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 68 focal events and 10 molecular subtypes across 577 patients, 259 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', 'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.
amp_3q26.33 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', and 'METHLYATION_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_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_12q14.1 cnv correlated to 'MIR_CNMF' and 'CN_CNMF'.
amp_13q34 cnv correlated to 'RPPA_CNMF'.
amp_14q32.33 cnv correlated to 'MIR_CNMF' and 'MRNASEQ_CNMF'.
amp_17p13.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_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_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', and 'METHLYATION_CNMF'.
del_1p36.23 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', and 'MRNASEQ_CNMF'.
del_1p22.1 cnv correlated to 'MIR_CHIERARCHICAL' and 'METHLYATION_CNMF'.
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_CNMF' and 'MRNA_CHIERARCHICAL'.
del_3p21.1 cnv correlated to 'CN_CNMF'.
del_3q13.31 cnv correlated to 'CN_CNMF'.
del_3q29 cnv correlated to 'RPPA_CNMF'.
del_4p16.3 cnv correlated to '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', 'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.
del_6q22.1 cnv correlated to 'RPPA_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_6q26 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_9p21.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_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', and 'MRNASEQ_CHIERARCHICAL'.
del_10q11.23 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 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_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', 'CN_CNMF', and 'MRNASEQ_CNMF'.
del_12p13.1 cnv correlated to 'MRNA_CHIERARCHICAL' and 'METHLYATION_CNMF'.
del_12q12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_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', 'CN_CNMF', and 'METHLYATION_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_17p13.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'METHLYATION_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 'CN_CNMF' and 'MRNASEQ_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 68 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, 259 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 (9.71e-05)	1e-05 (9.71e-05)	1e-05 (9.71e-05)	1e-05 (9.71e-05)	1e-05 (9.71e-05)	1e-05 (9.71e-05)	0.00085 (0.00459)	2e-05 (0.00016)	1e-05 (9.71e-05)	1e-05 (9.71e-05)
amp 7q11 21	464 (80%)	113	1e-05 (9.71e-05)	1e-05 (9.71e-05)	1e-05 (9.71e-05)	2e-05 (0.00016)	1e-05 (9.71e-05)	1e-05 (9.71e-05)	0.0257 (0.0788)	0.00556 (0.0221)	0.0049 (0.0201)	3e-05 (0.000227)
del 15q14	154 (27%)	423	1e-05 (9.71e-05)	1e-05 (9.71e-05)	0.00183 (0.0087)	7e-05 (0.000506)	1e-05 (9.71e-05)	0.00632 (0.0241)	0.041 (0.111)	0.0265 (0.0805)	0.00129 (0.0066)	0.0173 (0.0575)
del 9p21 3	421 (73%)	156	1e-05 (9.71e-05)	1e-05 (9.71e-05)	0.602 (0.73)	0.0357 (0.102)	1e-05 (9.71e-05)	0.00045 (0.00262)	0.042 (0.113)	0.0371 (0.106)	0.0378 (0.106)	0.00792 (0.0293)
del 10p15 3	470 (81%)	107	1e-05 (9.71e-05)	1e-05 (9.71e-05)	0.0223 (0.0692)	0.00362 (0.0157)	1e-05 (9.71e-05)	1e-05 (9.71e-05)	0.598 (0.729)	0.0007 (0.0039)	0.0212 (0.0664)	0.00019 (0.00119)
amp 7q31 2	473 (82%)	104	0.00199 (0.00933)	2e-05 (0.00016)	0.0191 (0.0611)	0.00571 (0.0224)	2e-05 (0.00016)	0.0405 (0.111)	0.352 (0.515)	0.00519 (0.021)	0.482 (0.625)	0.0099 (0.0361)
del 10p13	471 (82%)	106	1e-05 (9.71e-05)	1e-05 (9.71e-05)	0.00517 (0.021)	0.00118 (0.00613)	1e-05 (9.71e-05)	1e-05 (9.71e-05)	0.113 (0.227)	1e-05 (9.71e-05)	0.122 (0.24)	0.00267 (0.0122)
del 10p11 23	476 (82%)	101	1e-05 (9.71e-05)	1e-05 (9.71e-05)	0.00069 (0.00388)	3e-05 (0.000227)	1e-05 (9.71e-05)	1e-05 (9.71e-05)	0.192 (0.339)	0.00011 (0.000733)	0.0516 (0.134)	0.0011 (0.00575)
del 10q11 23	489 (85%)	88	1e-05 (9.71e-05)	1e-05 (9.71e-05)	0.00093 (0.00498)	2e-05 (0.00016)	1e-05 (9.71e-05)	1e-05 (9.71e-05)	0.0787 (0.182)	1e-05 (9.71e-05)	0.105 (0.218)	0.00376 (0.0162)
del 10q23 31	514 (89%)	63	3e-05 (0.000227)	1e-05 (9.71e-05)	0.0342 (0.0993)	0.00322 (0.0142)	1e-05 (9.71e-05)	0.00051 (0.00291)	0.186 (0.332)	0.00208 (0.00969)	0.366 (0.525)	0.041 (0.111)
del 11p15 5	132 (23%)	445	1e-05 (9.71e-05)	1e-05 (9.71e-05)	0.201 (0.352)	0.00164 (0.00797)	1e-05 (9.71e-05)	2e-05 (0.00016)	0.307 (0.466)	0.03 (0.0883)	0.006 (0.0233)	0.00228 (0.0105)
del 17q11 2	72 (12%)	505	1e-05 (9.71e-05)	2e-05 (0.00016)	0.00396 (0.0169)	0.0109 (0.0383)	0.00037 (0.00221)	7e-05 (0.000506)	0.00074 (0.00406)	0.0107 (0.038)	0.541 (0.683)	0.562 (0.699)
amp 7q21 2	480 (83%)	97	0.0001 (0.000687)	1e-05 (9.71e-05)	0.0588 (0.147)	0.0001 (0.000687)	1e-05 (9.71e-05)	0.00015 (0.000953)	0.0861 (0.191)	0.00328 (0.0144)	0.081 (0.184)	0.00238 (0.0109)
amp 8q24 21	69 (12%)	508	1e-05 (9.71e-05)	1e-05 (9.71e-05)	0.0206 (0.065)	0.237 (0.391)	0.0121 (0.0417)	0.00139 (0.00695)	0.0347 (0.101)	0.0242 (0.0745)	0.0607 (0.15)	0.258 (0.412)
amp 19p13 3	246 (43%)	331	1e-05 (9.71e-05)	3e-05 (0.000227)	0.0399 (0.11)	0.00277 (0.0126)	1e-05 (9.71e-05)	1e-05 (9.71e-05)	0.222 (0.375)	0.00011 (0.000733)	0.724 (0.825)	0.971 (0.991)
del 10q26 3	515 (89%)	62	1e-05 (9.71e-05)	2e-05 (0.00016)	0.0919 (0.198)	0.00147 (0.00729)	1e-05 (9.71e-05)	0.00015 (0.000953)	0.601 (0.729)	0.0168 (0.056)	0.29 (0.445)	0.0349 (0.101)
amp 19q12	216 (37%)	361	1e-05 (9.71e-05)	1e-05 (9.71e-05)	0.379 (0.538)	0.0043 (0.018)	1e-05 (9.71e-05)	1e-05 (9.71e-05)	0.485 (0.629)	0.00139 (0.00695)	0.0547 (0.141)	0.17 (0.312)
del 5q34	70 (12%)	507	2e-05 (0.00016)	1e-05 (9.71e-05)	6e-05 (0.000443)	0.00524 (0.0211)	0.125 (0.247)	0.00014 (0.000907)	0.622 (0.747)	0.0491 (0.129)	0.287 (0.443)	0.131 (0.255)
del 19q13 41	100 (17%)	477	0.0049 (0.0201)	8e-05 (0.000567)	0.0608 (0.15)	0.038 (0.106)	0.00039 (0.00229)	2e-05 (0.00016)	0.203 (0.354)	0.139 (0.267)	0.0269 (0.0811)	0.0941 (0.201)
amp 17p13 2	51 (9%)	526	0.00183 (0.0087)	0.0138 (0.0466)	0.0397 (0.11)	0.111 (0.226)	0.0668 (0.161)	0.0441 (0.117)	0.00612 (0.0236)	0.489 (0.631)	0.44 (0.586)	0.569 (0.705)
del 11p11 2	105 (18%)	472	1e-05 (9.71e-05)	1e-05 (9.71e-05)	0.599 (0.729)	0.0177 (0.058)	1e-05 (9.71e-05)	0.00148 (0.00729)	0.933 (0.97)	0.134 (0.262)	0.0566 (0.143)	0.0891 (0.195)
del 12q12	77 (13%)	500	0.0135 (0.0458)	0.00079 (0.0043)	0.423 (0.577)	0.0831 (0.185)	0.00011 (0.000733)	0.0228 (0.0705)	0.00966 (0.0355)	0.168 (0.309)	0.671 (0.787)	0.666 (0.783)
del 14q24 2	173 (30%)	404	1e-05 (9.71e-05)	2e-05 (0.00016)	0.0828 (0.185)	0.156 (0.29)	1e-05 (9.71e-05)	0.0111 (0.0389)	0.268 (0.426)	0.0492 (0.129)	0.0967 (0.205)	0.941 (0.974)
del 21q21 1	56 (10%)	521	0.00739 (0.0276)	0.00099 (0.00526)	0.0314 (0.0919)	0.21 (0.362)	0.514 (0.661)	0.0128 (0.0438)	0.258 (0.412)	0.0104 (0.0375)	1 (1.00)	1 (1.00)
amp 4q12	108 (19%)	469	0.00017 (0.00107)	0.00332 (0.0145)	0.588 (0.72)	0.472 (0.617)	0.022 (0.0685)	0.0117 (0.0402)	0.0675 (0.161)	0.435 (0.582)	0.149 (0.279)	0.416 (0.572)
amp 21q21 1	70 (12%)	507	0.0114 (0.0394)	0.0591 (0.147)	0.0262 (0.08)	0.00724 (0.0272)	0.0743 (0.174)	0.0425 (0.114)	0.0935 (0.201)	0.713 (0.819)	0.103 (0.216)	0.409 (0.568)
