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 29 focal events and 12 molecular subtypes across 528 patients, 205 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q24.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
amp_1q32.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
amp_3q26.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_4q32.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
amp_5q35.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_7q31.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_8q24.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_10p14 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_xq11.2 cnv correlated to 'CN_CNMF'.
amp_xq28 cnv correlated to 'RPPA_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_1p36.13 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_1p31.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_1q44 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_2q37.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_3p25.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p22.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p12.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_3p12.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_3p11.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_3q11.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_4q34.3 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q26 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_6q26 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_8p23.2 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_9p23 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_9p21.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_13q13.3 cnv correlated to 'MRNA_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_14q31.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 29 focal events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 205 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
del 3p25 3	463 (88%)	65	1e-05 (4.46e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	2e-05 (8e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	5e-05 (0.000171)	1e-05 (4.46e-05)	0.00191 (0.00482)	0.012 (0.0247)
del 3p22 2	465 (88%)	63	1e-05 (4.46e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	3e-05 (0.000116)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	4e-05 (0.000147)	1e-05 (4.46e-05)	0.00317 (0.00756)	0.0246 (0.0451)
del 9p21 3	159 (30%)	369	0.00256 (0.00619)	0.0164 (0.0316)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	0.00097 (0.0027)	0.00603 (0.0133)
del 9p23	152 (29%)	376	0.00638 (0.0139)	0.0361 (0.0637)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	0.00189 (0.0048)	0.0646 (0.107)
del 1p31 1	77 (15%)	451	0.0046 (0.0103)	0.00618 (0.0135)	0.0139 (0.028)	0.183 (0.246)	0.00113 (0.0031)	5e-05 (0.000171)	2e-05 (8e-05)	3e-05 (0.000116)	1e-05 (4.46e-05)	0.00181 (0.00463)	0.0126 (0.0259)	0.258 (0.324)
del 14q31 1	228 (43%)	300	2e-05 (8e-05)	0.00041 (0.00122)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	0.0311 (0.0561)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	0.232 (0.299)	0.145 (0.204)
amp 3q26 32	87 (16%)	441	0.0907 (0.144)	0.119 (0.175)	0.00037 (0.00113)	1e-05 (4.46e-05)	2e-05 (8e-05)	2e-05 (8e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	4e-05 (0.000147)	0.00205 (0.0051)	0.241 (0.308)
amp 8q24 22	79 (15%)	449	0.33 (0.401)	0.102 (0.157)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	0.116 (0.172)
del 1q44	44 (8%)	484	0.0147 (0.0291)	0.011 (0.0231)	0.0001 (0.000328)	0.0133 (0.027)	0.0211 (0.0391)	0.00337 (0.00792)	0.00036 (0.00112)	5e-05 (0.000171)	0.11 (0.164)	0.0225 (0.0414)	0.357 (0.425)	0.939 (0.95)
del 6q26	151 (29%)	377	0.0367 (0.0646)	0.0973 (0.151)	1e-05 (4.46e-05)	0.206 (0.271)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	0.00067 (0.00193)	0.00037 (0.00113)	0.00404 (0.00913)	0.00362 (0.00834)	0.0488 (0.0833)	0.152 (0.214)
del 6q26	151 (29%)	377	0.0381 (0.0662)	0.0977 (0.151)	1e-05 (4.46e-05)	0.205 (0.271)	2e-05 (8e-05)	1e-05 (4.46e-05)	0.00048 (0.00142)	0.0001 (0.000328)	0.0023 (0.00568)	0.00365 (0.00836)	0.0484 (0.0831)	0.153 (0.214)
amp 7q31 2	175 (33%)	353	0.585 (0.642)	0.714 (0.757)	1e-05 (4.46e-05)	0.0382 (0.0662)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	8e-05 (0.000268)	0.00149 (0.00393)	0.00744 (0.016)	0.0113 (0.0234)	0.115 (0.171)	0.908 (0.926)
del 1p36 13	99 (19%)	429	0.00103 (0.00284)	0.00165 (0.00425)	0.158 (0.221)	0.44 (0.508)	0.00011 (0.000358)	0.00234 (0.00573)	4e-05 (0.000147)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	0.00325 (0.00769)	0.0953 (0.149)	0.085 (0.135)
del 3p12 3	339 (64%)	189	0.00879 (0.0188)	0.0162 (0.0313)	1e-05 (4.46e-05)	0.0158 (0.0307)	0.17 (0.232)	0.0664 (0.11)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	0.0207 (0.0385)	0.0373 (0.0652)	0.168 (0.229)	0.801 (0.832)
del 13q13 3	81 (15%)	447	0.0196 (0.0368)	0.0851 (0.135)	0.0538 (0.09)	0.00201 (0.00503)	1e-05 (4.46e-05)	0.00121 (0.00329)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	1e-05 (4.46e-05)	5e-05 (0.000171)	0.104 (0.158)	0.339 (0.41)
del 2q37 3	50 (9%)	478	0.0041 (0.00921)	0.00041 (0.00122)	0.00151 (0.00395)	0.0178 (0.034)	0.416 (0.484)	0.238 (0.305)	0.00024 (0.000759)	2e-05 (8e-05)	0.0817 (0.132)	0.0352 (0.0624)	0.299 (0.369)	0.341 (0.41)
del 4q34 3	78 (15%)	450	0.215 (0.281)	0.494 (0.561)	0.122 (0.176)	0.00255 (0.00619)	8e-05 (0.000268)	0.00344 (0.00803)	0.00926 (0.0196)	1e-05 (4.46e-05)	0.286 (0.356)	0.0196 (0.0368)	0.244 (0.31)	0.00361 (0.00834)
amp 5q35 1	332 (63%)	196	0.0332 (0.0596)	0.0492 (0.0836)	1e-05 (4.46e-05)	0.529 (0.59)	0.0714 (0.117)	0.00087 (0.00246)	5e-05 (0.000171)	5e-05 (0.000171)	0.108 (0.163)	0.128 (0.185)	0.7 (0.749)	0.76 (0.799)
del 8p23 2	154 (29%)	374	0.312 (0.38)	0.245 (0.311)	0.0113 (0.0234)	0.209 (0.275)	0.0137 (0.0278)	0.728 (0.77)	5e-05 (0.000171)	4e-05 (0.000147)	0.00124 (0.00335)	0.00052 (0.00152)	0.135 (0.194)	0.552 (0.609)
del 10q23 31	96 (18%)	432	0.553 (0.609)	0.548 (0.607)	0.00658 (0.0142)	0.0458 (0.0789)	0.685 (0.743)	0.0144 (0.0288)	0.228 (0.294)	0.00029 (0.000909)	0.00039 (0.00118)	0.00137 (0.00364)	0.93 (0.945)	0.519 (0.583)
amp 10p14	20 (4%)	508	0.217 (0.283)	0.775 (0.813)	0.0147 (0.0291)	0.514 (0.579)	0.0152 (0.0298)	0.0671 (0.11)	0.00279 (0.0067)	3e-05 (0.000116)	0.115 (0.171)	0.0271 (0.0495)	1 (1.00)	0.141 (0.201)
amp 1q24 1	62 (12%)	466	0.357 (0.425)	0.784 (0.819)	1e-05 (4.46e-05)	0.204 (0.271)	0.368 (0.437)	0.401 (0.468)	0.00092 (0.00258)	0.00376 (0.00855)	0.0007 (0.002)	0.155 (0.216)	0.513 (0.579)	0.829 (0.859)
amp 1q32 1	62 (12%)	466	0.466 (0.534)	0.9 (0.924)	1e-05 (4.46e-05)	0.0718 (0.117)	0.167 (0.229)	0.121 (0.176)	0.00012 (0.000387)	0.00161 (0.00418)	0.00055 (0.00159)	0.179 (0.242)	0.388 (0.455)	0.903 (0.924)
del 3q11 2	161 (30%)	367	0.457 (0.525)	0.164 (0.226)	1e-05 (4.46e-05)	0.118 (0.174)	0.857 (0.885)	0.137 (0.196)	0.00133 (0.00356)	2e-05 (8e-05)	0.00606 (0.0133)	0.931 (0.945)	0.701 (0.749)	0.705 (0.75)
amp 4q32 1	16 (3%)	512			0.0196 (0.0368)	0.117 (0.172)	0.346 (0.416)	0.0932 (0.146)	0.103 (0.157)	0.0106 (0.0225)	0.0152 (0.0298)	0.304 (0.372)	0.288 (0.356)	0.875 (0.9)
del 3p12 2	305 (58%)	223	0.103 (0.157)	0.064 (0.106)	1e-05 (4.46e-05)	0.19 (0.254)	0.274 (0.343)	0.191 (0.255)	4e-05 (0.000147)	1e-05 (4.46e-05)	0.0739 (0.12)	0.249 (0.314)	0.457 (0.525)	0.654 (0.711)
del 3p11 1	237 (45%)	291	0.377 (0.446)	0.38 (0.446)	1e-05 (4.46e-05)	0.0508 (0.0858)	0.626 (0.685)	0.301 (0.37)	0.00018 (0.000575)	2e-05 (8e-05)	0.168 (0.229)	0.961 (0.969)	0.693 (0.748)	0.528 (0.59)
amp xq28	37 (7%)	491	0.511 (0.579)	0.701 (0.749)	0.439 (0.508)	0.694 (0.748)	0.0195 (0.0368)	0.093 (0.146)	0.38 (0.446)	0.0343 (0.0612)	0.0838 (0.134)	0.219 (0.285)	0.792 (0.825)	0.239 (0.306)
amp xq11 2	29 (5%)	499	0.18 (0.243)	0.161 (0.223)	0.0306 (0.0555)	0.486 (0.555)	0.144 (0.204)	0.0526 (0.0885)	0.109 (0.164)	0.309 (0.378)	0.639 (0.697)	0.287 (0.356)	0.541 (0.602)	0.752 (0.793)

