7.2e-05)	0.00488 (0.012)	0.0225 (0.0418)	0.00116 (0.0037)	0.00275 (0.00776)	0.0409 (0.0689)	0.028 (0.0499)	0.247 (0.306)	0.0322 (0.0561)	0.104 (0.149)
del 17p11 2	195 (53%)	175	1e-05 (7.2e-05)	0.00991 (0.0219)	0.0756 (0.113)	0.0205 (0.0389)	1e-05 (7.2e-05)	0.0793 (0.117)	4e-05 (0.000219)	0.00071 (0.00238)	7e-05 (0.000347)	2e-05 (0.00012)
del 19p13 3	93 (25%)	277	1e-05 (7.2e-05)	0.00629 (0.0149)	0.245 (0.305)	0.0173 (0.0342)	0.00058 (0.00205)	0.00055 (0.00197)	0.111 (0.158)	0.0147 (0.0299)	0.0422 (0.0708)	0.00067 (0.00227)
amp 1q42 2	268 (72%)	102	1e-05 (7.2e-05)	1e-05 (7.2e-05)	0.536 (0.592)	0.576 (0.626)	0.0001 (0.000472)	2e-05 (0.00012)	0.0185 (0.0363)	0.00184 (0.00554)	0.115 (0.162)	0.0016 (0.00497)
amp 6q12	83 (22%)	287	1e-05 (7.2e-05)	0.00164 (0.00507)	0.0119 (0.0251)	0.0435 (0.0723)	0.0198 (0.0378)	0.00996 (0.0219)	0.457 (0.513)	0.0749 (0.112)	0.00075 (0.0025)	0.342 (0.399)
amp 11q13 3	57 (15%)	313	0.0419 (0.0704)	0.025 (0.0457)	0.0738 (0.111)	0.991 (0.991)	0.00023 (0.000969)	0.004 (0.0102)	0.0097 (0.0217)	0.00443 (0.0111)	0.053 (0.0848)	0.00247 (0.00711)
amp 13q34	68 (18%)	302	1e-05 (7.2e-05)	0.013 (0.027)	0.654 (0.697)	0.0533 (0.085)	0.00681 (0.0158)	0.0107 (0.023)	0.00911 (0.0204)	0.416 (0.473)	0.00035 (0.00137)	0.0259 (0.0471)
amp xq28	87 (24%)	283	0.00031 (0.00124)	0.196 (0.251)	0.523 (0.583)	0.0347 (0.0599)	0.0611 (0.0956)	0.00209 (0.00613)	0.00796 (0.0181)	0.00257 (0.00735)	0.0019 (0.00563)	0.00036 (0.00138)
amp 3q26 31	77 (21%)	293	1e-05 (7.2e-05)	0.00063 (0.0022)	0.142 (0.195)	0.694 (0.731)	0.0188 (0.0365)	0.283 (0.341)	0.105 (0.15)	0.0354 (0.0609)	0.00618 (0.0148)	0.0277 (0.0497)
amp 5p15 33	163 (44%)	207	1e-05 (7.2e-05)	0.00218 (0.00637)	0.149 (0.201)	0.0491 (0.0794)	0.0109 (0.0233)	0.0786 (0.117)	0.0519 (0.0835)	0.00979 (0.0218)	0.0627 (0.0971)	0.0102 (0.0223)
amp 6p25 2	159 (43%)	211	1e-05 (7.2e-05)	0.00124 (0.00391)	0.0956 (0.139)	0.251 (0.308)	0.011 (0.0235)	0.0128 (0.0266)	0.069 (0.105)	0.0473 (0.0773)	0.00333 (0.00897)	0.37 (0.426)
amp 2p24 1	65 (18%)	305	0.0028 (0.00787)	0.0037 (0.00962)	0.875 (0.886)	0.18 (0.235)	0.00536 (0.0131)	0.19 (0.244)	0.0749 (0.112)	0.0462 (0.0761)	0.0058 (0.0141)	0.149 (0.201)
amp 2q33 1	64 (17%)	306	0.00294 (0.00814)	0.00452 (0.0113)	0.87 (0.882)	0.64 (0.687)	0.0377 (0.0639)	0.0445 (0.0736)	0.0948 (0.138)	0.171 (0.226)	0.00011 (0.000511)	0.249 (0.307)
amp 6p21 1	158 (43%)	212	1e-05 (7.2e-05)	0.00682 (0.0158)	0.00368 (0.00961)	0.0578 (0.092)	0.0986 (0.142)	0.181 (0.235)	0.436 (0.495)	0.007 (0.0161)	0.0435 (0.0723)	0.399 (0.456)
del 2q37 3	62 (17%)	308	1e-05 (7.2e-05)	0.0826 (0.122)	0.564 (0.616)	0.163 (0.218)	0.00012 (0.00054)	0.00291 (0.0081)	0.175 (0.229)	0.00635 (0.0149)	0.124 (0.174)	0.00347 (0.00918)
del 4p16 3	85 (23%)	285	1e-05 (7.2e-05)	0.0134 (0.0276)	0.011 (0.0235)	0.225 (0.283)	0.109 (0.155)	0.0618 (0.0962)	0.147 (0.199)	0.00483 (0.0119)	0.0777 (0.116)	0.00011 (0.000511)
del 11q14 1	77 (21%)	293	0.0105 (0.0226)	0.0293 (0.0519)	0.704 (0.739)	0.856 (0.872)	0.0221 (0.0411)	0.123 (0.173)	0.695 (0.731)	0.129 (0.18)	0.00451 (0.0113)	0.0298 (0.0524)
amp 6q12	109 (29%)	261	1e-05 (7.2e-05)	0.00906 (0.0204)	0.135 (0.187)	0.504 (0.564)	0.137 (0.189)	0.0295 (0.0521)	0.202 (0.258)	0.304 (0.364)	0.00391 (0.01)	0.25 (0.307)
amp 9q34 2	47 (13%)	323	0.00632 (0.0149)	0.247 (0.306)	0.183 (0.237)	0.174 (0.228)	0.0251 (0.0458)	0.165 (0.219)	0.0976 (0.141)	0.0281 (0.0499)	0.0233 (0.043)	0.145 (0.196)
amp 12q14 1	56 (15%)	314	0.149 (0.201)	0.68 (0.718)	0.204 (0.26)	0.0469 (0.0769)	0.00189 (0.00563)	0.0019 (0.00563)	0.13 (0.181)	0.131 (0.182)	0.0479 (0.0781)	0.186 (0.241)
del 8p23 2	247 (67%)	123	4e-05 (0.000219)	0.00023 (0.000969)	0.828 (0.85)	0.813 (0.836)	0.188 (0.242)	0.027 (0.0488)	0.532 (0.59)	0.0597 (0.0944)	0.45 (0.507)	0.0427 (0.0715)
del 8p12	242 (65%)	128	1e-05 (7.2e-05)	0.00123 (0.0039)	0.393 (0.451)	0.737 (0.769)	0.128 (0.179)	0.0102 (0.0223)	0.54 (0.595)	0.0188 (0.0365)	0.141 (0.194)	0.179 (0.233)
del 12p12 1	78 (21%)	292	0.00308 (0.00841)	0.0165 (0.0328)	0.58 (0.629)	0.721 (0.756)	0.0467 (0.0767)	0.274 (0.333)	0.1 (0.144)	0.019 (0.0367)	0.05 (0.0806)	0.0606 (0.0951)
del 18q21 2	94 (25%)	276	0.0214 (0.0404)	0.00384 (0.00989)	0.969 (0.974)	0.923 (0.931)	0.68 (0.718)	0.00997 (0.0219)	0.306 (0.365)	0.17 (0.225)	0.0247 (0.0455)	0.207 (0.262)
del xq26 2	67 (18%)	303	1e-05 (7.2e-05)	0.00682 (0.0158)	0.365 (0.422)	0.311 (0.369)	0.00088 (0.00287)	0.448 (0.505)	0.0308 (0.0538)	0.48 (0.538)	0.0747 (0.112)	0.887 (0.896)
amp 5q35 3	135 (36%)	235	0.00167 (0.00513)	0.438 (0.496)	0.635 (0.683)	0.627 (0.676)	0.0187 (0.0365)	0.248 (0.307)	0.0355 (0.0609)	0.274 (0.333)	0.0867 (0.127)	0.788 (0.816)
del 2q22 1	52 (14%)	318	0.00031 (0.00124)	0.0275 (0.0495)	0.648 (0.694)	0.322 (0.381)	0.0217 (0.0407)	0.0689 (0.105)	0.653 (0.697)	0.14 (0.193)	0.726 (0.759)	0.226 (0.283)
del 11q25	94 (25%)	276	0.0122 (0.0256)	0.0613 (0.0956)	0.318 (0.376)	0.619 (0.669)	0.207 (0.262)	0.0491 (0.0794)	0.509 (0.569)	0.212 (0.268)	0.0602 (0.095)	0.019 (0.0367)
del 22q13 32	83 (22%)	287	1e-05 (7.2e-05)	0.0787 (0.117)	0.00489 (0.012)	0.984 (0.987)	0.00434 (0.011)	0.165 (0.219)	0.68 (0.718)	0.0719 (0.109)	0.0655 (0.101)	0.279 (0.338)
amp 7q31 2	120 (32%)	250	0.0241 (0.0444)	0.0023 (0.00668)	0.173 (0.228)	0.657 (0.697)	0.764 (0.794)	0.797 (0.823)	0.342 (0.399)	0.798 (0.824)	0.635 (0.683)	0.525 (0.584)
amp 15q26 3	54 (15%)	316	0.0596 (0.0944)	0.657 (0.697)	0.767 (0.795)	0.0849 (0.125)	0.0366 (0.0623)	0.00787 (0.0179)	0.867 (0.881)	0.144 (0.196)	0.367 (0.424)	0.432 (0.491)
del 6q27	136 (37%)	234	0.00052 (0.00187)	0.0195 (0.0373)	0.143 (0.195)	0.327 (0.386)	0.207 (0.263)	0.575 (0.626)	0.222 (0.279)	0.349 (0.405)	0.237 (0.296)	0.188 (0.242)
del 22q12 1	79 (21%)	291	5e-05 (0.000261)	0.151 (0.202)	0.00343 (0.00912)	0.968 (0.974)	0.164 (0.218)	0.115 (0.162)	0.543 (0.597)	0.103 (0.148)	0.0851 (0.125)	0.197 (0.253)
del 12q24 33	59 (16%)	311	0.00045 (0.00165)	0.208 (0.263)	0.13 (0.181)	0.989 (0.99)	0.589 (0.638)	0.844 (0.865)	0.548 (0.6)	0.846 (0.865)	0.358 (0.414)	0.656 (0.697)
amp 17p11 2	46 (12%)	324	0.156 (0.209)	0.0721 (0.109)	0.372 (0.427)	0.535 (0.592)	0.26 (0.317)	0.343 (0.399)	0.753 (0.785)	0.286 (0.343)	0.309 (0.368)	0.334 (0.393)
del 20p12 1	29 (8%)	341	0.143 (0.195)	0.85 (0.868)	0.547 (0.599)	0.512 (0.571)	0.541 (0.595)	0.764 (0.794)	0.302 (0.361)	0.805 (0.829)	0.57 (0.621)	0.867 (0.881)

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
AMP PEAK 1(1Q21.3) MUTATED	47	98	126
AMP PEAK 1(1Q21.3) WILD-TYPE	54	33	12

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

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S2. Gene #1: 'amp_1q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
AMP PEAK 1(1Q21.3) MUTATED	41	123	87	20
AMP PEAK 1(1Q21.3) WILD-TYPE	20	40	12	27

Figure S2. Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0211 (Fisher's exact test), Q value = 0.04

Table S3. Gene #1: 'amp_1q21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	45	38	18	38
AMP PEAK 1(1Q21.3) MUTATED	28	25	30	17	27
AMP PEAK 1(1Q21.3) WILD-TYPE	11	20	8	1	11

Figure S3. Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00079

Table S4. Gene #1: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
AMP PEAK 1(1Q21.3) MUTATED	99	61	39	57	10
AMP PEAK 1(1Q21.3) WILD-TYPE	26	28	11	15	18

Figure S4. Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00031

Table S5. Gene #1: 'amp_1q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
AMP PEAK 1(1Q21.3) MUTATED	118	98	50	0
AMP PEAK 1(1Q21.3) WILD-TYPE	33	47	11	7

Figure S5. Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_CNMF'

P value = 0.00694 (Fisher's exact test), Q value = 0.016

Table S6. Gene #1: 'amp_1q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	45	60	103	45	63	37	12
AMP PEAK 1(1Q21.3) MUTATED	39	38	73	35	49	29	4
AMP PEAK 1(1Q21.3) WILD-TYPE	6	22	30	10	14	8	8

Figure S6. Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00079

Table S7. Gene #1: 'amp_1q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
AMP PEAK 1(1Q21.3) MUTATED	36	51	43	91	44	2
AMP PEAK 1(1Q21.3) WILD-TYPE	5	35	9	30	13	6

Figure S7. Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0044 (Fisher's exact test), Q value = 0.011

Table S8. Gene #1: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
AMP PEAK 1(1Q21.3) MUTATED	29	43	59	7	37	58	19
AMP PEAK 1(1Q21.3) WILD-TYPE	12	11	9	11	16	24	5

Figure S8. Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 0.033

Table S9. Gene #1: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
AMP PEAK 1(1Q21.3) MUTATED	101	30	52	34	34	1
AMP PEAK 1(1Q21.3) WILD-TYPE	27	20	19	6	13	3

Figure S9. Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q42.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S10. Gene #2: 'amp_1q42.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
AMP PEAK 2(1Q42.2) MUTATED	57	87	124
AMP PEAK 2(1Q42.2) WILD-TYPE	44	44	14

Figure S10. Get High-res Image Gene #2: 'amp_1q42.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q42.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S11. Gene #2: 'amp_1q42.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
AMP PEAK 2(1Q42.2) MUTATED	42	123	84	19
AMP PEAK 2(1Q42.2) WILD-TYPE	19	40	15	28

Figure S11. Get High-res Image Gene #2: 'amp_1q42.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q42.2' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00047

Table S12. Gene #2: 'amp_1q42.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
AMP PEAK 2(1Q42.2) MUTATED	98	56	40	58	11
AMP PEAK 2(1Q42.2) WILD-TYPE	27	33	10	14	17

Figure S12. Get High-res Image Gene #2: 'amp_1q42.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q42.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S13. Gene #2: 'amp_1q42.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
AMP PEAK 2(1Q42.2) MUTATED	118	94	51	0
AMP PEAK 2(1Q42.2) WILD-TYPE	33	51	10	7

Figure S13. Get High-res Image Gene #2: 'amp_1q42.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1q42.2' versus 'MIRSEQ_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.036

Table S14. Gene #2: 'amp_1q42.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	45	60	103	45	63	37	12
AMP PEAK 2(1Q42.2) MUTATED	33	38	74	37	51	27	4
AMP PEAK 2(1Q42.2) WILD-TYPE	12	22	29	8	12	10	8

Figure S14. Get High-res Image Gene #2: 'amp_1q42.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q42.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00184 (Fisher's exact test), Q value = 0.0055

Table S15. Gene #2: 'amp_1q42.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
AMP PEAK 2(1Q42.2) MUTATED	30	52	42	91	47	2
AMP PEAK 2(1Q42.2) WILD-TYPE	11	34	10	30	10	6

Figure S15. Get High-res Image Gene #2: 'amp_1q42.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1q42.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0016 (Fisher's exact test), Q value = 0.005

Table S16. Gene #2: 'amp_1q42.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
AMP PEAK 2(1Q42.2) MUTATED	103	26	53	29	37	1
AMP PEAK 2(1Q42.2) WILD-TYPE	25	24	18	11	10	3

Figure S16. Get High-res Image Gene #2: 'amp_1q42.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_2p24.1' versus 'CN_CNMF'

