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 71 focal events and 10 molecular subtypes across 577 patients, 271 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p36.21 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_1q32.1 cnv correlated to 'CN_CNMF'.
amp_1q44 cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.
amp_2p24.3 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.
amp_3q26.33 cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.
amp_4q12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'METHLYATION_CNMF'.
amp_7p11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_7q11.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_7q21.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.
amp_7q31.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', and 'RPPA_CHIERARCHICAL'.
amp_12p13.32 cnv correlated to 'CN_CNMF'.
amp_12q14.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
amp_12q15 cnv correlated to 'CN_CNMF'.
amp_13q34 cnv correlated to 'MIR_CNMF' and 'RPPA_CNMF'.
amp_14q32.33 cnv correlated to 'MRNASEQ_CNMF'.
amp_17p13.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CNMF'.
amp_17q25.1 cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.
amp_19p13.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.
amp_19p13.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.
amp_19q12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.
amp_21q21.1 cnv correlated to 'MRNA_CNMF', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', and 'METHLYATION_CNMF'.
del_1p36.23 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_1p22.1 cnv correlated to 'MIR_CHIERARCHICAL'.
del_1q42.11 cnv correlated to 'RPPA_CHIERARCHICAL'.
del_2q22.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', and 'CN_CNMF'.
del_2q37.1 cnv correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.
del_3p21.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_3q13.31 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_3q22.1 cnv correlated to 'CN_CNMF'.
del_3q29 cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.
del_4p16.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'METHLYATION_CNMF'.
del_4q34.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'METHLYATION_CNMF'.
del_5q34 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.
del_6q22.31 cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.
del_6q26 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_9p21.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_10p15.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_10p13 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.
del_10p11.23 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.
del_10q26.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.
del_11p15.5 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_11p11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', and 'METHLYATION_CNMF'.
del_11q14.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', and 'CN_CNMF'.
del_12p13.1 cnv correlated to 'MRNA_CHIERARCHICAL'.
del_12q12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'RPPA_CNMF'.
del_12q15 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', and 'CN_CNMF'.
del_13q14.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'METHLYATION_CNMF'.
del_13q22.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', and 'CN_CNMF'.
del_14q13.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'METHLYATION_CNMF'.
del_14q24.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.
del_15q14 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_16q23.1 cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.
del_17p13.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', and 'CN_CNMF'.
del_17p13.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', and 'CN_CNMF'.
del_17q11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', and 'RPPA_CHIERARCHICAL'.
del_18q22.3 cnv correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.
del_19q13.41 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
del_21q21.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.
del_22q13.32 cnv correlated to 'MIR_CNMF', 'CN_CNMF', and 'MRNASEQ_CNMF'.
del_xp22.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'METHLYATION_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 71 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, 271 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	MIR CNMF	MIR CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ 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
amp 7p11 2	507 (88%)	70	1e-05 (8.35e-05)	1e-05 (8.35e-05)	2e-05 (0.000151)	1e-05 (8.35e-05)	1e-05 (8.35e-05)	1e-05 (8.35e-05)	0.00075 (0.00389)	1e-05 (8.35e-05)	4e-05 (0.000273)	1e-05 (8.35e-05)
amp 7q11 21	464 (80%)	113	2e-05 (0.000151)	1e-05 (8.35e-05)	6e-05 (0.00038)	1e-05 (8.35e-05)	1e-05 (8.35e-05)	1e-05 (8.35e-05)	0.0261 (0.0778)	0.0055 (0.0207)	0.00407 (0.0164)	6e-05 (0.00038)
del 15q14	154 (27%)	423	2e-05 (0.000151)	1e-05 (8.35e-05)	0.00102 (0.00493)	6e-05 (0.00038)	1e-05 (8.35e-05)	0.00482 (0.0189)	0.0404 (0.113)	0.0265 (0.0783)	0.0008 (0.00406)	0.0172 (0.0543)
del 10p15 3	470 (81%)	107	3e-05 (0.000217)	1e-05 (8.35e-05)	0.0085 (0.0302)	0.00345 (0.0141)	1e-05 (8.35e-05)	1e-05 (8.35e-05)	0.596 (0.721)	0.00077 (0.00393)	0.0146 (0.0475)	0.00013 (0.000763)
del 10p11 23	476 (82%)	101	1e-05 (8.35e-05)	1e-05 (8.35e-05)	9e-05 (0.000546)	1e-05 (8.35e-05)	1e-05 (8.35e-05)	1e-05 (8.35e-05)	0.195 (0.342)	9e-05 (0.000546)	0.0448 (0.12)	0.00087 (0.00432)
amp 7q21 2	480 (83%)	97	4e-05 (0.000273)	1e-05 (8.35e-05)	0.0498 (0.13)	0.0001 (0.000602)	1e-05 (8.35e-05)	9e-05 (0.000546)	0.0879 (0.2)	0.00368 (0.0149)	0.0623 (0.157)	0.00278 (0.0117)
amp 7q31 2	473 (82%)	104	0.00183 (0.00812)	1e-05 (8.35e-05)	0.0108 (0.0371)	0.00531 (0.0204)	5e-05 (0.000332)	0.0105 (0.0362)	0.355 (0.509)	0.00547 (0.0207)	0.408 (0.564)	0.00975 (0.0343)
del 9p21 3	421 (73%)	156	1e-05 (8.35e-05)	1e-05 (8.35e-05)	0.701 (0.805)	0.0371 (0.106)	1e-05 (8.35e-05)	0.139 (0.274)	0.043 (0.118)	0.0371 (0.106)	0.0274 (0.0809)	0.00804 (0.0287)
del 10p13	471 (82%)	106	1e-05 (8.35e-05)	1e-05 (8.35e-05)	0.00236 (0.0102)	0.00124 (0.00583)	1e-05 (8.35e-05)	1e-05 (8.35e-05)	0.114 (0.233)	3e-05 (0.000217)	0.087 (0.199)	0.00289 (0.0119)
del 10q23 31	514 (89%)	63	1e-05 (8.35e-05)	1e-05 (8.35e-05)	0.0122 (0.041)	0.0028 (0.0118)	1e-05 (8.35e-05)	0.00053 (0.00283)	0.187 (0.333)	0.00244 (0.0105)	0.37 (0.524)	0.0411 (0.114)
del 10q26 3	515 (89%)	62	1e-05 (8.35e-05)	5e-05 (0.000332)	0.0437 (0.119)	0.0014 (0.0065)	1e-05 (8.35e-05)	1e-05 (8.35e-05)	0.602 (0.726)	0.0175 (0.055)	0.252 (0.406)	0.0351 (0.101)
del 11p15 5	129 (22%)	448	1e-05 (8.35e-05)	1e-05 (8.35e-05)	0.161 (0.303)	0.00162 (0.00728)	1e-05 (8.35e-05)	1e-05 (8.35e-05)	0.321 (0.478)	0.0402 (0.113)	0.00286 (0.0119)	0.0016 (0.00724)
del 17q11 2	72 (12%)	505	1e-05 (8.35e-05)	1e-05 (8.35e-05)	0.00258 (0.011)	0.0115 (0.0392)	1e-05 (8.35e-05)	0.00025 (0.00137)	0.00087 (0.00432)	0.0104 (0.0361)	0.541 (0.681)	0.565 (0.696)
amp 8q24 21	70 (12%)	507	1e-05 (8.35e-05)	3e-05 (0.000217)	0.0263 (0.0781)	0.29 (0.445)	1e-05 (8.35e-05)	7e-05 (0.000436)	0.0343 (0.0994)	0.0244 (0.0731)	0.0888 (0.2)	0.272 (0.429)
amp 19p13 3	244 (42%)	333	1e-05 (8.35e-05)	1e-05 (8.35e-05)	0.0388 (0.11)	0.00143 (0.00659)	1e-05 (8.35e-05)	1e-05 (8.35e-05)	0.219 (0.371)	7e-05 (0.000436)	0.819 (0.892)	0.969 (0.993)
del 5q34	70 (12%)	507	1e-05 (8.35e-05)	1e-05 (8.35e-05)	4e-05 (0.000273)	0.00531 (0.0204)	0.00751 (0.0273)	1e-05 (8.35e-05)	0.621 (0.741)	0.0485 (0.128)	0.256 (0.41)	0.13 (0.261)
amp 17p13 2	51 (9%)	526	0.00081 (0.00408)	0.0138 (0.0453)	0.0472 (0.126)	0.112 (0.231)	0.00223 (0.00977)	0.0123 (0.041)	0.00611 (0.0226)	0.492 (0.637)	0.403 (0.561)	0.57 (0.699)
amp 19p13 2	249 (43%)	328	1e-05 (8.35e-05)	2e-05 (0.000151)	0.147 (0.283)	0.00112 (0.00534)	1e-05 (8.35e-05)	1e-05 (8.35e-05)	0.342 (0.495)	0.00014 (0.000802)	0.165 (0.31)	0.808 (0.888)
amp 19q12	216 (37%)	361	1e-05 (8.35e-05)	1e-05 (8.35e-05)	0.283 (0.438)	0.00498 (0.0194)	1e-05 (8.35e-05)	1e-05 (8.35e-05)	0.483 (0.634)	0.00131 (0.00612)	0.0632 (0.159)	0.172 (0.316)
del 19q13 41	99 (17%)	478	0.00466 (0.0185)	4e-05 (0.000273)	0.0759 (0.181)	0.0429 (0.118)	0.00115 (0.00544)	2e-05 (0.000151)	0.203 (0.352)	0.141 (0.276)	0.0363 (0.104)	0.0935 (0.205)
amp 21q21 1	70 (12%)	507	0.00504 (0.0196)	0.0608 (0.155)	0.018 (0.0561)	0.00781 (0.028)	0.00011 (0.000656)	0.0183 (0.0568)	0.0912 (0.202)	0.715 (0.815)	0.0963 (0.21)	0.407 (0.564)
del 11p11 2	105 (18%)	472	1e-05 (8.35e-05)	1e-05 (8.35e-05)	0.505 (0.651)	0.0177 (0.0555)	1e-05 (8.35e-05)	0.00262 (0.0111)	0.933 (0.97)	0.136 (0.271)	0.0942 (0.206)	0.0874 (0.199)
del 14q24 2	173 (30%)	404	1e-05 (8.35e-05)	2e-05 (0.000151)	0.0586 (0.15)	0.158 (0.298)	1e-05 (8.35e-05)	0.00408 (0.0164)	0.268 (0.424)	0.0483 (0.128)	0.088 (0.2)	0.94 (0.975)
del 21q21 1	56 (10%)	521	0.0104 (0.0362)	0.00089 (0.00439)	0.0159 (0.0512)	0.207 (0.359)	0.0889 (0.2)	0.00059 (0.0031)	0.258 (0.411)	0.0109 (0.0372)	0.661 (0.774)	1 (1.00)
amp 2p24 3	49 (8%)	528	0.0994 (0.215)	0.0172 (0.0543)	0.428 (0.584)	0.979 (0.999)	0.00106 (0.00509)	0.0162 (0.0517)	0.28 (0.436)	0.034 (0.0989)	0.886 (0.935)	0.627 (0.743)
amp 4q12	108 (19%)	469	0.00066 (0.00345)	0.00343 (0.0141)	0.537 (0.679)	0.473 (0.627)	3e-05 (0.000217)	0.0103 (0.0359)	0.0658 (0.164)	0.435 (0.588)	0.156 (0.297)	0.417 (0.572)
del 4p16 3	78 (14%)	499	0.0471 (0.126)	0.00461 (0.0184)	0.323 (0.48)	0.249 (0.405)	0.0023 (0.01)	0.00014 (0.000802)	0.753 (0.848)	0.858 (0.918)	0.873 (0.927)	0.947 (0.978)
del 4q34 3	93 (16%)	484	0.00549 (0.0207)	0.00029 (0.00157)	0.0757 (0.181)	0.0964 (0.21)	1e-05 (8.35e-05)	0.00778 (0.028)	0.209 (0.36)	0.0781 (0.185)	0.126 (0.256)	0.136 (0.271)
del 6q26	179 (31%)	398	0.743 (0.839)	0.756 (0.848)	0.478 (0.632)	0.548 (0.687)	0.00097 (0.00475)	0.0168 (0.0536)	0.00013 (0.000763)	0.0541 (0.14)	0.758 (0.849)	0.0185 (0.057)
del 12q12	77 (13%)	500	0.0131 (0.0434)	0.00077 (0.00393)	0.268 (0.424)	0.0854 (0.198)	0.00014 (0.000802)	0.0643 (0.161)	0.00925 (0.0327)	0.166 (0.311)	1 (1.00)	0.663 (0.774)
del 13q14 2	241 (42%)	336	1e-05 (8.35e-05)	2e-05 (0.000151)	0.35 (0.504)	0.145 (0.281)	1e-05 (8.35e-05)	0.00102 (0.00493)	0.83 (0.9)	0.109 (0.229)	0.0796 (0.188)	0.0668 (0.166)
del 14q13 1	178 (31%)	399	1e-05 (8.35e-05)	0.00018 (0.00101)	0.611 (0.73)	0.664 (0.774)	1e-05 (8.35e-05)	0.0445 (0.12)	0.411 (0.567)	0.455 (0.607)	0.447 (0.598)	0.941 (0.975)
del xp22 2	118 (20%)	459	0.0059 (0.0219)	0.0015 (0.00687)	0.111 (0.23)	0.169 (0.313)	1e-05 (8.35e-05)	0.00155 (0.00705)	0.072 (0.173)	0.213 (0.365)	0.305 (0.461)	0.673 (0.779)
amp 1p36 21	92 (16%)	485	0.59 (0.715)	0.432 (0.587)	0.405 (0.563)	0.114 (0.233)	1e-05 (8.35e-05)	0.57 (0.699)	0.0835 (0.196)	0.169 (0.313)	0.0116 (0.0392)	0.0197 (0.0601)
del 2q22 1	47 (8%)	530	0.00537 (0.0205)	0.0283 (0.083)	0.389 (0.547)	0.551 (0.687)	1e-05 (8.35e-05)	0.452 (0.604)	0.0922 (0.204)	0.81 (0.889)	0.183 (0.33)	0.429 (0.584)
del 11q14 1	96 (17%)	481	1e-05 (8.35e-05)	0.00057 (0.00302)	0.881 (0.931)	0.139 (0.274)	1e-05 (8.35e-05)	0.332 (0.489)	0.375 (0.53)	0.425 (0.581)	0.119 (0.242)	0.16 (0.302)
del 12q15	79 (14%)	498	0.00017 (0.000958)	0.00189 (0.00833)	0.488 (0.637)	0.423 (0.579)	1e-05 (8.35e-05)	0.242 (0.402)	0.068 (0.166)	0.576 (0.703)	0.712 (0.815)	0.396 (0.554)
del 13q22 1	230 (40%)	347	1e-05 (8.35e-05)	0.00017 (0.000958)	0.508 (0.654)	0.339 (0.494)	1e-05 (8.35e-05)	0.0711 (0.171)	0.834 (0.902)	0.248 (0.405)	0.525 (0.67)	0.284 (0.438)
del 17p13 2	88 (15%)	489	0.00287 (0.0119)	0.0244 (0.0731)	0.95 (0.979)	0.948 (0.979)	1e-05 (8.35e-05)	0.0766 (0.182)	0.646 (0.76)	0.195 (0.342)	0.586 (0.711)	0.818 (0.892)
del 17p13 1	98 (17%)	479	0.00023 (0.00128)	0.00171 (0.00764)	0.628 (0.743)	0.896 (0.943)	1e-05 (8.35e-05)	0.11 (0.229)	0.341 (0.495)	0.098 (0.213)	0.643 (0.758)	0.662 (0.774)
del 22q13 32	212 (37%)	365	0.713 (0.815)	0.972 (0.994)	0.0392 (0.111)	0.414 (0.569)	2e-05 (0.000151)	0.268 (0.424)	0.294 (0.449)	0.369 (0.524)	0.0492 (0.129)	0.0843 (0.196)
amp 1q44	99 (17%)	478	0.145 (0.281)	0.622 (0.741)	0.606 (0.727)	0.31 (0.467)	1e-05 (8.35e-05)	0.599 (0.723)	0.0189 (0.0581)	0.218 (0.37)	0.96 (0.985)	0.552 (0.687)
amp 3q26 33	111 (19%)	466	0.00773 (0.028)	0.211 (0.363)	0.443 (0.596)	0.057 (0.147)	1e-05 (8.35e-05)	0.0672 (0.166)	0.103 (0.221)	0.924 (0.964)	0.276 (0.431)	0.696 (0.801)
amp 12q14 1	134 (23%)	443	0.0671 (0.166)	0.148 (0.283)	0.0982 (0.213)	0.087 (0.199)	1e-05 (8.35e-05)	0.483 (0.634)	0.276 (0.431)	0.145 (0.281)	0.0419 (0.116)	0.139 (0.274)
amp 13q34	32 (6%)	545	0.26 (0.414)	0.201 (0.35)	0.0291 (0.085)	0.48 (0.632)	0.058 (0.149)	0.237 (0.395)	0.0412 (0.114)	0.103 (0.221)	0.492 (0.637)	0.801 (0.883)
amp 17q25 1	84 (15%)	493	0.0136 (0.0449)	0.257 (0.411)	0.282 (0.438)	0.731 (0.828)	4e-05 (0.000273)	0.169 (0.313)	0.0683 (0.167)	0.254 (0.408)	0.865 (0.923)	0.693 (0.799)
del 1p36 23	136 (24%)	441	0.07 (0.169)	0.186 (0.333)	0.57 (0.699)	0.558 (0.689)	0.00024 (0.00132)	0.549 (0.687)	0.673 (0.779)	0.196 (0.343)	0.0147 (0.0476)	0.0691 (0.167)
del 2q37 1	55 (10%)	522	0.101 (0.218)	0.00566 (0.0212)	0.315 (0.473)	0.822 (0.894)	0.0192 (0.0588)	0.222 (0.373)	0.135 (0.27)	0.532 (0.677)	0.182 (0.33)	0.0519 (0.135)
del 3p21 1	53 (9%)	524	0.243 (0.402)	0.134 (0.27)	0.676 (0.782)	0.48 (0.632)	6e-05 (0.00038)	0.0455 (0.122)	0.163 (0.306)	0.84 (0.906)	0.461 (0.614)	0.108 (0.228)
del 3q13 31	56 (10%)	521	0.572 (0.701)	0.345 (0.499)	0.607 (0.727)	0.509 (0.654)	6e-05 (0.00038)	0.0237 (0.0716)	0.168 (0.313)	0.104 (0.221)	1 (1.00)	0.179 (0.327)
del 3q29	65 (11%)	512	0.0902 (0.201)	0.186 (0.333)	0.536 (0.679)	0.875 (0.928)	0.0446 (0.12)	0.326 (0.481)	0.0439 (0.119)	0.117 (0.24)	0.954 (0.982)	0.794 (0.88)
del 6q22 31	158 (27%)	419	0.632 (0.746)	0.99 (1.00)	0.294 (0.449)	0.285 (0.438)	1e-05 (8.35e-05)	0.251 (0.406)	0.00616 (0.0227)	0.12 (0.244)	0.795 (0.88)	0.11 (0.23)
del 16q23 1	101 (18%)	476	0.0152 (0.049)	0.489 (0.637)	0.874 (0.927)	0.535 (0.679)	0.0123 (0.041)	0.857 (0.918)	0.222 (0.373)	0.113 (0.233)	0.878 (0.929)	0.785 (0.876)
del 18q22 3	82 (14%)	495	0.128 (0.258)	0.0862 (0.199)	0.786 (0.876)	0.39 (0.547)	5e-05 (0.000332)	0.187 (0.333)	0.296 (0.451)	0.0206 (0.0626)	0.197 (0.343)	0.273 (0.43)
amp 1q32 1	160 (28%)	417	0.819 (0.892)	0.0632 (0.159)	0.334 (0.489)	0.148 (0.283)	1e-05 (8.35e-05)	0.305 (0.461)	0.109 (0.229)	0.339 (0.494)	0.555 (0.689)	0.0896 (0.201)
amp 12p13 32	84 (15%)	493	0.665 (0.774)	0.386 (0.543)	0.342 (0.495)	0.433 (0.587)	4e-05 (0.000273)	0.47 (0.625)	0.529 (0.674)	0.272 (0.429)	0.319 (0.477)	0.551 (0.687)
amp 12q15	93 (16%)	484	0.733 (0.828)	0.317 (0.475)	0.707 (0.81)	0.277 (0.432)	2e-05 (0.000151)	0.495 (0.641)	0.579 (0.705)	0.324 (0.48)	0.318 (0.476)	0.9 (0.946)
amp 14q32 33	36 (6%)	541	0.187 (0.333)	0.661 (0.774)	0.0907 (0.202)	0.92 (0.961)	0.251 (0.406)	0.539 (0.681)	0.171 (0.316)	0.0534 (0.138)	0.0394 (0.111)	0.0677 (0.166)
del 1p22 1	48 (8%)	529	0.977 (0.998)	0.553 (0.688)	0.811 (0.889)	0.00483 (0.0189)	0.141 (0.276)	0.09 (0.201)	0.362 (0.517)	0.607 (0.727)	1 (1.00)	0.324 (0.48)
del 1q42 11	51 (9%)	526	0.222 (0.373)	0.826 (0.896)	0.514 (0.659)	0.285 (0.438)	0.606 (0.727)	0.556 (0.689)	0.903 (0.947)	0.00683 (0.025)	0.687 (0.793)	0.194 (0.342)
del 3q22 1	58 (10%)	519	0.791 (0.879)	0.624 (0.741)	0.956 (0.983)	1 (1.00)	0.00045 (0.00242)	0.0839 (0.196)	0.105 (0.223)	0.124 (0.252)	1 (1.00)	0.217 (0.369)
del 12p13 1	72 (12%)	505	0.0503 (0.131)	0.0142 (0.0464)	0.251 (0.406)	0.232 (0.387)	0.086 (0.199)	0.153 (0.292)	0.416 (0.571)	0.19 (0.337)	1 (1.00)	0.933 (0.97)
amp 4p16 3	48 (8%)	529	0.308 (0.465)	0.73 (0.828)	0.859 (0.918)	0.0826 (0.194)	0.185 (0.332)	0.558 (0.689)	0.411 (0.567)	0.754 (0.848)	1 (1.00)	1 (1.00)
amp 11p13	31 (5%)	546	0.787 (0.876)	0.351 (0.505)	0.55 (0.687)	0.248 (0.405)	0.353 (0.507)	0.904 (0.947)	0.193 (0.341)	1 (1.00)	1 (1.00)	0.887 (0.935)
amp 13q34	30 (5%)	547	0.139 (0.274)	0.211 (0.363)	0.217 (0.369)	0.787 (0.876)	0.0623 (0.157)	0.488 (0.637)	0.148 (0.283)	0.183 (0.33)	0.369 (0.524)	0.792 (0.879)
del 1p36 32	100 (17%)	477	0.92 (0.961)	0.715 (0.815)	0.585 (0.711)	0.172 (0.316)	0.509 (0.654)	0.182 (0.33)	0.624 (0.741)	0.144 (0.28)	0.253 (0.408)	0.579 (0.705)
del 1p32 3	61 (11%)	516	0.245 (0.404)	0.365 (0.52)	0.831 (0.9)	0.157 (0.298)	0.491 (0.637)	0.841 (0.906)	0.857 (0.918)	0.755 (0.848)	0.806 (0.887)	0.106 (0.224)
del 1q44	35 (6%)	542	0.812 (0.889)	0.473 (0.627)	0.729 (0.828)	0.247 (0.404)	0.215 (0.368)	1 (1.00)	0.8 (0.883)	0.35 (0.504)	0.541 (0.681)	0.324 (0.48)
del 8p23 2	66 (11%)	511	0.376 (0.53)	0.247 (0.404)	0.18 (0.327)	0.275 (0.431)	0.489 (0.637)	0.327 (0.482)	0.996 (1.00)	0.87 (0.927)	0.722 (0.821)	0.438 (0.591)
del 9q34 2	79 (14%)	498	0.215 (0.368)	0.107 (0.227)	0.519 (0.664)	0.23 (0.386)	0.396 (0.554)	0.845 (0.909)	0.0923 (0.204)	0.668 (0.776)	0.445 (0.597)	0.304 (0.461)
del 16p12 2	92 (16%)	485	0.246 (0.404)	0.233 (0.388)	0.397 (0.554)	0.87 (0.927)	0.174 (0.318)	0.0691 (0.167)	0.943 (0.976)	0.646 (0.76)	0.443 (0.596)	0.334 (0.489)