'amp_1q24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S1. Gene #1: 'amp_1q24.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	80	156	82	80	69
AMP PEAK 1(1Q24.1) MUTATED	5	4	42	9	2	0
AMP PEAK 1(1Q24.1) WILD-TYPE	56	76	114	73	78	69

Figure S1. Get High-res Image Gene #1: 'amp_1q24.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q24.1' versus 'MRNASEQ_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.0026

Table S2. Gene #1: 'amp_1q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	170	81	153	40
AMP PEAK 1(1Q24.1) MUTATED	5	15	7	32	1
AMP PEAK 1(1Q24.1) WILD-TYPE	76	155	74	121	39

Figure S2. Get High-res Image Gene #1: 'amp_1q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00376 (Fisher's exact test), Q value = 0.0086

Table S3. Gene #1: 'amp_1q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
AMP PEAK 1(1Q24.1) MUTATED	7	3	18	25	7	0
AMP PEAK 1(1Q24.1) WILD-TYPE	110	30	165	107	28	25

Figure S3. Get High-res Image Gene #1: 'amp_1q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q24.1' versus 'MIRSEQ_CNMF'

P value = 7e-04 (Fisher's exact test), Q value = 0.002

Table S4. Gene #1: 'amp_1q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	57	186	119	57
AMP PEAK 1(1Q24.1) MUTATED	4	9	16	26	5
AMP PEAK 1(1Q24.1) WILD-TYPE	87	48	170	93	52

Figure S4. Get High-res Image Gene #1: 'amp_1q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q32.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S5. Gene #2: 'amp_1q32.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	80	156	82	80	69
AMP PEAK 2(1Q32.1) MUTATED	4	5	44	8	0	1
AMP PEAK 2(1Q32.1) WILD-TYPE	57	75	112	74	80	68

Figure S5. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q32.1' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00039

Table S6. Gene #2: 'amp_1q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	170	81	153	40
AMP PEAK 2(1Q32.1) MUTATED	3	14	8	33	2
AMP PEAK 2(1Q32.1) WILD-TYPE	78	156	73	120	38

Figure S6. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q32.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00161 (Fisher's exact test), Q value = 0.0042

Table S7. Gene #2: 'amp_1q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
AMP PEAK 2(1Q32.1) MUTATED	7	2	18	26	7	0
AMP PEAK 2(1Q32.1) WILD-TYPE	110	31	165	106	28	25

Figure S7. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q32.1' versus 'MIRSEQ_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0016

Table S8. Gene #2: 'amp_1q32.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	57	186	119	57
AMP PEAK 2(1Q32.1) MUTATED	4	8	16	27	5
AMP PEAK 2(1Q32.1) WILD-TYPE	87	49	170	92	52

Figure S8. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.32' versus 'CN_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0011

Table S9. Gene #3: 'amp_3q26.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	80	156	82	80	69
AMP PEAK 3(3Q26.32) MUTATED	11	8	40	5	17	6
AMP PEAK 3(3Q26.32) WILD-TYPE	50	72	116	77	63	63

Figure S9. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S10. Gene #3: 'amp_3q26.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	70	96	81
AMP PEAK 3(3Q26.32) MUTATED	10	13	27	1
AMP PEAK 3(3Q26.32) WILD-TYPE	57	57	69	80

Figure S10. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.32' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8e-05

Table S11. Gene #3: 'amp_3q26.32' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	86	90	82	92	33
AMP PEAK 3(3Q26.32) MUTATED	19	9	32	10	10	1
AMP PEAK 3(3Q26.32) WILD-TYPE	69	77	58	72	82	32

Figure S11. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_3q26.32' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8e-05

Table S12. Gene #3: 'amp_3q26.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	112	85	139
AMP PEAK 3(3Q26.32) MUTATED	13	23	29	16
AMP PEAK 3(3Q26.32) WILD-TYPE	122	89	56	123

Figure S12. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_3q26.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S13. Gene #3: 'amp_3q26.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	170	81	153	40
AMP PEAK 3(3Q26.32) MUTATED	18	12	11	42	4
AMP PEAK 3(3Q26.32) WILD-TYPE	63	158	70	111	36

Figure S13. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S14. Gene #3: 'amp_3q26.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
AMP PEAK 3(3Q26.32) MUTATED	14	4	14	43	8	4
AMP PEAK 3(3Q26.32) WILD-TYPE	103	29	169	89	27	21

Figure S14. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S15. Gene #3: 'amp_3q26.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	57	186	119	57
AMP PEAK 3(3Q26.32) MUTATED	10	13	14	37	10
AMP PEAK 3(3Q26.32) WILD-TYPE	81	44	172	82	47

Figure S15. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00015

Table S16. Gene #3: 'amp_3q26.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	209	128
AMP PEAK 3(3Q26.32) MUTATED	35	17	32
AMP PEAK 3(3Q26.32) WILD-TYPE	138	192	96

Figure S16. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00205 (Fisher's exact test), Q value = 0.0051

Table S17. Gene #3: 'amp_3q26.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	21	44	38
AMP PEAK 3(3Q26.32) MUTATED	2	1	3	12
AMP PEAK 3(3Q26.32) WILD-TYPE	37	20	41	26

Figure S17. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_4q32.1' versus 'CN_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.037

Table S18. Gene #4: 'amp_4q32.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	80	156	82	80	69
AMP PEAK 4(4Q32.1) MUTATED	2	3	5	0	0	6
AMP PEAK 4(4Q32.1) WILD-TYPE	59	77	151	82	80	63

Figure S18. Get High-res Image Gene #4: 'amp_4q32.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_4q32.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0106 (Fisher's exact test), Q value = 0.022

Table S19. Gene #4: 'amp_4q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
AMP PEAK 4(4Q32.1) MUTATED	5	0	2	4	0	4
AMP PEAK 4(4Q32.1) WILD-TYPE	112	33	181	128	35	21

Figure S19. Get High-res Image Gene #4: 'amp_4q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_4q32.1' versus 'MIRSEQ_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.03

Table S20. Gene #4: 'amp_4q32.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	57	186	119	57
AMP PEAK 4(4Q32.1) MUTATED	3	4	1	7	1
AMP PEAK 4(4Q32.1) WILD-TYPE	88	53	185	112	56

Figure S20. Get High-res Image Gene #4: 'amp_4q32.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_5q35.1' versus 'MRNA_CNMF'

P value = 0.0332 (Fisher's exact test), Q value = 0.06

Table S21. Gene #5: 'amp_5q35.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	25	14
AMP PEAK 5(5Q35.1) MUTATED	19	15	3
AMP PEAK 5(5Q35.1) WILD-TYPE	12	10	11

Figure S21. Get High-res Image Gene #5: 'amp_5q35.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_5q35.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0492 (Fisher's exact test), Q value = 0.084

Table S22. Gene #5: 'amp_5q35.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	11	12	4	11	13	9	10
AMP PEAK 5(5Q35.1) MUTATED	8	5	0	9	7	5	3
AMP PEAK 5(5Q35.1) WILD-TYPE	3	7	4	2	6	4	7

Figure S22. Get High-res Image Gene #5: 'amp_5q35.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_5q35.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S23. Gene #5: 'amp_5q35.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	80	156	82	80	69
AMP PEAK 5(5Q35.1) MUTATED	61	48	92	47	56	28
AMP PEAK 5(5Q35.1) WILD-TYPE	0	32	64	35	24	41

Figure S23. Get High-res Image Gene #5: 'amp_5q35.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5q35.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00087 (Fisher's exact test), Q value = 0.0025

Table S24. Gene #5: 'amp_5q35.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	112	85	139
AMP PEAK 5(5Q35.1) MUTATED	84	68	43	106
AMP PEAK 5(5Q35.1) WILD-TYPE	51	44	42	33

Figure S24. Get High-res Image Gene #5: 'amp_5q35.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_5q35.1' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00017

Table S25. Gene #5: 'amp_5q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	170	81	153	40
AMP PEAK 5(5Q35.1) MUTATED	34	113	45	111	27
AMP PEAK 5(5Q35.1) WILD-TYPE	47	57	36	42	13

Figure S25. Get High-res Image Gene #5: 'amp_5q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00017

Table S26. Gene #5: 'amp_5q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
AMP PEAK 5(5Q35.1) MUTATED	79	15	121	84	26	5
AMP PEAK 5(5Q35.1) WILD-TYPE	38	18	62	48	9	20

Figure S26. Get High-res Image Gene #5: 'amp_5q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S27. Gene #6: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	80	156	82	80	69
AMP PEAK 6(7Q31.2) MUTATED	39	34	55	10	23	14
AMP PEAK 6(7Q31.2) WILD-TYPE	22	46	101	72	57	55

