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

Prostate Adenocarcinoma (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C11Z439T

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 65 focal events and 10 molecular subtypes across 492 patients, 201 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_3q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3q26.2 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_4p16.3 cnv correlated to 'CN_CNMF'.
amp_4q13.3 cnv correlated to 'CN_CNMF'.
amp_5q35.3 cnv correlated to 'CN_CNMF'.
amp_7p14.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_7q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_8p11.23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_9q33.3 cnv correlated to 'CN_CNMF'.
amp_11q13.2 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
amp_12q23.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_13q12.11 cnv correlated to 'CN_CNMF'.
amp_14q21.1 cnv correlated to 'CN_CNMF'.
amp_16q11.2 cnv correlated to 'CN_CNMF'.
amp_17q23.2 cnv correlated to 'CN_CNMF'.
amp_19q13.43 cnv correlated to 'CN_CNMF'.
amp_20q13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_xp22.11 cnv correlated to 'CN_CNMF'.
amp_xp22.11 cnv correlated to 'CN_CNMF'.
amp_xp21.1 cnv correlated to 'CN_CNMF'.
amp_xq27.1 cnv correlated to 'MIRSEQ_CHIERARCHICAL'.
del_1p31.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_1p22.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_1q42.3 cnv correlated to 'METHLYATION_CNMF'.
del_2p21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
del_2q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_2q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_4q28.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
del_5q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_6p25.1 cnv correlated to 'CN_CNMF'.
del_6q14.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_7q31.33 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_8p23.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_8p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p23 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p11.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_12p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_12q24.32 cnv correlated to 'CN_CNMF'.
del_13q14.13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q22.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q24.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17q21.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_18q21.31 cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q23 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19q13.2 cnv correlated to 'CN_CNMF'.
del_21q22.2 cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_21q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 65 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, 201 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 15q21 3	67 (14%)	425	1e-05 (0.00648)	0.0001 (0.0488)	0.00194 (0.788)	0.00691 (1.00)	1e-05 (0.00648)	0.00016 (0.0765)	1e-05 (0.00648)	5e-05 (0.0251)	0.00013 (0.0628)	1e-05 (0.00648)
del 16q22 3	191 (39%)	301	1e-05 (0.00648)	1e-05 (0.00648)	0.423 (1.00)	0.218 (1.00)	1e-05 (0.00648)	1e-05 (0.00648)	3e-05 (0.0153)	1e-05 (0.00648)	1e-05 (0.00648)	1e-05 (0.00648)
amp 8q22 1	157 (32%)	335	1e-05 (0.00648)	1e-05 (0.00648)	0.00618 (1.00)	0.00661 (1.00)	9e-05 (0.0441)	0.0173 (1.00)	3e-05 (0.0153)	1e-05 (0.00648)	1e-05 (0.00648)	7e-05 (0.0349)
amp 8q24 21	152 (31%)	340	1e-05 (0.00648)	1e-05 (0.00648)	0.00617 (1.00)	0.0065 (1.00)	2e-05 (0.0105)	0.00118 (0.503)	1e-05 (0.00648)	1e-05 (0.00648)	1e-05 (0.00648)	0.00044 (0.2)
del 8p21 3	294 (60%)	198	1e-05 (0.00648)	1e-05 (0.00648)	0.0309 (1.00)	0.0511 (1.00)	1e-05 (0.00648)	2e-05 (0.0105)	3e-05 (0.0153)	1e-05 (0.00648)	0.0092 (1.00)	1e-05 (0.00648)
del 13q14 13	227 (46%)	265	1e-05 (0.00648)	1e-05 (0.00648)	0.0774 (1.00)	0.223 (1.00)	2e-05 (0.0105)	0.00267 (1.00)	0.00011 (0.0535)	0.0004 (0.183)	0.00016 (0.0765)	8e-05 (0.0395)
del 16q24 1	213 (43%)	279	1e-05 (0.00648)	1e-05 (0.00648)	0.679 (1.00)	0.495 (1.00)	1e-05 (0.00648)	1e-05 (0.00648)	0.00028 (0.129)	1e-05 (0.00648)	0.00262 (1.00)	1e-05 (0.00648)
del 17p13 1	163 (33%)	329	1e-05 (0.00648)	1e-05 (0.00648)	0.0321 (1.00)	0.0491 (1.00)	1e-05 (0.00648)	1e-05 (0.00648)	0.00015 (0.0718)	1e-05 (0.00648)	0.00151 (0.631)	1e-05 (0.00648)
amp 7q22 1	101 (21%)	391	1e-05 (0.00648)	1e-05 (0.00648)	0.409 (1.00)	0.583 (1.00)	1e-05 (0.00648)	9e-05 (0.0441)	0.00582 (1.00)	1e-05 (0.00648)	0.00045 (0.203)	0.00363 (1.00)
del 2q22 1	92 (19%)	400	1e-05 (0.00648)	1e-05 (0.00648)	0.0247 (1.00)	0.0627 (1.00)	1e-05 (0.00648)	0.00027 (0.125)	2e-05 (0.0105)	1e-05 (0.00648)	0.00173 (0.714)	0.00115 (0.491)
del 2q22 3	85 (17%)	407	1e-05 (0.00648)	1e-05 (0.00648)	0.244 (1.00)	0.0867 (1.00)	4e-05 (0.0202)	0.0018 (0.738)	0.00026 (0.121)	1e-05 (0.00648)	0.0131 (1.00)	0.0002 (0.0948)
del 6q14 3	180 (37%)	312	1e-05 (0.00648)	1e-05 (0.00648)	0.00747 (1.00)	0.00242 (0.97)	1e-05 (0.00648)	1e-05 (0.00648)	1e-05 (0.00648)	5e-05 (0.0251)	0.0018 (0.738)	0.00493 (1.00)
del 8p23 2	224 (46%)	268	1e-05 (0.00648)	1e-05 (0.00648)	0.00612 (1.00)	0.051 (1.00)	1e-05 (0.00648)	0.00011 (0.0535)	0.0002 (0.0948)	0.00041 (0.187)	0.0348 (1.00)	0.00146 (0.612)
del 10q23 31	157 (32%)	335	1e-05 (0.00648)	1e-05 (0.00648)	0.0667 (1.00)	0.142 (1.00)	1e-05 (0.00648)	1e-05 (0.00648)	0.0141 (1.00)	1e-05 (0.00648)	0.0391 (1.00)	1e-05 (0.00648)
del 21q22 3	147 (30%)	345	1e-05 (0.00648)	1e-05 (0.00648)	0.0781 (1.00)	0.367 (1.00)	1e-05 (0.00648)	1e-05 (0.00648)	0.0321 (1.00)	2e-05 (0.0105)	0.77 (1.00)	1e-05 (0.00648)
amp 8p11 23	67 (14%)	425	1e-05 (0.00648)	1e-05 (0.00648)	0.0967 (1.00)	0.162 (1.00)	8e-05 (0.0395)	0.019 (1.00)	0.046 (1.00)	0.0013 (0.549)	1e-05 (0.00648)	0.00054 (0.242)
amp 20q13 2	45 (9%)	447	1e-05 (0.00648)	2e-05 (0.0105)	0.305 (1.00)	0.327 (1.00)	0.0127 (1.00)	0.0135 (1.00)	0.00044 (0.2)	6e-05 (0.03)	0.16 (1.00)	7e-05 (0.0349)
del 5q11 2	100 (20%)	392	1e-05 (0.00648)	1e-05 (0.00648)	0.00441 (1.00)	0.0314 (1.00)	0.00621 (1.00)	0.00371 (1.00)	0.0001 (0.0488)	1e-05 (0.00648)	0.00113 (0.484)	0.00021 (0.0989)
del 5q13 2	99 (20%)	393	1e-05 (0.00648)	4e-05 (0.0202)	0.0212 (1.00)	0.183 (1.00)	0.0156 (1.00)	0.144 (1.00)	0.00025 (0.117)	1e-05 (0.00648)	0.00214 (0.867)	0.00027 (0.125)
del 5q21 1	109 (22%)	383	1e-05 (0.00648)	1e-05 (0.00648)	0.12 (1.00)	0.0961 (1.00)	1e-05 (0.00648)	2e-05 (0.0105)	0.00029 (0.134)	0.00295 (1.00)	0.0999 (1.00)	0.00483 (1.00)
amp 3q21 3	75 (15%)	417	1e-05 (0.00648)	7e-05 (0.0349)	0.174 (1.00)	0.201 (1.00)	0.00311 (1.00)	0.00574 (1.00)	0.0173 (1.00)	0.00041 (0.187)	0.00931 (1.00)	0.00025 (0.117)
amp 7p14 3	104 (21%)	388	1e-05 (0.00648)	1e-05 (0.00648)	0.355 (1.00)	0.564 (1.00)	1e-05 (0.00648)	0.00039 (0.179)	0.00363 (1.00)	0.00059 (0.263)	0.00111 (0.476)	0.00876 (1.00)
del 1p31 3	60 (12%)	432	1e-05 (0.00648)	1e-05 (0.00648)	0.336 (1.00)	0.528 (1.00)	1e-05 (0.00648)	1e-05 (0.00648)	0.00181 (0.738)	0.166 (1.00)	0.00551 (1.00)	0.00124 (0.525)
