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

Overview

Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 56 focal events and 10 molecular subtypes across 184 patients, 238 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p34.2 cnv correlated to 'RPPA_CHIERARCHICAL'.
amp_1q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_2q36.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3p12.2 cnv correlated to 'METHLYATION_CNMF'.
amp_3q26.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_4p16.3 cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6p21.31 cnv correlated to 'MIRSEQ_CNMF'.
amp_7q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8p11.22 cnv correlated to 'CN_CNMF'.
amp_8p11.21 cnv correlated to 'CN_CNMF'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
amp_12p13.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12p11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12q15 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_15q26.1 cnv correlated to 'CN_CNMF'.
amp_17p11.2 cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q12 cnv correlated to 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_18q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19q13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
amp_20p11.23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_xq28 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_2q14.3 cnv correlated to 'MIRSEQ_CNMF'.
del_3p21.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_4q22.1 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q34.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_5q14.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_6p25.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6p22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_7q36.1 cnv correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.
del_8p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10p15.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q23.33 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p15.4 cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.
del_12p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12q24.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q11.2 cnv correlated to 'METHLYATION_CNMF'.
del_15q15.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q23.1 cnv correlated to 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17q22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_18p11.31 cnv correlated to 'CN_CNMF'.
del_18q21.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_19p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19q13.33 cnv correlated to 'CN_CNMF'.
del_21q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_22q13.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_22q13.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_xp21.1 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xq11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 56 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, 238 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 6q25 3	91 (49%)	93	1e-05 (0.000224)	1e-05 (0.000224)	0.0119 (0.0436)	0.404 (0.511)	2e-05 (0.000329)	0.00507 (0.022)	0.00427 (0.0199)	0.00021 (0.00187)	0.00063 (0.00454)	0.00973 (0.0368)
del xq11 2	23 (12%)	161	0.00965 (0.0368)	0.00373 (0.0185)	0.00164 (0.00996)	0.288 (0.406)	0.03 (0.0786)	0.0199 (0.061)	0.0167 (0.0544)	0.0226 (0.0646)	0.0214 (0.0634)	0.0161 (0.0543)
del 9p21 3	116 (63%)	68	1e-05 (0.000224)	1e-05 (0.000224)	0.151 (0.255)	0.571 (0.658)	1e-05 (0.000224)	8e-05 (0.000878)	1e-05 (0.000224)	1e-05 (0.000224)	1e-05 (0.000224)	1e-05 (0.000224)
del 12p13 1	29 (16%)	155	0.00019 (0.00177)	0.00014 (0.00138)	0.00915 (0.0351)	0.0514 (0.12)	0.00087 (0.00587)	0.0012 (0.00764)	0.3 (0.417)	6e-05 (0.000715)	0.0465 (0.111)	0.00442 (0.0202)
del 12q24 33	43 (23%)	141	0.00309 (0.0163)	0.00046 (0.00358)	0.0145 (0.0511)	0.0151 (0.0522)	0.0101 (0.0379)	0.00325 (0.0169)	0.115 (0.21)	0.00064 (0.00454)	0.138 (0.24)	0.0249 (0.0694)
del 17p12	89 (48%)	95	1e-05 (0.000224)	1e-05 (0.000224)	0.225 (0.343)	0.461 (0.566)	1e-05 (0.000224)	4e-05 (0.000546)	5e-05 (0.000636)	8e-05 (0.000878)	1e-05 (0.000224)	3e-05 (0.000442)
del 17q22	49 (27%)	135	1e-05 (0.000224)	0.00083 (0.00567)	0.00405 (0.0194)	0.0582 (0.131)	0.00902 (0.0351)	0.0149 (0.052)	0.0222 (0.0638)	0.0262 (0.071)	0.00016 (0.00154)	0.318 (0.432)
del 18q21 2	126 (68%)	58	1e-05 (0.000224)	1e-05 (0.000224)	0.244 (0.365)	0.61 (0.687)	2e-05 (0.000329)	5e-05 (0.000636)	0.0002 (0.00181)	6e-05 (0.000715)	0.00124 (0.0078)	1e-05 (0.000224)
amp 1q21 3	62 (34%)	122	0.00057 (0.00431)	6e-05 (0.000715)	0.0666 (0.146)	0.0787 (0.163)	0.0165 (0.0543)	0.0105 (0.0391)	0.0133 (0.0476)	0.0158 (0.0538)	0.00757 (0.0307)	0.135 (0.237)
amp 2q36 2	26 (14%)	158	0.0186 (0.0579)	9e-05 (0.000933)	0.0557 (0.128)	0.314 (0.428)	0.0191 (0.0588)	0.021 (0.0632)	0.485 (0.589)	0.00383 (0.0188)	0.0309 (0.0804)	0.0319 (0.0827)
amp 7q22 1	56 (30%)	128	3e-05 (0.000442)	0.0201 (0.0612)	0.0324 (0.0836)	0.678 (0.742)	0.0253 (0.0701)	0.311 (0.425)	0.106 (0.199)	0.0376 (0.0941)	0.0024 (0.0133)	0.00477 (0.0212)
del 6p25 2	74 (40%)	110	1e-05 (0.000224)	2e-05 (0.000329)	0.00242 (0.0133)	0.179 (0.289)	0.00346 (0.0175)	0.0123 (0.0449)	0.063 (0.139)	0.00046 (0.00358)	0.177 (0.288)	0.00104 (0.00677)
del 6p22 2	70 (38%)	114	1e-05 (0.000224)	2e-05 (0.000329)	0.0362 (0.0917)	0.56 (0.65)	0.00471 (0.0212)	0.0221 (0.0637)	0.142 (0.245)	0.00094 (0.00627)	0.254 (0.374)	0.00167 (0.00996)
del 19p13 2	28 (15%)	156	0.00061 (0.00449)	2e-05 (0.000329)	0.572 (0.658)	0.0834 (0.169)	8e-05 (0.000878)	0.00325 (0.0169)	0.0972 (0.188)	0.00039 (0.00312)	0.00292 (0.0156)	0.0119 (0.0436)
del 22q13 31	60 (33%)	124	1e-05 (0.000224)	9e-05 (0.000933)	0.47 (0.575)	0.894 (0.919)	0.0217 (0.0636)	0.0801 (0.164)	0.0156 (0.0533)	0.0165 (0.0543)	0.0029 (0.0156)	0.0412 (0.101)
amp 3q26 2	32 (17%)	152	0.00394 (0.0192)	3e-05 (0.000442)	0.214 (0.33)	0.0166 (0.0543)	2e-05 (0.000329)	0.0526 (0.122)	0.59 (0.672)	0.0171 (0.0547)	0.136 (0.238)	0.0184 (0.0579)
amp 12q15	29 (16%)	155	0.00028 (0.00231)	0.00417 (0.0198)	0.289 (0.406)	0.0751 (0.16)	0.00689 (0.0286)	0.329 (0.443)	0.0326 (0.0838)	0.0769 (0.161)	0.0467 (0.111)	0.00144 (0.00896)
amp 18q11 2	56 (30%)	128	5e-05 (0.000636)	0.00106 (0.00682)	0.0751 (0.16)	0.102 (0.194)	0.00066 (0.00456)	0.0756 (0.16)	0.0219 (0.0636)	0.00054 (0.00414)	0.189 (0.301)	0.00022 (0.00192)
del 10p15 3	41 (22%)	143	2e-05 (0.000329)	0.235 (0.353)	0.896 (0.919)	0.674 (0.741)	0.00101 (0.00665)	0.0126 (0.0457)	0.657 (0.73)	0.0242 (0.0684)	0.00038 (0.00308)	0.0155 (0.0532)
del 19p13 3	36 (20%)	148	2e-05 (0.000329)	1e-05 (0.000224)	0.782 (0.829)	0.253 (0.374)	0.00013 (0.0013)	0.00183 (0.0106)	0.452 (0.559)	0.00914 (0.0351)	0.0476 (0.112)	0.115 (0.21)
amp 4p16 3	15 (8%)	169	0.157 (0.262)	0.676 (0.741)	0.137 (0.239)	0.0713 (0.155)	0.043 (0.105)	0.0184 (0.0579)	0.186 (0.297)	0.0255 (0.0701)	0.0386 (0.0961)	0.00168 (0.00996)
amp 12p13 33	39 (21%)	145	0.00023 (0.00198)	0.0002 (0.00181)	0.401 (0.509)	0.276 (0.394)	0.0133 (0.0476)	0.552 (0.645)	0.058 (0.131)	0.197 (0.309)	0.0149 (0.052)	0.00368 (0.0184)
amp 12p11 21	43 (23%)	141	3e-05 (0.000442)	2e-05 (0.000329)	0.498 (0.602)	0.463 (0.568)	0.00059 (0.00441)	0.31 (0.425)	0.0733 (0.157)	0.0079 (0.0318)	0.0895 (0.177)	0.0188 (0.0581)
amp 20p11 23	38 (21%)	146	0.00624 (0.0266)	0.00671 (0.028)	0.0775 (0.161)	0.119 (0.215)	0.0757 (0.16)	0.395 (0.503)	0.0496 (0.117)	0.0259 (0.0707)	0.272 (0.39)	0.00443 (0.0202)
del 1p36 11	68 (37%)	116	8e-05 (0.000878)	1e-05 (0.000224)	0.0163 (0.0543)	0.284 (0.401)	0.00018 (0.00171)	0.0184 (0.0579)	0.192 (0.303)	0.0855 (0.17)	0.0956 (0.185)	0.167 (0.276)
del 8p21 3	62 (34%)	122	1e-05 (0.000224)	0.00475 (0.0212)	0.41 (0.516)	0.147 (0.251)	0.0186 (0.0579)	0.028 (0.0754)	0.645 (0.721)	0.0286 (0.076)	0.339 (0.45)	0.348 (0.453)
del 15q15 1	36 (20%)	148	0.00496 (0.0219)	0.0563 (0.129)	0.265 (0.385)	0.437 (0.545)	0.0168 (0.0544)	0.00331 (0.017)	0.67 (0.737)	0.034 (0.087)	0.588 (0.672)	0.0088 (0.0345)
del 22q13 32	61 (33%)	123	1e-05 (0.000224)	9e-05 (0.000933)	0.756 (0.808)	0.943 (0.956)	0.0468 (0.111)	0.0721 (0.155)	0.0377 (0.0941)	0.165 (0.275)	0.00733 (0.03)	0.286 (0.403)
del 3p21 31	51 (28%)	133	0.017 (0.0546)	0.0055 (0.0237)	0.237 (0.356)	0.544 (0.639)	0.00423 (0.0199)	0.788 (0.832)	0.105 (0.198)	0.0434 (0.105)	0.632 (0.709)	0.113 (0.207)
del 4q22 1	27 (15%)	157	0.387 (0.495)	0.00806 (0.032)	0.336 (0.448)	0.144 (0.248)	0.00631 (0.0266)	0.0883 (0.175)	0.345 (0.451)	0.0016 (0.00985)	0.156 (0.261)	0.0262 (0.071)
del 10q23 33	35 (19%)	149	4e-05 (0.000546)	0.799 (0.839)	0.567 (0.656)	0.309 (0.425)	0.0219 (0.0636)	0.179 (0.289)	0.148 (0.251)	0.538 (0.633)	0.0162 (0.0543)	0.0398 (0.0978)
del 16q23 1	19 (10%)	165	0.404 (0.511)	0.769 (0.819)	0.189 (0.3)	0.00631 (0.0266)	0.417 (0.524)	0.0465 (0.111)	0.0246 (0.0689)	0.338 (0.449)	0.251 (0.372)	0.0136 (0.0483)
del xp21 1	28 (15%)	156	0.00841 (0.0332)	0.211 (0.329)	0.0389 (0.0963)	0.656 (0.73)	0.28 (0.399)	0.293 (0.408)	0.0295 (0.0776)	0.655 (0.73)	0.0601 (0.134)	0.0215 (0.0634)
amp 8q24 21	74 (40%)	110	1e-05 (0.000224)	0.00025 (0.00212)	0.108 (0.201)	0.14 (0.243)	0.00333 (0.017)	0.0613 (0.136)	0.123 (0.222)	0.0562 (0.129)	0.105 (0.198)	0.0818 (0.167)
amp 17q12	31 (17%)	153	0.0844 (0.169)	0.0855 (0.17)	0.961 (0.97)	0.986 (0.987)	0.0283 (0.0755)	0.214 (0.33)	0.0227 (0.0646)	0.0601 (0.134)	0.502 (0.602)	0.00264 (0.0144)
amp 19q13 2	47 (26%)	137	0.00012 (0.00122)	0.00993 (0.0373)	0.343 (0.451)	0.512 (0.609)	0.00503 (0.022)	0.872 (0.901)	0.429 (0.536)	0.227 (0.344)	0.308 (0.425)	0.352 (0.456)
del 21q11 2	62 (34%)	122	4e-05 (0.000546)	0.00225 (0.0126)	0.344 (0.451)	0.213 (0.33)	0.129 (0.229)	0.0579 (0.131)	0.22 (0.338)	0.0211 (0.0632)	0.0771 (0.161)	0.36 (0.465)
amp xq28	20 (11%)	164	0.00432 (0.02)	0.459 (0.565)	0.283 (0.401)	0.135 (0.237)	0.245 (0.366)	0.215 (0.33)	0.0949 (0.184)	0.327 (0.442)	0.0911 (0.178)	0.0294 (0.0776)
del 4q34 3	35 (19%)	149	0.0255 (0.0701)	0.0352 (0.0896)	0.107 (0.201)	0.0538 (0.124)	0.0776 (0.161)	0.622 (0.699)	0.799 (0.839)	0.17 (0.28)	0.446 (0.554)	0.138 (0.24)
del 5q14 2	35 (19%)	149	0.00175 (0.0102)	0.0905 (0.178)	0.292 (0.408)	0.148 (0.251)	0.00196 (0.0112)	0.221 (0.338)	0.291 (0.408)	0.177 (0.288)	0.148 (0.251)	0.18 (0.289)
del 7q36 1	15 (8%)	169	0.0397 (0.0978)	0.129 (0.229)	0.152 (0.256)	0.0213 (0.0634)	0.177 (0.288)	0.605 (0.684)	0.827 (0.863)	0.341 (0.451)	0.536 (0.632)	0.161 (0.268)
del 11p15 4	29 (16%)	155	0.00729 (0.03)	0.5 (0.602)	0.00213 (0.012)	0.0833 (0.169)	0.593 (0.674)	0.784 (0.83)	0.51 (0.609)	0.55 (0.643)	0.692 (0.751)	0.56 (0.65)
amp 1p34 2	13 (7%)	171	0.336 (0.448)	0.812 (0.85)	0.171 (0.28)	0.0433 (0.105)	0.916 (0.934)	0.265 (0.385)	0.486 (0.589)	0.918 (0.935)	0.263 (0.384)	0.752 (0.806)
amp 3p12 2	12 (7%)	172	0.127 (0.227)	0.0283 (0.0755)	0.0844 (0.169)	0.771 (0.819)	0.146 (0.25)	0.92 (0.935)	0.608 (0.686)	1 (1.00)	0.637 (0.713)	0.98 (0.984)
amp 6p21 31	12 (7%)	172	0.109 (0.201)	0.248 (0.369)	0.683 (0.744)	0.683 (0.744)	0.42 (0.526)	0.855 (0.885)	0.0372 (0.0939)	0.716 (0.772)	0.572 (0.658)	0.38 (0.489)
amp 8p11 22	34 (18%)	150	0.0205 (0.062)	0.268 (0.386)	0.124 (0.224)	0.336 (0.448)	0.375 (0.482)	0.698 (0.755)	0.512 (0.609)	0.69 (0.751)	0.352 (0.456)	0.67 (0.737)
amp 8p11 21	34 (18%)	150	0.00066 (0.00456)	0.128 (0.229)	0.234 (0.353)	0.457 (0.563)	0.329 (0.443)	0.697 (0.755)	0.342 (0.451)	0.212 (0.33)	0.0902 (0.178)	0.486 (0.589)
amp 15q26 1	22 (12%)	162	0.00064 (0.00454)	0.102 (0.194)	0.335 (0.448)	0.67 (0.737)	0.835 (0.87)	0.111 (0.205)	0.585 (0.67)	0.535 (0.632)	0.077 (0.161)	0.347 (0.453)
amp 17p11 2	15 (8%)	169	0.895 (0.919)	0.269 (0.386)	0.371 (0.479)	0.408 (0.515)	0.102 (0.194)	0.0505 (0.118)	0.302 (0.419)	0.112 (0.207)	0.0683 (0.149)	0.00169 (0.00996)
del 2q14 3	9 (5%)	175	0.256 (0.376)	0.189 (0.3)	0.344 (0.451)	0.196 (0.309)	0.315 (0.428)	0.482 (0.588)	0.00028 (0.00231)	0.718 (0.773)	0.514 (0.61)	0.116 (0.212)
del 14q11 2	20 (11%)	164	0.45 (0.557)	0.00397 (0.0192)	0.909 (0.931)	0.737 (0.79)	0.0688 (0.15)	0.134 (0.237)	0.057 (0.13)	0.248 (0.369)	0.282 (0.4)	0.789 (0.832)
del 18p11 31	54 (29%)	130	0.00805 (0.032)	0.666 (0.737)	0.267 (0.386)	0.18 (0.29)	0.5 (0.602)	0.975 (0.98)	0.101 (0.194)	0.853 (0.885)	0.125 (0.224)	0.192 (0.303)
del 19q13 33	22 (12%)	162	0.0245 (0.0689)	0.0718 (0.155)	0.59 (0.672)	0.531 (0.629)	0.227 (0.344)	0.227 (0.344)	0.385 (0.494)	0.0841 (0.169)	0.6 (0.68)	0.262 (0.383)
amp 1p12	27 (15%)	157	0.104 (0.197)	0.916 (0.934)	0.168 (0.278)	0.202 (0.316)	0.8 (0.839)	0.442 (0.551)	0.945 (0.957)	0.26 (0.382)	0.0923 (0.18)	0.669 (0.737)
amp 9p13 3	24 (13%)	160	0.17 (0.279)	0.888 (0.916)	0.947 (0.957)	0.311 (0.425)	0.827 (0.863)	0.392 (0.5)	0.58 (0.666)	0.0799 (0.164)	0.975 (0.98)	0.104 (0.197)
del 7q31 1	15 (8%)	169	0.268 (0.386)	0.735 (0.79)	0.559 (0.65)	0.0584 (0.131)	0.501 (0.602)	0.308 (0.425)	0.851 (0.884)	0.51 (0.609)	0.77 (0.819)	0.546 (0.64)