Figure S27. Get High-res Image Gene #6: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q31.2' versus 'METHLYATION_CNMF'

P value = 0.0382 (Fisher's exact test), Q value = 0.066

Table S28. Gene #6: 'amp_7q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	70	96	81
AMP PEAK 6(7Q31.2) MUTATED	12	24	35	20
AMP PEAK 6(7Q31.2) WILD-TYPE	55	46	61	61

Figure S28. Get High-res Image Gene #6: 'amp_7q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7q31.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S29. Gene #6: 'amp_7q31.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	86	90	82	92	33
AMP PEAK 6(7Q31.2) MUTATED	32	21	52	23	23	5
AMP PEAK 6(7Q31.2) WILD-TYPE	56	65	38	59	69	28

Figure S29. Get High-res Image Gene #6: 'amp_7q31.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_7q31.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S30. Gene #6: 'amp_7q31.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	112	85	139
AMP PEAK 6(7Q31.2) MUTATED	36	50	41	29
AMP PEAK 6(7Q31.2) WILD-TYPE	99	62	44	110

Figure S30. Get High-res Image Gene #6: 'amp_7q31.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_7q31.2' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00027

Table S31. Gene #6: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	170	81	153	40
AMP PEAK 6(7Q31.2) MUTATED	26	36	27	72	12
AMP PEAK 6(7Q31.2) WILD-TYPE	55	134	54	81	28

Figure S31. Get High-res Image Gene #6: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00149 (Fisher's exact test), Q value = 0.0039

Table S32. Gene #6: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
AMP PEAK 6(7Q31.2) MUTATED	38	11	43	61	14	6
AMP PEAK 6(7Q31.2) WILD-TYPE	79	22	140	71	21	19

Figure S32. Get High-res Image Gene #6: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_CNMF'

P value = 0.00744 (Fisher's exact test), Q value = 0.016

Table S33. Gene #6: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	57	186	119	57
AMP PEAK 6(7Q31.2) MUTATED	27	27	53	51	14
AMP PEAK 6(7Q31.2) WILD-TYPE	64	30	133	68	43

Figure S33. Get High-res Image Gene #6: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.023

Table S34. Gene #6: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	209	128
AMP PEAK 6(7Q31.2) MUTATED	62	56	54
AMP PEAK 6(7Q31.2) WILD-TYPE	111	153	74

Figure S34. Get High-res Image Gene #6: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S35. Gene #7: 'amp_8q24.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	80	156	82	80	69
AMP PEAK 7(8Q24.22) MUTATED	7	12	43	5	10	2
AMP PEAK 7(8Q24.22) WILD-TYPE	54	68	113	77	70	67

Figure S35. Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.22' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S36. Gene #7: 'amp_8q24.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	70	96	81
AMP PEAK 7(8Q24.22) MUTATED	4	15	31	3
AMP PEAK 7(8Q24.22) WILD-TYPE	63	55	65	78

Figure S36. Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.22' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S37. Gene #7: 'amp_8q24.22' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	86	90	82	92	33
AMP PEAK 7(8Q24.22) MUTATED	13	5	36	7	12	1
AMP PEAK 7(8Q24.22) WILD-TYPE	75	81	54	75	80	32

Figure S37. Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_8q24.22' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S38. Gene #7: 'amp_8q24.22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	112	85	139
AMP PEAK 7(8Q24.22) MUTATED	9	31	25	9
AMP PEAK 7(8Q24.22) WILD-TYPE	126	81	60	130

Figure S38. Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_8q24.22' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S39. Gene #7: 'amp_8q24.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	170	81	153	40
AMP PEAK 7(8Q24.22) MUTATED	4	6	13	51	4
AMP PEAK 7(8Q24.22) WILD-TYPE	77	164	68	102	36

Figure S39. Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S40. Gene #7: 'amp_8q24.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
AMP PEAK 7(8Q24.22) MUTATED	9	2	8	54	4	1
AMP PEAK 7(8Q24.22) WILD-TYPE	108	31	175	78	31	24

Figure S40. Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.22' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S41. Gene #7: 'amp_8q24.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	57	186	119	57
AMP PEAK 7(8Q24.22) MUTATED	11	12	10	39	5
AMP PEAK 7(8Q24.22) WILD-TYPE	80	45	176	80	52

Figure S41. Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S42. Gene #7: 'amp_8q24.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	209	128
AMP PEAK 7(8Q24.22) MUTATED	41	13	23
AMP PEAK 7(8Q24.22) WILD-TYPE	132	196	105

Figure S42. Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S43. Gene #7: 'amp_8q24.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	21	44	38
AMP PEAK 7(8Q24.22) MUTATED	3	1	0	15
AMP PEAK 7(8Q24.22) WILD-TYPE	36	20	44	23

Figure S43. Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_10p14' versus 'CN_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.029

Table S44. Gene #8: 'amp_10p14' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	80	156	82	80	69
AMP PEAK 8(10P14) MUTATED	3	2	12	0	3	0
AMP PEAK 8(10P14) WILD-TYPE	58	78	144	82	77	69

Figure S44. Get High-res Image Gene #8: 'amp_10p14' versus Molecular Subtype #3: 'CN_CNMF'

'amp_10p14' versus 'RPPA_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.03

Table S45. Gene #8: 'amp_10p14' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	86	90	82	92	33
AMP PEAK 8(10P14) MUTATED	1	2	10	2	2	2
AMP PEAK 8(10P14) WILD-TYPE	87	84	80	80	90	31

Figure S45. Get High-res Image Gene #8: 'amp_10p14' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_10p14' versus 'MRNASEQ_CNMF'

P value = 0.00279 (Fisher's exact test), Q value = 0.0067

Table S46. Gene #8: 'amp_10p14' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	170	81	153	40
AMP PEAK 8(10P14) MUTATED	3	1	3	13	0
AMP PEAK 8(10P14) WILD-TYPE	78	169	78	140	40

Figure S46. Get High-res Image Gene #8: 'amp_10p14' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_10p14' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

Table S47. Gene #8: 'amp_10p14' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
AMP PEAK 8(10P14) MUTATED	2	2	0	14	2	0
AMP PEAK 8(10P14) WILD-TYPE	115	31	183	118	33	25

Figure S47. Get High-res Image Gene #8: 'amp_10p14' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10p14' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0271 (Fisher's exact test), Q value = 0.049

Table S48. Gene #8: 'amp_10p14' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	209	128
AMP PEAK 8(10P14) MUTATED	11	3	6
AMP PEAK 8(10P14) WILD-TYPE	162	206	122

Figure S48. Get High-res Image Gene #8: 'amp_10p14' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_xq11.2' versus 'CN_CNMF'

P value = 0.0306 (Fisher's exact test), Q value = 0.055

Table S49. Gene #9: 'amp_xq11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	80	156	82	80	69
AMP PEAK 9(XQ11.2) MUTATED	9	5	5	2	3	5
AMP PEAK 9(XQ11.2) WILD-TYPE	52	75	151	80	77	64

Figure S49. Get High-res Image Gene #9: 'amp_xq11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xq28' versus 'RPPA_CNMF'

P value = 0.0195 (Fisher's exact test), Q value = 0.037

Table S50. Gene #10: 'amp_xq28' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	86	90	82	92	33
AMP PEAK 10(XQ28) MUTATED	8	1	11	8	6	0
AMP PEAK 10(XQ28) WILD-TYPE	80	85	79	74	86	33

Figure S50. Get High-res Image Gene #10: 'amp_xq28' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_xq28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0343 (Fisher's exact test), Q value = 0.061

Table S51. Gene #10: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
AMP PEAK 10(XQ28) MUTATED	5	2	9	14	6	0
AMP PEAK 10(XQ28) WILD-TYPE	112	31	174	118	29	25

Figure S51. Get High-res Image Gene #10: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.13' versus 'MRNA_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.0028

Table S52. Gene #11: 'del_1p36.13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	25	14
DEL PEAK 1(1P36.13) MUTATED	2	7	8
DEL PEAK 1(1P36.13) WILD-TYPE	29	18	6

Figure S52. Get High-res Image Gene #11: 'del_1p36.13' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.13' versus 'MRNA_CHIERARCHICAL'

P value = 0.00165 (Fisher's exact test), Q value = 0.0043

Table S53. Gene #11: 'del_1p36.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	11	12	4	11	13	9	10
DEL PEAK 1(1P36.13) MUTATED	0	2	2	4	1	1	7
DEL PEAK 1(1P36.13) WILD-TYPE	11	10	2	7	12	8	3

Figure S53. Get High-res Image Gene #11: 'del_1p36.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p36.13' versus 'RPPA_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00036

Table S54. Gene #11: 'del_1p36.13' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	86	90	82	92	33
DEL PEAK 1(1P36.13) MUTATED	24	6	27	17	10	5
DEL PEAK 1(1P36.13) WILD-TYPE	64	80	63	65	82	28

Figure S54. Get High-res Image Gene #11: 'del_1p36.13' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p36.13' versus 'RPPA_CHIERARCHICAL'

P value = 0.00234 (Fisher's exact test), Q value = 0.0057

Table S55. Gene #11: 'del_1p36.13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	112	85	139
DEL PEAK 1(1P36.13) MUTATED	16	29	24	20
DEL PEAK 1(1P36.13) WILD-TYPE	119	83	61	119

