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 50 focal events and 10 molecular subtypes across 150 patients, 267 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q21.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
amp_2p24.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3p13 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3q27.3 cnv correlated to 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_4q12 cnv correlated to 'CN_CNMF'.
amp_7p22.1 cnv correlated to 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7q11.22 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q11.23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q23.3 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12p13.33 cnv correlated to 'RPPA_CHIERARCHICAL'.
amp_12p11.21 cnv correlated to 'RPPA_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_16q21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20q11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_22q11.21 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.31 cnv correlated to 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p31.1 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_1q42.12 cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q37.3 cnv correlated to 'METHLYATION_CNMF'.
del_3p26.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q22.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5p15.2 cnv correlated to 'CN_CNMF'.
del_5p14.3 cnv correlated to 'RPPA_CNMF'.
del_5q12.1 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6p22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q26 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_7q11.22 cnv correlated to 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_7q35 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p24.3 cnv correlated to 'CN_CNMF'.
del_9p23 cnv correlated to 'CN_CNMF'.
del_9q33.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_9q34.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_10p15.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q26.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p15.5 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p12 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q12.3 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q24.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q34 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q23.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18p11.32 cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
del_18q22.3 cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19q13.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19q13.42 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_20p12.1 cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp21.1 cnv correlated to 'METHLYATION_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xq27.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 50 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 267 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
amp 8q11 23	122 (81%)	28	0.00015 (0.00142)	0.00834 (0.0253)	0.00061 (0.00401)	0.00013 (0.00127)	1e-05 (0.000161)	2e-05 (0.000303)	9e-05 (0.001)	1e-05 (0.000161)	3e-05 (0.000417)	5e-05 (0.000581)
amp 16q21	21 (14%)	129	0.00532 (0.018)	0.0191 (0.0466)	0.00335 (0.0131)	0.00119 (0.00626)	0.0465 (0.088)	0.00777 (0.0242)	0.0014 (0.0068)	0.00841 (0.0253)	0.00234 (0.00975)	0.00287 (0.0117)
del 6p22 3	24 (16%)	126	0.00024 (0.00197)	0.00233 (0.00975)	0.00017 (0.00152)	0.00078 (0.00459)	0.022 (0.0509)	0.0116 (0.0323)	0.00501 (0.0175)	0.00345 (0.0133)	0.00334 (0.0131)	0.00553 (0.0184)
del 10p15 3	84 (56%)	66	0.00015 (0.00142)	0.0201 (0.0479)	0.00408 (0.0151)	0.00267 (0.0109)	0.00542 (0.0182)	0.00126 (0.00649)	0.0346 (0.071)	0.00065 (0.00411)	0.0003 (0.00238)	0.00144 (0.00686)
del 10q23 1	71 (47%)	79	0.00052 (0.00366)	0.00403 (0.015)	0.0244 (0.0542)	0.0136 (0.0356)	0.00216 (0.00927)	0.00037 (0.00276)	0.0234 (0.0529)	3e-05 (0.000417)	0.0001 (0.00104)	3e-05 (0.000417)
del 10q26 3	76 (51%)	74	1e-05 (0.000161)	0.00078 (0.00459)	0.0122 (0.0325)	0.00308 (0.0123)	0.00041 (0.00301)	0.00011 (0.00112)	0.0441 (0.0845)	5e-05 (0.000581)	5e-05 (0.000581)	4e-05 (0.000513)
del 19q13 33	58 (39%)	92	1e-05 (0.000161)	1e-05 (0.000161)	1e-05 (0.000161)	1e-05 (0.000161)	1e-05 (0.000161)	1e-05 (0.000161)	1e-05 (0.000161)	1e-05 (0.000161)	1e-05 (0.000161)	1e-05 (0.000161)
del 19q13 42	57 (38%)	93	1e-05 (0.000161)	1e-05 (0.000161)	1e-05 (0.000161)	1e-05 (0.000161)	1e-05 (0.000161)	1e-05 (0.000161)	1e-05 (0.000161)	1e-05 (0.000161)	1e-05 (0.000161)	1e-05 (0.000161)
amp 8q23 3	108 (72%)	42	0.103 (0.163)	0.00183 (0.00832)	0.0241 (0.0538)	0.011 (0.0318)	0.00033 (0.0025)	0.00057 (0.00396)	2e-05 (0.000303)	0.0001 (0.00104)	0.00032 (0.00246)	0.00886 (0.0265)
amp 20q11 21	51 (34%)	99	0.0366 (0.0741)	0.00099 (0.00544)	0.0195 (0.047)	0.0145 (0.037)	0.0835 (0.137)	0.0337 (0.0694)	0.0115 (0.0322)	0.00687 (0.0219)	0.0102 (0.0296)	0.0421 (0.082)
amp 22q11 21	57 (38%)	93	1e-05 (0.000161)	0.0749 (0.127)	0.0118 (0.0323)	0.00574 (0.019)	1e-05 (0.000161)	1e-05 (0.000161)	0.0249 (0.0543)	0.00019 (0.00161)	0.00025 (0.00202)	5e-05 (0.000581)
del 6q26	26 (17%)	124	0.102 (0.162)	0.0397 (0.078)	0.0247 (0.0542)	0.0144 (0.0368)	0.00077 (0.00459)	0.0013 (0.0065)	0.0179 (0.0438)	0.00505 (0.0175)	0.00446 (0.0159)	0.0234 (0.0529)
del 11q12 3	114 (76%)	36	0.0009 (0.00506)	0.188 (0.26)	0.0324 (0.0672)	0.0217 (0.0507)	4e-05 (0.000513)	1e-05 (0.000161)	1e-05 (0.000161)	1e-05 (0.000161)	8e-05 (0.000909)	1e-05 (0.000161)
amp 2p24 1	62 (41%)	88	0.00838 (0.0253)	0.00031 (0.00242)	0.194 (0.265)	0.129 (0.193)	0.0391 (0.0776)	0.0436 (0.0842)	0.0274 (0.0593)	0.0389 (0.0775)	0.0433 (0.0838)	0.012 (0.0323)
amp 3p13	34 (23%)	116	0.0162 (0.0402)	0.153 (0.219)	0.00012 (0.0012)	0.00159 (0.00743)	0.00059 (0.00399)	0.0176 (0.0433)	0.141 (0.206)	0.0207 (0.049)	0.0169 (0.0418)	0.0336 (0.0694)
amp 3q27 3	49 (33%)	101	0.419 (0.492)	0.0592 (0.105)	0.00233 (0.00975)	0.00088 (0.00506)	0.00018 (0.00155)	0.00784 (0.0242)	0.00135 (0.00668)	0.00242 (0.01)	0.00106 (0.00575)	0.00972 (0.0286)
amp 7q11 22	120 (80%)	30	0.0633 (0.111)	0.0246 (0.0542)	0.0114 (0.0322)	0.058 (0.104)	1e-05 (0.000161)	0.00203 (0.00891)	0.0002 (0.00167)	0.00018 (0.00155)	0.0001 (0.00104)	0.00089 (0.00506)
del 3p26 2	41 (27%)	109	0.0246 (0.0542)	0.00349 (0.0133)	0.0897 (0.146)	0.505 (0.565)	0.00789 (0.0242)	0.00442 (0.0159)	0.0037 (0.014)	0.00348 (0.0133)	0.0013 (0.0065)	0.00016 (0.00148)
del 4q22 2	110 (73%)	40	0.025 (0.0544)	0.0867 (0.141)	0.68 (0.719)	0.559 (0.616)	0.00924 (0.0273)	0.00142 (0.00683)	0.00066 (0.00412)	0.00421 (0.0155)	0.0294 (0.0624)	0.00494 (0.0174)
del 5q12 1	105 (70%)	45	0.00063 (0.00404)	0.0667 (0.115)	0.0111 (0.0319)	0.332 (0.409)	0.0118 (0.0323)	0.00745 (0.0236)	0.451 (0.521)	0.0239 (0.0536)	0.029 (0.0621)	0.0395 (0.078)
del 11q24 3	122 (81%)	28	0.00061 (0.00401)	0.572 (0.624)	0.588 (0.638)	0.309 (0.388)	0.00205 (0.00891)	0.00059 (0.00399)	0.00314 (0.0125)	0.00608 (0.02)	0.0155 (0.0391)	0.00047 (0.00341)
del 7q11 22	4 (3%)	146	0.101 (0.162)	0.0627 (0.11)	0.12 (0.184)	0.0282 (0.0607)	0.0792 (0.132)	0.0293 (0.0623)	0.00531 (0.018)	0.00894 (0.0266)	0.0102 (0.0296)	0.0226 (0.0517)
del 11p15 5	94 (63%)	56	0.18 (0.249)	0.0486 (0.0917)	0.159 (0.225)	0.45 (0.521)	0.0828 (0.137)	0.00427 (0.0156)	0.00217 (0.00927)	0.00204 (0.00891)	0.00618 (0.0202)	0.0119 (0.0323)
del 11p12	99 (66%)	51	0.421 (0.493)	0.0465 (0.088)	0.138 (0.203)	0.489 (0.553)	0.109 (0.17)	0.00529 (0.018)	0.00077 (0.00459)	0.00128 (0.0065)	0.00634 (0.0205)	0.0126 (0.0336)
del 16q23 3	67 (45%)	83	0.00138 (0.00676)	0.00304 (0.0123)	0.764 (0.794)	0.192 (0.265)	0.045 (0.0858)	0.0854 (0.14)	0.00177 (0.00819)	0.0218 (0.0508)	0.172 (0.239)	0.0142 (0.0366)
del xq27 3	30 (20%)	120	0.00149 (0.00703)	0.00124 (0.00646)	0.117 (0.181)	0.744 (0.775)	0.00631 (0.0205)	0.0631 (0.111)	0.0137 (0.0356)	0.012 (0.0323)	0.102 (0.162)	0.0212 (0.0498)
amp 7p22 1	126 (84%)	24	0.208 (0.279)	0.0721 (0.122)	0.125 (0.19)	0.091 (0.147)	0.0316 (0.0661)	0.104 (0.164)	0.012 (0.0323)	0.0113 (0.0322)	0.0221 (0.051)	0.0386 (0.0771)
del 1p36 31	34 (23%)	116	0.64 (0.686)	0.0561 (0.103)	0.158 (0.224)	0.0574 (0.104)	0.0668 (0.115)	0.0502 (0.0936)	0.00524 (0.018)	0.00473 (0.0168)	0.00195 (0.00878)	0.0146 (0.0371)
del 13q34	113 (75%)	37	0.0132 (0.0348)	0.316 (0.395)	0.112 (0.174)	0.159 (0.225)	0.00074 (0.00457)	0.00198 (0.00884)	0.165 (0.23)	0.131 (0.195)	0.219 (0.291)	0.00112 (0.00596)
del 18q22 3	125 (83%)	25	0.0119 (0.0323)	0.138 (0.203)	0.72 (0.755)	0.952 (0.958)	0.207 (0.278)	0.135 (0.199)	0.0236 (0.0532)	0.0405 (0.0791)	0.235 (0.311)	0.00765 (0.0241)
amp 12p11 21	144 (96%)	6	0.096 (0.154)	0.193 (0.265)	0.153 (0.219)	0.0361 (0.0734)	0.156 (0.221)	0.496 (0.56)	0.206 (0.278)	0.0361 (0.0734)	0.0382 (0.0767)	0.194 (0.265)
del 1p31 1	27 (18%)	123	0.02 (0.0479)	0.272 (0.351)	0.355 (0.431)	0.0489 (0.0917)	0.676 (0.719)	0.727 (0.76)	0.00787 (0.0242)	0.153 (0.219)	0.0642 (0.112)	0.43 (0.499)
del 7q35	13 (9%)	137	0.0137 (0.0356)	0.404 (0.479)	0.587 (0.638)	0.0578 (0.104)	0.142 (0.207)	0.0115 (0.0322)	0.267 (0.346)	0.808 (0.831)	0.43 (0.499)	0.0322 (0.0672)
del 9q34 2	60 (40%)	90	0.00099 (0.00544)	0.0682 (0.116)	0.128 (0.193)	0.0554 (0.102)	0.0593 (0.105)	0.00402 (0.015)	0.537 (0.595)	0.0284 (0.061)	0.143 (0.207)	0.131 (0.195)
del 16q23 1	66 (44%)	84	0.00063 (0.00404)	0.0223 (0.0511)	0.679 (0.719)	0.381 (0.459)	0.295 (0.37)	0.395 (0.472)	0.0562 (0.103)	0.207 (0.278)	0.568 (0.622)	0.0161 (0.0402)
del xp21 1	28 (19%)	122	0.0754 (0.127)	0.00441 (0.0159)	0.901 (0.915)	0.622 (0.67)	0.0762 (0.128)	0.0513 (0.0954)	0.0572 (0.104)	0.0722 (0.122)	0.049 (0.0917)	0.00675 (0.0216)
amp 1q21 2	69 (46%)	81	0.00107 (0.00575)	0.395 (0.472)	0.319 (0.398)	0.916 (0.927)	0.141 (0.206)	0.00086 (0.005)	0.134 (0.199)	0.933 (0.94)	0.673 (0.719)	0.13 (0.194)
del 9q33 3	60 (40%)	90	0.00017 (0.00152)	0.123 (0.188)	0.127 (0.192)	0.0549 (0.102)	0.0679 (0.116)	0.0156 (0.0391)	0.678 (0.719)	0.0553 (0.102)	0.164 (0.23)	0.242 (0.316)
del 18p11 32	118 (79%)	32	0.502 (0.563)	0.155 (0.22)	0.71 (0.746)	0.959 (0.963)	0.627 (0.674)	0.248 (0.322)	0.044 (0.0845)	0.0193 (0.0469)	0.281 (0.36)	0.0676 (0.116)
del 20p12 1	29 (19%)	121	0.219 (0.291)	0.397 (0.472)	0.414 (0.487)	0.454 (0.523)	0.0783 (0.13)	0.0938 (0.151)	0.0312 (0.0656)	0.241 (0.316)	0.0611 (0.108)	0.00179 (0.00821)
amp 4q12	20 (13%)	130	4e-05 (0.000513)	0.807 (0.831)	0.804 (0.83)	0.457 (0.525)	0.197 (0.267)	0.396 (0.472)	0.339 (0.415)	0.333 (0.41)	0.278 (0.357)	0.242 (0.316)
amp 12p13 33	145 (97%)	5	0.195 (0.266)	0.397 (0.472)	0.15 (0.217)	0.0373 (0.0753)	0.216 (0.288)	0.685 (0.723)	0.32 (0.398)	0.0828 (0.137)	0.0868 (0.141)	0.473 (0.54)
del 1q42 12	9 (6%)	141	0.0943 (0.152)	0.0667 (0.115)	0.831 (0.853)	0.288 (0.365)	0.62 (0.67)	0.196 (0.266)	0.123 (0.188)	0.127 (0.192)	0.501 (0.562)	0.013 (0.0345)
del 2q37 3	15 (10%)	135	0.561 (0.616)	0.02 (0.0479)	0.411 (0.485)	0.252 (0.327)	0.344 (0.418)	0.173 (0.241)	0.381 (0.459)	0.117 (0.181)	0.109 (0.17)	0.242 (0.316)
del 5p15 2	101 (67%)	49	0.0398 (0.078)	0.407 (0.481)	0.119 (0.183)	0.488 (0.553)	0.489 (0.553)	0.458 (0.525)	0.55 (0.607)	0.241 (0.316)	0.284 (0.362)	0.286 (0.363)
del 5p14 3	103 (69%)	47	0.0591 (0.105)	0.168 (0.235)	0.0209 (0.0494)	0.705 (0.742)	0.278 (0.357)	0.295 (0.37)	0.795 (0.825)	0.152 (0.219)	0.198 (0.267)	0.282 (0.36)
del 9p24 3	70 (47%)	80	0.0308 (0.0649)	0.329 (0.407)	0.668 (0.715)	0.424 (0.495)	0.465 (0.532)	0.803 (0.83)	0.339 (0.415)	0.678 (0.719)	1 (1.00)	0.871 (0.891)
del 9p23	66 (44%)	84	0.00049 (0.0035)	0.608 (0.658)	0.52 (0.579)	0.342 (0.417)	0.377 (0.457)	0.527 (0.584)	0.585 (0.637)	0.91 (0.923)	0.932 (0.94)	0.888 (0.904)
amp 12p12 1	147 (98%)	3	0.108 (0.169)	0.104 (0.163)	0.294 (0.37)	0.234 (0.309)	0.0775 (0.13)	0.562 (0.616)	0.0589 (0.105)	0.339 (0.415)	0.326 (0.405)	0.125 (0.189)
amp 12q15	100 (67%)	50	0.869 (0.89)	0.887 (0.904)	0.39 (0.468)	1 (1.00)	0.497 (0.56)	0.735 (0.767)	0.43 (0.499)	0.512 (0.571)	0.524 (0.583)	0.478 (0.544)

