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 63 focal events and 10 molecular subtypes across 295 patients, 260 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p31.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_1q21.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_2p24.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_2q33.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_3q26.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_4q12 cnv correlated to 'RPPA_CNMF'.
amp_5p15.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6p21.33 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_7p11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_8q24.21 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_9p24.1 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.
amp_11q13.3 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_11q22.1 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'.
amp_15q26.1 cnv correlated to 'CN_CNMF'.
amp_17q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_17q25.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
amp_19p13.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_19p13.2 cnv correlated to 'CN_CNMF'.
amp_19q13.13 cnv correlated to 'CN_CNMF'.
amp_20q11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_xq28 cnv correlated to 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.23 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p13.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_2q22.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_2q37.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4p16.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q21.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_4q22.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_4q35.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q12.1 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_5q35.2 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
del_6p24.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_6q26 cnv correlated to 'CN_CNMF'.
del_8p23.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_8p23.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_10q23.31 cnv correlated to 'CN_CNMF'.
del_11p15.1 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q23.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q25 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q12.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q32.31 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q21.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q23.1 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p12 cnv correlated to 'CN_CNMF'.
del_17q25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q21.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19q13.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_20p12.1 cnv correlated to 'MRNASEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_21q11.2 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.
del_22q13.32 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_xp11.3 cnv correlated to 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xq21.33 cnv correlated to 'RPPA_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 63 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, 260 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 11q22 1	47 (16%)	248	1e-05 (0.000185)	0.00137 (0.00872)	0.00264 (0.0145)	1e-05 (0.000185)	2e-05 (0.00028)	1e-05 (0.000185)	0.00072 (0.00547)	1e-05 (0.000185)	3e-05 (0.000386)	0.00022 (0.00227)
del 3p14 2	134 (45%)	161	1e-05 (0.000185)	0.00064 (0.00499)	0.142 (0.256)	0.0466 (0.114)	0.00161 (0.00972)	2e-05 (0.00028)	0.0039 (0.0195)	0.00046 (0.00392)	0.02 (0.0613)	0.00014 (0.00147)
amp 5p15 33	138 (47%)	157	1e-05 (0.000185)	0.0305 (0.0827)	0.241 (0.373)	0.376 (0.513)	0.00663 (0.0278)	0.00539 (0.0238)	0.00259 (0.0143)	0.00077 (0.00571)	0.00388 (0.0195)	0.0148 (0.0501)
del 2q37 1	129 (44%)	166	0.00155 (0.00957)	0.00043 (0.00376)	0.357 (0.496)	0.106 (0.208)	3e-05 (0.000386)	1e-05 (0.000185)	0.00676 (0.0279)	0.00124 (0.00805)	0.00763 (0.0308)	9e-05 (0.000978)
del 3p22 1	113 (38%)	182	1e-05 (0.000185)	0.00393 (0.0195)	0.0368 (0.0943)	0.00139 (0.00876)	0.00729 (0.0296)	3e-05 (0.000386)	0.174 (0.298)	0.00062 (0.00499)	0.236 (0.37)	0.00093 (0.00672)
del 13q12 11	98 (33%)	197	1e-05 (0.000185)	0.00173 (0.0102)	0.431 (0.568)	0.0919 (0.188)	0.0188 (0.0592)	0.00033 (0.0032)	0.00187 (0.0109)	0.00483 (0.0229)	0.0351 (0.0911)	0.00545 (0.0238)
del 18q21 2	82 (28%)	213	0.00063 (0.00499)	0.00113 (0.00757)	0.511 (0.642)	0.0553 (0.129)	1e-05 (0.000185)	3e-05 (0.000386)	0.0231 (0.0685)	1e-05 (0.000185)	0.0029 (0.0154)	1e-05 (0.000185)
amp 3q26 31	227 (77%)	68	1e-05 (0.000185)	0.00224 (0.0126)	0.572 (0.693)	0.885 (0.911)	0.00041 (0.00369)	1e-05 (0.000185)	0.127 (0.235)	2e-05 (0.00028)	0.0434 (0.107)	1e-05 (0.000185)
amp 7p11 2	52 (18%)	243	4e-05 (0.000504)	0.0144 (0.0495)	0.0298 (0.0817)	0.00841 (0.0335)	0.0316 (0.085)	0.0674 (0.152)	0.00025 (0.00254)	0.0889 (0.185)	7e-05 (0.000802)	0.135 (0.245)
amp 17q12	55 (19%)	240	0.00169 (0.01)	0.00391 (0.0195)	0.728 (0.808)	0.0377 (0.0954)	0.00496 (0.023)	0.00343 (0.018)	0.116 (0.221)	0.0325 (0.0865)	0.0158 (0.0523)	0.114 (0.22)
amp 20q11 21	135 (46%)	160	1e-05 (0.000185)	0.0136 (0.0472)	0.596 (0.708)	0.00361 (0.0188)	0.0419 (0.104)	0.0373 (0.0949)	0.103 (0.204)	0.0345 (0.0903)	0.0475 (0.115)	0.247 (0.377)
del 13q14 2	118 (40%)	177	2e-05 (0.00028)	0.0201 (0.0613)	0.898 (0.92)	0.628 (0.737)	0.00122 (0.00801)	0.00216 (0.0124)	0.00507 (0.0231)	0.00059 (0.00489)	0.0872 (0.182)	0.00998 (0.0376)
del 16q11 2	53 (18%)	242	0.0297 (0.0817)	0.00036 (0.00334)	0.505 (0.636)	0.156 (0.278)	0.0472 (0.115)	0.00979 (0.0372)	0.0165 (0.054)	0.0105 (0.039)	0.131 (0.241)	0.00035 (0.00334)