Figure S55. Get High-res Image Gene #11: 'del_1p36.13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_1p36.13' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00015

Table S56. Gene #11: 'del_1p36.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	170	81	153	40
DEL PEAK 1(1P36.13) MUTATED	26	22	5	41	5
DEL PEAK 1(1P36.13) WILD-TYPE	55	148	76	112	35

Figure S56. Get High-res Image Gene #11: 'del_1p36.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S57. Gene #11: 'del_1p36.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 1(1P36.13) MUTATED	11	6	23	38	9	12
DEL PEAK 1(1P36.13) WILD-TYPE	106	27	160	94	26	13

Figure S57. Get High-res Image Gene #11: 'del_1p36.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.13' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S58. Gene #11: 'del_1p36.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	57	186	119	57
DEL PEAK 1(1P36.13) MUTATED	16	9	22	48	4
DEL PEAK 1(1P36.13) WILD-TYPE	75	48	164	71	53

Figure S58. Get High-res Image Gene #11: 'del_1p36.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00325 (Fisher's exact test), Q value = 0.0077

Table S59. Gene #11: 'del_1p36.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	209	128
DEL PEAK 1(1P36.13) MUTATED	41	26	32
DEL PEAK 1(1P36.13) WILD-TYPE	132	183	96

Figure S59. Get High-res Image Gene #11: 'del_1p36.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p31.1' versus 'MRNA_CNMF'

P value = 0.0046 (Fisher's exact test), Q value = 0.01

Table S60. Gene #12: 'del_1p31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	25	14
DEL PEAK 2(1P31.1) MUTATED	2	5	7
DEL PEAK 2(1P31.1) WILD-TYPE	29	20	7

Figure S60. Get High-res Image Gene #12: 'del_1p31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p31.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00618 (Fisher's exact test), Q value = 0.014

Table S61. Gene #12: 'del_1p31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	11	12	4	11	13	9	10
DEL PEAK 2(1P31.1) MUTATED	0	3	2	1	1	1	6
DEL PEAK 2(1P31.1) WILD-TYPE	11	9	2	10	12	8	4

Figure S61. Get High-res Image Gene #12: 'del_1p31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p31.1' versus 'CN_CNMF'

P value = 0.0139 (Fisher's exact test), Q value = 0.028

Table S62. Gene #12: 'del_1p31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	80	156	82	80	69
DEL PEAK 2(1P31.1) MUTATED	4	8	29	7	12	17
DEL PEAK 2(1P31.1) WILD-TYPE	57	72	127	75	68	52

Figure S62. Get High-res Image Gene #12: 'del_1p31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p31.1' versus 'RPPA_CNMF'

P value = 0.00113 (Fisher's exact test), Q value = 0.0031

Table S63. Gene #12: 'del_1p31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	86	90	82	92	33
DEL PEAK 2(1P31.1) MUTATED	20	7	21	11	5	4
DEL PEAK 2(1P31.1) WILD-TYPE	68	79	69	71	87	29

Figure S63. Get High-res Image Gene #12: 'del_1p31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p31.1' versus 'RPPA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00017

Table S64. Gene #12: 'del_1p31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	112	85	139
DEL PEAK 2(1P31.1) MUTATED	6	23	21	18
DEL PEAK 2(1P31.1) WILD-TYPE	129	89	64	121

Figure S64. Get High-res Image Gene #12: 'del_1p31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_1p31.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8e-05

Table S65. Gene #12: 'del_1p31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	170	81	153	40
DEL PEAK 2(1P31.1) MUTATED	24	17	3	29	4
DEL PEAK 2(1P31.1) WILD-TYPE	57	153	78	124	36

Figure S65. Get High-res Image Gene #12: 'del_1p31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

Table S66. Gene #12: 'del_1p31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 2(1P31.1) MUTATED	11	6	16	28	4	12
DEL PEAK 2(1P31.1) WILD-TYPE	106	27	167	104	31	13

Figure S66. Get High-res Image Gene #12: 'del_1p31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p31.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S67. Gene #12: 'del_1p31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	57	186	119	57
DEL PEAK 2(1P31.1) MUTATED	10	6	18	39	4
DEL PEAK 2(1P31.1) WILD-TYPE	81	51	168	80	53

Figure S67. Get High-res Image Gene #12: 'del_1p31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00181 (Fisher's exact test), Q value = 0.0046

Table S68. Gene #12: 'del_1p31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	209	128
DEL PEAK 2(1P31.1) MUTATED	23	22	32
DEL PEAK 2(1P31.1) WILD-TYPE	150	187	96

Figure S68. Get High-res Image Gene #12: 'del_1p31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p31.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.026

Table S69. Gene #12: 'del_1p31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	21	44	38
DEL PEAK 2(1P31.1) MUTATED	6	0	2	9
DEL PEAK 2(1P31.1) WILD-TYPE	33	21	42	29

Figure S69. Get High-res Image Gene #12: 'del_1p31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1q44' versus 'MRNA_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.029

Table S70. Gene #13: 'del_1q44' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	25	14
DEL PEAK 3(1Q44) MUTATED	2	1	5
DEL PEAK 3(1Q44) WILD-TYPE	29	24	9

Figure S70. Get High-res Image Gene #13: 'del_1q44' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1q44' versus 'MRNA_CHIERARCHICAL'

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

Table S71. Gene #13: 'del_1q44' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	11	12	4	11	13	9	10
DEL PEAK 3(1Q44) MUTATED	0	1	0	0	1	1	5
DEL PEAK 3(1Q44) WILD-TYPE	11	11	4	11	12	8	5

Figure S71. Get High-res Image Gene #13: 'del_1q44' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1q44' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00033

Table S72. Gene #13: 'del_1q44' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	80	156	82	80	69
DEL PEAK 3(1Q44) MUTATED	1	5	6	5	12	15
DEL PEAK 3(1Q44) WILD-TYPE	60	75	150	77	68	54

Figure S72. Get High-res Image Gene #13: 'del_1q44' versus Molecular Subtype #3: 'CN_CNMF'

'del_1q44' versus 'METHLYATION_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.027

Table S73. Gene #13: 'del_1q44' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	70	96	81
DEL PEAK 3(1Q44) MUTATED	11	1	7	6
DEL PEAK 3(1Q44) WILD-TYPE	56	69	89	75

Figure S73. Get High-res Image Gene #13: 'del_1q44' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1q44' versus 'RPPA_CNMF'

P value = 0.0211 (Fisher's exact test), Q value = 0.039

Table S74. Gene #13: 'del_1q44' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	86	90	82	92	33
DEL PEAK 3(1Q44) MUTATED	14	8	8	4	2	2
DEL PEAK 3(1Q44) WILD-TYPE	74	78	82	78	90	31

Figure S74. Get High-res Image Gene #13: 'del_1q44' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1q44' versus 'RPPA_CHIERARCHICAL'

P value = 0.00337 (Fisher's exact test), Q value = 0.0079

Table S75. Gene #13: 'del_1q44' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	112	85	139
DEL PEAK 3(1Q44) MUTATED	5	10	15	8
DEL PEAK 3(1Q44) WILD-TYPE	130	102	70	131

Figure S75. Get High-res Image Gene #13: 'del_1q44' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_1q44' versus 'MRNASEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0011

Table S76. Gene #13: 'del_1q44' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	170	81	153	40
DEL PEAK 3(1Q44) MUTATED	17	12	1	11	3
DEL PEAK 3(1Q44) WILD-TYPE	64	158	80	142	37

Figure S76. Get High-res Image Gene #13: 'del_1q44' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1q44' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00017

Table S77. Gene #13: 'del_1q44' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 3(1Q44) MUTATED	6	1	14	10	2	11
DEL PEAK 3(1Q44) WILD-TYPE	111	32	169	122	33	14

Figure S77. Get High-res Image Gene #13: 'del_1q44' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1q44' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0225 (Fisher's exact test), Q value = 0.041

Table S78. Gene #13: 'del_1q44' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	209	128
DEL PEAK 3(1Q44) MUTATED	11	14	19
DEL PEAK 3(1Q44) WILD-TYPE	162	195	109

Figure S78. Get High-res Image Gene #13: 'del_1q44' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MRNA_CNMF'

P value = 0.0041 (Fisher's exact test), Q value = 0.0092

Table S79. Gene #14: 'del_2q37.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	25	14
DEL PEAK 4(2Q37.3) MUTATED	1	4	6
DEL PEAK 4(2Q37.3) WILD-TYPE	30	21	8

Figure S79. Get High-res Image Gene #14: 'del_2q37.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_2q37.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0012

Table S80. Gene #14: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	11	12	4	11	13	9	10
DEL PEAK 4(2Q37.3) MUTATED	0	4	0	0	1	0	6
DEL PEAK 4(2Q37.3) WILD-TYPE	11	8	4	11	12	9	4

Figure S80. Get High-res Image Gene #14: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 0.00151 (Fisher's exact test), Q value = 0.004

Table S81. Gene #14: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	80	156	82	80	69
DEL PEAK 4(2Q37.3) MUTATED	1	5	19	11	2	12
DEL PEAK 4(2Q37.3) WILD-TYPE	60	75	137	71	78	57

Figure S81. Get High-res Image Gene #14: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 0.0178 (Fisher's exact test), Q value = 0.034