'amp_1q21.2' versus 'CN_CNMF'

P value = 0.00107 (Fisher's exact test), Q value = 0.0058

Table S1. Gene #1: 'amp_1q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
AMP PEAK 1(1Q21.2) MUTATED	16	23	28	2
AMP PEAK 1(1Q21.2) WILD-TYPE	32	11	26	12

Figure S1. Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00086 (Fisher's exact test), Q value = 0.005

Table S2. Gene #1: 'amp_1q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
AMP PEAK 1(1Q21.2) MUTATED	12	19	3	16	3	13	3
AMP PEAK 1(1Q21.2) WILD-TYPE	31	8	9	8	5	10	10

Figure S2. Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_2p24.1' versus 'CN_CNMF'

P value = 0.00838 (Fisher's exact test), Q value = 0.025

Table S3. Gene #2: 'amp_2p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
AMP PEAK 2(2P24.1) MUTATED	11	17	29	5
AMP PEAK 2(2P24.1) WILD-TYPE	37	17	25	9

Figure S3. Get High-res Image Gene #2: 'amp_2p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2p24.1' versus 'METHLYATION_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0024

Table S4. Gene #2: 'amp_2p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	20	34	51
AMP PEAK 2(2P24.1) MUTATED	9	7	14	32
AMP PEAK 2(2P24.1) WILD-TYPE	36	13	20	19

Figure S4. Get High-res Image Gene #2: 'amp_2p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_2p24.1' versus 'MRNASEQ_CNMF'

P value = 0.0391 (Fisher's exact test), Q value = 0.078

Table S5. Gene #2: 'amp_2p24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	34	30	33	22	8	22	1
AMP PEAK 2(2P24.1) MUTATED	8	14	12	10	3	15	0
AMP PEAK 2(2P24.1) WILD-TYPE	26	16	21	12	5	7	1

Figure S5. Get High-res Image Gene #2: 'amp_2p24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_2p24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0436 (Fisher's exact test), Q value = 0.084

Table S6. Gene #2: 'amp_2p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
AMP PEAK 2(2P24.1) MUTATED	10	13	6	14	2	9	8
AMP PEAK 2(2P24.1) WILD-TYPE	33	14	6	10	6	14	5

Figure S6. Get High-res Image Gene #2: 'amp_2p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_2p24.1' versus 'MIRSEQ_CNMF'

P value = 0.0274 (Fisher's exact test), Q value = 0.059

Table S7. Gene #2: 'amp_2p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	57	42
AMP PEAK 2(2P24.1) MUTATED	15	23	24
AMP PEAK 2(2P24.1) WILD-TYPE	36	34	18

Figure S7. Get High-res Image Gene #2: 'amp_2p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_2p24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0389 (Fisher's exact test), Q value = 0.077

Table S8. Gene #2: 'amp_2p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
AMP PEAK 2(2P24.1) MUTATED	23	15	24
AMP PEAK 2(2P24.1) WILD-TYPE	47	23	18

Figure S8. Get High-res Image Gene #2: 'amp_2p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_2p24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0433 (Fisher's exact test), Q value = 0.084

Table S9. Gene #2: 'amp_2p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
AMP PEAK 2(2P24.1) MUTATED	22	15	25
AMP PEAK 2(2P24.1) WILD-TYPE	47	21	20

Figure S9. Get High-res Image Gene #2: 'amp_2p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_2p24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.032

Table S10. Gene #2: 'amp_2p24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
AMP PEAK 2(2P24.1) MUTATED	7	16	10	17	5	7
AMP PEAK 2(2P24.1) WILD-TYPE	27	20	9	10	14	8

Figure S10. Get High-res Image Gene #2: 'amp_2p24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3p13' versus 'CN_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.04

Table S11. Gene #3: 'amp_3p13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
AMP PEAK 3(3P13) MUTATED	8	7	19	0
AMP PEAK 3(3P13) WILD-TYPE	40	27	35	14

Figure S11. Get High-res Image Gene #3: 'amp_3p13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3p13' versus 'RPPA_CNMF'

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

Table S12. Gene #3: 'amp_3p13' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
AMP PEAK 3(3P13) MUTATED	4	0	0	17	6
AMP PEAK 3(3P13) WILD-TYPE	41	8	10	20	12

Figure S12. Get High-res Image Gene #3: 'amp_3p13' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_3p13' versus 'RPPA_CHIERARCHICAL'

P value = 0.00159 (Fisher's exact test), Q value = 0.0074

Table S13. Gene #3: 'amp_3p13' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
AMP PEAK 3(3P13) MUTATED	4	7	16
AMP PEAK 3(3P13) WILD-TYPE	47	18	26

Figure S13. Get High-res Image Gene #3: 'amp_3p13' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_3p13' versus 'MRNASEQ_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.004

Table S14. Gene #3: 'amp_3p13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	34	30	33	22	8	22	1
AMP PEAK 3(3P13) MUTATED	4	4	7	4	1	14	0
AMP PEAK 3(3P13) WILD-TYPE	30	26	26	18	7	8	1

Figure S14. Get High-res Image Gene #3: 'amp_3p13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0176 (Fisher's exact test), Q value = 0.043

Table S15. Gene #3: 'amp_3p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
AMP PEAK 3(3P13) MUTATED	5	4	4	6	2	5	8
AMP PEAK 3(3P13) WILD-TYPE	38	23	8	18	6	18	5

Figure S15. Get High-res Image Gene #3: 'amp_3p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0207 (Fisher's exact test), Q value = 0.049

Table S16. Gene #3: 'amp_3p13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
AMP PEAK 3(3P13) MUTATED	9	11	14
AMP PEAK 3(3P13) WILD-TYPE	61	27	28

Figure S16. Get High-res Image Gene #3: 'amp_3p13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.042

Table S17. Gene #3: 'amp_3p13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
AMP PEAK 3(3P13) MUTATED	9	9	16
AMP PEAK 3(3P13) WILD-TYPE	60	27	29

Figure S17. Get High-res Image Gene #3: 'amp_3p13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_3p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0336 (Fisher's exact test), Q value = 0.069

Table S18. Gene #3: 'amp_3p13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
AMP PEAK 3(3P13) MUTATED	6	3	7	10	3	5
AMP PEAK 3(3P13) WILD-TYPE	28	33	12	17	16	10

Figure S18. Get High-res Image Gene #3: 'amp_3p13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q27.3' versus 'RPPA_CNMF'

P value = 0.00233 (Fisher's exact test), Q value = 0.0097

Table S19. Gene #4: 'amp_3q27.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
AMP PEAK 4(3Q27.3) MUTATED	6	1	5	18	7
AMP PEAK 4(3Q27.3) WILD-TYPE	39	7	5	19	11

Figure S19. Get High-res Image Gene #4: 'amp_3q27.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_3q27.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00088 (Fisher's exact test), Q value = 0.0051

Table S20. Gene #4: 'amp_3q27.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
AMP PEAK 4(3Q27.3) MUTATED	7	11	19
AMP PEAK 4(3Q27.3) WILD-TYPE	44	14	23

Figure S20. Get High-res Image Gene #4: 'amp_3q27.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_3q27.3' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0016

Table S21. Gene #4: 'amp_3q27.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	34	30	33	22	8	22	1
AMP PEAK 4(3Q27.3) MUTATED	2	10	13	7	3	14	0
AMP PEAK 4(3Q27.3) WILD-TYPE	32	20	20	15	5	8	1

Figure S21. Get High-res Image Gene #4: 'amp_3q27.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3q27.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00784 (Fisher's exact test), Q value = 0.024

Table S22. Gene #4: 'amp_3q27.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
AMP PEAK 4(3Q27.3) MUTATED	5	8	6	9	4	10	7
AMP PEAK 4(3Q27.3) WILD-TYPE	38	19	6	15	4	13	6

Figure S22. Get High-res Image Gene #4: 'amp_3q27.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3q27.3' versus 'MIRSEQ_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.0067

Table S23. Gene #4: 'amp_3q27.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	57	42
AMP PEAK 4(3Q27.3) MUTATED	7	24	18
AMP PEAK 4(3Q27.3) WILD-TYPE	44	33	24

Figure S23. Get High-res Image Gene #4: 'amp_3q27.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_3q27.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00242 (Fisher's exact test), Q value = 0.01

Table S24. Gene #4: 'amp_3q27.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
AMP PEAK 4(3Q27.3) MUTATED	13	18	18
AMP PEAK 4(3Q27.3) WILD-TYPE	57	20	24

Figure S24. Get High-res Image Gene #4: 'amp_3q27.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3q27.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.0058

Table S25. Gene #4: 'amp_3q27.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
AMP PEAK 4(3Q27.3) MUTATED	12	17	20
AMP PEAK 4(3Q27.3) WILD-TYPE	57	19	25

Figure S25. Get High-res Image Gene #4: 'amp_3q27.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_3q27.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00972 (Fisher's exact test), Q value = 0.029

Table S26. Gene #4: 'amp_3q27.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
AMP PEAK 4(3Q27.3) MUTATED	4	9	9	11	8	8
AMP PEAK 4(3Q27.3) WILD-TYPE	30	27	10	16	11	7

Figure S26. Get High-res Image Gene #4: 'amp_3q27.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q12' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00051

Table S27. Gene #5: 'amp_4q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
AMP PEAK 5(4Q12) MUTATED	1	13	4	2
AMP PEAK 5(4Q12) WILD-TYPE	47	21	50	12

Figure S27. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p22.1' versus 'MRNASEQ_CNMF'