del 4q34 3	93 (16%)	484	0.00757 (0.0281)	0.0003 (0.00184)	0.059 (0.147)	0.0974 (0.206)	0.00071 (0.00393)	0.0111 (0.0389)	0.209 (0.361)	0.0802 (0.183)	0.0945 (0.201)	0.137 (0.264)
del 11q14 1	96 (17%)	481	1e-05 (9.71e-05)	0.0006 (0.0034)	0.842 (0.902)	0.137 (0.264)	1e-05 (9.71e-05)	0.182 (0.327)	0.376 (0.536)	0.426 (0.579)	0.0394 (0.109)	0.16 (0.295)
del 13q14 2	241 (42%)	336	1e-05 (9.71e-05)	2e-05 (0.00016)	0.178 (0.322)	0.145 (0.276)	1e-05 (9.71e-05)	0.00012 (0.000792)	0.83 (0.892)	0.111 (0.226)	0.0926 (0.199)	0.0674 (0.161)
del 13q22 1	230 (40%)	347	2e-05 (0.00016)	0.0001 (0.000687)	0.389 (0.546)	0.34 (0.503)	1e-05 (9.71e-05)	3e-05 (0.000227)	0.836 (0.897)	0.247 (0.405)	0.517 (0.663)	0.282 (0.438)
del 14q13 1	178 (31%)	399	2e-05 (0.00016)	0.00033 (0.002)	0.711 (0.819)	0.663 (0.783)	1e-05 (9.71e-05)	0.0376 (0.106)	0.414 (0.572)	0.453 (0.599)	0.442 (0.588)	0.943 (0.974)
del 17p13 1	98 (17%)	479	0.00125 (0.00644)	0.00162 (0.00793)	0.649 (0.77)	0.896 (0.942)	1e-05 (9.71e-05)	0.0428 (0.115)	0.335 (0.499)	0.096 (0.204)	0.745 (0.841)	0.665 (0.783)
amp 1p36 21	92 (16%)	485	0.324 (0.485)	0.429 (0.58)	0.359 (0.52)	0.115 (0.228)	0.00013 (0.00085)	0.783 (0.863)	0.0825 (0.185)	0.171 (0.312)	0.00302 (0.0135)	0.0193 (0.0612)
amp 2p24 3	49 (8%)	528	0.0656 (0.16)	0.0168 (0.056)	0.586 (0.719)	0.98 (0.994)	0.201 (0.352)	0.0186 (0.0609)	0.282 (0.438)	0.0333 (0.0971)	1 (1.00)	0.626 (0.748)
amp 3q26 33	111 (19%)	466	0.00321 (0.0142)	0.211 (0.362)	0.316 (0.477)	0.0555 (0.141)	0.00039 (0.00229)	0.0376 (0.106)	0.104 (0.217)	0.925 (0.965)	0.25 (0.406)	0.698 (0.811)
del 1p36 23	135 (23%)	442	0.02 (0.0633)	0.227 (0.38)	0.776 (0.861)	0.624 (0.747)	0.0352 (0.101)	0.569 (0.705)	0.742 (0.84)	0.225 (0.378)	0.0056 (0.0221)	0.074 (0.174)
del 2q22 1	47 (8%)	530	0.00035 (0.00211)	0.0287 (0.0849)	0.609 (0.734)	0.547 (0.686)	0.00174 (0.00839)	0.156 (0.29)	0.0911 (0.198)	0.811 (0.879)	0.218 (0.372)	0.431 (0.58)
del 4p16 3	78 (14%)	499	0.055 (0.141)	0.00454 (0.0189)	0.106 (0.219)	0.251 (0.406)	0.0106 (0.0378)	0.00048 (0.00277)	0.753 (0.846)	0.859 (0.912)	0.797 (0.872)	0.946 (0.975)
del 6q26	179 (31%)	398	0.785 (0.863)	0.758 (0.848)	0.384 (0.542)	0.548 (0.686)	1 (1.00)	0.00138 (0.00695)	8e-05 (0.000567)	0.0553 (0.141)	0.742 (0.84)	0.0189 (0.0611)
del 12q15	79 (14%)	498	0.00106 (0.00559)	0.00193 (0.00911)	0.267 (0.425)	0.423 (0.577)	4e-05 (0.000299)	0.0505 (0.132)	0.0652 (0.16)	0.571 (0.706)	0.536 (0.679)	0.397 (0.555)
amp 1q44	99 (17%)	478	0.129 (0.253)	0.623 (0.747)	0.356 (0.519)	0.307 (0.466)	2e-05 (0.00016)	0.234 (0.387)	0.0191 (0.0611)	0.217 (0.372)	0.961 (0.984)	0.552 (0.69)
amp 12q14 1	134 (23%)	443	0.113 (0.227)	0.147 (0.277)	0.00994 (0.0361)	0.0885 (0.195)	0.00287 (0.0129)	0.597 (0.729)	0.276 (0.435)	0.146 (0.276)	0.062 (0.153)	0.139 (0.267)
amp 14q32 33	36 (6%)	541	0.0751 (0.175)	0.657 (0.779)	0.0386 (0.108)	0.92 (0.961)	0.0912 (0.198)	0.347 (0.51)	0.174 (0.316)	0.0527 (0.137)	0.0282 (0.0838)	0.0664 (0.161)
amp 17q25 1	84 (15%)	493	0.0279 (0.0834)	0.255 (0.409)	0.159 (0.294)	0.731 (0.831)	0.00527 (0.0211)	0.0825 (0.185)	0.0696 (0.165)	0.254 (0.409)	0.905 (0.947)	0.692 (0.805)
del 1p22 1	48 (8%)	529	0.976 (0.992)	0.553 (0.69)	0.957 (0.982)	0.00486 (0.0201)	0.0673 (0.161)	0.0272 (0.0814)	0.365 (0.525)	0.606 (0.732)	0.642 (0.765)	0.318 (0.478)
del 2q37 1	55 (10%)	522	0.0176 (0.058)	0.00619 (0.0238)	0.548 (0.686)	0.823 (0.888)	0.0796 (0.183)	0.114 (0.228)	0.136 (0.263)	0.529 (0.673)	0.218 (0.372)	0.0535 (0.138)
del 6q22 1	155 (27%)	422	0.975 (0.992)	0.944 (0.974)	0.113 (0.227)	0.604 (0.73)	0.277 (0.435)	0.401 (0.56)	0.0269 (0.0811)	0.359 (0.52)	0.525 (0.673)	0.0472 (0.125)
del 12p13 1	72 (12%)	505	0.0565 (0.143)	0.0136 (0.046)	0.458 (0.603)	0.234 (0.387)	0.22 (0.375)	0.00684 (0.0258)	0.415 (0.572)	0.19 (0.338)	0.944 (0.974)	0.931 (0.97)
del 16q23 1	101 (18%)	476	0.0106 (0.0378)	0.489 (0.631)	0.872 (0.921)	0.541 (0.683)	0.0103 (0.0373)	0.809 (0.879)	0.221 (0.375)	0.114 (0.228)	0.848 (0.905)	0.785 (0.863)
del 18q22 3	82 (14%)	495	0.059 (0.147)	0.0864 (0.191)	0.402 (0.56)	0.388 (0.546)	0.00398 (0.0169)	0.284 (0.44)	0.292 (0.447)	0.0191 (0.0611)	0.365 (0.525)	0.271 (0.43)
del 22q13 32	212 (37%)	365	0.819 (0.886)	0.972 (0.991)	0.0831 (0.185)	0.417 (0.573)	1e-05 (9.71e-05)	0.48 (0.625)	0.294 (0.449)	0.367 (0.526)	0.019 (0.0611)	0.0848 (0.188)
amp 1q32 1	160 (28%)	417	0.783 (0.863)	0.0621 (0.153)	0.289 (0.445)	0.147 (0.277)	0.00576 (0.0225)	0.0977 (0.206)	0.107 (0.219)	0.339 (0.503)	0.469 (0.615)	0.089 (0.195)
amp 13q34	32 (6%)	545	0.234 (0.387)	0.203 (0.354)	0.0683 (0.162)	0.48 (0.625)	0.0658 (0.16)	0.528 (0.673)	0.041 (0.111)	0.104 (0.217)	0.769 (0.856)	0.804 (0.875)
del 1q42 11	51 (9%)	526	0.233 (0.387)	0.824 (0.888)	0.457 (0.603)	0.286 (0.441)	0.195 (0.343)	0.775 (0.861)	0.903 (0.946)	0.00675 (0.0256)	0.429 (0.58)	0.192 (0.339)
del 3p21 1	54 (9%)	523	0.249 (0.405)	0.135 (0.262)	0.669 (0.786)	0.393 (0.551)	0.00423 (0.0179)	0.38 (0.538)	0.0801 (0.183)	0.715 (0.82)	0.463 (0.609)	0.106 (0.219)
del 3q13 31	56 (10%)	521	0.421 (0.577)	0.343 (0.507)	0.952 (0.979)	0.514 (0.661)	0.00024 (0.00148)	0.206 (0.357)	0.171 (0.312)	0.102 (0.215)	1 (1.00)	0.18 (0.324)
del 3q29	65 (11%)	512	0.0791 (0.182)	0.186 (0.331)	0.699 (0.811)	0.875 (0.923)	0.628 (0.749)	0.253 (0.409)	0.0439 (0.117)	0.115 (0.229)	0.953 (0.979)	0.793 (0.868)
amp 4p16 3	48 (8%)	529	0.223 (0.376)	0.724 (0.825)	0.708 (0.818)	0.0823 (0.185)	0.962 (0.984)	0.758 (0.848)	0.415 (0.572)	0.753 (0.846)	1 (1.00)	1 (1.00)
amp 11p13	31 (5%)	546	0.811 (0.879)	0.35 (0.512)	0.533 (0.676)	0.248 (0.405)	0.422 (0.577)	0.683 (0.798)	0.194 (0.341)	1 (1.00)	1 (1.00)	0.888 (0.934)
amp 12p13 32	84 (15%)	493	0.764 (0.853)	0.382 (0.541)	0.444 (0.589)	0.432 (0.58)	0.107 (0.219)	0.766 (0.854)	0.529 (0.673)	0.276 (0.435)	0.357 (0.52)	0.546 (0.686)
amp 12q15	93 (16%)	484	0.675 (0.79)	0.315 (0.476)	0.477 (0.622)	0.279 (0.436)	0.0776 (0.18)	0.855 (0.911)	0.578 (0.712)	0.325 (0.486)	0.377 (0.536)	0.9 (0.945)
amp 13q34	30 (5%)	547	0.278 (0.435)	0.209 (0.361)	0.305 (0.464)	0.788 (0.865)	0.0728 (0.172)	0.869 (0.921)	0.147 (0.277)	0.186 (0.331)	0.747 (0.843)	0.792 (0.868)
del 1p36 32	100 (17%)	477	0.8 (0.873)	0.713 (0.819)	0.581 (0.714)	0.173 (0.316)	0.375 (0.536)	0.282 (0.438)	0.623 (0.747)	0.141 (0.268)	0.181 (0.325)	0.577 (0.712)
del 1p32 3	61 (11%)	516	0.36 (0.521)	0.366 (0.525)	0.599 (0.729)	0.158 (0.293)	0.414 (0.572)	0.716 (0.82)	0.857 (0.912)	0.754 (0.846)	0.734 (0.833)	0.106 (0.219)
del 1q44	35 (6%)	542	0.846 (0.905)	0.472 (0.617)	0.711 (0.819)	0.246 (0.405)	0.56 (0.698)	0.691 (0.805)	0.801 (0.873)	0.347 (0.51)	0.529 (0.673)	0.322 (0.484)
del 8p23 2	66 (11%)	511	0.254 (0.409)	0.249 (0.405)	0.178 (0.322)	0.275 (0.434)	0.225 (0.378)	0.779 (0.863)	0.996 (1.00)	0.872 (0.921)	0.724 (0.825)	0.436 (0.583)
del 9q34 2	79 (14%)	498	0.128 (0.251)	0.108 (0.22)	0.443 (0.588)	0.227 (0.38)	0.827 (0.89)	0.7 (0.811)	0.0918 (0.198)	0.664 (0.783)	0.435 (0.582)	0.305 (0.464)
del 16p12 2	92 (16%)	485	0.43 (0.58)	0.229 (0.382)	0.342 (0.506)	0.87 (0.921)	0.141 (0.268)	0.0772 (0.18)	0.944 (0.974)	0.643 (0.765)	0.428 (0.58)	0.333 (0.496)