del 3p13	78 (16%)	414	0.0005 (0.224)	1e-05 (0.00648)	0.84 (1.00)	0.919 (1.00)	1e-05 (0.00648)	1e-05 (0.00648)	0.293 (1.00)	0.0643 (1.00)	0.0293 (1.00)	0.168 (1.00)
del 12p13 1	124 (25%)	368	1e-05 (0.00648)	3e-05 (0.0153)	0.0594 (1.00)	0.0796 (1.00)	0.00084 (0.37)	0.00364 (1.00)	0.0632 (1.00)	3e-05 (0.0153)	7e-05 (0.0349)	0.00295 (1.00)
del 17q21 31	96 (20%)	396	1e-05 (0.00648)	1e-05 (0.00648)	0.523 (1.00)	0.749 (1.00)	1e-05 (0.00648)	1e-05 (0.00648)	0.555 (1.00)	0.0543 (1.00)	0.171 (1.00)	0.313 (1.00)
amp 1q22	40 (8%)	452	1e-05 (0.00648)	0.00044 (0.2)	0.00162 (0.674)	0.0207 (1.00)	0.00099 (0.431)	0.00176 (0.723)	0.0129 (1.00)	0.0004 (0.183)	0.0394 (1.00)	0.0191 (1.00)
del 2p21	46 (9%)	446	1e-05 (0.00648)	0.00022 (0.103)	0.144 (1.00)	0.582 (1.00)	0.0002 (0.0948)	0.00975 (1.00)	0.00066 (0.294)	0.0725 (1.00)	0.0332 (1.00)	0.0145 (1.00)
del 4q28 2	51 (10%)	441	1e-05 (0.00648)	1e-05 (0.00648)	0.0905 (1.00)	0.0974 (1.00)	2e-05 (0.0105)	0.0358 (1.00)	0.0921 (1.00)	0.0151 (1.00)	0.00105 (0.454)	0.0246 (1.00)
del 7q31 33	28 (6%)	464	0.00014 (0.0672)	0.0361 (1.00)	0.0281 (1.00)	0.0145 (1.00)	0.00013 (0.0628)	0.0619 (1.00)	0.001 (0.434)	0.00021 (0.0989)	0.752 (1.00)	0.0479 (1.00)
del 13q22 1	176 (36%)	316	1e-05 (0.00648)	0.00066 (0.294)	0.00892 (1.00)	0.0399 (1.00)	4e-05 (0.0202)	0.00254 (1.00)	0.00497 (1.00)	0.00123 (0.523)	0.00175 (0.721)	0.00011 (0.0535)
del 18q21 31	131 (27%)	361	1e-05 (0.00648)	0.00191 (0.777)	0.286 (1.00)	0.218 (1.00)	0.00162 (0.674)	0.0673 (1.00)	0.00021 (0.0989)	0.0178 (1.00)	0.0035 (1.00)	1e-05 (0.00648)
del 18q23	137 (28%)	355	1e-05 (0.00648)	0.016 (1.00)	0.92 (1.00)	0.307 (1.00)	0.00031 (0.143)	0.0225 (1.00)	0.011 (1.00)	0.00729 (1.00)	0.00934 (1.00)	1e-05 (0.00648)
amp 3q26 2	86 (17%)	406	1e-05 (0.00648)	0.0929 (1.00)	0.151 (1.00)	0.398 (1.00)	0.0131 (1.00)	0.0512 (1.00)	0.0821 (1.00)	0.00779 (1.00)	0.00742 (1.00)	2e-05 (0.0105)
amp 11q13 2	48 (10%)	444	1e-05 (0.00648)	0.0267 (1.00)	0.522 (1.00)	0.524 (1.00)	0.0283 (1.00)	0.00076 (0.337)	0.0321 (1.00)	0.00018 (0.0855)	0.00713 (1.00)	0.0296 (1.00)
amp 12q23 1	36 (7%)	456	2e-05 (0.0105)	8e-05 (0.0395)	0.0571 (1.00)	0.111 (1.00)	0.161 (1.00)	0.0204 (1.00)	0.65 (1.00)	0.00214 (0.867)	0.288 (1.00)	0.124 (1.00)
del 1p22 1	58 (12%)	434	1e-05 (0.00648)	8e-05 (0.0395)	0.23 (1.00)	0.0933 (1.00)	0.00336 (1.00)	0.035 (1.00)	0.00794 (1.00)	0.00308 (1.00)	0.0101 (1.00)	0.00722 (1.00)
del 9p23	45 (9%)	447	1e-05 (0.00648)	0.0861 (1.00)	0.00331 (1.00)	0.0304 (1.00)	0.00016 (0.0765)	0.0123 (1.00)	0.0271 (1.00)	0.0815 (1.00)	0.0755 (1.00)	0.0166 (1.00)
del 11p11 2	34 (7%)	458	1e-05 (0.00648)	0.0603 (1.00)	0.041 (1.00)	0.339 (1.00)	0.00045 (0.203)	0.0866 (1.00)	0.0306 (1.00)	0.024 (1.00)	0.00789 (1.00)	0.475 (1.00)
del 21q22 2	52 (11%)	440	0.00056 (0.25)	0.00351 (1.00)	0.42 (1.00)	0.765 (1.00)	2e-05 (0.0105)	1e-05 (0.00648)	0.165 (1.00)	0.0406 (1.00)	0.833 (1.00)	0.00322 (1.00)
amp 4p16 3	20 (4%)	472	1e-05 (0.00648)	0.0394 (1.00)	0.507 (1.00)	0.284 (1.00)	0.016 (1.00)	0.0767 (1.00)	0.408 (1.00)	0.0732 (1.00)	0.746 (1.00)	0.584 (1.00)
amp 4q13 3	22 (4%)	470	1e-05 (0.00648)	0.39 (1.00)	0.471 (1.00)	0.781 (1.00)	0.201 (1.00)	0.255 (1.00)	0.0269 (1.00)	0.0665 (1.00)	0.0363 (1.00)	0.164 (1.00)
amp 5q35 3	28 (6%)	464	1e-05 (0.00648)	0.0235 (1.00)	0.111 (1.00)	0.193 (1.00)	0.0672 (1.00)	0.0702 (1.00)	0.183 (1.00)	0.00092 (0.402)	0.0167 (1.00)	0.296 (1.00)
amp 9q33 3	62 (13%)	430	1e-05 (0.00648)	0.00252 (1.00)	0.0572 (1.00)	0.043 (1.00)	0.00386 (1.00)	0.00219 (0.88)	0.0188 (1.00)	0.00096 (0.419)	0.0168 (1.00)	0.00842 (1.00)
amp 13q12 11	25 (5%)	467	1e-05 (0.00648)	0.0129 (1.00)	0.0426 (1.00)	0.0333 (1.00)	0.00657 (1.00)	0.125 (1.00)	0.0146 (1.00)	0.0323 (1.00)	0.067 (1.00)	0.0739 (1.00)
amp 14q21 1	30 (6%)	462	1e-05 (0.00648)	0.127 (1.00)	0.167 (1.00)	0.18 (1.00)	0.0935 (1.00)	0.0554 (1.00)	0.00815 (1.00)	0.0108 (1.00)	0.0678 (1.00)	0.0288 (1.00)
amp 16q11 2	30 (6%)	462	1e-05 (0.00648)	0.00091 (0.399)	1 (1.00)	1 (1.00)	0.179 (1.00)	0.0152 (1.00)	0.0017 (0.704)	0.00109 (0.469)	0.0816 (1.00)	0.242 (1.00)
amp 17q23 2	25 (5%)	467	1e-05 (0.00648)	0.00299 (1.00)	1 (1.00)	0.321 (1.00)	0.0828 (1.00)	0.218 (1.00)	0.521 (1.00)	0.0141 (1.00)	0.379 (1.00)	0.0899 (1.00)
amp 19q13 43	19 (4%)	473	1e-05 (0.00648)	0.134 (1.00)	0.45 (1.00)	0.386 (1.00)	0.18 (1.00)	0.166 (1.00)	0.00631 (1.00)	0.00139 (0.584)	0.152 (1.00)	0.0118 (1.00)
amp xp22 11	26 (5%)	466	1e-05 (0.00648)	0.236 (1.00)			0.0939 (1.00)	0.0972 (1.00)	0.0154 (1.00)	0.00508 (1.00)	0.045 (1.00)	0.311 (1.00)
amp xp22 11	25 (5%)	467	2e-05 (0.0105)	0.253 (1.00)	0.0938 (1.00)	0.186 (1.00)	0.0388 (1.00)	0.0115 (1.00)	0.0079 (1.00)	0.00986 (1.00)	0.0464 (1.00)	0.234 (1.00)
amp xp21 1	23 (5%)	469	2e-05 (0.0105)	0.00732 (1.00)	0.85 (1.00)	0.736 (1.00)	0.0672 (1.00)	0.0682 (1.00)	0.0201 (1.00)	0.00914 (1.00)	0.00525 (1.00)	0.146 (1.00)
amp xq27 1	19 (4%)	473	0.00424 (1.00)	0.0706 (1.00)	0.418 (1.00)	0.217 (1.00)	0.131 (1.00)	0.263 (1.00)	0.00103 (0.446)	0.00013 (0.0628)	0.036 (1.00)	0.126 (1.00)
del 1q42 3	47 (10%)	445	0.00108 (0.465)	7e-05 (0.0349)	0.933 (1.00)	0.106 (1.00)	0.107 (1.00)	0.456 (1.00)	0.111 (1.00)	0.032 (1.00)	0.698 (1.00)	0.0472 (1.00)
del 6p25 1	46 (9%)	446	1e-05 (0.00648)	0.012 (1.00)	0.696 (1.00)	0.932 (1.00)	0.00803 (1.00)	0.00158 (0.659)	0.148 (1.00)	0.0491 (1.00)	0.387 (1.00)	0.0165 (1.00)
del 12q24 32	43 (9%)	449	5e-05 (0.0251)	0.313 (1.00)	1 (1.00)	0.829 (1.00)	0.215 (1.00)	0.194 (1.00)	0.63 (1.00)	0.549 (1.00)	0.392 (1.00)	0.0729 (1.00)
del 19q13 2	52 (11%)	440	1e-05 (0.00648)	0.0723 (1.00)	0.355 (1.00)	0.358 (1.00)	0.00515 (1.00)	0.044 (1.00)	0.00274 (1.00)	0.00076 (0.337)	0.00218 (0.879)	0.00123 (0.523)
amp 15q11 2	16 (3%)	476	0.00965 (1.00)	0.0687 (1.00)	0.785 (1.00)	0.781 (1.00)	0.948 (1.00)	0.563 (1.00)	0.133 (1.00)	0.685 (1.00)	0.532 (1.00)	0.154 (1.00)
amp xq21 1	16 (3%)	476	0.00089 (0.391)	0.182 (1.00)	0.484 (1.00)	0.641 (1.00)	0.0115 (1.00)	0.0657 (1.00)	0.313 (1.00)	0.454 (1.00)	0.45 (1.00)	0.393 (1.00)
amp xq21 1	14 (3%)	478	0.00252 (1.00)	0.184 (1.00)	0.449 (1.00)	1 (1.00)	0.0826 (1.00)	0.0118 (1.00)	0.0521 (1.00)	0.236 (1.00)	0.301 (1.00)	0.777 (1.00)
amp xq25	19 (4%)	473	0.00263 (1.00)	0.00325 (1.00)	1 (1.00)	0.878 (1.00)	0.138 (1.00)	0.0252 (1.00)	0.203 (1.00)	0.151 (1.00)	0.73 (1.00)	0.143 (1.00)
del 1q23 1	28 (6%)	464	0.00502 (1.00)	0.00083 (0.366)	0.241 (1.00)	0.286 (1.00)	0.00131 (0.552)	0.034 (1.00)	0.0449 (1.00)	0.0536 (1.00)	0.0203 (1.00)	0.188 (1.00)
del 3q29	32 (7%)	460	0.612 (1.00)	0.207 (1.00)	0.728 (1.00)	0.137 (1.00)	0.0638 (1.00)	0.00334 (1.00)	0.312 (1.00)	0.252 (1.00)	0.119 (1.00)	0.601 (1.00)
del 11q22 3	43 (9%)	449	0.0435 (1.00)	0.01 (1.00)	0.163 (1.00)	0.378 (1.00)	0.293 (1.00)	0.0345 (1.00)	0.862 (1.00)	0.781 (1.00)	0.156 (1.00)	0.0123 (1.00)
del 11q23 2	48 (10%)	444	0.133 (1.00)	0.192 (1.00)	0.234 (1.00)	0.159 (1.00)	0.81 (1.00)	0.893 (1.00)	0.233 (1.00)	0.465 (1.00)	0.304 (1.00)	0.259 (1.00)