Table S82. Gene #14: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	70	96	81
DEL PEAK 4(2Q37.3) MUTATED	11	5	11	2
DEL PEAK 4(2Q37.3) WILD-TYPE	56	65	85	79

Figure S82. Get High-res Image Gene #14: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00076

Table S83. Gene #14: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	170	81	153	40
DEL PEAK 4(2Q37.3) MUTATED	14	6	14	14	1
DEL PEAK 4(2Q37.3) WILD-TYPE	67	164	67	139	39

Figure S83. Get High-res Image Gene #14: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8e-05

Table S84. Gene #14: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 4(2Q37.3) MUTATED	13	1	7	18	1	9
DEL PEAK 4(2Q37.3) WILD-TYPE	104	32	176	114	34	16

Figure S84. Get High-res Image Gene #14: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0352 (Fisher's exact test), Q value = 0.062

Table S85. Gene #14: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	209	128
DEL PEAK 4(2Q37.3) MUTATED	16	13	19
DEL PEAK 4(2Q37.3) WILD-TYPE	157	196	109

Figure S85. Get High-res Image Gene #14: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p25.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S86. Gene #15: 'del_3p25.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	25	14
DEL PEAK 5(3P25.3) MUTATED	30	23	4
DEL PEAK 5(3P25.3) WILD-TYPE	1	2	10

Figure S86. Get High-res Image Gene #15: 'del_3p25.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p25.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S87. Gene #15: 'del_3p25.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	11	12	4	11	13	9	10
DEL PEAK 5(3P25.3) MUTATED	11	11	1	11	12	9	2
DEL PEAK 5(3P25.3) WILD-TYPE	0	1	3	0	1	0	8

Figure S87. Get High-res Image Gene #15: 'del_3p25.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p25.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S88. Gene #15: 'del_3p25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	80	156	82	80	69
DEL PEAK 5(3P25.3) MUTATED	59	46	150	77	77	54
DEL PEAK 5(3P25.3) WILD-TYPE	2	34	6	5	3	15

Figure S88. Get High-res Image Gene #15: 'del_3p25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p25.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S89. Gene #15: 'del_3p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	70	96	81
DEL PEAK 5(3P25.3) MUTATED	49	57	93	79
DEL PEAK 5(3P25.3) WILD-TYPE	18	13	3	2

Figure S89. Get High-res Image Gene #15: 'del_3p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p25.3' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8e-05

Table S90. Gene #15: 'del_3p25.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	86	90	82	92	33
DEL PEAK 5(3P25.3) MUTATED	66	85	82	76	78	30
DEL PEAK 5(3P25.3) WILD-TYPE	22	1	8	6	14	3

Figure S90. Get High-res Image Gene #15: 'del_3p25.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p25.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S91. Gene #15: 'del_3p25.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	112	85	139
DEL PEAK 5(3P25.3) MUTATED	114	107	62	134
DEL PEAK 5(3P25.3) WILD-TYPE	21	5	23	5

Figure S91. Get High-res Image Gene #15: 'del_3p25.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p25.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S92. Gene #15: 'del_3p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	170	81	153	40
DEL PEAK 5(3P25.3) MUTATED	41	167	74	140	38
DEL PEAK 5(3P25.3) WILD-TYPE	40	3	7	13	2

Figure S92. Get High-res Image Gene #15: 'del_3p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S93. Gene #15: 'del_3p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 5(3P25.3) MUTATED	109	20	179	115	35	2
DEL PEAK 5(3P25.3) WILD-TYPE	8	13	4	17	0	23

Figure S93. Get High-res Image Gene #15: 'del_3p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p25.3' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00017

Table S94. Gene #15: 'del_3p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	57	186	119	57
DEL PEAK 5(3P25.3) MUTATED	75	50	178	92	51
DEL PEAK 5(3P25.3) WILD-TYPE	16	7	8	27	6

Figure S94. Get High-res Image Gene #15: 'del_3p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S95. Gene #15: 'del_3p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	209	128
DEL PEAK 5(3P25.3) MUTATED	142	202	102
DEL PEAK 5(3P25.3) WILD-TYPE	31	7	26

Figure S95. Get High-res Image Gene #15: 'del_3p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p25.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00191 (Fisher's exact test), Q value = 0.0048

Table S96. Gene #15: 'del_3p25.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	21	44	38
DEL PEAK 5(3P25.3) MUTATED	27	16	43	30
DEL PEAK 5(3P25.3) WILD-TYPE	12	5	1	8

Figure S96. Get High-res Image Gene #15: 'del_3p25.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.025

Table S97. Gene #15: 'del_3p25.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	52	28	22
DEL PEAK 5(3P25.3) MUTATED	28	41	25	22
DEL PEAK 5(3P25.3) WILD-TYPE	12	11	3	0

Figure S97. Get High-res Image Gene #15: 'del_3p25.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p22.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S98. Gene #16: 'del_3p22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	25	14
DEL PEAK 6(3P22.2) MUTATED	30	23	4
DEL PEAK 6(3P22.2) WILD-TYPE	1	2	10

Figure S98. Get High-res Image Gene #16: 'del_3p22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p22.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S99. Gene #16: 'del_3p22.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	11	12	4	11	13	9	10
DEL PEAK 6(3P22.2) MUTATED	11	11	1	11	12	9	2
DEL PEAK 6(3P22.2) WILD-TYPE	0	1	3	0	1	0	8

Figure S99. Get High-res Image Gene #16: 'del_3p22.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S100. Gene #16: 'del_3p22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	80	156	82	80	69
DEL PEAK 6(3P22.2) MUTATED	60	45	151	77	78	54
DEL PEAK 6(3P22.2) WILD-TYPE	1	35	5	5	2	15

Figure S100. Get High-res Image Gene #16: 'del_3p22.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p22.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S101. Gene #16: 'del_3p22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	70	96	81
DEL PEAK 6(3P22.2) MUTATED	48	57	93	79
DEL PEAK 6(3P22.2) WILD-TYPE	19	13	3	2

Figure S101. Get High-res Image Gene #16: 'del_3p22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p22.2' versus 'RPPA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

Table S102. Gene #16: 'del_3p22.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	86	90	82	92	33
DEL PEAK 6(3P22.2) MUTATED	66	85	84	76	78	30
DEL PEAK 6(3P22.2) WILD-TYPE	22	1	6	6	14	3

Figure S102. Get High-res Image Gene #16: 'del_3p22.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p22.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S103. Gene #16: 'del_3p22.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	112	85	139
DEL PEAK 6(3P22.2) MUTATED	114	107	65	133
DEL PEAK 6(3P22.2) WILD-TYPE	21	5	20	6

Figure S103. Get High-res Image Gene #16: 'del_3p22.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p22.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S104. Gene #16: 'del_3p22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	170	81	153	40
DEL PEAK 6(3P22.2) MUTATED	41	167	74	141	39
DEL PEAK 6(3P22.2) WILD-TYPE	40	3	7	12	1

Figure S104. Get High-res Image Gene #16: 'del_3p22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S105. Gene #16: 'del_3p22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 6(3P22.2) MUTATED	110	19	179	116	35	3
DEL PEAK 6(3P22.2) WILD-TYPE	7	14	4	16	0	22

Figure S105. Get High-res Image Gene #16: 'del_3p22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p22.2' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00015

Table S106. Gene #16: 'del_3p22.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	57	186	119	57
DEL PEAK 6(3P22.2) MUTATED	74	51	179	93	51
DEL PEAK 6(3P22.2) WILD-TYPE	17	6	7	26	6

Figure S106. Get High-res Image Gene #16: 'del_3p22.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S107. Gene #16: 'del_3p22.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	209	128
DEL PEAK 6(3P22.2) MUTATED	142	202	104
DEL PEAK 6(3P22.2) WILD-TYPE	31	7	24

Figure S107. Get High-res Image Gene #16: 'del_3p22.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00317 (Fisher's exact test), Q value = 0.0076

Table S108. Gene #16: 'del_3p22.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	21	44	38
DEL PEAK 6(3P22.2) MUTATED	29	15	43	30
DEL PEAK 6(3P22.2) WILD-TYPE	10	6	1	8

Figure S108. Get High-res Image Gene #16: 'del_3p22.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0246 (Fisher's exact test), Q value = 0.045

Table S109. Gene #16: 'del_3p22.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	52	28	22
DEL PEAK 6(3P22.2) MUTATED	30	40	25	22
DEL PEAK 6(3P22.2) WILD-TYPE	10	12	3	0

Figure S109. Get High-res Image Gene #16: 'del_3p22.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p12.3' versus 'MRNA_CNMF'

P value = 0.00879 (Fisher's exact test), Q value = 0.019

Table S110. Gene #17: 'del_3p12.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	25	14
DEL PEAK 7(3P12.3) MUTATED	19	18	3
DEL PEAK 7(3P12.3) WILD-TYPE	12	7	11

Figure S110. Get High-res Image Gene #17: 'del_3p12.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p12.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0162 (Fisher's exact test), Q value = 0.031

Table S111. Gene #17: 'del_3p12.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	11	12	4	11	13	9	10
DEL PEAK 7(3P12.3) MUTATED	7	9	1	8	7	7	1
DEL PEAK 7(3P12.3) WILD-TYPE	4	3	3	3	6	2	9