del 16q23 1	55 (19%)	240	0.105 (0.207)	0.00642 (0.0271)	0.579 (0.698)	0.186 (0.31)	0.00065 (0.00499)	0.00036 (0.00334)	0.0374 (0.0949)	0.0006 (0.00491)	0.0228 (0.0681)	9e-05 (0.000978)
del 17q25 3	51 (17%)	244	0.00948 (0.0364)	1e-05 (0.000185)	0.396 (0.528)	0.952 (0.965)	1e-05 (0.000185)	0.00094 (0.00672)	0.00189 (0.0109)	0.00086 (0.0063)	0.0513 (0.123)	0.0286 (0.0802)
del 19p13 3	105 (36%)	190	1e-05 (0.000185)	0.987 (0.991)	0.371 (0.508)	0.0844 (0.178)	8e-05 (9e-04)	1e-05 (0.000185)	0.0194 (0.0603)	5e-05 (0.000606)	0.0156 (0.0523)	0.00096 (0.00672)
amp 11q13 3	41 (14%)	254	7e-05 (0.000802)	0.7 (0.795)	0.0671 (0.152)	0.031 (0.0839)	0.0296 (0.0817)	7e-05 (0.000802)	0.0502 (0.121)	2e-05 (0.00028)	0.00045 (0.00388)	0.141 (0.254)
del 4p16 3	127 (43%)	168	1e-05 (0.000185)	0.0214 (0.0645)	0.862 (0.899)	0.997 (0.998)	0.00466 (0.0222)	0.001 (0.00692)	0.227 (0.362)	0.00038 (0.00347)	0.515 (0.645)	0.00491 (0.023)
del 11p15 1	102 (35%)	193	1e-05 (0.000185)	0.0747 (0.164)	0.0103 (0.0385)	0.00932 (0.036)	0.029 (0.0809)	0.0194 (0.0603)	0.402 (0.535)	0.0766 (0.167)	0.742 (0.817)	0.0354 (0.0913)
del 14q32 31	50 (17%)	245	0.71 (0.802)	0.00677 (0.0279)	0.0944 (0.191)	0.00808 (0.0324)	0.0111 (0.0406)	0.00922 (0.0359)	0.525 (0.654)	0.0255 (0.0734)	0.269 (0.398)	0.0242 (0.0708)
del 15q21 1	70 (24%)	225	0.0249 (0.0721)	0.464 (0.594)	0.74 (0.817)	0.551 (0.677)	0.135 (0.245)	0.0472 (0.115)	0.00492 (0.023)	0.0317 (0.085)	0.0192 (0.0603)	0.00885 (0.0346)
amp 1q21 3	158 (54%)	137	1e-05 (0.000185)	0.449 (0.583)	0.25 (0.379)	0.246 (0.377)	0.0366 (0.0941)	0.0112 (0.0406)	0.751 (0.822)	0.00095 (0.00672)	0.537 (0.663)	0.0154 (0.0521)
del 1p36 23	40 (14%)	255	0.0768 (0.167)	0.022 (0.0661)	0.714 (0.803)	0.0969 (0.194)	0.00065 (0.00499)	2e-05 (0.00028)	0.25 (0.379)	0.0001 (0.00107)	0.232 (0.367)	0.00505 (0.0231)
del 8p23 3	104 (35%)	191	1e-05 (0.000185)	0.83 (0.879)	0.258 (0.386)	0.0915 (0.188)	0.0005 (0.0042)	0.0256 (0.0734)	0.0839 (0.178)	0.0173 (0.0559)	0.0112 (0.0406)	0.298 (0.432)
del 8p23 1	97 (33%)	198	1e-05 (0.000185)	0.962 (0.969)	0.531 (0.658)	0.0904 (0.187)	0.0022 (0.0125)	0.159 (0.28)	0.0249 (0.0721)	0.0211 (0.0639)	0.00442 (0.0214)	0.217 (0.349)
del 11q23 3	162 (55%)	133	1e-05 (0.000185)	0.183 (0.308)	0.637 (0.743)	0.135 (0.245)	0.041 (0.102)	0.00373 (0.0193)	0.841 (0.883)	0.00237 (0.0132)	0.104 (0.206)	0.0114 (0.0407)
del 11q25	160 (54%)	135	1e-05 (0.000185)	0.157 (0.278)	0.866 (0.9)	0.188 (0.311)	0.0271 (0.0766)	0.00549 (0.0238)	0.812 (0.869)	0.00576 (0.0247)	0.0548 (0.129)	0.0196 (0.0606)
del xp11 3	72 (24%)	223	0.0829 (0.176)	0.0105 (0.039)	0.444 (0.578)	0.655 (0.758)	0.0752 (0.165)	0.245 (0.377)	2e-05 (0.00028)	0.032 (0.0853)	0.00275 (0.0148)	0.0145 (0.0495)
amp 1p31 3	96 (33%)	199	1e-05 (0.000185)	0.429 (0.567)	0.463 (0.594)	0.711 (0.802)	0.0245 (0.0715)	0.00159 (0.00972)	0.24 (0.373)	0.00101 (0.00692)	0.394 (0.528)	0.174 (0.298)