'amp_1q22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S1. Gene #1: 'amp_1q22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 1(1Q22) MUTATED	11	28	1
AMP PEAK 1(1Q22) WILD-TYPE	262	106	84

Figure S1. Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q22' versus 'METHLYATION_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.2

Table S2. Gene #1: 'amp_1q22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
AMP PEAK 1(1Q22) MUTATED	1	14	13	3
AMP PEAK 1(1Q22) WILD-TYPE	133	112	108	36

Figure S2. Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.18

Table S3. Gene #1: 'amp_1q22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 1(1Q22) MUTATED	5	7	5	22	1
AMP PEAK 1(1Q22) WILD-TYPE	142	91	54	106	55

Figure S3. Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S4. Gene #2: 'amp_3q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 2(3Q21.3) MUTATED	15	48	12
AMP PEAK 2(3Q21.3) WILD-TYPE	258	86	73

Figure S4. Get High-res Image Gene #2: 'amp_3q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q21.3' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.035

Table S5. Gene #2: 'amp_3q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
AMP PEAK 2(3Q21.3) MUTATED	7	28	15	10
AMP PEAK 2(3Q21.3) WILD-TYPE	127	98	106	29

Figure S5. Get High-res Image Gene #2: 'amp_3q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.19

Table S6. Gene #2: 'amp_3q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 2(3Q21.3) MUTATED	12	15	6	35	6
AMP PEAK 2(3Q21.3) WILD-TYPE	135	83	53	93	50

Figure S6. Get High-res Image Gene #2: 'amp_3q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.12

Table S7. Gene #2: 'amp_3q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
AMP PEAK 2(3Q21.3) MUTATED	5	4	16	14	1	6
AMP PEAK 2(3Q21.3) WILD-TYPE	65	37	24	68	24	54

Figure S7. Get High-res Image Gene #2: 'amp_3q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S8. Gene #3: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 3(3Q26.2) MUTATED	22	51	13
AMP PEAK 3(3Q26.2) WILD-TYPE	251	83	72

Figure S8. Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S9. Gene #3: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
AMP PEAK 3(3Q26.2) MUTATED	4	6	17	19	4	3
AMP PEAK 3(3Q26.2) WILD-TYPE	66	35	23	63	21	57

Figure S9. Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4p16.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S10. Gene #4: 'amp_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 4(4P16.3) MUTATED	2	17	1
AMP PEAK 4(4P16.3) WILD-TYPE	271	117	84

Figure S10. Get High-res Image Gene #4: 'amp_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S11. Gene #5: 'amp_4q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 5(4Q13.3) MUTATED	5	17	0
AMP PEAK 5(4Q13.3) WILD-TYPE	268	117	85

Figure S11. Get High-res Image Gene #5: 'amp_4q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q35.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S12. Gene #6: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 6(5Q35.3) MUTATED	4	24	0
AMP PEAK 6(5Q35.3) WILD-TYPE	269	110	85

Figure S12. Get High-res Image Gene #6: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p14.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S13. Gene #7: 'amp_7p14.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 7(7P14.3) MUTATED	13	69	22
AMP PEAK 7(7P14.3) WILD-TYPE	260	65	63

Figure S13. Get High-res Image Gene #7: 'amp_7p14.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p14.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S14. Gene #7: 'amp_7p14.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
AMP PEAK 7(7P14.3) MUTATED	11	45	17	13
AMP PEAK 7(7P14.3) WILD-TYPE	123	81	104	26

Figure S14. Get High-res Image Gene #7: 'amp_7p14.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p14.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S15. Gene #7: 'amp_7p14.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
AMP PEAK 7(7P14.3) MUTATED	13	58	30
AMP PEAK 7(7P14.3) WILD-TYPE	132	104	145

Figure S15. Get High-res Image Gene #7: 'amp_7p14.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p14.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.18

Table S16. Gene #7: 'amp_7p14.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	173	166
AMP PEAK 7(7P14.3) MUTATED	18	53	30
AMP PEAK 7(7P14.3) WILD-TYPE	125	120	136

Figure S16. Get High-res Image Gene #7: 'amp_7p14.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S17. Gene #8: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 8(7Q22.1) MUTATED	13	66	22
AMP PEAK 8(7Q22.1) WILD-TYPE	260	68	63

Figure S17. Get High-res Image Gene #8: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S18. Gene #8: 'amp_7q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
AMP PEAK 8(7Q22.1) MUTATED	10	44	17	10
AMP PEAK 8(7Q22.1) WILD-TYPE	124	82	104	29

Figure S18. Get High-res Image Gene #8: 'amp_7q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S19. Gene #8: 'amp_7q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
AMP PEAK 8(7Q22.1) MUTATED	13	57	27
AMP PEAK 8(7Q22.1) WILD-TYPE	132	105	148

Figure S19. Get High-res Image Gene #8: 'amp_7q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.044

Table S20. Gene #8: 'amp_7q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	173	166
AMP PEAK 8(7Q22.1) MUTATED	18	53	26
AMP PEAK 8(7Q22.1) WILD-TYPE	125	120	140

Figure S20. Get High-res Image Gene #8: 'amp_7q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S21. Gene #8: 'amp_7q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 8(7Q22.1) MUTATED	13	30	16	36	5
AMP PEAK 8(7Q22.1) WILD-TYPE	134	68	43	92	51

Figure S21. Get High-res Image Gene #8: 'amp_7q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.2

Table S22. Gene #8: 'amp_7q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
AMP PEAK 8(7Q22.1) MUTATED	4	35	12	18
AMP PEAK 8(7Q22.1) WILD-TYPE	58	71	48	72