Figure S111. Get High-res Image Gene #17: 'del_3p12.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p12.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S112. Gene #17: 'del_3p12.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	80	156	82	80	69
DEL PEAK 7(3P12.3) MUTATED	45	29	137	69	7	52
DEL PEAK 7(3P12.3) WILD-TYPE	16	51	19	13	73	17

Figure S112. Get High-res Image Gene #17: 'del_3p12.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p12.3' versus 'METHLYATION_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.031

Table S113. Gene #17: 'del_3p12.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	70	96	81
DEL PEAK 7(3P12.3) MUTATED	35	42	71	58
DEL PEAK 7(3P12.3) WILD-TYPE	32	28	25	23

Figure S113. Get High-res Image Gene #17: 'del_3p12.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p12.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S114. Gene #17: 'del_3p12.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	170	81	153	40
DEL PEAK 7(3P12.3) MUTATED	28	122	55	110	23
DEL PEAK 7(3P12.3) WILD-TYPE	53	48	26	43	17

Figure S114. Get High-res Image Gene #17: 'del_3p12.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p12.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S115. Gene #17: 'del_3p12.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 7(3P12.3) MUTATED	82	14	125	92	23	2
DEL PEAK 7(3P12.3) WILD-TYPE	35	19	58	40	12	23

Figure S115. Get High-res Image Gene #17: 'del_3p12.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p12.3' versus 'MIRSEQ_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.038

Table S116. Gene #17: 'del_3p12.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	57	186	119	57
DEL PEAK 7(3P12.3) MUTATED	46	40	130	73	39
DEL PEAK 7(3P12.3) WILD-TYPE	45	17	56	46	18

Figure S116. Get High-res Image Gene #17: 'del_3p12.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p12.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0373 (Fisher's exact test), Q value = 0.065

Table S117. Gene #17: 'del_3p12.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	209	128
DEL PEAK 7(3P12.3) MUTATED	100	147	81
DEL PEAK 7(3P12.3) WILD-TYPE	73	62	47

Figure S117. Get High-res Image Gene #17: 'del_3p12.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S118. Gene #18: 'del_3p12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	80	156	82	80	69
DEL PEAK 8(3P12.2) MUTATED	41	27	128	59	1	49
DEL PEAK 8(3P12.2) WILD-TYPE	20	53	28	23	79	20

Figure S118. Get High-res Image Gene #18: 'del_3p12.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p12.2' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00015

Table S119. Gene #18: 'del_3p12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	170	81	153	40
DEL PEAK 8(3P12.2) MUTATED	28	104	53	99	20
DEL PEAK 8(3P12.2) WILD-TYPE	53	66	28	54	20

Figure S119. Get High-res Image Gene #18: 'del_3p12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S120. Gene #18: 'del_3p12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 8(3P12.2) MUTATED	75	13	109	84	21	2
DEL PEAK 8(3P12.2) WILD-TYPE	42	20	74	48	14	23

Figure S120. Get High-res Image Gene #18: 'del_3p12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p11.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S121. Gene #19: 'del_3p11.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	80	156	82	80	69
DEL PEAK 9(3P11.1) MUTATED	32	25	100	45	0	35
DEL PEAK 9(3P11.1) WILD-TYPE	29	55	56	37	80	34

Figure S121. Get High-res Image Gene #19: 'del_3p11.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p11.1' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00057

Table S122. Gene #19: 'del_3p11.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	170	81	153	40
DEL PEAK 9(3P11.1) MUTATED	21	78	46	78	13
DEL PEAK 9(3P11.1) WILD-TYPE	60	92	35	75	27

Figure S122. Get High-res Image Gene #19: 'del_3p11.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p11.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8e-05

Table S123. Gene #19: 'del_3p11.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 9(3P11.1) MUTATED	63	8	80	71	12	2
DEL PEAK 9(3P11.1) WILD-TYPE	54	25	103	61	23	23

Figure S123. Get High-res Image Gene #19: 'del_3p11.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S124. Gene #20: 'del_3q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	80	156	82	80	69
DEL PEAK 10(3Q11.2) MUTATED	21	22	58	39	1	20
DEL PEAK 10(3Q11.2) WILD-TYPE	40	58	98	43	79	49

Figure S124. Get High-res Image Gene #20: 'del_3q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00133 (Fisher's exact test), Q value = 0.0036

Table S125. Gene #20: 'del_3q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	170	81	153	40
DEL PEAK 10(3Q11.2) MUTATED	15	49	39	48	10
DEL PEAK 10(3Q11.2) WILD-TYPE	66	121	42	105	30

Figure S125. Get High-res Image Gene #20: 'del_3q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8e-05

Table S126. Gene #20: 'del_3q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 10(3Q11.2) MUTATED	49	6	50	50	5	1
DEL PEAK 10(3Q11.2) WILD-TYPE	68	27	133	82	30	24

Figure S126. Get High-res Image Gene #20: 'del_3q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00606 (Fisher's exact test), Q value = 0.013

Table S127. Gene #20: 'del_3q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	57	186	119	57
DEL PEAK 10(3Q11.2) MUTATED	19	11	59	41	26
DEL PEAK 10(3Q11.2) WILD-TYPE	72	46	127	78	31

Figure S127. Get High-res Image Gene #20: 'del_3q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 0.00255 (Fisher's exact test), Q value = 0.0062

Table S128. Gene #21: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	70	96	81
DEL PEAK 11(4Q34.3) MUTATED	5	12	27	9
DEL PEAK 11(4Q34.3) WILD-TYPE	62	58	69	72

Figure S128. Get High-res Image Gene #21: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q34.3' versus 'RPPA_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00027

Table S129. Gene #21: 'del_4q34.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	86	90	82	92	33
DEL PEAK 11(4Q34.3) MUTATED	8	11	30	11	13	1
DEL PEAK 11(4Q34.3) WILD-TYPE	80	75	60	71	79	32

Figure S129. Get High-res Image Gene #21: 'del_4q34.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4q34.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00344 (Fisher's exact test), Q value = 0.008

Table S130. Gene #21: 'del_4q34.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	112	85	139
DEL PEAK 11(4Q34.3) MUTATED	12	25	20	17
DEL PEAK 11(4Q34.3) WILD-TYPE	123	87	65	122

Figure S130. Get High-res Image Gene #21: 'del_4q34.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 0.00926 (Fisher's exact test), Q value = 0.02

Table S131. Gene #21: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	170	81	153	40
DEL PEAK 11(4Q34.3) MUTATED	6	18	12	34	8
DEL PEAK 11(4Q34.3) WILD-TYPE	75	152	69	119	32

Figure S131. Get High-res Image Gene #21: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S132. Gene #21: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 11(4Q34.3) MUTATED	15	1	18	38	6	0
DEL PEAK 11(4Q34.3) WILD-TYPE	102	32	165	94	29	25

Figure S132. Get High-res Image Gene #21: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0196 (Fisher's exact test), Q value = 0.037

Table S133. Gene #21: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	209	128
DEL PEAK 11(4Q34.3) MUTATED	37	26	14
DEL PEAK 11(4Q34.3) WILD-TYPE	136	183	114

Figure S133. Get High-res Image Gene #21: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00361 (Fisher's exact test), Q value = 0.0083

Table S134. Gene #21: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	52	28	22
DEL PEAK 11(4Q34.3) MUTATED	3	15	4	0
DEL PEAK 11(4Q34.3) WILD-TYPE	37	37	24	22

Figure S134. Get High-res Image Gene #21: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q26' versus 'MRNA_CNMF'

P value = 0.0367 (Fisher's exact test), Q value = 0.065

Table S135. Gene #22: 'del_6q26' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	25	14
DEL PEAK 12(6Q26) MUTATED	7	12	8
DEL PEAK 12(6Q26) WILD-TYPE	24	13	6

Figure S135. Get High-res Image Gene #22: 'del_6q26' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S136. Gene #22: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	80	156	82	80	69
DEL PEAK 12(6Q26) MUTATED	9	10	103	0	16	13
DEL PEAK 12(6Q26) WILD-TYPE	52	70	53	82	64	56

Figure S136. Get High-res Image Gene #22: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q26' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S137. Gene #22: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	86	90	82	92	33
DEL PEAK 12(6Q26) MUTATED	23	27	41	29	9	6
DEL PEAK 12(6Q26) WILD-TYPE	65	59	49	53	83	27

Figure S137. Get High-res Image Gene #22: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_6q26' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S138. Gene #22: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	112	85	139
DEL PEAK 12(6Q26) MUTATED	17	48	34	36
DEL PEAK 12(6Q26) WILD-TYPE	118	64	51	103

Figure S138. Get High-res Image Gene #22: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0019

Table S139. Gene #22: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	170	81	153	40
DEL PEAK 12(6Q26) MUTATED	22	42	14	63	8
DEL PEAK 12(6Q26) WILD-TYPE	59	128	67	90	32

Figure S139. Get High-res Image Gene #22: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.0011

Table S140. Gene #22: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 12(6Q26) MUTATED	26	6	40	58	10	9
DEL PEAK 12(6Q26) WILD-TYPE	91	27	143	74	25	16

Figure S140. Get High-res Image Gene #22: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CNMF'