'amp_1p34.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0433 (Fisher's exact test), Q value = 0.1

Table S1. Gene #1: 'amp_1p34.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	25	16	16	18
AMP PEAK 1(1P34.2) MUTATED	1	3	0	3	0
AMP PEAK 1(1P34.2) WILD-TYPE	46	22	16	13	18

Figure S1. Get High-res Image Gene #1: 'amp_1p34.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_1q21.3' versus 'CN_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0043

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
AMP PEAK 3(1Q21.3) MUTATED	8	33	5	16
AMP PEAK 3(1Q21.3) WILD-TYPE	18	41	41	22

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

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00071

Table S3. Gene #3: 'amp_1q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
AMP PEAK 3(1Q21.3) MUTATED	27	10	19	6
AMP PEAK 3(1Q21.3) WILD-TYPE	18	39	33	31

Figure S3. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.054

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
AMP PEAK 3(1Q21.3) MUTATED	20	7	16	12	4
AMP PEAK 3(1Q21.3) WILD-TYPE	19	19	27	27	26

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

'amp_1q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.039

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
AMP PEAK 3(1Q21.3) MUTATED	22	33	4
AMP PEAK 3(1Q21.3) WILD-TYPE	52	42	24

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

'amp_1q21.3' versus 'MIRSEQ_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.048

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	52	47	25	31	22
AMP PEAK 3(1Q21.3) MUTATED	26	8	7	11	7
AMP PEAK 3(1Q21.3) WILD-TYPE	26	39	18	20	15

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

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0158 (Fisher's exact test), Q value = 0.054

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
AMP PEAK 3(1Q21.3) MUTATED	42	12	5
AMP PEAK 3(1Q21.3) WILD-TYPE	60	30	28

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

'amp_1q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00757 (Fisher's exact test), Q value = 0.031

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	27	11	27	13	51	27	17
AMP PEAK 3(1Q21.3) MUTATED	9	5	9	2	26	6	1
AMP PEAK 3(1Q21.3) WILD-TYPE	18	6	18	11	25	21	16

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

'amp_2q36.2' versus 'CN_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.058

Table S9. Gene #4: 'amp_2q36.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
AMP PEAK 4(2Q36.2) MUTATED	5	15	1	5
AMP PEAK 4(2Q36.2) WILD-TYPE	21	59	45	33

Figure S9. Get High-res Image Gene #4: 'amp_2q36.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2q36.2' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00093

Table S10. Gene #4: 'amp_2q36.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
AMP PEAK 4(2Q36.2) MUTATED	10	2	13	0
AMP PEAK 4(2Q36.2) WILD-TYPE	35	47	39	37

Figure S10. Get High-res Image Gene #4: 'amp_2q36.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_2q36.2' versus 'MRNASEQ_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.059

Table S11. Gene #4: 'amp_2q36.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
AMP PEAK 4(2Q36.2) MUTATED	7	2	12	3	1
AMP PEAK 4(2Q36.2) WILD-TYPE	32	24	31	36	29

Figure S11. Get High-res Image Gene #4: 'amp_2q36.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_2q36.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.021 (Fisher's exact test), Q value = 0.063

Table S12. Gene #4: 'amp_2q36.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
AMP PEAK 4(2Q36.2) MUTATED	10	15	0
AMP PEAK 4(2Q36.2) WILD-TYPE	64	60	28

Figure S12. Get High-res Image Gene #4: 'amp_2q36.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_2q36.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00383 (Fisher's exact test), Q value = 0.019

Table S13. Gene #4: 'amp_2q36.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
AMP PEAK 4(2Q36.2) MUTATED	22	2	1
AMP PEAK 4(2Q36.2) WILD-TYPE	80	40	32

Figure S13. Get High-res Image Gene #4: 'amp_2q36.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_2q36.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0309 (Fisher's exact test), Q value = 0.08

Table S14. Gene #4: 'amp_2q36.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	27	11	27	13	51	27	17
AMP PEAK 4(2Q36.2) MUTATED	1	2	6	1	13	2	0
AMP PEAK 4(2Q36.2) WILD-TYPE	26	9	21	12	38	25	17

Figure S14. Get High-res Image Gene #4: 'amp_2q36.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_2q36.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0319 (Fisher's exact test), Q value = 0.083

Table S15. Gene #4: 'amp_2q36.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	23	44	19	53	26	8
AMP PEAK 4(2Q36.2) MUTATED	6	11	3	4	1	0
AMP PEAK 4(2Q36.2) WILD-TYPE	17	33	16	49	25	8

Figure S15. Get High-res Image Gene #4: 'amp_2q36.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3p12.2' versus 'METHLYATION_CNMF'

P value = 0.0283 (Fisher's exact test), Q value = 0.075

Table S16. Gene #5: 'amp_3p12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
AMP PEAK 5(3P12.2) MUTATED	6	1	5	0
AMP PEAK 5(3P12.2) WILD-TYPE	39	48	47	37

Figure S16. Get High-res Image Gene #5: 'amp_3p12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'CN_CNMF'

P value = 0.00394 (Fisher's exact test), Q value = 0.019

Table S17. Gene #6: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
AMP PEAK 6(3Q26.2) MUTATED	5	21	2	4
AMP PEAK 6(3Q26.2) WILD-TYPE	21	53	44	34