Figure S22. Get High-res Image Gene #8: 'amp_7q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S23. Gene #9: 'amp_8p11.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 9(8P11.23) MUTATED	9	49	9
AMP PEAK 9(8P11.23) WILD-TYPE	264	85	76

Figure S23. Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p11.23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S24. Gene #9: 'amp_8p11.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
AMP PEAK 9(8P11.23) MUTATED	5	30	7	8
AMP PEAK 9(8P11.23) WILD-TYPE	129	96	114	31

Figure S24. Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8p11.23' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.04

Table S25. Gene #9: 'amp_8p11.23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
AMP PEAK 9(8P11.23) MUTATED	12	37	15
AMP PEAK 9(8P11.23) WILD-TYPE	133	125	160

Figure S25. Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8p11.23' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S26. Gene #9: 'amp_8p11.23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
AMP PEAK 9(8P11.23) MUTATED	2	31	4	8
AMP PEAK 9(8P11.23) WILD-TYPE	60	75	56	82

Figure S26. Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8p11.23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.24

Table S27. Gene #9: 'amp_8p11.23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
AMP PEAK 9(8P11.23) MUTATED	5	5	4	25	1	5
AMP PEAK 9(8P11.23) WILD-TYPE	65	36	36	57	24	55

Figure S27. Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S28. Gene #10: 'amp_8q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 10(8Q22.1) MUTATED	45	100	12
AMP PEAK 10(8Q22.1) WILD-TYPE	228	34	73

Figure S28. Get High-res Image Gene #10: 'amp_8q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S29. Gene #10: 'amp_8q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
AMP PEAK 10(8Q22.1) MUTATED	14	60	29	18
AMP PEAK 10(8Q22.1) WILD-TYPE	120	66	92	21

Figure S29. Get High-res Image Gene #10: 'amp_8q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q22.1' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.044

Table S30. Gene #10: 'amp_8q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
AMP PEAK 10(8Q22.1) MUTATED	28	67	58
AMP PEAK 10(8Q22.1) WILD-TYPE	117	95	117

Figure S30. Get High-res Image Gene #10: 'amp_8q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8q22.1' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S31. Gene #10: 'amp_8q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
AMP PEAK 10(8Q22.1) MUTATED	38	36	81
AMP PEAK 10(8Q22.1) WILD-TYPE	120	111	102

Figure S31. Get High-res Image Gene #10: 'amp_8q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S32. Gene #10: 'amp_8q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 10(8Q22.1) MUTATED	25	29	24	65	12
AMP PEAK 10(8Q22.1) WILD-TYPE	122	69	35	63	44

Figure S32. Get High-res Image Gene #10: 'amp_8q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S33. Gene #10: 'amp_8q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
AMP PEAK 10(8Q22.1) MUTATED	10	56	12	23
AMP PEAK 10(8Q22.1) WILD-TYPE	52	50	48	67

Figure S33. Get High-res Image Gene #10: 'amp_8q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.035

Table S34. Gene #10: 'amp_8q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
AMP PEAK 10(8Q22.1) MUTATED	12	9	16	43	6	15
AMP PEAK 10(8Q22.1) WILD-TYPE	58	32	24	39	19	45

Figure S34. Get High-res Image Gene #10: 'amp_8q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S35. Gene #11: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 11(8Q24.21) MUTATED	43	98	11
AMP PEAK 11(8Q24.21) WILD-TYPE	230	36	74

Figure S35. Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S36. Gene #11: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
AMP PEAK 11(8Q24.21) MUTATED	15	59	27	17
AMP PEAK 11(8Q24.21) WILD-TYPE	119	67	94	22

Figure S36. Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S37. Gene #11: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
AMP PEAK 11(8Q24.21) MUTATED	25	68	54
AMP PEAK 11(8Q24.21) WILD-TYPE	120	94	121

Figure S37. Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S38. Gene #11: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
AMP PEAK 11(8Q24.21) MUTATED	33	35	82
AMP PEAK 11(8Q24.21) WILD-TYPE	125	112	101

Figure S38. Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S39. Gene #11: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 11(8Q24.21) MUTATED	21	29	23	65	12
AMP PEAK 11(8Q24.21) WILD-TYPE	126	69	36	63	44

Figure S39. Get High-res Image Gene #11: '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 = 0.0065

Table S40. Gene #11: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
AMP PEAK 11(8Q24.21) MUTATED	10	53	14	21
AMP PEAK 11(8Q24.21) WILD-TYPE	52	53	46	69

Figure S40. Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.2

Table S41. Gene #11: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
AMP PEAK 11(8Q24.21) MUTATED	13	9	15	41	6	14
AMP PEAK 11(8Q24.21) WILD-TYPE	57	32	25	41	19	46

Figure S41. Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9q33.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S42. Gene #12: 'amp_9q33.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 12(9Q33.3) MUTATED	9	53	0
AMP PEAK 12(9Q33.3) WILD-TYPE	264	81	85

Figure S42. Get High-res Image Gene #12: 'amp_9q33.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S43. Gene #13: 'amp_11q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 13(11Q13.2) MUTATED	7	39	2
AMP PEAK 13(11Q13.2) WILD-TYPE	266	95	83

Figure S43. Get High-res Image Gene #13: 'amp_11q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.085

Table S44. Gene #13: 'amp_11q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 13(11Q13.2) MUTATED	6	11	5	24	1
AMP PEAK 13(11Q13.2) WILD-TYPE	141	87	54	104	55

Figure S44. Get High-res Image Gene #13: 'amp_11q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_12q23.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S45. Gene #14: 'amp_12q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 14(12Q23.1) MUTATED	12	23	1
AMP PEAK 14(12Q23.1) WILD-TYPE	261	111	84

Figure S45. Get High-res Image Gene #14: 'amp_12q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q23.1' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.04

Table S46. Gene #14: 'amp_12q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
AMP PEAK 14(12Q23.1) MUTATED	4	15	1	6
AMP PEAK 14(12Q23.1) WILD-TYPE	130	111	120	33

Figure S46. Get High-res Image Gene #14: 'amp_12q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q12.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S47. Gene #15: 'amp_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 15(13Q12.11) MUTATED	4	20	1
AMP PEAK 15(13Q12.11) WILD-TYPE	269	114	84

Figure S47. Get High-res Image Gene #15: 'amp_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

'amp_14q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S48. Gene #16: 'amp_14q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 16(14Q21.1) MUTATED	1	25	4
AMP PEAK 16(14Q21.1) WILD-TYPE	272	109	81

Figure S48. Get High-res Image Gene #16: 'amp_14q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_16q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S49. Gene #18: 'amp_16q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 18(16Q11.2) MUTATED	8	21	1
AMP PEAK 18(16Q11.2) WILD-TYPE	265	113	84

Figure S49. Get High-res Image Gene #18: 'amp_16q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S50. Gene #19: 'amp_17q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 19(17Q23.2) MUTATED	6	19	0
AMP PEAK 19(17Q23.2) WILD-TYPE	267	115	85

Figure S50. Get High-res Image Gene #19: 'amp_17q23.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q13.43' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S51. Gene #20: 'amp_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 20(19Q13.43) MUTATED	0	19	0
AMP PEAK 20(19Q13.43) WILD-TYPE	273	115	85

Figure S51. Get High-res Image Gene #20: 'amp_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S52. Gene #21: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 21(20Q13.2) MUTATED	5	37	3
AMP PEAK 21(20Q13.2) WILD-TYPE	268	97	82

Figure S52. Get High-res Image Gene #21: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S53. Gene #21: 'amp_20q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
AMP PEAK 21(20Q13.2) MUTATED	2	19	6	7
AMP PEAK 21(20Q13.2) WILD-TYPE	132	107	115	32

Figure S53. Get High-res Image Gene #21: 'amp_20q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q13.2' versus 'MIRSEQ_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.2

Table S54. Gene #21: 'amp_20q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
AMP PEAK 21(20Q13.2) MUTATED	5	12	28
AMP PEAK 21(20Q13.2) WILD-TYPE	153	135	155

Figure S54. Get High-res Image Gene #21: 'amp_20q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_20q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.03

Table S55. Gene #21: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 21(20Q13.2) MUTATED	5	13	1	23	3
AMP PEAK 21(20Q13.2) WILD-TYPE	142	85	58	105	53

Figure S55. Get High-res Image Gene #21: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.035

Table S56. Gene #21: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
AMP PEAK 21(20Q13.2) MUTATED	1	1	12	5	2	6
AMP PEAK 21(20Q13.2) WILD-TYPE	69	40	28	77	23	54

Figure S56. Get High-res Image Gene #21: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xp22.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S57. Gene #22: 'amp_xp22.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 22(XP22.11) MUTATED	5	19	2
AMP PEAK 22(XP22.11) WILD-TYPE	268	115	83

Figure S57. Get High-res Image Gene #22: 'amp_xp22.11' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp22.11' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S58. Gene #23: 'amp_xp22.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 23(XP22.11) MUTATED	5	18	2
AMP PEAK 23(XP22.11) WILD-TYPE	268	116	83

Figure S58. Get High-res Image Gene #23: 'amp_xp22.11' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp21.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S59. Gene #24: 'amp_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
AMP PEAK 24(XP21.1) MUTATED	4	17	2
AMP PEAK 24(XP21.1) WILD-TYPE	269	117	83