P value = 0.0316 (Fisher's exact test), Q value = 0.066

Table S28. Gene #6: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	34	30	33	22	8	22	1
AMP PEAK 6(7P22.1) MUTATED	32	26	29	14	7	18	0
AMP PEAK 6(7P22.1) WILD-TYPE	2	4	4	8	1	4	1

Figure S28. Get High-res Image Gene #6: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p22.1' versus 'MIRSEQ_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.032

Table S29. Gene #6: 'amp_7p22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	57	42
AMP PEAK 6(7P22.1) MUTATED	45	52	29
AMP PEAK 6(7P22.1) WILD-TYPE	6	5	13

Figure S29. Get High-res Image Gene #6: 'amp_7p22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7p22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.032

Table S30. Gene #6: 'amp_7p22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
AMP PEAK 6(7P22.1) MUTATED	62	35	29
AMP PEAK 6(7P22.1) WILD-TYPE	8	3	13

Figure S30. Get High-res Image Gene #6: 'amp_7p22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7p22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.051

Table S31. Gene #6: 'amp_7p22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
AMP PEAK 6(7P22.1) MUTATED	61	33	32
AMP PEAK 6(7P22.1) WILD-TYPE	8	3	13

Figure S31. Get High-res Image Gene #6: 'amp_7p22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7p22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0386 (Fisher's exact test), Q value = 0.077

Table S32. Gene #6: 'amp_7p22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
AMP PEAK 6(7P22.1) MUTATED	32	30	17	18	18	11
AMP PEAK 6(7P22.1) WILD-TYPE	2	6	2	9	1	4

Figure S32. Get High-res Image Gene #6: 'amp_7p22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q11.22' versus 'METHLYATION_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 0.054

Table S33. Gene #7: 'amp_7q11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	20	34	51
AMP PEAK 7(7Q11.22) MUTATED	39	16	31	34
AMP PEAK 7(7Q11.22) WILD-TYPE	6	4	3	17

Figure S33. Get High-res Image Gene #7: 'amp_7q11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q11.22' versus 'RPPA_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.032

Table S34. Gene #7: 'amp_7q11.22' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
AMP PEAK 7(7Q11.22) MUTATED	39	8	7	22	16
AMP PEAK 7(7Q11.22) WILD-TYPE	6	0	3	15	2

Figure S34. Get High-res Image Gene #7: 'amp_7q11.22' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_7q11.22' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S35. Gene #7: 'amp_7q11.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	34	30	33	22	8	22	1
AMP PEAK 7(7Q11.22) MUTATED	32	27	29	9	7	16	0
AMP PEAK 7(7Q11.22) WILD-TYPE	2	3	4	13	1	6	1

Figure S35. Get High-res Image Gene #7: 'amp_7q11.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7q11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00203 (Fisher's exact test), Q value = 0.0089

Table S36. Gene #7: 'amp_7q11.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
AMP PEAK 7(7Q11.22) MUTATED	39	24	8	14	7	21	7
AMP PEAK 7(7Q11.22) WILD-TYPE	4	3	4	10	1	2	6

Figure S36. Get High-res Image Gene #7: 'amp_7q11.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q11.22' versus 'MIRSEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0017

Table S37. Gene #7: 'amp_7q11.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	57	42
AMP PEAK 7(7Q11.22) MUTATED	45	51	24
AMP PEAK 7(7Q11.22) WILD-TYPE	6	6	18

Figure S37. Get High-res Image Gene #7: 'amp_7q11.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7q11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.0016

Table S38. Gene #7: 'amp_7q11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
AMP PEAK 7(7Q11.22) MUTATED	63	33	24
AMP PEAK 7(7Q11.22) WILD-TYPE	7	5	18

Figure S38. Get High-res Image Gene #7: 'amp_7q11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q11.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.001

Table S39. Gene #7: 'amp_7q11.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
AMP PEAK 7(7Q11.22) MUTATED	62	32	26
AMP PEAK 7(7Q11.22) WILD-TYPE	7	4	19

Figure S39. Get High-res Image Gene #7: 'amp_7q11.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7q11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00089 (Fisher's exact test), Q value = 0.0051

Table S40. Gene #7: 'amp_7q11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
AMP PEAK 7(7Q11.22) MUTATED	31	32	15	14	18	10
AMP PEAK 7(7Q11.22) WILD-TYPE	3	4	4	13	1	5

Figure S40. Get High-res Image Gene #7: 'amp_7q11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q11.23' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0014

Table S41. Gene #8: 'amp_8q11.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
AMP PEAK 8(8Q11.23) MUTATED	33	34	41	14
AMP PEAK 8(8Q11.23) WILD-TYPE	15	0	13	0

Figure S41. Get High-res Image Gene #8: 'amp_8q11.23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q11.23' versus 'METHLYATION_CNMF'

P value = 0.00834 (Fisher's exact test), Q value = 0.025

Table S42. Gene #8: 'amp_8q11.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	20	34	51
AMP PEAK 8(8Q11.23) MUTATED	40	20	26	36
AMP PEAK 8(8Q11.23) WILD-TYPE	5	0	8	15

Figure S42. Get High-res Image Gene #8: 'amp_8q11.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q11.23' versus 'RPPA_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.004

Table S43. Gene #8: 'amp_8q11.23' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
AMP PEAK 8(8Q11.23) MUTATED	44	6	6	25	14
AMP PEAK 8(8Q11.23) WILD-TYPE	1	2	4	12	4

Figure S43. Get High-res Image Gene #8: 'amp_8q11.23' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_8q11.23' versus 'RPPA_CHIERARCHICAL'

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

Table S44. Gene #8: 'amp_8q11.23' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
AMP PEAK 8(8Q11.23) MUTATED	49	15	31
AMP PEAK 8(8Q11.23) WILD-TYPE	2	10	11

Figure S44. Get High-res Image Gene #8: 'amp_8q11.23' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_8q11.23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S45. Gene #8: 'amp_8q11.23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	34	30	33	22	8	22	1
AMP PEAK 8(8Q11.23) MUTATED	33	30	27	17	5	9	1
AMP PEAK 8(8Q11.23) WILD-TYPE	1	0	6	5	3	13	0

Figure S45. Get High-res Image Gene #8: 'amp_8q11.23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8q11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3e-04

Table S46. Gene #8: 'amp_8q11.23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
AMP PEAK 8(8Q11.23) MUTATED	40	27	8	18	6	19	4
AMP PEAK 8(8Q11.23) WILD-TYPE	3	0	4	6	2	4	9

Figure S46. Get High-res Image Gene #8: 'amp_8q11.23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q11.23' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.001

Table S47. Gene #8: 'amp_8q11.23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	57	42
AMP PEAK 8(8Q11.23) MUTATED	48	49	25
AMP PEAK 8(8Q11.23) WILD-TYPE	3	8	17

Figure S47. Get High-res Image Gene #8: 'amp_8q11.23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8q11.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S48. Gene #8: 'amp_8q11.23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
AMP PEAK 8(8Q11.23) MUTATED	67	30	25
AMP PEAK 8(8Q11.23) WILD-TYPE	3	8	17

Figure S48. Get High-res Image Gene #8: 'amp_8q11.23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q11.23' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00042

Table S49. Gene #8: 'amp_8q11.23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
AMP PEAK 8(8Q11.23) MUTATED	66	28	28
AMP PEAK 8(8Q11.23) WILD-TYPE	3	8	17

Figure S49. Get High-res Image Gene #8: 'amp_8q11.23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8q11.23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00058

Table S50. Gene #8: 'amp_8q11.23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
AMP PEAK 8(8Q11.23) MUTATED	31	36	16	16	14	9
AMP PEAK 8(8Q11.23) WILD-TYPE	3	0	3	11	5	6

Figure S50. Get High-res Image Gene #8: 'amp_8q11.23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q23.3' versus 'METHLYATION_CNMF'

P value = 0.00183 (Fisher's exact test), Q value = 0.0083

Table S51. Gene #9: 'amp_8q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	20	34	51
AMP PEAK 9(8Q23.3) MUTATED	41	15	22	30
AMP PEAK 9(8Q23.3) WILD-TYPE	4	5	12	21

Figure S51. Get High-res Image Gene #9: 'amp_8q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q23.3' versus 'RPPA_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.054

Table S52. Gene #9: 'amp_8q23.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
AMP PEAK 9(8Q23.3) MUTATED	38	7	6	20	12
AMP PEAK 9(8Q23.3) WILD-TYPE	7	1	4	17	6

Figure S52. Get High-res Image Gene #9: 'amp_8q23.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_8q23.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.032

Table S53. Gene #9: 'amp_8q23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
AMP PEAK 9(8Q23.3) MUTATED	43	14	26
AMP PEAK 9(8Q23.3) WILD-TYPE	8	11	16

Figure S53. Get High-res Image Gene #9: 'amp_8q23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_8q23.3' versus 'MRNASEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0025

Table S54. Gene #9: 'amp_8q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	34	30	33	22	8	22	1
AMP PEAK 9(8Q23.3) MUTATED	32	24	24	13	5	9	1
AMP PEAK 9(8Q23.3) WILD-TYPE	2	6	9	9	3	13	0

Figure S54. Get High-res Image Gene #9: 'amp_8q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00057 (Fisher's exact test), Q value = 0.004

Table S55. Gene #9: 'amp_8q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
AMP PEAK 9(8Q23.3) MUTATED	38	22	9	15	5	16	3
AMP PEAK 9(8Q23.3) WILD-TYPE	5	5	3	9	3	7	10

Figure S55. Get High-res Image Gene #9: 'amp_8q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q23.3' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3e-04

Table S56. Gene #9: 'amp_8q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	57	42
AMP PEAK 9(8Q23.3) MUTATED	46	42	20
AMP PEAK 9(8Q23.3) WILD-TYPE	5	15	22

Figure S56. Get High-res Image Gene #9: 'amp_8q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.001

Table S57. Gene #9: 'amp_8q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
AMP PEAK 9(8Q23.3) MUTATED	60	28	20
AMP PEAK 9(8Q23.3) WILD-TYPE	10	10	22

Figure S57. Get High-res Image Gene #9: 'amp_8q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0025

Table S58. Gene #9: 'amp_8q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
AMP PEAK 9(8Q23.3) MUTATED	60	23	25
AMP PEAK 9(8Q23.3) WILD-TYPE	9	13	20

Figure S58. Get High-res Image Gene #9: 'amp_8q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00886 (Fisher's exact test), Q value = 0.027

Table S59. Gene #9: 'amp_8q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
AMP PEAK 9(8Q23.3) MUTATED	30	30	13	14	13	8
AMP PEAK 9(8Q23.3) WILD-TYPE	4	6	6	13	6	7

Figure S59. Get High-res Image Gene #9: 'amp_8q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p13.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.0373 (Fisher's exact test), Q value = 0.075

Table S60. Gene #10: 'amp_12p13.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
AMP PEAK 10(12P13.33) MUTATED	46	25	42
AMP PEAK 10(12P13.33) WILD-TYPE	5	0	0

Figure S60. Get High-res Image Gene #10: 'amp_12p13.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_12p11.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.0361 (Fisher's exact test), Q value = 0.073

Table S61. Gene #12: 'amp_12p11.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
AMP PEAK 12(12P11.21) MUTATED	46	25	42
AMP PEAK 12(12P11.21) WILD-TYPE	5	0	0

Figure S61. Get High-res Image Gene #12: 'amp_12p11.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_12p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0361 (Fisher's exact test), Q value = 0.073

Table S62. Gene #12: 'amp_12p11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
AMP PEAK 12(12P11.21) MUTATED	64	38	42
AMP PEAK 12(12P11.21) WILD-TYPE	6	0	0

Figure S62. Get High-res Image Gene #12: 'amp_12p11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_12p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0382 (Fisher's exact test), Q value = 0.077

Table S63. Gene #12: 'amp_12p11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
AMP PEAK 12(12P11.21) MUTATED	63	36	45
AMP PEAK 12(12P11.21) WILD-TYPE	6	0	0

Figure S63. Get High-res Image Gene #12: 'amp_12p11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_16q21' versus 'CN_CNMF'

P value = 0.00532 (Fisher's exact test), Q value = 0.018

Table S64. Gene #14: 'amp_16q21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
AMP PEAK 14(16Q21) MUTATED	3	3	15	0
AMP PEAK 14(16Q21) WILD-TYPE	45	31	39	14

Figure S64. Get High-res Image Gene #14: 'amp_16q21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_16q21' versus 'METHLYATION_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.047

Table S65. Gene #14: 'amp_16q21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	20	34	51
AMP PEAK 14(16Q21) MUTATED	1	4	5	11
AMP PEAK 14(16Q21) WILD-TYPE	44	16	29	40

Figure S65. Get High-res Image Gene #14: 'amp_16q21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_16q21' versus 'RPPA_CNMF'

P value = 0.00335 (Fisher's exact test), Q value = 0.013

Table S66. Gene #14: 'amp_16q21' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
AMP PEAK 14(16Q21) MUTATED	1	0	2	11	2
AMP PEAK 14(16Q21) WILD-TYPE	44	8	8	26	16

Figure S66. Get High-res Image Gene #14: 'amp_16q21' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_16q21' versus 'RPPA_CHIERARCHICAL'