amp xq28	75 (25%)	220	0.985 (0.99)	0.0186 (0.0589)	0.576 (0.695)	0.909 (0.928)	0.678 (0.78)	0.557 (0.679)	0.00132 (0.00849)	0.168 (0.292)	0.0233 (0.069)	0.0339 (0.0889)
del 1p13 2	34 (12%)	261	0.0159 (0.0523)	0.0601 (0.139)	0.134 (0.245)	0.263 (0.391)	5e-05 (0.000606)	0.0689 (0.154)	0.00551 (0.0238)	0.178 (0.304)	0.00958 (0.0366)	0.0558 (0.13)
del 4q22 1	100 (34%)	195	1e-05 (0.000185)	0.153 (0.273)	0.569 (0.691)	0.871 (0.903)	0.0172 (0.0558)	0.0114 (0.0407)	0.48 (0.608)	0.0442 (0.109)	0.574 (0.695)	0.0869 (0.182)
del 4q35 2	114 (39%)	181	1e-05 (0.000185)	0.199 (0.326)	0.958 (0.969)	0.998 (0.998)	0.00675 (0.0279)	0.00272 (0.0148)	0.254 (0.382)	0.122 (0.229)	0.722 (0.805)	0.00546 (0.0238)
amp 2p24 3	79 (27%)	216	2e-05 (0.00028)	0.492 (0.623)	0.253 (0.381)	0.0538 (0.127)	0.104 (0.206)	0.0429 (0.107)	0.0854 (0.18)	2e-05 (0.00028)	0.0537 (0.127)	0.0924 (0.188)
amp 2q33 1	41 (14%)	254	1e-05 (0.000185)	0.185 (0.31)	0.198 (0.324)	0.444 (0.578)	0.00033 (0.0032)	0.0539 (0.127)	0.419 (0.557)	0.00726 (0.0296)	0.269 (0.398)	0.246 (0.377)
amp 6p21 33	82 (28%)	213	0.00033 (0.0032)	0.367 (0.504)	0.541 (0.667)	0.0626 (0.143)	0.0186 (0.0589)	0.159 (0.28)	0.817 (0.872)	0.0147 (0.0501)	0.358 (0.496)	0.0738 (0.164)
amp 8q24 21	127 (43%)	168	0.241 (0.373)	0.00113 (0.00757)	0.0901 (0.187)	0.146 (0.261)	0.441 (0.577)	0.0395 (0.0995)	0.109 (0.212)	0.0967 (0.194)	0.133 (0.245)	0.0137 (0.0476)
amp 9p24 1	63 (21%)	232	0.00043 (0.00376)	0.353 (0.492)	0.0974 (0.195)	0.0119 (0.0423)	0.359 (0.496)	0.0333 (0.0878)	0.527 (0.655)	0.0686 (0.154)	0.389 (0.524)	0.172 (0.297)
amp 17q25 1	74 (25%)	221	2e-05 (0.00028)	0.00595 (0.0253)	0.342 (0.484)	0.0805 (0.173)	0.027 (0.0766)	0.508 (0.639)	0.555 (0.677)	0.942 (0.957)	0.341 (0.484)	0.884 (0.911)
amp 19p13 3	39 (13%)	256	0.0126 (0.0442)	0.0638 (0.145)	0.144 (0.258)	0.589 (0.704)	0.187 (0.311)	0.00122 (0.00801)	0.289 (0.424)	0.0184 (0.0589)	0.358 (0.496)	0.0809 (0.173)
del 4q21 3	103 (35%)	192	1e-05 (0.000185)	0.0565 (0.131)	0.678 (0.78)	0.802 (0.86)	0.00852 (0.0338)	0.00537 (0.0238)	0.234 (0.368)	0.237 (0.371)	0.803 (0.86)	0.166 (0.289)
del 5q12 1	76 (26%)	219	1e-05 (0.000185)	0.764 (0.833)	0.115 (0.221)	0.03 (0.0818)	0.396 (0.528)	0.939 (0.956)	0.0349 (0.0909)	0.348 (0.489)	0.213 (0.342)	0.189 (0.312)
del 6p24 2	46 (16%)	249	0.0159 (0.0523)	0.0741 (0.164)	0.35 (0.491)	0.183 (0.308)	0.0917 (0.188)	0.0401 (0.101)	0.458 (0.592)	0.0261 (0.0743)	0.225 (0.359)	0.361 (0.497)
del 19q13 33	38 (13%)	257	0.0197 (0.0607)	0.0296 (0.0817)	0.429 (0.567)	0.59 (0.704)	0.147 (0.262)	0.183 (0.308)	0.119 (0.225)	0.168 (0.292)	0.0617 (0.142)	0.0122 (0.043)
del 20p12 1	36 (12%)	259	0.461 (0.594)	0.829 (0.879)	0.258 (0.386)	0.125 (0.233)	0.00535 (0.0238)	0.124 (0.233)	0.0929 (0.189)	0.144 (0.258)	0.00152 (0.00948)	0.00162 (0.00972)
del 21q11 2	58 (20%)	237	0.00394 (0.0195)	0.519 (0.648)	0.203 (0.33)	0.00449 (0.0216)	0.0539 (0.127)	0.00872 (0.0343)	0.613 (0.724)	0.231 (0.367)	0.654 (0.758)	0.257 (0.385)