P value = 0.0028 (Fisher's exact test), Q value = 0.0079

Table S17. Gene #3: 'amp_2p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
AMP PEAK 3(2P24.1) MUTATED	8	32	25
AMP PEAK 3(2P24.1) WILD-TYPE	93	99	113

Figure S17. Get High-res Image Gene #3: 'amp_2p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2p24.1' versus 'METHLYATION_CNMF'

P value = 0.0037 (Fisher's exact test), Q value = 0.0096

Table S18. Gene #3: 'amp_2p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
AMP PEAK 3(2P24.1) MUTATED	16	29	19	1
AMP PEAK 3(2P24.1) WILD-TYPE	45	134	80	46

Figure S18. Get High-res Image Gene #3: 'amp_2p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_2p24.1' versus 'MRNASEQ_CNMF'

P value = 0.00536 (Fisher's exact test), Q value = 0.013

Table S19. Gene #3: 'amp_2p24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
AMP PEAK 3(2P24.1) MUTATED	30	20	4	8	1
AMP PEAK 3(2P24.1) WILD-TYPE	95	69	46	64	27

Figure S19. Get High-res Image Gene #3: 'amp_2p24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_2p24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0462 (Fisher's exact test), Q value = 0.076

Table S20. Gene #3: 'amp_2p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
AMP PEAK 3(2P24.1) MUTATED	13	18	10	18	5	0
AMP PEAK 3(2P24.1) WILD-TYPE	28	68	42	103	52	8

Figure S20. Get High-res Image Gene #3: 'amp_2p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_2p24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0058 (Fisher's exact test), Q value = 0.014

Table S21. Gene #3: 'amp_2p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
AMP PEAK 3(2P24.1) MUTATED	6	17	18	0	5	11	4
AMP PEAK 3(2P24.1) WILD-TYPE	35	37	50	18	48	71	20

Figure S21. Get High-res Image Gene #3: 'amp_2p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_2q33.1' versus 'CN_CNMF'

P value = 0.00294 (Fisher's exact test), Q value = 0.0081

Table S22. Gene #4: 'amp_2q33.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
AMP PEAK 4(2Q33.1) MUTATED	7	29	28
AMP PEAK 4(2Q33.1) WILD-TYPE	94	102	110

Figure S22. Get High-res Image Gene #4: 'amp_2q33.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2q33.1' versus 'METHLYATION_CNMF'

P value = 0.00452 (Fisher's exact test), Q value = 0.011

Table S23. Gene #4: 'amp_2q33.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
AMP PEAK 4(2Q33.1) MUTATED	13	27	23	1
AMP PEAK 4(2Q33.1) WILD-TYPE	48	136	76	46

Figure S23. Get High-res Image Gene #4: 'amp_2q33.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_2q33.1' versus 'MRNASEQ_CNMF'

P value = 0.0377 (Fisher's exact test), Q value = 0.064

Table S24. Gene #4: 'amp_2q33.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
AMP PEAK 4(2Q33.1) MUTATED	31	13	6	11	1
AMP PEAK 4(2Q33.1) WILD-TYPE	94	76	44	61	27

Figure S24. Get High-res Image Gene #4: 'amp_2q33.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_2q33.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0445 (Fisher's exact test), Q value = 0.074

Table S25. Gene #4: 'amp_2q33.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
AMP PEAK 4(2Q33.1) MUTATED	35	17	10	0
AMP PEAK 4(2Q33.1) WILD-TYPE	116	128	51	7

Figure S25. Get High-res Image Gene #4: 'amp_2q33.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_2q33.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00051

Table S26. Gene #4: 'amp_2q33.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
AMP PEAK 4(2Q33.1) MUTATED	7	16	20	0	5	6	7
AMP PEAK 4(2Q33.1) WILD-TYPE	34	38	48	18	48	76	17

Figure S26. Get High-res Image Gene #4: 'amp_2q33.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S27. Gene #5: 'amp_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
AMP PEAK 5(3Q26.31) MUTATED	6	47	24
AMP PEAK 5(3Q26.31) WILD-TYPE	95	84	114

Figure S27. Get High-res Image Gene #5: 'amp_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.31' versus 'METHLYATION_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.0022

Table S28. Gene #5: 'amp_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
AMP PEAK 5(3Q26.31) MUTATED	17	40	19	1
AMP PEAK 5(3Q26.31) WILD-TYPE	44	123	80	46

Figure S28. Get High-res Image Gene #5: 'amp_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q26.31' versus 'MRNASEQ_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.037

Table S29. Gene #5: 'amp_3q26.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
AMP PEAK 5(3Q26.31) MUTATED	32	26	5	10	4
AMP PEAK 5(3Q26.31) WILD-TYPE	93	63	45	62	24

Figure S29. Get High-res Image Gene #5: 'amp_3q26.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3q26.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0354 (Fisher's exact test), Q value = 0.061

Table S30. Gene #5: 'amp_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
AMP PEAK 5(3Q26.31) MUTATED	15	20	10	25	6	0
AMP PEAK 5(3Q26.31) WILD-TYPE	26	66	42	96	51	8

Figure S30. Get High-res Image Gene #5: 'amp_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00618 (Fisher's exact test), Q value = 0.015

Table S31. Gene #5: 'amp_3q26.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
AMP PEAK 5(3Q26.31) MUTATED	7	20	14	0	12	11	7
AMP PEAK 5(3Q26.31) WILD-TYPE	34	34	54	18	41	71	17

Figure S31. Get High-res Image Gene #5: 'amp_3q26.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0277 (Fisher's exact test), Q value = 0.05

Table S32. Gene #5: 'amp_3q26.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
AMP PEAK 5(3Q26.31) MUTATED	24	12	16	15	4	0
AMP PEAK 5(3Q26.31) WILD-TYPE	104	38	55	25	43	4

Figure S32. Get High-res Image Gene #5: 'amp_3q26.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4p14' versus 'CN_CNMF'

P value = 0.00859 (Fisher's exact test), Q value = 0.019

Table S33. Gene #6: 'amp_4p14' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
AMP PEAK 6(4P14) MUTATED	6	24	24
AMP PEAK 6(4P14) WILD-TYPE	95	107	114

Figure S33. Get High-res Image Gene #6: 'amp_4p14' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4p14' versus 'METHLYATION_CNMF'

P value = 0.00323 (Fisher's exact test), Q value = 0.0087

Table S34. Gene #6: 'amp_4p14' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
AMP PEAK 6(4P14) MUTATED	8	19	25	2
AMP PEAK 6(4P14) WILD-TYPE	53	144	74	45

Figure S34. Get High-res Image Gene #6: 'amp_4p14' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_4p14' versus 'RPPA_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.026

Table S35. Gene #6: 'amp_4p14' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	73	19	22	22	1
AMP PEAK 6(4P14) MUTATED	5	6	7	4	4	1
AMP PEAK 6(4P14) WILD-TYPE	36	67	12	18	18	0

Figure S35. Get High-res Image Gene #6: 'amp_4p14' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_4p14' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S36. Gene #6: 'amp_4p14' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
AMP PEAK 6(4P14) MUTATED	31	15	6	1	0
AMP PEAK 6(4P14) WILD-TYPE	94	74	44	71	28

Figure S36. Get High-res Image Gene #6: 'amp_4p14' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_4p14' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.0016

Table S37. Gene #6: 'amp_4p14' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
AMP PEAK 6(4P14) MUTATED	33	19	1	0
AMP PEAK 6(4P14) WILD-TYPE	118	126	60	7

Figure S37. Get High-res Image Gene #6: 'amp_4p14' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_4p14' versus 'MIRSEQ_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.05

Table S38. Gene #6: 'amp_4p14' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	45	60	103	45	63	37	12
AMP PEAK 6(4P14) MUTATED	8	11	8	4	14	9	0
AMP PEAK 6(4P14) WILD-TYPE	37	49	95	41	49	28	12

Figure S38. Get High-res Image Gene #6: 'amp_4p14' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_4p14' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.028

Table S39. Gene #6: 'amp_4p14' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
AMP PEAK 6(4P14) MUTATED	7	13	10	23	1	0
AMP PEAK 6(4P14) WILD-TYPE	34	73	42	98	56	8

Figure S39. Get High-res Image Gene #6: 'amp_4p14' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_4p14' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00093 (Fisher's exact test), Q value = 0.003

Table S40. Gene #6: 'amp_4p14' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
AMP PEAK 6(4P14) MUTATED	2	13	19	1	10	5	4
AMP PEAK 6(4P14) WILD-TYPE	39	41	49	17	43	77	20

Figure S40. Get High-res Image Gene #6: 'amp_4p14' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S41. Gene #7: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
AMP PEAK 7(5P15.33) MUTATED	19	69	75
AMP PEAK 7(5P15.33) WILD-TYPE	82	62	63

Figure S41. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 0.00218 (Fisher's exact test), Q value = 0.0064

Table S42. Gene #7: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
AMP PEAK 7(5P15.33) MUTATED	27	79	48	9
AMP PEAK 7(5P15.33) WILD-TYPE	34	84	51	38

Figure S42. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.0491 (Fisher's exact test), Q value = 0.079

Table S43. Gene #7: 'amp_5p15.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	45	38	18	38
AMP PEAK 7(5P15.33) MUTATED	17	15	25	10	17
AMP PEAK 7(5P15.33) WILD-TYPE	22	30	13	8	21

Figure S43. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.023

Table S44. Gene #7: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
AMP PEAK 7(5P15.33) MUTATED	59	45	21	32	4
AMP PEAK 7(5P15.33) WILD-TYPE	66	44	29	40	24

Figure S44. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00979 (Fisher's exact test), Q value = 0.022

Table S45. Gene #7: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
AMP PEAK 7(5P15.33) MUTATED	23	42	30	44	20	1
AMP PEAK 7(5P15.33) WILD-TYPE	18	44	22	77	37	7

Figure S45. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.022

Table S46. Gene #7: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
AMP PEAK 7(5P15.33) MUTATED	64	26	23	23	16	0
AMP PEAK 7(5P15.33) WILD-TYPE	64	24	48	17	31	4

Figure S46. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5q35.3' versus 'CN_CNMF'

P value = 0.00167 (Fisher's exact test), Q value = 0.0051

Table S47. Gene #8: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
AMP PEAK 8(5Q35.3) MUTATED	27	42	66
AMP PEAK 8(5Q35.3) WILD-TYPE	74	89	72

Figure S47. Get High-res Image Gene #8: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q35.3' versus 'MRNASEQ_CNMF'

P value = 0.0187 (Fisher's exact test), Q value = 0.037

Table S48. Gene #8: 'amp_5q35.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
AMP PEAK 8(5Q35.3) MUTATED	42	30	23	33	4
AMP PEAK 8(5Q35.3) WILD-TYPE	83	59	27	39	24

Figure S48. Get High-res Image Gene #8: 'amp_5q35.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5q35.3' versus 'MIRSEQ_CNMF'

P value = 0.0355 (Fisher's exact test), Q value = 0.061

Table S49. Gene #8: 'amp_5q35.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	45	60	103	45	63	37	12
AMP PEAK 8(5Q35.3) MUTATED	15	28	37	22	16	13	1
AMP PEAK 8(5Q35.3) WILD-TYPE	30	32	66	23	47	24	11

Figure S49. Get High-res Image Gene #8: 'amp_5q35.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6p25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S50. Gene #9: 'amp_6p25.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
AMP PEAK 9(6P25.2) MUTATED	15	64	80
AMP PEAK 9(6P25.2) WILD-TYPE	86	67	58

Figure S50. Get High-res Image Gene #9: 'amp_6p25.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p25.2' versus 'METHLYATION_CNMF'

P value = 0.00124 (Fisher's exact test), Q value = 0.0039

Table S51. Gene #9: 'amp_6p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
AMP PEAK 9(6P25.2) MUTATED	21	76	52	10
AMP PEAK 9(6P25.2) WILD-TYPE	40	87	47	37

Figure S51. Get High-res Image Gene #9: 'amp_6p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p25.2' versus 'MRNASEQ_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.023

Table S52. Gene #9: 'amp_6p25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
AMP PEAK 9(6P25.2) MUTATED	61	37	18	38	5
AMP PEAK 9(6P25.2) WILD-TYPE	64	52	32	34	23

Figure S52. Get High-res Image Gene #9: 'amp_6p25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6p25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0128 (Fisher's exact test), Q value = 0.027

Table S53. Gene #9: 'amp_6p25.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
AMP PEAK 9(6P25.2) MUTATED	76	51	31	1
AMP PEAK 9(6P25.2) WILD-TYPE	75	94	30	6

Figure S53. Get High-res Image Gene #9: 'amp_6p25.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6p25.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0473 (Fisher's exact test), Q value = 0.077

Table S54. Gene #9: 'amp_6p25.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
AMP PEAK 9(6P25.2) MUTATED	22	28	24	50	30	1
AMP PEAK 9(6P25.2) WILD-TYPE	19	58	28	71	27	7

Figure S54. Get High-res Image Gene #9: 'amp_6p25.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6p25.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00333 (Fisher's exact test), Q value = 0.009

Table S55. Gene #9: 'amp_6p25.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
AMP PEAK 9(6P25.2) MUTATED	13	29	38	2	19	30	10
AMP PEAK 9(6P25.2) WILD-TYPE	28	25	30	16	34	52	14

Figure S55. Get High-res Image Gene #9: 'amp_6p25.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_6p21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S56. Gene #10: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
AMP PEAK 10(6P21.1) MUTATED	17	65	76
AMP PEAK 10(6P21.1) WILD-TYPE	84	66	62

Figure S56. Get High-res Image Gene #10: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p21.1' versus 'METHLYATION_CNMF'

P value = 0.00682 (Fisher's exact test), Q value = 0.016

Table S57. Gene #10: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
AMP PEAK 10(6P21.1) MUTATED	21	79	47	11
AMP PEAK 10(6P21.1) WILD-TYPE	40	84	52	36

Figure S57. Get High-res Image Gene #10: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p21.1' versus 'RPPA_CNMF'

P value = 0.00368 (Fisher's exact test), Q value = 0.0096

Table S58. Gene #10: 'amp_6p21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	73	19	22	22	1
AMP PEAK 10(6P21.1) MUTATED	13	31	8	17	14	1
AMP PEAK 10(6P21.1) WILD-TYPE	28	42	11	5	8	0

Figure S58. Get High-res Image Gene #10: 'amp_6p21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_6p21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.007 (Fisher's exact test), Q value = 0.016

Table S59. Gene #10: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
AMP PEAK 10(6P21.1) MUTATED	23	25	23	53	31	1
AMP PEAK 10(6P21.1) WILD-TYPE	18	61	29	68	26	7

Figure S59. Get High-res Image Gene #10: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0435 (Fisher's exact test), Q value = 0.072

Table S60. Gene #10: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
AMP PEAK 10(6P21.1) MUTATED	12	31	30	6	19	30	14
AMP PEAK 10(6P21.1) WILD-TYPE	29	23	38	12	34	52	10

Figure S60. Get High-res Image Gene #10: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_6q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S61. Gene #11: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
AMP PEAK 11(6Q12) MUTATED	8	53	48
AMP PEAK 11(6Q12) WILD-TYPE	93	78	90

Figure S61. Get High-res Image Gene #11: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q12' versus 'METHLYATION_CNMF'

P value = 0.00906 (Fisher's exact test), Q value = 0.02

Table S62. Gene #11: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
AMP PEAK 11(6Q12) MUTATED	18	50	36	5
AMP PEAK 11(6Q12) WILD-TYPE	43	113	63	42

Figure S62. Get High-res Image Gene #11: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0295 (Fisher's exact test), Q value = 0.052

Table S63. Gene #11: 'amp_6q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
AMP PEAK 11(6Q12) MUTATED	58	35	15	1
AMP PEAK 11(6Q12) WILD-TYPE	93	110	46	6

Figure S63. Get High-res Image Gene #11: 'amp_6q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00391 (Fisher's exact test), Q value = 0.01