'amp_1p36.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S1. Gene #1: 'amp_1p36.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
AMP PEAK 1(1P36.21) MUTATED	52	22	18
AMP PEAK 1(1P36.21) WILD-TYPE	110	196	179

Figure S1. Get High-res Image Gene #1: 'amp_1p36.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_1p36.21' versus 'MRNASEQ_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 0.039

Table S2. Gene #1: 'amp_1p36.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	67	36
AMP PEAK 1(1P36.21) MUTATED	4	20	4
AMP PEAK 1(1P36.21) WILD-TYPE	40	47	32

Figure S2. Get High-res Image Gene #1: 'amp_1p36.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_1p36.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0197 (Fisher's exact test), Q value = 0.06

Table S3. Gene #1: 'amp_1p36.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	92	25
AMP PEAK 1(1P36.21) MUTATED	2	24	2
AMP PEAK 1(1P36.21) WILD-TYPE	28	68	23

Figure S3. Get High-res Image Gene #1: 'amp_1p36.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_1q32.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S4. Gene #2: 'amp_1q32.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
AMP PEAK 2(1Q32.1) MUTATED	75	47	38
AMP PEAK 2(1Q32.1) WILD-TYPE	87	171	159

Figure S4. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #5: 'CN_CNMF'

'amp_1q44' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S5. Gene #3: 'amp_1q44' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
AMP PEAK 3(1Q44) MUTATED	57	22	20
AMP PEAK 3(1Q44) WILD-TYPE	105	196	177

Figure S5. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #5: 'CN_CNMF'

'amp_1q44' versus 'RPPA_CNMF'

P value = 0.0189 (Fisher's exact test), Q value = 0.058

Table S6. Gene #3: 'amp_1q44' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	57	44	30	45
AMP PEAK 3(1Q44) MUTATED	3	7	6	11	7
AMP PEAK 3(1Q44) WILD-TYPE	41	50	38	19	38

Figure S6. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_2p24.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0172 (Fisher's exact test), Q value = 0.054

Table S7. Gene #4: 'amp_2p24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
AMP PEAK 4(2P24.3) MUTATED	11	17	4	13
AMP PEAK 4(2P24.3) WILD-TYPE	137	85	96	145

Figure S7. Get High-res Image Gene #4: 'amp_2p24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_2p24.3' versus 'CN_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.0051

Table S8. Gene #4: 'amp_2p24.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
AMP PEAK 4(2P24.3) MUTATED	24	9	16
AMP PEAK 4(2P24.3) WILD-TYPE	138	209	181

Figure S8. Get High-res Image Gene #4: 'amp_2p24.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_2p24.3' versus 'METHLYATION_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.052