Figure S17. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00044

Table S18. Gene #6: 'amp_3q26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
AMP PEAK 6(3Q26.2) MUTATED	11	1	18	2
AMP PEAK 6(3Q26.2) WILD-TYPE	34	48	34	35

Figure S18. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 0.054

Table S19. Gene #6: 'amp_3q26.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	25	16	16	18
AMP PEAK 6(3Q26.2) MUTATED	9	3	1	2	9
AMP PEAK 6(3Q26.2) WILD-TYPE	38	22	15	14	9

Figure S19. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_3q26.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00033

Table S20. Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
AMP PEAK 6(3Q26.2) MUTATED	5	1	20	3	2
AMP PEAK 6(3Q26.2) WILD-TYPE	34	25	23	36	28

Figure S20. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3q26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0171 (Fisher's exact test), Q value = 0.055

Table S21. Gene #6: 'amp_3q26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
AMP PEAK 6(3Q26.2) MUTATED	25	3	3
AMP PEAK 6(3Q26.2) WILD-TYPE	77	39	30

Figure S21. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0184 (Fisher's exact test), Q value = 0.058

Table S22. Gene #6: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	23	44	19	53	26	8
AMP PEAK 6(3Q26.2) MUTATED	2	16	2	7	3	0
AMP PEAK 6(3Q26.2) WILD-TYPE	21	28	17	46	23	8

Figure S22. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4p16.3' versus 'MRNASEQ_CNMF'

P value = 0.043 (Fisher's exact test), Q value = 0.1

Table S23. Gene #7: 'amp_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
AMP PEAK 7(4P16.3) MUTATED	3	5	3	0	4
AMP PEAK 7(4P16.3) WILD-TYPE	36	21	40	39	26

Figure S23. Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0184 (Fisher's exact test), Q value = 0.058

Table S24. Gene #7: 'amp_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
AMP PEAK 7(4P16.3) MUTATED	2	8	5
AMP PEAK 7(4P16.3) WILD-TYPE	72	67	23

Figure S24. Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0255 (Fisher's exact test), Q value = 0.07

Table S25. Gene #7: 'amp_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
AMP PEAK 7(4P16.3) MUTATED	10	0	5
AMP PEAK 7(4P16.3) WILD-TYPE	92	42	28

Figure S25. Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0386 (Fisher's exact test), Q value = 0.096

Table S26. Gene #7: 'amp_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	27	11	27	13	51	27	17
AMP PEAK 7(4P16.3) MUTATED	0	1	1	3	5	1	4
AMP PEAK 7(4P16.3) WILD-TYPE	27	10	26	10	46	26	13

Figure S26. Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00168 (Fisher's exact test), Q value = 0.01

Table S27. Gene #7: 'amp_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	23	44	19	53	26	8
AMP PEAK 7(4P16.3) MUTATED	1	5	3	1	1	4
AMP PEAK 7(4P16.3) WILD-TYPE	22	39	16	52	25	4

Figure S27. Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6p21.31' versus 'MIRSEQ_CNMF'

P value = 0.0372 (Fisher's exact test), Q value = 0.094

Table S28. Gene #8: 'amp_6p21.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	52	47	25	31	22
AMP PEAK 8(6P21.31) MUTATED	3	1	2	6	0
AMP PEAK 8(6P21.31) WILD-TYPE	49	46	23	25	22

Figure S28. Get High-res Image Gene #8: 'amp_6p21.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7q22.1' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00044

Table S29. Gene #9: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
AMP PEAK 9(7Q22.1) MUTATED	6	30	3	17
AMP PEAK 9(7Q22.1) WILD-TYPE	20	44	43	21

Figure S29. Get High-res Image Gene #9: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q22.1' versus 'METHLYATION_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.061

Table S30. Gene #9: 'amp_7q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
AMP PEAK 9(7Q22.1) MUTATED	15	11	23	6
AMP PEAK 9(7Q22.1) WILD-TYPE	30	38	29	31

Figure S30. Get High-res Image Gene #9: 'amp_7q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q22.1' versus 'RPPA_CNMF'

P value = 0.0324 (Fisher's exact test), Q value = 0.084

Table S31. Gene #9: 'amp_7q22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	25	20	15	23
AMP PEAK 9(7Q22.1) MUTATED	14	8	1	2	9
AMP PEAK 9(7Q22.1) WILD-TYPE	25	17	19	13	14

Figure S31. Get High-res Image Gene #9: 'amp_7q22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_7q22.1' versus 'MRNASEQ_CNMF'

P value = 0.0253 (Fisher's exact test), Q value = 0.07

Table S32. Gene #9: 'amp_7q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
AMP PEAK 9(7Q22.1) MUTATED	15	10	17	7	4
AMP PEAK 9(7Q22.1) WILD-TYPE	24	16	26	32	26

Figure S32. Get High-res Image Gene #9: 'amp_7q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0376 (Fisher's exact test), Q value = 0.094

Table S33. Gene #9: 'amp_7q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
AMP PEAK 9(7Q22.1) MUTATED	38	7	8
AMP PEAK 9(7Q22.1) WILD-TYPE	64	35	25

Figure S33. Get High-res Image Gene #9: 'amp_7q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0024 (Fisher's exact test), Q value = 0.013

Table S34. Gene #9: 'amp_7q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	27	11	27	13	51	27	17
AMP PEAK 9(7Q22.1) MUTATED	5	6	8	0	23	4	6
AMP PEAK 9(7Q22.1) WILD-TYPE	22	5	19	13	28	23	11

Figure S34. Get High-res Image Gene #9: 'amp_7q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00477 (Fisher's exact test), Q value = 0.021

Table S35. Gene #9: 'amp_7q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	23	44	19	53	26	8
AMP PEAK 9(7Q22.1) MUTATED	7	18	7	11	3	6
AMP PEAK 9(7Q22.1) WILD-TYPE	16	26	12	42	23	2

Figure S35. Get High-res Image Gene #9: 'amp_7q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p11.22' versus 'CN_CNMF'

P value = 0.0205 (Fisher's exact test), Q value = 0.062

Table S36. Gene #10: 'amp_8p11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
AMP PEAK 10(8P11.22) MUTATED	6	11	4	13
AMP PEAK 10(8P11.22) WILD-TYPE	20	63	42	25

Figure S36. Get High-res Image Gene #10: 'amp_8p11.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p11.21' versus 'CN_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0046

Table S37. Gene #11: 'amp_8p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
AMP PEAK 11(8P11.21) MUTATED	7	11	2	14
AMP PEAK 11(8P11.21) WILD-TYPE	19	63	44	24

Figure S37. Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S38. Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
AMP PEAK 12(8Q24.21) MUTATED	6	49	3	16
AMP PEAK 12(8Q24.21) WILD-TYPE	20	25	43	22

Figure S38. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0021

Table S39. Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
AMP PEAK 12(8Q24.21) MUTATED	25	13	28	7
AMP PEAK 12(8Q24.21) WILD-TYPE	20	36	24	30

Figure S39. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 0.00333 (Fisher's exact test), Q value = 0.017

Table S40. Gene #12: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
AMP PEAK 12(8Q24.21) MUTATED	18	9	26	14	5
AMP PEAK 12(8Q24.21) WILD-TYPE	21	17	17	25	25

Figure S40. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_12p13.33' versus 'CN_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.002

Table S41. Gene #14: 'amp_12p13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
AMP PEAK 14(12P13.33) MUTATED	1	25	3	10
AMP PEAK 14(12P13.33) WILD-TYPE	25	49	43	28

Figure S41. Get High-res Image Gene #14: 'amp_12p13.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p13.33' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0018

Table S42. Gene #14: 'amp_12p13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
AMP PEAK 14(12P13.33) MUTATED	14	9	16	0
AMP PEAK 14(12P13.33) WILD-TYPE	31	40	36	37

Figure S42. Get High-res Image Gene #14: 'amp_12p13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12p13.33' versus 'MRNASEQ_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.048

Table S43. Gene #14: 'amp_12p13.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
AMP PEAK 14(12P13.33) MUTATED	9	9	13	6	1
AMP PEAK 14(12P13.33) WILD-TYPE	30	17	30	33	29

Figure S43. Get High-res Image Gene #14: 'amp_12p13.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_12p13.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.052

Table S44. Gene #14: 'amp_12p13.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	27	11	27	13	51	27	17
AMP PEAK 14(12P13.33) MUTATED	5	2	5	0	15	2	8
AMP PEAK 14(12P13.33) WILD-TYPE	22	9	22	13	36	25	9

Figure S44. Get High-res Image Gene #14: 'amp_12p13.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_12p13.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00368 (Fisher's exact test), Q value = 0.018

Table S45. Gene #14: 'amp_12p13.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	23	44	19	53	26	8
AMP PEAK 14(12P13.33) MUTATED	2	12	4	11	2	6
AMP PEAK 14(12P13.33) WILD-TYPE	21	32	15	42	24	2

Figure S45. Get High-res Image Gene #14: 'amp_12p13.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p11.21' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00044

Table S46. Gene #15: 'amp_12p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
AMP PEAK 15(12P11.21) MUTATED	2	28	2	11
AMP PEAK 15(12P11.21) WILD-TYPE	24	46	44	27

Figure S46. Get High-res Image Gene #15: 'amp_12p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p11.21' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00033

Table S47. Gene #15: 'amp_12p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
AMP PEAK 15(12P11.21) MUTATED	20	7	16	0
AMP PEAK 15(12P11.21) WILD-TYPE	25	42	36	37

Figure S47. Get High-res Image Gene #15: 'amp_12p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12p11.21' versus 'MRNASEQ_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.0044

Table S48. Gene #15: 'amp_12p11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
AMP PEAK 15(12P11.21) MUTATED	10	10	16	3	2
AMP PEAK 15(12P11.21) WILD-TYPE	29	16	27	36	28

Figure S48. Get High-res Image Gene #15: 'amp_12p11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_12p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0079 (Fisher's exact test), Q value = 0.032

Table S49. Gene #15: 'amp_12p11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
AMP PEAK 15(12P11.21) MUTATED	27	3	11
AMP PEAK 15(12P11.21) WILD-TYPE	75	39	22

Figure S49. Get High-res Image Gene #15: 'amp_12p11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_12p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0188 (Fisher's exact test), Q value = 0.058

Table S50. Gene #15: 'amp_12p11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	23	44	19	53	26	8
AMP PEAK 15(12P11.21) MUTATED	4	13	4	9	4	6
AMP PEAK 15(12P11.21) WILD-TYPE	19	31	15	44	22	2

Figure S50. Get High-res Image Gene #15: 'amp_12p11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0023

Table S51. Gene #16: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
AMP PEAK 16(12Q15) MUTATED	0	20	2	7
AMP PEAK 16(12Q15) WILD-TYPE	26	54	44	31

Figure S51. Get High-res Image Gene #16: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 0.00417 (Fisher's exact test), Q value = 0.02

Table S52. Gene #16: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
AMP PEAK 16(12Q15) MUTATED	10	7	12	0
AMP PEAK 16(12Q15) WILD-TYPE	35	42	40	37

Figure S52. Get High-res Image Gene #16: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12q15' versus 'MRNASEQ_CNMF'

P value = 0.00689 (Fisher's exact test), Q value = 0.029

Table S53. Gene #16: 'amp_12q15' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
AMP PEAK 16(12Q15) MUTATED	5	9	10	3	1
AMP PEAK 16(12Q15) WILD-TYPE	34	17	33	36	29

Figure S53. Get High-res Image Gene #16: 'amp_12q15' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_12q15' versus 'MIRSEQ_CNMF'

P value = 0.0326 (Fisher's exact test), Q value = 0.084

Table S54. Gene #16: 'amp_12q15' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	52	47	25	31	22
AMP PEAK 16(12Q15) MUTATED	10	2	3	9	4
AMP PEAK 16(12Q15) WILD-TYPE	42	45	22	22	18