Table S64. Gene #11: 'amp_6q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
AMP PEAK 11(6Q12) MUTATED	11	22	25	1	15	15	11
AMP PEAK 11(6Q12) WILD-TYPE	30	32	43	17	38	67	13

Figure S64. Get High-res Image Gene #11: 'amp_6q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_6q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S65. Gene #12: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
AMP PEAK 12(6Q12) MUTATED	5	37	41
AMP PEAK 12(6Q12) WILD-TYPE	96	94	97

Figure S65. Get High-res Image Gene #12: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q12' versus 'METHLYATION_CNMF'

P value = 0.00164 (Fisher's exact test), Q value = 0.0051

Table S66. Gene #12: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
AMP PEAK 12(6Q12) MUTATED	13	34	33	3
AMP PEAK 12(6Q12) WILD-TYPE	48	129	66	44

Figure S66. Get High-res Image Gene #12: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q12' versus 'RPPA_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.025

Table S67. Gene #12: 'amp_6q12' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	73	19	22	22	1
AMP PEAK 12(6Q12) MUTATED	8	13	6	8	12	0
AMP PEAK 12(6Q12) WILD-TYPE	33	60	13	14	10	1

Figure S67. Get High-res Image Gene #12: 'amp_6q12' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_6q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.0435 (Fisher's exact test), Q value = 0.072

Table S68. Gene #12: 'amp_6q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	45	38	18	38
AMP PEAK 12(6Q12) MUTATED	11	6	12	9	9
AMP PEAK 12(6Q12) WILD-TYPE	28	39	26	9	29

Figure S68. Get High-res Image Gene #12: 'amp_6q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_6q12' versus 'MRNASEQ_CNMF'

P value = 0.0198 (Fisher's exact test), Q value = 0.038

Table S69. Gene #12: 'amp_6q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
AMP PEAK 12(6Q12) MUTATED	39	14	12	16	2
AMP PEAK 12(6Q12) WILD-TYPE	86	75	38	56	26

Figure S69. Get High-res Image Gene #12: 'amp_6q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00996 (Fisher's exact test), Q value = 0.022

Table S70. Gene #12: 'amp_6q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
AMP PEAK 12(6Q12) MUTATED	47	24	12	0
AMP PEAK 12(6Q12) WILD-TYPE	104	121	49	7

Figure S70. Get High-res Image Gene #12: 'amp_6q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00075 (Fisher's exact test), Q value = 0.0025

Table S71. Gene #12: 'amp_6q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
AMP PEAK 12(6Q12) MUTATED	5	17	23	1	11	10	10
AMP PEAK 12(6Q12) WILD-TYPE	36	37	45	17	42	72	14

Figure S71. Get High-res Image Gene #12: 'amp_6q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7q31.2' versus 'CN_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.044

Table S72. Gene #13: 'amp_7q31.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
AMP PEAK 13(7Q31.2) MUTATED	22	49	49
AMP PEAK 13(7Q31.2) WILD-TYPE	79	82	89

Figure S72. Get High-res Image Gene #13: 'amp_7q31.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q31.2' versus 'METHLYATION_CNMF'

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

Table S73. Gene #13: 'amp_7q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
AMP PEAK 13(7Q31.2) MUTATED	22	66	25	7
AMP PEAK 13(7Q31.2) WILD-TYPE	39	97	74	40

Figure S73. Get High-res Image Gene #13: 'amp_7q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S74. Gene #14: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
AMP PEAK 14(8Q24.21) MUTATED	53	63	115
AMP PEAK 14(8Q24.21) WILD-TYPE	48	68	23

Figure S74. Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0013

Table S75. Gene #14: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
AMP PEAK 14(8Q24.21) MUTATED	44	95	73	19
AMP PEAK 14(8Q24.21) WILD-TYPE	17	68	26	28

Figure S75. Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S76. Gene #14: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
AMP PEAK 14(8Q24.21) MUTATED	90	33	41	53	9
AMP PEAK 14(8Q24.21) WILD-TYPE	35	56	9	19	19

Figure S76. Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S77. Gene #14: 'amp_8q24.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
AMP PEAK 14(8Q24.21) MUTATED	110	70	45	1
AMP PEAK 14(8Q24.21) WILD-TYPE	41	75	16	6

Figure S77. Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.04

Table S78. Gene #14: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	45	60	103	45	63	37	12
AMP PEAK 14(8Q24.21) MUTATED	25	28	66	33	46	24	5
AMP PEAK 14(8Q24.21) WILD-TYPE	20	32	37	12	17	13	7

Figure S78. Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S79. Gene #14: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
AMP PEAK 14(8Q24.21) MUTATED	22	38	34	88	43	2
AMP PEAK 14(8Q24.21) WILD-TYPE	19	48	18	33	14	6

Figure S79. Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S80. Gene #14: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
AMP PEAK 14(8Q24.21) MUTATED	24	23	57	5	37	52	19
AMP PEAK 14(8Q24.21) WILD-TYPE	17	31	11	13	16	30	5

Figure S80. Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00087

Table S81. Gene #14: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
AMP PEAK 14(8Q24.21) MUTATED	86	20	51	22	37	1
AMP PEAK 14(8Q24.21) WILD-TYPE	42	30	20	18	10	3

Figure S81. Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9q34.2' versus 'CN_CNMF'

P value = 0.00632 (Fisher's exact test), Q value = 0.015

Table S82. Gene #15: 'amp_9q34.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
AMP PEAK 15(9Q34.2) MUTATED	5	24	18
AMP PEAK 15(9Q34.2) WILD-TYPE	96	107	120

Figure S82. Get High-res Image Gene #15: 'amp_9q34.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9q34.2' versus 'MRNASEQ_CNMF'

P value = 0.0251 (Fisher's exact test), Q value = 0.046

Table S83. Gene #15: 'amp_9q34.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
AMP PEAK 15(9Q34.2) MUTATED	21	16	4	3	2
AMP PEAK 15(9Q34.2) WILD-TYPE	104	73	46	69	26

Figure S83. Get High-res Image Gene #15: 'amp_9q34.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_9q34.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0281 (Fisher's exact test), Q value = 0.05

Table S84. Gene #15: 'amp_9q34.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
AMP PEAK 15(9Q34.2) MUTATED	10	16	7	11	3	0
AMP PEAK 15(9Q34.2) WILD-TYPE	31	70	45	110	54	8

Figure S84. Get High-res Image Gene #15: 'amp_9q34.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_9q34.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0233 (Fisher's exact test), Q value = 0.043

Table S85. Gene #15: 'amp_9q34.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
AMP PEAK 15(9Q34.2) MUTATED	3	15	11	2	7	6	1
AMP PEAK 15(9Q34.2) WILD-TYPE	38	39	57	16	46	76	23

Figure S85. Get High-res Image Gene #15: 'amp_9q34.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_11q13.3' versus 'CN_CNMF'

P value = 0.0419 (Fisher's exact test), Q value = 0.07

Table S86. Gene #16: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
AMP PEAK 16(11Q13.3) MUTATED	15	28	14
AMP PEAK 16(11Q13.3) WILD-TYPE	86	103	124

Figure S86. Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 0.046

Table S87. Gene #16: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
AMP PEAK 16(11Q13.3) MUTATED	15	27	13	2
AMP PEAK 16(11Q13.3) WILD-TYPE	46	136	86	45

Figure S87. Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00097

Table S88. Gene #16: 'amp_11q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
AMP PEAK 16(11Q13.3) MUTATED	24	23	4	3	1
AMP PEAK 16(11Q13.3) WILD-TYPE	101	66	46	69	27

Figure S88. Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.004 (Fisher's exact test), Q value = 0.01

Table S89. Gene #16: 'amp_11q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
AMP PEAK 16(11Q13.3) MUTATED	22	31	2	0
AMP PEAK 16(11Q13.3) WILD-TYPE	129	114	59	7

Figure S89. Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

P value = 0.0097 (Fisher's exact test), Q value = 0.022

Table S90. Gene #16: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	45	60	103	45	63	37	12
AMP PEAK 16(11Q13.3) MUTATED	10	16	7	6	12	6	0
AMP PEAK 16(11Q13.3) WILD-TYPE	35	44	96	39	51	31	12

Figure S90. Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00443 (Fisher's exact test), Q value = 0.011

Table S91. Gene #16: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
AMP PEAK 16(11Q13.3) MUTATED	11	20	6	18	2	0
AMP PEAK 16(11Q13.3) WILD-TYPE	30	66	46	103	55	8

Figure S91. Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00247 (Fisher's exact test), Q value = 0.0071

Table S92. Gene #16: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
AMP PEAK 16(11Q13.3) MUTATED	25	10	9	10	0	0
AMP PEAK 16(11Q13.3) WILD-TYPE	103	40	62	30	47	4

Figure S92. Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q14.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0469 (Fisher's exact test), Q value = 0.077

Table S93. Gene #17: 'amp_12q14.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	45	38	18	38
AMP PEAK 17(12Q14.1) MUTATED	7	5	11	4	2
AMP PEAK 17(12Q14.1) WILD-TYPE	32	40	27	14	36

Figure S93. Get High-res Image Gene #17: 'amp_12q14.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_12q14.1' versus 'MRNASEQ_CNMF'

P value = 0.00189 (Fisher's exact test), Q value = 0.0056

Table S94. Gene #17: 'amp_12q14.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
AMP PEAK 17(12Q14.1) MUTATED	31	13	7	4	1
AMP PEAK 17(12Q14.1) WILD-TYPE	94	76	43	68	27

Figure S94. Get High-res Image Gene #17: 'amp_12q14.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0019 (Fisher's exact test), Q value = 0.0056

Table S95. Gene #17: 'amp_12q14.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
AMP PEAK 17(12Q14.1) MUTATED	34	19	2	1
AMP PEAK 17(12Q14.1) WILD-TYPE	117	126	59	6

Figure S95. Get High-res Image Gene #17: 'amp_12q14.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0479 (Fisher's exact test), Q value = 0.078

Table S96. Gene #17: 'amp_12q14.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
AMP PEAK 17(12Q14.1) MUTATED	10	10	11	2	12	5	2
AMP PEAK 17(12Q14.1) WILD-TYPE	31	44	57	16	41	77	22

Figure S96. Get High-res Image Gene #17: 'amp_12q14.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_13q32.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S97. Gene #18: 'amp_13q32.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
AMP PEAK 18(13Q32.3) MUTATED	1	34	32
AMP PEAK 18(13Q32.3) WILD-TYPE	100	97	106

Figure S97. Get High-res Image Gene #18: 'amp_13q32.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q32.3' versus 'METHLYATION_CNMF'

P value = 0.015 (Fisher's exact test), Q value = 0.03

Table S98. Gene #18: 'amp_13q32.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
AMP PEAK 18(13Q32.3) MUTATED	13	25	26	3
AMP PEAK 18(13Q32.3) WILD-TYPE	48	138	73	44

Figure S98. Get High-res Image Gene #18: 'amp_13q32.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q32.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0364 (Fisher's exact test), Q value = 0.062

Table S99. Gene #18: 'amp_13q32.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	45	38	18	38
AMP PEAK 18(13Q32.3) MUTATED	8	3	9	7	7
AMP PEAK 18(13Q32.3) WILD-TYPE	31	42	29	11	31

Figure S99. Get High-res Image Gene #18: 'amp_13q32.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_13q32.3' versus 'MRNASEQ_CNMF'

P value = 0.00258 (Fisher's exact test), Q value = 0.0074

Table S100. Gene #18: 'amp_13q32.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
AMP PEAK 18(13Q32.3) MUTATED	34	15	8	9	0
AMP PEAK 18(13Q32.3) WILD-TYPE	91	74	42	63	28

Figure S100. Get High-res Image Gene #18: 'amp_13q32.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_13q32.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.023

Table S101. Gene #18: 'amp_13q32.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
AMP PEAK 18(13Q32.3) MUTATED	39	21	6	0
AMP PEAK 18(13Q32.3) WILD-TYPE	112	124	55	7

Figure S101. Get High-res Image Gene #18: 'amp_13q32.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_13q32.3' versus 'MIRSEQ_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.026

Table S102. Gene #18: 'amp_13q32.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	45	60	103	45	63	37	12
AMP PEAK 18(13Q32.3) MUTATED	14	10	12	6	13	12	0
AMP PEAK 18(13Q32.3) WILD-TYPE	31	50	91	39	50	25	12

Figure S102. Get High-res Image Gene #18: 'amp_13q32.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_13q32.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0019

Table S103. Gene #18: 'amp_13q32.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
AMP PEAK 18(13Q32.3) MUTATED	4	13	22	0	8	8	8
AMP PEAK 18(13Q32.3) WILD-TYPE	37	41	46	18	45	74	16

Figure S103. Get High-res Image Gene #18: 'amp_13q32.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_13q32.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00335 (Fisher's exact test), Q value = 0.009

Table S104. Gene #18: 'amp_13q32.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
AMP PEAK 18(13Q32.3) MUTATED	30	6	15	11	1	0
AMP PEAK 18(13Q32.3) WILD-TYPE	98	44	56	29	46	4

Figure S104. Get High-res Image Gene #18: 'amp_13q32.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S105. Gene #19: 'amp_13q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
AMP PEAK 19(13Q34) MUTATED	3	32	33
AMP PEAK 19(13Q34) WILD-TYPE	98	99	105

Figure S105. Get High-res Image Gene #19: 'amp_13q34' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q34' versus 'METHLYATION_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.027

Table S106. Gene #19: 'amp_13q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
AMP PEAK 19(13Q34) MUTATED	12	26	27	3
AMP PEAK 19(13Q34) WILD-TYPE	49	137	72	44

Figure S106. Get High-res Image Gene #19: 'amp_13q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q34' versus 'MRNASEQ_CNMF'

P value = 0.00681 (Fisher's exact test), Q value = 0.016

Table S107. Gene #19: 'amp_13q34' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
AMP PEAK 19(13Q34) MUTATED	33	14	8	12	0
AMP PEAK 19(13Q34) WILD-TYPE	92	75	42	60	28

Figure S107. Get High-res Image Gene #19: 'amp_13q34' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0107 (Fisher's exact test), Q value = 0.023

Table S108. Gene #19: 'amp_13q34' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
AMP PEAK 19(13Q34) MUTATED	40	19	8	0
AMP PEAK 19(13Q34) WILD-TYPE	111	126	53	7

Figure S108. Get High-res Image Gene #19: 'amp_13q34' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_13q34' versus 'MIRSEQ_CNMF'

P value = 0.00911 (Fisher's exact test), Q value = 0.02

Table S109. Gene #19: 'amp_13q34' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	45	60	103	45	63	37	12
AMP PEAK 19(13Q34) MUTATED	14	8	14	6	13	13	0
AMP PEAK 19(13Q34) WILD-TYPE	31	52	89	39	50	24	12

Figure S109. Get High-res Image Gene #19: 'amp_13q34' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_13q34' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0014

Table S110. Gene #19: 'amp_13q34' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
AMP PEAK 19(13Q34) MUTATED	2	13	22	0	8	11	8
AMP PEAK 19(13Q34) WILD-TYPE	39	41	46	18	45	71	16

Figure S110. Get High-res Image Gene #19: 'amp_13q34' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_13q34' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0259 (Fisher's exact test), Q value = 0.047

Table S111. Gene #19: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
AMP PEAK 19(13Q34) MUTATED	28	7	16	11	2	0
AMP PEAK 19(13Q34) WILD-TYPE	100	43	55	29	45	4

Figure S111. Get High-res Image Gene #19: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_15q26.3' versus 'MRNASEQ_CNMF'

P value = 0.0366 (Fisher's exact test), Q value = 0.062

Table S112. Gene #20: 'amp_15q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
AMP PEAK 20(15Q26.3) MUTATED	27	14	4	5	3
AMP PEAK 20(15Q26.3) WILD-TYPE	98	75	46	67	25

Figure S112. Get High-res Image Gene #20: 'amp_15q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00787 (Fisher's exact test), Q value = 0.018