'amp_1p36.21' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00085

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
AMP PEAK 1(1P36.21) MUTATED	35	48	9
AMP PEAK 1(1P36.21) WILD-TYPE	220	149	116

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 = 0.00302 (Fisher's exact test), Q value = 0.014

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	68	34
AMP PEAK 1(1P36.21) MUTATED	4	21	3
AMP PEAK 1(1P36.21) WILD-TYPE	41	47	31

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 = 0.0193 (Fisher's exact test), Q value = 0.061

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 = 0.00576 (Fisher's exact test), Q value = 0.023

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
AMP PEAK 2(1Q32.1) MUTATED	62	71	27
AMP PEAK 2(1Q32.1) WILD-TYPE	193	126	98

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

'amp_1q44' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
AMP PEAK 3(1Q44) MUTATED	37	53	9
AMP PEAK 3(1Q44) WILD-TYPE	218	144	116

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

'amp_1q44' versus 'RPPA_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.061

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 = 0.0168 (Fisher's exact test), Q value = 0.056

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 'METHLYATION_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.061

Table S8. Gene #4: 'amp_2p24.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
AMP PEAK 4(2P24.3) MUTATED	3	2	6	15
AMP PEAK 4(2P24.3) WILD-TYPE	67	40	75	67

Figure S8. Get High-res Image Gene #4: 'amp_2p24.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_2p24.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0333 (Fisher's exact test), Q value = 0.097

Table S9. 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 S9. Get High-res Image Gene #4: 'amp_2p24.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_3q26.33' versus 'MRNA_CNMF'

P value = 0.00321 (Fisher's exact test), Q value = 0.014

Table S10. Gene #5: 'amp_3q26.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
AMP PEAK 5(3Q26.33) MUTATED	30	28	15	28
AMP PEAK 5(3Q26.33) WILD-TYPE	128	68	122	89

Figure S10. Get High-res Image Gene #5: 'amp_3q26.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.33' versus 'CN_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0023

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
AMP PEAK 5(3Q26.33) MUTATED	53	48	10
AMP PEAK 5(3Q26.33) WILD-TYPE	202	149	115

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

'amp_3q26.33' versus 'METHLYATION_CNMF'

P value = 0.0376 (Fisher's exact test), Q value = 0.11

Table S12. Gene #5: 'amp_3q26.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
AMP PEAK 5(3Q26.33) MUTATED	9	3	19	20
AMP PEAK 5(3Q26.33) WILD-TYPE	61	39	62	62

Figure S12. Get High-res Image Gene #5: 'amp_3q26.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_4q12' versus 'MRNA_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0011

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
AMP PEAK 7(4Q12) MUTATED	22	34	19	24
AMP PEAK 7(4Q12) WILD-TYPE	136	62	118	93

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

'amp_4q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00332 (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 = 0.022 (Fisher's exact test), Q value = 0.068

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
AMP PEAK 7(4Q12) MUTATED	48	46	14
AMP PEAK 7(4Q12) WILD-TYPE	207	151	111

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

'amp_4q12' versus 'METHLYATION_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 0.04

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
AMP PEAK 7(4Q12) MUTATED	9	3	15	24
AMP PEAK 7(4Q12) WILD-TYPE	61	39	66	58

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 = 9.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
AMP PEAK 8(7P11.2) MUTATED	150	69	132	92
AMP PEAK 8(7P11.2) WILD-TYPE	8	27	5	25

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 = 9.7e-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 = 1e-05 (Fisher's exact test), Q value = 9.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	187	90	126
AMP PEAK 8(7P11.2) MUTATED	139	151	74	116
AMP PEAK 8(7P11.2) WILD-TYPE	4	36	16	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 = 9.7e-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 = 9.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
AMP PEAK 8(7P11.2) MUTATED	190	192	125
AMP PEAK 8(7P11.2) WILD-TYPE	65	5	0

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 = 9.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
AMP PEAK 8(7P11.2) MUTATED	67	41	79	54
AMP PEAK 8(7P11.2) WILD-TYPE	3	1	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 = 0.00085 (Fisher's exact test), Q value = 0.0046

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 = 2e-05 (Fisher's exact test), Q value = 0.00016

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 = 1e-05 (Fisher's exact test), Q value = 9.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	68	34
AMP PEAK 8(7P11.2) MUTATED	32	67	32
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 = 9.7e-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 = 1e-05 (Fisher's exact test), Q value = 9.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
AMP PEAK 9(7Q11.21) MUTATED	142	63	113	85
AMP PEAK 9(7Q11.21) WILD-TYPE	16	33	24	32

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 = 9.7e-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 = 1e-05 (Fisher's exact test), Q value = 9.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	187	90	126
AMP PEAK 9(7Q11.21) MUTATED	131	138	63	108
AMP PEAK 9(7Q11.21) WILD-TYPE	12	49	27	18

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 = 2e-05 (Fisher's exact test), Q value = 0.00016

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 = 9.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
AMP PEAK 9(7Q11.21) MUTATED	179	183	102
AMP PEAK 9(7Q11.21) WILD-TYPE	76	14	23

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 = 9.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
AMP PEAK 9(7Q11.21) MUTATED	65	38	67	50
AMP PEAK 9(7Q11.21) WILD-TYPE	5	4	14	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 = 0.0257 (Fisher's exact test), Q value = 0.079

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 = 0.00556 (Fisher's exact test), Q value = 0.022

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 = 0.0049 (Fisher's exact test), Q value = 0.02

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	68	34
AMP PEAK 9(7Q11.21) MUTATED	29	61	28
AMP PEAK 9(7Q11.21) WILD-TYPE	16	7	6

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 = 3e-05 (Fisher's exact test), Q value = 0.00023

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 = 1e-04 (Fisher's exact test), Q value = 0.00069

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
AMP PEAK 10(7Q21.2) MUTATED	141	66	120	91
AMP PEAK 10(7Q21.2) WILD-TYPE	17	30	17	26

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 = 9.7e-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_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00069

Table S39. 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 S39. 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 = 9.7e-05

Table S40. Gene #10: 'amp_7q21.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
AMP PEAK 10(7Q21.2) MUTATED	184	187	109
AMP PEAK 10(7Q21.2) WILD-TYPE	71	10	16

Figure S40. Get High-res Image Gene #10: 'amp_7q21.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_7q21.2' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00095

Table S41. Gene #10: 'amp_7q21.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
AMP PEAK 10(7Q21.2) MUTATED	62	40	67	54
AMP PEAK 10(7Q21.2) WILD-TYPE	8	2	14	28

Figure S41. Get High-res Image Gene #10: 'amp_7q21.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_7q21.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00328 (Fisher's exact test), Q value = 0.014

Table S42. 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 S42. Get High-res Image Gene #10: 'amp_7q21.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_7q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00238 (Fisher's exact test), Q value = 0.011

Table S43. 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 S43. Get High-res Image Gene #10: 'amp_7q21.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MRNA_CNMF'

P value = 0.00199 (Fisher's exact test), Q value = 0.0093

Table S44. Gene #11: 'amp_7q31.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
AMP PEAK 11(7Q31.2) MUTATED	141	68	113	91
AMP PEAK 11(7Q31.2) WILD-TYPE	17	28	24	26

Figure S44. Get High-res Image Gene #11: 'amp_7q31.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_7q31.2' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

Table S45. 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 S45. Get High-res Image Gene #11: 'amp_7q31.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7q31.2' versus 'MIR_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.061

Table S46. Gene #11: 'amp_7q31.2' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	187	90	126
AMP PEAK 11(7Q31.2) MUTATED	126	141	72	107
AMP PEAK 11(7Q31.2) WILD-TYPE	17	46	18	19

Figure S46. Get High-res Image Gene #11: 'amp_7q31.2' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_7q31.2' versus 'MIR_CHIERARCHICAL'

P value = 0.00571 (Fisher's exact test), Q value = 0.022

Table S47. 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 S47. Get High-res Image Gene #11: 'amp_7q31.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_7q31.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

Table S48. Gene #11: 'amp_7q31.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
AMP PEAK 11(7Q31.2) MUTATED	190	180	103
AMP PEAK 11(7Q31.2) WILD-TYPE	65	17	22

Figure S48. Get High-res Image Gene #11: 'amp_7q31.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_7q31.2' versus 'METHLYATION_CNMF'

P value = 0.0405 (Fisher's exact test), Q value = 0.11

Table S49. Gene #11: 'amp_7q31.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
AMP PEAK 11(7Q31.2) MUTATED	62	36	65	58
AMP PEAK 11(7Q31.2) WILD-TYPE	8	6	16	24

Figure S49. Get High-res Image Gene #11: 'amp_7q31.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_7q31.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00519 (Fisher's exact test), Q value = 0.021

Table S50. 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 S50. Get High-res Image Gene #11: 'amp_7q31.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_7q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0099 (Fisher's exact test), Q value = 0.036

Table S51. 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 S51. 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 = 9.7e-05

Table S52. Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
AMP PEAK 12(8Q24.21) MUTATED	8	25	6	22
AMP PEAK 12(8Q24.21) WILD-TYPE	150	71	131	95

Figure S52. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8q24.21' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S53. 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	16
AMP PEAK 12(8Q24.21) WILD-TYPE	138	73	94	142

Figure S53. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8q24.21' versus 'MIR_CNMF'

P value = 0.0206 (Fisher's exact test), Q value = 0.065

Table S54. Gene #12: 'amp_8q24.21' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	187	90	126
AMP PEAK 12(8Q24.21) MUTATED	10	31	13	10
AMP PEAK 12(8Q24.21) WILD-TYPE	133	156	77	116

Figure S54. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.042

Table S55. Gene #12: 'amp_8q24.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
AMP PEAK 12(8Q24.21) MUTATED	37	26	6
AMP PEAK 12(8Q24.21) WILD-TYPE	218	171	119

Figure S55. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 0.00139 (Fisher's exact test), Q value = 0.0069

Table S56. Gene #12: 'amp_8q24.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
AMP PEAK 12(8Q24.21) MUTATED	4	3	11	22
AMP PEAK 12(8Q24.21) WILD-TYPE	66	39	70	60

Figure S56. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'RPPA_CNMF'

P value = 0.0347 (Fisher's exact test), Q value = 0.1

Table S57. 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 S57. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_8q24.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.0242 (Fisher's exact test), Q value = 0.074

Table S58. 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 S58. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_12q14.1' versus 'MIR_CNMF'

P value = 0.00994 (Fisher's exact test), Q value = 0.036

Table S59. Gene #15: 'amp_12q14.1' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	187	90	126
AMP PEAK 15(12Q14.1) MUTATED	25	60	18	26
AMP PEAK 15(12Q14.1) WILD-TYPE	118	127	72	100

Figure S59. Get High-res Image Gene #15: 'amp_12q14.1' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_12q14.1' versus 'CN_CNMF'

P value = 0.00287 (Fisher's exact test), Q value = 0.013

Table S60. Gene #15: 'amp_12q14.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
AMP PEAK 15(12Q14.1) MUTATED	56	60	18
AMP PEAK 15(12Q14.1) WILD-TYPE	199	137	107

Figure S60. Get High-res Image Gene #15: 'amp_12q14.1' versus Molecular Subtype #5: 'CN_CNMF'

'amp_13q34' versus 'RPPA_CNMF'

P value = 0.041 (Fisher's exact test), Q value = 0.11

Table S61. 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 S61. Get High-res Image Gene #17: 'amp_13q34' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_14q32.33' versus 'MIR_CNMF'

P value = 0.0386 (Fisher's exact test), Q value = 0.11

Table S62. Gene #19: 'amp_14q32.33' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	187	90	126
AMP PEAK 19(14Q32.33) MUTATED	12	10	10	3
AMP PEAK 19(14Q32.33) WILD-TYPE	131	177	80	123

Figure S62. Get High-res Image Gene #19: 'amp_14q32.33' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_14q32.33' versus 'MRNASEQ_CNMF'

P value = 0.0282 (Fisher's exact test), Q value = 0.084

Table S63. Gene #19: 'amp_14q32.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	68	34
AMP PEAK 19(14Q32.33) MUTATED	1	3	6
AMP PEAK 19(14Q32.33) WILD-TYPE	44	65	28