Figure S54. Get High-res Image Gene #16: 'amp_12q15' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_12q15' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0467 (Fisher's exact test), Q value = 0.11

Table S55. Gene #16: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	27	11	27	13	51	27	17
AMP PEAK 16(12Q15) MUTATED	3	0	3	0	10	4	7
AMP PEAK 16(12Q15) WILD-TYPE	24	11	24	13	41	23	10

Figure S55. Get High-res Image Gene #16: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_12q15' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00144 (Fisher's exact test), Q value = 0.009

Table S56. Gene #16: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	23	44	19	53	26	8
AMP PEAK 16(12Q15) MUTATED	1	9	2	6	3	6
AMP PEAK 16(12Q15) WILD-TYPE	22	35	17	47	23	2

Figure S56. Get High-res Image Gene #16: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_15q26.1' versus 'CN_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.0045

Table S57. Gene #17: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
AMP PEAK 17(15Q26.1) MUTATED	4	16	0	2
AMP PEAK 17(15Q26.1) WILD-TYPE	22	58	46	36

Figure S57. Get High-res Image Gene #17: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00169 (Fisher's exact test), Q value = 0.01

Table S58. Gene #18: 'amp_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	23	44	19	53	26	8
AMP PEAK 18(17P11.2) MUTATED	1	4	1	3	1	5
AMP PEAK 18(17P11.2) WILD-TYPE	22	40	18	50	25	3

Figure S58. Get High-res Image Gene #18: 'amp_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 0.0283 (Fisher's exact test), Q value = 0.075

Table S59. Gene #19: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
AMP PEAK 19(17Q12) MUTATED	7	8	11	2	3
AMP PEAK 19(17Q12) WILD-TYPE	32	18	32	37	27

Figure S59. Get High-res Image Gene #19: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.065

Table S60. Gene #19: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	52	47	25	31	22
AMP PEAK 19(17Q12) MUTATED	13	6	0	8	4
AMP PEAK 19(17Q12) WILD-TYPE	39	41	25	23	18

Figure S60. Get High-res Image Gene #19: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00264 (Fisher's exact test), Q value = 0.014

Table S61. Gene #19: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	23	44	19	53	26	8
AMP PEAK 19(17Q12) MUTATED	3	13	1	5	4	5
AMP PEAK 19(17Q12) WILD-TYPE	20	31	18	48	22	3

Figure S61. Get High-res Image Gene #19: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18q11.2' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00064

Table S62. Gene #20: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
AMP PEAK 20(18Q11.2) MUTATED	8	33	3	12
AMP PEAK 20(18Q11.2) WILD-TYPE	18	41	43	26

Figure S62. Get High-res Image Gene #20: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.0068

Table S63. Gene #20: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
AMP PEAK 20(18Q11.2) MUTATED	20	10	21	4
AMP PEAK 20(18Q11.2) WILD-TYPE	25	39	31	33

Figure S63. Get High-res Image Gene #20: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0046

Table S64. Gene #20: 'amp_18q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
AMP PEAK 20(18Q11.2) MUTATED	21	6	16	8	3
AMP PEAK 20(18Q11.2) WILD-TYPE	18	20	27	31	27

Figure S64. Get High-res Image Gene #20: 'amp_18q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CNMF'

P value = 0.0219 (Fisher's exact test), Q value = 0.064

Table S65. Gene #20: 'amp_18q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	52	47	25	31	22
AMP PEAK 20(18Q11.2) MUTATED	24	10	6	11	3
AMP PEAK 20(18Q11.2) WILD-TYPE	28	37	19	20	19

Figure S65. Get High-res Image Gene #20: 'amp_18q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.0041

Table S66. Gene #20: 'amp_18q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
AMP PEAK 20(18Q11.2) MUTATED	42	9	3
AMP PEAK 20(18Q11.2) WILD-TYPE	60	33	30

Figure S66. Get High-res Image Gene #20: 'amp_18q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.0019

Table S67. Gene #20: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	23	44	19	53	26	8
AMP PEAK 20(18Q11.2) MUTATED	11	20	6	13	0	3
AMP PEAK 20(18Q11.2) WILD-TYPE	12	24	13	40	26	5

Figure S67. Get High-res Image Gene #20: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q13.2' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0012

Table S68. Gene #21: 'amp_19q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
AMP PEAK 21(19Q13.2) MUTATED	6	29	2	10
AMP PEAK 21(19Q13.2) WILD-TYPE	20	45	44	28

Figure S68. Get High-res Image Gene #21: 'amp_19q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q13.2' versus 'METHLYATION_CNMF'

P value = 0.00993 (Fisher's exact test), Q value = 0.037

Table S69. Gene #21: 'amp_19q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
AMP PEAK 21(19Q13.2) MUTATED	11	9	22	5
AMP PEAK 21(19Q13.2) WILD-TYPE	34	40	30	32

Figure S69. Get High-res Image Gene #21: 'amp_19q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q13.2' versus 'MRNASEQ_CNMF'

P value = 0.00503 (Fisher's exact test), Q value = 0.022

Table S70. Gene #21: 'amp_19q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
AMP PEAK 21(19Q13.2) MUTATED	9	12	16	4	5
AMP PEAK 21(19Q13.2) WILD-TYPE	30	14	27	35	25

Figure S70. Get High-res Image Gene #21: 'amp_19q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_20p11.23' versus 'CN_CNMF'

P value = 0.00624 (Fisher's exact test), Q value = 0.027

Table S71. Gene #22: 'amp_20p11.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
AMP PEAK 22(20P11.23) MUTATED	2	19	4	13
AMP PEAK 22(20P11.23) WILD-TYPE	24	55	42	25

Figure S71. Get High-res Image Gene #22: 'amp_20p11.23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20p11.23' versus 'METHLYATION_CNMF'

P value = 0.00671 (Fisher's exact test), Q value = 0.028

Table S72. Gene #22: 'amp_20p11.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
AMP PEAK 22(20P11.23) MUTATED	16	8	11	2
AMP PEAK 22(20P11.23) WILD-TYPE	29	41	41	35

Figure S72. Get High-res Image Gene #22: 'amp_20p11.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20p11.23' versus 'MIRSEQ_CNMF'

P value = 0.0496 (Fisher's exact test), Q value = 0.12

Table S73. Gene #22: 'amp_20p11.23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	52	47	25	31	22
AMP PEAK 22(20P11.23) MUTATED	13	6	3	12	3
AMP PEAK 22(20P11.23) WILD-TYPE	39	41	22	19	19

Figure S73. Get High-res Image Gene #22: 'amp_20p11.23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_20p11.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0259 (Fisher's exact test), Q value = 0.071

Table S74. Gene #22: 'amp_20p11.23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
AMP PEAK 22(20P11.23) MUTATED	27	3	7
AMP PEAK 22(20P11.23) WILD-TYPE	75	39	26

Figure S74. Get High-res Image Gene #22: 'amp_20p11.23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20p11.23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00443 (Fisher's exact test), Q value = 0.02

Table S75. Gene #22: 'amp_20p11.23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	23	44	19	53	26	8
AMP PEAK 22(20P11.23) MUTATED	3	12	7	7	2	5
AMP PEAK 22(20P11.23) WILD-TYPE	20	32	12	46	24	3

Figure S75. Get High-res Image Gene #22: 'amp_20p11.23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xq28' versus 'CN_CNMF'

P value = 0.00432 (Fisher's exact test), Q value = 0.02

Table S76. Gene #23: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
AMP PEAK 23(XQ28) MUTATED	0	14	1	5
AMP PEAK 23(XQ28) WILD-TYPE	26	60	45	33

Figure S76. Get High-res Image Gene #23: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq28' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0294 (Fisher's exact test), Q value = 0.078

Table S77. Gene #23: 'amp_xq28' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	23	44	19	53	26	8
AMP PEAK 23(XQ28) MUTATED	3	6	0	5	2	4
AMP PEAK 23(XQ28) WILD-TYPE	20	38	19	48	24	4

Figure S77. Get High-res Image Gene #23: 'amp_xq28' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.11' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00088

Table S78. Gene #24: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
DEL PEAK 1(1P36.11) MUTATED	8	40	6	14
DEL PEAK 1(1P36.11) WILD-TYPE	18	34	40	24

Figure S78. Get High-res Image Gene #24: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S79. Gene #24: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
DEL PEAK 1(1P36.11) MUTATED	33	15	18	2
DEL PEAK 1(1P36.11) WILD-TYPE	12	34	34	35

Figure S79. Get High-res Image Gene #24: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.11' versus 'RPPA_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 0.054

Table S80. Gene #24: 'del_1p36.11' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	25	20	15	23
DEL PEAK 1(1P36.11) MUTATED	24	6	9	4	7
DEL PEAK 1(1P36.11) WILD-TYPE	15	19	11	11	16

Figure S80. Get High-res Image Gene #24: 'del_1p36.11' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0017

Table S81. Gene #24: 'del_1p36.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
DEL PEAK 1(1P36.11) MUTATED	23	9	15	15	2
DEL PEAK 1(1P36.11) WILD-TYPE	16	17	28	24	28

Figure S81. Get High-res Image Gene #24: 'del_1p36.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0184 (Fisher's exact test), Q value = 0.058

Table S82. Gene #24: 'del_1p36.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 1(1P36.11) MUTATED	27	33	4
DEL PEAK 1(1P36.11) WILD-TYPE	47	42	24

Figure S82. Get High-res Image Gene #24: 'del_1p36.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q14.3' versus 'MIRSEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0023

Table S83. Gene #25: 'del_2q14.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	52	47	25	31	22
DEL PEAK 2(2Q14.3) MUTATED	2	0	0	7	0
DEL PEAK 2(2Q14.3) WILD-TYPE	50	47	25	24	22

Figure S83. Get High-res Image Gene #25: 'del_2q14.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p21.31' versus 'CN_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 0.055

Table S84. Gene #26: 'del_3p21.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
DEL PEAK 3(3P21.31) MUTATED	10	23	5	13
DEL PEAK 3(3P21.31) WILD-TYPE	16	51	41	25

Figure S84. Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p21.31' versus 'METHLYATION_CNMF'

P value = 0.0055 (Fisher's exact test), Q value = 0.024

Table S85. Gene #26: 'del_3p21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
DEL PEAK 3(3P21.31) MUTATED	18	10	19	4
DEL PEAK 3(3P21.31) WILD-TYPE	27	39	33	33

Figure S85. Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p21.31' versus 'MRNASEQ_CNMF'

P value = 0.00423 (Fisher's exact test), Q value = 0.02

Table S86. Gene #26: 'del_3p21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
DEL PEAK 3(3P21.31) MUTATED	16	5	18	7	3
DEL PEAK 3(3P21.31) WILD-TYPE	23	21	25	32	27

Figure S86. Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0434 (Fisher's exact test), Q value = 0.1

Table S87. Gene #26: 'del_3p21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 3(3P21.31) MUTATED	35	6	8
DEL PEAK 3(3P21.31) WILD-TYPE	67	36	25

Figure S87. Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 0.00806 (Fisher's exact test), Q value = 0.032

Table S88. Gene #27: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
DEL PEAK 4(4Q22.1) MUTATED	11	1	9	6
DEL PEAK 4(4Q22.1) WILD-TYPE	34	48	43	31

Figure S88. Get High-res Image Gene #27: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00631 (Fisher's exact test), Q value = 0.027

Table S89. Gene #27: 'del_4q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
DEL PEAK 4(4Q22.1) MUTATED	6	3	10	0	7
DEL PEAK 4(4Q22.1) WILD-TYPE	33	23	33	39	23

Figure S89. Get High-res Image Gene #27: 'del_4q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0016 (Fisher's exact test), Q value = 0.0098

Table S90. Gene #27: 'del_4q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 4(4Q22.1) MUTATED	19	0	7
DEL PEAK 4(4Q22.1) WILD-TYPE	83	42	26