del 2q22 1	65 (22%)	230	0.0159 (0.0523)	0.173 (0.297)	0.3 (0.433)	0.722 (0.805)	0.0182 (0.0584)	0.118 (0.224)	0.905 (0.926)	0.182 (0.308)	0.388 (0.523)	0.452 (0.584)
del 5q35 2	71 (24%)	224	2e-05 (0.00028)	0.732 (0.81)	0.652 (0.758)	0.548 (0.675)	0.874 (0.904)	0.84 (0.883)	0.0287 (0.0802)	0.554 (0.677)	0.249 (0.379)	0.395 (0.528)
del 22q13 32	87 (29%)	208	0.00406 (0.0198)	0.803 (0.86)	0.124 (0.233)	0.674 (0.778)	0.19 (0.313)	0.0236 (0.0694)	0.765 (0.833)	0.588 (0.704)	0.833 (0.879)	0.867 (0.9)
amp 4q12	21 (7%)	274	0.162 (0.284)	0.387 (0.523)	0.00396 (0.0195)	0.433 (0.57)	0.248 (0.379)	0.891 (0.914)	0.959 (0.969)	0.372 (0.508)	0.111 (0.215)	0.082 (0.175)
amp 15q26 1	76 (26%)	219	0.0112 (0.0406)	0.835 (0.879)	0.305 (0.439)	0.33 (0.472)	0.701 (0.795)	0.593 (0.706)	0.928 (0.946)	0.606 (0.717)	0.692 (0.791)	0.958 (0.969)
amp 19p13 2	43 (15%)	252	0.0329 (0.087)	0.289 (0.424)	0.172 (0.297)	0.582 (0.7)	0.477 (0.606)	0.0794 (0.172)	0.778 (0.842)	0.0951 (0.192)	0.346 (0.487)	0.321 (0.46)
amp 19q13 13	93 (32%)	202	1e-05 (0.000185)	0.47 (0.599)	0.835 (0.879)	0.251 (0.379)	0.351 (0.492)	0.435 (0.571)	0.7 (0.795)	0.27 (0.398)	0.554 (0.677)	0.656 (0.758)
del 6q26	100 (34%)	195	0.00279 (0.0149)	0.0674 (0.152)	0.619 (0.729)	0.748 (0.821)	0.451 (0.584)	0.0855 (0.18)	0.115 (0.221)	0.319 (0.459)	0.172 (0.297)	0.235 (0.369)
del 10q23 31	86 (29%)	209	0.00534 (0.0238)	0.344 (0.485)	0.32 (0.459)	0.761 (0.831)	0.124 (0.233)	0.331 (0.472)	0.709 (0.802)	0.239 (0.371)	0.471 (0.599)	0.0772 (0.168)
del 17p12	109 (37%)	186	0.00073 (0.00547)	0.111 (0.215)	0.0576 (0.133)	0.721 (0.805)	0.233 (0.368)	0.271 (0.399)	0.211 (0.34)	0.202 (0.33)	0.776 (0.842)	0.832 (0.879)
del xq21 33	59 (20%)	236	0.296 (0.43)	0.051 (0.123)	0.0796 (0.172)	0.0114 (0.0407)	0.859 (0.897)	0.781 (0.842)	0.213 (0.342)	0.97 (0.976)	0.53 (0.658)	0.749 (0.821)
amp 11p12	23 (8%)	272	0.183 (0.308)	0.824 (0.878)	0.727 (0.808)	0.864 (0.899)	0.367 (0.504)	0.296 (0.43)	0.604 (0.717)	0.0691 (0.154)	0.238 (0.371)	0.563 (0.684)
amp 13q22 1	65 (22%)	230	0.108 (0.212)	0.13 (0.24)	0.184 (0.308)	0.519 (0.648)	0.116 (0.221)	0.743 (0.817)	0.72 (0.805)	0.427 (0.567)	0.64 (0.745)	0.206 (0.334)
amp 13q34	69 (23%)	226	0.295 (0.43)	0.853 (0.893)	0.631 (0.737)	0.589 (0.704)	0.696 (0.793)	0.614 (0.724)	0.715 (0.803)	0.77 (0.837)	0.85 (0.891)	0.379 (0.515)
amp 16p13 13	65 (22%)	230	0.163 (0.285)	0.112 (0.216)	0.63 (0.737)	0.887 (0.911)	0.193 (0.317)	0.379 (0.515)	0.499 (0.63)	0.221 (0.353)	0.685 (0.784)	0.336 (0.478)
amp 21q22 13	48 (16%)	247	0.129 (0.239)	0.728 (0.808)	0.63 (0.737)	0.798 (0.859)	0.0625 (0.143)	0.442 (0.577)	0.78 (0.842)	0.834 (0.879)	0.881 (0.91)	0.382 (0.518)
del 7q34	60 (20%)	235	0.103 (0.204)	0.296 (0.43)	0.204 (0.331)	0.463 (0.594)	0.733 (0.81)	0.695 (0.793)	0.681 (0.781)	0.468 (0.598)	0.259 (0.386)	0.353 (0.492)