P value = 0.00119 (Fisher's exact test), Q value = 0.0063

Table S67. Gene #14: 'amp_16q21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
AMP PEAK 14(16Q21) MUTATED	1	7	8
AMP PEAK 14(16Q21) WILD-TYPE	50	18	34

Figure S67. Get High-res Image Gene #14: 'amp_16q21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_16q21' versus 'MRNASEQ_CNMF'

P value = 0.0465 (Fisher's exact test), Q value = 0.088

Table S68. Gene #14: 'amp_16q21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	34	30	33	22	8	22	1
AMP PEAK 14(16Q21) MUTATED	1	3	5	5	0	7	0
AMP PEAK 14(16Q21) WILD-TYPE	33	27	28	17	8	15	1

Figure S68. Get High-res Image Gene #14: 'amp_16q21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_16q21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00777 (Fisher's exact test), Q value = 0.024

Table S69. Gene #14: 'amp_16q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
AMP PEAK 14(16Q21) MUTATED	1	3	3	8	0	3	3
AMP PEAK 14(16Q21) WILD-TYPE	42	24	9	16	8	20	10

Figure S69. Get High-res Image Gene #14: 'amp_16q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_16q21' versus 'MIRSEQ_CNMF'

P value = 0.0014 (Fisher's exact test), Q value = 0.0068

Table S70. Gene #14: 'amp_16q21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	57	42
AMP PEAK 14(16Q21) MUTATED	1	9	11
AMP PEAK 14(16Q21) WILD-TYPE	50	48	31

Figure S70. Get High-res Image Gene #14: 'amp_16q21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_16q21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00841 (Fisher's exact test), Q value = 0.025

Table S71. Gene #14: 'amp_16q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
AMP PEAK 14(16Q21) MUTATED	4	6	11
AMP PEAK 14(16Q21) WILD-TYPE	66	32	31

Figure S71. Get High-res Image Gene #14: 'amp_16q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_16q21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00234 (Fisher's exact test), Q value = 0.0097

Table S72. Gene #14: 'amp_16q21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
AMP PEAK 14(16Q21) MUTATED	4	4	13
AMP PEAK 14(16Q21) WILD-TYPE	65	32	32

Figure S72. Get High-res Image Gene #14: 'amp_16q21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_16q21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00287 (Fisher's exact test), Q value = 0.012

Table S73. Gene #14: 'amp_16q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
AMP PEAK 14(16Q21) MUTATED	0	4	4	8	1	4
AMP PEAK 14(16Q21) WILD-TYPE	34	32	15	19	18	11

Figure S73. Get High-res Image Gene #14: 'amp_16q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q11.21' versus 'CN_CNMF'

P value = 0.0366 (Fisher's exact test), Q value = 0.074

Table S74. Gene #15: 'amp_20q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
AMP PEAK 15(20Q11.21) MUTATED	11	9	23	8
AMP PEAK 15(20Q11.21) WILD-TYPE	37	25	31	6

Figure S74. Get High-res Image Gene #15: 'amp_20q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q11.21' versus 'METHLYATION_CNMF'

P value = 0.00099 (Fisher's exact test), Q value = 0.0054

Table S75. Gene #15: 'amp_20q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	20	34	51
AMP PEAK 15(20Q11.21) MUTATED	7	4	14	26
AMP PEAK 15(20Q11.21) WILD-TYPE	38	16	20	25

Figure S75. Get High-res Image Gene #15: 'amp_20q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'RPPA_CNMF'

P value = 0.0195 (Fisher's exact test), Q value = 0.047

Table S76. Gene #15: 'amp_20q11.21' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
AMP PEAK 15(20Q11.21) MUTATED	10	1	6	15	10
AMP PEAK 15(20Q11.21) WILD-TYPE	35	7	4	22	8

Figure S76. Get High-res Image Gene #15: 'amp_20q11.21' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_20q11.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.0145 (Fisher's exact test), Q value = 0.037

Table S77. Gene #15: 'amp_20q11.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
AMP PEAK 15(20Q11.21) MUTATED	11	13	18
AMP PEAK 15(20Q11.21) WILD-TYPE	40	12	24

Figure S77. Get High-res Image Gene #15: 'amp_20q11.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0337 (Fisher's exact test), Q value = 0.069

Table S78. Gene #15: 'amp_20q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
AMP PEAK 15(20Q11.21) MUTATED	11	5	3	14	2	9	7
AMP PEAK 15(20Q11.21) WILD-TYPE	32	22	9	10	6	14	6

Figure S78. Get High-res Image Gene #15: 'amp_20q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.032

Table S79. Gene #15: 'amp_20q11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	57	42
AMP PEAK 15(20Q11.21) MUTATED	12	17	22
AMP PEAK 15(20Q11.21) WILD-TYPE	39	40	20

Figure S79. Get High-res Image Gene #15: 'amp_20q11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_20q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00687 (Fisher's exact test), Q value = 0.022

Table S80. Gene #15: 'amp_20q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
AMP PEAK 15(20Q11.21) MUTATED	16	13	22
AMP PEAK 15(20Q11.21) WILD-TYPE	54	25	20

Figure S80. Get High-res Image Gene #15: 'amp_20q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.03

Table S81. Gene #15: 'amp_20q11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
AMP PEAK 15(20Q11.21) MUTATED	16	12	23
AMP PEAK 15(20Q11.21) WILD-TYPE	53	24	22

Figure S81. Get High-res Image Gene #15: 'amp_20q11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0421 (Fisher's exact test), Q value = 0.082

Table S82. Gene #15: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
AMP PEAK 15(20Q11.21) MUTATED	6	10	7	15	6	7
AMP PEAK 15(20Q11.21) WILD-TYPE	28	26	12	12	13	8

Figure S82. Get High-res Image Gene #15: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_22q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S83. Gene #16: 'amp_22q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
AMP PEAK 16(22Q11.21) MUTATED	13	27	12	5
AMP PEAK 16(22Q11.21) WILD-TYPE	35	7	42	9

Figure S83. Get High-res Image Gene #16: 'amp_22q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_22q11.21' versus 'RPPA_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.032

Table S84. Gene #16: 'amp_22q11.21' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
AMP PEAK 16(22Q11.21) MUTATED	24	2	4	8	3
AMP PEAK 16(22Q11.21) WILD-TYPE	21	6	6	29	15

Figure S84. Get High-res Image Gene #16: 'amp_22q11.21' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_22q11.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.00574 (Fisher's exact test), Q value = 0.019

Table S85. Gene #16: 'amp_22q11.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
AMP PEAK 16(22Q11.21) MUTATED	26	5	10
AMP PEAK 16(22Q11.21) WILD-TYPE	25	20	32

Figure S85. Get High-res Image Gene #16: 'amp_22q11.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_22q11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S86. Gene #16: 'amp_22q11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	34	30	33	22	8	22	1
AMP PEAK 16(22Q11.21) MUTATED	12	25	9	4	2	5	0
AMP PEAK 16(22Q11.21) WILD-TYPE	22	5	24	18	6	17	1

Figure S86. Get High-res Image Gene #16: 'amp_22q11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_22q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S87. Gene #16: 'amp_22q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
AMP PEAK 16(22Q11.21) MUTATED	16	23	4	5	1	5	3
AMP PEAK 16(22Q11.21) WILD-TYPE	27	4	8	19	7	18	10

Figure S87. Get High-res Image Gene #16: 'amp_22q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_22q11.21' versus 'MIRSEQ_CNMF'

P value = 0.0249 (Fisher's exact test), Q value = 0.054

Table S88. Gene #16: 'amp_22q11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	57	42
AMP PEAK 16(22Q11.21) MUTATED	24	24	9
AMP PEAK 16(22Q11.21) WILD-TYPE	27	33	33

Figure S88. Get High-res Image Gene #16: 'amp_22q11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_22q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.0016

Table S89. Gene #16: 'amp_22q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
AMP PEAK 16(22Q11.21) MUTATED	39	9	9
AMP PEAK 16(22Q11.21) WILD-TYPE	31	29	33

Figure S89. Get High-res Image Gene #16: 'amp_22q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_22q11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.002

Table S90. Gene #16: 'amp_22q11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
AMP PEAK 16(22Q11.21) MUTATED	38	10	9
AMP PEAK 16(22Q11.21) WILD-TYPE	31	26	36

Figure S90. Get High-res Image Gene #16: 'amp_22q11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_22q11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00058

Table S91. Gene #16: 'amp_22q11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
AMP PEAK 16(22Q11.21) MUTATED	13	26	6	4	4	4
AMP PEAK 16(22Q11.21) WILD-TYPE	21	10	13	23	15	11

Figure S91. Get High-res Image Gene #16: 'amp_22q11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.31' versus 'MIRSEQ_CNMF'

P value = 0.00524 (Fisher's exact test), Q value = 0.018

Table S92. Gene #17: 'del_1p36.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	57	42
DEL PEAK 1(1P36.31) MUTATED	12	6	16
DEL PEAK 1(1P36.31) WILD-TYPE	39	51	26

Figure S92. Get High-res Image Gene #17: 'del_1p36.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p36.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00473 (Fisher's exact test), Q value = 0.017

Table S93. Gene #17: 'del_1p36.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 1(1P36.31) MUTATED	15	3	16
DEL PEAK 1(1P36.31) WILD-TYPE	55	35	26

Figure S93. Get High-res Image Gene #17: 'del_1p36.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00195 (Fisher's exact test), Q value = 0.0088

Table S94. Gene #17: 'del_1p36.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 1(1P36.31) MUTATED	15	2	17
DEL PEAK 1(1P36.31) WILD-TYPE	54	34	28

Figure S94. Get High-res Image Gene #17: 'del_1p36.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p36.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0146 (Fisher's exact test), Q value = 0.037

Table S95. Gene #17: 'del_1p36.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
DEL PEAK 1(1P36.31) MUTATED	7	8	3	9	0	7
DEL PEAK 1(1P36.31) WILD-TYPE	27	28	16	18	19	8

Figure S95. Get High-res Image Gene #17: 'del_1p36.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p31.1' versus 'CN_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 0.048

Table S96. Gene #18: 'del_1p31.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
DEL PEAK 2(1P31.1) MUTATED	5	9	7	6
DEL PEAK 2(1P31.1) WILD-TYPE	43	25	47	8

Figure S96. Get High-res Image Gene #18: 'del_1p31.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p31.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0489 (Fisher's exact test), Q value = 0.092

Table S97. Gene #18: 'del_1p31.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
DEL PEAK 2(1P31.1) MUTATED	13	5	3
DEL PEAK 2(1P31.1) WILD-TYPE	38	20	39

Figure S97. Get High-res Image Gene #18: 'del_1p31.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_1p31.1' versus 'MIRSEQ_CNMF'

P value = 0.00787 (Fisher's exact test), Q value = 0.024

Table S98. Gene #18: 'del_1p31.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	57	42
DEL PEAK 2(1P31.1) MUTATED	15	4	8
DEL PEAK 2(1P31.1) WILD-TYPE	36	53	34

Figure S98. Get High-res Image Gene #18: 'del_1p31.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1q42.12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.013 (Fisher's exact test), Q value = 0.034

Table S99. Gene #19: 'del_1q42.12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
DEL PEAK 3(1Q42.12) MUTATED	0	6	2	0	0	1
DEL PEAK 3(1Q42.12) WILD-TYPE	34	30	17	27	19	14

Figure S99. Get High-res Image Gene #19: 'del_1q42.12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 0.048

Table S100. Gene #20: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	20	34	51
DEL PEAK 4(2Q37.3) MUTATED	2	0	8	5
DEL PEAK 4(2Q37.3) WILD-TYPE	43	20	26	46

Figure S100. Get High-res Image Gene #20: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p26.2' versus 'CN_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 0.054

Table S101. Gene #21: 'del_3p26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
DEL PEAK 5(3P26.2) MUTATED	11	8	13	9
DEL PEAK 5(3P26.2) WILD-TYPE	37	26	41	5

Figure S101. Get High-res Image Gene #21: 'del_3p26.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p26.2' versus 'METHLYATION_CNMF'

P value = 0.00349 (Fisher's exact test), Q value = 0.013

Table S102. Gene #21: 'del_3p26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	20	34	51
DEL PEAK 5(3P26.2) MUTATED	14	5	16	6
DEL PEAK 5(3P26.2) WILD-TYPE	31	15	18	45

Figure S102. Get High-res Image Gene #21: 'del_3p26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p26.2' versus 'MRNASEQ_CNMF'

P value = 0.00789 (Fisher's exact test), Q value = 0.024

Table S103. Gene #21: 'del_3p26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	34	30	33	22	8	22	1
DEL PEAK 5(3P26.2) MUTATED	14	6	14	2	3	2	0
DEL PEAK 5(3P26.2) WILD-TYPE	20	24	19	20	5	20	1

Figure S103. Get High-res Image Gene #21: 'del_3p26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00442 (Fisher's exact test), Q value = 0.016

Table S104. Gene #21: 'del_3p26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 5(3P26.2) MUTATED	17	5	2	2	2	12	1
DEL PEAK 5(3P26.2) WILD-TYPE	26	22	10	22	6	11	12

Figure S104. Get High-res Image Gene #21: 'del_3p26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_CNMF'