Figure S90. Get High-res Image Gene #27: 'del_4q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0262 (Fisher's exact test), Q value = 0.071

Table S91. Gene #27: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	23	44	19	53	26	8
DEL PEAK 4(4Q22.1) MUTATED	3	9	5	2	6	0
DEL PEAK 4(4Q22.1) WILD-TYPE	20	35	14	51	20	8

Figure S91. Get High-res Image Gene #27: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 0.0255 (Fisher's exact test), Q value = 0.07

Table S92. Gene #28: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
DEL PEAK 5(4Q34.3) MUTATED	2	22	5	6
DEL PEAK 5(4Q34.3) WILD-TYPE	24	52	41	32

Figure S92. Get High-res Image Gene #28: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 0.0352 (Fisher's exact test), Q value = 0.09

Table S93. Gene #28: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
DEL PEAK 5(4Q34.3) MUTATED	12	4	14	5
DEL PEAK 5(4Q34.3) WILD-TYPE	33	45	38	32

Figure S93. Get High-res Image Gene #28: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q14.2' versus 'CN_CNMF'

P value = 0.00175 (Fisher's exact test), Q value = 0.01

Table S94. Gene #29: 'del_5q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
DEL PEAK 6(5Q14.2) MUTATED	5	23	2	5
DEL PEAK 6(5Q14.2) WILD-TYPE	21	51	44	33

Figure S94. Get High-res Image Gene #29: 'del_5q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q14.2' versus 'MRNASEQ_CNMF'

P value = 0.00196 (Fisher's exact test), Q value = 0.011

Table S95. Gene #29: 'del_5q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
DEL PEAK 6(5Q14.2) MUTATED	7	0	16	7	4
DEL PEAK 6(5Q14.2) WILD-TYPE	32	26	27	32	26

Figure S95. Get High-res Image Gene #29: 'del_5q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6p25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S96. Gene #30: 'del_6p25.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
DEL PEAK 7(6P25.2) MUTATED	17	38	0	19
DEL PEAK 7(6P25.2) WILD-TYPE	9	36	46	19

Figure S96. Get High-res Image Gene #30: 'del_6p25.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00033

Table S97. Gene #30: 'del_6p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
DEL PEAK 7(6P25.2) MUTATED	25	11	31	6
DEL PEAK 7(6P25.2) WILD-TYPE	20	38	21	31

Figure S97. Get High-res Image Gene #30: 'del_6p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p25.2' versus 'RPPA_CNMF'

P value = 0.00242 (Fisher's exact test), Q value = 0.013

Table S98. Gene #30: 'del_6p25.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	25	20	15	23
DEL PEAK 7(6P25.2) MUTATED	26	5	8	4	8
DEL PEAK 7(6P25.2) WILD-TYPE	13	20	12	11	15

Figure S98. Get High-res Image Gene #30: 'del_6p25.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_6p25.2' versus 'MRNASEQ_CNMF'

P value = 0.00346 (Fisher's exact test), Q value = 0.017

Table S99. Gene #30: 'del_6p25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
DEL PEAK 7(6P25.2) MUTATED	21	8	24	11	6
DEL PEAK 7(6P25.2) WILD-TYPE	18	18	19	28	24

Figure S99. Get High-res Image Gene #30: 'del_6p25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6p25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0123 (Fisher's exact test), Q value = 0.045

Table S100. Gene #30: 'del_6p25.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 7(6P25.2) MUTATED	28	37	5
DEL PEAK 7(6P25.2) WILD-TYPE	46	38	23

Figure S100. Get High-res Image Gene #30: 'del_6p25.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6p25.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.0036

Table S101. Gene #30: 'del_6p25.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 7(6P25.2) MUTATED	53	10	7
DEL PEAK 7(6P25.2) WILD-TYPE	49	32	26

Figure S101. Get High-res Image Gene #30: 'del_6p25.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6p25.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00104 (Fisher's exact test), Q value = 0.0068

Table S102. Gene #30: 'del_6p25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	23	44	19	53	26	8
DEL PEAK 7(6P25.2) MUTATED	13	26	7	18	3	3
DEL PEAK 7(6P25.2) WILD-TYPE	10	18	12	35	23	5

Figure S102. Get High-res Image Gene #30: 'del_6p25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S103. Gene #31: 'del_6p22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
DEL PEAK 8(6P22.2) MUTATED	14	36	0	20
DEL PEAK 8(6P22.2) WILD-TYPE	12	38	46	18

Figure S103. Get High-res Image Gene #31: 'del_6p22.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p22.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00033

Table S104. Gene #31: 'del_6p22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
DEL PEAK 8(6P22.2) MUTATED	23	10	30	6
DEL PEAK 8(6P22.2) WILD-TYPE	22	39	22	31

Figure S104. Get High-res Image Gene #31: 'del_6p22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p22.2' versus 'RPPA_CNMF'

P value = 0.0362 (Fisher's exact test), Q value = 0.092

Table S105. Gene #31: 'del_6p22.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	25	20	15	23
DEL PEAK 8(6P22.2) MUTATED	23	6	8	4	7
DEL PEAK 8(6P22.2) WILD-TYPE	16	19	12	11	16

Figure S105. Get High-res Image Gene #31: 'del_6p22.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_6p22.2' versus 'MRNASEQ_CNMF'

P value = 0.00471 (Fisher's exact test), Q value = 0.021

Table S106. Gene #31: 'del_6p22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
DEL PEAK 8(6P22.2) MUTATED	17	8	25	10	6
DEL PEAK 8(6P22.2) WILD-TYPE	22	18	18	29	24

Figure S106. Get High-res Image Gene #31: 'del_6p22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6p22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0221 (Fisher's exact test), Q value = 0.064

Table S107. Gene #31: 'del_6p22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 8(6P22.2) MUTATED	26	35	5
DEL PEAK 8(6P22.2) WILD-TYPE	48	40	23

Figure S107. Get High-res Image Gene #31: 'del_6p22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6p22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00094 (Fisher's exact test), Q value = 0.0063

Table S108. Gene #31: 'del_6p22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 8(6P22.2) MUTATED	50	9	7
DEL PEAK 8(6P22.2) WILD-TYPE	52	33	26

Figure S108. Get High-res Image Gene #31: 'del_6p22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6p22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00167 (Fisher's exact test), Q value = 0.01

Table S109. Gene #31: 'del_6p22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	23	44	19	53	26	8
DEL PEAK 8(6P22.2) MUTATED	11	26	7	16	3	3
DEL PEAK 8(6P22.2) WILD-TYPE	12	18	12	37	23	5

Figure S109. Get High-res Image Gene #31: 'del_6p22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q25.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S110. Gene #32: 'del_6q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
DEL PEAK 9(6Q25.3) MUTATED	18	48	0	25
DEL PEAK 9(6Q25.3) WILD-TYPE	8	26	46	13

Figure S110. Get High-res Image Gene #32: 'del_6q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q25.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S111. Gene #32: 'del_6q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
DEL PEAK 9(6Q25.3) MUTATED	30	13	38	9
DEL PEAK 9(6Q25.3) WILD-TYPE	15	36	14	28

Figure S111. Get High-res Image Gene #32: 'del_6q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q25.3' versus 'RPPA_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.044

Table S112. Gene #32: 'del_6q25.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	25	20	15	23
DEL PEAK 9(6Q25.3) MUTATED	27	8	11	4	13
DEL PEAK 9(6Q25.3) WILD-TYPE	12	17	9	11	10

Figure S112. Get High-res Image Gene #32: 'del_6q25.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_6q25.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00033

Table S113. Gene #32: 'del_6q25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
DEL PEAK 9(6Q25.3) MUTATED	23	9	33	13	8
DEL PEAK 9(6Q25.3) WILD-TYPE	16	17	10	26	22

Figure S113. Get High-res Image Gene #32: 'del_6q25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00507 (Fisher's exact test), Q value = 0.022

Table S114. Gene #32: 'del_6q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 9(6Q25.3) MUTATED	34	45	7
DEL PEAK 9(6Q25.3) WILD-TYPE	40	30	21

Figure S114. Get High-res Image Gene #32: 'del_6q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q25.3' versus 'MIRSEQ_CNMF'

P value = 0.00427 (Fisher's exact test), Q value = 0.02

Table S115. Gene #32: 'del_6q25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	52	47	25	31	22
DEL PEAK 9(6Q25.3) MUTATED	36	18	11	15	6
DEL PEAK 9(6Q25.3) WILD-TYPE	16	29	14	16	16

Figure S115. Get High-res Image Gene #32: 'del_6q25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6q25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.0019

Table S116. Gene #32: 'del_6q25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 9(6Q25.3) MUTATED	63	12	11
DEL PEAK 9(6Q25.3) WILD-TYPE	39	30	22

Figure S116. Get High-res Image Gene #32: 'del_6q25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q25.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.0045

Table S117. Gene #32: 'del_6q25.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	27	11	27	13	51	27	17
DEL PEAK 9(6Q25.3) MUTATED	11	7	10	3	38	10	6
DEL PEAK 9(6Q25.3) WILD-TYPE	16	4	17	10	13	17	11

Figure S117. Get High-res Image Gene #32: 'del_6q25.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6q25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00973 (Fisher's exact test), Q value = 0.037

Table S118. Gene #32: 'del_6q25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	23	44	19	53	26	8
DEL PEAK 9(6Q25.3) MUTATED	13	30	9	24	6	3
DEL PEAK 9(6Q25.3) WILD-TYPE	10	14	10	29	20	5

Figure S118. Get High-res Image Gene #32: 'del_6q25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q36.1' versus 'CN_CNMF'

P value = 0.0397 (Fisher's exact test), Q value = 0.098

Table S119. Gene #34: 'del_7q36.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
DEL PEAK 11(7Q36.1) MUTATED	2	10	0	3
DEL PEAK 11(7Q36.1) WILD-TYPE	24	64	46	35

Figure S119. Get High-res Image Gene #34: 'del_7q36.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q36.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0213 (Fisher's exact test), Q value = 0.063

Table S120. Gene #34: 'del_7q36.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	25	16	16	18
DEL PEAK 11(7Q36.1) MUTATED	1	4	2	0	4
DEL PEAK 11(7Q36.1) WILD-TYPE	46	21	14	16	14

Figure S120. Get High-res Image Gene #34: 'del_7q36.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_8p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S121. Gene #35: 'del_8p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
DEL PEAK 12(8P21.3) MUTATED	7	48	5	2
DEL PEAK 12(8P21.3) WILD-TYPE	19	26	41	36

Figure S121. Get High-res Image Gene #35: 'del_8p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p21.3' versus 'METHLYATION_CNMF'

P value = 0.00475 (Fisher's exact test), Q value = 0.021

Table S122. Gene #35: 'del_8p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
DEL PEAK 12(8P21.3) MUTATED	17	11	26	7
DEL PEAK 12(8P21.3) WILD-TYPE	28	38	26	30

Figure S122. Get High-res Image Gene #35: 'del_8p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p21.3' versus 'MRNASEQ_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.058

Table S123. Gene #35: 'del_8p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
DEL PEAK 12(8P21.3) MUTATED	14	8	23	9	6
DEL PEAK 12(8P21.3) WILD-TYPE	25	18	20	30	24

Figure S123. Get High-res Image Gene #35: 'del_8p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.028 (Fisher's exact test), Q value = 0.075

Table S124. Gene #35: 'del_8p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 12(8P21.3) MUTATED	22	33	5
DEL PEAK 12(8P21.3) WILD-TYPE	52	42	23

Figure S124. Get High-res Image Gene #35: 'del_8p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0286 (Fisher's exact test), Q value = 0.076

Table S125. Gene #35: 'del_8p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 12(8P21.3) MUTATED	43	9	8
DEL PEAK 12(8P21.3) WILD-TYPE	59	33	25

Figure S125. Get High-res Image Gene #35: 'del_8p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S126. Gene #36: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
DEL PEAK 13(9P21.3) MUTATED	20	66	7	23
DEL PEAK 13(9P21.3) WILD-TYPE	6	8	39	15