Table S9. Gene #4: 'amp_2p24.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
AMP PEAK 4(2P24.3) MUTATED	5	7	14
AMP PEAK 4(2P24.3) WILD-TYPE	84	101	64

Figure S9. Get High-res Image Gene #4: 'amp_2p24.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_2p24.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.034 (Fisher's exact test), Q value = 0.099

Table S10. Gene #4: 'amp_2p24.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
AMP PEAK 4(2P24.3) MUTATED	5	13	6
AMP PEAK 4(2P24.3) WILD-TYPE	85	57	54

Figure S10. Get High-res Image Gene #4: 'amp_2p24.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_3q26.33' versus 'MRNA_CNMF'

P value = 0.00773 (Fisher's exact test), Q value = 0.028

Table S11. Gene #5: 'amp_3q26.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 5(3Q26.33) MUTATED	27	28	19	27
AMP PEAK 5(3Q26.33) WILD-TYPE	120	68	133	86

Figure S11. Get High-res Image Gene #5: 'amp_3q26.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S12. Gene #5: 'amp_3q26.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
AMP PEAK 5(3Q26.33) MUTATED	61	24	26
AMP PEAK 5(3Q26.33) WILD-TYPE	101	194	171

Figure S12. Get High-res Image Gene #5: 'amp_3q26.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_4q12' versus 'MRNA_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0034

Table S13. Gene #7: 'amp_4q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 7(4Q12) MUTATED	22	32	20	25
AMP PEAK 7(4Q12) WILD-TYPE	125	64	132	88

Figure S13. Get High-res Image Gene #7: 'amp_4q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_4q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00343 (Fisher's exact test), Q value = 0.014

Table S14. Gene #7: 'amp_4q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
AMP PEAK 7(4Q12) MUTATED	18	31	16	34
AMP PEAK 7(4Q12) WILD-TYPE	130	71	84	124

Figure S14. Get High-res Image Gene #7: 'amp_4q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_4q12' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00022

Table S15. Gene #7: 'amp_4q12' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
AMP PEAK 7(4Q12) MUTATED	50	26	32
AMP PEAK 7(4Q12) WILD-TYPE	112	192	165

Figure S15. Get High-res Image Gene #7: 'amp_4q12' versus Molecular Subtype #5: 'CN_CNMF'

'amp_4q12' versus 'METHLYATION_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.036

Table S16. Gene #7: 'amp_4q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
AMP PEAK 7(4Q12) MUTATED	10	18	23
AMP PEAK 7(4Q12) WILD-TYPE	79	90	55

Figure S16. Get High-res Image Gene #7: 'amp_4q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S17. Gene #8: 'amp_7p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 8(7P11.2) MUTATED	139	68	147	89
AMP PEAK 8(7P11.2) WILD-TYPE	8	28	5	24

Figure S17. Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_7p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S18. Gene #8: 'amp_7p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
AMP PEAK 8(7P11.2) MUTATED	136	60	99	148
AMP PEAK 8(7P11.2) WILD-TYPE	12	42	1	10

Figure S18. Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7p11.2' versus 'MIR_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S19. Gene #8: 'amp_7p11.2' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
AMP PEAK 8(7P11.2) MUTATED	151	146	73	110
AMP PEAK 8(7P11.2) WILD-TYPE	5	37	14	10

Figure S19. Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_7p11.2' versus 'MIR_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S20. Gene #8: 'amp_7p11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
AMP PEAK 8(7P11.2) MUTATED	234	120	126
AMP PEAK 8(7P11.2) WILD-TYPE	59	4	3

Figure S20. Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S21. Gene #8: 'amp_7p11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
AMP PEAK 8(7P11.2) MUTATED	153	217	137
AMP PEAK 8(7P11.2) WILD-TYPE	9	1	60

Figure S21. Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S22. Gene #8: 'amp_7p11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
AMP PEAK 8(7P11.2) MUTATED	85	106	50
AMP PEAK 8(7P11.2) WILD-TYPE	4	2	28

Figure S22. Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'RPPA_CNMF'

P value = 0.00075 (Fisher's exact test), Q value = 0.0039

Table S23. Gene #8: 'amp_7p11.2' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	57	44	30	45
AMP PEAK 8(7P11.2) MUTATED	43	51	32	26	44
AMP PEAK 8(7P11.2) WILD-TYPE	1	6	12	4	1

Figure S23. Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_7p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S24. Gene #8: 'amp_7p11.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
AMP PEAK 8(7P11.2) MUTATED	84	52	60
AMP PEAK 8(7P11.2) WILD-TYPE	6	18	0

Figure S24. Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00027

Table S25. Gene #8: 'amp_7p11.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	67	36
AMP PEAK 8(7P11.2) MUTATED	31	66	34
AMP PEAK 8(7P11.2) WILD-TYPE	13	1	2

Figure S25. Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S26. Gene #8: 'amp_7p11.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	92	25
AMP PEAK 8(7P11.2) MUTATED	17	90	24
AMP PEAK 8(7P11.2) WILD-TYPE	13	2	1

Figure S26. Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_7q11.21' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S27. Gene #9: 'amp_7q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 9(7Q11.21) MUTATED	133	64	124	82
AMP PEAK 9(7Q11.21) WILD-TYPE	14	32	28	31

Figure S27. Get High-res Image Gene #9: 'amp_7q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_7q11.21' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S28. Gene #9: 'amp_7q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
AMP PEAK 9(7Q11.21) MUTATED	129	55	82	137
AMP PEAK 9(7Q11.21) WILD-TYPE	19	47	18	21

Figure S28. Get High-res Image Gene #9: 'amp_7q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7q11.21' versus 'MIR_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00038

Table S29. Gene #9: 'amp_7q11.21' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
AMP PEAK 9(7Q11.21) MUTATED	141	133	63	103
AMP PEAK 9(7Q11.21) WILD-TYPE	15	50	24	17

Figure S29. Get High-res Image Gene #9: 'amp_7q11.21' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_7q11.21' versus 'MIR_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S30. Gene #9: 'amp_7q11.21' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
AMP PEAK 9(7Q11.21) MUTATED	216	114	110
AMP PEAK 9(7Q11.21) WILD-TYPE	77	10	19

Figure S30. Get High-res Image Gene #9: 'amp_7q11.21' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_7q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S31. Gene #9: 'amp_7q11.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
AMP PEAK 9(7Q11.21) MUTATED	145	189	130
AMP PEAK 9(7Q11.21) WILD-TYPE	17	29	67

Figure S31. Get High-res Image Gene #9: 'amp_7q11.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_7q11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S32. Gene #9: 'amp_7q11.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
AMP PEAK 9(7Q11.21) MUTATED	83	91	46
AMP PEAK 9(7Q11.21) WILD-TYPE	6	17	32

Figure S32. Get High-res Image Gene #9: 'amp_7q11.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_7q11.21' versus 'RPPA_CNMF'

P value = 0.0261 (Fisher's exact test), Q value = 0.078

Table S33. Gene #9: 'amp_7q11.21' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	57	44	30	45
AMP PEAK 9(7Q11.21) MUTATED	41	46	29	25	38
AMP PEAK 9(7Q11.21) WILD-TYPE	3	11	15	5	7

Figure S33. Get High-res Image Gene #9: 'amp_7q11.21' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_7q11.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.0055 (Fisher's exact test), Q value = 0.021

Table S34. Gene #9: 'amp_7q11.21' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
AMP PEAK 9(7Q11.21) MUTATED	79	48	52
AMP PEAK 9(7Q11.21) WILD-TYPE	11	22	8

Figure S34. Get High-res Image Gene #9: 'amp_7q11.21' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_7q11.21' versus 'MRNASEQ_CNMF'

P value = 0.00407 (Fisher's exact test), Q value = 0.016

Table S35. Gene #9: 'amp_7q11.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	67	36
AMP PEAK 9(7Q11.21) MUTATED	29	61	28
AMP PEAK 9(7Q11.21) WILD-TYPE	15	6	8

Figure S35. Get High-res Image Gene #9: 'amp_7q11.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_7q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00038

Table S36. Gene #9: 'amp_7q11.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	92	25
AMP PEAK 9(7Q11.21) MUTATED	15	82	21
AMP PEAK 9(7Q11.21) WILD-TYPE	15	10	4

Figure S36. Get High-res Image Gene #9: 'amp_7q11.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00027

Table S37. Gene #10: 'amp_7q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 10(7Q21.2) MUTATED	131	64	134	89
AMP PEAK 10(7Q21.2) WILD-TYPE	16	32	18	24

Figure S37. Get High-res Image Gene #10: 'amp_7q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_7q21.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S38. Gene #10: 'amp_7q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
AMP PEAK 10(7Q21.2) MUTATED	126	62	89	141
AMP PEAK 10(7Q21.2) WILD-TYPE	22	40	11	17

Figure S38. Get High-res Image Gene #10: 'amp_7q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7q21.2' versus 'MIR_CNMF'

P value = 0.0498 (Fisher's exact test), Q value = 0.13

Table S39. Gene #10: 'amp_7q21.2' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
AMP PEAK 10(7Q21.2) MUTATED	138	142	70	102
AMP PEAK 10(7Q21.2) WILD-TYPE	18	41	17	18

Figure S39. Get High-res Image Gene #10: 'amp_7q21.2' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_7q21.2' versus 'MIR_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 6e-04

Table S40. Gene #10: 'amp_7q21.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
AMP PEAK 10(7Q21.2) MUTATED	224	111	117
AMP PEAK 10(7Q21.2) WILD-TYPE	69	13	12

Figure S40. Get High-res Image Gene #10: 'amp_7q21.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_7q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S41. Gene #10: 'amp_7q21.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
AMP PEAK 10(7Q21.2) MUTATED	144	199	137
AMP PEAK 10(7Q21.2) WILD-TYPE	18	19	60

Figure S41. Get High-res Image Gene #10: 'amp_7q21.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_7q21.2' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00055

Table S42. Gene #10: 'amp_7q21.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
AMP PEAK 10(7Q21.2) MUTATED	80	93	50
AMP PEAK 10(7Q21.2) WILD-TYPE	9	15	28

Figure S42. Get High-res Image Gene #10: 'amp_7q21.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_7q21.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00368 (Fisher's exact test), Q value = 0.015

Table S43. Gene #10: 'amp_7q21.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
AMP PEAK 10(7Q21.2) MUTATED	80	50	55
AMP PEAK 10(7Q21.2) WILD-TYPE	10	20	5

Figure S43. Get High-res Image Gene #10: 'amp_7q21.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_7q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00278 (Fisher's exact test), Q value = 0.012

Table S44. Gene #10: 'amp_7q21.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	92	25
AMP PEAK 10(7Q21.2) MUTATED	20	85	21
AMP PEAK 10(7Q21.2) WILD-TYPE	10	7	4

Figure S44. Get High-res Image Gene #10: 'amp_7q21.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MRNA_CNMF'

P value = 0.00183 (Fisher's exact test), Q value = 0.0081

Table S45. Gene #11: 'amp_7q31.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 11(7Q31.2) MUTATED	131	67	126	89
AMP PEAK 11(7Q31.2) WILD-TYPE	16	29	26	24

Figure S45. Get High-res Image Gene #11: 'amp_7q31.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_7q31.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S46. Gene #11: 'amp_7q31.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
AMP PEAK 11(7Q31.2) MUTATED	131	63	83	136
AMP PEAK 11(7Q31.2) WILD-TYPE	17	39	17	22

Figure S46. Get High-res Image Gene #11: 'amp_7q31.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7q31.2' versus 'MIR_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.037

Table S47. Gene #11: 'amp_7q31.2' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
AMP PEAK 11(7Q31.2) MUTATED	137	136	71	102
AMP PEAK 11(7Q31.2) WILD-TYPE	19	47	16	18

Figure S47. Get High-res Image Gene #11: 'amp_7q31.2' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_7q31.2' versus 'MIR_CHIERARCHICAL'

P value = 0.00531 (Fisher's exact test), Q value = 0.02

Table S48. Gene #11: 'amp_7q31.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
AMP PEAK 11(7Q31.2) MUTATED	225	110	111
AMP PEAK 11(7Q31.2) WILD-TYPE	68	14	18

Figure S48. Get High-res Image Gene #11: 'amp_7q31.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_7q31.2' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00033

Table S49. Gene #11: 'amp_7q31.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
AMP PEAK 11(7Q31.2) MUTATED	140	193	140
AMP PEAK 11(7Q31.2) WILD-TYPE	22	25	57

Figure S49. Get High-res Image Gene #11: 'amp_7q31.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_7q31.2' versus 'METHLYATION_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.036

Table S50. Gene #11: 'amp_7q31.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
AMP PEAK 11(7Q31.2) MUTATED	78	89	54
AMP PEAK 11(7Q31.2) WILD-TYPE	11	19	24

Figure S50. Get High-res Image Gene #11: 'amp_7q31.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_7q31.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00547 (Fisher's exact test), Q value = 0.021

Table S51. Gene #11: 'amp_7q31.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
AMP PEAK 11(7Q31.2) MUTATED	80	49	53
AMP PEAK 11(7Q31.2) WILD-TYPE	10	21	7

Figure S51. Get High-res Image Gene #11: 'amp_7q31.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_7q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00975 (Fisher's exact test), Q value = 0.034

Table S52. Gene #11: 'amp_7q31.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	92	25
AMP PEAK 11(7Q31.2) MUTATED	20	83	20
AMP PEAK 11(7Q31.2) WILD-TYPE	10	9	5

Figure S52. Get High-res Image Gene #11: 'amp_7q31.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S53. Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 12(8Q24.21) MUTATED	9	25	7	21
AMP PEAK 12(8Q24.21) WILD-TYPE	138	71	145	92

Figure S53. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8q24.21' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00022

Table S54. Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
AMP PEAK 12(8Q24.21) MUTATED	10	29	6	17
AMP PEAK 12(8Q24.21) WILD-TYPE	138	73	94	141