'amp_1p31.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S1. Gene #1: 'amp_1p31.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
AMP PEAK 1(1P31.3) MUTATED	3	38	34	6	15
AMP PEAK 1(1P31.3) WILD-TYPE	12	74	22	53	38

Figure S1. Get High-res Image Gene #1: 'amp_1p31.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1p31.3' versus 'MRNASEQ_CNMF'

P value = 0.0245 (Fisher's exact test), Q value = 0.072

Table S2. Gene #1: 'amp_1p31.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
AMP PEAK 1(1P31.3) MUTATED	20	42	17	16
AMP PEAK 1(1P31.3) WILD-TYPE	37	56	52	52

Figure S2. Get High-res Image Gene #1: 'amp_1p31.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1p31.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00159 (Fisher's exact test), Q value = 0.0097

Table S3. Gene #1: 'amp_1p31.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
AMP PEAK 1(1P31.3) MUTATED	15	74	6
AMP PEAK 1(1P31.3) WILD-TYPE	57	111	29

Figure S3. Get High-res Image Gene #1: 'amp_1p31.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1p31.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00101 (Fisher's exact test), Q value = 0.0069

Table S4. Gene #1: 'amp_1p31.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
AMP PEAK 1(1P31.3) MUTATED	12	36	32	10	6
AMP PEAK 1(1P31.3) WILD-TYPE	48	59	40	15	37

Figure S4. Get High-res Image Gene #1: 'amp_1p31.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S5. Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
AMP PEAK 2(1Q21.3) MUTATED	7	67	44	16	24
AMP PEAK 2(1Q21.3) WILD-TYPE	8	45	12	43	29

Figure S5. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 0.0366 (Fisher's exact test), Q value = 0.094

Table S6. Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
AMP PEAK 2(1Q21.3) MUTATED	31	63	32	30
AMP PEAK 2(1Q21.3) WILD-TYPE	26	35	37	38

Figure S6. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 0.041

Table S7. Gene #2: 'amp_1q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
AMP PEAK 2(1Q21.3) MUTATED	29	111	16
AMP PEAK 2(1Q21.3) WILD-TYPE	43	74	19

Figure S7. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00095 (Fisher's exact test), Q value = 0.0067

Table S8. Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
AMP PEAK 2(1Q21.3) MUTATED	23	62	42	16	15
AMP PEAK 2(1Q21.3) WILD-TYPE	37	33	30	9	28

Figure S8. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0154 (Fisher's exact test), Q value = 0.052

Table S9. Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	79	99	42	33
AMP PEAK 2(1Q21.3) MUTATED	14	46	62	16	12
AMP PEAK 2(1Q21.3) WILD-TYPE	15	33	37	26	21

Figure S9. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_2p24.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S10. Gene #3: 'amp_2p24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
AMP PEAK 3(2P24.3) MUTATED	1	50	9	8	11
AMP PEAK 3(2P24.3) WILD-TYPE	14	62	47	51	42

Figure S10. Get High-res Image Gene #3: 'amp_2p24.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2p24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0429 (Fisher's exact test), Q value = 0.11

Table S11. Gene #3: 'amp_2p24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
AMP PEAK 3(2P24.3) MUTATED	25	41	13
AMP PEAK 3(2P24.3) WILD-TYPE	47	144	22

Figure S11. Get High-res Image Gene #3: 'amp_2p24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_2p24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S12. Gene #3: 'amp_2p24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
AMP PEAK 3(2P24.3) MUTATED	21	26	6	13	13
AMP PEAK 3(2P24.3) WILD-TYPE	39	69	66	12	30

Figure S12. Get High-res Image Gene #3: 'amp_2p24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_2q33.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S13. Gene #4: 'amp_2q33.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
AMP PEAK 4(2Q33.1) MUTATED	0	32	2	3	4
AMP PEAK 4(2Q33.1) WILD-TYPE	15	80	54	56	49

Figure S13. Get High-res Image Gene #4: 'amp_2q33.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2q33.1' versus 'MRNASEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0032

Table S14. Gene #4: 'amp_2q33.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
AMP PEAK 4(2Q33.1) MUTATED	12	3	10	15
AMP PEAK 4(2Q33.1) WILD-TYPE	45	95	59	53

Figure S14. Get High-res Image Gene #4: 'amp_2q33.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_2q33.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00726 (Fisher's exact test), Q value = 0.03

Table S15. Gene #4: 'amp_2q33.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
AMP PEAK 4(2Q33.1) MUTATED	12	10	4	3	12
AMP PEAK 4(2Q33.1) WILD-TYPE	48	85	68	22	31