Figure S63. Get High-res Image Gene #19: 'amp_14q32.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_17p13.2' versus 'MRNA_CNMF'

P value = 0.00183 (Fisher's exact test), Q value = 0.0087

Table S64. Gene #20: 'amp_17p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
AMP PEAK 20(17P13.2) MUTATED	9	13	6	19
AMP PEAK 20(17P13.2) WILD-TYPE	149	83	131	98

Figure S64. 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 = 0.047

Table S65. 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 S65. Get High-res Image Gene #20: 'amp_17p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17p13.2' versus 'MIR_CNMF'

P value = 0.0397 (Fisher's exact test), Q value = 0.11

Table S66. Gene #20: 'amp_17p13.2' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	187	90	126
AMP PEAK 20(17P13.2) MUTATED	5	22	8	13
AMP PEAK 20(17P13.2) WILD-TYPE	138	165	82	113

Figure S66. Get High-res Image Gene #20: 'amp_17p13.2' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_17p13.2' versus 'METHLYATION_CNMF'

P value = 0.0441 (Fisher's exact test), Q value = 0.12

Table S67. Gene #20: 'amp_17p13.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
AMP PEAK 20(17P13.2) MUTATED	4	1	5	13
AMP PEAK 20(17P13.2) WILD-TYPE	66	41	76	69

Figure S67. Get High-res Image Gene #20: 'amp_17p13.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_17p13.2' versus 'RPPA_CNMF'

P value = 0.00612 (Fisher's exact test), Q value = 0.024

Table S68. 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 S68. Get High-res Image Gene #20: 'amp_17p13.2' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_17q25.1' versus 'MRNA_CNMF'

P value = 0.0279 (Fisher's exact test), Q value = 0.083

Table S69. Gene #21: 'amp_17q25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
AMP PEAK 21(17Q25.1) MUTATED	19	22	13	19
AMP PEAK 21(17Q25.1) WILD-TYPE	139	74	124	98

Figure S69. Get High-res Image Gene #21: 'amp_17q25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q25.1' versus 'CN_CNMF'

P value = 0.00527 (Fisher's exact test), Q value = 0.021

Table S70. Gene #21: 'amp_17q25.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
AMP PEAK 21(17Q25.1) MUTATED	39	37	8
AMP PEAK 21(17Q25.1) WILD-TYPE	216	160	117

Figure S70. 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 = 9.7e-05

Table S71. Gene #22: 'amp_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
AMP PEAK 22(19P13.3) MUTATED	63	35	90	29
AMP PEAK 22(19P13.3) WILD-TYPE	95	61	47	88

Figure S71. Get High-res Image Gene #22: 'amp_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19p13.3' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00023

Table S72. 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	31	62	57
AMP PEAK 22(19P13.3) WILD-TYPE	81	71	38	101

Figure S72. Get High-res Image Gene #22: 'amp_19p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19p13.3' versus 'MIR_CNMF'

P value = 0.0399 (Fisher's exact test), Q value = 0.11

Table S73. Gene #22: 'amp_19p13.3' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	187	90	126
AMP PEAK 22(19P13.3) MUTATED	59	89	27	57
AMP PEAK 22(19P13.3) WILD-TYPE	84	98	63	69

Figure S73. Get High-res Image Gene #22: 'amp_19p13.3' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_19p13.3' versus 'MIR_CHIERARCHICAL'

P value = 0.00277 (Fisher's exact test), Q value = 0.013

Table S74. 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	108	53	71
AMP PEAK 22(19P13.3) WILD-TYPE	185	71	58

Figure S74. 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 = 9.7e-05

Table S75. Gene #22: 'amp_19p13.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
AMP PEAK 22(19P13.3) MUTATED	75	63	108
AMP PEAK 22(19P13.3) WILD-TYPE	180	134	17

Figure S75. 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 = 9.7e-05

Table S76. Gene #22: 'amp_19p13.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
AMP PEAK 22(19P13.3) MUTATED	26	20	55	19
AMP PEAK 22(19P13.3) WILD-TYPE	44	22	26	63

Figure S76. Get High-res Image Gene #22: 'amp_19p13.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_19p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00073

Table S77. 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 S77. Get High-res Image Gene #22: 'amp_19p13.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_19q12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S78. Gene #23: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
AMP PEAK 23(19Q12) MUTATED	60	31	79	18
AMP PEAK 23(19Q12) WILD-TYPE	98	65	58	99

Figure S78. Get High-res Image Gene #23: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19q12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S79. Gene #23: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
AMP PEAK 23(19Q12) MUTATED	62	21	54	51
AMP PEAK 23(19Q12) WILD-TYPE	86	81	46	107

Figure S79. Get High-res Image Gene #23: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q12' versus 'MIR_CHIERARCHICAL'

P value = 0.0043 (Fisher's exact test), Q value = 0.018

Table S80. Gene #23: 'amp_19q12' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
AMP PEAK 23(19Q12) MUTATED	91	49	61
AMP PEAK 23(19Q12) WILD-TYPE	202	75	68

Figure S80. Get High-res Image Gene #23: 'amp_19q12' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S81. Gene #23: 'amp_19q12' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
AMP PEAK 23(19Q12) MUTATED	63	51	102
AMP PEAK 23(19Q12) WILD-TYPE	192	146	23

Figure S81. Get High-res Image Gene #23: 'amp_19q12' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S82. Gene #23: 'amp_19q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
AMP PEAK 23(19Q12) MUTATED	27	18	49	11
AMP PEAK 23(19Q12) WILD-TYPE	43	24	32	71

Figure S82. Get High-res Image Gene #23: 'amp_19q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_19q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00139 (Fisher's exact test), Q value = 0.0069

Table S83. Gene #23: 'amp_19q12' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
AMP PEAK 23(19Q12) MUTATED	31	17	33
AMP PEAK 23(19Q12) WILD-TYPE	59	53	27

Figure S83. Get High-res Image Gene #23: 'amp_19q12' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_21q21.1' versus 'MRNA_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.039

Table S84. Gene #24: 'amp_21q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
AMP PEAK 24(21Q21.1) MUTATED	29	12	9	10
AMP PEAK 24(21Q21.1) WILD-TYPE	129	84	128	107

Figure S84. Get High-res Image Gene #24: 'amp_21q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_21q21.1' versus 'MIR_CNMF'

P value = 0.0262 (Fisher's exact test), Q value = 0.08

Table S85. Gene #24: 'amp_21q21.1' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	187	90	126
AMP PEAK 24(21Q21.1) MUTATED	25	19	5	19
AMP PEAK 24(21Q21.1) WILD-TYPE	118	168	85	107

Figure S85. Get High-res Image Gene #24: 'amp_21q21.1' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_21q21.1' versus 'MIR_CHIERARCHICAL'

P value = 0.00724 (Fisher's exact test), Q value = 0.027

Table S86. Gene #24: 'amp_21q21.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
AMP PEAK 24(21Q21.1) MUTATED	29	26	13
AMP PEAK 24(21Q21.1) WILD-TYPE	264	98	116

Figure S86. Get High-res Image Gene #24: 'amp_21q21.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_21q21.1' versus 'METHLYATION_CNMF'

P value = 0.0425 (Fisher's exact test), Q value = 0.11

Table S87. Gene #24: 'amp_21q21.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
AMP PEAK 24(21Q21.1) MUTATED	16	3	7	9
AMP PEAK 24(21Q21.1) WILD-TYPE	54	39	74	73

Figure S87. Get High-res Image Gene #24: 'amp_21q21.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_1p36.23' versus 'MRNA_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 0.063

Table S88. Gene #26: 'del_1p36.23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
DEL PEAK 2(1P36.23) MUTATED	36	14	44	27
DEL PEAK 2(1P36.23) WILD-TYPE	122	82	93	90

Figure S88. Get High-res Image Gene #26: 'del_1p36.23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.23' versus 'CN_CNMF'

P value = 0.0352 (Fisher's exact test), Q value = 0.1

Table S89. Gene #26: 'del_1p36.23' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
DEL PEAK 2(1P36.23) MUTATED	49	47	39
DEL PEAK 2(1P36.23) WILD-TYPE	206	150	86

Figure S89. Get High-res Image Gene #26: 'del_1p36.23' versus Molecular Subtype #5: 'CN_CNMF'

'del_1p36.23' versus 'MRNASEQ_CNMF'

P value = 0.0056 (Fisher's exact test), Q value = 0.022

Table S90. Gene #26: 'del_1p36.23' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	68	34
DEL PEAK 2(1P36.23) MUTATED	6	14	15
DEL PEAK 2(1P36.23) WILD-TYPE	39	54	19

Figure S90. Get High-res Image Gene #26: 'del_1p36.23' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_1p22.1' versus 'MIR_CHIERARCHICAL'

P value = 0.00486 (Fisher's exact test), Q value = 0.02

Table S91. Gene #28: '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 S91. Get High-res Image Gene #28: 'del_1p22.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_1p22.1' versus 'METHLYATION_CNMF'

P value = 0.0272 (Fisher's exact test), Q value = 0.081

Table S92. Gene #28: 'del_1p22.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
DEL PEAK 4(1P22.1) MUTATED	2	4	14	7
DEL PEAK 4(1P22.1) WILD-TYPE	68	38	67	75

Figure S92. Get High-res Image Gene #28: 'del_1p22.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_1q42.11' versus 'RPPA_CHIERARCHICAL'

P value = 0.00675 (Fisher's exact test), Q value = 0.026

Table S93. Gene #29: '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 S93. Get High-res Image Gene #29: 'del_1q42.11' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_2q22.1' versus 'MRNA_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0021

Table S94. Gene #31: 'del_2q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
DEL PEAK 7(2Q22.1) MUTATED	9	19	6	7
DEL PEAK 7(2Q22.1) WILD-TYPE	149	77	131	110

Figure S94. Get High-res Image Gene #31: 'del_2q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_2q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0287 (Fisher's exact test), Q value = 0.085

Table S95. Gene #31: '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 S95. Get High-res Image Gene #31: 'del_2q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_2q22.1' versus 'CN_CNMF'

P value = 0.00174 (Fisher's exact test), Q value = 0.0084

Table S96. Gene #31: 'del_2q22.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
DEL PEAK 7(2Q22.1) MUTATED	22	23	2
DEL PEAK 7(2Q22.1) WILD-TYPE	233	174	123

Figure S96. Get High-res Image Gene #31: 'del_2q22.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_2q37.1' versus 'MRNA_CNMF'

P value = 0.0176 (Fisher's exact test), Q value = 0.058

Table S97. Gene #32: 'del_2q37.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
DEL PEAK 8(2Q37.1) MUTATED	12	18	9	10
DEL PEAK 8(2Q37.1) WILD-TYPE	146	78	128	107

Figure S97. Get High-res Image Gene #32: 'del_2q37.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_2q37.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00619 (Fisher's exact test), Q value = 0.024

Table S98. Gene #32: '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 S98. Get High-res Image Gene #32: 'del_2q37.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p21.1' versus 'CN_CNMF'

P value = 0.00423 (Fisher's exact test), Q value = 0.018

Table S99. Gene #33: 'del_3p21.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
DEL PEAK 9(3P21.1) MUTATED	29	22	3
DEL PEAK 9(3P21.1) WILD-TYPE	226	175	122

Figure S99. Get High-res Image Gene #33: 'del_3p21.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_3q13.31' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0015

Table S100. Gene #34: 'del_3q13.31' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
DEL PEAK 10(3Q13.31) MUTATED	34	20	2
DEL PEAK 10(3Q13.31) WILD-TYPE	221	177	123