Table S113. Gene #20: 'amp_15q26.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
AMP PEAK 20(15Q26.3) MUTATED	30	21	2	0
AMP PEAK 20(15Q26.3) WILD-TYPE	121	124	59	7

Figure S113. Get High-res Image Gene #20: 'amp_15q26.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q25.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S114. Gene #22: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
AMP PEAK 22(17Q25.3) MUTATED	20	69	56
AMP PEAK 22(17Q25.3) WILD-TYPE	81	62	82

Figure S114. Get High-res Image Gene #22: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q25.3' versus 'METHLYATION_CNMF'

P value = 0.00633 (Fisher's exact test), Q value = 0.015

Table S115. Gene #22: 'amp_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
AMP PEAK 22(17Q25.3) MUTATED	27	74	35	9
AMP PEAK 22(17Q25.3) WILD-TYPE	34	89	64	38

Figure S115. Get High-res Image Gene #22: 'amp_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q25.3' versus 'RPPA_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.028

Table S116. Gene #22: 'amp_17q25.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	73	19	22	22	1
AMP PEAK 22(17Q25.3) MUTATED	21	28	8	7	17	0
AMP PEAK 22(17Q25.3) WILD-TYPE	20	45	11	15	5	1

Figure S116. Get High-res Image Gene #22: 'amp_17q25.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_17q25.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0304 (Fisher's exact test), Q value = 0.053

Table S117. Gene #22: 'amp_17q25.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	45	38	18	38
AMP PEAK 22(17Q25.3) MUTATED	14	15	25	9	18
AMP PEAK 22(17Q25.3) WILD-TYPE	25	30	13	9	20

Figure S117. Get High-res Image Gene #22: 'amp_17q25.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_17q25.3' versus 'MRNASEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.001

Table S118. Gene #22: 'amp_17q25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
AMP PEAK 22(17Q25.3) MUTATED	53	41	11	34	3
AMP PEAK 22(17Q25.3) WILD-TYPE	72	48	39	38	25

Figure S118. Get High-res Image Gene #22: 'amp_17q25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q25.3' versus 'MIRSEQ_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.038

Table S119. Gene #22: 'amp_17q25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	45	60	103	45	63	37	12
AMP PEAK 22(17Q25.3) MUTATED	25	27	46	14	21	9	2
AMP PEAK 22(17Q25.3) WILD-TYPE	20	33	57	31	42	28	10

Figure S119. Get High-res Image Gene #22: 'amp_17q25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_17q25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00595 (Fisher's exact test), Q value = 0.014

Table S120. Gene #22: 'amp_17q25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
AMP PEAK 22(17Q25.3) MUTATED	24	36	24	33	25	2
AMP PEAK 22(17Q25.3) WILD-TYPE	17	50	28	88	32	6

Figure S120. Get High-res Image Gene #22: 'amp_17q25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_17q25.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0249 (Fisher's exact test), Q value = 0.046

Table S121. Gene #22: 'amp_17q25.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
AMP PEAK 22(17Q25.3) MUTATED	18	26	25	1	18	38	10
AMP PEAK 22(17Q25.3) WILD-TYPE	23	28	43	17	35	44	14

Figure S121. Get High-res Image Gene #22: 'amp_17q25.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_17q25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00361 (Fisher's exact test), Q value = 0.0095

Table S122. Gene #22: 'amp_17q25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
AMP PEAK 22(17Q25.3) MUTATED	54	24	17	23	18	0
AMP PEAK 22(17Q25.3) WILD-TYPE	74	26	54	17	29	4

Figure S122. Get High-res Image Gene #22: 'amp_17q25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.12' versus 'CN_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0016

Table S123. Gene #23: 'amp_19p13.12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
AMP PEAK 23(19P13.12) MUTATED	10	19	40
AMP PEAK 23(19P13.12) WILD-TYPE	91	112	98

Figure S123. Get High-res Image Gene #23: 'amp_19p13.12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19p13.12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S124. Gene #23: 'amp_19p13.12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
AMP PEAK 23(19P13.12) MUTATED	16	18	34	1
AMP PEAK 23(19P13.12) WILD-TYPE	45	145	65	46

Figure S124. Get High-res Image Gene #23: 'amp_19p13.12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19p13.12' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S125. Gene #23: 'amp_19p13.12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
AMP PEAK 23(19P13.12) MUTATED	37	8	15	6	2
AMP PEAK 23(19P13.12) WILD-TYPE	88	81	35	66	26

Figure S125. Get High-res Image Gene #23: 'amp_19p13.12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19p13.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.0023

Table S126. Gene #23: 'amp_19p13.12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
AMP PEAK 23(19P13.12) MUTATED	42	22	4	0
AMP PEAK 23(19P13.12) WILD-TYPE	109	123	57	7

Figure S126. Get High-res Image Gene #23: 'amp_19p13.12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.12' versus 'MIRSEQ_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.031

Table S127. Gene #23: 'amp_19p13.12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	45	60	103	45	63	37	12
AMP PEAK 23(19P13.12) MUTATED	4	10	13	11	21	8	1
AMP PEAK 23(19P13.12) WILD-TYPE	41	50	90	34	42	29	11

Figure S127. Get High-res Image Gene #23: 'amp_19p13.12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_19p13.12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0015

Table S128. Gene #23: 'amp_19p13.12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
AMP PEAK 23(19P13.12) MUTATED	3	14	14	34	3	0
AMP PEAK 23(19P13.12) WILD-TYPE	38	72	38	87	54	8

Figure S128. Get High-res Image Gene #23: 'amp_19p13.12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_19p13.12' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00035

Table S129. Gene #23: 'amp_19p13.12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
AMP PEAK 23(19P13.12) MUTATED	7	5	26	0	13	8	5
AMP PEAK 23(19P13.12) WILD-TYPE	34	49	42	18	40	74	19

Figure S129. Get High-res Image Gene #23: 'amp_19p13.12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_19p13.12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S130. Gene #23: 'amp_19p13.12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
AMP PEAK 23(19P13.12) MUTATED	39	4	16	3	2	0
AMP PEAK 23(19P13.12) WILD-TYPE	89	46	55	37	45	4

Figure S130. Get High-res Image Gene #23: 'amp_19p13.12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q13.11' versus 'CN_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0014

Table S131. Gene #24: 'amp_19q13.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
AMP PEAK 24(19Q13.11) MUTATED	11	38	42
AMP PEAK 24(19Q13.11) WILD-TYPE	90	93	96

Figure S131. Get High-res Image Gene #24: 'amp_19q13.11' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q13.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S132. Gene #24: 'amp_19q13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
AMP PEAK 24(19Q13.11) MUTATED	23	33	34	1
AMP PEAK 24(19Q13.11) WILD-TYPE	38	130	65	46

Figure S132. Get High-res Image Gene #24: 'amp_19q13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q13.11' versus 'RPPA_CHIERARCHICAL'

P value = 0.0299 (Fisher's exact test), Q value = 0.053

Table S133. Gene #24: 'amp_19q13.11' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	45	38	18	38
AMP PEAK 24(19Q13.11) MUTATED	17	11	9	7	5
AMP PEAK 24(19Q13.11) WILD-TYPE	22	34	29	11	33

Figure S133. Get High-res Image Gene #24: 'amp_19q13.11' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_19q13.11' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00031

Table S134. Gene #24: 'amp_19q13.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
AMP PEAK 24(19Q13.11) MUTATED	46	18	16	6	4
AMP PEAK 24(19Q13.11) WILD-TYPE	79	71	34	66	24

Figure S134. Get High-res Image Gene #24: 'amp_19q13.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19q13.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 9e-04

Table S135. Gene #24: 'amp_19q13.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
AMP PEAK 24(19Q13.11) MUTATED	51	34	5	0
AMP PEAK 24(19Q13.11) WILD-TYPE	100	111	56	7

Figure S135. Get High-res Image Gene #24: 'amp_19q13.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19q13.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.001

Table S136. Gene #24: 'amp_19q13.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
AMP PEAK 24(19Q13.11) MUTATED	13	19	17	38	3	0
AMP PEAK 24(19Q13.11) WILD-TYPE	28	67	35	83	54	8

Figure S136. Get High-res Image Gene #24: 'amp_19q13.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_19q13.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00047

Table S137. Gene #24: 'amp_19q13.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
AMP PEAK 24(19Q13.11) MUTATED	9	16	28	2	15	7	8
AMP PEAK 24(19Q13.11) WILD-TYPE	32	38	40	16	38	75	16

Figure S137. Get High-res Image Gene #24: 'amp_19q13.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_19q13.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00054

Table S138. Gene #24: 'amp_19q13.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
AMP PEAK 24(19Q13.11) MUTATED	44	9	17	13	1	1
AMP PEAK 24(19Q13.11) WILD-TYPE	84	41	54	27	46	3

Figure S138. Get High-res Image Gene #24: 'amp_19q13.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.13' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S139. Gene #25: 'amp_20q13.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
AMP PEAK 25(20Q13.13) MUTATED	14	57	53
AMP PEAK 25(20Q13.13) WILD-TYPE	87	74	85

Figure S139. Get High-res Image Gene #25: 'amp_20q13.13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.13' versus 'METHLYATION_CNMF'

P value = 0.0017 (Fisher's exact test), Q value = 0.0052

Table S140. Gene #25: 'amp_20q13.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
AMP PEAK 25(20Q13.13) MUTATED	25	57	37	5
AMP PEAK 25(20Q13.13) WILD-TYPE	36	106	62	42

Figure S140. Get High-res Image Gene #25: 'amp_20q13.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q13.13' versus 'RPPA_CHIERARCHICAL'

P value = 0.0162 (Fisher's exact test), Q value = 0.032

Table S141. Gene #25: 'amp_20q13.13' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	45	38	18	38
AMP PEAK 25(20Q13.13) MUTATED	19	14	14	12	9
AMP PEAK 25(20Q13.13) WILD-TYPE	20	31	24	6	29

Figure S141. Get High-res Image Gene #25: 'amp_20q13.13' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_20q13.13' versus 'MRNASEQ_CNMF'

P value = 0.00462 (Fisher's exact test), Q value = 0.011

Table S142. Gene #25: 'amp_20q13.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
AMP PEAK 25(20Q13.13) MUTATED	52	31	21	14	5
AMP PEAK 25(20Q13.13) WILD-TYPE	73	58	29	58	23

Figure S142. Get High-res Image Gene #25: 'amp_20q13.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_20q13.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.0014

Table S143. Gene #25: 'amp_20q13.13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
AMP PEAK 25(20Q13.13) MUTATED	61	53	9	0
AMP PEAK 25(20Q13.13) WILD-TYPE	90	92	52	7

Figure S143. Get High-res Image Gene #25: 'amp_20q13.13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.13' versus 'MIRSEQ_CNMF'

P value = 0.0491 (Fisher's exact test), Q value = 0.079

Table S144. Gene #25: 'amp_20q13.13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	45	60	103	45	63	37	12
AMP PEAK 25(20Q13.13) MUTATED	19	22	24	14	24	18	2
AMP PEAK 25(20Q13.13) WILD-TYPE	26	38	79	31	39	19	10

Figure S144. Get High-res Image Gene #25: 'amp_20q13.13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_20q13.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0149 (Fisher's exact test), Q value = 0.03

Table S145. Gene #25: 'amp_20q13.13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
AMP PEAK 25(20Q13.13) MUTATED	19	26	24	42	11	1
AMP PEAK 25(20Q13.13) WILD-TYPE	22	60	28	79	46	7

Figure S145. Get High-res Image Gene #25: 'amp_20q13.13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S146. Gene #25: 'amp_20q13.13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
AMP PEAK 25(20Q13.13) MUTATED	14	26	30	2	13	15	16
AMP PEAK 25(20Q13.13) WILD-TYPE	27	28	38	16	40	67	8

Figure S146. Get High-res Image Gene #25: 'amp_20q13.13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0169 (Fisher's exact test), Q value = 0.033

Table S147. Gene #25: 'amp_20q13.13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
AMP PEAK 25(20Q13.13) MUTATED	49	12	27	19	9	0
AMP PEAK 25(20Q13.13) WILD-TYPE	79	38	44	21	38	4

Figure S147. Get High-res Image Gene #25: 'amp_20q13.13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xq28' versus 'CN_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0012

Table S148. Gene #26: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
AMP PEAK 26(XQ28) MUTATED	27	16	44
AMP PEAK 26(XQ28) WILD-TYPE	74	115	94

Figure S148. Get High-res Image Gene #26: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq28' versus 'RPPA_CHIERARCHICAL'

P value = 0.0347 (Fisher's exact test), Q value = 0.06

Table S149. Gene #26: 'amp_xq28' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	45	38	18	38
AMP PEAK 26(XQ28) MUTATED	3	7	10	6	12
AMP PEAK 26(XQ28) WILD-TYPE	36	38	28	12	26

Figure S149. Get High-res Image Gene #26: 'amp_xq28' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_xq28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00209 (Fisher's exact test), Q value = 0.0061

Table S150. Gene #26: 'amp_xq28' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
AMP PEAK 26(XQ28) MUTATED	25	37	24	0
AMP PEAK 26(XQ28) WILD-TYPE	126	108	37	7

Figure S150. Get High-res Image Gene #26: 'amp_xq28' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_CNMF'

P value = 0.00796 (Fisher's exact test), Q value = 0.018

Table S151. Gene #26: 'amp_xq28' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	45	60	103	45	63	37	12
AMP PEAK 26(XQ28) MUTATED	4	14	37	8	14	5	3
AMP PEAK 26(XQ28) WILD-TYPE	41	46	66	37	49	32	9

Figure S151. Get High-res Image Gene #26: 'amp_xq28' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_xq28' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00257 (Fisher's exact test), Q value = 0.0074

Table S152. Gene #26: 'amp_xq28' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
AMP PEAK 26(XQ28) MUTATED	4	21	11	23	25	1
AMP PEAK 26(XQ28) WILD-TYPE	37	65	41	98	32	7

Figure S152. Get High-res Image Gene #26: 'amp_xq28' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0019 (Fisher's exact test), Q value = 0.0056

Table S153. Gene #26: 'amp_xq28' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
AMP PEAK 26(XQ28) MUTATED	10	5	15	3	11	32	2
AMP PEAK 26(XQ28) WILD-TYPE	31	49	53	15	42	50	22

Figure S153. Get High-res Image Gene #26: 'amp_xq28' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_xq28' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.0014

Table S154. Gene #26: 'amp_xq28' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
AMP PEAK 26(XQ28) MUTATED	31	11	11	3	22	0
AMP PEAK 26(XQ28) WILD-TYPE	97	39	60	37	25	4

Figure S154. Get High-res Image Gene #26: 'amp_xq28' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S155. Gene #27: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 1(1P36.31) MUTATED	20	49	93
DEL PEAK 1(1P36.31) WILD-TYPE	81	82	45

Figure S155. Get High-res Image Gene #27: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S156. Gene #27: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
DEL PEAK 1(1P36.31) MUTATED	23	59	70	10
DEL PEAK 1(1P36.31) WILD-TYPE	38	104	29	37

Figure S156. Get High-res Image Gene #27: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S157. Gene #27: 'del_1p36.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
DEL PEAK 1(1P36.31) MUTATED	77	32	24	20	6
DEL PEAK 1(1P36.31) WILD-TYPE	48	57	26	52	22

Figure S157. Get High-res Image Gene #27: 'del_1p36.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p36.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S158. Gene #27: 'del_1p36.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
DEL PEAK 1(1P36.31) MUTATED	88	54	17	0
DEL PEAK 1(1P36.31) WILD-TYPE	63	91	44	7

Figure S158. Get High-res Image Gene #27: 'del_1p36.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.31' versus 'MIRSEQ_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0023

Table S159. Gene #27: 'del_1p36.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	45	60	103	45	63	37	12
DEL PEAK 1(1P36.31) MUTATED	14	26	37	19	42	19	2
DEL PEAK 1(1P36.31) WILD-TYPE	31	34	66	26	21	18	10