Figure S59. Get High-res Image Gene #24: 'amp_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq27.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.063

Table S60. Gene #28: 'amp_xq27.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
AMP PEAK 28(XQ27.1) MUTATED	0	7	0	6	6
AMP PEAK 28(XQ27.1) WILD-TYPE	147	91	59	122	50

Figure S60. Get High-res Image Gene #28: 'amp_xq27.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p31.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S61. Gene #29: 'del_1p31.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 1(1P31.3) MUTATED	17	39	4
DEL PEAK 1(1P31.3) WILD-TYPE	256	95	81

Figure S61. Get High-res Image Gene #29: 'del_1p31.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p31.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S62. Gene #29: 'del_1p31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
DEL PEAK 1(1P31.3) MUTATED	2	14	24	8
DEL PEAK 1(1P31.3) WILD-TYPE	132	112	97	31

Figure S62. Get High-res Image Gene #29: 'del_1p31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p31.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S63. Gene #29: 'del_1p31.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
DEL PEAK 1(1P31.3) MUTATED	5	16	39
DEL PEAK 1(1P31.3) WILD-TYPE	140	146	136

Figure S63. Get High-res Image Gene #29: 'del_1p31.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p31.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S64. Gene #29: 'del_1p31.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	173	166
DEL PEAK 1(1P31.3) MUTATED	4	21	35
DEL PEAK 1(1P31.3) WILD-TYPE	139	152	131

Figure S64. Get High-res Image Gene #29: 'del_1p31.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S65. Gene #30: 'del_1p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 2(1P22.1) MUTATED	11	38	9
DEL PEAK 2(1P22.1) WILD-TYPE	262	96	76

Figure S65. Get High-res Image Gene #30: 'del_1p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p22.1' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.04

Table S66. Gene #30: 'del_1p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
DEL PEAK 2(1P22.1) MUTATED	3	20	17	8
DEL PEAK 2(1P22.1) WILD-TYPE	131	106	104	31

Figure S66. Get High-res Image Gene #30: 'del_1p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1q42.3' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.035

Table S67. Gene #32: 'del_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
DEL PEAK 4(1Q42.3) MUTATED	6	24	9	0
DEL PEAK 4(1Q42.3) WILD-TYPE	128	102	112	39

Figure S67. Get High-res Image Gene #32: 'del_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2p21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S68. Gene #33: 'del_2p21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 5(2P21) MUTATED	14	28	4
DEL PEAK 5(2P21) WILD-TYPE	259	106	81

Figure S68. Get High-res Image Gene #33: 'del_2p21' versus Molecular Subtype #1: 'CN_CNMF'

'del_2p21' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.1

Table S69. Gene #33: 'del_2p21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
DEL PEAK 5(2P21) MUTATED	2	10	19	4
DEL PEAK 5(2P21) WILD-TYPE	132	116	102	35

Figure S69. Get High-res Image Gene #33: 'del_2p21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2p21' versus 'MRNASEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.095

Table S70. Gene #33: 'del_2p21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
DEL PEAK 5(2P21) MUTATED	5	11	28
DEL PEAK 5(2P21) WILD-TYPE	140	151	147

Figure S70. Get High-res Image Gene #33: 'del_2p21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S71. Gene #34: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 6(2Q22.1) MUTATED	13	49	30
DEL PEAK 6(2Q22.1) WILD-TYPE	260	85	55

Figure S71. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S72. Gene #34: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
DEL PEAK 6(2Q22.1) MUTATED	6	43	14	9
DEL PEAK 6(2Q22.1) WILD-TYPE	128	83	107	30

Figure S72. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S73. Gene #34: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
DEL PEAK 6(2Q22.1) MUTATED	11	50	28
DEL PEAK 6(2Q22.1) WILD-TYPE	134	112	147

Figure S73. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.13

Table S74. Gene #34: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	173	166
DEL PEAK 6(2Q22.1) MUTATED	17	49	23
DEL PEAK 6(2Q22.1) WILD-TYPE	126	124	143

Figure S74. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S75. Gene #34: 'del_2q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 6(2Q22.1) MUTATED	15	21	56
DEL PEAK 6(2Q22.1) WILD-TYPE	143	126	127

Figure S75. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S76. Gene #34: 'del_2q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 6(2Q22.1) MUTATED	16	20	3	39	14
DEL PEAK 6(2Q22.1) WILD-TYPE	131	78	56	89	42

Figure S76. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S77. Gene #35: 'del_2q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 7(2Q22.3) MUTATED	11	46	28
DEL PEAK 7(2Q22.3) WILD-TYPE	262	88	57

Figure S77. Get High-res Image Gene #35: 'del_2q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S78. Gene #35: 'del_2q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
DEL PEAK 7(2Q22.3) MUTATED	6	36	15	8
DEL PEAK 7(2Q22.3) WILD-TYPE	128	90	106	31

Figure S78. Get High-res Image Gene #35: 'del_2q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.3' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S79. Gene #35: 'del_2q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
DEL PEAK 7(2Q22.3) MUTATED	12	44	25
DEL PEAK 7(2Q22.3) WILD-TYPE	133	118	150

Figure S79. Get High-res Image Gene #35: 'del_2q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q22.3' versus 'MIRSEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.12

Table S80. Gene #35: 'del_2q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 7(2Q22.3) MUTATED	17	19	49
DEL PEAK 7(2Q22.3) WILD-TYPE	141	128	134

Figure S80. Get High-res Image Gene #35: 'del_2q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S81. Gene #35: 'del_2q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 7(2Q22.3) MUTATED	14	15	4	36	16
DEL PEAK 7(2Q22.3) WILD-TYPE	133	83	55	92	40

Figure S81. Get High-res Image Gene #35: 'del_2q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.095

Table S82. Gene #35: 'del_2q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 7(2Q22.3) MUTATED	5	5	11	24	0	11
DEL PEAK 7(2Q22.3) WILD-TYPE	65	36	29	58	25	49

Figure S82. Get High-res Image Gene #35: 'del_2q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p13' versus 'CN_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.22

Table S83. Gene #36: 'del_3p13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 8(3P13) MUTATED	58	15	5
DEL PEAK 8(3P13) WILD-TYPE	215	119	80

Figure S83. Get High-res Image Gene #36: 'del_3p13' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S84. Gene #36: 'del_3p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
DEL PEAK 8(3P13) MUTATED	15	7	39	6
DEL PEAK 8(3P13) WILD-TYPE	119	119	82	33

Figure S84. Get High-res Image Gene #36: 'del_3p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S85. Gene #36: 'del_3p13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
DEL PEAK 8(3P13) MUTATED	16	8	52
DEL PEAK 8(3P13) WILD-TYPE	129	154	123

Figure S85. Get High-res Image Gene #36: 'del_3p13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S86. Gene #36: 'del_3p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	173	166
DEL PEAK 8(3P13) MUTATED	12	16	48
DEL PEAK 8(3P13) WILD-TYPE	131	157	118

Figure S86. Get High-res Image Gene #36: 'del_3p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q28.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S87. Gene #38: 'del_4q28.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 10(4Q28.2) MUTATED	7	30	14
DEL PEAK 10(4Q28.2) WILD-TYPE	266	104	71

Figure S87. Get High-res Image Gene #38: 'del_4q28.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q28.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S88. Gene #38: 'del_4q28.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
DEL PEAK 10(4Q28.2) MUTATED	2	23	5	6
DEL PEAK 10(4Q28.2) WILD-TYPE	132	103	116	33

Figure S88. Get High-res Image Gene #38: 'del_4q28.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q28.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S89. Gene #38: 'del_4q28.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
DEL PEAK 10(4Q28.2) MUTATED	4	30	13
DEL PEAK 10(4Q28.2) WILD-TYPE	141	132	162

Figure S89. Get High-res Image Gene #38: 'del_4q28.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S90. Gene #39: 'del_5q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 11(5Q11.2) MUTATED	23	64	13
DEL PEAK 11(5Q11.2) WILD-TYPE	250	70	72

Figure S90. Get High-res Image Gene #39: 'del_5q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S91. Gene #39: 'del_5q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
DEL PEAK 11(5Q11.2) MUTATED	6	33	25	10
DEL PEAK 11(5Q11.2) WILD-TYPE	128	93	96	29

Figure S91. Get High-res Image Gene #39: 'del_5q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q11.2' versus 'MIRSEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.049

Table S92. Gene #39: 'del_5q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 11(5Q11.2) MUTATED	23	20	56
DEL PEAK 11(5Q11.2) WILD-TYPE	135	127	127

Figure S92. Get High-res Image Gene #39: 'del_5q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S93. Gene #39: 'del_5q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 11(5Q11.2) MUTATED	19	9	15	45	11
DEL PEAK 11(5Q11.2) WILD-TYPE	128	89	44	83	45

Figure S93. Get High-res Image Gene #39: 'del_5q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.099

Table S94. Gene #39: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 11(5Q11.2) MUTATED	9	4	16	28	2	10
DEL PEAK 11(5Q11.2) WILD-TYPE	61	37	24	54	23	50