P value = 0.0037 (Fisher's exact test), Q value = 0.014

Table S105. Gene #21: 'del_3p26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	57	42
DEL PEAK 5(3P26.2) MUTATED	15	22	4
DEL PEAK 5(3P26.2) WILD-TYPE	36	35	38

Figure S105. Get High-res Image Gene #21: 'del_3p26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00348 (Fisher's exact test), Q value = 0.013

Table S106. Gene #21: 'del_3p26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 5(3P26.2) MUTATED	22	15	4
DEL PEAK 5(3P26.2) WILD-TYPE	48	23	38

Figure S106. Get High-res Image Gene #21: 'del_3p26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0013 (Fisher's exact test), Q value = 0.0065

Table S107. Gene #21: 'del_3p26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 5(3P26.2) MUTATED	22	15	4
DEL PEAK 5(3P26.2) WILD-TYPE	47	21	41

Figure S107. Get High-res Image Gene #21: 'del_3p26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S108. Gene #21: 'del_3p26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
DEL PEAK 5(3P26.2) MUTATED	15	7	5	1	11	2
DEL PEAK 5(3P26.2) WILD-TYPE	19	29	14	26	8	13

Figure S108. Get High-res Image Gene #21: 'del_3p26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.2' versus 'CN_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 0.054

Table S109. Gene #22: 'del_4q22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
DEL PEAK 6(4Q22.2) MUTATED	29	29	39	13
DEL PEAK 6(4Q22.2) WILD-TYPE	19	5	15	1

Figure S109. Get High-res Image Gene #22: 'del_4q22.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q22.2' versus 'MRNASEQ_CNMF'

P value = 0.00924 (Fisher's exact test), Q value = 0.027

Table S110. Gene #22: 'del_4q22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	34	30	33	22	8	22	1
DEL PEAK 6(4Q22.2) MUTATED	21	27	29	15	5	12	1
DEL PEAK 6(4Q22.2) WILD-TYPE	13	3	4	7	3	10	0

Figure S110. Get High-res Image Gene #22: 'del_4q22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00142 (Fisher's exact test), Q value = 0.0068

Table S111. Gene #22: 'del_4q22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 6(4Q22.2) MUTATED	27	25	10	14	7	21	6
DEL PEAK 6(4Q22.2) WILD-TYPE	16	2	2	10	1	2	7

Figure S111. Get High-res Image Gene #22: 'del_4q22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.2' versus 'MIRSEQ_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0041

Table S112. Gene #22: 'del_4q22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	57	42
DEL PEAK 6(4Q22.2) MUTATED	35	51	24
DEL PEAK 6(4Q22.2) WILD-TYPE	16	6	18

Figure S112. Get High-res Image Gene #22: 'del_4q22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00421 (Fisher's exact test), Q value = 0.015

Table S113. Gene #22: 'del_4q22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 6(4Q22.2) MUTATED	52	34	24
DEL PEAK 6(4Q22.2) WILD-TYPE	18	4	18

Figure S113. Get High-res Image Gene #22: 'del_4q22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 0.062

Table S114. Gene #22: 'del_4q22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 6(4Q22.2) MUTATED	52	31	27
DEL PEAK 6(4Q22.2) WILD-TYPE	17	5	18

Figure S114. Get High-res Image Gene #22: 'del_4q22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00494 (Fisher's exact test), Q value = 0.017

Table S115. Gene #22: 'del_4q22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
DEL PEAK 6(4Q22.2) MUTATED	22	30	15	13	18	12
DEL PEAK 6(4Q22.2) WILD-TYPE	12	6	4	14	1	3

Figure S115. Get High-res Image Gene #22: 'del_4q22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5p15.2' versus 'CN_CNMF'

P value = 0.0398 (Fisher's exact test), Q value = 0.078

Table S116. Gene #23: 'del_5p15.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
DEL PEAK 7(5P15.2) MUTATED	32	29	33	7
DEL PEAK 7(5P15.2) WILD-TYPE	16	5	21	7

Figure S116. Get High-res Image Gene #23: 'del_5p15.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5p14.3' versus 'RPPA_CNMF'

P value = 0.0209 (Fisher's exact test), Q value = 0.049

Table S117. Gene #24: 'del_5p14.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
DEL PEAK 8(5P14.3) MUTATED	30	7	4	28	7
DEL PEAK 8(5P14.3) WILD-TYPE	15	1	6	9	11

Figure S117. Get High-res Image Gene #24: 'del_5p14.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_5q12.1' versus 'CN_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.004

Table S118. Gene #25: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
DEL PEAK 9(5Q12.1) MUTATED	31	32	36	6
DEL PEAK 9(5Q12.1) WILD-TYPE	17	2	18	8

Figure S118. Get High-res Image Gene #25: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q12.1' versus 'RPPA_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.032

Table S119. Gene #25: 'del_5q12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
DEL PEAK 9(5Q12.1) MUTATED	33	7	4	28	7
DEL PEAK 9(5Q12.1) WILD-TYPE	12	1	6	9	11

Figure S119. Get High-res Image Gene #25: 'del_5q12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_5q12.1' versus 'MRNASEQ_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.032

Table S120. Gene #25: 'del_5q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	34	30	33	22	8	22	1
DEL PEAK 9(5Q12.1) MUTATED	24	28	18	16	4	14	1
DEL PEAK 9(5Q12.1) WILD-TYPE	10	2	15	6	4	8	0

Figure S120. Get High-res Image Gene #25: 'del_5q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00745 (Fisher's exact test), Q value = 0.024

Table S121. Gene #25: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 9(5Q12.1) MUTATED	30	26	9	15	4	12	9
DEL PEAK 9(5Q12.1) WILD-TYPE	13	1	3	9	4	11	4

Figure S121. Get High-res Image Gene #25: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0239 (Fisher's exact test), Q value = 0.054

Table S122. Gene #25: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 9(5Q12.1) MUTATED	56	21	28
DEL PEAK 9(5Q12.1) WILD-TYPE	14	17	14

Figure S122. Get High-res Image Gene #25: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.029 (Fisher's exact test), Q value = 0.062

Table S123. Gene #25: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 9(5Q12.1) MUTATED	55	20	30
DEL PEAK 9(5Q12.1) WILD-TYPE	14	16	15

Figure S123. Get High-res Image Gene #25: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5q12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0395 (Fisher's exact test), Q value = 0.078

Table S124. Gene #25: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
DEL PEAK 9(5Q12.1) MUTATED	25	31	10	17	10	12
DEL PEAK 9(5Q12.1) WILD-TYPE	9	5	9	10	9	3

Figure S124. Get High-res Image Gene #25: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p22.3' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.002

Table S125. Gene #26: 'del_6p22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
DEL PEAK 10(6P22.3) MUTATED	2	3	18	1
DEL PEAK 10(6P22.3) WILD-TYPE	46	31	36	13

Figure S125. Get High-res Image Gene #26: 'del_6p22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p22.3' versus 'METHLYATION_CNMF'

P value = 0.00233 (Fisher's exact test), Q value = 0.0097

Table S126. Gene #26: 'del_6p22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	20	34	51
DEL PEAK 10(6P22.3) MUTATED	1	2	10	11
DEL PEAK 10(6P22.3) WILD-TYPE	44	18	24	40

Figure S126. Get High-res Image Gene #26: 'del_6p22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p22.3' versus 'RPPA_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0015

Table S127. Gene #26: 'del_6p22.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
DEL PEAK 10(6P22.3) MUTATED	2	0	0	11	8
DEL PEAK 10(6P22.3) WILD-TYPE	43	8	10	26	10

Figure S127. Get High-res Image Gene #26: 'del_6p22.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_6p22.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.0046

Table S128. Gene #26: 'del_6p22.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
DEL PEAK 10(6P22.3) MUTATED	2	6	13
DEL PEAK 10(6P22.3) WILD-TYPE	49	19	29

Figure S128. Get High-res Image Gene #26: 'del_6p22.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_6p22.3' versus 'MRNASEQ_CNMF'

P value = 0.022 (Fisher's exact test), Q value = 0.051

Table S129. Gene #26: 'del_6p22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	34	30	33	22	8	22	1
DEL PEAK 10(6P22.3) MUTATED	2	2	8	4	0	8	0
DEL PEAK 10(6P22.3) WILD-TYPE	32	28	25	18	8	14	1

Figure S129. Get High-res Image Gene #26: 'del_6p22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6p22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0116 (Fisher's exact test), Q value = 0.032

Table S130. Gene #26: 'del_6p22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 10(6P22.3) MUTATED	2	2	3	4	1	7	5
DEL PEAK 10(6P22.3) WILD-TYPE	41	25	9	20	7	16	8

Figure S130. Get High-res Image Gene #26: 'del_6p22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6p22.3' versus 'MIRSEQ_CNMF'

P value = 0.00501 (Fisher's exact test), Q value = 0.018

Table S131. Gene #26: 'del_6p22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	57	42
DEL PEAK 10(6P22.3) MUTATED	2	11	11
DEL PEAK 10(6P22.3) WILD-TYPE	49	46	31

Figure S131. Get High-res Image Gene #26: 'del_6p22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6p22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00345 (Fisher's exact test), Q value = 0.013

Table S132. Gene #26: 'del_6p22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 10(6P22.3) MUTATED	4	9	11
DEL PEAK 10(6P22.3) WILD-TYPE	66	29	31

Figure S132. Get High-res Image Gene #26: 'del_6p22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6p22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00334 (Fisher's exact test), Q value = 0.013

Table S133. Gene #26: 'del_6p22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 10(6P22.3) MUTATED	4	10	10
DEL PEAK 10(6P22.3) WILD-TYPE	65	26	35

Figure S133. Get High-res Image Gene #26: 'del_6p22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6p22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00553 (Fisher's exact test), Q value = 0.018

Table S134. Gene #26: 'del_6p22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
DEL PEAK 10(6P22.3) MUTATED	1	3	7	8	3	2
DEL PEAK 10(6P22.3) WILD-TYPE	33	33	12	19	16	13

Figure S134. Get High-res Image Gene #26: 'del_6p22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 0.0397 (Fisher's exact test), Q value = 0.078

Table S135. Gene #27: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	20	34	51
DEL PEAK 11(6Q26) MUTATED	4	1	10	11
DEL PEAK 11(6Q26) WILD-TYPE	41	19	24	40

Figure S135. Get High-res Image Gene #27: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q26' versus 'RPPA_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.054

Table S136. Gene #27: 'del_6q26' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
DEL PEAK 11(6Q26) MUTATED	4	0	2	10	7
DEL PEAK 11(6Q26) WILD-TYPE	41	8	8	27	11

Figure S136. Get High-res Image Gene #27: 'del_6q26' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_6q26' versus 'RPPA_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.037

Table S137. Gene #27: 'del_6q26' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
DEL PEAK 11(6Q26) MUTATED	4	7	12
DEL PEAK 11(6Q26) WILD-TYPE	47	18	30

Figure S137. Get High-res Image Gene #27: 'del_6q26' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.0046

Table S138. Gene #27: 'del_6q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	34	30	33	22	8	22	1
DEL PEAK 11(6Q26) MUTATED	1	4	9	2	0	10	0
DEL PEAK 11(6Q26) WILD-TYPE	33	26	24	20	8	12	1

Figure S138. Get High-res Image Gene #27: 'del_6q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0013 (Fisher's exact test), Q value = 0.0065

Table S139. Gene #27: 'del_6q26' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 11(6Q26) MUTATED	1	4	3	3	3	6	6
DEL PEAK 11(6Q26) WILD-TYPE	42	23	9	21	5	17	7

Figure S139. Get High-res Image Gene #27: 'del_6q26' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.044

Table S140. Gene #27: 'del_6q26' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	57	42
DEL PEAK 11(6Q26) MUTATED	3	13	10
DEL PEAK 11(6Q26) WILD-TYPE	48	44	32

Figure S140. Get High-res Image Gene #27: 'del_6q26' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00505 (Fisher's exact test), Q value = 0.018

Table S141. Gene #27: 'del_6q26' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 11(6Q26) MUTATED	5	11	10
DEL PEAK 11(6Q26) WILD-TYPE	65	27	32

Figure S141. Get High-res Image Gene #27: 'del_6q26' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00446 (Fisher's exact test), Q value = 0.016

Table S142. Gene #27: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 11(6Q26) MUTATED	5	11	10
DEL PEAK 11(6Q26) WILD-TYPE	64	25	35

Figure S142. Get High-res Image Gene #27: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0234 (Fisher's exact test), Q value = 0.053

Table S143. Gene #27: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
DEL PEAK 11(6Q26) MUTATED	1	4	5	7	6	3
DEL PEAK 11(6Q26) WILD-TYPE	33	32	14	20	13	12

Figure S143. Get High-res Image Gene #27: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q11.22' versus 'RPPA_CHIERARCHICAL'

P value = 0.0282 (Fisher's exact test), Q value = 0.061

Table S144. Gene #28: 'del_7q11.22' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
DEL PEAK 12(7Q11.22) MUTATED	0	0	4
DEL PEAK 12(7Q11.22) WILD-TYPE	51	25	38

Figure S144. Get High-res Image Gene #28: 'del_7q11.22' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_7q11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0293 (Fisher's exact test), Q value = 0.062