Figure S126. Get High-res Image Gene #36: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S127. Gene #36: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
DEL PEAK 13(9P21.3) MUTATED	38	17	47	13
DEL PEAK 13(9P21.3) WILD-TYPE	7	32	5	24

Figure S127. Get High-res Image Gene #36: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S128. Gene #36: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
DEL PEAK 13(9P21.3) MUTATED	33	7	40	17	12
DEL PEAK 13(9P21.3) WILD-TYPE	6	19	3	22	18

Figure S128. Get High-res Image Gene #36: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00088

Table S129. Gene #36: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 13(9P21.3) MUTATED	44	57	8
DEL PEAK 13(9P21.3) WILD-TYPE	30	18	20

Figure S129. Get High-res Image Gene #36: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S130. Gene #36: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	52	47	25	31	22
DEL PEAK 13(9P21.3) MUTATED	49	22	14	15	9
DEL PEAK 13(9P21.3) WILD-TYPE	3	25	11	16	13

Figure S130. Get High-res Image Gene #36: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S131. Gene #36: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 13(9P21.3) MUTATED	80	17	12
DEL PEAK 13(9P21.3) WILD-TYPE	22	25	21

Figure S131. Get High-res Image Gene #36: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S132. Gene #36: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	27	11	27	13	51	27	17
DEL PEAK 13(9P21.3) MUTATED	13	9	15	4	46	16	5
DEL PEAK 13(9P21.3) WILD-TYPE	14	2	12	9	5	11	12

Figure S132. Get High-res Image Gene #36: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S133. Gene #36: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	23	44	19	53	26	8
DEL PEAK 13(9P21.3) MUTATED	19	40	9	28	11	1
DEL PEAK 13(9P21.3) WILD-TYPE	4	4	10	25	15	7

Figure S133. Get High-res Image Gene #36: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00033

Table S134. Gene #37: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
DEL PEAK 14(10P15.3) MUTATED	11	18	0	12
DEL PEAK 14(10P15.3) WILD-TYPE	15	56	46	26

Figure S134. Get High-res Image Gene #37: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 0.00101 (Fisher's exact test), Q value = 0.0067

Table S135. Gene #37: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
DEL PEAK 14(10P15.3) MUTATED	5	6	20	6	3
DEL PEAK 14(10P15.3) WILD-TYPE	34	20	23	33	27

Figure S135. Get High-res Image Gene #37: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0126 (Fisher's exact test), Q value = 0.046

Table S136. Gene #37: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 14(10P15.3) MUTATED	10	25	5
DEL PEAK 14(10P15.3) WILD-TYPE	64	50	23

Figure S136. Get High-res Image Gene #37: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0242 (Fisher's exact test), Q value = 0.068

Table S137. Gene #37: 'del_10p15.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 14(10P15.3) MUTATED	30	4	6
DEL PEAK 14(10P15.3) WILD-TYPE	72	38	27

Figure S137. Get High-res Image Gene #37: 'del_10p15.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0031

Table S138. Gene #37: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	27	11	27	13	51	27	17
DEL PEAK 14(10P15.3) MUTATED	2	7	2	2	17	3	6
DEL PEAK 14(10P15.3) WILD-TYPE	25	4	25	11	34	24	11

Figure S138. Get High-res Image Gene #37: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10p15.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0155 (Fisher's exact test), Q value = 0.053

Table S139. Gene #37: 'del_10p15.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	23	44	19	53	26	8
DEL PEAK 14(10P15.3) MUTATED	6	15	6	8	1	3
DEL PEAK 14(10P15.3) WILD-TYPE	17	29	13	45	25	5

Figure S139. Get High-res Image Gene #37: 'del_10p15.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.33' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00055

Table S140. Gene #38: 'del_10q23.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
DEL PEAK 15(10Q23.33) MUTATED	10	17	0	8
DEL PEAK 15(10Q23.33) WILD-TYPE	16	57	46	30

Figure S140. Get High-res Image Gene #38: 'del_10q23.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.33' versus 'MRNASEQ_CNMF'

P value = 0.0219 (Fisher's exact test), Q value = 0.064

Table S141. Gene #38: 'del_10q23.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
DEL PEAK 15(10Q23.33) MUTATED	3	5	15	7	3
DEL PEAK 15(10Q23.33) WILD-TYPE	36	21	28	32	27

Figure S141. Get High-res Image Gene #38: 'del_10q23.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.054

Table S142. Gene #38: 'del_10q23.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	27	11	27	13	51	27	17
DEL PEAK 15(10Q23.33) MUTATED	1	5	6	2	10	2	6
DEL PEAK 15(10Q23.33) WILD-TYPE	26	6	21	11	41	25	11

Figure S142. Get High-res Image Gene #38: 'del_10q23.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q23.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0398 (Fisher's exact test), Q value = 0.098

Table S143. Gene #38: 'del_10q23.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	23	44	19	53	26	8
DEL PEAK 15(10Q23.33) MUTATED	5	9	5	10	0	3
DEL PEAK 15(10Q23.33) WILD-TYPE	18	35	14	43	26	5

Figure S143. Get High-res Image Gene #38: 'del_10q23.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.4' versus 'CN_CNMF'

P value = 0.00729 (Fisher's exact test), Q value = 0.03

Table S144. Gene #39: 'del_11p15.4' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
DEL PEAK 16(11P15.4) MUTATED	5	13	1	10
DEL PEAK 16(11P15.4) WILD-TYPE	21	61	45	28

Figure S144. Get High-res Image Gene #39: 'del_11p15.4' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.4' versus 'RPPA_CNMF'

P value = 0.00213 (Fisher's exact test), Q value = 0.012

Table S145. Gene #39: 'del_11p15.4' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	25	20	15	23
DEL PEAK 16(11P15.4) MUTATED	10	1	0	1	8
DEL PEAK 16(11P15.4) WILD-TYPE	29	24	20	14	15

Figure S145. Get High-res Image Gene #39: 'del_11p15.4' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_12p13.1' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0018

Table S146. Gene #40: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
DEL PEAK 17(12P13.1) MUTATED	10	15	1	3
DEL PEAK 17(12P13.1) WILD-TYPE	16	59	45	35

Figure S146. Get High-res Image Gene #40: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0014

Table S147. Gene #40: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
DEL PEAK 17(12P13.1) MUTATED	9	1	16	3
DEL PEAK 17(12P13.1) WILD-TYPE	36	48	36	34

Figure S147. Get High-res Image Gene #40: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12p13.1' versus 'RPPA_CNMF'

P value = 0.00915 (Fisher's exact test), Q value = 0.035

Table S148. Gene #40: 'del_12p13.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	25	20	15	23
DEL PEAK 17(12P13.1) MUTATED	12	2	0	1	2
DEL PEAK 17(12P13.1) WILD-TYPE	27	23	20	14	21

Figure S148. Get High-res Image Gene #40: 'del_12p13.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_12p13.1' versus 'MRNASEQ_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0059

Table S149. Gene #40: 'del_12p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
DEL PEAK 17(12P13.1) MUTATED	13	2	9	1	2
DEL PEAK 17(12P13.1) WILD-TYPE	26	24	34	38	28

Figure S149. Get High-res Image Gene #40: 'del_12p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0012 (Fisher's exact test), Q value = 0.0076

Table S150. Gene #40: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 17(12P13.1) MUTATED	6	20	1
DEL PEAK 17(12P13.1) WILD-TYPE	68	55	27

Figure S150. Get High-res Image Gene #40: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00071

Table S151. Gene #40: 'del_12p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 17(12P13.1) MUTATED	25	0	2
DEL PEAK 17(12P13.1) WILD-TYPE	77	42	31

Figure S151. Get High-res Image Gene #40: 'del_12p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0465 (Fisher's exact test), Q value = 0.11

Table S152. Gene #40: 'del_12p13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	27	11	27	13	51	27	17
DEL PEAK 17(12P13.1) MUTATED	2	3	1	1	14	4	1
DEL PEAK 17(12P13.1) WILD-TYPE	25	8	26	12	37	23	16

Figure S152. Get High-res Image Gene #40: 'del_12p13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_12p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00442 (Fisher's exact test), Q value = 0.02

Table S153. Gene #40: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	23	44	19	53	26	8
DEL PEAK 17(12P13.1) MUTATED	7	11	4	2	2	0
DEL PEAK 17(12P13.1) WILD-TYPE	16	33	15	51	24	8

Figure S153. Get High-res Image Gene #40: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q24.33' versus 'CN_CNMF'

P value = 0.00309 (Fisher's exact test), Q value = 0.016

Table S154. Gene #41: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
DEL PEAK 18(12Q24.33) MUTATED	11	22	4	6
DEL PEAK 18(12Q24.33) WILD-TYPE	15	52	42	32

Figure S154. Get High-res Image Gene #41: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q24.33' versus 'METHLYATION_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0036

Table S155. Gene #41: 'del_12q24.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
DEL PEAK 18(12Q24.33) MUTATED	12	5	22	4
DEL PEAK 18(12Q24.33) WILD-TYPE	33	44	30	33

Figure S155. Get High-res Image Gene #41: 'del_12q24.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12q24.33' versus 'RPPA_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.051

Table S156. Gene #41: 'del_12q24.33' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	25	20	15	23
DEL PEAK 18(12Q24.33) MUTATED	15	3	4	0	4
DEL PEAK 18(12Q24.33) WILD-TYPE	24	22	16	15	19

Figure S156. Get High-res Image Gene #41: 'del_12q24.33' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_12q24.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.0151 (Fisher's exact test), Q value = 0.052

Table S157. Gene #41: 'del_12q24.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	25	16	16	18
DEL PEAK 18(12Q24.33) MUTATED	14	3	2	0	7
DEL PEAK 18(12Q24.33) WILD-TYPE	33	22	14	16	11

Figure S157. Get High-res Image Gene #41: 'del_12q24.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_12q24.33' versus 'MRNASEQ_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.038

Table S158. Gene #41: 'del_12q24.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
DEL PEAK 18(12Q24.33) MUTATED	10	3	18	7	3
DEL PEAK 18(12Q24.33) WILD-TYPE	29	23	25	32	27

Figure S158. Get High-res Image Gene #41: 'del_12q24.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_12q24.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00325 (Fisher's exact test), Q value = 0.017

Table S159. Gene #41: 'del_12q24.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 18(12Q24.33) MUTATED	15	25	1
DEL PEAK 18(12Q24.33) WILD-TYPE	59	50	27

Figure S159. Get High-res Image Gene #41: 'del_12q24.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12q24.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00064 (Fisher's exact test), Q value = 0.0045

Table S160. Gene #41: 'del_12q24.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 18(12Q24.33) MUTATED	34	5	2
DEL PEAK 18(12Q24.33) WILD-TYPE	68	37	31

Figure S160. Get High-res Image Gene #41: 'del_12q24.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_12q24.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0249 (Fisher's exact test), Q value = 0.069

Table S161. Gene #41: 'del_12q24.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	23	44	19	53	26	8
DEL PEAK 18(12Q24.33) MUTATED	6	15	6	12	1	0
DEL PEAK 18(12Q24.33) WILD-TYPE	17	29	13	41	25	8

Figure S161. Get High-res Image Gene #41: 'del_12q24.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q11.2' versus 'METHLYATION_CNMF'

P value = 0.00397 (Fisher's exact test), Q value = 0.019

Table S162. Gene #42: 'del_14q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
DEL PEAK 19(14Q11.2) MUTATED	8	1	10	1
DEL PEAK 19(14Q11.2) WILD-TYPE	37	48	42	36

Figure S162. Get High-res Image Gene #42: 'del_14q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q15.1' versus 'CN_CNMF'

P value = 0.00496 (Fisher's exact test), Q value = 0.022

Table S163. Gene #43: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
DEL PEAK 20(15Q15.1) MUTATED	5	22	2	7
DEL PEAK 20(15Q15.1) WILD-TYPE	21	52	44	31