Figure S94. Get High-res Image Gene #39: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S95. Gene #40: 'del_5q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 12(5Q13.2) MUTATED	19	67	13
DEL PEAK 12(5Q13.2) WILD-TYPE	254	67	72

Figure S95. Get High-res Image Gene #40: 'del_5q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q13.2' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S96. Gene #40: 'del_5q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
DEL PEAK 12(5Q13.2) MUTATED	9	35	21	11
DEL PEAK 12(5Q13.2) WILD-TYPE	125	91	100	28

Figure S96. Get High-res Image Gene #40: 'del_5q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q13.2' versus 'MIRSEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.12

Table S97. Gene #40: 'del_5q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 12(5Q13.2) MUTATED	32	15	51
DEL PEAK 12(5Q13.2) WILD-TYPE	126	132	132

Figure S97. Get High-res Image Gene #40: 'del_5q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S98. Gene #40: 'del_5q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 12(5Q13.2) MUTATED	27	7	14	44	6
DEL PEAK 12(5Q13.2) WILD-TYPE	120	91	45	84	50

Figure S98. Get High-res Image Gene #40: 'del_5q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.13

Table S99. Gene #40: 'del_5q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 12(5Q13.2) MUTATED	10	3	14	27	4	6
DEL PEAK 12(5Q13.2) WILD-TYPE	60	38	26	55	21	54

Figure S99. Get High-res Image Gene #40: 'del_5q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S100. Gene #41: 'del_5q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 13(5Q21.1) MUTATED	13	60	36
DEL PEAK 13(5Q21.1) WILD-TYPE	260	74	49

Figure S100. Get High-res Image Gene #41: 'del_5q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S101. Gene #41: 'del_5q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
DEL PEAK 13(5Q21.1) MUTATED	8	51	16	7
DEL PEAK 13(5Q21.1) WILD-TYPE	126	75	105	32

Figure S101. Get High-res Image Gene #41: 'del_5q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q21.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S102. Gene #41: 'del_5q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
DEL PEAK 13(5Q21.1) MUTATED	13	64	28
DEL PEAK 13(5Q21.1) WILD-TYPE	132	98	147

Figure S102. Get High-res Image Gene #41: 'del_5q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S103. Gene #41: 'del_5q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	173	166
DEL PEAK 13(5Q21.1) MUTATED	22	59	24
DEL PEAK 13(5Q21.1) WILD-TYPE	121	114	142

Figure S103. Get High-res Image Gene #41: 'del_5q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q21.1' versus 'MIRSEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.13

Table S104. Gene #41: 'del_5q21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 13(5Q21.1) MUTATED	30	20	58
DEL PEAK 13(5Q21.1) WILD-TYPE	128	127	125

Figure S104. Get High-res Image Gene #41: 'del_5q21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6p25.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S105. Gene #42: 'del_6p25.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 14(6P25.1) MUTATED	12	30	4
DEL PEAK 14(6P25.1) WILD-TYPE	261	104	81

Figure S105. Get High-res Image Gene #42: 'del_6p25.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q14.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S106. Gene #43: 'del_6q14.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 15(6Q14.3) MUTATED	50	76	54
DEL PEAK 15(6Q14.3) WILD-TYPE	223	58	31

Figure S106. Get High-res Image Gene #43: 'del_6q14.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q14.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S107. Gene #43: 'del_6q14.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
DEL PEAK 15(6Q14.3) MUTATED	18	89	27	14
DEL PEAK 15(6Q14.3) WILD-TYPE	116	37	94	25

Figure S107. Get High-res Image Gene #43: 'del_6q14.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q14.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S108. Gene #43: 'del_6q14.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
DEL PEAK 15(6Q14.3) MUTATED	31	93	49
DEL PEAK 15(6Q14.3) WILD-TYPE	114	69	126

Figure S108. Get High-res Image Gene #43: 'del_6q14.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q14.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S109. Gene #43: 'del_6q14.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	173	166
DEL PEAK 15(6Q14.3) MUTATED	35	91	47
DEL PEAK 15(6Q14.3) WILD-TYPE	108	82	119

Figure S109. Get High-res Image Gene #43: 'del_6q14.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q14.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S110. Gene #43: 'del_6q14.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 15(6Q14.3) MUTATED	43	42	94
DEL PEAK 15(6Q14.3) WILD-TYPE	115	105	89

Figure S110. Get High-res Image Gene #43: 'del_6q14.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6q14.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.025

Table S111. Gene #43: 'del_6q14.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 15(6Q14.3) MUTATED	38	35	14	68	24
DEL PEAK 15(6Q14.3) WILD-TYPE	109	63	45	60	32

Figure S111. Get High-res Image Gene #43: 'del_6q14.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_7q31.33' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.067

Table S112. Gene #44: 'del_7q31.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 16(7Q31.33) MUTATED	7	18	3
DEL PEAK 16(7Q31.33) WILD-TYPE	266	116	82

Figure S112. Get High-res Image Gene #44: 'del_7q31.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q31.33' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.063

Table S113. Gene #44: 'del_7q31.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
DEL PEAK 16(7Q31.33) MUTATED	0	14	13
DEL PEAK 16(7Q31.33) WILD-TYPE	145	148	162

Figure S113. Get High-res Image Gene #44: 'del_7q31.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_7q31.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.099

Table S114. Gene #44: 'del_7q31.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 16(7Q31.33) MUTATED	4	1	2	18	3
DEL PEAK 16(7Q31.33) WILD-TYPE	143	97	57	110	53

Figure S114. Get High-res Image Gene #44: 'del_7q31.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S115. Gene #45: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 17(8P23.2) MUTATED	123	90	11
DEL PEAK 17(8P23.2) WILD-TYPE	150	44	74

Figure S115. Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S116. Gene #45: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
DEL PEAK 17(8P23.2) MUTATED	32	62	68	21
DEL PEAK 17(8P23.2) WILD-TYPE	102	64	53	18

Figure S116. Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S117. Gene #45: 'del_8p23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
DEL PEAK 17(8P23.2) MUTATED	47	69	105
DEL PEAK 17(8P23.2) WILD-TYPE	98	93	70

Figure S117. Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.053

Table S118. Gene #45: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	173	166
DEL PEAK 17(8P23.2) MUTATED	45	84	92
DEL PEAK 17(8P23.2) WILD-TYPE	98	89	74

Figure S118. Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.095

Table S119. Gene #45: 'del_8p23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 17(8P23.2) MUTATED	61	56	105
DEL PEAK 17(8P23.2) WILD-TYPE	97	91	78

Figure S119. Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.19

Table S120. Gene #45: 'del_8p23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 17(8P23.2) MUTATED	53	34	31	75	29
DEL PEAK 17(8P23.2) WILD-TYPE	94	64	28	53	27

Figure S120. Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S121. Gene #46: 'del_8p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 18(8P21.3) MUTATED	161	107	26
DEL PEAK 18(8P21.3) WILD-TYPE	112	27	59

Figure S121. Get High-res Image Gene #46: 'del_8p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S122. Gene #46: 'del_8p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
DEL PEAK 18(8P21.3) MUTATED	43	80	88	30
DEL PEAK 18(8P21.3) WILD-TYPE	91	46	33	9

Figure S122. Get High-res Image Gene #46: 'del_8p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S123. Gene #46: 'del_8p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
DEL PEAK 18(8P21.3) MUTATED	62	91	136
DEL PEAK 18(8P21.3) WILD-TYPE	83	71	39

Figure S123. Get High-res Image Gene #46: 'del_8p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S124. Gene #46: 'del_8p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	173	166
DEL PEAK 18(8P21.3) MUTATED	63	106	120
DEL PEAK 18(8P21.3) WILD-TYPE	80	67	46

Figure S124. Get High-res Image Gene #46: 'del_8p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p21.3' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S125. Gene #46: 'del_8p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 18(8P21.3) MUTATED	81	77	134
DEL PEAK 18(8P21.3) WILD-TYPE	77	70	49

Figure S125. Get High-res Image Gene #46: 'del_8p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S126. Gene #46: 'del_8p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 18(8P21.3) MUTATED	67	50	42	97	36
DEL PEAK 18(8P21.3) WILD-TYPE	80	48	17	31	20

Figure S126. Get High-res Image Gene #46: 'del_8p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S127. Gene #46: 'del_8p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 18(8P21.3) MUTATED	24	17	32	53	14	38
DEL PEAK 18(8P21.3) WILD-TYPE	46	24	8	29	11	22

Figure S127. Get High-res Image Gene #46: 'del_8p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S128. Gene #47: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 19(9P23) MUTATED	15	28	2
DEL PEAK 19(9P23) WILD-TYPE	258	106	83

Figure S128. Get High-res Image Gene #47: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.076

Table S129. Gene #47: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
DEL PEAK 19(9P23) MUTATED	3	16	26
DEL PEAK 19(9P23) WILD-TYPE	142	146	149

Figure S129. Get High-res Image Gene #47: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S130. Gene #48: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 20(10Q23.31) MUTATED	78	68	11
DEL PEAK 20(10Q23.31) WILD-TYPE	195	66	74

Figure S130. Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S131. Gene #48: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
DEL PEAK 20(10Q23.31) MUTATED	19	23	63	21
DEL PEAK 20(10Q23.31) WILD-TYPE	115	103	58	18