Figure S54. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8q24.21' versus 'MIR_CNMF'

P value = 0.0263 (Fisher's exact test), Q value = 0.078

Table S55. Gene #12: 'amp_8q24.21' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
AMP PEAK 12(8Q24.21) MUTATED	12	32	11	10
AMP PEAK 12(8Q24.21) WILD-TYPE	144	151	76	110

Figure S55. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S56. Gene #12: 'amp_8q24.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
AMP PEAK 12(8Q24.21) MUTATED	39	8	23
AMP PEAK 12(8Q24.21) WILD-TYPE	123	210	174

Figure S56. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00044

Table S57. Gene #12: 'amp_8q24.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
AMP PEAK 12(8Q24.21) MUTATED	5	12	23
AMP PEAK 12(8Q24.21) WILD-TYPE	84	96	55

Figure S57. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'RPPA_CNMF'

P value = 0.0343 (Fisher's exact test), Q value = 0.099

Table S58. Gene #12: 'amp_8q24.21' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	57	44	30	45
AMP PEAK 12(8Q24.21) MUTATED	2	7	5	9	4
AMP PEAK 12(8Q24.21) WILD-TYPE	42	50	39	21	41

Figure S58. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_8q24.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.0244 (Fisher's exact test), Q value = 0.073

Table S59. Gene #12: 'amp_8q24.21' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
AMP PEAK 12(8Q24.21) MUTATED	7	15	5
AMP PEAK 12(8Q24.21) WILD-TYPE	83	55	55

Figure S59. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_12p13.32' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00027

Table S60. Gene #14: 'amp_12p13.32' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
AMP PEAK 14(12P13.32) MUTATED	40	18	26
AMP PEAK 14(12P13.32) WILD-TYPE	122	200	171

Figure S60. Get High-res Image Gene #14: 'amp_12p13.32' versus Molecular Subtype #5: 'CN_CNMF'

'amp_12q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S61. Gene #15: 'amp_12q14.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
AMP PEAK 15(12Q14.1) MUTATED	65	39	30
AMP PEAK 15(12Q14.1) WILD-TYPE	97	179	167

Figure S61. Get High-res Image Gene #15: 'amp_12q14.1' versus Molecular Subtype #5: 'CN_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CNMF'

P value = 0.0419 (Fisher's exact test), Q value = 0.12

Table S62. Gene #15: 'amp_12q14.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	67	36
AMP PEAK 15(12Q14.1) MUTATED	19	15	8
AMP PEAK 15(12Q14.1) WILD-TYPE	25	52	28

Figure S62. Get High-res Image Gene #15: 'amp_12q14.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_12q15' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S63. Gene #16: 'amp_12q15' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
AMP PEAK 16(12Q15) MUTATED	48	25	20
AMP PEAK 16(12Q15) WILD-TYPE	114	193	177

Figure S63. Get High-res Image Gene #16: 'amp_12q15' versus Molecular Subtype #5: 'CN_CNMF'

'amp_13q34' versus 'MIR_CNMF'

P value = 0.0291 (Fisher's exact test), Q value = 0.085

Table S64. Gene #17: 'amp_13q34' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
AMP PEAK 17(13Q34) MUTATED	3	17	5	6
AMP PEAK 17(13Q34) WILD-TYPE	153	166	82	114

Figure S64. Get High-res Image Gene #17: 'amp_13q34' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_13q34' versus 'RPPA_CNMF'

P value = 0.0412 (Fisher's exact test), Q value = 0.11

Table S65. Gene #17: 'amp_13q34' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	57	44	30	45
AMP PEAK 17(13Q34) MUTATED	0	3	0	3	4
AMP PEAK 17(13Q34) WILD-TYPE	44	54	44	27	41

Figure S65. Get High-res Image Gene #17: 'amp_13q34' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_14q32.33' versus 'MRNASEQ_CNMF'

P value = 0.0394 (Fisher's exact test), Q value = 0.11

Table S66. Gene #19: 'amp_14q32.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	67	36
AMP PEAK 19(14Q32.33) MUTATED	1	3	6
AMP PEAK 19(14Q32.33) WILD-TYPE	43	64	30

Figure S66. Get High-res Image Gene #19: 'amp_14q32.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_17p13.2' versus 'MRNA_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.0041

Table S67. Gene #20: 'amp_17p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 20(17P13.2) MUTATED	9	12	6	20
AMP PEAK 20(17P13.2) WILD-TYPE	138	84	146	93

Figure S67. Get High-res Image Gene #20: 'amp_17p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17p13.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0138 (Fisher's exact test), Q value = 0.045

Table S68. Gene #20: 'amp_17p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
AMP PEAK 20(17P13.2) MUTATED	10	18	5	14
AMP PEAK 20(17P13.2) WILD-TYPE	138	84	95	144

Figure S68. Get High-res Image Gene #20: 'amp_17p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17p13.2' versus 'MIR_CNMF'

P value = 0.0472 (Fisher's exact test), Q value = 0.13

Table S69. Gene #20: 'amp_17p13.2' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
AMP PEAK 20(17P13.2) MUTATED	6	21	8	13
AMP PEAK 20(17P13.2) WILD-TYPE	150	162	79	107

Figure S69. Get High-res Image Gene #20: 'amp_17p13.2' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_17p13.2' versus 'CN_CNMF'

P value = 0.00223 (Fisher's exact test), Q value = 0.0098

Table S70. Gene #20: 'amp_17p13.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
AMP PEAK 20(17P13.2) MUTATED	25	11	15
AMP PEAK 20(17P13.2) WILD-TYPE	137	207	182

Figure S70. Get High-res Image Gene #20: 'amp_17p13.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_17p13.2' versus 'METHLYATION_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.041

Table S71. Gene #20: 'amp_17p13.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
AMP PEAK 20(17P13.2) MUTATED	5	5	13
AMP PEAK 20(17P13.2) WILD-TYPE	84	103	65

Figure S71. Get High-res Image Gene #20: 'amp_17p13.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_17p13.2' versus 'RPPA_CNMF'

P value = 0.00611 (Fisher's exact test), Q value = 0.023

Table S72. Gene #20: 'amp_17p13.2' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	57	44	30	45
AMP PEAK 20(17P13.2) MUTATED	5	9	2	6	0
AMP PEAK 20(17P13.2) WILD-TYPE	39	48	42	24	45

Figure S72. Get High-res Image Gene #20: 'amp_17p13.2' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_17q25.1' versus 'MRNA_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.045

Table S73. Gene #21: 'amp_17q25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 21(17Q25.1) MUTATED	19	22	13	19
AMP PEAK 21(17Q25.1) WILD-TYPE	128	74	139	94

Figure S73. Get High-res Image Gene #21: 'amp_17q25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q25.1' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00027

Table S74. Gene #21: 'amp_17q25.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
AMP PEAK 21(17Q25.1) MUTATED	42	20	22
AMP PEAK 21(17Q25.1) WILD-TYPE	120	198	175

Figure S74. Get High-res Image Gene #21: 'amp_17q25.1' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19p13.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S75. Gene #22: 'amp_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 22(19P13.3) MUTATED	58	34	95	28
AMP PEAK 22(19P13.3) WILD-TYPE	89	62	57	85

Figure S75. Get High-res Image Gene #22: 'amp_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19p13.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S76. Gene #22: 'amp_19p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
AMP PEAK 22(19P13.3) MUTATED	67	30	62	56
AMP PEAK 22(19P13.3) WILD-TYPE	81	72	38	102

Figure S76. Get High-res Image Gene #22: 'amp_19p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19p13.3' versus 'MIR_CNMF'

P value = 0.0388 (Fisher's exact test), Q value = 0.11

Table S77. Gene #22: 'amp_19p13.3' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
AMP PEAK 22(19P13.3) MUTATED	67	86	25	52
AMP PEAK 22(19P13.3) WILD-TYPE	89	97	62	68

Figure S77. Get High-res Image Gene #22: 'amp_19p13.3' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_19p13.3' versus 'MIR_CHIERARCHICAL'

P value = 0.00143 (Fisher's exact test), Q value = 0.0066

Table S78. Gene #22: 'amp_19p13.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
AMP PEAK 22(19P13.3) MUTATED	106	53	71
AMP PEAK 22(19P13.3) WILD-TYPE	187	71	58

Figure S78. Get High-res Image Gene #22: 'amp_19p13.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S79. Gene #22: 'amp_19p13.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
AMP PEAK 22(19P13.3) MUTATED	46	148	50
AMP PEAK 22(19P13.3) WILD-TYPE	116	70	147

Figure S79. Get High-res Image Gene #22: 'amp_19p13.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S80. Gene #22: 'amp_19p13.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
AMP PEAK 22(19P13.3) MUTATED	29	72	17
AMP PEAK 22(19P13.3) WILD-TYPE	60	36	61

Figure S80. Get High-res Image Gene #22: 'amp_19p13.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_19p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00044

Table S81. Gene #22: 'amp_19p13.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
AMP PEAK 22(19P13.3) MUTATED	32	21	39
AMP PEAK 22(19P13.3) WILD-TYPE	58	49	21

Figure S81. Get High-res Image Gene #22: 'amp_19p13.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_19p13.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S82. Gene #23: 'amp_19p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 23(19P13.2) MUTATED	57	38	101	25
AMP PEAK 23(19P13.2) WILD-TYPE	90	58	51	88

Figure S82. Get High-res Image Gene #23: 'amp_19p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19p13.2' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S83. Gene #23: 'amp_19p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
AMP PEAK 23(19P13.2) MUTATED	66	32	66	57
AMP PEAK 23(19P13.2) WILD-TYPE	82	70	34	101

Figure S83. Get High-res Image Gene #23: 'amp_19p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19p13.2' versus 'MIR_CHIERARCHICAL'

P value = 0.00112 (Fisher's exact test), Q value = 0.0053

Table S84. Gene #23: 'amp_19p13.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
AMP PEAK 23(19P13.2) MUTATED	109	54	73
AMP PEAK 23(19P13.2) WILD-TYPE	184	70	56

Figure S84. Get High-res Image Gene #23: 'amp_19p13.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S85. Gene #23: 'amp_19p13.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
AMP PEAK 23(19P13.2) MUTATED	50	150	49
AMP PEAK 23(19P13.2) WILD-TYPE	112	68	148

Figure S85. Get High-res Image Gene #23: 'amp_19p13.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19p13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S86. Gene #23: 'amp_19p13.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
AMP PEAK 23(19P13.2) MUTATED	31	74	19
AMP PEAK 23(19P13.2) WILD-TYPE	58	34	59

Figure S86. Get High-res Image Gene #23: 'amp_19p13.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 8e-04

Table S87. Gene #23: 'amp_19p13.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
AMP PEAK 23(19P13.2) MUTATED	34	20	39
AMP PEAK 23(19P13.2) WILD-TYPE	56	50	21

Figure S87. Get High-res Image Gene #23: 'amp_19p13.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_19q12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S88. Gene #24: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 24(19Q12) MUTATED	55	31	85	17
AMP PEAK 24(19Q12) WILD-TYPE	92	65	67	96

Figure S88. Get High-res Image Gene #24: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19q12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S89. Gene #24: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
AMP PEAK 24(19Q12) MUTATED	62	21	54	51
AMP PEAK 24(19Q12) WILD-TYPE	86	81	46	107

Figure S89. Get High-res Image Gene #24: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q12' versus 'MIR_CHIERARCHICAL'

P value = 0.00498 (Fisher's exact test), Q value = 0.019

Table S90. Gene #24: 'amp_19q12' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
AMP PEAK 24(19Q12) MUTATED	91	49	61
AMP PEAK 24(19Q12) WILD-TYPE	202	75	68

Figure S90. Get High-res Image Gene #24: 'amp_19q12' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S91. Gene #24: 'amp_19q12' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
AMP PEAK 24(19Q12) MUTATED	44	132	40
AMP PEAK 24(19Q12) WILD-TYPE	118	86	157

Figure S91. Get High-res Image Gene #24: 'amp_19q12' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S92. Gene #24: 'amp_19q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
AMP PEAK 24(19Q12) MUTATED	31	64	10
AMP PEAK 24(19Q12) WILD-TYPE	58	44	68

Figure S92. Get High-res Image Gene #24: 'amp_19q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_19q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00131 (Fisher's exact test), Q value = 0.0061

Table S93. Gene #24: 'amp_19q12' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
AMP PEAK 24(19Q12) MUTATED	31	17	33
AMP PEAK 24(19Q12) WILD-TYPE	59	53	27

Figure S93. Get High-res Image Gene #24: 'amp_19q12' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_21q21.1' versus 'MRNA_CNMF'

P value = 0.00504 (Fisher's exact test), Q value = 0.02

Table S94. Gene #25: 'amp_21q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 25(21Q21.1) MUTATED	28	13	11	8
AMP PEAK 25(21Q21.1) WILD-TYPE	119	83	141	105

Figure S94. Get High-res Image Gene #25: 'amp_21q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_21q21.1' versus 'MIR_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.056

Table S95. Gene #25: 'amp_21q21.1' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
AMP PEAK 25(21Q21.1) MUTATED	26	19	4	19
AMP PEAK 25(21Q21.1) WILD-TYPE	130	164	83	101

Figure S95. Get High-res Image Gene #25: 'amp_21q21.1' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_21q21.1' versus 'MIR_CHIERARCHICAL'

P value = 0.00781 (Fisher's exact test), Q value = 0.028

Table S96. Gene #25: 'amp_21q21.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
AMP PEAK 25(21Q21.1) MUTATED	29	26	13
AMP PEAK 25(21Q21.1) WILD-TYPE	264	98	116

Figure S96. Get High-res Image Gene #25: 'amp_21q21.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_21q21.1' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00066