Figure S159. Get High-res Image Gene #27: 'del_1p36.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p36.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.0026

Table S160. Gene #27: 'del_1p36.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
DEL PEAK 1(1P36.31) MUTATED	13	34	29	66	16	1
DEL PEAK 1(1P36.31) WILD-TYPE	28	52	23	55	41	7

Figure S160. Get High-res Image Gene #27: 'del_1p36.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00039

Table S161. Gene #27: 'del_1p36.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
DEL PEAK 1(1P36.31) MUTATED	14	19	47	5	27	27	11
DEL PEAK 1(1P36.31) WILD-TYPE	27	35	21	13	26	55	13

Figure S161. Get High-res Image Gene #27: 'del_1p36.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p36.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.0013

Table S162. Gene #27: 'del_1p36.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
DEL PEAK 1(1P36.31) MUTATED	65	18	42	13	12	0
DEL PEAK 1(1P36.31) WILD-TYPE	63	32	29	27	35	4

Figure S162. Get High-res Image Gene #27: 'del_1p36.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S163. Gene #28: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 2(1P36.11) MUTATED	12	46	84
DEL PEAK 2(1P36.11) WILD-TYPE	89	85	54

Figure S163. Get High-res Image Gene #28: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S164. Gene #28: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
DEL PEAK 2(1P36.11) MUTATED	19	47	68	8
DEL PEAK 2(1P36.11) WILD-TYPE	42	116	31	39

Figure S164. Get High-res Image Gene #28: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S165. Gene #28: 'del_1p36.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
DEL PEAK 2(1P36.11) MUTATED	72	25	20	20	3
DEL PEAK 2(1P36.11) WILD-TYPE	53	64	30	52	25

Figure S165. Get High-res Image Gene #28: 'del_1p36.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S166. Gene #28: 'del_1p36.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
DEL PEAK 2(1P36.11) MUTATED	82	41	17	0
DEL PEAK 2(1P36.11) WILD-TYPE	69	104	44	7

Figure S166. Get High-res Image Gene #28: 'del_1p36.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S167. Gene #28: 'del_1p36.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	45	60	103	45	63	37	12
DEL PEAK 2(1P36.11) MUTATED	9	15	35	19	40	20	1
DEL PEAK 2(1P36.11) WILD-TYPE	36	45	68	26	23	17	11

Figure S167. Get High-res Image Gene #28: 'del_1p36.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p36.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S168. Gene #28: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
DEL PEAK 2(1P36.11) MUTATED	8	25	24	67	14	1
DEL PEAK 2(1P36.11) WILD-TYPE	33	61	28	54	43	7

Figure S168. Get High-res Image Gene #28: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S169. Gene #28: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
DEL PEAK 2(1P36.11) MUTATED	16	12	47	2	24	21	10
DEL PEAK 2(1P36.11) WILD-TYPE	25	42	21	16	29	61	14

Figure S169. Get High-res Image Gene #28: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S170. Gene #28: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
DEL PEAK 2(1P36.11) MUTATED	59	12	42	9	10	0
DEL PEAK 2(1P36.11) WILD-TYPE	69	38	29	31	37	4

Figure S170. Get High-res Image Gene #28: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q22.1' versus 'CN_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0012

Table S171. Gene #29: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 3(2Q22.1) MUTATED	5	30	17
DEL PEAK 3(2Q22.1) WILD-TYPE	96	101	121

Figure S171. Get High-res Image Gene #29: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 0.0275 (Fisher's exact test), Q value = 0.049

Table S172. Gene #29: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
DEL PEAK 3(2Q22.1) MUTATED	9	23	19	1
DEL PEAK 3(2Q22.1) WILD-TYPE	52	140	80	46

Figure S172. Get High-res Image Gene #29: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.041

Table S173. Gene #29: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
DEL PEAK 3(2Q22.1) MUTATED	22	18	7	4	1
DEL PEAK 3(2Q22.1) WILD-TYPE	103	71	43	68	27

Figure S173. Get High-res Image Gene #29: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S174. Gene #30: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 4(2Q37.3) MUTATED	3	37	22
DEL PEAK 4(2Q37.3) WILD-TYPE	98	94	116

Figure S174. Get High-res Image Gene #30: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00054

Table S175. Gene #30: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
DEL PEAK 4(2Q37.3) MUTATED	29	23	6	3	1
DEL PEAK 4(2Q37.3) WILD-TYPE	96	66	44	69	27

Figure S175. Get High-res Image Gene #30: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00291 (Fisher's exact test), Q value = 0.0081

Table S176. Gene #30: 'del_2q37.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
DEL PEAK 4(2Q37.3) MUTATED	31	29	2	0
DEL PEAK 4(2Q37.3) WILD-TYPE	120	116	59	7

Figure S176. Get High-res Image Gene #30: 'del_2q37.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00635 (Fisher's exact test), Q value = 0.015

Table S177. Gene #30: 'del_2q37.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
DEL PEAK 4(2Q37.3) MUTATED	11	14	16	16	4	0
DEL PEAK 4(2Q37.3) WILD-TYPE	30	72	36	105	53	8

Figure S177. Get High-res Image Gene #30: 'del_2q37.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00347 (Fisher's exact test), Q value = 0.0092

Table S178. Gene #30: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
DEL PEAK 4(2Q37.3) MUTATED	32	5	7	11	3	0
DEL PEAK 4(2Q37.3) WILD-TYPE	96	45	64	29	44	4

Figure S178. Get High-res Image Gene #30: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p13' versus 'CN_CNMF'

P value = 0.00356 (Fisher's exact test), Q value = 0.0094

Table S179. Gene #31: 'del_3p13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 5(3P13) MUTATED	9	30	34
DEL PEAK 5(3P13) WILD-TYPE	92	101	104

Figure S179. Get High-res Image Gene #31: 'del_3p13' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p13' versus 'METHLYATION_CNMF'

P value = 0.00173 (Fisher's exact test), Q value = 0.0052

Table S180. Gene #31: 'del_3p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
DEL PEAK 5(3P13) MUTATED	13	23	32	5
DEL PEAK 5(3P13) WILD-TYPE	48	140	67	42

Figure S180. Get High-res Image Gene #31: 'del_3p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p13' versus 'RPPA_CNMF'

P value = 0.0361 (Fisher's exact test), Q value = 0.062

Table S181. Gene #31: 'del_3p13' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	73	19	22	22	1
DEL PEAK 5(3P13) MUTATED	8	8	5	6	9	0
DEL PEAK 5(3P13) WILD-TYPE	33	65	14	16	13	1

Figure S181. Get High-res Image Gene #31: 'del_3p13' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_3p13' versus 'RPPA_CHIERARCHICAL'

P value = 0.022 (Fisher's exact test), Q value = 0.041

Table S182. Gene #31: 'del_3p13' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	45	38	18	38
DEL PEAK 5(3P13) MUTATED	14	5	6	6	5
DEL PEAK 5(3P13) WILD-TYPE	25	40	32	12	33

Figure S182. Get High-res Image Gene #31: 'del_3p13' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_3p13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S183. Gene #31: 'del_3p13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
DEL PEAK 5(3P13) MUTATED	46	8	8	7	3
DEL PEAK 5(3P13) WILD-TYPE	79	81	42	65	25

Figure S183. Get High-res Image Gene #31: 'del_3p13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S184. Gene #31: 'del_3p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
DEL PEAK 5(3P13) MUTATED	51	16	5	0
DEL PEAK 5(3P13) WILD-TYPE	100	129	56	7

Figure S184. Get High-res Image Gene #31: 'del_3p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p13' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S185. Gene #31: 'del_3p13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	45	60	103	45	63	37	12
DEL PEAK 5(3P13) MUTATED	5	7	14	8	31	5	1
DEL PEAK 5(3P13) WILD-TYPE	40	53	89	37	32	32	11

Figure S185. Get High-res Image Gene #31: 'del_3p13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00299 (Fisher's exact test), Q value = 0.0082

Table S186. Gene #31: 'del_3p13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
DEL PEAK 5(3P13) MUTATED	5	11	12	37	6	0
DEL PEAK 5(3P13) WILD-TYPE	36	75	40	84	51	8

Figure S186. Get High-res Image Gene #31: 'del_3p13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0014

Table S187. Gene #31: 'del_3p13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
DEL PEAK 5(3P13) MUTATED	11	8	22	2	16	5	3
DEL PEAK 5(3P13) WILD-TYPE	30	46	46	16	37	77	21

Figure S187. Get High-res Image Gene #31: 'del_3p13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00301 (Fisher's exact test), Q value = 0.0083

Table S188. Gene #31: 'del_3p13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
DEL PEAK 5(3P13) MUTATED	35	6	19	4	3	0
DEL PEAK 5(3P13) WILD-TYPE	93	44	52	36	44	4

Figure S188. Get High-res Image Gene #31: 'del_3p13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4p16.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S189. Gene #32: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 6(4P16.3) MUTATED	5	44	36
DEL PEAK 6(4P16.3) WILD-TYPE	96	87	102

Figure S189. Get High-res Image Gene #32: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4p16.3' versus 'METHLYATION_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.028

Table S190. Gene #32: 'del_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
DEL PEAK 6(4P16.3) MUTATED	13	41	28	3
DEL PEAK 6(4P16.3) WILD-TYPE	48	122	71	44

Figure S190. Get High-res Image Gene #32: 'del_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4p16.3' versus 'RPPA_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.023

Table S191. Gene #32: 'del_4p16.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	73	19	22	22	1
DEL PEAK 6(4P16.3) MUTATED	8	14	1	10	9	0
DEL PEAK 6(4P16.3) WILD-TYPE	33	59	18	12	13	1

Figure S191. Get High-res Image Gene #32: 'del_4p16.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00483 (Fisher's exact test), Q value = 0.012

Table S192. Gene #32: 'del_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
DEL PEAK 6(4P16.3) MUTATED	6	16	19	36	7	0
DEL PEAK 6(4P16.3) WILD-TYPE	35	70	33	85	50	8

Figure S192. Get High-res Image Gene #32: 'del_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00051

Table S193. Gene #32: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
DEL PEAK 6(4P16.3) MUTATED	48	8	12	6	4	0
DEL PEAK 6(4P16.3) WILD-TYPE	80	42	59	34	43	4

Figure S193. Get High-res Image Gene #32: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S194. Gene #33: 'del_4q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 7(4Q21.3) MUTATED	6	94	71
DEL PEAK 7(4Q21.3) WILD-TYPE	95	37	67

Figure S194. Get High-res Image Gene #33: 'del_4q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S195. Gene #33: 'del_4q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
DEL PEAK 7(4Q21.3) MUTATED	29	66	66	10
DEL PEAK 7(4Q21.3) WILD-TYPE	32	97	33	37

Figure S195. Get High-res Image Gene #33: 'del_4q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q21.3' versus 'RPPA_CNMF'

P value = 0.0193 (Fisher's exact test), Q value = 0.037

Table S196. Gene #33: 'del_4q21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	73	19	22	22	1
DEL PEAK 7(4Q21.3) MUTATED	17	28	11	14	16	0
DEL PEAK 7(4Q21.3) WILD-TYPE	24	45	8	8	6	1

Figure S196. Get High-res Image Gene #33: 'del_4q21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_4q21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S197. Gene #33: 'del_4q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
DEL PEAK 7(4Q21.3) MUTATED	81	48	18	18	4
DEL PEAK 7(4Q21.3) WILD-TYPE	44	41	32	54	24

Figure S197. Get High-res Image Gene #33: 'del_4q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S198. Gene #33: 'del_4q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
DEL PEAK 7(4Q21.3) MUTATED	85	69	15	0
DEL PEAK 7(4Q21.3) WILD-TYPE	66	76	46	7

Figure S198. Get High-res Image Gene #33: 'del_4q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q21.3' versus 'MIRSEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00097

Table S199. Gene #33: 'del_4q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	45	60	103	45	63	37	12
DEL PEAK 7(4Q21.3) MUTATED	22	26	37	20	38	26	1
DEL PEAK 7(4Q21.3) WILD-TYPE	23	34	66	25	25	11	11

Figure S199. Get High-res Image Gene #33: 'del_4q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S200. Gene #33: 'del_4q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
DEL PEAK 7(4Q21.3) MUTATED	19	39	30	69	13	0
DEL PEAK 7(4Q21.3) WILD-TYPE	22	47	22	52	44	8

Figure S200. Get High-res Image Gene #33: 'del_4q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S201. Gene #33: 'del_4q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
DEL PEAK 7(4Q21.3) MUTATED	21	30	48	4	19	25	16
DEL PEAK 7(4Q21.3) WILD-TYPE	20	24	20	14	34	57	8

Figure S201. Get High-res Image Gene #33: 'del_4q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S202. Gene #33: 'del_4q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
DEL PEAK 7(4Q21.3) MUTATED	82	18	36	18	9	0
DEL PEAK 7(4Q21.3) WILD-TYPE	46	32	35	22	38	4

Figure S202. Get High-res Image Gene #33: 'del_4q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q24' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S203. Gene #34: 'del_4q24' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 8(4Q24) MUTATED	5	96	72
DEL PEAK 8(4Q24) WILD-TYPE	96	35	66

Figure S203. Get High-res Image Gene #34: 'del_4q24' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q24' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S204. Gene #34: 'del_4q24' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
DEL PEAK 8(4Q24) MUTATED	31	66	67	9
DEL PEAK 8(4Q24) WILD-TYPE	30	97	32	38

Figure S204. Get High-res Image Gene #34: 'del_4q24' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q24' versus 'RPPA_CNMF'

P value = 0.0383 (Fisher's exact test), Q value = 0.065

Table S205. Gene #34: 'del_4q24' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	73	19	22	22	1
DEL PEAK 8(4Q24) MUTATED	17	30	11	14	16	0
DEL PEAK 8(4Q24) WILD-TYPE	24	43	8	8	6	1

Figure S205. Get High-res Image Gene #34: 'del_4q24' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_4q24' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S206. Gene #34: 'del_4q24' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
DEL PEAK 8(4Q24) MUTATED	82	47	19	18	4
DEL PEAK 8(4Q24) WILD-TYPE	43	42	31	54	24

Figure S206. Get High-res Image Gene #34: 'del_4q24' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q24' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S207. Gene #34: 'del_4q24' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
DEL PEAK 8(4Q24) MUTATED	87	69	14	0
DEL PEAK 8(4Q24) WILD-TYPE	64	76	47	7

Figure S207. Get High-res Image Gene #34: 'del_4q24' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q24' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00054

Table S208. Gene #34: 'del_4q24' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	45	60	103	45	63	37	12
DEL PEAK 8(4Q24) MUTATED	25	25	37	20	38	26	1
DEL PEAK 8(4Q24) WILD-TYPE	20	35	66	25	25	11	11

Figure S208. Get High-res Image Gene #34: 'del_4q24' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q24' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S209. Gene #34: 'del_4q24' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
DEL PEAK 8(4Q24) MUTATED	22	38	31	69	12	0
DEL PEAK 8(4Q24) WILD-TYPE	19	48	21	52	45	8

Figure S209. Get High-res Image Gene #34: 'del_4q24' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q24' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S210. Gene #34: 'del_4q24' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
DEL PEAK 8(4Q24) MUTATED	20	31	48	4	20	25	17
DEL PEAK 8(4Q24) WILD-TYPE	21	23	20	14	33	57	7

Figure S210. Get High-res Image Gene #34: 'del_4q24' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q24' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S211. Gene #34: 'del_4q24' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
DEL PEAK 8(4Q24) MUTATED	83	17	36	21	8	0
DEL PEAK 8(4Q24) WILD-TYPE	45	33	35	19	39	4

Figure S211. Get High-res Image Gene #34: 'del_4q24' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q35.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S212. Gene #35: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 9(4Q35.1) MUTATED	8	87	77
DEL PEAK 9(4Q35.1) WILD-TYPE	93	44	61