Table S145. Gene #28: 'del_7q11.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 12(7Q11.22) MUTATED	0	0	1	1	0	0	2
DEL PEAK 12(7Q11.22) WILD-TYPE	43	27	11	23	8	23	11

Figure S145. Get High-res Image Gene #28: 'del_7q11.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_7q11.22' versus 'MIRSEQ_CNMF'

P value = 0.00531 (Fisher's exact test), Q value = 0.018

Table S146. Gene #28: 'del_7q11.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	57	42
DEL PEAK 12(7Q11.22) MUTATED	0	0	4
DEL PEAK 12(7Q11.22) WILD-TYPE	51	57	38

Figure S146. Get High-res Image Gene #28: 'del_7q11.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_7q11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00894 (Fisher's exact test), Q value = 0.027

Table S147. Gene #28: 'del_7q11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 12(7Q11.22) MUTATED	0	0	4
DEL PEAK 12(7Q11.22) WILD-TYPE	70	38	38

Figure S147. Get High-res Image Gene #28: 'del_7q11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_7q11.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.03

Table S148. Gene #28: 'del_7q11.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 12(7Q11.22) MUTATED	0	0	4
DEL PEAK 12(7Q11.22) WILD-TYPE	69	36	41

Figure S148. Get High-res Image Gene #28: 'del_7q11.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_7q11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0226 (Fisher's exact test), Q value = 0.052

Table S149. Gene #28: 'del_7q11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
DEL PEAK 12(7Q11.22) MUTATED	0	0	0	2	0	2
DEL PEAK 12(7Q11.22) WILD-TYPE	34	36	19	25	19	13

Figure S149. Get High-res Image Gene #28: 'del_7q11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q35' versus 'CN_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.036

Table S150. Gene #29: 'del_7q35' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
DEL PEAK 13(7Q35) MUTATED	0	6	6	1
DEL PEAK 13(7Q35) WILD-TYPE	48	28	48	13

Figure S150. Get High-res Image Gene #29: 'del_7q35' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q35' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0115 (Fisher's exact test), Q value = 0.032

Table S151. Gene #29: 'del_7q35' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 13(7Q35) MUTATED	0	5	3	1	0	2	2
DEL PEAK 13(7Q35) WILD-TYPE	43	22	9	23	8	21	11

Figure S151. Get High-res Image Gene #29: 'del_7q35' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_7q35' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0322 (Fisher's exact test), Q value = 0.067

Table S152. Gene #29: 'del_7q35' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
DEL PEAK 13(7Q35) MUTATED	0	5	3	2	0	3
DEL PEAK 13(7Q35) WILD-TYPE	34	31	16	25	19	12

Figure S152. Get High-res Image Gene #29: 'del_7q35' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p24.3' versus 'CN_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.065

Table S153. Gene #30: 'del_9p24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
DEL PEAK 14(9P24.3) MUTATED	16	19	31	4
DEL PEAK 14(9P24.3) WILD-TYPE	32	15	23	10

Figure S153. Get High-res Image Gene #30: 'del_9p24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'CN_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0035

Table S154. Gene #31: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
DEL PEAK 15(9P23) MUTATED	15	19	31	1
DEL PEAK 15(9P23) WILD-TYPE	33	15	23	13

Figure S154. Get High-res Image Gene #31: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q33.3' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0015

Table S155. Gene #32: 'del_9q33.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
DEL PEAK 16(9Q33.3) MUTATED	11	14	33	2
DEL PEAK 16(9Q33.3) WILD-TYPE	37	20	21	12

Figure S155. Get High-res Image Gene #32: 'del_9q33.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q33.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0156 (Fisher's exact test), Q value = 0.039

Table S156. Gene #32: 'del_9q33.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 16(9Q33.3) MUTATED	14	8	9	12	1	13	3
DEL PEAK 16(9Q33.3) WILD-TYPE	29	19	3	12	7	10	10

Figure S156. Get High-res Image Gene #32: 'del_9q33.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9q34.2' versus 'CN_CNMF'

P value = 0.00099 (Fisher's exact test), Q value = 0.0054

Table S157. Gene #33: 'del_9q34.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
DEL PEAK 17(9Q34.2) MUTATED	11	14	32	3
DEL PEAK 17(9Q34.2) WILD-TYPE	37	20	22	11

Figure S157. Get High-res Image Gene #33: 'del_9q34.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q34.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00402 (Fisher's exact test), Q value = 0.015

Table S158. Gene #33: 'del_9q34.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 17(9Q34.2) MUTATED	14	8	9	12	1	14	2
DEL PEAK 17(9Q34.2) WILD-TYPE	29	19	3	12	7	9	11

Figure S158. Get High-res Image Gene #33: 'del_9q34.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9q34.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0284 (Fisher's exact test), Q value = 0.061

Table S159. Gene #33: 'del_9q34.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 17(9Q34.2) MUTATED	22	22	16
DEL PEAK 17(9Q34.2) WILD-TYPE	48	16	26

Figure S159. Get High-res Image Gene #33: 'del_9q34.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0014

Table S160. Gene #34: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
DEL PEAK 18(10P15.3) MUTATED	20	13	42	9
DEL PEAK 18(10P15.3) WILD-TYPE	28	21	12	5

Figure S160. Get High-res Image Gene #34: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.048

Table S161. Gene #34: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	20	34	51
DEL PEAK 18(10P15.3) MUTATED	19	10	26	29
DEL PEAK 18(10P15.3) WILD-TYPE	26	10	8	22

Figure S161. Get High-res Image Gene #34: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p15.3' versus 'RPPA_CNMF'

P value = 0.00408 (Fisher's exact test), Q value = 0.015

Table S162. Gene #34: 'del_10p15.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
DEL PEAK 18(10P15.3) MUTATED	17	3	5	25	15
DEL PEAK 18(10P15.3) WILD-TYPE	28	5	5	12	3

Figure S162. Get High-res Image Gene #34: 'del_10p15.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_10p15.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00267 (Fisher's exact test), Q value = 0.011

Table S163. Gene #34: 'del_10p15.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
DEL PEAK 18(10P15.3) MUTATED	19	16	30
DEL PEAK 18(10P15.3) WILD-TYPE	32	9	12

Figure S163. Get High-res Image Gene #34: 'del_10p15.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 0.00542 (Fisher's exact test), Q value = 0.018

Table S164. Gene #34: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	34	30	33	22	8	22	1
DEL PEAK 18(10P15.3) MUTATED	13	13	26	12	4	16	0
DEL PEAK 18(10P15.3) WILD-TYPE	21	17	7	10	4	6	1

Figure S164. Get High-res Image Gene #34: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00126 (Fisher's exact test), Q value = 0.0065

Table S165. Gene #34: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 18(10P15.3) MUTATED	16	12	8	14	5	21	8
DEL PEAK 18(10P15.3) WILD-TYPE	27	15	4	10	3	2	5

Figure S165. Get High-res Image Gene #34: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_CNMF'

P value = 0.0346 (Fisher's exact test), Q value = 0.071

Table S166. Gene #34: 'del_10p15.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	57	42
DEL PEAK 18(10P15.3) MUTATED	21	36	27
DEL PEAK 18(10P15.3) WILD-TYPE	30	21	15

Figure S166. Get High-res Image Gene #34: 'del_10p15.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10p15.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00065 (Fisher's exact test), Q value = 0.0041

Table S167. Gene #34: 'del_10p15.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 18(10P15.3) MUTATED	28	29	27
DEL PEAK 18(10P15.3) WILD-TYPE	42	9	15

Figure S167. Get High-res Image Gene #34: 'del_10p15.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0024

Table S168. Gene #34: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 18(10P15.3) MUTATED	28	29	27
DEL PEAK 18(10P15.3) WILD-TYPE	41	7	18

Figure S168. Get High-res Image Gene #34: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10p15.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00144 (Fisher's exact test), Q value = 0.0069

Table S169. Gene #34: 'del_10p15.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
DEL PEAK 18(10P15.3) MUTATED	11	17	16	15	14	11
DEL PEAK 18(10P15.3) WILD-TYPE	23	19	3	12	5	4

Figure S169. Get High-res Image Gene #34: 'del_10p15.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.1' versus 'CN_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0037

Table S170. Gene #35: 'del_10q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
DEL PEAK 19(10Q23.1) MUTATED	18	9	37	7
DEL PEAK 19(10Q23.1) WILD-TYPE	30	25	17	7

Figure S170. Get High-res Image Gene #35: 'del_10q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.1' versus 'METHLYATION_CNMF'

P value = 0.00403 (Fisher's exact test), Q value = 0.015

Table S171. Gene #35: 'del_10q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	20	34	51
DEL PEAK 19(10Q23.1) MUTATED	16	7	25	23
DEL PEAK 19(10Q23.1) WILD-TYPE	29	13	9	28

Figure S171. Get High-res Image Gene #35: 'del_10q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.1' versus 'RPPA_CNMF'

P value = 0.0244 (Fisher's exact test), Q value = 0.054

Table S172. Gene #35: 'del_10q23.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
DEL PEAK 19(10Q23.1) MUTATED	15	2	4	21	13
DEL PEAK 19(10Q23.1) WILD-TYPE	30	6	6	16	5

Figure S172. Get High-res Image Gene #35: 'del_10q23.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_10q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.036

Table S173. Gene #35: 'del_10q23.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
DEL PEAK 19(10Q23.1) MUTATED	16	14	25
DEL PEAK 19(10Q23.1) WILD-TYPE	35	11	17

Figure S173. Get High-res Image Gene #35: 'del_10q23.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_10q23.1' versus 'MRNASEQ_CNMF'

P value = 0.00216 (Fisher's exact test), Q value = 0.0093

Table S174. Gene #35: 'del_10q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	34	30	33	22	8	22	1
DEL PEAK 19(10Q23.1) MUTATED	12	8	25	10	4	12	0
DEL PEAK 19(10Q23.1) WILD-TYPE	22	22	8	12	4	10	1

Figure S174. Get High-res Image Gene #35: 'del_10q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.0028

Table S175. Gene #35: 'del_10q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 19(10Q23.1) MUTATED	14	8	9	12	5	19	4
DEL PEAK 19(10Q23.1) WILD-TYPE	29	19	3	12	3	4	9

Figure S175. Get High-res Image Gene #35: 'del_10q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.1' versus 'MIRSEQ_CNMF'

P value = 0.0234 (Fisher's exact test), Q value = 0.053

Table S176. Gene #35: 'del_10q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	57	42
DEL PEAK 19(10Q23.1) MUTATED	17	34	20
DEL PEAK 19(10Q23.1) WILD-TYPE	34	23	22

Figure S176. Get High-res Image Gene #35: 'del_10q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00042

Table S177. Gene #35: 'del_10q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 19(10Q23.1) MUTATED	22	29	20
DEL PEAK 19(10Q23.1) WILD-TYPE	48	9	22

Figure S177. Get High-res Image Gene #35: 'del_10q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.001

Table S178. Gene #35: 'del_10q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 19(10Q23.1) MUTATED	22	27	22
DEL PEAK 19(10Q23.1) WILD-TYPE	47	9	23

Figure S178. Get High-res Image Gene #35: 'del_10q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00042

Table S179. Gene #35: 'del_10q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
DEL PEAK 19(10Q23.1) MUTATED	9	13	15	9	14	11
DEL PEAK 19(10Q23.1) WILD-TYPE	25	23	4	18	5	4

Figure S179. Get High-res Image Gene #35: 'del_10q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S180. Gene #36: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
DEL PEAK 20(10Q26.3) MUTATED	17	9	41	9
DEL PEAK 20(10Q26.3) WILD-TYPE	31	25	13	5

Figure S180. Get High-res Image Gene #36: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q26.3' versus 'METHLYATION_CNMF'

P value = 0.00078 (Fisher's exact test), Q value = 0.0046

Table S181. Gene #36: 'del_10q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	20	34	51
DEL PEAK 20(10Q26.3) MUTATED	17	7	27	25
DEL PEAK 20(10Q26.3) WILD-TYPE	28	13	7	26

Figure S181. Get High-res Image Gene #36: 'del_10q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q26.3' versus 'RPPA_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.033

Table S182. Gene #36: 'del_10q26.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
DEL PEAK 20(10Q26.3) MUTATED	15	2	5	23	13
DEL PEAK 20(10Q26.3) WILD-TYPE	30	6	5	14	5

Figure S182. Get High-res Image Gene #36: 'del_10q26.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_10q26.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00308 (Fisher's exact test), Q value = 0.012

Table S183. Gene #36: 'del_10q26.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
DEL PEAK 20(10Q26.3) MUTATED	16	15	27
DEL PEAK 20(10Q26.3) WILD-TYPE	35	10	15

Figure S183. Get High-res Image Gene #36: 'del_10q26.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.003

Table S184. Gene #36: 'del_10q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	34	30	33	22	8	22	1
DEL PEAK 20(10Q26.3) MUTATED	14	8	27	11	4	12	0
DEL PEAK 20(10Q26.3) WILD-TYPE	20	22	6	11	4	10	1

Figure S184. Get High-res Image Gene #36: 'del_10q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.0011