P value = 0.00404 (Fisher's exact test), Q value = 0.0091

Table S141. Gene #22: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	57	186	119	57
DEL PEAK 12(6Q26) MUTATED	26	19	39	49	14
DEL PEAK 12(6Q26) WILD-TYPE	65	38	147	70	43

Figure S141. Get High-res Image Gene #22: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00362 (Fisher's exact test), Q value = 0.0083

Table S142. Gene #22: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	209	128
DEL PEAK 12(6Q26) MUTATED	56	44	47
DEL PEAK 12(6Q26) WILD-TYPE	117	165	81

Figure S142. Get High-res Image Gene #22: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0488 (Fisher's exact test), Q value = 0.083

Table S143. Gene #22: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	21	44	38
DEL PEAK 12(6Q26) MUTATED	7	2	12	15
DEL PEAK 12(6Q26) WILD-TYPE	32	19	32	23

Figure S143. Get High-res Image Gene #22: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6q26' versus 'MRNA_CNMF'

P value = 0.0381 (Fisher's exact test), Q value = 0.066

Table S144. Gene #23: 'del_6q26' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	25	14
DEL PEAK 13(6Q26) MUTATED	7	12	8
DEL PEAK 13(6Q26) WILD-TYPE	24	13	6

Figure S144. Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S145. Gene #23: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	80	156	82	80	69
DEL PEAK 13(6Q26) MUTATED	9	10	103	0	16	13
DEL PEAK 13(6Q26) WILD-TYPE	52	70	53	82	64	56

Figure S145. Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q26' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8e-05

Table S146. Gene #23: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	86	90	82	92	33
DEL PEAK 13(6Q26) MUTATED	23	26	42	29	9	6
DEL PEAK 13(6Q26) WILD-TYPE	65	60	48	53	83	27

Figure S146. Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_6q26' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S147. Gene #23: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	112	85	139
DEL PEAK 13(6Q26) MUTATED	17	49	33	36
DEL PEAK 13(6Q26) WILD-TYPE	118	63	52	103

Figure S147. Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.0014

Table S148. Gene #23: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	170	81	153	40
DEL PEAK 13(6Q26) MUTATED	21	42	14	64	8
DEL PEAK 13(6Q26) WILD-TYPE	60	128	67	89	32

Figure S148. Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00033

Table S149. Gene #23: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 13(6Q26) MUTATED	26	6	40	59	9	9
DEL PEAK 13(6Q26) WILD-TYPE	91	27	143	73	26	16

Figure S149. Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CNMF'

P value = 0.0023 (Fisher's exact test), Q value = 0.0057

Table S150. Gene #23: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	57	186	119	57
DEL PEAK 13(6Q26) MUTATED	25	19	39	50	14
DEL PEAK 13(6Q26) WILD-TYPE	66	38	147	69	43

Figure S150. Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00365 (Fisher's exact test), Q value = 0.0084

Table S151. Gene #23: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	209	128
DEL PEAK 13(6Q26) MUTATED	56	44	47
DEL PEAK 13(6Q26) WILD-TYPE	117	165	81

Figure S151. Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0484 (Fisher's exact test), Q value = 0.083

Table S152. Gene #23: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	21	44	38
DEL PEAK 13(6Q26) MUTATED	7	2	12	15
DEL PEAK 13(6Q26) WILD-TYPE	32	19	32	23

Figure S152. Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'CN_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.023

Table S153. Gene #24: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	80	156	82	80	69
DEL PEAK 14(8P23.2) MUTATED	15	24	62	15	19	19
DEL PEAK 14(8P23.2) WILD-TYPE	46	56	94	67	61	50

Figure S153. Get High-res Image Gene #24: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'RPPA_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.028

Table S154. Gene #24: 'del_8p23.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	86	90	82	92	33
DEL PEAK 14(8P23.2) MUTATED	24	15	38	27	26	8
DEL PEAK 14(8P23.2) WILD-TYPE	64	71	52	55	66	25

Figure S154. Get High-res Image Gene #24: 'del_8p23.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00017

Table S155. Gene #24: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	170	81	153	40
DEL PEAK 14(8P23.2) MUTATED	15	40	18	68	12
DEL PEAK 14(8P23.2) WILD-TYPE	66	130	63	85	28

Figure S155. Get High-res Image Gene #24: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00015

Table S156. Gene #24: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 14(8P23.2) MUTATED	31	3	48	60	6	5
DEL PEAK 14(8P23.2) WILD-TYPE	86	30	135	72	29	20

Figure S156. Get High-res Image Gene #24: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 0.00124 (Fisher's exact test), Q value = 0.0033

Table S157. Gene #24: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	57	186	119	57
DEL PEAK 14(8P23.2) MUTATED	27	16	42	53	13
DEL PEAK 14(8P23.2) WILD-TYPE	64	41	144	66	44

Figure S157. Get High-res Image Gene #24: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.0015

Table S158. Gene #24: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	209	128
DEL PEAK 14(8P23.2) MUTATED	70	47	34
DEL PEAK 14(8P23.2) WILD-TYPE	103	162	94

Figure S158. Get High-res Image Gene #24: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MRNA_CNMF'

P value = 0.00638 (Fisher's exact test), Q value = 0.014

Table S159. Gene #25: 'del_9p23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	25	14
DEL PEAK 15(9P23) MUTATED	5	12	1
DEL PEAK 15(9P23) WILD-TYPE	26	13	13

Figure S159. Get High-res Image Gene #25: 'del_9p23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p23' versus 'MRNA_CHIERARCHICAL'

P value = 0.0361 (Fisher's exact test), Q value = 0.064

Table S160. Gene #25: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	11	12	4	11	13	9	10
DEL PEAK 15(9P23) MUTATED	2	7	0	5	1	2	1
DEL PEAK 15(9P23) WILD-TYPE	9	5	4	6	12	7	9

Figure S160. Get High-res Image Gene #25: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S161. Gene #25: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	80	156	82	80	69
DEL PEAK 15(9P23) MUTATED	7	21	86	17	21	0
DEL PEAK 15(9P23) WILD-TYPE	54	59	70	65	59	69

Figure S161. Get High-res Image Gene #25: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S162. Gene #25: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	70	96	81
DEL PEAK 15(9P23) MUTATED	9	25	58	3
DEL PEAK 15(9P23) WILD-TYPE	58	45	38	78

Figure S162. Get High-res Image Gene #25: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p23' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S163. Gene #25: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	86	90	82	92	33
DEL PEAK 15(9P23) MUTATED	16	14	56	24	25	6
DEL PEAK 15(9P23) WILD-TYPE	72	72	34	58	67	27

Figure S163. Get High-res Image Gene #25: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p23' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S164. Gene #25: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	112	85	139
DEL PEAK 15(9P23) MUTATED	25	55	37	24
DEL PEAK 15(9P23) WILD-TYPE	110	57	48	115

Figure S164. Get High-res Image Gene #25: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S165. Gene #25: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	170	81	153	40
DEL PEAK 15(9P23) MUTATED	15	15	22	92	7
DEL PEAK 15(9P23) WILD-TYPE	66	155	59	61	33

Figure S165. Get High-res Image Gene #25: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S166. Gene #25: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 15(9P23) MUTATED	32	3	15	84	13	4
DEL PEAK 15(9P23) WILD-TYPE	85	30	168	48	22	21

Figure S166. Get High-res Image Gene #25: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S167. Gene #25: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	57	186	119	57
DEL PEAK 15(9P23) MUTATED	20	24	26	64	13
DEL PEAK 15(9P23) WILD-TYPE	71	33	160	55	44

Figure S167. Get High-res Image Gene #25: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S168. Gene #25: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	209	128
DEL PEAK 15(9P23) MUTATED	71	24	52
DEL PEAK 15(9P23) WILD-TYPE	102	185	76

Figure S168. Get High-res Image Gene #25: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00189 (Fisher's exact test), Q value = 0.0048

Table S169. Gene #25: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	21	44	38
DEL PEAK 15(9P23) MUTATED	8	4	4	17
DEL PEAK 15(9P23) WILD-TYPE	31	17	40	21

Figure S169. Get High-res Image Gene #25: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MRNA_CNMF'

P value = 0.00256 (Fisher's exact test), Q value = 0.0062

Table S170. Gene #26: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	25	14
DEL PEAK 16(9P21.3) MUTATED	5	13	1
DEL PEAK 16(9P21.3) WILD-TYPE	26	12	13

Figure S170. Get High-res Image Gene #26: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p21.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 0.032

Table S171. Gene #26: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	11	12	4	11	13	9	10
DEL PEAK 16(9P21.3) MUTATED	2	7	0	6	1	2	1
DEL PEAK 16(9P21.3) WILD-TYPE	9	5	4	5	12	7	9

Figure S171. Get High-res Image Gene #26: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S172. Gene #26: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	80	156	82	80	69
DEL PEAK 16(9P21.3) MUTATED	7	23	89	17	22	1
DEL PEAK 16(9P21.3) WILD-TYPE	54	57	67	65	58	68

Figure S172. Get High-res Image Gene #26: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S173. Gene #26: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	70	96	81
DEL PEAK 16(9P21.3) MUTATED	9	28	57	4
DEL PEAK 16(9P21.3) WILD-TYPE	58	42	39	77