Table S97. Gene #25: 'amp_21q21.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
AMP PEAK 25(21Q21.1) MUTATED	34	13	23
AMP PEAK 25(21Q21.1) WILD-TYPE	128	205	174

Figure S97. Get High-res Image Gene #25: 'amp_21q21.1' versus Molecular Subtype #5: 'CN_CNMF'

'amp_21q21.1' versus 'METHLYATION_CNMF'

P value = 0.0183 (Fisher's exact test), Q value = 0.057

Table S98. Gene #25: 'amp_21q21.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
AMP PEAK 25(21Q21.1) MUTATED	19	9	7
AMP PEAK 25(21Q21.1) WILD-TYPE	70	99	71

Figure S98. Get High-res Image Gene #25: 'amp_21q21.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_1p36.23' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0013

Table S99. Gene #27: 'del_1p36.23' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 2(1P36.23) MUTATED	34	71	31
DEL PEAK 2(1P36.23) WILD-TYPE	128	147	166

Figure S99. Get High-res Image Gene #27: 'del_1p36.23' versus Molecular Subtype #5: 'CN_CNMF'

'del_1p36.23' versus 'MRNASEQ_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.048

Table S100. Gene #27: 'del_1p36.23' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	67	36
DEL PEAK 2(1P36.23) MUTATED	6	15	15
DEL PEAK 2(1P36.23) WILD-TYPE	38	52	21

Figure S100. Get High-res Image Gene #27: 'del_1p36.23' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_1p22.1' versus 'MIR_CHIERARCHICAL'

P value = 0.00483 (Fisher's exact test), Q value = 0.019

Table S101. Gene #29: 'del_1p22.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 4(1P22.1) MUTATED	25	3	17
DEL PEAK 4(1P22.1) WILD-TYPE	268	121	112

Figure S101. Get High-res Image Gene #29: 'del_1p22.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_1q42.11' versus 'RPPA_CHIERARCHICAL'

P value = 0.00683 (Fisher's exact test), Q value = 0.025

Table S102. Gene #30: 'del_1q42.11' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
DEL PEAK 5(1Q42.11) MUTATED	15	9	1
DEL PEAK 5(1Q42.11) WILD-TYPE	75	61	59

Figure S102. Get High-res Image Gene #30: 'del_1q42.11' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_2q22.1' versus 'MRNA_CNMF'

P value = 0.00537 (Fisher's exact test), Q value = 0.02

Table S103. Gene #32: 'del_2q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 7(2Q22.1) MUTATED	9	17	8	7
DEL PEAK 7(2Q22.1) WILD-TYPE	138	79	144	106

Figure S103. Get High-res Image Gene #32: 'del_2q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_2q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0283 (Fisher's exact test), Q value = 0.083

Table S104. Gene #32: 'del_2q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 7(2Q22.1) MUTATED	9	16	5	11
DEL PEAK 7(2Q22.1) WILD-TYPE	139	86	95	147

Figure S104. Get High-res Image Gene #32: 'del_2q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_2q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S105. Gene #32: 'del_2q22.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 7(2Q22.1) MUTATED	29	6	12
DEL PEAK 7(2Q22.1) WILD-TYPE	133	212	185

Figure S105. Get High-res Image Gene #32: 'del_2q22.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_2q37.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00566 (Fisher's exact test), Q value = 0.021

Table S106. Gene #33: 'del_2q37.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 8(2Q37.1) MUTATED	10	20	7	12
DEL PEAK 8(2Q37.1) WILD-TYPE	138	82	93	146

Figure S106. Get High-res Image Gene #33: 'del_2q37.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_2q37.1' versus 'CN_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.059

Table S107. Gene #33: 'del_2q37.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 8(2Q37.1) MUTATED	22	12	21
DEL PEAK 8(2Q37.1) WILD-TYPE	140	206	176

Figure S107. Get High-res Image Gene #33: 'del_2q37.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_3p21.1' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00038

Table S108. Gene #34: 'del_3p21.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 9(3P21.1) MUTATED	25	7	21
DEL PEAK 9(3P21.1) WILD-TYPE	137	211	176

Figure S108. Get High-res Image Gene #34: 'del_3p21.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_3p21.1' versus 'METHLYATION_CNMF'

P value = 0.0455 (Fisher's exact test), Q value = 0.12

Table S109. Gene #34: 'del_3p21.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
DEL PEAK 9(3P21.1) MUTATED	8	6	13
DEL PEAK 9(3P21.1) WILD-TYPE	81	102	65

Figure S109. Get High-res Image Gene #34: 'del_3p21.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_3q13.31' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00038

Table S110. Gene #35: 'del_3q13.31' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 10(3Q13.31) MUTATED	26	7	23
DEL PEAK 10(3Q13.31) WILD-TYPE	136	211	174

Figure S110. Get High-res Image Gene #35: 'del_3q13.31' versus Molecular Subtype #5: 'CN_CNMF'

'del_3q13.31' versus 'METHLYATION_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 0.072

Table S111. Gene #35: 'del_3q13.31' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
DEL PEAK 10(3Q13.31) MUTATED	12	5	12
DEL PEAK 10(3Q13.31) WILD-TYPE	77	103	66

Figure S111. Get High-res Image Gene #35: 'del_3q13.31' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_3q22.1' versus 'CN_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0024

Table S112. Gene #36: 'del_3q22.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 11(3Q22.1) MUTATED	24	9	25
DEL PEAK 11(3Q22.1) WILD-TYPE	138	209	172

Figure S112. Get High-res Image Gene #36: 'del_3q22.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_3q29' versus 'CN_CNMF'

P value = 0.0446 (Fisher's exact test), Q value = 0.12

Table S113. Gene #37: 'del_3q29' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 12(3Q29) MUTATED	26	17	22
DEL PEAK 12(3Q29) WILD-TYPE	136	201	175

Figure S113. Get High-res Image Gene #37: 'del_3q29' versus Molecular Subtype #5: 'CN_CNMF'

'del_3q29' versus 'RPPA_CNMF'

P value = 0.0439 (Fisher's exact test), Q value = 0.12

Table S114. Gene #37: 'del_3q29' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	57	44	30	45
DEL PEAK 12(3Q29) MUTATED	2	7	3	5	11
DEL PEAK 12(3Q29) WILD-TYPE	42	50	41	25	34

Figure S114. Get High-res Image Gene #37: 'del_3q29' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_4p16.3' versus 'MRNA_CNMF'

P value = 0.0471 (Fisher's exact test), Q value = 0.13

Table S115. Gene #38: 'del_4p16.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 13(4P16.3) MUTATED	17	21	15	18
DEL PEAK 13(4P16.3) WILD-TYPE	130	75	137	95

Figure S115. Get High-res Image Gene #38: 'del_4p16.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4p16.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00461 (Fisher's exact test), Q value = 0.018

Table S116. Gene #38: 'del_4p16.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 13(4P16.3) MUTATED	19	25	7	20
DEL PEAK 13(4P16.3) WILD-TYPE	129	77	93	138

Figure S116. Get High-res Image Gene #38: 'del_4p16.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4p16.3' versus 'CN_CNMF'

P value = 0.0023 (Fisher's exact test), Q value = 0.01

Table S117. Gene #38: 'del_4p16.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 13(4P16.3) MUTATED	35	20	23
DEL PEAK 13(4P16.3) WILD-TYPE	127	198	174

Figure S117. Get High-res Image Gene #38: 'del_4p16.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_4p16.3' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 8e-04

Table S118. Gene #38: 'del_4p16.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
DEL PEAK 13(4P16.3) MUTATED	2	13	18
DEL PEAK 13(4P16.3) WILD-TYPE	87	95	60

Figure S118. Get High-res Image Gene #38: 'del_4p16.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNA_CNMF'

P value = 0.00549 (Fisher's exact test), Q value = 0.021

Table S119. Gene #39: 'del_4q34.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 14(4Q34.3) MUTATED	16	25	18	22
DEL PEAK 14(4Q34.3) WILD-TYPE	131	71	134	91

Figure S119. Get High-res Image Gene #39: 'del_4q34.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q34.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.0016

Table S120. Gene #39: 'del_4q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 14(4Q34.3) MUTATED	17	31	10	23
DEL PEAK 14(4Q34.3) WILD-TYPE	131	71	90	135

Figure S120. Get High-res Image Gene #39: 'del_4q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S121. Gene #39: 'del_4q34.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 14(4Q34.3) MUTATED	47	20	26
DEL PEAK 14(4Q34.3) WILD-TYPE	115	198	171

Figure S121. Get High-res Image Gene #39: 'del_4q34.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 0.00778 (Fisher's exact test), Q value = 0.028

Table S122. Gene #39: 'del_4q34.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
DEL PEAK 14(4Q34.3) MUTATED	7	18	20
DEL PEAK 14(4Q34.3) WILD-TYPE	82	90	58

Figure S122. Get High-res Image Gene #39: 'del_4q34.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_5q34' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S123. Gene #40: 'del_5q34' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 15(5Q34) MUTATED	8	26	12	17
DEL PEAK 15(5Q34) WILD-TYPE	139	70	140	96

Figure S123. Get High-res Image Gene #40: 'del_5q34' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q34' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S124. Gene #40: 'del_5q34' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 15(5Q34) MUTATED	10	31	11	11
DEL PEAK 15(5Q34) WILD-TYPE	138	71	89	147

Figure S124. Get High-res Image Gene #40: 'del_5q34' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q34' versus 'MIR_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00027

Table S125. Gene #40: 'del_5q34' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
DEL PEAK 15(5Q34) MUTATED	6	36	9	11
DEL PEAK 15(5Q34) WILD-TYPE	150	147	78	109

Figure S125. Get High-res Image Gene #40: 'del_5q34' versus Molecular Subtype #3: 'MIR_CNMF'

'del_5q34' versus 'MIR_CHIERARCHICAL'

P value = 0.00531 (Fisher's exact test), Q value = 0.02

Table S126. Gene #40: 'del_5q34' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 15(5Q34) MUTATED	42	5	15
DEL PEAK 15(5Q34) WILD-TYPE	251	119	114

Figure S126. Get High-res Image Gene #40: 'del_5q34' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_5q34' versus 'CN_CNMF'

P value = 0.00751 (Fisher's exact test), Q value = 0.027

Table S127. Gene #40: 'del_5q34' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 15(5Q34) MUTATED	26	15	29
DEL PEAK 15(5Q34) WILD-TYPE	136	203	168

Figure S127. Get High-res Image Gene #40: 'del_5q34' versus Molecular Subtype #5: 'CN_CNMF'

'del_5q34' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S128. Gene #40: 'del_5q34' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
DEL PEAK 15(5Q34) MUTATED	2	11	22
DEL PEAK 15(5Q34) WILD-TYPE	87	97	56

Figure S128. Get High-res Image Gene #40: 'del_5q34' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_5q34' versus 'RPPA_CHIERARCHICAL'

P value = 0.0485 (Fisher's exact test), Q value = 0.13

Table S129. Gene #40: 'del_5q34' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
DEL PEAK 15(5Q34) MUTATED	8	14	4
DEL PEAK 15(5Q34) WILD-TYPE	82	56	56

Figure S129. Get High-res Image Gene #40: 'del_5q34' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_6q22.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S130. Gene #41: 'del_6q22.31' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 16(6Q22.31) MUTATED	71	48	39
DEL PEAK 16(6Q22.31) WILD-TYPE	91	170	158

Figure S130. Get High-res Image Gene #41: 'del_6q22.31' versus Molecular Subtype #5: 'CN_CNMF'

'del_6q22.31' versus 'RPPA_CNMF'

P value = 0.00616 (Fisher's exact test), Q value = 0.023

Table S131. Gene #41: 'del_6q22.31' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	57	44	30	45
DEL PEAK 16(6Q22.31) MUTATED	16	14	3	9	15
DEL PEAK 16(6Q22.31) WILD-TYPE	28	43	41	21	30

Figure S131. Get High-res Image Gene #41: 'del_6q22.31' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_6q26' versus 'CN_CNMF'

P value = 0.00097 (Fisher's exact test), Q value = 0.0047

Table S132. Gene #42: 'del_6q26' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 17(6Q26) MUTATED	67	66	46
DEL PEAK 17(6Q26) WILD-TYPE	95	152	151

Figure S132. Get High-res Image Gene #42: 'del_6q26' versus Molecular Subtype #5: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

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

Table S133. Gene #42: 'del_6q26' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
DEL PEAK 17(6Q26) MUTATED	32	37	14
DEL PEAK 17(6Q26) WILD-TYPE	57	71	64

Figure S133. Get High-res Image Gene #42: 'del_6q26' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_6q26' versus 'RPPA_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00076

Table S134. Gene #42: 'del_6q26' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	57	44	30	45
DEL PEAK 17(6Q26) MUTATED	20	19	3	11	21
DEL PEAK 17(6Q26) WILD-TYPE	24	38	41	19	24

Figure S134. Get High-res Image Gene #42: 'del_6q26' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0185 (Fisher's exact test), Q value = 0.057

Table S135. Gene #42: 'del_6q26' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	92	25
DEL PEAK 17(6Q26) MUTATED	5	39	12
DEL PEAK 17(6Q26) WILD-TYPE	25	53	13

Figure S135. Get High-res Image Gene #42: 'del_6q26' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S136. Gene #44: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 19(9P21.3) MUTATED	100	61	133	75
DEL PEAK 19(9P21.3) WILD-TYPE	47	35	19	38

Figure S136. Get High-res Image Gene #44: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p21.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S137. Gene #44: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 19(9P21.3) MUTATED	102	61	91	115
DEL PEAK 19(9P21.3) WILD-TYPE	46	41	9	43

Figure S137. Get High-res Image Gene #44: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p21.3' versus 'MIR_CHIERARCHICAL'