Table S185. Gene #36: 'del_10q26.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 20(10Q26.3) MUTATED	16	8	10	13	6	19	4
DEL PEAK 20(10Q26.3) WILD-TYPE	27	19	2	11	2	4	9

Figure S185. Get High-res Image Gene #36: 'del_10q26.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_CNMF'

P value = 0.0441 (Fisher's exact test), Q value = 0.084

Table S186. Gene #36: 'del_10q26.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	57	42
DEL PEAK 20(10Q26.3) MUTATED	19	35	22
DEL PEAK 20(10Q26.3) WILD-TYPE	32	22	20

Figure S186. Get High-res Image Gene #36: 'del_10q26.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00058

Table S187. Gene #36: 'del_10q26.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 20(10Q26.3) MUTATED	24	30	22
DEL PEAK 20(10Q26.3) WILD-TYPE	46	8	20

Figure S187. Get High-res Image Gene #36: 'del_10q26.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00058

Table S188. Gene #36: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 20(10Q26.3) MUTATED	24	29	23
DEL PEAK 20(10Q26.3) WILD-TYPE	45	7	22

Figure S188. Get High-res Image Gene #36: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00051

Table S189. Gene #36: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
DEL PEAK 20(10Q26.3) MUTATED	10	14	17	10	14	11
DEL PEAK 20(10Q26.3) WILD-TYPE	24	22	2	17	5	4

Figure S189. Get High-res Image Gene #36: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 0.0486 (Fisher's exact test), Q value = 0.092

Table S190. Gene #37: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	20	34	51
DEL PEAK 21(11P15.5) MUTATED	32	16	21	25
DEL PEAK 21(11P15.5) WILD-TYPE	13	4	13	26

Figure S190. Get High-res Image Gene #37: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00427 (Fisher's exact test), Q value = 0.016

Table S191. Gene #37: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 21(11P15.5) MUTATED	31	20	8	12	4	17	2
DEL PEAK 21(11P15.5) WILD-TYPE	12	7	4	12	4	6	11

Figure S191. Get High-res Image Gene #37: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 0.00217 (Fisher's exact test), Q value = 0.0093

Table S192. Gene #37: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	57	42
DEL PEAK 21(11P15.5) MUTATED	35	42	17
DEL PEAK 21(11P15.5) WILD-TYPE	16	15	25

Figure S192. Get High-res Image Gene #37: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00204 (Fisher's exact test), Q value = 0.0089

Table S193. Gene #37: 'del_11p15.5' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 21(11P15.5) MUTATED	51	26	17
DEL PEAK 21(11P15.5) WILD-TYPE	19	12	25

Figure S193. Get High-res Image Gene #37: 'del_11p15.5' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00618 (Fisher's exact test), Q value = 0.02

Table S194. Gene #37: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 21(11P15.5) MUTATED	51	23	20
DEL PEAK 21(11P15.5) WILD-TYPE	18	13	25

Figure S194. Get High-res Image Gene #37: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0119 (Fisher's exact test), Q value = 0.032

Table S195. Gene #37: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
DEL PEAK 21(11P15.5) MUTATED	24	27	15	10	11	7
DEL PEAK 21(11P15.5) WILD-TYPE	10	9	4	17	8	8

Figure S195. Get High-res Image Gene #37: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p12' versus 'METHLYATION_CNMF'

P value = 0.0465 (Fisher's exact test), Q value = 0.088

Table S196. Gene #38: 'del_11p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	20	34	51
DEL PEAK 22(11P12) MUTATED	33	16	24	26
DEL PEAK 22(11P12) WILD-TYPE	12	4	10	25

Figure S196. Get High-res Image Gene #38: 'del_11p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00529 (Fisher's exact test), Q value = 0.018

Table S197. Gene #38: 'del_11p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 22(11P12) MUTATED	31	21	8	12	5	19	3
DEL PEAK 22(11P12) WILD-TYPE	12	6	4	12	3	4	10

Figure S197. Get High-res Image Gene #38: 'del_11p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11p12' versus 'MIRSEQ_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.0046

Table S198. Gene #38: 'del_11p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	57	42
DEL PEAK 22(11P12) MUTATED	36	45	18
DEL PEAK 22(11P12) WILD-TYPE	15	12	24

Figure S198. Get High-res Image Gene #38: 'del_11p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00128 (Fisher's exact test), Q value = 0.0065

Table S199. Gene #38: 'del_11p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 22(11P12) MUTATED	52	29	18
DEL PEAK 22(11P12) WILD-TYPE	18	9	24

Figure S199. Get High-res Image Gene #38: 'del_11p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00634 (Fisher's exact test), Q value = 0.02

Table S200. Gene #38: 'del_11p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 22(11P12) MUTATED	51	27	21
DEL PEAK 22(11P12) WILD-TYPE	18	9	24

Figure S200. Get High-res Image Gene #38: 'del_11p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0126 (Fisher's exact test), Q value = 0.034

Table S201. Gene #38: 'del_11p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
DEL PEAK 22(11P12) MUTATED	25	27	15	10	14	8
DEL PEAK 22(11P12) WILD-TYPE	9	9	4	17	5	7

Figure S201. Get High-res Image Gene #38: 'del_11p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q12.3' versus 'CN_CNMF'

P value = 9e-04 (Fisher's exact test), Q value = 0.0051

Table S202. Gene #39: 'del_11q12.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
DEL PEAK 23(11Q12.3) MUTATED	29	31	40	14
DEL PEAK 23(11Q12.3) WILD-TYPE	19	3	14	0

Figure S202. Get High-res Image Gene #39: 'del_11q12.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q12.3' versus 'RPPA_CNMF'

P value = 0.0324 (Fisher's exact test), Q value = 0.067

Table S203. Gene #39: 'del_11q12.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
DEL PEAK 23(11Q12.3) MUTATED	39	7	5	23	13
DEL PEAK 23(11Q12.3) WILD-TYPE	6	1	5	14	5

Figure S203. Get High-res Image Gene #39: 'del_11q12.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_11q12.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0217 (Fisher's exact test), Q value = 0.051

Table S204. Gene #39: 'del_11q12.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
DEL PEAK 23(11Q12.3) MUTATED	44	16	27
DEL PEAK 23(11Q12.3) WILD-TYPE	7	9	15

Figure S204. Get High-res Image Gene #39: 'del_11q12.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_11q12.3' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00051

Table S205. Gene #39: 'del_11q12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	34	30	33	22	8	22	1
DEL PEAK 23(11Q12.3) MUTATED	27	30	26	13	7	11	0
DEL PEAK 23(11Q12.3) WILD-TYPE	7	0	7	9	1	11	1

Figure S205. Get High-res Image Gene #39: 'del_11q12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q12.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S206. Gene #39: 'del_11q12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 23(11Q12.3) MUTATED	35	27	9	14	6	20	3
DEL PEAK 23(11Q12.3) WILD-TYPE	8	0	3	10	2	3	10

Figure S206. Get High-res Image Gene #39: 'del_11q12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q12.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S207. Gene #39: 'del_11q12.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	57	42
DEL PEAK 23(11Q12.3) MUTATED	43	51	20
DEL PEAK 23(11Q12.3) WILD-TYPE	8	6	22

Figure S207. Get High-res Image Gene #39: 'del_11q12.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11q12.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S208. Gene #39: 'del_11q12.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 23(11Q12.3) MUTATED	62	32	20
DEL PEAK 23(11Q12.3) WILD-TYPE	8	6	22

Figure S208. Get High-res Image Gene #39: 'del_11q12.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11q12.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00091

Table S209. Gene #39: 'del_11q12.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 23(11Q12.3) MUTATED	61	30	23
DEL PEAK 23(11Q12.3) WILD-TYPE	8	6	22

Figure S209. Get High-res Image Gene #39: 'del_11q12.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q12.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S210. Gene #39: 'del_11q12.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
DEL PEAK 23(11Q12.3) MUTATED	27	35	15	12	16	9
DEL PEAK 23(11Q12.3) WILD-TYPE	7	1	4	15	3	6

Figure S210. Get High-res Image Gene #39: 'del_11q12.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q24.3' versus 'CN_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.004

Table S211. Gene #40: 'del_11q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
DEL PEAK 24(11Q24.3) MUTATED	32	33	43	14
DEL PEAK 24(11Q24.3) WILD-TYPE	16	1	11	0

Figure S211. Get High-res Image Gene #40: 'del_11q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q24.3' versus 'MRNASEQ_CNMF'

P value = 0.00205 (Fisher's exact test), Q value = 0.0089

Table S212. Gene #40: 'del_11q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	34	30	33	22	8	22	1
DEL PEAK 24(11Q24.3) MUTATED	28	30	28	16	6	14	0
DEL PEAK 24(11Q24.3) WILD-TYPE	6	0	5	6	2	8	1

Figure S212. Get High-res Image Gene #40: 'del_11q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00059 (Fisher's exact test), Q value = 0.004

Table S213. Gene #40: 'del_11q24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 24(11Q24.3) MUTATED	35	27	10	18	7	20	5
DEL PEAK 24(11Q24.3) WILD-TYPE	8	0	2	6	1	3	8

Figure S213. Get High-res Image Gene #40: 'del_11q24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q24.3' versus 'MIRSEQ_CNMF'

P value = 0.00314 (Fisher's exact test), Q value = 0.012

Table S214. Gene #40: 'del_11q24.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	57	42
DEL PEAK 24(11Q24.3) MUTATED	43	52	27
DEL PEAK 24(11Q24.3) WILD-TYPE	8	5	15

Figure S214. Get High-res Image Gene #40: 'del_11q24.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00608 (Fisher's exact test), Q value = 0.02

Table S215. Gene #40: 'del_11q24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 24(11Q24.3) MUTATED	62	33	27
DEL PEAK 24(11Q24.3) WILD-TYPE	8	5	15

Figure S215. Get High-res Image Gene #40: 'del_11q24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11q24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 0.039

Table S216. Gene #40: 'del_11q24.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 24(11Q24.3) MUTATED	61	31	30
DEL PEAK 24(11Q24.3) WILD-TYPE	8	5	15

Figure S216. Get High-res Image Gene #40: 'del_11q24.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.0034

Table S217. Gene #40: 'del_11q24.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
DEL PEAK 24(11Q24.3) MUTATED	26	36	15	16	17	12
DEL PEAK 24(11Q24.3) WILD-TYPE	8	0	4	11	2	3

Figure S217. Get High-res Image Gene #40: 'del_11q24.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q34' versus 'CN_CNMF'

P value = 0.0132 (Fisher's exact test), Q value = 0.035

Table S218. Gene #41: 'del_13q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
DEL PEAK 25(13Q34) MUTATED	32	32	40	9
DEL PEAK 25(13Q34) WILD-TYPE	16	2	14	5

Figure S218. Get High-res Image Gene #41: 'del_13q34' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q34' versus 'MRNASEQ_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.0046

Table S219. Gene #41: 'del_13q34' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	34	30	33	22	8	22	1
DEL PEAK 25(13Q34) MUTATED	23	30	26	16	4	13	1
DEL PEAK 25(13Q34) WILD-TYPE	11	0	7	6	4	9	0

Figure S219. Get High-res Image Gene #41: 'del_13q34' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00198 (Fisher's exact test), Q value = 0.0088

Table S220. Gene #41: 'del_13q34' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 25(13Q34) MUTATED	30	27	11	15	6	17	7
DEL PEAK 25(13Q34) WILD-TYPE	13	0	1	9	2	6	6

Figure S220. Get High-res Image Gene #41: 'del_13q34' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q34' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00112 (Fisher's exact test), Q value = 0.006

Table S221. Gene #41: 'del_13q34' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
DEL PEAK 25(13Q34) MUTATED	22	35	14	15	15	12
DEL PEAK 25(13Q34) WILD-TYPE	12	1	5	12	4	3

Figure S221. Get High-res Image Gene #41: 'del_13q34' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.004

Table S222. Gene #42: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
DEL PEAK 26(16Q23.1) MUTATED	12	20	23	11
DEL PEAK 26(16Q23.1) WILD-TYPE	36	14	31	3

Figure S222. Get High-res Image Gene #42: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 0.0223 (Fisher's exact test), Q value = 0.051

Table S223. Gene #42: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	20	34	51
DEL PEAK 26(16Q23.1) MUTATED	17	14	18	17
DEL PEAK 26(16Q23.1) WILD-TYPE	28	6	16	34

Figure S223. Get High-res Image Gene #42: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0161 (Fisher's exact test), Q value = 0.04

Table S224. Gene #42: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
DEL PEAK 26(16Q23.1) MUTATED	11	21	8	6	10	10
DEL PEAK 26(16Q23.1) WILD-TYPE	23	15	11	21	9	5

Figure S224. Get High-res Image Gene #42: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.3' versus 'CN_CNMF'

P value = 0.00138 (Fisher's exact test), Q value = 0.0068

Table S225. Gene #43: 'del_16q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
DEL PEAK 27(16Q23.3) MUTATED	13	20	23	11
DEL PEAK 27(16Q23.3) WILD-TYPE	35	14	31	3

Figure S225. Get High-res Image Gene #43: 'del_16q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.3' versus 'METHLYATION_CNMF'