Figure S212. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q35.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S213. Gene #35: 'del_4q35.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
DEL PEAK 9(4Q35.1) MUTATED	27	67	66	12
DEL PEAK 9(4Q35.1) WILD-TYPE	34	96	33	35

Figure S213. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q35.1' versus 'RPPA_CNMF'

P value = 0.0329 (Fisher's exact test), Q value = 0.057

Table S214. Gene #35: 'del_4q35.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	73	19	22	22	1
DEL PEAK 9(4Q35.1) MUTATED	16	28	10	13	16	0
DEL PEAK 9(4Q35.1) WILD-TYPE	25	45	9	9	6	1

Figure S214. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_4q35.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S215. Gene #35: 'del_4q35.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
DEL PEAK 9(4Q35.1) MUTATED	78	44	21	22	4
DEL PEAK 9(4Q35.1) WILD-TYPE	47	45	29	50	24

Figure S215. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00026

Table S216. Gene #35: 'del_4q35.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
DEL PEAK 9(4Q35.1) MUTATED	87	64	18	0
DEL PEAK 9(4Q35.1) WILD-TYPE	64	81	43	7

Figure S216. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MIRSEQ_CNMF'

P value = 0.00141 (Fisher's exact test), Q value = 0.0044

Table S217. Gene #35: 'del_4q35.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	45	60	103	45	63	37	12
DEL PEAK 9(4Q35.1) MUTATED	24	23	40	19	37	26	2
DEL PEAK 9(4Q35.1) WILD-TYPE	21	37	63	26	26	11	10

Figure S217. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q35.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00022

Table S218. Gene #35: 'del_4q35.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
DEL PEAK 9(4Q35.1) MUTATED	21	36	32	68	14	0
DEL PEAK 9(4Q35.1) WILD-TYPE	20	50	20	53	43	8

Figure S218. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S219. Gene #35: 'del_4q35.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
DEL PEAK 9(4Q35.1) MUTATED	18	29	47	3	20	27	17
DEL PEAK 9(4Q35.1) WILD-TYPE	23	25	21	15	33	55	7

Figure S219. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q35.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S220. Gene #35: 'del_4q35.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
DEL PEAK 9(4Q35.1) MUTATED	77	15	39	21	9	0
DEL PEAK 9(4Q35.1) WILD-TYPE	51	35	32	19	38	4

Figure S220. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q27' versus 'CN_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0019

Table S221. Gene #36: 'del_6q27' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 10(6Q27) MUTATED	21	57	58
DEL PEAK 10(6Q27) WILD-TYPE	80	74	80

Figure S221. Get High-res Image Gene #36: 'del_6q27' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q27' versus 'METHLYATION_CNMF'

P value = 0.0195 (Fisher's exact test), Q value = 0.037

Table S222. Gene #36: 'del_6q27' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
DEL PEAK 10(6Q27) MUTATED	19	69	39	9
DEL PEAK 10(6Q27) WILD-TYPE	42	94	60	38

Figure S222. Get High-res Image Gene #36: 'del_6q27' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.2' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00022

Table S223. Gene #37: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 11(8P23.2) MUTATED	54	82	111
DEL PEAK 11(8P23.2) WILD-TYPE	47	49	27

Figure S223. Get High-res Image Gene #37: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00097

Table S224. Gene #37: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
DEL PEAK 11(8P23.2) MUTATED	43	114	72	18
DEL PEAK 11(8P23.2) WILD-TYPE	18	49	27	29

Figure S224. Get High-res Image Gene #37: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.027 (Fisher's exact test), Q value = 0.049

Table S225. Gene #37: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
DEL PEAK 11(8P23.2) MUTATED	106	94	40	1
DEL PEAK 11(8P23.2) WILD-TYPE	45	51	21	6

Figure S225. Get High-res Image Gene #37: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0427 (Fisher's exact test), Q value = 0.071

Table S226. Gene #37: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
DEL PEAK 11(8P23.2) MUTATED	94	28	42	29	34	1
DEL PEAK 11(8P23.2) WILD-TYPE	34	22	29	11	13	3

Figure S226. Get High-res Image Gene #37: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S227. Gene #38: 'del_8p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 12(8P12) MUTATED	51	79	112
DEL PEAK 12(8P12) WILD-TYPE	50	52	26

Figure S227. Get High-res Image Gene #38: 'del_8p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p12' versus 'METHLYATION_CNMF'

P value = 0.00123 (Fisher's exact test), Q value = 0.0039

Table S228. Gene #38: 'del_8p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
DEL PEAK 12(8P12) MUTATED	43	107	73	19
DEL PEAK 12(8P12) WILD-TYPE	18	56	26	28

Figure S228. Get High-res Image Gene #38: 'del_8p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.022

Table S229. Gene #38: 'del_8p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
DEL PEAK 12(8P12) MUTATED	108	89	39	1
DEL PEAK 12(8P12) WILD-TYPE	43	56	22	6

Figure S229. Get High-res Image Gene #38: 'del_8p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0188 (Fisher's exact test), Q value = 0.037

Table S230. Gene #38: 'del_8p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
DEL PEAK 12(8P12) MUTATED	30	47	39	80	40	2
DEL PEAK 12(8P12) WILD-TYPE	11	39	13	41	17	6

Figure S230. Get High-res Image Gene #38: 'del_8p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S231. Gene #39: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 13(9P21.3) MUTATED	15	64	71
DEL PEAK 13(9P21.3) WILD-TYPE	86	67	67

Figure S231. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S232. Gene #39: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
DEL PEAK 13(9P21.3) MUTATED	29	53	58	10
DEL PEAK 13(9P21.3) WILD-TYPE	32	110	41	37

Figure S232. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S233. Gene #39: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
DEL PEAK 13(9P21.3) MUTATED	72	31	19	22	3
DEL PEAK 13(9P21.3) WILD-TYPE	53	58	31	50	25

Figure S233. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S234. Gene #39: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
DEL PEAK 13(9P21.3) MUTATED	82	48	17	0
DEL PEAK 13(9P21.3) WILD-TYPE	69	97	44	7

Figure S234. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0023

Table S235. Gene #39: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	45	60	103	45	63	37	12
DEL PEAK 13(9P21.3) MUTATED	23	18	34	19	30	24	1
DEL PEAK 13(9P21.3) WILD-TYPE	22	42	69	26	33	13	11

Figure S235. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.0012

Table S236. Gene #39: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
DEL PEAK 13(9P21.3) MUTATED	19	26	31	58	14	1
DEL PEAK 13(9P21.3) WILD-TYPE	22	60	21	63	43	7

Figure S236. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.001

Table S237. Gene #39: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
DEL PEAK 13(9P21.3) MUTATED	14	24	42	5	20	22	15
DEL PEAK 13(9P21.3) WILD-TYPE	27	30	26	13	33	60	9

Figure S237. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S238. Gene #39: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
DEL PEAK 13(9P21.3) MUTATED	70	11	34	19	8	0
DEL PEAK 13(9P21.3) WILD-TYPE	58	39	37	21	39	4

Figure S238. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q31.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S239. Gene #40: 'del_9q31.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 14(9Q31.3) MUTATED	9	59	51
DEL PEAK 14(9Q31.3) WILD-TYPE	92	72	87

Figure S239. Get High-res Image Gene #40: 'del_9q31.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q31.3' versus 'METHLYATION_CNMF'

P value = 0.00101 (Fisher's exact test), Q value = 0.0032

Table S240. Gene #40: 'del_9q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
DEL PEAK 14(9Q31.3) MUTATED	21	44	46	8
DEL PEAK 14(9Q31.3) WILD-TYPE	40	119	53	39

Figure S240. Get High-res Image Gene #40: 'del_9q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9q31.3' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00044

Table S241. Gene #40: 'del_9q31.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
DEL PEAK 14(9Q31.3) MUTATED	49	38	17	12	2
DEL PEAK 14(9Q31.3) WILD-TYPE	76	51	33	60	26

Figure S241. Get High-res Image Gene #40: 'del_9q31.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9q31.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S242. Gene #40: 'del_9q31.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
DEL PEAK 14(9Q31.3) MUTATED	67	43	8	0
DEL PEAK 14(9Q31.3) WILD-TYPE	84	102	53	7

Figure S242. Get High-res Image Gene #40: 'del_9q31.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9q31.3' versus 'MIRSEQ_CNMF'

P value = 0.0268 (Fisher's exact test), Q value = 0.049

Table S243. Gene #40: 'del_9q31.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	45	60	103	45	63	37	12
DEL PEAK 14(9Q31.3) MUTATED	18	16	26	18	25	13	0
DEL PEAK 14(9Q31.3) WILD-TYPE	27	44	77	27	38	24	12

Figure S243. Get High-res Image Gene #40: 'del_9q31.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9q31.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0029 (Fisher's exact test), Q value = 0.0081

Table S244. Gene #40: 'del_9q31.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
DEL PEAK 14(9Q31.3) MUTATED	17	26	22	43	7	1
DEL PEAK 14(9Q31.3) WILD-TYPE	24	60	30	78	50	7

Figure S244. Get High-res Image Gene #40: 'del_9q31.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9q31.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00088 (Fisher's exact test), Q value = 0.0029

Table S245. Gene #40: 'del_9q31.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
DEL PEAK 14(9Q31.3) MUTATED	15	23	28	2	19	13	11
DEL PEAK 14(9Q31.3) WILD-TYPE	26	31	40	16	34	69	13

Figure S245. Get High-res Image Gene #40: 'del_9q31.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9q31.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S246. Gene #40: 'del_9q31.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
DEL PEAK 14(9Q31.3) MUTATED	56	12	24	17	2	0
DEL PEAK 14(9Q31.3) WILD-TYPE	72	38	47	23	45	4

Figure S246. Get High-res Image Gene #40: 'del_9q31.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S247. Gene #41: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 15(10Q23.31) MUTATED	11	66	20
DEL PEAK 15(10Q23.31) WILD-TYPE	90	65	118

Figure S247. Get High-res Image Gene #41: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S248. Gene #41: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
DEL PEAK 15(10Q23.31) MUTATED	28	45	21	3
DEL PEAK 15(10Q23.31) WILD-TYPE	33	118	78	44

Figure S248. Get High-res Image Gene #41: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'RPPA_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0015

Table S249. Gene #41: 'del_10q23.31' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	73	19	22	22	1
DEL PEAK 15(10Q23.31) MUTATED	19	17	1	7	13	0
DEL PEAK 15(10Q23.31) WILD-TYPE	22	56	18	15	9	1

Figure S249. Get High-res Image Gene #41: 'del_10q23.31' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_10q23.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00337 (Fisher's exact test), Q value = 0.009

Table S250. Gene #41: 'del_10q23.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	45	38	18	38
DEL PEAK 15(10Q23.31) MUTATED	13	7	19	9	9
DEL PEAK 15(10Q23.31) WILD-TYPE	26	38	19	9	29

Figure S250. Get High-res Image Gene #41: 'del_10q23.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S251. Gene #41: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
DEL PEAK 15(10Q23.31) MUTATED	37	38	10	6	3
DEL PEAK 15(10Q23.31) WILD-TYPE	88	51	40	66	25

Figure S251. Get High-res Image Gene #41: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00156 (Fisher's exact test), Q value = 0.0049

Table S252. Gene #41: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
DEL PEAK 15(10Q23.31) MUTATED	41	47	6	0
DEL PEAK 15(10Q23.31) WILD-TYPE	110	98	55	7

Figure S252. Get High-res Image Gene #41: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S253. Gene #41: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	45	60	103	45	63	37	12
DEL PEAK 15(10Q23.31) MUTATED	16	30	17	4	22	7	1
DEL PEAK 15(10Q23.31) WILD-TYPE	29	30	86	41	41	30	11

Figure S253. Get High-res Image Gene #41: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00047

Table S254. Gene #41: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
DEL PEAK 15(10Q23.31) MUTATED	15	35	16	26	5	0
DEL PEAK 15(10Q23.31) WILD-TYPE	26	51	36	95	52	8

Figure S254. Get High-res Image Gene #41: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0012

Table S255. Gene #41: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
DEL PEAK 15(10Q23.31) MUTATED	15	28	19	3	12	12	5
DEL PEAK 15(10Q23.31) WILD-TYPE	26	26	49	15	41	70	19

Figure S255. Get High-res Image Gene #41: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00039

Table S256. Gene #41: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
DEL PEAK 15(10Q23.31) MUTATED	41	21	16	14	2	0
DEL PEAK 15(10Q23.31) WILD-TYPE	87	29	55	26	45	4

Figure S256. Get High-res Image Gene #41: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q26.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S257. Gene #42: 'del_10q26.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 16(10Q26.13) MUTATED	14	70	21
DEL PEAK 16(10Q26.13) WILD-TYPE	87	61	117

Figure S257. Get High-res Image Gene #42: 'del_10q26.13' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q26.13' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00079

Table S258. Gene #42: 'del_10q26.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
DEL PEAK 16(10Q26.13) MUTATED	31	45	23	6
DEL PEAK 16(10Q26.13) WILD-TYPE	30	118	76	41

Figure S258. Get High-res Image Gene #42: 'del_10q26.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q26.13' versus 'RPPA_CNMF'

P value = 0.00199 (Fisher's exact test), Q value = 0.0059

Table S259. Gene #42: 'del_10q26.13' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	73	19	22	22	1
DEL PEAK 16(10Q26.13) MUTATED	17	18	2	8	14	0
DEL PEAK 16(10Q26.13) WILD-TYPE	24	55	17	14	8	1

Figure S259. Get High-res Image Gene #42: 'del_10q26.13' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_10q26.13' versus 'RPPA_CHIERARCHICAL'

P value = 0.0114 (Fisher's exact test), Q value = 0.024

Table S260. Gene #42: 'del_10q26.13' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	45	38	18	38
DEL PEAK 16(10Q26.13) MUTATED	14	7	19	8	11
DEL PEAK 16(10Q26.13) WILD-TYPE	25	38	19	10	27

Figure S260. Get High-res Image Gene #42: 'del_10q26.13' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_10q26.13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S261. Gene #42: 'del_10q26.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
DEL PEAK 16(10Q26.13) MUTATED	41	40	12	6	3
DEL PEAK 16(10Q26.13) WILD-TYPE	84	49	38	66	25

Figure S261. Get High-res Image Gene #42: 'del_10q26.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q26.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.0019

Table S262. Gene #42: 'del_10q26.13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
DEL PEAK 16(10Q26.13) MUTATED	47	49	6	0
DEL PEAK 16(10Q26.13) WILD-TYPE	104	96	55	7

Figure S262. Get High-res Image Gene #42: 'del_10q26.13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.13' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00026

Table S263. Gene #42: 'del_10q26.13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	45	60	103	45	63	37	12
DEL PEAK 16(10Q26.13) MUTATED	15	29	19	6	27	8	1
DEL PEAK 16(10Q26.13) WILD-TYPE	30	31	84	39	36	29	11

Figure S263. Get High-res Image Gene #42: 'del_10q26.13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q26.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00031

Table S264. Gene #42: 'del_10q26.13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
DEL PEAK 16(10Q26.13) MUTATED	14	39	15	31	5	1
DEL PEAK 16(10Q26.13) WILD-TYPE	27	47	37	90	52	7

Figure S264. Get High-res Image Gene #42: 'del_10q26.13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q26.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0168 (Fisher's exact test), Q value = 0.033

Table S265. Gene #42: 'del_10q26.13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
DEL PEAK 16(10Q26.13) MUTATED	17	24	20	4	15	14	8
DEL PEAK 16(10Q26.13) WILD-TYPE	24	30	48	14	38	68	16

Figure S265. Get High-res Image Gene #42: 'del_10q26.13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q26.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00022

Table S266. Gene #42: 'del_10q26.13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
DEL PEAK 16(10Q26.13) MUTATED	41	23	22	14	2	0
DEL PEAK 16(10Q26.13) WILD-TYPE	87	27	49	26	45	4

Figure S266. Get High-res Image Gene #42: 'del_10q26.13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q14.1' versus 'CN_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.023