Figure S163. Get High-res Image Gene #43: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q15.1' versus 'MRNASEQ_CNMF'

P value = 0.0168 (Fisher's exact test), Q value = 0.054

Table S164. Gene #43: 'del_15q15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
DEL PEAK 20(15Q15.1) MUTATED	8	2	16	4	5
DEL PEAK 20(15Q15.1) WILD-TYPE	31	24	27	35	25

Figure S164. Get High-res Image Gene #43: 'del_15q15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00331 (Fisher's exact test), Q value = 0.017

Table S165. Gene #43: 'del_15q15.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 20(15Q15.1) MUTATED	11	23	1
DEL PEAK 20(15Q15.1) WILD-TYPE	63	52	27

Figure S165. Get High-res Image Gene #43: 'del_15q15.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.034 (Fisher's exact test), Q value = 0.087

Table S166. Gene #43: 'del_15q15.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 20(15Q15.1) MUTATED	27	5	3
DEL PEAK 20(15Q15.1) WILD-TYPE	75	37	30

Figure S166. Get High-res Image Gene #43: 'del_15q15.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0088 (Fisher's exact test), Q value = 0.034

Table S167. Gene #43: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	23	44	19	53	26	8
DEL PEAK 20(15Q15.1) MUTATED	3	13	8	7	1	1
DEL PEAK 20(15Q15.1) WILD-TYPE	20	31	11	46	25	7

Figure S167. Get High-res Image Gene #43: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00631 (Fisher's exact test), Q value = 0.027

Table S168. Gene #44: 'del_16q23.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	25	16	16	18
DEL PEAK 21(16Q23.1) MUTATED	1	0	1	4	0
DEL PEAK 21(16Q23.1) WILD-TYPE	46	25	15	12	18

Figure S168. Get High-res Image Gene #44: 'del_16q23.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0465 (Fisher's exact test), Q value = 0.11

Table S169. Gene #44: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 21(16Q23.1) MUTATED	3	12	3
DEL PEAK 21(16Q23.1) WILD-TYPE	71	63	25

Figure S169. Get High-res Image Gene #44: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 0.069

Table S170. Gene #44: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	52	47	25	31	22
DEL PEAK 21(16Q23.1) MUTATED	2	4	1	8	3
DEL PEAK 21(16Q23.1) WILD-TYPE	50	43	24	23	19

Figure S170. Get High-res Image Gene #44: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.048

Table S171. Gene #44: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	23	44	19	53	26	8
DEL PEAK 21(16Q23.1) MUTATED	4	2	4	3	1	3
DEL PEAK 21(16Q23.1) WILD-TYPE	19	42	15	50	25	5

Figure S171. Get High-res Image Gene #44: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S172. Gene #45: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
DEL PEAK 22(17P12) MUTATED	10	55	2	22
DEL PEAK 22(17P12) WILD-TYPE	16	19	44	16

Figure S172. Get High-res Image Gene #45: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S173. Gene #45: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
DEL PEAK 22(17P12) MUTATED	28	11	42	8
DEL PEAK 22(17P12) WILD-TYPE	17	38	10	29

Figure S173. Get High-res Image Gene #45: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S174. Gene #45: 'del_17p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
DEL PEAK 22(17P12) MUTATED	27	6	33	13	7
DEL PEAK 22(17P12) WILD-TYPE	12	20	10	26	23

Figure S174. Get High-res Image Gene #45: 'del_17p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00055

Table S175. Gene #45: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 22(17P12) MUTATED	40	43	3
DEL PEAK 22(17P12) WILD-TYPE	34	32	25

Figure S175. Get High-res Image Gene #45: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00064

Table S176. Gene #45: 'del_17p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	52	47	25	31	22
DEL PEAK 22(17P12) MUTATED	40	16	13	11	6
DEL PEAK 22(17P12) WILD-TYPE	12	31	12	20	16

Figure S176. Get High-res Image Gene #45: 'del_17p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00088

Table S177. Gene #45: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 22(17P12) MUTATED	63	16	7
DEL PEAK 22(17P12) WILD-TYPE	39	26	26

Figure S177. Get High-res Image Gene #45: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S178. Gene #45: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	27	11	27	13	51	27	17
DEL PEAK 22(17P12) MUTATED	10	4	14	0	41	12	4
DEL PEAK 22(17P12) WILD-TYPE	17	7	13	13	10	15	13

Figure S178. Get High-res Image Gene #45: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00044

Table S179. Gene #45: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	23	44	19	53	26	8
DEL PEAK 22(17P12) MUTATED	13	34	7	24	7	0
DEL PEAK 22(17P12) WILD-TYPE	10	10	12	29	19	8

Figure S179. Get High-res Image Gene #45: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S180. Gene #46: 'del_17q22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
DEL PEAK 23(17Q22) MUTATED	5	33	1	10
DEL PEAK 23(17Q22) WILD-TYPE	21	41	45	28

Figure S180. Get High-res Image Gene #46: 'del_17q22' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q22' versus 'METHLYATION_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.0057

Table S181. Gene #46: 'del_17q22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
DEL PEAK 23(17Q22) MUTATED	18	6	20	5
DEL PEAK 23(17Q22) WILD-TYPE	27	43	32	32

Figure S181. Get High-res Image Gene #46: 'del_17q22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q22' versus 'RPPA_CNMF'

P value = 0.00405 (Fisher's exact test), Q value = 0.019

Table S182. Gene #46: 'del_17q22' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	25	20	15	23
DEL PEAK 23(17Q22) MUTATED	19	5	1	3	8
DEL PEAK 23(17Q22) WILD-TYPE	20	20	19	12	15

Figure S182. Get High-res Image Gene #46: 'del_17q22' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_17q22' versus 'MRNASEQ_CNMF'

P value = 0.00902 (Fisher's exact test), Q value = 0.035

Table S183. Gene #46: 'del_17q22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
DEL PEAK 23(17Q22) MUTATED	18	4	14	6	5
DEL PEAK 23(17Q22) WILD-TYPE	21	22	29	33	25

Figure S183. Get High-res Image Gene #46: 'del_17q22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17q22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0149 (Fisher's exact test), Q value = 0.052

Table S184. Gene #46: 'del_17q22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 23(17Q22) MUTATED	19	26	2
DEL PEAK 23(17Q22) WILD-TYPE	55	49	26

Figure S184. Get High-res Image Gene #46: 'del_17q22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17q22' versus 'MIRSEQ_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 0.064

Table S185. Gene #46: 'del_17q22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	52	47	25	31	22
DEL PEAK 23(17Q22) MUTATED	23	8	6	6	4
DEL PEAK 23(17Q22) WILD-TYPE	29	39	19	25	18

Figure S185. Get High-res Image Gene #46: 'del_17q22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17q22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0262 (Fisher's exact test), Q value = 0.071

Table S186. Gene #46: 'del_17q22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 23(17Q22) MUTATED	35	7	5
DEL PEAK 23(17Q22) WILD-TYPE	67	35	28

Figure S186. Get High-res Image Gene #46: 'del_17q22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17q22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0015

Table S187. Gene #46: 'del_17q22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	27	11	27	13	51	27	17
DEL PEAK 23(17Q22) MUTATED	5	1	6	1	27	5	1
DEL PEAK 23(17Q22) WILD-TYPE	22	10	21	12	24	22	16

Figure S187. Get High-res Image Gene #46: 'del_17q22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_18p11.31' versus 'CN_CNMF'

P value = 0.00805 (Fisher's exact test), Q value = 0.032

Table S188. Gene #47: 'del_18p11.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
DEL PEAK 24(18P11.31) MUTATED	5	22	8	19
DEL PEAK 24(18P11.31) WILD-TYPE	21	52	38	19

Figure S188. Get High-res Image Gene #47: 'del_18p11.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S189. Gene #48: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
DEL PEAK 25(18Q21.2) MUTATED	18	70	10	28
DEL PEAK 25(18Q21.2) WILD-TYPE	8	4	36	10

Figure S189. Get High-res Image Gene #48: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S190. Gene #48: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
DEL PEAK 25(18Q21.2) MUTATED	37	23	47	18
DEL PEAK 25(18Q21.2) WILD-TYPE	8	26	5	19

Figure S190. Get High-res Image Gene #48: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00033

Table S191. Gene #48: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
DEL PEAK 25(18Q21.2) MUTATED	31	14	39	23	13
DEL PEAK 25(18Q21.2) WILD-TYPE	8	12	4	16	17

Figure S191. Get High-res Image Gene #48: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00064

Table S192. Gene #48: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 25(18Q21.2) MUTATED	51	60	9
DEL PEAK 25(18Q21.2) WILD-TYPE	23	15	19

Figure S192. Get High-res Image Gene #48: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0018

Table S193. Gene #48: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	52	47	25	31	22
DEL PEAK 25(18Q21.2) MUTATED	46	27	19	14	14
DEL PEAK 25(18Q21.2) WILD-TYPE	6	20	6	17	8

Figure S193. Get High-res Image Gene #48: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00071

Table S194. Gene #48: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 25(18Q21.2) MUTATED	82	25	13
DEL PEAK 25(18Q21.2) WILD-TYPE	20	17	20

Figure S194. Get High-res Image Gene #48: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00124 (Fisher's exact test), Q value = 0.0078

Table S195. Gene #48: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	27	11	27	13	51	27	17
DEL PEAK 25(18Q21.2) MUTATED	18	9	16	6	44	18	6
DEL PEAK 25(18Q21.2) WILD-TYPE	9	2	11	7	7	9	11

Figure S195. Get High-res Image Gene #48: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_18q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S196. Gene #48: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	23	44	19	53	26	8
DEL PEAK 25(18Q21.2) MUTATED	20	38	12	36	11	0
DEL PEAK 25(18Q21.2) WILD-TYPE	3	6	7	17	15	8

Figure S196. Get High-res Image Gene #48: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00033

Table S197. Gene #49: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
DEL PEAK 26(19P13.3) MUTATED	7	24	0	5
DEL PEAK 26(19P13.3) WILD-TYPE	19	50	46	33

Figure S197. Get High-res Image Gene #49: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S198. Gene #49: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
DEL PEAK 26(19P13.3) MUTATED	10	1	22	3
DEL PEAK 26(19P13.3) WILD-TYPE	35	48	30	34

Figure S198. Get High-res Image Gene #49: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0013

Table S199. Gene #49: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
DEL PEAK 26(19P13.3) MUTATED	7	2	20	3	4
DEL PEAK 26(19P13.3) WILD-TYPE	32	24	23	36	26

Figure S199. Get High-res Image Gene #49: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00183 (Fisher's exact test), Q value = 0.011

Table S200. Gene #49: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 26(19P13.3) MUTATED	11	24	1
DEL PEAK 26(19P13.3) WILD-TYPE	63	51	27

Figure S200. Get High-res Image Gene #49: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00914 (Fisher's exact test), Q value = 0.035

Table S201. Gene #49: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 26(19P13.3) MUTATED	29	4	3
DEL PEAK 26(19P13.3) WILD-TYPE	73	38	30

Figure S201. Get High-res Image Gene #49: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0476 (Fisher's exact test), Q value = 0.11

Table S202. Gene #49: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	27	11	27	13	51	27	17
DEL PEAK 26(19P13.3) MUTATED	5	4	4	2	17	2	1
DEL PEAK 26(19P13.3) WILD-TYPE	22	7	23	11	34	25	16

Figure S202. Get High-res Image Gene #49: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19p13.2' versus 'CN_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.0045

Table S203. Gene #50: 'del_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
DEL PEAK 27(19P13.2) MUTATED	6	17	0	5
DEL PEAK 27(19P13.2) WILD-TYPE	20	57	46	33

Figure S203. Get High-res Image Gene #50: 'del_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00033

Table S204. Gene #50: 'del_19p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
DEL PEAK 27(19P13.2) MUTATED	6	1	19	2
DEL PEAK 27(19P13.2) WILD-TYPE	39	48	33	35