Figure S100. Get High-res Image Gene #34: 'del_3q13.31' versus Molecular Subtype #5: 'CN_CNMF'

'del_3q29' versus 'RPPA_CNMF'

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

Table S101. Gene #35: '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 11(3Q29) MUTATED	2	7	3	5	11
DEL PEAK 11(3Q29) WILD-TYPE	42	50	41	25	34

Figure S101. Get High-res Image Gene #35: 'del_3q29' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_4p16.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00454 (Fisher's exact test), Q value = 0.019

Table S102. Gene #36: '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 12(4P16.3) MUTATED	19	25	7	20
DEL PEAK 12(4P16.3) WILD-TYPE	129	77	93	138

Figure S102. Get High-res Image Gene #36: 'del_4p16.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4p16.3' versus 'CN_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.038

Table S103. Gene #36: 'del_4p16.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
DEL PEAK 12(4P16.3) MUTATED	32	37	9
DEL PEAK 12(4P16.3) WILD-TYPE	223	160	116

Figure S103. Get High-res Image Gene #36: 'del_4p16.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_4p16.3' versus 'METHLYATION_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.0028

Table S104. Gene #36: 'del_4p16.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
DEL PEAK 12(4P16.3) MUTATED	2	2	10	19
DEL PEAK 12(4P16.3) WILD-TYPE	68	40	71	63

Figure S104. Get High-res Image Gene #36: 'del_4p16.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNA_CNMF'

P value = 0.00757 (Fisher's exact test), Q value = 0.028

Table S105. Gene #37: 'del_4q34.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
DEL PEAK 13(4Q34.3) MUTATED	18	23	15	25
DEL PEAK 13(4Q34.3) WILD-TYPE	140	73	122	92

Figure S105. Get High-res Image Gene #37: 'del_4q34.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q34.3' versus 'MRNA_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0018

Table S106. Gene #37: '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 13(4Q34.3) MUTATED	17	31	10	23
DEL PEAK 13(4Q34.3) WILD-TYPE	131	71	90	135

Figure S106. Get High-res Image Gene #37: 'del_4q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0039

Table S107. Gene #37: 'del_4q34.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
DEL PEAK 13(4Q34.3) MUTATED	42	43	8
DEL PEAK 13(4Q34.3) WILD-TYPE	213	154	117

Figure S107. Get High-res Image Gene #37: 'del_4q34.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.039

Table S108. Gene #37: 'del_4q34.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
DEL PEAK 13(4Q34.3) MUTATED	6	3	15	21
DEL PEAK 13(4Q34.3) WILD-TYPE	64	39	66	61

Figure S108. Get High-res Image Gene #37: 'del_4q34.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_5q34' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

Table S109. Gene #38: 'del_5q34' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
DEL PEAK 14(5Q34) MUTATED	8	26	12	17
DEL PEAK 14(5Q34) WILD-TYPE	150	70	125	100

Figure S109. Get High-res Image Gene #38: 'del_5q34' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q34' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S110. Gene #38: 'del_5q34' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 14(5Q34) MUTATED	10	31	11	11
DEL PEAK 14(5Q34) WILD-TYPE	138	71	89	147

Figure S110. Get High-res Image Gene #38: 'del_5q34' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q34' versus 'MIR_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00044

Table S111. Gene #38: 'del_5q34' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	187	90	126
DEL PEAK 14(5Q34) MUTATED	5	37	9	11
DEL PEAK 14(5Q34) WILD-TYPE	138	150	81	115

Figure S111. Get High-res Image Gene #38: 'del_5q34' versus Molecular Subtype #3: 'MIR_CNMF'

'del_5q34' versus 'MIR_CHIERARCHICAL'

P value = 0.00524 (Fisher's exact test), Q value = 0.021

Table S112. Gene #38: 'del_5q34' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 14(5Q34) MUTATED	42	5	15
DEL PEAK 14(5Q34) WILD-TYPE	251	119	114

Figure S112. Get High-res Image Gene #38: 'del_5q34' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_5q34' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00091

Table S113. Gene #38: 'del_5q34' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
DEL PEAK 14(5Q34) MUTATED	3	1	10	21
DEL PEAK 14(5Q34) WILD-TYPE	67	41	71	61

Figure S113. Get High-res Image Gene #38: 'del_5q34' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_5q34' versus 'RPPA_CHIERARCHICAL'

P value = 0.0491 (Fisher's exact test), Q value = 0.13

Table S114. Gene #38: 'del_5q34' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

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

Figure S114. Get High-res Image Gene #38: 'del_5q34' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_6q22.1' versus 'RPPA_CNMF'

P value = 0.0269 (Fisher's exact test), Q value = 0.081

Table S115. Gene #39: 'del_6q22.1' 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 15(6Q22.1) MUTATED	15	13	4	9	15
DEL PEAK 15(6Q22.1) WILD-TYPE	29	44	40	21	30

Figure S115. Get High-res Image Gene #39: 'del_6q22.1' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_6q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0472 (Fisher's exact test), Q value = 0.12

Table S116. Gene #39: 'del_6q22.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	92	25
DEL PEAK 15(6Q22.1) MUTATED	5	37	10
DEL PEAK 15(6Q22.1) WILD-TYPE	25	55	15

Figure S116. Get High-res Image Gene #39: 'del_6q22.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 0.00138 (Fisher's exact test), Q value = 0.0069

Table S117. Gene #40: 'del_6q26' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
DEL PEAK 16(6Q26) MUTATED	24	21	24	14
DEL PEAK 16(6Q26) WILD-TYPE	46	21	57	68

Figure S117. Get High-res Image Gene #40: 'del_6q26' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_6q26' versus 'RPPA_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00057

Table S118. Gene #40: '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 16(6Q26) MUTATED	20	19	3	11	21
DEL PEAK 16(6Q26) WILD-TYPE	24	38	41	19	24

Figure S118. Get High-res Image Gene #40: 'del_6q26' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.061

Table S119. Gene #40: 'del_6q26' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	92	25
DEL PEAK 16(6Q26) MUTATED	5	39	12
DEL PEAK 16(6Q26) WILD-TYPE	25	53	13

Figure S119. Get High-res Image Gene #40: 'del_6q26' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S120. Gene #42: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
DEL PEAK 18(9P21.3) MUTATED	107	63	121	78
DEL PEAK 18(9P21.3) WILD-TYPE	51	33	16	39

Figure S120. Get High-res Image Gene #42: '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 = 9.7e-05

Table S121. Gene #42: '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 18(9P21.3) MUTATED	102	61	91	115
DEL PEAK 18(9P21.3) WILD-TYPE	46	41	9	43

Figure S121. Get High-res Image Gene #42: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p21.3' versus 'MIR_CHIERARCHICAL'

P value = 0.0357 (Fisher's exact test), Q value = 0.1

Table S122. Gene #42: 'del_9p21.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 18(9P21.3) MUTATED	199	96	101
DEL PEAK 18(9P21.3) WILD-TYPE	94	28	28

Figure S122. Get High-res Image Gene #42: '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 = 9.7e-05

Table S123. Gene #42: 'del_9p21.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
DEL PEAK 18(9P21.3) MUTATED	165	136	120
DEL PEAK 18(9P21.3) WILD-TYPE	90	61	5

Figure S123. Get High-res Image Gene #42: 'del_9p21.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0026

Table S124. Gene #42: 'del_9p21.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
DEL PEAK 18(9P21.3) MUTATED	43	39	67	58
DEL PEAK 18(9P21.3) WILD-TYPE	27	3	14	24

Figure S124. Get High-res Image Gene #42: 'del_9p21.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

P value = 0.042 (Fisher's exact test), Q value = 0.11

Table S125. Gene #42: '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 18(9P21.3) MUTATED	36	46	32	19	41
DEL PEAK 18(9P21.3) WILD-TYPE	8	11	12	11	4

Figure S125. Get High-res Image Gene #42: '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 S126. Gene #42: 'del_9p21.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

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

Figure S126. Get High-res Image Gene #42: 'del_9p21.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 0.0378 (Fisher's exact test), Q value = 0.11

Table S127. Gene #42: 'del_9p21.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	68	34
DEL PEAK 18(9P21.3) MUTATED	25	53	25
DEL PEAK 18(9P21.3) WILD-TYPE	20	15	9

Figure S127. Get High-res Image Gene #42: 'del_9p21.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00792 (Fisher's exact test), Q value = 0.029

Table S128. Gene #42: 'del_9p21.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

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

Figure S128. Get High-res Image Gene #42: 'del_9p21.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S129. Gene #44: 'del_10p15.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
DEL PEAK 20(10P15.3) MUTATED	136	61	125	86
DEL PEAK 20(10P15.3) WILD-TYPE	22	35	12	31

Figure S129. Get High-res Image Gene #44: '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 = 9.7e-05

Table S130. Gene #44: '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 20(10P15.3) MUTATED	125	59	89	135
DEL PEAK 20(10P15.3) WILD-TYPE	23	43	11	23

Figure S130. Get High-res Image Gene #44: 'del_10p15.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10p15.3' versus 'MIR_CNMF'

P value = 0.0223 (Fisher's exact test), Q value = 0.069

Table S131. Gene #44: 'del_10p15.3' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	187	90	126
DEL PEAK 20(10P15.3) MUTATED	127	142	71	103
DEL PEAK 20(10P15.3) WILD-TYPE	16	45	19	23

Figure S131. Get High-res Image Gene #44: 'del_10p15.3' versus Molecular Subtype #3: 'MIR_CNMF'

'del_10p15.3' versus 'MIR_CHIERARCHICAL'

P value = 0.00362 (Fisher's exact test), Q value = 0.016

Table S132. Gene #44: 'del_10p15.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 20(10P15.3) MUTATED	223	105	115
DEL PEAK 20(10P15.3) WILD-TYPE	70	19	14

Figure S132. Get High-res Image Gene #44: '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 = 9.7e-05

Table S133. Gene #44: 'del_10p15.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
DEL PEAK 20(10P15.3) MUTATED	174	187	109
DEL PEAK 20(10P15.3) WILD-TYPE	81	10	16

Figure S133. Get High-res Image Gene #44: '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 = 9.7e-05

Table S134. Gene #44: 'del_10p15.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
DEL PEAK 20(10P15.3) MUTATED	62	38	72	48
DEL PEAK 20(10P15.3) WILD-TYPE	8	4	9	34

Figure S134. Get High-res Image Gene #44: 'del_10p15.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_10p15.3' versus 'RPPA_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.0039

Table S135. Gene #44: 'del_10p15.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
DEL PEAK 20(10P15.3) MUTATED	82	49	54
DEL PEAK 20(10P15.3) WILD-TYPE	8	21	6

Figure S135. Get High-res Image Gene #44: 'del_10p15.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.066

Table S136. Gene #44: 'del_10p15.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	68	34
DEL PEAK 20(10P15.3) MUTATED	34	60	33
DEL PEAK 20(10P15.3) WILD-TYPE	11	8	1

Figure S136. Get High-res Image Gene #44: 'del_10p15.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.0012

Table S137. Gene #44: 'del_10p15.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	92	25
DEL PEAK 20(10P15.3) MUTATED	19	83	25
DEL PEAK 20(10P15.3) WILD-TYPE	11	9	0

Figure S137. Get High-res Image Gene #44: 'del_10p15.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_10p13' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S138. Gene #45: 'del_10p13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
DEL PEAK 21(10P13) MUTATED	139	63	125	83
DEL PEAK 21(10P13) WILD-TYPE	19	33	12	34