Table S267. Gene #43: 'del_11q14.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 17(11Q14.1) MUTATED	11	34	32
DEL PEAK 17(11Q14.1) WILD-TYPE	90	97	106

Figure S267. Get High-res Image Gene #43: 'del_11q14.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q14.1' versus 'METHLYATION_CNMF'

P value = 0.0293 (Fisher's exact test), Q value = 0.052

Table S268. Gene #43: 'del_11q14.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
DEL PEAK 17(11Q14.1) MUTATED	17	35	22	3
DEL PEAK 17(11Q14.1) WILD-TYPE	44	128	77	44

Figure S268. Get High-res Image Gene #43: 'del_11q14.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q14.1' versus 'MRNASEQ_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.041

Table S269. Gene #43: 'del_11q14.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
DEL PEAK 17(11Q14.1) MUTATED	38	15	8	13	2
DEL PEAK 17(11Q14.1) WILD-TYPE	87	74	42	59	26

Figure S269. Get High-res Image Gene #43: 'del_11q14.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00451 (Fisher's exact test), Q value = 0.011

Table S270. Gene #43: 'del_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
DEL PEAK 17(11Q14.1) MUTATED	9	16	23	2	6	9	6
DEL PEAK 17(11Q14.1) WILD-TYPE	32	38	45	16	47	73	18

Figure S270. Get High-res Image Gene #43: 'del_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0298 (Fisher's exact test), Q value = 0.052

Table S271. Gene #43: 'del_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
DEL PEAK 17(11Q14.1) MUTATED	39	8	11	8	5	0
DEL PEAK 17(11Q14.1) WILD-TYPE	89	42	60	32	42	4

Figure S271. Get High-res Image Gene #43: 'del_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q25' versus 'CN_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.026

Table S272. Gene #44: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 18(11Q25) MUTATED	15	40	39
DEL PEAK 18(11Q25) WILD-TYPE	86	91	99

Figure S272. Get High-res Image Gene #44: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q25' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0491 (Fisher's exact test), Q value = 0.079

Table S273. Gene #44: 'del_11q25' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
DEL PEAK 18(11Q25) MUTATED	49	31	13	0
DEL PEAK 18(11Q25) WILD-TYPE	102	114	48	7

Figure S273. Get High-res Image Gene #44: 'del_11q25' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q25' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.019 (Fisher's exact test), Q value = 0.037

Table S274. Gene #44: 'del_11q25' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
DEL PEAK 18(11Q25) MUTATED	46	12	14	7	7	0
DEL PEAK 18(11Q25) WILD-TYPE	82	38	57	33	40	4

Figure S274. Get High-res Image Gene #44: 'del_11q25' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12p12.1' versus 'CN_CNMF'

P value = 0.00308 (Fisher's exact test), Q value = 0.0084

Table S275. Gene #45: 'del_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 19(12P12.1) MUTATED	12	39	27
DEL PEAK 19(12P12.1) WILD-TYPE	89	92	111

Figure S275. Get High-res Image Gene #45: 'del_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p12.1' versus 'METHLYATION_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.033

Table S276. Gene #45: 'del_12p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
DEL PEAK 19(12P12.1) MUTATED	20	36	18	4
DEL PEAK 19(12P12.1) WILD-TYPE	41	127	81	43

Figure S276. Get High-res Image Gene #45: 'del_12p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12p12.1' versus 'MRNASEQ_CNMF'

P value = 0.0467 (Fisher's exact test), Q value = 0.077

Table S277. Gene #45: 'del_12p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
DEL PEAK 19(12P12.1) MUTATED	25	28	11	12	2
DEL PEAK 19(12P12.1) WILD-TYPE	100	61	39	60	26

Figure S277. Get High-res Image Gene #45: 'del_12p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_12p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.019 (Fisher's exact test), Q value = 0.037

Table S278. Gene #45: 'del_12p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
DEL PEAK 19(12P12.1) MUTATED	14	26	7	20	8	1
DEL PEAK 19(12P12.1) WILD-TYPE	27	60	45	101	49	7

Figure S278. Get High-res Image Gene #45: 'del_12p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_12q24.33' versus 'CN_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0016

Table S279. Gene #46: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 20(12Q24.33) MUTATED	6	32	21
DEL PEAK 20(12Q24.33) WILD-TYPE	95	99	117

Figure S279. Get High-res Image Gene #46: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S280. Gene #47: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 21(13Q14.2) MUTATED	24	96	59
DEL PEAK 21(13Q14.2) WILD-TYPE	77	35	79

Figure S280. Get High-res Image Gene #47: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 0.00318 (Fisher's exact test), Q value = 0.0086

Table S281. Gene #47: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
DEL PEAK 21(13Q14.2) MUTATED	33	75	58	13
DEL PEAK 21(13Q14.2) WILD-TYPE	28	88	41	34

Figure S281. Get High-res Image Gene #47: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q14.2' versus 'RPPA_CNMF'

P value = 0.0343 (Fisher's exact test), Q value = 0.059

Table S282. Gene #47: 'del_13q14.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	73	19	22	22	1
DEL PEAK 21(13Q14.2) MUTATED	22	26	12	10	15	0
DEL PEAK 21(13Q14.2) WILD-TYPE	19	47	7	12	7	1

Figure S282. Get High-res Image Gene #47: 'del_13q14.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_13q14.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.044 (Fisher's exact test), Q value = 0.073

Table S283. Gene #47: 'del_13q14.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	45	38	18	38
DEL PEAK 21(13Q14.2) MUTATED	25	14	20	9	17
DEL PEAK 21(13Q14.2) WILD-TYPE	14	31	18	9	21

Figure S283. Get High-res Image Gene #47: 'del_13q14.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S284. Gene #47: 'del_13q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
DEL PEAK 21(13Q14.2) MUTATED	71	60	20	20	5
DEL PEAK 21(13Q14.2) WILD-TYPE	54	29	30	52	23

Figure S284. Get High-res Image Gene #47: 'del_13q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S285. Gene #47: 'del_13q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
DEL PEAK 21(13Q14.2) MUTATED	90	71	15	0
DEL PEAK 21(13Q14.2) WILD-TYPE	61	74	46	7

Figure S285. Get High-res Image Gene #47: 'del_13q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S286. Gene #47: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	45	60	103	45	63	37	12
DEL PEAK 21(13Q14.2) MUTATED	30	34	35	23	40	14	1
DEL PEAK 21(13Q14.2) WILD-TYPE	15	26	68	22	23	23	11

Figure S286. Get High-res Image Gene #47: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00026

Table S287. Gene #47: 'del_13q14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
DEL PEAK 21(13Q14.2) MUTATED	27	48	27	61	13	1
DEL PEAK 21(13Q14.2) WILD-TYPE	14	38	25	60	44	7

Figure S287. Get High-res Image Gene #47: 'del_13q14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.023

Table S288. Gene #47: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
DEL PEAK 21(13Q14.2) MUTATED	21	35	39	6	26	28	13
DEL PEAK 21(13Q14.2) WILD-TYPE	20	19	29	12	27	54	11

Figure S288. Get High-res Image Gene #47: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S289. Gene #47: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
DEL PEAK 21(13Q14.2) MUTATED	72	27	35	26	8	0
DEL PEAK 21(13Q14.2) WILD-TYPE	56	23	36	14	39	4

Figure S289. Get High-res Image Gene #47: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S290. Gene #48: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 22(14Q23.3) MUTATED	12	71	48
DEL PEAK 22(14Q23.3) WILD-TYPE	89	60	90

Figure S290. Get High-res Image Gene #48: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q23.3' versus 'METHLYATION_CNMF'

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

Table S291. Gene #48: 'del_14q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
DEL PEAK 22(14Q23.3) MUTATED	29	50	44	8
DEL PEAK 22(14Q23.3) WILD-TYPE	32	113	55	39

Figure S291. Get High-res Image Gene #48: 'del_14q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q23.3' versus 'RPPA_CNMF'

P value = 0.00275 (Fisher's exact test), Q value = 0.0078

Table S292. Gene #48: 'del_14q23.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	73	19	22	22	1
DEL PEAK 22(14Q23.3) MUTATED	24	17	7	8	12	0
DEL PEAK 22(14Q23.3) WILD-TYPE	17	56	12	14	10	1

Figure S292. Get High-res Image Gene #48: 'del_14q23.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_14q23.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00378 (Fisher's exact test), Q value = 0.0098

Table S293. Gene #48: 'del_14q23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	45	38	18	38
DEL PEAK 22(14Q23.3) MUTATED	15	10	24	7	12
DEL PEAK 22(14Q23.3) WILD-TYPE	24	35	14	11	26

Figure S293. Get High-res Image Gene #48: 'del_14q23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_14q23.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S294. Gene #48: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
DEL PEAK 22(14Q23.3) MUTATED	65	30	14	18	2
DEL PEAK 22(14Q23.3) WILD-TYPE	60	59	36	54	26

Figure S294. Get High-res Image Gene #48: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00064 (Fisher's exact test), Q value = 0.0022

Table S295. Gene #48: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
DEL PEAK 22(14Q23.3) MUTATED	70	44	15	0
DEL PEAK 22(14Q23.3) WILD-TYPE	81	101	46	7

Figure S295. Get High-res Image Gene #48: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q23.3' versus 'MIRSEQ_CNMF'

P value = 0.00721 (Fisher's exact test), Q value = 0.017

Table S296. Gene #48: 'del_14q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	45	60	103	45	63	37	12
DEL PEAK 22(14Q23.3) MUTATED	22	22	30	14	30	12	0
DEL PEAK 22(14Q23.3) WILD-TYPE	23	38	73	31	33	25	12

Figure S296. Get High-res Image Gene #48: 'del_14q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_14q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00593 (Fisher's exact test), Q value = 0.014

Table S297. Gene #48: 'del_14q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
DEL PEAK 22(14Q23.3) MUTATED	20	26	24	47	13	0
DEL PEAK 22(14Q23.3) WILD-TYPE	21	60	28	74	44	8

Figure S297. Get High-res Image Gene #48: 'del_14q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_14q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00035

Table S298. Gene #48: 'del_14q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
DEL PEAK 22(14Q23.3) MUTATED	20	27	33	1	17	18	9
DEL PEAK 22(14Q23.3) WILD-TYPE	21	27	35	17	36	64	15

Figure S298. Get High-res Image Gene #48: 'del_14q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_14q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00765 (Fisher's exact test), Q value = 0.017

Table S299. Gene #48: 'del_14q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
DEL PEAK 22(14Q23.3) MUTATED	54	15	26	21	9	0
DEL PEAK 22(14Q23.3) WILD-TYPE	74	35	45	19	38	4

Figure S299. Get High-res Image Gene #48: 'del_14q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q32.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S300. Gene #49: 'del_14q32.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 23(14Q32.33) MUTATED	12	72	49
DEL PEAK 23(14Q32.33) WILD-TYPE	89	59	89

Figure S300. Get High-res Image Gene #49: 'del_14q32.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.33' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00054

Table S301. Gene #49: 'del_14q32.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
DEL PEAK 23(14Q32.33) MUTATED	30	46	48	9
DEL PEAK 23(14Q32.33) WILD-TYPE	31	117	51	38

Figure S301. Get High-res Image Gene #49: 'del_14q32.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q32.33' versus 'RPPA_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.029

Table S302. Gene #49: 'del_14q32.33' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	73	19	22	22	1
DEL PEAK 23(14Q32.33) MUTATED	21	18	7	8	13	0
DEL PEAK 23(14Q32.33) WILD-TYPE	20	55	12	14	9	1

Figure S302. Get High-res Image Gene #49: 'del_14q32.33' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_14q32.33' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00058

Table S303. Gene #49: 'del_14q32.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
DEL PEAK 23(14Q32.33) MUTATED	62	32	17	17	3
DEL PEAK 23(14Q32.33) WILD-TYPE	63	57	33	55	25

Figure S303. Get High-res Image Gene #49: 'del_14q32.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q32.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.001

Table S304. Gene #49: 'del_14q32.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
DEL PEAK 23(14Q32.33) MUTATED	73	42	16	0
DEL PEAK 23(14Q32.33) WILD-TYPE	78	103	45	7

Figure S304. Get High-res Image Gene #49: 'del_14q32.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.33' versus 'MIRSEQ_CNMF'

P value = 0.00428 (Fisher's exact test), Q value = 0.011

Table S305. Gene #49: 'del_14q32.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	45	60	103	45	63	37	12
DEL PEAK 23(14Q32.33) MUTATED	22	20	30	17	31	11	0
DEL PEAK 23(14Q32.33) WILD-TYPE	23	40	73	28	32	26	12

Figure S305. Get High-res Image Gene #49: 'del_14q32.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_14q32.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.022

Table S306. Gene #49: 'del_14q32.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
DEL PEAK 23(14Q32.33) MUTATED	19	27	24	48	13	0
DEL PEAK 23(14Q32.33) WILD-TYPE	22	59	28	73	44	8

Figure S306. Get High-res Image Gene #49: 'del_14q32.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_14q32.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.002

Table S307. Gene #49: 'del_14q32.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
DEL PEAK 23(14Q32.33) MUTATED	19	25	31	2	23	16	10
DEL PEAK 23(14Q32.33) WILD-TYPE	22	29	37	16	30	66	14

Figure S307. Get High-res Image Gene #49: 'del_14q32.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_14q32.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00614 (Fisher's exact test), Q value = 0.015

Table S308. Gene #49: 'del_14q32.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
DEL PEAK 23(14Q32.33) MUTATED	56	14	27	20	9	0
DEL PEAK 23(14Q32.33) WILD-TYPE	72	36	44	20	38	4

Figure S308. Get High-res Image Gene #49: 'del_14q32.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S309. Gene #50: 'del_15q26.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 24(15Q26.3) MUTATED	9	46	24
DEL PEAK 24(15Q26.3) WILD-TYPE	92	85	114

Figure S309. Get High-res Image Gene #50: 'del_15q26.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q26.3' versus 'METHLYATION_CNMF'

P value = 0.00488 (Fisher's exact test), Q value = 0.012

Table S310. Gene #50: 'del_15q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
DEL PEAK 24(15Q26.3) MUTATED	19	28	28	4
DEL PEAK 24(15Q26.3) WILD-TYPE	42	135	71	43

Figure S310. Get High-res Image Gene #50: 'del_15q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q26.3' versus 'RPPA_CNMF'

P value = 0.0225 (Fisher's exact test), Q value = 0.042

Table S311. Gene #50: 'del_15q26.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	73	19	22	22	1
DEL PEAK 24(15Q26.3) MUTATED	14	11	4	3	10	0
DEL PEAK 24(15Q26.3) WILD-TYPE	27	62	15	19	12	1

Figure S311. Get High-res Image Gene #50: 'del_15q26.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_15q26.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00116 (Fisher's exact test), Q value = 0.0037

Table S312. Gene #50: 'del_15q26.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	45	38	18	38
DEL PEAK 24(15Q26.3) MUTATED	9	3	17	3	10
DEL PEAK 24(15Q26.3) WILD-TYPE	30	42	21	15	28

Figure S312. Get High-res Image Gene #50: 'del_15q26.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_15q26.3' versus 'MRNASEQ_CNMF'

P value = 0.00275 (Fisher's exact test), Q value = 0.0078

Table S313. Gene #50: 'del_15q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
DEL PEAK 24(15Q26.3) MUTATED	40	18	8	11	1
DEL PEAK 24(15Q26.3) WILD-TYPE	85	71	42	61	27

Figure S313. Get High-res Image Gene #50: 'del_15q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0409 (Fisher's exact test), Q value = 0.069

Table S314. Gene #50: 'del_15q26.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
DEL PEAK 24(15Q26.3) MUTATED	43	25	10	0
DEL PEAK 24(15Q26.3) WILD-TYPE	108	120	51	7

Figure S314. Get High-res Image Gene #50: 'del_15q26.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q26.3' versus 'MIRSEQ_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.05