Figure S131. Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S132. Gene #48: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
DEL PEAK 20(10Q23.31) MUTATED	21	27	105
DEL PEAK 20(10Q23.31) WILD-TYPE	124	135	70

Figure S132. Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S133. Gene #48: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	173	166
DEL PEAK 20(10Q23.31) MUTATED	19	33	101
DEL PEAK 20(10Q23.31) WILD-TYPE	124	140	65

Figure S133. Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S134. Gene #48: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 20(10Q23.31) MUTATED	41	12	25	57	20
DEL PEAK 20(10Q23.31) WILD-TYPE	106	86	34	71	36

Figure S134. Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S135. Gene #48: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 20(10Q23.31) MUTATED	10	3	32	31	9	26
DEL PEAK 20(10Q23.31) WILD-TYPE	60	38	8	51	16	34

Figure S135. Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S136. Gene #49: 'del_11p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 21(11P11.2) MUTATED	5	23	6
DEL PEAK 21(11P11.2) WILD-TYPE	268	111	79

Figure S136. Get High-res Image Gene #49: 'del_11p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p11.2' versus 'MRNASEQ_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.2

Table S137. Gene #49: 'del_11p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
DEL PEAK 21(11P11.2) MUTATED	5	22	6
DEL PEAK 21(11P11.2) WILD-TYPE	140	140	169

Figure S137. Get High-res Image Gene #49: 'del_11p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_12p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S138. Gene #52: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 24(12P13.1) MUTATED	59	54	11
DEL PEAK 24(12P13.1) WILD-TYPE	214	80	74

Figure S138. Get High-res Image Gene #52: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S139. Gene #52: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
DEL PEAK 24(12P13.1) MUTATED	13	37	39	11
DEL PEAK 24(12P13.1) WILD-TYPE	121	89	82	28

Figure S139. Get High-res Image Gene #52: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S140. Gene #52: 'del_12p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 24(12P13.1) MUTATED	31	10	18	47	15
DEL PEAK 24(12P13.1) WILD-TYPE	116	88	41	81	41

Figure S140. Get High-res Image Gene #52: 'del_12p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.035

Table S141. Gene #52: 'del_12p13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
DEL PEAK 24(12P13.1) MUTATED	5	41	12	21
DEL PEAK 24(12P13.1) WILD-TYPE	57	65	48	69

Figure S141. Get High-res Image Gene #52: 'del_12p13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_12q24.32' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.025

Table S142. Gene #53: 'del_12q24.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 25(12Q24.32) MUTATED	15	25	3
DEL PEAK 25(12Q24.32) WILD-TYPE	258	109	82

Figure S142. Get High-res Image Gene #53: 'del_12q24.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S143. Gene #54: 'del_13q14.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 26(13Q14.13) MUTATED	86	90	51
DEL PEAK 26(13Q14.13) WILD-TYPE	187	44	34

Figure S143. Get High-res Image Gene #54: 'del_13q14.13' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S144. Gene #54: 'del_13q14.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
DEL PEAK 26(13Q14.13) MUTATED	29	69	55	27
DEL PEAK 26(13Q14.13) WILD-TYPE	105	57	66	12

Figure S144. Get High-res Image Gene #54: 'del_13q14.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q14.13' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S145. Gene #54: 'del_13q14.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
DEL PEAK 26(13Q14.13) MUTATED	44	83	95
DEL PEAK 26(13Q14.13) WILD-TYPE	101	79	80

Figure S145. Get High-res Image Gene #54: 'del_13q14.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q14.13' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.053

Table S146. Gene #54: 'del_13q14.13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 26(13Q14.13) MUTATED	60	58	108
DEL PEAK 26(13Q14.13) WILD-TYPE	98	89	75

Figure S146. Get High-res Image Gene #54: 'del_13q14.13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_13q14.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.18

Table S147. Gene #54: 'del_13q14.13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 26(13Q14.13) MUTATED	55	37	25	78	31
DEL PEAK 26(13Q14.13) WILD-TYPE	92	61	34	50	25

Figure S147. Get High-res Image Gene #54: 'del_13q14.13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.076

Table S148. Gene #54: 'del_13q14.13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
DEL PEAK 26(13Q14.13) MUTATED	19	66	21	46
DEL PEAK 26(13Q14.13) WILD-TYPE	43	40	39	44

Figure S148. Get High-res Image Gene #54: 'del_13q14.13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_13q14.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.04

Table S149. Gene #54: 'del_13q14.13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 26(13Q14.13) MUTATED	19	14	23	53	11	32
DEL PEAK 26(13Q14.13) WILD-TYPE	51	27	17	29	14	28

Figure S149. Get High-res Image Gene #54: 'del_13q14.13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S150. Gene #55: 'del_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 27(13Q22.1) MUTATED	56	88	32
DEL PEAK 27(13Q22.1) WILD-TYPE	217	46	53

Figure S150. Get High-res Image Gene #55: 'del_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q22.1' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S151. Gene #55: 'del_13q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
DEL PEAK 27(13Q22.1) MUTATED	30	65	77
DEL PEAK 27(13Q22.1) WILD-TYPE	115	97	98

Figure S151. Get High-res Image Gene #55: 'del_13q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.053

Table S152. Gene #55: 'del_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 27(13Q22.1) MUTATED	17	9	22	44	6	21
DEL PEAK 27(13Q22.1) WILD-TYPE	53	32	18	38	19	39

Figure S152. Get High-res Image Gene #55: 'del_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S153. Gene #56: 'del_15q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 28(15Q21.3) MUTATED	17	47	3
DEL PEAK 28(15Q21.3) WILD-TYPE	256	87	82

Figure S153. Get High-res Image Gene #56: 'del_15q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q21.3' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.049

Table S154. Gene #56: 'del_15q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
DEL PEAK 28(15Q21.3) MUTATED	3	17	22	6
DEL PEAK 28(15Q21.3) WILD-TYPE	131	109	99	33

Figure S154. Get High-res Image Gene #56: 'del_15q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S155. Gene #56: 'del_15q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
DEL PEAK 28(15Q21.3) MUTATED	4	25	36
DEL PEAK 28(15Q21.3) WILD-TYPE	141	137	139

Figure S155. Get High-res Image Gene #56: 'del_15q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.076

Table S156. Gene #56: 'del_15q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	173	166
DEL PEAK 28(15Q21.3) MUTATED	6	28	31
DEL PEAK 28(15Q21.3) WILD-TYPE	137	145	135

Figure S156. Get High-res Image Gene #56: 'del_15q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S157. Gene #56: 'del_15q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 28(15Q21.3) MUTATED	8	15	42
DEL PEAK 28(15Q21.3) WILD-TYPE	150	132	141

Figure S157. Get High-res Image Gene #56: 'del_15q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_15q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.025

Table S158. Gene #56: 'del_15q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 28(15Q21.3) MUTATED	7	8	10	28	12
DEL PEAK 28(15Q21.3) WILD-TYPE	140	90	49	100	44

Figure S158. Get High-res Image Gene #56: 'del_15q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.063

Table S159. Gene #56: 'del_15q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
DEL PEAK 28(15Q21.3) MUTATED	1	26	5	12
DEL PEAK 28(15Q21.3) WILD-TYPE	61	80	55	78

Figure S159. Get High-res Image Gene #56: 'del_15q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_15q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S160. Gene #56: 'del_15q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 28(15Q21.3) MUTATED	0	2	14	18	1	9
DEL PEAK 28(15Q21.3) WILD-TYPE	70	39	26	64	24	51

Figure S160. Get High-res Image Gene #56: 'del_15q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S161. Gene #57: 'del_16q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 29(16Q22.3) MUTATED	88	93	10
DEL PEAK 29(16Q22.3) WILD-TYPE	185	41	75

Figure S161. Get High-res Image Gene #57: 'del_16q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S162. Gene #57: 'del_16q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
DEL PEAK 29(16Q22.3) MUTATED	24	49	59	26
DEL PEAK 29(16Q22.3) WILD-TYPE	110	77	62	13

Figure S162. Get High-res Image Gene #57: 'del_16q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S163. Gene #57: 'del_16q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
DEL PEAK 29(16Q22.3) MUTATED	35	55	97
DEL PEAK 29(16Q22.3) WILD-TYPE	110	107	78

Figure S163. Get High-res Image Gene #57: 'del_16q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S164. Gene #57: 'del_16q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	173	166
DEL PEAK 29(16Q22.3) MUTATED	34	63	90
DEL PEAK 29(16Q22.3) WILD-TYPE	109	110	76

Figure S164. Get High-res Image Gene #57: 'del_16q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q22.3' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S165. Gene #57: 'del_16q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 29(16Q22.3) MUTATED	56	39	94
DEL PEAK 29(16Q22.3) WILD-TYPE	102	108	89

Figure S165. Get High-res Image Gene #57: 'del_16q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S166. Gene #57: 'del_16q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 29(16Q22.3) MUTATED	44	22	28	78	17
DEL PEAK 29(16Q22.3) WILD-TYPE	103	76	31	50	39

Figure S166. Get High-res Image Gene #57: 'del_16q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S167. Gene #57: 'del_16q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
DEL PEAK 29(16Q22.3) MUTATED	10	57	16	31
DEL PEAK 29(16Q22.3) WILD-TYPE	52	49	44	59