P value = 0.0371 (Fisher's exact test), Q value = 0.11

Table S138. Gene #44: 'del_9p21.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 19(9P21.3) MUTATED	199	96	101
DEL PEAK 19(9P21.3) WILD-TYPE	94	28	28

Figure S138. Get High-res Image Gene #44: 'del_9p21.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S139. Gene #44: 'del_9p21.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 19(9P21.3) MUTATED	102	195	124
DEL PEAK 19(9P21.3) WILD-TYPE	60	23	73

Figure S139. Get High-res Image Gene #44: 'del_9p21.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

P value = 0.043 (Fisher's exact test), Q value = 0.12

Table S140. Gene #44: 'del_9p21.3' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	57	44	30	45
DEL PEAK 19(9P21.3) MUTATED	36	46	32	19	41
DEL PEAK 19(9P21.3) WILD-TYPE	8	11	12	11	4

Figure S140. Get High-res Image Gene #44: 'del_9p21.3' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0371 (Fisher's exact test), Q value = 0.11

Table S141. Gene #44: 'del_9p21.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
DEL PEAK 19(9P21.3) MUTATED	72	49	53
DEL PEAK 19(9P21.3) WILD-TYPE	18	21	7

Figure S141. Get High-res Image Gene #44: 'del_9p21.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 0.0274 (Fisher's exact test), Q value = 0.081

Table S142. Gene #44: 'del_9p21.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	67	36
DEL PEAK 19(9P21.3) MUTATED	24	52	27
DEL PEAK 19(9P21.3) WILD-TYPE	20	15	9

Figure S142. Get High-res Image Gene #44: 'del_9p21.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00804 (Fisher's exact test), Q value = 0.029

Table S143. Gene #44: 'del_9p21.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	92	25
DEL PEAK 19(9P21.3) MUTATED	14	71	18
DEL PEAK 19(9P21.3) WILD-TYPE	16	21	7

Figure S143. Get High-res Image Gene #44: 'del_9p21.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00022

Table S144. Gene #46: 'del_10p15.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 21(10P15.3) MUTATED	129	63	134	82
DEL PEAK 21(10P15.3) WILD-TYPE	18	33	18	31

Figure S144. Get High-res Image Gene #46: 'del_10p15.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10p15.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S145. Gene #46: 'del_10p15.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 21(10P15.3) MUTATED	125	59	89	135
DEL PEAK 21(10P15.3) WILD-TYPE	23	43	11	23

Figure S145. Get High-res Image Gene #46: 'del_10p15.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10p15.3' versus 'MIR_CNMF'

P value = 0.0085 (Fisher's exact test), Q value = 0.03

Table S146. Gene #46: 'del_10p15.3' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
DEL PEAK 21(10P15.3) MUTATED	139	137	70	97
DEL PEAK 21(10P15.3) WILD-TYPE	17	46	17	23

Figure S146. Get High-res Image Gene #46: 'del_10p15.3' versus Molecular Subtype #3: 'MIR_CNMF'

'del_10p15.3' versus 'MIR_CHIERARCHICAL'

P value = 0.00345 (Fisher's exact test), Q value = 0.014

Table S147. Gene #46: 'del_10p15.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 21(10P15.3) MUTATED	223	105	115
DEL PEAK 21(10P15.3) WILD-TYPE	70	19	14

Figure S147. Get High-res Image Gene #46: 'del_10p15.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S148. Gene #46: 'del_10p15.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 21(10P15.3) MUTATED	147	206	117
DEL PEAK 21(10P15.3) WILD-TYPE	15	12	80

Figure S148. Get High-res Image Gene #46: 'del_10p15.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S149. Gene #46: 'del_10p15.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
DEL PEAK 21(10P15.3) MUTATED	78	97	45
DEL PEAK 21(10P15.3) WILD-TYPE	11	11	33

Figure S149. Get High-res Image Gene #46: 'del_10p15.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_10p15.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00077 (Fisher's exact test), Q value = 0.0039

Table S150. Gene #46: 'del_10p15.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
DEL PEAK 21(10P15.3) MUTATED	82	49	54
DEL PEAK 21(10P15.3) WILD-TYPE	8	21	6

Figure S150. Get High-res Image Gene #46: 'del_10p15.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 0.0146 (Fisher's exact test), Q value = 0.047

Table S151. Gene #46: 'del_10p15.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	67	36
DEL PEAK 21(10P15.3) MUTATED	33	59	35
DEL PEAK 21(10P15.3) WILD-TYPE	11	8	1

Figure S151. Get High-res Image Gene #46: 'del_10p15.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00076

Table S152. Gene #46: 'del_10p15.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	92	25
DEL PEAK 21(10P15.3) MUTATED	19	83	25
DEL PEAK 21(10P15.3) WILD-TYPE	11	9	0

Figure S152. Get High-res Image Gene #46: 'del_10p15.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_10p13' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S153. Gene #47: 'del_10p13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 22(10P13) MUTATED	131	65	135	79
DEL PEAK 22(10P13) WILD-TYPE	16	31	17	34

Figure S153. Get High-res Image Gene #47: 'del_10p13' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10p13' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S154. Gene #47: 'del_10p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 22(10P13) MUTATED	129	58	89	134
DEL PEAK 22(10P13) WILD-TYPE	19	44	11	24

Figure S154. Get High-res Image Gene #47: 'del_10p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10p13' versus 'MIR_CNMF'

P value = 0.00236 (Fisher's exact test), Q value = 0.01

Table S155. Gene #47: 'del_10p13' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
DEL PEAK 22(10P13) MUTATED	141	138	68	99
DEL PEAK 22(10P13) WILD-TYPE	15	45	19	21

Figure S155. Get High-res Image Gene #47: 'del_10p13' versus Molecular Subtype #3: 'MIR_CNMF'

'del_10p13' versus 'MIR_CHIERARCHICAL'

P value = 0.00124 (Fisher's exact test), Q value = 0.0058

Table S156. Gene #47: 'del_10p13' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 22(10P13) MUTATED	223	108	115
DEL PEAK 22(10P13) WILD-TYPE	70	16	14

Figure S156. Get High-res Image Gene #47: 'del_10p13' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_10p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S157. Gene #47: 'del_10p13' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 22(10P13) MUTATED	147	208	116
DEL PEAK 22(10P13) WILD-TYPE	15	10	81

Figure S157. Get High-res Image Gene #47: 'del_10p13' versus Molecular Subtype #5: 'CN_CNMF'

'del_10p13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S158. Gene #47: 'del_10p13' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
DEL PEAK 22(10P13) MUTATED	78	96	44
DEL PEAK 22(10P13) WILD-TYPE	11	12	34

Figure S158. Get High-res Image Gene #47: 'del_10p13' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_10p13' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00022

Table S159. Gene #47: 'del_10p13' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
DEL PEAK 22(10P13) MUTATED	83	45	55
DEL PEAK 22(10P13) WILD-TYPE	7	25	5

Figure S159. Get High-res Image Gene #47: 'del_10p13' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_10p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00289 (Fisher's exact test), Q value = 0.012

Table S160. Gene #47: 'del_10p13' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	92	25
DEL PEAK 22(10P13) MUTATED	20	83	24
DEL PEAK 22(10P13) WILD-TYPE	10	9	1

Figure S160. Get High-res Image Gene #47: 'del_10p13' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_10p11.23' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S161. Gene #48: 'del_10p11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 23(10P11.23) MUTATED	130	61	142	83
DEL PEAK 23(10P11.23) WILD-TYPE	17	35	10	30

Figure S161. Get High-res Image Gene #48: 'del_10p11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10p11.23' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S162. Gene #48: 'del_10p11.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 23(10P11.23) MUTATED	127	60	93	136
DEL PEAK 23(10P11.23) WILD-TYPE	21	42	7	22

Figure S162. Get High-res Image Gene #48: 'del_10p11.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10p11.23' versus 'MIR_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00055

Table S163. Gene #48: 'del_10p11.23' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
DEL PEAK 23(10P11.23) MUTATED	145	139	67	99
DEL PEAK 23(10P11.23) WILD-TYPE	11	44	20	21

Figure S163. Get High-res Image Gene #48: 'del_10p11.23' versus Molecular Subtype #3: 'MIR_CNMF'

'del_10p11.23' versus 'MIR_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S164. Gene #48: 'del_10p11.23' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 23(10P11.23) MUTATED	223	106	121
DEL PEAK 23(10P11.23) WILD-TYPE	70	18	8

Figure S164. Get High-res Image Gene #48: 'del_10p11.23' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_10p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S165. Gene #48: 'del_10p11.23' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 23(10P11.23) MUTATED	148	212	116
DEL PEAK 23(10P11.23) WILD-TYPE	14	6	81

Figure S165. Get High-res Image Gene #48: 'del_10p11.23' versus Molecular Subtype #5: 'CN_CNMF'

'del_10p11.23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S166. Gene #48: 'del_10p11.23' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
DEL PEAK 23(10P11.23) MUTATED	79	96	45
DEL PEAK 23(10P11.23) WILD-TYPE	10	12	33

Figure S166. Get High-res Image Gene #48: 'del_10p11.23' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_10p11.23' versus 'RPPA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00055

Table S167. Gene #48: 'del_10p11.23' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
DEL PEAK 23(10P11.23) MUTATED	81	49	57
DEL PEAK 23(10P11.23) WILD-TYPE	9	21	3

Figure S167. Get High-res Image Gene #48: 'del_10p11.23' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_10p11.23' versus 'MRNASEQ_CNMF'

P value = 0.0448 (Fisher's exact test), Q value = 0.12

Table S168. Gene #48: 'del_10p11.23' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	67	36
DEL PEAK 23(10P11.23) MUTATED	34	61	34
DEL PEAK 23(10P11.23) WILD-TYPE	10	6	2

Figure S168. Get High-res Image Gene #48: 'del_10p11.23' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_10p11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00087 (Fisher's exact test), Q value = 0.0043

Table S169. Gene #48: 'del_10p11.23' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	92	25
DEL PEAK 23(10P11.23) MUTATED	20	85	24
DEL PEAK 23(10P11.23) WILD-TYPE	10	7	1

Figure S169. Get High-res Image Gene #48: 'del_10p11.23' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S170. Gene #49: 'del_10q23.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 24(10Q23.31) MUTATED	136	75	147	91
DEL PEAK 24(10Q23.31) WILD-TYPE	11	21	5	22

Figure S170. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q23.31' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S171. Gene #49: 'del_10q23.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 24(10Q23.31) MUTATED	132	75	98	144
DEL PEAK 24(10Q23.31) WILD-TYPE	16	27	2	14

Figure S171. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q23.31' versus 'MIR_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.041

Table S172. Gene #49: 'del_10q23.31' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
DEL PEAK 24(10Q23.31) MUTATED	148	158	72	107
DEL PEAK 24(10Q23.31) WILD-TYPE	8	25	15	13

Figure S172. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #3: 'MIR_CNMF'

'del_10q23.31' versus 'MIR_CHIERARCHICAL'

P value = 0.0028 (Fisher's exact test), Q value = 0.012

Table S173. Gene #49: 'del_10q23.31' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 24(10Q23.31) MUTATED	248	115	122
DEL PEAK 24(10Q23.31) WILD-TYPE	45	9	7

Figure S173. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S174. Gene #49: 'del_10q23.31' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 24(10Q23.31) MUTATED	154	216	144
DEL PEAK 24(10Q23.31) WILD-TYPE	8	2	53

Figure S174. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #5: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.0028

Table S175. Gene #49: 'del_10q23.31' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
DEL PEAK 24(10Q23.31) MUTATED	81	103	60
DEL PEAK 24(10Q23.31) WILD-TYPE	8	5	18

Figure S175. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_10q23.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00244 (Fisher's exact test), Q value = 0.01

Table S176. Gene #49: 'del_10q23.31' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
DEL PEAK 24(10Q23.31) MUTATED	85	56	58
DEL PEAK 24(10Q23.31) WILD-TYPE	5	14	2

Figure S176. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0411 (Fisher's exact test), Q value = 0.11

Table S177. Gene #49: 'del_10q23.31' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	92	25
DEL PEAK 24(10Q23.31) MUTATED	24	87	23
DEL PEAK 24(10Q23.31) WILD-TYPE	6	5	2

Figure S177. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S178. Gene #50: 'del_10q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 25(10Q26.3) MUTATED	136	75	148	91
DEL PEAK 25(10Q26.3) WILD-TYPE	11	21	4	22

Figure S178. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q26.3' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00033

Table S179. Gene #50: 'del_10q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 25(10Q26.3) MUTATED	132	77	97	144
DEL PEAK 25(10Q26.3) WILD-TYPE	16	25	3	14

Figure S179. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q26.3' versus 'MIR_CNMF'

P value = 0.0437 (Fisher's exact test), Q value = 0.12

Table S180. Gene #50: 'del_10q26.3' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
DEL PEAK 25(10Q26.3) MUTATED	146	162	71	107
DEL PEAK 25(10Q26.3) WILD-TYPE	10	21	16	13

Figure S180. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #3: 'MIR_CNMF'

'del_10q26.3' versus 'MIR_CHIERARCHICAL'

P value = 0.0014 (Fisher's exact test), Q value = 0.0065

Table S181. Gene #50: 'del_10q26.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 25(10Q26.3) MUTATED	252	109	125
DEL PEAK 25(10Q26.3) WILD-TYPE	41	15	4

Figure S181. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_10q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S182. Gene #50: 'del_10q26.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 25(10Q26.3) MUTATED	151	216	148
DEL PEAK 25(10Q26.3) WILD-TYPE	11	2	49

Figure S182. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_10q26.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S183. Gene #50: 'del_10q26.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
DEL PEAK 25(10Q26.3) MUTATED	79	105	58
DEL PEAK 25(10Q26.3) WILD-TYPE	10	3	20