Table S315. Gene #50: 'del_15q26.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	45	60	103	45	63	37	12
DEL PEAK 24(15Q26.3) MUTATED	9	11	18	5	22	12	1
DEL PEAK 24(15Q26.3) WILD-TYPE	36	49	85	40	41	25	11

Figure S315. Get High-res Image Gene #50: 'del_15q26.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_15q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0322 (Fisher's exact test), Q value = 0.056

Table S316. Gene #50: 'del_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
DEL PEAK 24(15Q26.3) MUTATED	11	13	21	3	8	10	9
DEL PEAK 24(15Q26.3) WILD-TYPE	30	41	47	15	45	72	15

Figure S316. Get High-res Image Gene #50: 'del_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S317. Gene #51: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 25(16Q23.1) MUTATED	11	73	78
DEL PEAK 25(16Q23.1) WILD-TYPE	90	58	60

Figure S317. Get High-res Image Gene #51: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S318. Gene #51: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
DEL PEAK 25(16Q23.1) MUTATED	26	56	71	9
DEL PEAK 25(16Q23.1) WILD-TYPE	35	107	28	38

Figure S318. Get High-res Image Gene #51: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.1' versus 'RPPA_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.0028

Table S319. Gene #51: 'del_16q23.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	73	19	22	22	1
DEL PEAK 25(16Q23.1) MUTATED	16	23	13	13	16	0
DEL PEAK 25(16Q23.1) WILD-TYPE	25	50	6	9	6	1

Figure S319. Get High-res Image Gene #51: 'del_16q23.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_16q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00059 (Fisher's exact test), Q value = 0.0021

Table S320. Gene #51: 'del_16q23.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	45	38	18	38
DEL PEAK 25(16Q23.1) MUTATED	22	11	20	14	14
DEL PEAK 25(16Q23.1) WILD-TYPE	17	34	18	4	24

Figure S320. Get High-res Image Gene #51: 'del_16q23.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S321. Gene #51: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
DEL PEAK 25(16Q23.1) MUTATED	85	45	16	10	4
DEL PEAK 25(16Q23.1) WILD-TYPE	40	44	34	62	24

Figure S321. Get High-res Image Gene #51: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S322. Gene #51: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
DEL PEAK 25(16Q23.1) MUTATED	91	61	8	0
DEL PEAK 25(16Q23.1) WILD-TYPE	60	84	53	7

Figure S322. Get High-res Image Gene #51: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S323. Gene #51: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	45	60	103	45	63	37	12
DEL PEAK 25(16Q23.1) MUTATED	22	25	31	20	35	26	1
DEL PEAK 25(16Q23.1) WILD-TYPE	23	35	72	25	28	11	11

Figure S323. Get High-res Image Gene #51: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S324. Gene #51: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
DEL PEAK 25(16Q23.1) MUTATED	19	31	34	66	9	1
DEL PEAK 25(16Q23.1) WILD-TYPE	22	55	18	55	48	7

Figure S324. Get High-res Image Gene #51: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S325. Gene #51: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
DEL PEAK 25(16Q23.1) MUTATED	18	28	48	2	22	22	14
DEL PEAK 25(16Q23.1) WILD-TYPE	23	26	20	16	31	60	10

Figure S325. Get High-res Image Gene #51: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0015

Table S326. Gene #51: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
DEL PEAK 25(16Q23.1) MUTATED	64	22	41	18	9	0
DEL PEAK 25(16Q23.1) WILD-TYPE	64	28	30	22	38	4

Figure S326. Get High-res Image Gene #51: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S327. Gene #52: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 26(17P13.1) MUTATED	39	122	65
DEL PEAK 26(17P13.1) WILD-TYPE	62	9	73

Figure S327. Get High-res Image Gene #52: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.1' versus 'METHLYATION_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0023

Table S328. Gene #52: 'del_17p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
DEL PEAK 26(17P13.1) MUTATED	43	109	57	17
DEL PEAK 26(17P13.1) WILD-TYPE	18	54	42	30

Figure S328. Get High-res Image Gene #52: 'del_17p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p13.1' versus 'RPPA_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.036

Table S329. Gene #52: 'del_17p13.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	73	19	22	22	1
DEL PEAK 26(17P13.1) MUTATED	31	40	8	17	16	0
DEL PEAK 26(17P13.1) WILD-TYPE	10	33	11	5	6	1

Figure S329. Get High-res Image Gene #52: 'del_17p13.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_17p13.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00168 (Fisher's exact test), Q value = 0.0051

Table S330. Gene #52: 'del_17p13.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	45	38	18	38
DEL PEAK 26(17P13.1) MUTATED	21	21	33	12	25
DEL PEAK 26(17P13.1) WILD-TYPE	18	24	5	6	13

Figure S330. Get High-res Image Gene #52: 'del_17p13.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_17p13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S331. Gene #52: 'del_17p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
DEL PEAK 26(17P13.1) MUTATED	79	75	27	34	6
DEL PEAK 26(17P13.1) WILD-TYPE	46	14	23	38	22

Figure S331. Get High-res Image Gene #52: 'del_17p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00233 (Fisher's exact test), Q value = 0.0067

Table S332. Gene #52: 'del_17p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
DEL PEAK 26(17P13.1) MUTATED	88	101	31	1
DEL PEAK 26(17P13.1) WILD-TYPE	63	44	30	6

Figure S332. Get High-res Image Gene #52: 'del_17p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S333. Gene #52: 'del_17p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	45	60	103	45	63	37	12
DEL PEAK 26(17P13.1) MUTATED	40	47	52	22	38	21	4
DEL PEAK 26(17P13.1) WILD-TYPE	5	13	51	23	25	16	8

Figure S333. Get High-res Image Gene #52: 'del_17p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00026

Table S334. Gene #52: 'del_17p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
DEL PEAK 26(17P13.1) MUTATED	36	62	30	67	26	3
DEL PEAK 26(17P13.1) WILD-TYPE	5	24	22	54	31	5

Figure S334. Get High-res Image Gene #52: 'del_17p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S335. Gene #52: 'del_17p13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
DEL PEAK 26(17P13.1) MUTATED	23	50	38	8	29	49	17
DEL PEAK 26(17P13.1) WILD-TYPE	18	4	30	10	24	33	7

Figure S335. Get High-res Image Gene #52: 'del_17p13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S336. Gene #52: 'del_17p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
DEL PEAK 26(17P13.1) MUTATED	78	40	41	36	19	0
DEL PEAK 26(17P13.1) WILD-TYPE	50	10	30	4	28	4

Figure S336. Get High-res Image Gene #52: 'del_17p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S337. Gene #53: 'del_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 27(17P11.2) MUTATED	33	109	53
DEL PEAK 27(17P11.2) WILD-TYPE	68	22	85

Figure S337. Get High-res Image Gene #53: 'del_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p11.2' versus 'METHLYATION_CNMF'

P value = 0.00991 (Fisher's exact test), Q value = 0.022

Table S338. Gene #53: 'del_17p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
DEL PEAK 27(17P11.2) MUTATED	40	90	49	16
DEL PEAK 27(17P11.2) WILD-TYPE	21	73	50	31

Figure S338. Get High-res Image Gene #53: 'del_17p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0205 (Fisher's exact test), Q value = 0.039

Table S339. Gene #53: 'del_17p11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	45	38	18	38
DEL PEAK 27(17P11.2) MUTATED	16	20	28	12	22
DEL PEAK 27(17P11.2) WILD-TYPE	23	25	10	6	16

Figure S339. Get High-res Image Gene #53: 'del_17p11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_17p11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S340. Gene #53: 'del_17p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
DEL PEAK 27(17P11.2) MUTATED	69	64	24	30	5
DEL PEAK 27(17P11.2) WILD-TYPE	56	25	26	42	23

Figure S340. Get High-res Image Gene #53: 'del_17p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17p11.2' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00022

Table S341. Gene #53: 'del_17p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	45	60	103	45	63	37	12
DEL PEAK 27(17P11.2) MUTATED	37	39	45	21	29	19	3
DEL PEAK 27(17P11.2) WILD-TYPE	8	21	58	24	34	18	9

Figure S341. Get High-res Image Gene #53: 'del_17p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00071 (Fisher's exact test), Q value = 0.0024

Table S342. Gene #53: 'del_17p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
DEL PEAK 27(17P11.2) MUTATED	34	48	26	58	24	3
DEL PEAK 27(17P11.2) WILD-TYPE	7	38	26	63	33	5

Figure S342. Get High-res Image Gene #53: 'del_17p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00035

Table S343. Gene #53: 'del_17p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
DEL PEAK 27(17P11.2) MUTATED	21	46	32	6	28	39	12
DEL PEAK 27(17P11.2) WILD-TYPE	20	8	36	12	25	43	12

Figure S343. Get High-res Image Gene #53: 'del_17p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S344. Gene #53: 'del_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
DEL PEAK 27(17P11.2) MUTATED	65	33	35	34	17	0
DEL PEAK 27(17P11.2) WILD-TYPE	63	17	36	6	30	4

Figure S344. Get High-res Image Gene #53: 'del_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q21.2' versus 'CN_CNMF'

P value = 0.0214 (Fisher's exact test), Q value = 0.04

Table S345. Gene #54: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 28(18Q21.2) MUTATED	16	41	37
DEL PEAK 28(18Q21.2) WILD-TYPE	85	90	101

Figure S345. Get High-res Image Gene #54: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 0.00384 (Fisher's exact test), Q value = 0.0099

Table S346. Gene #54: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
DEL PEAK 28(18Q21.2) MUTATED	11	35	39	9
DEL PEAK 28(18Q21.2) WILD-TYPE	50	128	60	38

Figure S346. Get High-res Image Gene #54: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00997 (Fisher's exact test), Q value = 0.022

Table S347. Gene #54: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
DEL PEAK 28(18Q21.2) MUTATED	51	27	16	0
DEL PEAK 28(18Q21.2) WILD-TYPE	100	118	45	7

Figure S347. Get High-res Image Gene #54: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.045

Table S348. Gene #54: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
DEL PEAK 28(18Q21.2) MUTATED	9	11	28	1	11	18	7
DEL PEAK 28(18Q21.2) WILD-TYPE	32	43	40	17	42	64	17

Figure S348. Get High-res Image Gene #54: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S349. Gene #55: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 29(19P13.3) MUTATED	6	57	30
DEL PEAK 29(19P13.3) WILD-TYPE	95	74	108

Figure S349. Get High-res Image Gene #55: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 0.00629 (Fisher's exact test), Q value = 0.015

Table S350. Gene #55: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
DEL PEAK 29(19P13.3) MUTATED	19	35	34	5
DEL PEAK 29(19P13.3) WILD-TYPE	42	128	65	42

Figure S350. Get High-res Image Gene #55: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0173 (Fisher's exact test), Q value = 0.034

Table S351. Gene #55: 'del_19p13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	45	38	18	38
DEL PEAK 29(19P13.3) MUTATED	8	5	16	5	12
DEL PEAK 29(19P13.3) WILD-TYPE	31	40	22	13	26

Figure S351. Get High-res Image Gene #55: 'del_19p13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.002

Table S352. Gene #55: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
DEL PEAK 29(19P13.3) MUTATED	44	25	10	11	1
DEL PEAK 29(19P13.3) WILD-TYPE	81	64	40	61	27

Figure S352. Get High-res Image Gene #55: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.002

Table S353. Gene #55: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	145	61	7
DEL PEAK 29(19P13.3) MUTATED	54	28	9	0
DEL PEAK 29(19P13.3) WILD-TYPE	97	117	52	7

Figure S353. Get High-res Image Gene #55: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0147 (Fisher's exact test), Q value = 0.03

Table S354. Gene #55: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	86	52	121	57	8
DEL PEAK 29(19P13.3) MUTATED	16	20	20	26	10	0
DEL PEAK 29(19P13.3) WILD-TYPE	25	66	32	95	47	8

Figure S354. Get High-res Image Gene #55: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.071

Table S355. Gene #55: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	41	54	68	18	53	82	24
DEL PEAK 29(19P13.3) MUTATED	12	18	23	1	10	16	9
DEL PEAK 29(19P13.3) WILD-TYPE	29	36	45	17	43	66	15

Figure S355. Get High-res Image Gene #55: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00067 (Fisher's exact test), Q value = 0.0023

Table S356. Gene #55: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	128	50	71	40	47	4
DEL PEAK 29(19P13.3) MUTATED	47	10	12	15	5	0
DEL PEAK 29(19P13.3) WILD-TYPE	81	40	59	25	42	4

Figure S356. Get High-res Image Gene #55: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q12.1' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00026

Table S357. Gene #57: 'del_22q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 31(22Q12.1) MUTATED	17	46	16
DEL PEAK 31(22Q12.1) WILD-TYPE	84	85	122

Figure S357. Get High-res Image Gene #57: 'del_22q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q12.1' versus 'RPPA_CNMF'

P value = 0.00343 (Fisher's exact test), Q value = 0.0091

Table S358. Gene #57: 'del_22q12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	73	19	22	22	1
DEL PEAK 31(22Q12.1) MUTATED	11	18	1	4	13	0
DEL PEAK 31(22Q12.1) WILD-TYPE	30	55	18	18	9	1

Figure S358. Get High-res Image Gene #57: 'del_22q12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S359. Gene #58: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 32(22Q13.32) MUTATED	17	48	18
DEL PEAK 32(22Q13.32) WILD-TYPE	84	83	120

Figure S359. Get High-res Image Gene #58: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.32' versus 'RPPA_CNMF'

P value = 0.00489 (Fisher's exact test), Q value = 0.012

Table S360. Gene #58: 'del_22q13.32' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	73	19	22	22	1
DEL PEAK 32(22Q13.32) MUTATED	15	20	2	3	13	0
DEL PEAK 32(22Q13.32) WILD-TYPE	26	53	17	19	9	1

Figure S360. Get High-res Image Gene #58: 'del_22q13.32' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 0.00434 (Fisher's exact test), Q value = 0.011

Table S361. Gene #58: 'del_22q13.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
DEL PEAK 32(22Q13.32) MUTATED	29	32	8	12	2
DEL PEAK 32(22Q13.32) WILD-TYPE	96	57	42	60	26

Figure S361. Get High-res Image Gene #58: 'del_22q13.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xq26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S362. Gene #59: 'del_xq26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	131	138
DEL PEAK 33(XQ26.2) MUTATED	5	40	22
DEL PEAK 33(XQ26.2) WILD-TYPE	96	91	116

Figure S362. Get High-res Image Gene #59: 'del_xq26.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq26.2' versus 'METHLYATION_CNMF'

P value = 0.00682 (Fisher's exact test), Q value = 0.016

Table S363. Gene #59: 'del_xq26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	163	99	47
DEL PEAK 33(XQ26.2) MUTATED	6	29	28	4
DEL PEAK 33(XQ26.2) WILD-TYPE	55	134	71	43

Figure S363. Get High-res Image Gene #59: 'del_xq26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq26.2' versus 'MRNASEQ_CNMF'

P value = 0.00088 (Fisher's exact test), Q value = 0.0029

Table S364. Gene #59: 'del_xq26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	125	89	50	72	28
DEL PEAK 33(XQ26.2) MUTATED	29	25	3	9	1
DEL PEAK 33(XQ26.2) WILD-TYPE	96	64	47	63	27

Figure S364. Get High-res Image Gene #59: 'del_xq26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xq26.2' versus 'MIRSEQ_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.054

Table S365. Gene #59: 'del_xq26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	45	60	103	45	63	37	12
DEL PEAK 33(XQ26.2) MUTATED	9	7	22	3	17	9	0
DEL PEAK 33(XQ26.2) WILD-TYPE	36	53	81	42	46	28	12

Figure S365. Get High-res Image Gene #59: 'del_xq26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LIHC/26854194/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LIHC/26874120/LIHC.transferedmergedcluster.txt
Number of patients = 370
Number of significantly focal cnvs = 59
Number of molecular subtypes = 10
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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