Figure S173. Get High-res Image Gene #26: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S174. Gene #26: 'del_9p21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	86	90	82	92	33
DEL PEAK 16(9P21.3) MUTATED	17	15	59	23	27	6
DEL PEAK 16(9P21.3) WILD-TYPE	71	71	31	59	65	27

Figure S174. Get High-res Image Gene #26: 'del_9p21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S175. Gene #26: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	112	85	139
DEL PEAK 16(9P21.3) MUTATED	28	53	41	25
DEL PEAK 16(9P21.3) WILD-TYPE	107	59	44	114

Figure S175. Get High-res Image Gene #26: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S176. Gene #26: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	170	81	153	40
DEL PEAK 16(9P21.3) MUTATED	16	17	24	94	7
DEL PEAK 16(9P21.3) WILD-TYPE	65	153	57	59	33

Figure S176. Get High-res Image Gene #26: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S177. Gene #26: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 16(9P21.3) MUTATED	32	2	16	90	14	4
DEL PEAK 16(9P21.3) WILD-TYPE	85	31	167	42	21	21

Figure S177. Get High-res Image Gene #26: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S178. Gene #26: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	57	186	119	57
DEL PEAK 16(9P21.3) MUTATED	23	24	27	65	14
DEL PEAK 16(9P21.3) WILD-TYPE	68	33	159	54	43

Figure S178. Get High-res Image Gene #26: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S179. Gene #26: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	209	128
DEL PEAK 16(9P21.3) MUTATED	77	25	51
DEL PEAK 16(9P21.3) WILD-TYPE	96	184	77

Figure S179. Get High-res Image Gene #26: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00097 (Fisher's exact test), Q value = 0.0027

Table S180. Gene #26: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	21	44	38
DEL PEAK 16(9P21.3) MUTATED	8	5	4	18
DEL PEAK 16(9P21.3) WILD-TYPE	31	16	40	20

Figure S180. Get High-res Image Gene #26: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00603 (Fisher's exact test), Q value = 0.013

Table S181. Gene #26: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	52	28	22
DEL PEAK 16(9P21.3) MUTATED	9	21	3	2
DEL PEAK 16(9P21.3) WILD-TYPE	31	31	25	20

Figure S181. Get High-res Image Gene #26: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 0.00658 (Fisher's exact test), Q value = 0.014

Table S182. Gene #27: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	80	156	82	80	69
DEL PEAK 17(10Q23.31) MUTATED	7	11	41	7	14	16
DEL PEAK 17(10Q23.31) WILD-TYPE	54	69	115	75	66	53

Figure S182. Get High-res Image Gene #27: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 0.0458 (Fisher's exact test), Q value = 0.079

Table S183. Gene #27: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	70	96	81
DEL PEAK 17(10Q23.31) MUTATED	8	12	27	12
DEL PEAK 17(10Q23.31) WILD-TYPE	59	58	69	69

Figure S183. Get High-res Image Gene #27: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q23.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.029

Table S184. Gene #27: 'del_10q23.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	112	85	139
DEL PEAK 17(10Q23.31) MUTATED	15	26	22	22
DEL PEAK 17(10Q23.31) WILD-TYPE	120	86	63	117

Figure S184. Get High-res Image Gene #27: 'del_10q23.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.00091

Table S185. Gene #27: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 17(10Q23.31) MUTATED	22	3	21	37	3	9
DEL PEAK 17(10Q23.31) WILD-TYPE	95	30	162	95	32	16

Figure S185. Get High-res Image Gene #27: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0012

Table S186. Gene #27: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	57	186	119	57
DEL PEAK 17(10Q23.31) MUTATED	15	4	25	36	14
DEL PEAK 17(10Q23.31) WILD-TYPE	76	53	161	83	43

Figure S186. Get High-res Image Gene #27: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00137 (Fisher's exact test), Q value = 0.0036

Table S187. Gene #27: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	209	128
DEL PEAK 17(10Q23.31) MUTATED	36	24	34
DEL PEAK 17(10Q23.31) WILD-TYPE	137	185	94

Figure S187. Get High-res Image Gene #27: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q13.3' versus 'MRNA_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.037

Table S188. Gene #28: 'del_13q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	25	14
DEL PEAK 18(13Q13.3) MUTATED	1	7	3
DEL PEAK 18(13Q13.3) WILD-TYPE	30	18	11

Figure S188. Get High-res Image Gene #28: 'del_13q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q13.3' versus 'METHLYATION_CNMF'

P value = 0.00201 (Fisher's exact test), Q value = 0.005

Table S189. Gene #28: 'del_13q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	70	96	81
DEL PEAK 18(13Q13.3) MUTATED	8	17	20	4
DEL PEAK 18(13Q13.3) WILD-TYPE	59	53	76	77

Figure S189. Get High-res Image Gene #28: 'del_13q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q13.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S190. Gene #28: 'del_13q13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	86	90	82	92	33
DEL PEAK 18(13Q13.3) MUTATED	11	3	33	10	12	3
DEL PEAK 18(13Q13.3) WILD-TYPE	77	83	57	72	80	30

Figure S190. Get High-res Image Gene #28: 'del_13q13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00121 (Fisher's exact test), Q value = 0.0033

Table S191. Gene #28: 'del_13q13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	112	85	139
DEL PEAK 18(13Q13.3) MUTATED	13	23	22	14
DEL PEAK 18(13Q13.3) WILD-TYPE	122	89	63	125

Figure S191. Get High-res Image Gene #28: 'del_13q13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_13q13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S192. Gene #28: 'del_13q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	170	81	153	40
DEL PEAK 18(13Q13.3) MUTATED	13	15	6	45	2
DEL PEAK 18(13Q13.3) WILD-TYPE	68	155	75	108	38

Figure S192. Get High-res Image Gene #28: 'del_13q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S193. Gene #28: 'del_13q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 18(13Q13.3) MUTATED	6	2	15	43	8	7
DEL PEAK 18(13Q13.3) WILD-TYPE	111	31	168	89	27	18

Figure S193. Get High-res Image Gene #28: 'del_13q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S194. Gene #28: 'del_13q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	57	186	119	57
DEL PEAK 18(13Q13.3) MUTATED	10	12	15	36	6
DEL PEAK 18(13Q13.3) WILD-TYPE	81	45	171	83	51

Figure S194. Get High-res Image Gene #28: 'del_13q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00017

Table S195. Gene #28: 'del_13q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	209	128
DEL PEAK 18(13Q13.3) MUTATED	35	15	29
DEL PEAK 18(13Q13.3) WILD-TYPE	138	194	99

Figure S195. Get High-res Image Gene #28: 'del_13q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q31.1' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8e-05

Table S196. Gene #29: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	25	14
DEL PEAK 19(14Q31.1) MUTATED	9	20	2
DEL PEAK 19(14Q31.1) WILD-TYPE	22	5	12

Figure S196. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q31.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0012

Table S197. Gene #29: 'del_14q31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	11	12	4	11	13	9	10
DEL PEAK 19(14Q31.1) MUTATED	4	7	1	11	5	1	2
DEL PEAK 19(14Q31.1) WILD-TYPE	7	5	3	0	8	8	8

Figure S197. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S198. Gene #29: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	80	156	82	80	69
DEL PEAK 19(14Q31.1) MUTATED	24	32	103	27	36	6
DEL PEAK 19(14Q31.1) WILD-TYPE	37	48	53	55	44	63

Figure S198. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q31.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S199. Gene #29: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	70	96	81
DEL PEAK 19(14Q31.1) MUTATED	19	36	60	18
DEL PEAK 19(14Q31.1) WILD-TYPE	48	34	36	63

Figure S199. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q31.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S200. Gene #29: 'del_14q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	86	90	82	92	33
DEL PEAK 19(14Q31.1) MUTATED	30	23	58	57	33	7
DEL PEAK 19(14Q31.1) WILD-TYPE	58	63	32	25	59	26

Figure S200. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_14q31.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0311 (Fisher's exact test), Q value = 0.056

Table S201. Gene #29: 'del_14q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	112	85	139
DEL PEAK 19(14Q31.1) MUTATED	49	56	46	57
DEL PEAK 19(14Q31.1) WILD-TYPE	86	56	39	82

Figure S201. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_14q31.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S202. Gene #29: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	170	81	153	40
DEL PEAK 19(14Q31.1) MUTATED	20	57	26	112	10
DEL PEAK 19(14Q31.1) WILD-TYPE	61	113	55	41	30

Figure S202. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S203. Gene #29: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 19(14Q31.1) MUTATED	45	7	57	81	33	2
DEL PEAK 19(14Q31.1) WILD-TYPE	72	26	126	51	2	23

Figure S203. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q31.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S204. Gene #29: 'del_14q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	91	57	186	119	57
DEL PEAK 19(14Q31.1) MUTATED	30	35	64	79	14
DEL PEAK 19(14Q31.1) WILD-TYPE	61	22	122	40	43

Figure S204. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_14q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S205. Gene #29: 'del_14q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	209	128
DEL PEAK 19(14Q31.1) MUTATED	75	69	78
DEL PEAK 19(14Q31.1) WILD-TYPE	98	140	50

Figure S205. Get High-res Image Gene #29: 'del_14q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRC-TP/22531283/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIRC-TP/22555002/KIRC-TP.transferedmergedcluster.txt
Number of patients = 528
Number of significantly focal cnvs = 29
Number of molecular subtypes = 12
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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