Figure S138. Get High-res Image Gene #45: 'del_10p13' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10p13' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S139. Gene #45: 'del_10p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 21(10P13) MUTATED	129	58	89	134
DEL PEAK 21(10P13) WILD-TYPE	19	44	11	24

Figure S139. Get High-res Image Gene #45: 'del_10p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10p13' versus 'MIR_CNMF'

P value = 0.00517 (Fisher's exact test), Q value = 0.021

Table S140. Gene #45: 'del_10p13' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	187	90	126
DEL PEAK 21(10P13) MUTATED	129	143	69	105
DEL PEAK 21(10P13) WILD-TYPE	14	44	21	21

Figure S140. Get High-res Image Gene #45: 'del_10p13' versus Molecular Subtype #3: 'MIR_CNMF'

'del_10p13' versus 'MIR_CHIERARCHICAL'

P value = 0.00118 (Fisher's exact test), Q value = 0.0061

Table S141. Gene #45: 'del_10p13' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 21(10P13) MUTATED	223	108	115
DEL PEAK 21(10P13) WILD-TYPE	70	16	14

Figure S141. Get High-res Image Gene #45: 'del_10p13' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_10p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S142. Gene #45: 'del_10p13' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
DEL PEAK 21(10P13) MUTATED	174	187	110
DEL PEAK 21(10P13) WILD-TYPE	81	10	15

Figure S142. Get High-res Image Gene #45: 'del_10p13' versus Molecular Subtype #5: 'CN_CNMF'

'del_10p13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S143. Gene #45: 'del_10p13' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
DEL PEAK 21(10P13) MUTATED	62	38	72	46
DEL PEAK 21(10P13) WILD-TYPE	8	4	9	36

Figure S143. Get High-res Image Gene #45: 'del_10p13' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_10p13' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S144. Gene #45: 'del_10p13' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
DEL PEAK 21(10P13) MUTATED	83	45	55
DEL PEAK 21(10P13) WILD-TYPE	7	25	5

Figure S144. Get High-res Image Gene #45: 'del_10p13' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_10p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00267 (Fisher's exact test), Q value = 0.012

Table S145. Gene #45: 'del_10p13' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	92	25
DEL PEAK 21(10P13) MUTATED	20	83	24
DEL PEAK 21(10P13) WILD-TYPE	10	9	1

Figure S145. Get High-res Image Gene #45: 'del_10p13' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_10p11.23' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S146. Gene #46: 'del_10p11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
DEL PEAK 22(10P11.23) MUTATED	139	60	130	87
DEL PEAK 22(10P11.23) WILD-TYPE	19	36	7	30

Figure S146. Get High-res Image Gene #46: '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 = 9.7e-05

Table S147. Gene #46: '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 22(10P11.23) MUTATED	127	60	93	136
DEL PEAK 22(10P11.23) WILD-TYPE	21	42	7	22

Figure S147. Get High-res Image Gene #46: 'del_10p11.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10p11.23' versus 'MIR_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0039

Table S148. Gene #46: 'del_10p11.23' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	187	90	126
DEL PEAK 22(10P11.23) MUTATED	132	145	68	105
DEL PEAK 22(10P11.23) WILD-TYPE	11	42	22	21

Figure S148. Get High-res Image Gene #46: 'del_10p11.23' versus Molecular Subtype #3: 'MIR_CNMF'

'del_10p11.23' versus 'MIR_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00023

Table S149. Gene #46: 'del_10p11.23' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 22(10P11.23) MUTATED	223	106	121
DEL PEAK 22(10P11.23) WILD-TYPE	70	18	8

Figure S149. Get High-res Image Gene #46: '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 = 9.7e-05

Table S150. Gene #46: 'del_10p11.23' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
DEL PEAK 22(10P11.23) MUTATED	170	189	117
DEL PEAK 22(10P11.23) WILD-TYPE	85	8	8

Figure S150. Get High-res Image Gene #46: '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 = 9.7e-05

Table S151. Gene #46: 'del_10p11.23' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
DEL PEAK 22(10P11.23) MUTATED	62	39	72	47
DEL PEAK 22(10P11.23) WILD-TYPE	8	3	9	35

Figure S151. Get High-res Image Gene #46: 'del_10p11.23' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_10p11.23' versus 'RPPA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00073

Table S152. Gene #46: 'del_10p11.23' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
DEL PEAK 22(10P11.23) MUTATED	81	49	57
DEL PEAK 22(10P11.23) WILD-TYPE	9	21	3

Figure S152. Get High-res Image Gene #46: 'del_10p11.23' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_10p11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0011 (Fisher's exact test), Q value = 0.0058

Table S153. Gene #46: 'del_10p11.23' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	92	25
DEL PEAK 22(10P11.23) MUTATED	20	85	24
DEL PEAK 22(10P11.23) WILD-TYPE	10	7	1

Figure S153. Get High-res Image Gene #46: 'del_10p11.23' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_10q11.23' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S154. Gene #47: 'del_10q11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
DEL PEAK 23(10Q11.23) MUTATED	143	67	131	87
DEL PEAK 23(10Q11.23) WILD-TYPE	15	29	6	30

Figure S154. Get High-res Image Gene #47: 'del_10q11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q11.23' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S155. Gene #47: 'del_10q11.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 23(10Q11.23) MUTATED	129	64	96	139
DEL PEAK 23(10Q11.23) WILD-TYPE	19	38	4	19

Figure S155. Get High-res Image Gene #47: 'del_10q11.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q11.23' versus 'MIR_CNMF'

P value = 0.00093 (Fisher's exact test), Q value = 0.005

Table S156. Gene #47: 'del_10q11.23' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	187	90	126
DEL PEAK 23(10Q11.23) MUTATED	133	151	69	111
DEL PEAK 23(10Q11.23) WILD-TYPE	10	36	21	15

Figure S156. Get High-res Image Gene #47: 'del_10q11.23' versus Molecular Subtype #3: 'MIR_CNMF'

'del_10q11.23' versus 'MIR_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

Table S157. Gene #47: 'del_10q11.23' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 23(10Q11.23) MUTATED	229	112	123
DEL PEAK 23(10Q11.23) WILD-TYPE	64	12	6

Figure S157. Get High-res Image Gene #47: 'del_10q11.23' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_10q11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S158. Gene #47: 'del_10q11.23' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
DEL PEAK 23(10Q11.23) MUTATED	174	194	121
DEL PEAK 23(10Q11.23) WILD-TYPE	81	3	4

Figure S158. Get High-res Image Gene #47: 'del_10q11.23' versus Molecular Subtype #5: 'CN_CNMF'

'del_10q11.23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S159. Gene #47: 'del_10q11.23' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
DEL PEAK 23(10Q11.23) MUTATED	61	39	76	52
DEL PEAK 23(10Q11.23) WILD-TYPE	9	3	5	30

Figure S159. Get High-res Image Gene #47: 'del_10q11.23' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_10q11.23' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S160. Gene #47: 'del_10q11.23' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
DEL PEAK 23(10Q11.23) MUTATED	83	51	60
DEL PEAK 23(10Q11.23) WILD-TYPE	7	19	0

Figure S160. Get High-res Image Gene #47: 'del_10q11.23' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_10q11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00376 (Fisher's exact test), Q value = 0.016

Table S161. Gene #47: 'del_10q11.23' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	92	25
DEL PEAK 23(10Q11.23) MUTATED	22	87	24
DEL PEAK 23(10Q11.23) WILD-TYPE	8	5	1

Figure S161. Get High-res Image Gene #47: 'del_10q11.23' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00023

Table S162. Gene #48: 'del_10q23.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
DEL PEAK 24(10Q23.31) MUTATED	146	76	132	95
DEL PEAK 24(10Q23.31) WILD-TYPE	12	20	5	22

Figure S162. Get High-res Image Gene #48: '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 = 9.7e-05

Table S163. Gene #48: '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 S163. Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q23.31' versus 'MIR_CNMF'

P value = 0.0342 (Fisher's exact test), Q value = 0.099

Table S164. Gene #48: 'del_10q23.31' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	187	90	126
DEL PEAK 24(10Q23.31) MUTATED	135	162	75	113
DEL PEAK 24(10Q23.31) WILD-TYPE	8	25	15	13

Figure S164. Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #3: 'MIR_CNMF'

'del_10q23.31' versus 'MIR_CHIERARCHICAL'

P value = 0.00322 (Fisher's exact test), Q value = 0.014

Table S165. Gene #48: '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 S165. Get High-res Image Gene #48: '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 = 9.7e-05

Table S166. Gene #48: 'del_10q23.31' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
DEL PEAK 24(10Q23.31) MUTATED	198	194	122
DEL PEAK 24(10Q23.31) WILD-TYPE	57	3	3

Figure S166. Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #5: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0029

Table S167. Gene #48: 'del_10q23.31' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
DEL PEAK 24(10Q23.31) MUTATED	63	41	77	63
DEL PEAK 24(10Q23.31) WILD-TYPE	7	1	4	19

Figure S167. Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_10q23.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00208 (Fisher's exact test), Q value = 0.0097

Table S168. Gene #48: '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 S168. Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.041 (Fisher's exact test), Q value = 0.11

Table S169. Gene #48: '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 S169. Get High-res Image Gene #48: '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 = 9.7e-05

Table S170. Gene #49: 'del_10q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
DEL PEAK 25(10Q26.3) MUTATED	145	75	135	95
DEL PEAK 25(10Q26.3) WILD-TYPE	13	21	2	22

Figure S170. Get High-res Image Gene #49: 'del_10q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q26.3' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

Table S171. Gene #49: '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 S171. Get High-res Image Gene #49: 'del_10q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q26.3' versus 'MIR_CHIERARCHICAL'

P value = 0.00147 (Fisher's exact test), Q value = 0.0073

Table S172. Gene #49: '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 S172. Get High-res Image Gene #49: '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 = 9.7e-05

Table S173. Gene #49: 'del_10q26.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
DEL PEAK 25(10Q26.3) MUTATED	199	191	125
DEL PEAK 25(10Q26.3) WILD-TYPE	56	6	0

Figure S173. Get High-res Image Gene #49: 'del_10q26.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_10q26.3' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00095

Table S174. Gene #49: 'del_10q26.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
DEL PEAK 25(10Q26.3) MUTATED	61	41	78	62
DEL PEAK 25(10Q26.3) WILD-TYPE	9	1	3	20

Figure S174. Get High-res Image Gene #49: 'del_10q26.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_10q26.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.056

Table S175. Gene #49: '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 S175. Get High-res Image Gene #49: 'del_10q26.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0349 (Fisher's exact test), Q value = 0.1

Table S176. Gene #49: '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 S176. Get High-res Image Gene #49: '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 = 9.7e-05

Table S177. Gene #50: 'del_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
DEL PEAK 26(11P15.5) MUTATED	32	42	12	33
DEL PEAK 26(11P15.5) WILD-TYPE	126	54	125	84

Figure S177. Get High-res Image Gene #50: '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 = 9.7e-05

Table S178. Gene #50: '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	32
DEL PEAK 26(11P15.5) WILD-TYPE	118	54	91	126

Figure S178. Get High-res Image Gene #50: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11p15.5' versus 'MIR_CHIERARCHICAL'

P value = 0.00164 (Fisher's exact test), Q value = 0.008

Table S179. Gene #50: '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	85	24	18
DEL PEAK 26(11P15.5) WILD-TYPE	208	100	111

Figure S179. Get High-res Image Gene #50: '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 = 9.7e-05

Table S180. Gene #50: 'del_11p15.5' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
DEL PEAK 26(11P15.5) MUTATED	76	50	6
DEL PEAK 26(11P15.5) WILD-TYPE	179	147	119