Figure S183. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_10q26.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0175 (Fisher's exact test), Q value = 0.055

Table S184. Gene #50: 'del_10q26.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
DEL PEAK 25(10Q26.3) MUTATED	83	59	59
DEL PEAK 25(10Q26.3) WILD-TYPE	7	11	1

Figure S184. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0351 (Fisher's exact test), Q value = 0.1

Table S185. Gene #50: 'del_10q26.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	92	25
DEL PEAK 25(10Q26.3) MUTATED	24	85	25
DEL PEAK 25(10Q26.3) WILD-TYPE	6	7	0

Figure S185. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S186. Gene #51: 'del_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 26(11P15.5) MUTATED	32	42	13	31
DEL PEAK 26(11P15.5) WILD-TYPE	115	54	139	82

Figure S186. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11p15.5' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S187. Gene #51: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 26(11P15.5) MUTATED	30	48	9	31
DEL PEAK 26(11P15.5) WILD-TYPE	118	54	91	127

Figure S187. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11p15.5' versus 'MIR_CHIERARCHICAL'

P value = 0.00162 (Fisher's exact test), Q value = 0.0073

Table S188. Gene #51: 'del_11p15.5' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 26(11P15.5) MUTATED	84	23	18
DEL PEAK 26(11P15.5) WILD-TYPE	209	101	111

Figure S188. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S189. Gene #51: 'del_11p15.5' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 26(11P15.5) MUTATED	64	13	52
DEL PEAK 26(11P15.5) WILD-TYPE	98	205	145

Figure S189. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #5: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S190. Gene #51: 'del_11p15.5' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
DEL PEAK 26(11P15.5) MUTATED	13	20	36
DEL PEAK 26(11P15.5) WILD-TYPE	76	88	42

Figure S190. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_11p15.5' versus 'RPPA_CHIERARCHICAL'

P value = 0.0402 (Fisher's exact test), Q value = 0.11

Table S191. Gene #51: 'del_11p15.5' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
DEL PEAK 26(11P15.5) MUTATED	15	21	8
DEL PEAK 26(11P15.5) WILD-TYPE	75	49	52

Figure S191. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 0.00286 (Fisher's exact test), Q value = 0.012

Table S192. Gene #51: 'del_11p15.5' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	67	36
DEL PEAK 26(11P15.5) MUTATED	18	11	4
DEL PEAK 26(11P15.5) WILD-TYPE	26	56	32

Figure S192. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0016 (Fisher's exact test), Q value = 0.0072

Table S193. Gene #51: 'del_11p15.5' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	92	25
DEL PEAK 26(11P15.5) MUTATED	14	17	2
DEL PEAK 26(11P15.5) WILD-TYPE	16	75	23

Figure S193. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_11p11.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S194. Gene #52: 'del_11p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 27(11P11.2) MUTATED	27	35	10	23
DEL PEAK 27(11P11.2) WILD-TYPE	120	61	142	90

Figure S194. Get High-res Image Gene #52: 'del_11p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S195. Gene #52: 'del_11p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 27(11P11.2) MUTATED	27	36	5	27
DEL PEAK 27(11P11.2) WILD-TYPE	121	66	95	131

Figure S195. Get High-res Image Gene #52: 'del_11p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11p11.2' versus 'MIR_CHIERARCHICAL'

P value = 0.0177 (Fisher's exact test), Q value = 0.055

Table S196. Gene #52: 'del_11p11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 27(11P11.2) MUTATED	65	22	14
DEL PEAK 27(11P11.2) WILD-TYPE	228	102	115

Figure S196. Get High-res Image Gene #52: 'del_11p11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_11p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S197. Gene #52: 'del_11p11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 27(11P11.2) MUTATED	58	11	36
DEL PEAK 27(11P11.2) WILD-TYPE	104	207	161

Figure S197. Get High-res Image Gene #52: 'del_11p11.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_11p11.2' versus 'METHLYATION_CNMF'

P value = 0.00262 (Fisher's exact test), Q value = 0.011

Table S198. Gene #52: 'del_11p11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
DEL PEAK 27(11P11.2) MUTATED	15	17	28
DEL PEAK 27(11P11.2) WILD-TYPE	74	91	50

Figure S198. Get High-res Image Gene #52: 'del_11p11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_11q14.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S199. Gene #53: 'del_11q14.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 28(11Q14.1) MUTATED	30	33	12	13
DEL PEAK 28(11Q14.1) WILD-TYPE	117	63	140	100

Figure S199. Get High-res Image Gene #53: 'del_11q14.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11q14.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00057 (Fisher's exact test), Q value = 0.003

Table S200. Gene #53: 'del_11q14.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 28(11Q14.1) MUTATED	30	27	6	25
DEL PEAK 28(11Q14.1) WILD-TYPE	118	75	94	133

Figure S200. Get High-res Image Gene #53: 'del_11q14.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S201. Gene #53: 'del_11q14.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 28(11Q14.1) MUTATED	63	10	23
DEL PEAK 28(11Q14.1) WILD-TYPE	99	208	174

Figure S201. Get High-res Image Gene #53: 'del_11q14.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_12p13.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0142 (Fisher's exact test), Q value = 0.046

Table S202. Gene #54: 'del_12p13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 29(12P13.1) MUTATED	17	20	5	22
DEL PEAK 29(12P13.1) WILD-TYPE	131	82	95	136

Figure S202. Get High-res Image Gene #54: 'del_12p13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_12q12' versus 'MRNA_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.043

Table S203. Gene #55: 'del_12q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 30(12Q12) MUTATED	18	17	11	22
DEL PEAK 30(12Q12) WILD-TYPE	129	79	141	91

Figure S203. Get High-res Image Gene #55: 'del_12q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00077 (Fisher's exact test), Q value = 0.0039

Table S204. Gene #55: 'del_12q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 30(12Q12) MUTATED	19	26	6	17
DEL PEAK 30(12Q12) WILD-TYPE	129	76	94	141

Figure S204. Get High-res Image Gene #55: 'del_12q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_12q12' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 8e-04

Table S205. Gene #55: 'del_12q12' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 30(12Q12) MUTATED	35	15	27
DEL PEAK 30(12Q12) WILD-TYPE	127	203	170

Figure S205. Get High-res Image Gene #55: 'del_12q12' versus Molecular Subtype #5: 'CN_CNMF'

'del_12q12' versus 'RPPA_CNMF'

P value = 0.00925 (Fisher's exact test), Q value = 0.033

Table S206. Gene #55: 'del_12q12' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	57	44	30	45
DEL PEAK 30(12Q12) MUTATED	2	10	7	7	1
DEL PEAK 30(12Q12) WILD-TYPE	42	47	37	23	44

Figure S206. Get High-res Image Gene #55: 'del_12q12' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_12q15' versus 'MRNA_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00096

Table S207. Gene #56: 'del_12q15' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 31(12Q15) MUTATED	21	21	7	20
DEL PEAK 31(12Q15) WILD-TYPE	126	75	145	93

Figure S207. Get High-res Image Gene #56: 'del_12q15' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12q15' versus 'MRNA_CHIERARCHICAL'

P value = 0.00189 (Fisher's exact test), Q value = 0.0083

Table S208. Gene #56: 'del_12q15' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 31(12Q15) MUTATED	20	22	4	23
DEL PEAK 31(12Q15) WILD-TYPE	128	80	96	135

Figure S208. Get High-res Image Gene #56: 'del_12q15' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_12q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S209. Gene #56: 'del_12q15' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 31(12Q15) MUTATED	40	14	25
DEL PEAK 31(12Q15) WILD-TYPE	122	204	172

Figure S209. Get High-res Image Gene #56: 'del_12q15' versus Molecular Subtype #5: 'CN_CNMF'

'del_13q14.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S210. Gene #57: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 32(13Q14.2) MUTATED	81	45	36	53
DEL PEAK 32(13Q14.2) WILD-TYPE	66	51	116	60

Figure S210. Get High-res Image Gene #57: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q14.2' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S211. Gene #57: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 32(13Q14.2) MUTATED	68	50	21	76
DEL PEAK 32(13Q14.2) WILD-TYPE	80	52	79	82

Figure S211. Get High-res Image Gene #57: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S212. Gene #57: 'del_13q14.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 32(13Q14.2) MUTATED	123	37	81
DEL PEAK 32(13Q14.2) WILD-TYPE	39	181	116

Figure S212. Get High-res Image Gene #57: 'del_13q14.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.0049

Table S213. Gene #57: 'del_13q14.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
DEL PEAK 32(13Q14.2) MUTATED	44	34	45
DEL PEAK 32(13Q14.2) WILD-TYPE	45	74	33

Figure S213. Get High-res Image Gene #57: 'del_13q14.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_13q22.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S214. Gene #58: 'del_13q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 33(13Q22.1) MUTATED	81	40	34	50
DEL PEAK 33(13Q22.1) WILD-TYPE	66	56	118	63

Figure S214. Get High-res Image Gene #58: 'del_13q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00096

Table S215. Gene #58: 'del_13q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 33(13Q22.1) MUTATED	68	45	21	71
DEL PEAK 33(13Q22.1) WILD-TYPE	80	57	79	87

Figure S215. Get High-res Image Gene #58: 'del_13q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S216. Gene #58: 'del_13q22.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 33(13Q22.1) MUTATED	123	35	72
DEL PEAK 33(13Q22.1) WILD-TYPE	39	183	125

Figure S216. Get High-res Image Gene #58: 'del_13q22.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_14q13.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S217. Gene #59: 'del_14q13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 34(14Q13.1) MUTATED	54	39	25	43
DEL PEAK 34(14Q13.1) WILD-TYPE	93	57	127	70

Figure S217. Get High-res Image Gene #59: 'del_14q13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q13.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.001

Table S218. Gene #59: 'del_14q13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 34(14Q13.1) MUTATED	49	42	15	55
DEL PEAK 34(14Q13.1) WILD-TYPE	99	60	85	103

Figure S218. Get High-res Image Gene #59: 'del_14q13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S219. Gene #59: 'del_14q13.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 34(14Q13.1) MUTATED	91	29	58
DEL PEAK 34(14Q13.1) WILD-TYPE	71	189	139

Figure S219. Get High-res Image Gene #59: 'del_14q13.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_14q13.1' versus 'METHLYATION_CNMF'

P value = 0.0445 (Fisher's exact test), Q value = 0.12

Table S220. Gene #59: 'del_14q13.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
DEL PEAK 34(14Q13.1) MUTATED	30	25	31
DEL PEAK 34(14Q13.1) WILD-TYPE	59	83	47

Figure S220. Get High-res Image Gene #59: 'del_14q13.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_14q24.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S221. Gene #60: 'del_14q24.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 35(14Q24.2) MUTATED	51	43	22	45
DEL PEAK 35(14Q24.2) WILD-TYPE	96	53	130	68

Figure S221. Get High-res Image Gene #60: 'del_14q24.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q24.2' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S222. Gene #60: 'del_14q24.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 35(14Q24.2) MUTATED	48	46	14	53
DEL PEAK 35(14Q24.2) WILD-TYPE	100	56	86	105

Figure S222. Get High-res Image Gene #60: 'del_14q24.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q24.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S223. Gene #60: 'del_14q24.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 35(14Q24.2) MUTATED	91	21	61
DEL PEAK 35(14Q24.2) WILD-TYPE	71	197	136

Figure S223. Get High-res Image Gene #60: 'del_14q24.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_14q24.2' versus 'METHLYATION_CNMF'

P value = 0.00408 (Fisher's exact test), Q value = 0.016

Table S224. Gene #60: 'del_14q24.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
DEL PEAK 35(14Q24.2) MUTATED	27	25	36
DEL PEAK 35(14Q24.2) WILD-TYPE	62	83	42

Figure S224. Get High-res Image Gene #60: 'del_14q24.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_14q24.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0483 (Fisher's exact test), Q value = 0.13

Table S225. Gene #60: 'del_14q24.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
DEL PEAK 35(14Q24.2) MUTATED	29	24	10
DEL PEAK 35(14Q24.2) WILD-TYPE	61	46	50

Figure S225. Get High-res Image Gene #60: 'del_14q24.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_15q14' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S226. Gene #61: 'del_15q14' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 36(15Q14) MUTATED	36	37	23	42
DEL PEAK 36(15Q14) WILD-TYPE	111	59	129	71

Figure S226. Get High-res Image Gene #61: 'del_15q14' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q14' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S227. Gene #61: 'del_15q14' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 36(15Q14) MUTATED	34	47	12	45
DEL PEAK 36(15Q14) WILD-TYPE	114	55	88	113

Figure S227. Get High-res Image Gene #61: 'del_15q14' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q14' versus 'MIR_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.0049

Table S228. Gene #61: 'del_15q14' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
DEL PEAK 36(15Q14) MUTATED	35	66	22	20
DEL PEAK 36(15Q14) WILD-TYPE	121	117	65	100

Figure S228. Get High-res Image Gene #61: 'del_15q14' versus Molecular Subtype #3: 'MIR_CNMF'

'del_15q14' versus 'MIR_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00038

Table S229. Gene #61: 'del_15q14' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 36(15Q14) MUTATED	95	15	33
DEL PEAK 36(15Q14) WILD-TYPE	198	109	96

Figure S229. Get High-res Image Gene #61: 'del_15q14' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_15q14' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S230. Gene #61: 'del_15q14' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 36(15Q14) MUTATED	72	38	44
DEL PEAK 36(15Q14) WILD-TYPE	90	180	153

Figure S230. Get High-res Image Gene #61: 'del_15q14' versus Molecular Subtype #5: 'CN_CNMF'

'del_15q14' versus 'METHLYATION_CNMF'