P value = 0.00304 (Fisher's exact test), Q value = 0.012

Table S226. Gene #43: 'del_16q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	20	34	51
DEL PEAK 27(16Q23.3) MUTATED	16	13	22	16
DEL PEAK 27(16Q23.3) WILD-TYPE	29	7	12	35

Figure S226. Get High-res Image Gene #43: 'del_16q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.3' versus 'MRNASEQ_CNMF'

P value = 0.045 (Fisher's exact test), Q value = 0.086

Table S227. Gene #43: 'del_16q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	34	30	33	22	8	22	1
DEL PEAK 27(16Q23.3) MUTATED	10	17	21	9	3	7	0
DEL PEAK 27(16Q23.3) WILD-TYPE	24	13	12	13	5	15	1

Figure S227. Get High-res Image Gene #43: 'del_16q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.3' versus 'MIRSEQ_CNMF'

P value = 0.00177 (Fisher's exact test), Q value = 0.0082

Table S228. Gene #43: 'del_16q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	57	42
DEL PEAK 27(16Q23.3) MUTATED	17	36	14
DEL PEAK 27(16Q23.3) WILD-TYPE	34	21	28

Figure S228. Get High-res Image Gene #43: 'del_16q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 0.051

Table S229. Gene #43: 'del_16q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 27(16Q23.3) MUTATED	29	24	14
DEL PEAK 27(16Q23.3) WILD-TYPE	41	14	28

Figure S229. Get High-res Image Gene #43: 'del_16q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0142 (Fisher's exact test), Q value = 0.037

Table S230. Gene #43: 'del_16q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
DEL PEAK 27(16Q23.3) MUTATED	11	18	10	6	12	10
DEL PEAK 27(16Q23.3) WILD-TYPE	23	18	9	21	7	5

Figure S230. Get High-res Image Gene #43: 'del_16q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18p11.32' versus 'MIRSEQ_CNMF'

P value = 0.044 (Fisher's exact test), Q value = 0.084

Table S231. Gene #44: 'del_18p11.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	57	42
DEL PEAK 28(18P11.32) MUTATED	40	50	28
DEL PEAK 28(18P11.32) WILD-TYPE	11	7	14

Figure S231. Get High-res Image Gene #44: 'del_18p11.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18p11.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0193 (Fisher's exact test), Q value = 0.047

Table S232. Gene #44: 'del_18p11.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 28(18P11.32) MUTATED	55	35	28
DEL PEAK 28(18P11.32) WILD-TYPE	15	3	14

Figure S232. Get High-res Image Gene #44: 'del_18p11.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q22.3' versus 'CN_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.032

Table S233. Gene #45: 'del_18q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
DEL PEAK 29(18Q22.3) MUTATED	33	32	48	12
DEL PEAK 29(18Q22.3) WILD-TYPE	15	2	6	2

Figure S233. Get High-res Image Gene #45: 'del_18q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q22.3' versus 'MIRSEQ_CNMF'

P value = 0.0236 (Fisher's exact test), Q value = 0.053

Table S234. Gene #45: 'del_18q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	57	42
DEL PEAK 29(18Q22.3) MUTATED	41	53	31
DEL PEAK 29(18Q22.3) WILD-TYPE	10	4	11

Figure S234. Get High-res Image Gene #45: 'del_18q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0405 (Fisher's exact test), Q value = 0.079

Table S235. Gene #45: 'del_18q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 29(18Q22.3) MUTATED	58	36	31
DEL PEAK 29(18Q22.3) WILD-TYPE	12	2	11

Figure S235. Get High-res Image Gene #45: 'del_18q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00765 (Fisher's exact test), Q value = 0.024

Table S236. Gene #45: 'del_18q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
DEL PEAK 29(18Q22.3) MUTATED	24	34	17	18	18	14
DEL PEAK 29(18Q22.3) WILD-TYPE	10	2	2	9	1	1

Figure S236. Get High-res Image Gene #45: 'del_18q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S237. Gene #46: 'del_19q13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
DEL PEAK 30(19Q13.33) MUTATED	14	1	37	6
DEL PEAK 30(19Q13.33) WILD-TYPE	34	33	17	8

Figure S237. Get High-res Image Gene #46: 'del_19q13.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S238. Gene #46: 'del_19q13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	20	34	51
DEL PEAK 30(19Q13.33) MUTATED	5	0	29	24
DEL PEAK 30(19Q13.33) WILD-TYPE	40	20	5	27

Figure S238. Get High-res Image Gene #46: 'del_19q13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19q13.33' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S239. Gene #46: 'del_19q13.33' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
DEL PEAK 30(19Q13.33) MUTATED	1	2	4	25	15
DEL PEAK 30(19Q13.33) WILD-TYPE	44	6	6	12	3

Figure S239. Get High-res Image Gene #46: 'del_19q13.33' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_19q13.33' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S240. Gene #46: 'del_19q13.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
DEL PEAK 30(19Q13.33) MUTATED	1	15	31
DEL PEAK 30(19Q13.33) WILD-TYPE	50	10	11

Figure S240. Get High-res Image Gene #46: 'del_19q13.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_19q13.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S241. Gene #46: 'del_19q13.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	34	30	33	22	8	22	1
DEL PEAK 30(19Q13.33) MUTATED	0	1	28	14	1	14	0
DEL PEAK 30(19Q13.33) WILD-TYPE	34	29	5	8	7	8	1

Figure S241. Get High-res Image Gene #46: 'del_19q13.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S242. Gene #46: 'del_19q13.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 30(19Q13.33) MUTATED	0	1	11	14	5	20	7
DEL PEAK 30(19Q13.33) WILD-TYPE	43	26	1	10	3	3	6

Figure S242. Get High-res Image Gene #46: 'del_19q13.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S243. Gene #46: 'del_19q13.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	57	42
DEL PEAK 30(19Q13.33) MUTATED	1	32	25
DEL PEAK 30(19Q13.33) WILD-TYPE	50	25	17

Figure S243. Get High-res Image Gene #46: 'del_19q13.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19q13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S244. Gene #46: 'del_19q13.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 30(19Q13.33) MUTATED	1	32	25
DEL PEAK 30(19Q13.33) WILD-TYPE	69	6	17

Figure S244. Get High-res Image Gene #46: 'del_19q13.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S245. Gene #46: 'del_19q13.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 30(19Q13.33) MUTATED	1	28	29
DEL PEAK 30(19Q13.33) WILD-TYPE	68	8	16

Figure S245. Get High-res Image Gene #46: 'del_19q13.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19q13.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S246. Gene #46: 'del_19q13.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
DEL PEAK 30(19Q13.33) MUTATED	0	1	15	14	16	12
DEL PEAK 30(19Q13.33) WILD-TYPE	34	35	4	13	3	3

Figure S246. Get High-res Image Gene #46: 'del_19q13.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.42' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S247. Gene #47: 'del_19q13.42' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
DEL PEAK 31(19Q13.42) MUTATED	14	1	36	6
DEL PEAK 31(19Q13.42) WILD-TYPE	34	33	18	8

Figure S247. Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.42' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S248. Gene #47: 'del_19q13.42' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	20	34	51
DEL PEAK 31(19Q13.42) MUTATED	5	0	29	23
DEL PEAK 31(19Q13.42) WILD-TYPE	40	20	5	28

Figure S248. Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19q13.42' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S249. Gene #47: 'del_19q13.42' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
DEL PEAK 31(19Q13.42) MUTATED	1	2	4	24	15
DEL PEAK 31(19Q13.42) WILD-TYPE	44	6	6	13	3

Figure S249. Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_19q13.42' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S250. Gene #47: 'del_19q13.42' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
DEL PEAK 31(19Q13.42) MUTATED	1	15	30
DEL PEAK 31(19Q13.42) WILD-TYPE	50	10	12

Figure S250. Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_19q13.42' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S251. Gene #47: 'del_19q13.42' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	34	30	33	22	8	22	1
DEL PEAK 31(19Q13.42) MUTATED	0	1	28	13	1	14	0
DEL PEAK 31(19Q13.42) WILD-TYPE	34	29	5	9	7	8	1

Figure S251. Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19q13.42' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S252. Gene #47: 'del_19q13.42' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 31(19Q13.42) MUTATED	0	1	11	13	5	20	7
DEL PEAK 31(19Q13.42) WILD-TYPE	43	26	1	11	3	3	6

Figure S252. Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.42' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S253. Gene #47: 'del_19q13.42' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	57	42
DEL PEAK 31(19Q13.42) MUTATED	1	32	24
DEL PEAK 31(19Q13.42) WILD-TYPE	50	25	18

Figure S253. Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19q13.42' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S254. Gene #47: 'del_19q13.42' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 31(19Q13.42) MUTATED	1	32	24
DEL PEAK 31(19Q13.42) WILD-TYPE	69	6	18

Figure S254. Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.42' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S255. Gene #47: 'del_19q13.42' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 31(19Q13.42) MUTATED	1	28	28
DEL PEAK 31(19Q13.42) WILD-TYPE	68	8	17

Figure S255. Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19q13.42' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S256. Gene #47: 'del_19q13.42' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
DEL PEAK 31(19Q13.42) MUTATED	0	1	15	13	16	12
DEL PEAK 31(19Q13.42) WILD-TYPE	34	35	4	14	3	3

Figure S256. Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_CNMF'

P value = 0.0312 (Fisher's exact test), Q value = 0.066

Table S257. Gene #48: 'del_20p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	57	42
DEL PEAK 32(20P12.1) MUTATED	5	17	7
DEL PEAK 32(20P12.1) WILD-TYPE	46	40	35

Figure S257. Get High-res Image Gene #48: 'del_20p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_20p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00179 (Fisher's exact test), Q value = 0.0082

Table S258. Gene #48: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
DEL PEAK 32(20P12.1) MUTATED	1	10	9	5	3	1
DEL PEAK 32(20P12.1) WILD-TYPE	33	26	10	22	16	14

Figure S258. Get High-res Image Gene #48: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 0.00441 (Fisher's exact test), Q value = 0.016

Table S259. Gene #49: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	20	34	51
DEL PEAK 33(XP21.1) MUTATED	2	6	5	15
DEL PEAK 33(XP21.1) WILD-TYPE	43	14	29	36

Figure S259. Get High-res Image Gene #49: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.049 (Fisher's exact test), Q value = 0.092

Table S260. Gene #49: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 33(XP21.1) MUTATED	10	4	14
DEL PEAK 33(XP21.1) WILD-TYPE	59	32	31

Figure S260. Get High-res Image Gene #49: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xp21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00675 (Fisher's exact test), Q value = 0.022

Table S261. Gene #49: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
DEL PEAK 33(XP21.1) MUTATED	1	9	2	10	2	4
DEL PEAK 33(XP21.1) WILD-TYPE	33	27	17	17	17	11

Figure S261. Get High-res Image Gene #49: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xq27.3' versus 'CN_CNMF'

P value = 0.00149 (Fisher's exact test), Q value = 0.007

Table S262. Gene #50: 'del_xq27.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	34	54	14
DEL PEAK 34(XQ27.3) MUTATED	2	7	18	3
DEL PEAK 34(XQ27.3) WILD-TYPE	46	27	36	11

Figure S262. Get High-res Image Gene #50: 'del_xq27.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq27.3' versus 'METHLYATION_CNMF'

P value = 0.00124 (Fisher's exact test), Q value = 0.0065

Table S263. Gene #50: 'del_xq27.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	20	34	51
DEL PEAK 34(XQ27.3) MUTATED	2	6	5	17
DEL PEAK 34(XQ27.3) WILD-TYPE	43	14	29	34

Figure S263. Get High-res Image Gene #50: 'del_xq27.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq27.3' versus 'MRNASEQ_CNMF'

P value = 0.00631 (Fisher's exact test), Q value = 0.02

Table S264. Gene #50: 'del_xq27.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	34	30	33	22	8	22	1
DEL PEAK 34(XQ27.3) MUTATED	4	7	3	11	0	5	0
DEL PEAK 34(XQ27.3) WILD-TYPE	30	23	30	11	8	17	1

Figure S264. Get High-res Image Gene #50: 'del_xq27.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xq27.3' versus 'MIRSEQ_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.036

Table S265. Gene #50: 'del_xq27.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	57	42
DEL PEAK 34(XQ27.3) MUTATED	8	7	15
DEL PEAK 34(XQ27.3) WILD-TYPE	43	50	27

Figure S265. Get High-res Image Gene #50: 'del_xq27.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xq27.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.032

Table S266. Gene #50: 'del_xq27.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 34(XQ27.3) MUTATED	11	4	15
DEL PEAK 34(XQ27.3) WILD-TYPE	59	34	27

Figure S266. Get High-res Image Gene #50: 'del_xq27.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xq27.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0212 (Fisher's exact test), Q value = 0.05

Table S267. Gene #50: 'del_xq27.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	34	36	19	27	19	15
DEL PEAK 34(XQ27.3) MUTATED	4	7	5	10	0	4
DEL PEAK 34(XQ27.3) WILD-TYPE	30	29	14	17	19	11

Figure S267. Get High-res Image Gene #50: 'del_xq27.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/TGCT-TP/22533662/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/TGCT-TP/22541961/TGCT-TP.transferedmergedcluster.txt
Number of patients = 150
Number of significantly focal cnvs = 50
Number of molecular subtypes = 10
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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