Figure S180. Get High-res Image Gene #50: 'del_11p15.5' versus Molecular Subtype #5: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

Table S181. Gene #50: 'del_11p15.5' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
DEL PEAK 26(11P15.5) MUTATED	11	4	16	38
DEL PEAK 26(11P15.5) WILD-TYPE	59	38	65	44

Figure S181. Get High-res Image Gene #50: 'del_11p15.5' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_11p15.5' versus 'RPPA_CHIERARCHICAL'

P value = 0.03 (Fisher's exact test), Q value = 0.088

Table S182. Gene #50: '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	16	22	8
DEL PEAK 26(11P15.5) WILD-TYPE	74	48	52

Figure S182. Get High-res Image Gene #50: 'del_11p15.5' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 0.006 (Fisher's exact test), Q value = 0.023

Table S183. Gene #50: 'del_11p15.5' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	68	34
DEL PEAK 26(11P15.5) MUTATED	18	12	4
DEL PEAK 26(11P15.5) WILD-TYPE	27	56	30

Figure S183. Get High-res Image Gene #50: 'del_11p15.5' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00228 (Fisher's exact test), Q value = 0.011

Table S184. Gene #50: '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	18	2
DEL PEAK 26(11P15.5) WILD-TYPE	16	74	23

Figure S184. Get High-res Image Gene #50: '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 = 9.7e-05

Table S185. Gene #51: 'del_11p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
DEL PEAK 27(11P11.2) MUTATED	27	35	9	24
DEL PEAK 27(11P11.2) WILD-TYPE	131	61	128	93

Figure S185. Get High-res Image Gene #51: '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 = 9.7e-05

Table S186. Gene #51: '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 S186. Get High-res Image Gene #51: '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 = 0.058

Table S187. Gene #51: '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 S187. Get High-res Image Gene #51: '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 = 9.7e-05

Table S188. Gene #51: 'del_11p11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
DEL PEAK 27(11P11.2) MUTATED	60	42	3
DEL PEAK 27(11P11.2) WILD-TYPE	195	155	122

Figure S188. Get High-res Image Gene #51: 'del_11p11.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_11p11.2' versus 'METHLYATION_CNMF'

P value = 0.00148 (Fisher's exact test), Q value = 0.0073

Table S189. Gene #51: 'del_11p11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
DEL PEAK 27(11P11.2) MUTATED	13	4	13	30
DEL PEAK 27(11P11.2) WILD-TYPE	57	38	68	52

Figure S189. Get High-res Image Gene #51: '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 = 9.7e-05

Table S190. Gene #52: 'del_11q14.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
DEL PEAK 28(11Q14.1) MUTATED	30	33	11	14
DEL PEAK 28(11Q14.1) WILD-TYPE	128	63	126	103

Figure S190. Get High-res Image Gene #52: 'del_11q14.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11q14.1' versus 'MRNA_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.0034

Table S191. Gene #52: '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 S191. Get High-res Image Gene #52: '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 = 9.7e-05

Table S192. Gene #52: 'del_11q14.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
DEL PEAK 28(11Q14.1) MUTATED	47	46	3
DEL PEAK 28(11Q14.1) WILD-TYPE	208	151	122

Figure S192. Get High-res Image Gene #52: 'del_11q14.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_11q14.1' versus 'MRNASEQ_CNMF'

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

Table S193. Gene #52: 'del_11q14.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	68	34
DEL PEAK 28(11Q14.1) MUTATED	9	14	1
DEL PEAK 28(11Q14.1) WILD-TYPE	36	54	33

Figure S193. Get High-res Image Gene #52: 'del_11q14.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_12p13.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.046

Table S194. Gene #53: '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 S194. Get High-res Image Gene #53: 'del_12p13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_12p13.1' versus 'METHLYATION_CNMF'

P value = 0.00684 (Fisher's exact test), Q value = 0.026

Table S195. Gene #53: 'del_12p13.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
DEL PEAK 29(12P13.1) MUTATED	8	0	12	16
DEL PEAK 29(12P13.1) WILD-TYPE	62	42	69	66

Figure S195. Get High-res Image Gene #53: 'del_12p13.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_12q12' versus 'MRNA_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.046

Table S196. Gene #54: 'del_12q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
DEL PEAK 30(12Q12) MUTATED	18	19	10	21
DEL PEAK 30(12Q12) WILD-TYPE	140	77	127	96

Figure S196. Get High-res Image Gene #54: 'del_12q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.0043

Table S197. Gene #54: '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 S197. Get High-res Image Gene #54: 'del_12q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_12q12' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00073

Table S198. Gene #54: 'del_12q12' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
DEL PEAK 30(12Q12) MUTATED	38	35	4
DEL PEAK 30(12Q12) WILD-TYPE	217	162	121

Figure S198. Get High-res Image Gene #54: 'del_12q12' versus Molecular Subtype #5: 'CN_CNMF'

'del_12q12' versus 'METHLYATION_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 0.071

Table S199. Gene #54: 'del_12q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
DEL PEAK 30(12Q12) MUTATED	7	1	12	17
DEL PEAK 30(12Q12) WILD-TYPE	63	41	69	65

Figure S199. Get High-res Image Gene #54: 'del_12q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_12q12' versus 'RPPA_CNMF'

P value = 0.00966 (Fisher's exact test), Q value = 0.036

Table S200. Gene #54: '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 S200. Get High-res Image Gene #54: 'del_12q12' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_12q15' versus 'MRNA_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.0056

Table S201. Gene #55: 'del_12q15' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
DEL PEAK 31(12Q15) MUTATED	22	21	7	19
DEL PEAK 31(12Q15) WILD-TYPE	136	75	130	98

Figure S201. Get High-res Image Gene #55: 'del_12q15' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12q15' versus 'MRNA_CHIERARCHICAL'

P value = 0.00193 (Fisher's exact test), Q value = 0.0091

Table S202. Gene #55: '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 S202. Get High-res Image Gene #55: 'del_12q15' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_12q15' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 3e-04

Table S203. Gene #55: 'del_12q15' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
DEL PEAK 31(12Q15) MUTATED	36	39	4
DEL PEAK 31(12Q15) WILD-TYPE	219	158	121

Figure S203. Get High-res Image Gene #55: 'del_12q15' versus Molecular Subtype #5: 'CN_CNMF'

'del_13q14.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S204. Gene #56: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
DEL PEAK 32(13Q14.2) MUTATED	82	45	32	56
DEL PEAK 32(13Q14.2) WILD-TYPE	76	51	105	61

Figure S204. Get High-res Image Gene #56: '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 = 0.00016

Table S205. Gene #56: '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 S205. Get High-res Image Gene #56: '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 = 9.7e-05

Table S206. Gene #56: 'del_13q14.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
DEL PEAK 32(13Q14.2) MUTATED	126	97	18
DEL PEAK 32(13Q14.2) WILD-TYPE	129	100	107

Figure S206. Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00079

Table S207. Gene #56: 'del_13q14.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
DEL PEAK 32(13Q14.2) MUTATED	39	9	29	46
DEL PEAK 32(13Q14.2) WILD-TYPE	31	33	52	36

Figure S207. Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_13q22.1' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

Table S208. Gene #57: 'del_13q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
DEL PEAK 33(13Q22.1) MUTATED	82	40	30	53
DEL PEAK 33(13Q22.1) WILD-TYPE	76	56	107	64

Figure S208. Get High-res Image Gene #57: 'del_13q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00069

Table S209. Gene #57: '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 S209. Get High-res Image Gene #57: '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 = 9.7e-05

Table S210. Gene #57: 'del_13q22.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
DEL PEAK 33(13Q22.1) MUTATED	119	94	17
DEL PEAK 33(13Q22.1) WILD-TYPE	136	103	108

Figure S210. Get High-res Image Gene #57: 'del_13q22.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_13q22.1' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00023

Table S211. Gene #57: 'del_13q22.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
DEL PEAK 33(13Q22.1) MUTATED	39	6	32	42
DEL PEAK 33(13Q22.1) WILD-TYPE	31	36	49	40

Figure S211. Get High-res Image Gene #57: 'del_13q22.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_14q13.1' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

Table S212. Gene #58: 'del_14q13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
DEL PEAK 34(14Q13.1) MUTATED	56	39	21	45
DEL PEAK 34(14Q13.1) WILD-TYPE	102	57	116	72

Figure S212. Get High-res Image Gene #58: 'del_14q13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q13.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.002

Table S213. Gene #58: '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 S213. Get High-res Image Gene #58: '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 = 9.7e-05

Table S214. Gene #58: 'del_14q13.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
DEL PEAK 34(14Q13.1) MUTATED	93	72	13
DEL PEAK 34(14Q13.1) WILD-TYPE	162	125	112

Figure S214. Get High-res Image Gene #58: 'del_14q13.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_14q13.1' versus 'METHLYATION_CNMF'

P value = 0.0376 (Fisher's exact test), Q value = 0.11

Table S215. Gene #58: 'del_14q13.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
DEL PEAK 34(14Q13.1) MUTATED	26	6	24	30
DEL PEAK 34(14Q13.1) WILD-TYPE	44	36	57	52

Figure S215. Get High-res Image Gene #58: '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 = 9.7e-05

Table S216. Gene #59: 'del_14q24.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
DEL PEAK 35(14Q24.2) MUTATED	53	43	18	47
DEL PEAK 35(14Q24.2) WILD-TYPE	105	53	119	70

Figure S216. Get High-res Image Gene #59: '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 = 0.00016

Table S217. Gene #59: '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 S217. Get High-res Image Gene #59: '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 = 9.7e-05

Table S218. Gene #59: 'del_14q24.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
DEL PEAK 35(14Q24.2) MUTATED	99	70	4
DEL PEAK 35(14Q24.2) WILD-TYPE	156	127	121

Figure S218. Get High-res Image Gene #59: 'del_14q24.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_14q24.2' versus 'METHLYATION_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.039

Table S219. Gene #59: 'del_14q24.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
DEL PEAK 35(14Q24.2) MUTATED	23	6	24	35
DEL PEAK 35(14Q24.2) WILD-TYPE	47	36	57	47

Figure S219. Get High-res Image Gene #59: 'del_14q24.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_14q24.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0492 (Fisher's exact test), Q value = 0.13

Table S220. Gene #59: '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 S220. Get High-res Image Gene #59: 'del_14q24.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_15q14' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S221. Gene #60: 'del_15q14' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
DEL PEAK 36(15Q14) MUTATED	37	36	20	45
DEL PEAK 36(15Q14) WILD-TYPE	121	60	117	72

Figure S221. Get High-res Image Gene #60: 'del_15q14' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q14' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S222. Gene #60: '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 S222. Get High-res Image Gene #60: 'del_15q14' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q14' versus 'MIR_CNMF'

P value = 0.00183 (Fisher's exact test), Q value = 0.0087

Table S223. Gene #60: 'del_15q14' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	187	90	126
DEL PEAK 36(15Q14) MUTATED	30	66	25	22
DEL PEAK 36(15Q14) WILD-TYPE	113	121	65	104

Figure S223. Get High-res Image Gene #60: 'del_15q14' versus Molecular Subtype #3: 'MIR_CNMF'

'del_15q14' versus 'MIR_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00051

Table S224. Gene #60: '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 S224. Get High-res Image Gene #60: 'del_15q14' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_15q14' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S225. Gene #60: 'del_15q14' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
DEL PEAK 36(15Q14) MUTATED	74	71	9
DEL PEAK 36(15Q14) WILD-TYPE	181	126	116

Figure S225. Get High-res Image Gene #60: 'del_15q14' versus Molecular Subtype #5: 'CN_CNMF'