Figure S167. Get High-res Image Gene #57: 'del_16q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S168. Gene #57: 'del_16q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 29(16Q22.3) MUTATED	16	4	20	46	4	24
DEL PEAK 29(16Q22.3) WILD-TYPE	54	37	20	36	21	36

Figure S168. Get High-res Image Gene #57: 'del_16q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S169. Gene #58: 'del_16q24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 30(16Q24.1) MUTATED	105	101	7
DEL PEAK 30(16Q24.1) WILD-TYPE	168	33	78

Figure S169. Get High-res Image Gene #58: 'del_16q24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q24.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S170. Gene #58: 'del_16q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
DEL PEAK 30(16Q24.1) MUTATED	27	53	63	30
DEL PEAK 30(16Q24.1) WILD-TYPE	107	73	58	9

Figure S170. Get High-res Image Gene #58: 'del_16q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q24.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S171. Gene #58: 'del_16q24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
DEL PEAK 30(16Q24.1) MUTATED	45	60	104
DEL PEAK 30(16Q24.1) WILD-TYPE	100	102	71

Figure S171. Get High-res Image Gene #58: 'del_16q24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S172. Gene #58: 'del_16q24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	173	166
DEL PEAK 30(16Q24.1) MUTATED	41	72	96
DEL PEAK 30(16Q24.1) WILD-TYPE	102	101	70

Figure S172. Get High-res Image Gene #58: 'del_16q24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q24.1' versus 'MIRSEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.13

Table S173. Gene #58: 'del_16q24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 30(16Q24.1) MUTATED	64	47	99
DEL PEAK 30(16Q24.1) WILD-TYPE	94	100	84

Figure S173. Get High-res Image Gene #58: 'del_16q24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S174. Gene #58: 'del_16q24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 30(16Q24.1) MUTATED	50	25	32	86	17
DEL PEAK 30(16Q24.1) WILD-TYPE	97	73	27	42	39

Figure S174. Get High-res Image Gene #58: 'del_16q24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S175. Gene #58: 'del_16q24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 30(16Q24.1) MUTATED	16	7	22	49	8	27
DEL PEAK 30(16Q24.1) WILD-TYPE	54	34	18	33	17	33

Figure S175. Get High-res Image Gene #58: 'del_16q24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S176. Gene #59: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 31(17P13.1) MUTATED	71	85	7
DEL PEAK 31(17P13.1) WILD-TYPE	202	49	78

Figure S176. Get High-res Image Gene #59: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S177. Gene #59: 'del_17p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
DEL PEAK 31(17P13.1) MUTATED	24	26	59	23
DEL PEAK 31(17P13.1) WILD-TYPE	110	100	62	16

Figure S177. Get High-res Image Gene #59: 'del_17p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S178. Gene #59: 'del_17p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
DEL PEAK 31(17P13.1) MUTATED	30	31	99
DEL PEAK 31(17P13.1) WILD-TYPE	115	131	76

Figure S178. Get High-res Image Gene #59: 'del_17p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S179. Gene #59: 'del_17p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	173	166
DEL PEAK 31(17P13.1) MUTATED	27	39	94
DEL PEAK 31(17P13.1) WILD-TYPE	116	134	72

Figure S179. Get High-res Image Gene #59: 'del_17p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.1' versus 'MIRSEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.072

Table S180. Gene #59: 'del_17p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 31(17P13.1) MUTATED	46	34	81
DEL PEAK 31(17P13.1) WILD-TYPE	112	113	102

Figure S180. Get High-res Image Gene #59: 'del_17p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S181. Gene #59: 'del_17p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 31(17P13.1) MUTATED	36	15	34	60	16
DEL PEAK 31(17P13.1) WILD-TYPE	111	83	25	68	40

Figure S181. Get High-res Image Gene #59: 'del_17p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S182. Gene #59: 'del_17p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 31(17P13.1) MUTATED	16	3	28	40	8	18
DEL PEAK 31(17P13.1) WILD-TYPE	54	38	12	42	17	42

Figure S182. Get High-res Image Gene #59: 'del_17p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q21.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S183. Gene #60: 'del_17q21.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 32(17Q21.31) MUTATED	52	41	3
DEL PEAK 32(17Q21.31) WILD-TYPE	221	93	82

Figure S183. Get High-res Image Gene #60: 'del_17q21.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q21.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S184. Gene #60: 'del_17q21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
DEL PEAK 32(17Q21.31) MUTATED	19	10	50	6
DEL PEAK 32(17Q21.31) WILD-TYPE	115	116	71	33

Figure S184. Get High-res Image Gene #60: 'del_17q21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q21.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S185. Gene #60: 'del_17q21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
DEL PEAK 32(17Q21.31) MUTATED	21	13	62
DEL PEAK 32(17Q21.31) WILD-TYPE	124	149	113

Figure S185. Get High-res Image Gene #60: 'del_17q21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17q21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S186. Gene #60: 'del_17q21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	173	166
DEL PEAK 32(17Q21.31) MUTATED	19	20	57
DEL PEAK 32(17Q21.31) WILD-TYPE	124	153	109

Figure S186. Get High-res Image Gene #60: 'del_17q21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S187. Gene #61: 'del_18q21.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 33(18Q21.31) MUTATED	45	72	14
DEL PEAK 33(18Q21.31) WILD-TYPE	228	62	71

Figure S187. Get High-res Image Gene #61: 'del_18q21.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q21.31' versus 'MIRSEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.099

Table S188. Gene #61: 'del_18q21.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
DEL PEAK 33(18Q21.31) MUTATED	31	30	68
DEL PEAK 33(18Q21.31) WILD-TYPE	127	117	115

Figure S188. Get High-res Image Gene #61: 'del_18q21.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S189. Gene #61: 'del_18q21.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 33(18Q21.31) MUTATED	9	4	21	33	5	14
DEL PEAK 33(18Q21.31) WILD-TYPE	61	37	19	49	20	46

Figure S189. Get High-res Image Gene #61: 'del_18q21.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S190. Gene #62: 'del_18q23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 34(18Q23) MUTATED	48	77	12
DEL PEAK 34(18Q23) WILD-TYPE	225	57	73

Figure S190. Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q23' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.14

Table S191. Gene #62: 'del_18q23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
DEL PEAK 34(18Q23) MUTATED	25	43	65
DEL PEAK 34(18Q23) WILD-TYPE	120	119	110

Figure S191. Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S192. Gene #62: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 34(18Q23) MUTATED	11	3	21	32	6	18
DEL PEAK 34(18Q23) WILD-TYPE	59	38	19	50	19	42

Figure S192. Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S193. Gene #63: 'del_19q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 35(19Q13.2) MUTATED	14	32	6
DEL PEAK 35(19Q13.2) WILD-TYPE	259	102	79

Figure S193. Get High-res Image Gene #63: 'del_19q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q22.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S194. Gene #64: 'del_21q22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
DEL PEAK 36(21Q22.2) MUTATED	12	6	33
DEL PEAK 36(21Q22.2) WILD-TYPE	133	156	142

Figure S194. Get High-res Image Gene #64: 'del_21q22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_21q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S195. Gene #64: 'del_21q22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	173	166
DEL PEAK 36(21Q22.2) MUTATED	6	11	34
DEL PEAK 36(21Q22.2) WILD-TYPE	137	162	132

Figure S195. Get High-res Image Gene #64: 'del_21q22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_21q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S196. Gene #65: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
DEL PEAK 37(21Q22.3) MUTATED	95	49	3
DEL PEAK 37(21Q22.3) WILD-TYPE	178	85	82

Figure S196. Get High-res Image Gene #65: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S197. Gene #65: 'del_21q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
DEL PEAK 37(21Q22.3) MUTATED	24	8	77	16
DEL PEAK 37(21Q22.3) WILD-TYPE	110	118	44	23

Figure S197. Get High-res Image Gene #65: 'del_21q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S198. Gene #65: 'del_21q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
DEL PEAK 37(21Q22.3) MUTATED	27	11	108
DEL PEAK 37(21Q22.3) WILD-TYPE	118	151	67

Figure S198. Get High-res Image Gene #65: 'del_21q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_21q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S199. Gene #65: 'del_21q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	173	166
DEL PEAK 37(21Q22.3) MUTATED	16	15	115
DEL PEAK 37(21Q22.3) WILD-TYPE	127	158	51

Figure S199. Get High-res Image Gene #65: 'del_21q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_21q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S200. Gene #65: 'del_21q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
DEL PEAK 37(21Q22.3) MUTATED	44	15	33	39	14
DEL PEAK 37(21Q22.3) WILD-TYPE	103	83	26	89	42

Figure S200. Get High-res Image Gene #65: 'del_21q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_21q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0065

Table S201. Gene #65: 'del_21q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
DEL PEAK 37(21Q22.3) MUTATED	17	3	26	19	13	19
DEL PEAK 37(21Q22.3) WILD-TYPE	53	38	14	63	12	41

Figure S201. Get High-res Image Gene #65: 'del_21q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = PRAD-TP.transferedmergedcluster.txt
Number of patients = 492
Number of significantly focal cnvs = 65
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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