Figure S204. Get High-res Image Gene #50: 'del_19p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.2' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00088

Table S205. Gene #50: 'del_19p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
DEL PEAK 27(19P13.2) MUTATED	4	0	17	3	3
DEL PEAK 27(19P13.2) WILD-TYPE	35	26	26	36	27

Figure S205. Get High-res Image Gene #50: 'del_19p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00325 (Fisher's exact test), Q value = 0.017

Table S206. Gene #50: 'del_19p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 27(19P13.2) MUTATED	9	18	0
DEL PEAK 27(19P13.2) WILD-TYPE	65	57	28

Figure S206. Get High-res Image Gene #50: 'del_19p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0031

Table S207. Gene #50: 'del_19p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 27(19P13.2) MUTATED	24	3	0
DEL PEAK 27(19P13.2) WILD-TYPE	78	39	33

Figure S207. Get High-res Image Gene #50: 'del_19p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00292 (Fisher's exact test), Q value = 0.016

Table S208. Gene #50: 'del_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	27	11	27	13	51	27	17
DEL PEAK 27(19P13.2) MUTATED	3	3	3	2	15	0	0
DEL PEAK 27(19P13.2) WILD-TYPE	24	8	24	11	36	27	17

Figure S208. Get High-res Image Gene #50: 'del_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0119 (Fisher's exact test), Q value = 0.044

Table S209. Gene #50: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	23	44	19	53	26	8
DEL PEAK 27(19P13.2) MUTATED	3	12	5	6	0	0
DEL PEAK 27(19P13.2) WILD-TYPE	20	32	14	47	26	8

Figure S209. Get High-res Image Gene #50: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.33' versus 'CN_CNMF'

P value = 0.0245 (Fisher's exact test), Q value = 0.069

Table S210. Gene #51: 'del_19q13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
DEL PEAK 28(19Q13.33) MUTATED	5	13	1	3
DEL PEAK 28(19Q13.33) WILD-TYPE	21	61	45	35

Figure S210. Get High-res Image Gene #51: 'del_19q13.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q11.2' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00055

Table S211. Gene #52: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
DEL PEAK 29(21Q11.2) MUTATED	8	35	3	16
DEL PEAK 29(21Q11.2) WILD-TYPE	18	39	43	22

Figure S211. Get High-res Image Gene #52: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 0.00225 (Fisher's exact test), Q value = 0.013

Table S212. Gene #52: 'del_21q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
DEL PEAK 29(21Q11.2) MUTATED	18	10	26	7
DEL PEAK 29(21Q11.2) WILD-TYPE	27	39	26	30

Figure S212. Get High-res Image Gene #52: 'del_21q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0211 (Fisher's exact test), Q value = 0.063

Table S213. Gene #52: 'del_21q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 29(21Q11.2) MUTATED	41	12	5
DEL PEAK 29(21Q11.2) WILD-TYPE	61	30	28

Figure S213. Get High-res Image Gene #52: 'del_21q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S214. Gene #53: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
DEL PEAK 30(22Q13.31) MUTATED	1	42	2	15
DEL PEAK 30(22Q13.31) WILD-TYPE	25	32	44	23

Figure S214. Get High-res Image Gene #53: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.31' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00093

Table S215. Gene #53: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
DEL PEAK 30(22Q13.31) MUTATED	20	10	26	4
DEL PEAK 30(22Q13.31) WILD-TYPE	25	39	26	33

Figure S215. Get High-res Image Gene #53: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.31' versus 'MRNASEQ_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.064

Table S216. Gene #53: 'del_22q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
DEL PEAK 30(22Q13.31) MUTATED	18	7	18	10	4
DEL PEAK 30(22Q13.31) WILD-TYPE	21	19	25	29	26

Figure S216. Get High-res Image Gene #53: 'del_22q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.31' versus 'MIRSEQ_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.053

Table S217. Gene #53: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	52	47	25	31	22
DEL PEAK 30(22Q13.31) MUTATED	25	11	10	8	3
DEL PEAK 30(22Q13.31) WILD-TYPE	27	36	15	23	19

Figure S217. Get High-res Image Gene #53: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0165 (Fisher's exact test), Q value = 0.054

Table S218. Gene #53: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 30(22Q13.31) MUTATED	41	11	5
DEL PEAK 30(22Q13.31) WILD-TYPE	61	31	28

Figure S218. Get High-res Image Gene #53: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0029 (Fisher's exact test), Q value = 0.016

Table S219. Gene #53: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	27	11	27	13	51	27	17
DEL PEAK 30(22Q13.31) MUTATED	8	2	7	1	28	8	2
DEL PEAK 30(22Q13.31) WILD-TYPE	19	9	20	12	23	19	15

Figure S219. Get High-res Image Gene #53: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0412 (Fisher's exact test), Q value = 0.1

Table S220. Gene #53: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	23	44	19	53	26	8
DEL PEAK 30(22Q13.31) MUTATED	10	18	6	18	2	2
DEL PEAK 30(22Q13.31) WILD-TYPE	13	26	13	35	24	6

Figure S220. Get High-res Image Gene #53: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S221. Gene #54: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
DEL PEAK 31(22Q13.32) MUTATED	1	42	2	16
DEL PEAK 31(22Q13.32) WILD-TYPE	25	32	44	22

Figure S221. Get High-res Image Gene #54: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.32' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00093

Table S222. Gene #54: 'del_22q13.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
DEL PEAK 31(22Q13.32) MUTATED	21	11	25	4
DEL PEAK 31(22Q13.32) WILD-TYPE	24	38	27	33

Figure S222. Get High-res Image Gene #54: 'del_22q13.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 0.0468 (Fisher's exact test), Q value = 0.11

Table S223. Gene #54: 'del_22q13.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
DEL PEAK 31(22Q13.32) MUTATED	17	8	18	11	4
DEL PEAK 31(22Q13.32) WILD-TYPE	22	18	25	28	26

Figure S223. Get High-res Image Gene #54: 'del_22q13.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MIRSEQ_CNMF'

P value = 0.0377 (Fisher's exact test), Q value = 0.094

Table S224. Gene #54: 'del_22q13.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	52	47	25	31	22
DEL PEAK 31(22Q13.32) MUTATED	24	11	11	8	4
DEL PEAK 31(22Q13.32) WILD-TYPE	28	36	14	23	18

Figure S224. Get High-res Image Gene #54: 'del_22q13.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00733 (Fisher's exact test), Q value = 0.03

Table S225. Gene #54: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	27	11	27	13	51	27	17
DEL PEAK 31(22Q13.32) MUTATED	8	2	8	1	27	9	2
DEL PEAK 31(22Q13.32) WILD-TYPE	19	9	19	12	24	18	15

Figure S225. Get High-res Image Gene #54: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xp21.1' versus 'CN_CNMF'

P value = 0.00841 (Fisher's exact test), Q value = 0.033

Table S226. Gene #55: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
DEL PEAK 32(XP21.1) MUTATED	3	17	1	7
DEL PEAK 32(XP21.1) WILD-TYPE	23	57	45	31

Figure S226. Get High-res Image Gene #55: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp21.1' versus 'RPPA_CNMF'

P value = 0.0389 (Fisher's exact test), Q value = 0.096

Table S227. Gene #55: 'del_xp21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	25	20	15	23
DEL PEAK 32(XP21.1) MUTATED	8	0	1	1	5
DEL PEAK 32(XP21.1) WILD-TYPE	31	25	19	14	18

Figure S227. Get High-res Image Gene #55: 'del_xp21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_xp21.1' versus 'MIRSEQ_CNMF'

P value = 0.0295 (Fisher's exact test), Q value = 0.078

Table S228. Gene #55: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	52	47	25	31	22
DEL PEAK 32(XP21.1) MUTATED	14	3	3	6	1
DEL PEAK 32(XP21.1) WILD-TYPE	38	44	22	25	21

Figure S228. Get High-res Image Gene #55: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xp21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0215 (Fisher's exact test), Q value = 0.063

Table S229. Gene #55: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	23	44	19	53	26	8
DEL PEAK 32(XP21.1) MUTATED	3	13	0	6	2	2
DEL PEAK 32(XP21.1) WILD-TYPE	20	31	19	47	24	6

Figure S229. Get High-res Image Gene #55: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xq11.2' versus 'CN_CNMF'

P value = 0.00965 (Fisher's exact test), Q value = 0.037

Table S230. Gene #56: 'del_xq11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	74	46	38
DEL PEAK 33(XQ11.2) MUTATED	3	16	1	3
DEL PEAK 33(XQ11.2) WILD-TYPE	23	58	45	35

Figure S230. Get High-res Image Gene #56: 'del_xq11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq11.2' versus 'METHLYATION_CNMF'

P value = 0.00373 (Fisher's exact test), Q value = 0.018

Table S231. Gene #56: 'del_xq11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	49	52	37
DEL PEAK 33(XQ11.2) MUTATED	7	4	12	0
DEL PEAK 33(XQ11.2) WILD-TYPE	38	45	40	37

Figure S231. Get High-res Image Gene #56: 'del_xq11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq11.2' versus 'RPPA_CNMF'

P value = 0.00164 (Fisher's exact test), Q value = 0.01

Table S232. Gene #56: 'del_xq11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	25	20	15	23
DEL PEAK 33(XQ11.2) MUTATED	10	0	0	0	3
DEL PEAK 33(XQ11.2) WILD-TYPE	29	25	20	15	20

Figure S232. Get High-res Image Gene #56: 'del_xq11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_xq11.2' versus 'MRNASEQ_CNMF'

P value = 0.03 (Fisher's exact test), Q value = 0.079

Table S233. Gene #56: 'del_xq11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	26	43	39	30
DEL PEAK 33(XQ11.2) MUTATED	8	2	8	3	0
DEL PEAK 33(XQ11.2) WILD-TYPE	31	24	35	36	30

Figure S233. Get High-res Image Gene #56: 'del_xq11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xq11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0199 (Fisher's exact test), Q value = 0.061

Table S234. Gene #56: 'del_xq11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 33(XQ11.2) MUTATED	5	15	1
DEL PEAK 33(XQ11.2) WILD-TYPE	69	60	27

Figure S234. Get High-res Image Gene #56: 'del_xq11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xq11.2' versus 'MIRSEQ_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.054

Table S235. Gene #56: 'del_xq11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	52	47	25	31	22
DEL PEAK 33(XQ11.2) MUTATED	10	3	1	7	0
DEL PEAK 33(XQ11.2) WILD-TYPE	42	44	24	24	22

Figure S235. Get High-res Image Gene #56: 'del_xq11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xq11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0226 (Fisher's exact test), Q value = 0.065

Table S236. Gene #56: 'del_xq11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 33(XQ11.2) MUTATED	18	2	1
DEL PEAK 33(XQ11.2) WILD-TYPE	84	40	32

Figure S236. Get High-res Image Gene #56: 'del_xq11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xq11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0214 (Fisher's exact test), Q value = 0.063

Table S237. Gene #56: 'del_xq11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	27	11	27	13	51	27	17
DEL PEAK 33(XQ11.2) MUTATED	1	3	2	0	12	1	1
DEL PEAK 33(XQ11.2) WILD-TYPE	26	8	25	13	39	26	16

Figure S237. Get High-res Image Gene #56: 'del_xq11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xq11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0161 (Fisher's exact test), Q value = 0.054

Table S238. Gene #56: 'del_xq11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	23	44	19	53	26	8
DEL PEAK 33(XQ11.2) MUTATED	3	11	2	3	0	1
DEL PEAK 33(XQ11.2) WILD-TYPE	20	33	17	50	26	7

Figure S238. Get High-res Image Gene #56: 'del_xq11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PAAD-TP/22533736/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PAAD-TP/22541963/PAAD-TP.transferedmergedcluster.txt
Number of patients = 184
Number of significantly focal cnvs = 56
Number of molecular subtypes = 10
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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