'del_15q14' versus 'METHLYATION_CNMF'

P value = 0.00632 (Fisher's exact test), Q value = 0.024

Table S226. Gene #60: 'del_15q14' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
DEL PEAK 36(15Q14) MUTATED	17	8	19	36
DEL PEAK 36(15Q14) WILD-TYPE	53	34	62	46

Figure S226. Get High-res Image Gene #60: 'del_15q14' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_15q14' versus 'RPPA_CNMF'

P value = 0.041 (Fisher's exact test), Q value = 0.11

Table S227. Gene #60: '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 S227. Get High-res Image Gene #60: 'del_15q14' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_15q14' versus 'RPPA_CHIERARCHICAL'

P value = 0.0265 (Fisher's exact test), Q value = 0.081

Table S228. Gene #60: '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 S228. Get High-res Image Gene #60: 'del_15q14' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_15q14' versus 'MRNASEQ_CNMF'

P value = 0.00129 (Fisher's exact test), Q value = 0.0066

Table S229. Gene #60: 'del_15q14' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	68	34
DEL PEAK 36(15Q14) MUTATED	23	15	6
DEL PEAK 36(15Q14) WILD-TYPE	22	53	28

Figure S229. Get High-res Image Gene #60: 'del_15q14' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_15q14' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0173 (Fisher's exact test), Q value = 0.058

Table S230. Gene #60: '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 S230. Get High-res Image Gene #60: 'del_15q14' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MRNA_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.038

Table S231. Gene #62: 'del_16q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
DEL PEAK 38(16Q23.1) MUTATED	32	24	13	21
DEL PEAK 38(16Q23.1) WILD-TYPE	126	72	124	96

Figure S231. Get High-res Image Gene #62: 'del_16q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.037

Table S232. Gene #62: 'del_16q23.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
DEL PEAK 38(16Q23.1) MUTATED	50	40	11
DEL PEAK 38(16Q23.1) WILD-TYPE	205	157	114

Figure S232. Get High-res Image Gene #62: 'del_16q23.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_17p13.1' versus 'MRNA_CNMF'

P value = 0.00125 (Fisher's exact test), Q value = 0.0064

Table S233. Gene #63: 'del_17p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
DEL PEAK 39(17P13.1) MUTATED	33	26	12	17
DEL PEAK 39(17P13.1) WILD-TYPE	125	70	125	100

Figure S233. Get High-res Image Gene #63: 'del_17p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p13.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00162 (Fisher's exact test), Q value = 0.0079

Table S234. Gene #63: '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 39(17P13.1) MUTATED	32	27	9	20
DEL PEAK 39(17P13.1) WILD-TYPE	116	75	91	138

Figure S234. Get High-res Image Gene #63: '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 = 9.7e-05

Table S235. Gene #63: 'del_17p13.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
DEL PEAK 39(17P13.1) MUTATED	55	41	2
DEL PEAK 39(17P13.1) WILD-TYPE	200	156	123

Figure S235. Get High-res Image Gene #63: 'del_17p13.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_17p13.1' versus 'METHLYATION_CNMF'

P value = 0.0428 (Fisher's exact test), Q value = 0.11

Table S236. Gene #63: 'del_17p13.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
DEL PEAK 39(17P13.1) MUTATED	16	3	9	18
DEL PEAK 39(17P13.1) WILD-TYPE	54	39	72	64

Figure S236. Get High-res Image Gene #63: 'del_17p13.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_17q11.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S237. Gene #64: 'del_17q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
DEL PEAK 40(17Q11.2) MUTATED	36	9	11	5
DEL PEAK 40(17Q11.2) WILD-TYPE	122	87	126	112

Figure S237. Get High-res Image Gene #64: 'del_17q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

Table S238. Gene #64: '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 40(17Q11.2) MUTATED	35	7	9	10
DEL PEAK 40(17Q11.2) WILD-TYPE	113	95	91	148

Figure S238. Get High-res Image Gene #64: 'del_17q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17q11.2' versus 'MIR_CNMF'

P value = 0.00396 (Fisher's exact test), Q value = 0.017

Table S239. Gene #64: 'del_17q11.2' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	187	90	126
DEL PEAK 40(17Q11.2) MUTATED	27	18	4	19
DEL PEAK 40(17Q11.2) WILD-TYPE	116	169	86	107

Figure S239. Get High-res Image Gene #64: 'del_17q11.2' versus Molecular Subtype #3: 'MIR_CNMF'

'del_17q11.2' versus 'MIR_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.038

Table S240. Gene #64: 'del_17q11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 40(17Q11.2) MUTATED	26	24	18
DEL PEAK 40(17Q11.2) WILD-TYPE	267	100	111

Figure S240. Get High-res Image Gene #64: 'del_17q11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_17q11.2' versus 'CN_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0022

Table S241. Gene #64: 'del_17q11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
DEL PEAK 40(17Q11.2) MUTATED	41	27	4
DEL PEAK 40(17Q11.2) WILD-TYPE	214	170	121

Figure S241. Get High-res Image Gene #64: 'del_17q11.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_17q11.2' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00051

Table S242. Gene #64: 'del_17q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
DEL PEAK 40(17Q11.2) MUTATED	17	3	3	3
DEL PEAK 40(17Q11.2) WILD-TYPE	53	39	78	79

Figure S242. Get High-res Image Gene #64: 'del_17q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_17q11.2' versus 'RPPA_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.0041

Table S243. Gene #64: '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 40(17Q11.2) MUTATED	12	9	0	4	3
DEL PEAK 40(17Q11.2) WILD-TYPE	32	48	44	26	42

Figure S243. Get High-res Image Gene #64: 'del_17q11.2' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_17q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0107 (Fisher's exact test), Q value = 0.038

Table S244. Gene #64: 'del_17q11.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
DEL PEAK 40(17Q11.2) MUTATED	19	5	4
DEL PEAK 40(17Q11.2) WILD-TYPE	71	65	56

Figure S244. Get High-res Image Gene #64: 'del_17q11.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_18q22.3' versus 'CN_CNMF'

P value = 0.00398 (Fisher's exact test), Q value = 0.017

Table S245. Gene #65: 'del_18q22.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
DEL PEAK 41(18Q22.3) MUTATED	41	34	7
DEL PEAK 41(18Q22.3) WILD-TYPE	214	163	118

Figure S245. Get High-res Image Gene #65: 'del_18q22.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_18q22.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0191 (Fisher's exact test), Q value = 0.061

Table S246. Gene #65: 'del_18q22.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
DEL PEAK 41(18Q22.3) MUTATED	15	17	4
DEL PEAK 41(18Q22.3) WILD-TYPE	75	53	56

Figure S246. Get High-res Image Gene #65: 'del_18q22.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_19q13.41' versus 'MRNA_CNMF'

P value = 0.0049 (Fisher's exact test), Q value = 0.02

Table S247. Gene #66: 'del_19q13.41' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
DEL PEAK 42(19Q13.41) MUTATED	23	23	15	30
DEL PEAK 42(19Q13.41) WILD-TYPE	135	73	122	87

Figure S247. Get High-res Image Gene #66: 'del_19q13.41' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19q13.41' versus 'MRNA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00057

Table S248. Gene #66: '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 42(19Q13.41) MUTATED	24	34	8	25
DEL PEAK 42(19Q13.41) WILD-TYPE	124	68	92	133

Figure S248. Get High-res Image Gene #66: 'del_19q13.41' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19q13.41' versus 'MIR_CHIERARCHICAL'

P value = 0.038 (Fisher's exact test), Q value = 0.11

Table S249. Gene #66: 'del_19q13.41' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 42(19Q13.41) MUTATED	63	19	15
DEL PEAK 42(19Q13.41) WILD-TYPE	230	105	114

Figure S249. Get High-res Image Gene #66: 'del_19q13.41' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_19q13.41' versus 'CN_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0023

Table S250. Gene #66: 'del_19q13.41' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
DEL PEAK 42(19Q13.41) MUTATED	55	37	8
DEL PEAK 42(19Q13.41) WILD-TYPE	200	160	117

Figure S250. Get High-res Image Gene #66: '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 = 0.00016

Table S251. Gene #66: 'del_19q13.41' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
DEL PEAK 42(19Q13.41) MUTATED	9	2	8	29
DEL PEAK 42(19Q13.41) WILD-TYPE	61	40	73	53

Figure S251. Get High-res Image Gene #66: 'del_19q13.41' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_19q13.41' versus 'MRNASEQ_CNMF'

P value = 0.0269 (Fisher's exact test), Q value = 0.081

Table S252. Gene #66: 'del_19q13.41' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	68	34
DEL PEAK 42(19Q13.41) MUTATED	9	6	10
DEL PEAK 42(19Q13.41) WILD-TYPE	36	62	24

Figure S252. Get High-res Image Gene #66: 'del_19q13.41' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_21q21.1' versus 'MRNA_CNMF'

P value = 0.00739 (Fisher's exact test), Q value = 0.028

Table S253. Gene #67: 'del_21q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	96	137	117
DEL PEAK 43(21Q21.1) MUTATED	6	15	12	14
DEL PEAK 43(21Q21.1) WILD-TYPE	152	81	125	103

Figure S253. Get High-res Image Gene #67: 'del_21q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_21q21.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00099 (Fisher's exact test), Q value = 0.0053

Table S254. Gene #67: '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 43(21Q21.1) MUTATED	5	19	8	15
DEL PEAK 43(21Q21.1) WILD-TYPE	143	83	92	143

Figure S254. Get High-res Image Gene #67: 'del_21q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_21q21.1' versus 'MIR_CNMF'

P value = 0.0314 (Fisher's exact test), Q value = 0.092

Table S255. Gene #67: 'del_21q21.1' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	187	90	126
DEL PEAK 43(21Q21.1) MUTATED	8	24	13	8
DEL PEAK 43(21Q21.1) WILD-TYPE	135	163	77	118

Figure S255. Get High-res Image Gene #67: 'del_21q21.1' versus Molecular Subtype #3: 'MIR_CNMF'

'del_21q21.1' versus 'METHLYATION_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.044

Table S256. Gene #67: 'del_21q21.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	42	81	82
DEL PEAK 43(21Q21.1) MUTATED	1	4	8	13
DEL PEAK 43(21Q21.1) WILD-TYPE	69	38	73	69

Figure S256. Get High-res Image Gene #67: 'del_21q21.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_21q21.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.037

Table S257. Gene #67: 'del_21q21.1' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	70	60
DEL PEAK 43(21Q21.1) MUTATED	2	9	8
DEL PEAK 43(21Q21.1) WILD-TYPE	88	61	52

Figure S257. Get High-res Image Gene #67: 'del_21q21.1' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S258. Gene #68: 'del_22q13.32' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	255	197	125
DEL PEAK 44(22Q13.32) MUTATED	89	96	27
DEL PEAK 44(22Q13.32) WILD-TYPE	166	101	98

Figure S258. Get High-res Image Gene #68: 'del_22q13.32' versus Molecular Subtype #5: 'CN_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 0.019 (Fisher's exact test), Q value = 0.061

Table S259. Gene #68: 'del_22q13.32' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	68	34
DEL PEAK 44(22Q13.32) MUTATED	16	26	22
DEL PEAK 44(22Q13.32) WILD-TYPE	29	42	12

Figure S259. Get High-res Image Gene #68: 'del_22q13.32' versus Molecular Subtype #9: 'MRNASEQ_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/22538153/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/GBM-TP/22555065/GBM-TP.transferedmergedcluster.txt
Number of patients = 577
Number of significantly focal cnvs = 68
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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