P value = 0.00482 (Fisher's exact test), Q value = 0.019

Table S231. Gene #61: 'del_15q14' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
DEL PEAK 36(15Q14) MUTATED	21	25	34
DEL PEAK 36(15Q14) WILD-TYPE	68	83	44

Figure S231. Get High-res Image Gene #61: 'del_15q14' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_15q14' versus 'RPPA_CNMF'

P value = 0.0404 (Fisher's exact test), Q value = 0.11

Table S232. Gene #61: 'del_15q14' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	57	44	30	45
DEL PEAK 36(15Q14) MUTATED	10	13	14	14	7
DEL PEAK 36(15Q14) WILD-TYPE	34	44	30	16	38

Figure S232. Get High-res Image Gene #61: 'del_15q14' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_15q14' versus 'RPPA_CHIERARCHICAL'

P value = 0.0265 (Fisher's exact test), Q value = 0.078

Table S233. Gene #61: 'del_15q14' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
DEL PEAK 36(15Q14) MUTATED	24	25	9
DEL PEAK 36(15Q14) WILD-TYPE	66	45	51

Figure S233. Get High-res Image Gene #61: 'del_15q14' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_15q14' versus 'MRNASEQ_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0041

Table S234. Gene #61: 'del_15q14' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	67	36
DEL PEAK 36(15Q14) MUTATED	23	14	7
DEL PEAK 36(15Q14) WILD-TYPE	21	53	29

Figure S234. Get High-res Image Gene #61: 'del_15q14' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_15q14' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0172 (Fisher's exact test), Q value = 0.054

Table S235. Gene #61: 'del_15q14' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	92	25
DEL PEAK 36(15Q14) MUTATED	15	25	4
DEL PEAK 36(15Q14) WILD-TYPE	15	67	21

Figure S235. Get High-res Image Gene #61: 'del_15q14' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MRNA_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.049

Table S236. Gene #63: 'del_16q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 38(16Q23.1) MUTATED	31	24	16	19
DEL PEAK 38(16Q23.1) WILD-TYPE	116	72	136	94

Figure S236. Get High-res Image Gene #63: 'del_16q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.041

Table S237. Gene #63: 'del_16q23.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 38(16Q23.1) MUTATED	39	27	35
DEL PEAK 38(16Q23.1) WILD-TYPE	123	191	162

Figure S237. Get High-res Image Gene #63: 'del_16q23.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_17p13.2' versus 'MRNA_CNMF'

P value = 0.00287 (Fisher's exact test), Q value = 0.012

Table S238. Gene #64: 'del_17p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 39(17P13.2) MUTATED	28	23	13	13
DEL PEAK 39(17P13.2) WILD-TYPE	119	73	139	100

Figure S238. Get High-res Image Gene #64: 'del_17p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p13.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0244 (Fisher's exact test), Q value = 0.073

Table S239. Gene #64: 'del_17p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 39(17P13.2) MUTATED	28	22	11	16
DEL PEAK 39(17P13.2) WILD-TYPE	120	80	89	142

Figure S239. Get High-res Image Gene #64: 'del_17p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S240. Gene #64: 'del_17p13.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 39(17P13.2) MUTATED	47	9	32
DEL PEAK 39(17P13.2) WILD-TYPE	115	209	165

Figure S240. Get High-res Image Gene #64: 'del_17p13.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_17p13.1' versus 'MRNA_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0013

Table S241. Gene #65: 'del_17p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 40(17P13.1) MUTATED	32	27	13	16
DEL PEAK 40(17P13.1) WILD-TYPE	115	69	139	97

Figure S241. Get High-res Image Gene #65: 'del_17p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p13.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00171 (Fisher's exact test), Q value = 0.0076

Table S242. Gene #65: 'del_17p13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 40(17P13.1) MUTATED	32	27	9	20
DEL PEAK 40(17P13.1) WILD-TYPE	116	75	91	138

Figure S242. Get High-res Image Gene #65: 'del_17p13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S243. Gene #65: 'del_17p13.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 40(17P13.1) MUTATED	55	8	35
DEL PEAK 40(17P13.1) WILD-TYPE	107	210	162

Figure S243. Get High-res Image Gene #65: 'del_17p13.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_17q11.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S244. Gene #66: 'del_17q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 41(17Q11.2) MUTATED	35	9	12	5
DEL PEAK 41(17Q11.2) WILD-TYPE	112	87	140	108

Figure S244. Get High-res Image Gene #66: 'del_17q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S245. Gene #66: 'del_17q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 41(17Q11.2) MUTATED	35	7	9	10
DEL PEAK 41(17Q11.2) WILD-TYPE	113	95	91	148

Figure S245. Get High-res Image Gene #66: 'del_17q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17q11.2' versus 'MIR_CNMF'

P value = 0.00258 (Fisher's exact test), Q value = 0.011

Table S246. Gene #66: 'del_17q11.2' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
DEL PEAK 41(17Q11.2) MUTATED	29	16	4	19
DEL PEAK 41(17Q11.2) WILD-TYPE	127	167	83	101

Figure S246. Get High-res Image Gene #66: 'del_17q11.2' versus Molecular Subtype #3: 'MIR_CNMF'

'del_17q11.2' versus 'MIR_CHIERARCHICAL'

P value = 0.0115 (Fisher's exact test), Q value = 0.039

Table S247. Gene #66: 'del_17q11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 41(17Q11.2) MUTATED	26	24	18
DEL PEAK 41(17Q11.2) WILD-TYPE	267	100	111

Figure S247. Get High-res Image Gene #66: 'del_17q11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_17q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S248. Gene #66: 'del_17q11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 41(17Q11.2) MUTATED	33	9	30
DEL PEAK 41(17Q11.2) WILD-TYPE	129	209	167

Figure S248. Get High-res Image Gene #66: 'del_17q11.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_17q11.2' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0014

Table S249. Gene #66: 'del_17q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
DEL PEAK 41(17Q11.2) MUTATED	18	4	4
DEL PEAK 41(17Q11.2) WILD-TYPE	71	104	74

Figure S249. Get High-res Image Gene #66: 'del_17q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_17q11.2' versus 'RPPA_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0043

Table S250. Gene #66: 'del_17q11.2' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	57	44	30	45
DEL PEAK 41(17Q11.2) MUTATED	12	9	0	4	3
DEL PEAK 41(17Q11.2) WILD-TYPE	32	48	44	26	42

Figure S250. Get High-res Image Gene #66: 'del_17q11.2' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_17q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.036

Table S251. Gene #66: 'del_17q11.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
DEL PEAK 41(17Q11.2) MUTATED	19	5	4
DEL PEAK 41(17Q11.2) WILD-TYPE	71	65	56

Figure S251. Get High-res Image Gene #66: 'del_17q11.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_18q22.3' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00033

Table S252. Gene #67: 'del_18q22.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 42(18Q22.3) MUTATED	36	15	31
DEL PEAK 42(18Q22.3) WILD-TYPE	126	203	166

Figure S252. Get High-res Image Gene #67: 'del_18q22.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_18q22.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0206 (Fisher's exact test), Q value = 0.063

Table S253. Gene #67: 'del_18q22.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
DEL PEAK 42(18Q22.3) MUTATED	15	17	4
DEL PEAK 42(18Q22.3) WILD-TYPE	75	53	56

Figure S253. Get High-res Image Gene #67: 'del_18q22.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_19q13.41' versus 'MRNA_CNMF'

P value = 0.00466 (Fisher's exact test), Q value = 0.018

Table S254. Gene #68: 'del_19q13.41' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 43(19Q13.41) MUTATED	21	23	17	29
DEL PEAK 43(19Q13.41) WILD-TYPE	126	73	135	84

Figure S254. Get High-res Image Gene #68: 'del_19q13.41' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19q13.41' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00027

Table S255. Gene #68: 'del_19q13.41' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 43(19Q13.41) MUTATED	23	34	8	25
DEL PEAK 43(19Q13.41) WILD-TYPE	125	68	92	133

Figure S255. Get High-res Image Gene #68: 'del_19q13.41' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19q13.41' versus 'MIR_CHIERARCHICAL'

P value = 0.0429 (Fisher's exact test), Q value = 0.12

Table S256. Gene #68: 'del_19q13.41' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 43(19Q13.41) MUTATED	62	19	15
DEL PEAK 43(19Q13.41) WILD-TYPE	231	105	114

Figure S256. Get High-res Image Gene #68: 'del_19q13.41' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_19q13.41' versus 'CN_CNMF'

P value = 0.00115 (Fisher's exact test), Q value = 0.0054

Table S257. Gene #68: 'del_19q13.41' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 43(19Q13.41) MUTATED	32	22	45
DEL PEAK 43(19Q13.41) WILD-TYPE	130	196	152

Figure S257. Get High-res Image Gene #68: 'del_19q13.41' versus Molecular Subtype #5: 'CN_CNMF'

'del_19q13.41' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S258. Gene #68: 'del_19q13.41' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
DEL PEAK 43(19Q13.41) MUTATED	12	8	29
DEL PEAK 43(19Q13.41) WILD-TYPE	77	100	49

Figure S258. Get High-res Image Gene #68: 'del_19q13.41' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_19q13.41' versus 'MRNASEQ_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.1

Table S259. Gene #68: 'del_19q13.41' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	67	36
DEL PEAK 43(19Q13.41) MUTATED	9	6	10
DEL PEAK 43(19Q13.41) WILD-TYPE	35	61	26

Figure S259. Get High-res Image Gene #68: 'del_19q13.41' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_21q21.1' versus 'MRNA_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.036

Table S260. Gene #69: 'del_21q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 44(21Q21.1) MUTATED	5	14	15	13
DEL PEAK 44(21Q21.1) WILD-TYPE	142	82	137	100

Figure S260. Get High-res Image Gene #69: 'del_21q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_21q21.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00089 (Fisher's exact test), Q value = 0.0044

Table S261. Gene #69: 'del_21q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 44(21Q21.1) MUTATED	5	19	8	15
DEL PEAK 44(21Q21.1) WILD-TYPE	143	83	92	143

Figure S261. Get High-res Image Gene #69: 'del_21q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_21q21.1' versus 'MIR_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.051

Table S262. Gene #69: 'del_21q21.1' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
DEL PEAK 44(21Q21.1) MUTATED	8	24	13	8
DEL PEAK 44(21Q21.1) WILD-TYPE	148	159	74	112

Figure S262. Get High-res Image Gene #69: 'del_21q21.1' versus Molecular Subtype #3: 'MIR_CNMF'

'del_21q21.1' versus 'METHLYATION_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.0031

Table S263. Gene #69: 'del_21q21.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
DEL PEAK 44(21Q21.1) MUTATED	1	12	13
DEL PEAK 44(21Q21.1) WILD-TYPE	88	96	65

Figure S263. Get High-res Image Gene #69: 'del_21q21.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_21q21.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.037

Table S264. Gene #69: 'del_21q21.1' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
DEL PEAK 44(21Q21.1) MUTATED	2	9	8
DEL PEAK 44(21Q21.1) WILD-TYPE	88	61	52

Figure S264. Get High-res Image Gene #69: 'del_21q21.1' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_22q13.32' versus 'MIR_CNMF'

P value = 0.0392 (Fisher's exact test), Q value = 0.11

Table S265. Gene #70: 'del_22q13.32' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
DEL PEAK 45(22Q13.32) MUTATED	59	82	24	41
DEL PEAK 45(22Q13.32) WILD-TYPE	97	101	63	79

Figure S265. Get High-res Image Gene #70: 'del_22q13.32' versus Molecular Subtype #3: 'MIR_CNMF'

'del_22q13.32' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S266. Gene #70: 'del_22q13.32' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 45(22Q13.32) MUTATED	85	63	64
DEL PEAK 45(22Q13.32) WILD-TYPE	77	155	133

Figure S266. Get High-res Image Gene #70: 'del_22q13.32' versus Molecular Subtype #5: 'CN_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 0.0492 (Fisher's exact test), Q value = 0.13

Table S267. Gene #70: 'del_22q13.32' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	67	36
DEL PEAK 45(22Q13.32) MUTATED	16	26	22
DEL PEAK 45(22Q13.32) WILD-TYPE	28	41	14

Figure S267. Get High-res Image Gene #70: 'del_22q13.32' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_xp22.2' versus 'MRNA_CNMF'

P value = 0.0059 (Fisher's exact test), Q value = 0.022

Table S268. Gene #71: 'del_xp22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 46(XP22.2) MUTATED	24	32	25	27
DEL PEAK 46(XP22.2) WILD-TYPE	123	64	127	86

Figure S268. Get High-res Image Gene #71: 'del_xp22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_xp22.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0015 (Fisher's exact test), Q value = 0.0069

Table S269. Gene #71: 'del_xp22.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 46(XP22.2) MUTATED	22	36	18	32
DEL PEAK 46(XP22.2) WILD-TYPE	126	66	82	126

Figure S269. Get High-res Image Gene #71: 'del_xp22.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_xp22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S270. Gene #71: 'del_xp22.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	218	197
DEL PEAK 46(XP22.2) MUTATED	59	26	33
DEL PEAK 46(XP22.2) WILD-TYPE	103	192	164

Figure S270. Get High-res Image Gene #71: 'del_xp22.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_xp22.2' versus 'METHLYATION_CNMF'

P value = 0.00155 (Fisher's exact test), Q value = 0.0071

Table S271. Gene #71: 'del_xp22.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	108	78
DEL PEAK 46(XP22.2) MUTATED	12	19	28
DEL PEAK 46(XP22.2) WILD-TYPE	77	89	50

Figure S271. Get High-res Image Gene #71: 'del_xp22.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/GBM-TP/20146435/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/GBM-TP/20125497/GBM-TP.transferedmergedcluster.txt
Number of patients = 577
Number of significantly focal cnvs = 71
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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