Figure S15. Get High-res Image Gene #4: 'amp_2q33.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S16. Gene #5: 'amp_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
AMP PEAK 5(3Q26.31) MUTATED	9	96	51	33	38
AMP PEAK 5(3Q26.31) WILD-TYPE	6	16	5	26	15

Figure S16. Get High-res Image Gene #5: 'amp_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.31' versus 'METHLYATION_CNMF'

P value = 0.00224 (Fisher's exact test), Q value = 0.013

Table S17. Gene #5: 'amp_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	115	108
AMP PEAK 5(3Q26.31) MUTATED	48	100	79
AMP PEAK 5(3Q26.31) WILD-TYPE	24	15	29

Figure S17. Get High-res Image Gene #5: 'amp_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q26.31' versus 'MRNASEQ_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0037

Table S18. Gene #5: 'amp_3q26.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
AMP PEAK 5(3Q26.31) MUTATED	48	86	46	44
AMP PEAK 5(3Q26.31) WILD-TYPE	9	12	23	24

Figure S18. Get High-res Image Gene #5: 'amp_3q26.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3q26.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S19. Gene #5: 'amp_3q26.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
AMP PEAK 5(3Q26.31) MUTATED	43	160	21
AMP PEAK 5(3Q26.31) WILD-TYPE	29	25	14

Figure S19. Get High-res Image Gene #5: 'amp_3q26.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S20. Gene #5: 'amp_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
AMP PEAK 5(3Q26.31) MUTATED	34	81	65	20	27
AMP PEAK 5(3Q26.31) WILD-TYPE	26	14	7	5	16

Figure S20. Get High-res Image Gene #5: 'amp_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0434 (Fisher's exact test), Q value = 0.11

Table S21. Gene #5: 'amp_3q26.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	79	102
AMP PEAK 5(3Q26.31) MUTATED	69	66	81
AMP PEAK 5(3Q26.31) WILD-TYPE	32	13	21

Figure S21. Get High-res Image Gene #5: 'amp_3q26.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S22. Gene #5: 'amp_3q26.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	79	99	42	33
AMP PEAK 5(3Q26.31) MUTATED	17	70	87	22	20
AMP PEAK 5(3Q26.31) WILD-TYPE	12	9	12	20	13

Figure S22. Get High-res Image Gene #5: 'amp_3q26.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q12' versus 'RPPA_CNMF'

P value = 0.00396 (Fisher's exact test), Q value = 0.019

Table S23. Gene #6: 'amp_4q12' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	41	64
AMP PEAK 6(4Q12) MUTATED	3	0	11
AMP PEAK 6(4Q12) WILD-TYPE	56	41	53

Figure S23. Get High-res Image Gene #6: 'amp_4q12' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S24. Gene #7: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
AMP PEAK 7(5P15.33) MUTATED	6	82	30	10	10
AMP PEAK 7(5P15.33) WILD-TYPE	9	30	26	49	43

Figure S24. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 0.0305 (Fisher's exact test), Q value = 0.083

Table S25. Gene #7: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	115	108
AMP PEAK 7(5P15.33) MUTATED	24	59	55
AMP PEAK 7(5P15.33) WILD-TYPE	48	56	53

Figure S25. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 0.00663 (Fisher's exact test), Q value = 0.028

Table S26. Gene #7: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
AMP PEAK 7(5P15.33) MUTATED	23	48	23	42
AMP PEAK 7(5P15.33) WILD-TYPE	34	50	46	26

Figure S26. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00539 (Fisher's exact test), Q value = 0.024

Table S27. Gene #7: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
AMP PEAK 7(5P15.33) MUTATED	24	89	23
AMP PEAK 7(5P15.33) WILD-TYPE	48	96	12

Figure S27. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 0.00259 (Fisher's exact test), Q value = 0.014

Table S28. Gene #7: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	75	115
AMP PEAK 7(5P15.33) MUTATED	43	27	68
AMP PEAK 7(5P15.33) WILD-TYPE	62	48	47

Figure S28. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00077 (Fisher's exact test), Q value = 0.0057

Table S29. Gene #7: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
AMP PEAK 7(5P15.33) MUTATED	17	50	28	16	27
AMP PEAK 7(5P15.33) WILD-TYPE	43	45	44	9	16

Figure S29. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00388 (Fisher's exact test), Q value = 0.019

Table S30. Gene #7: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	79	102
AMP PEAK 7(5P15.33) MUTATED	46	26	59
AMP PEAK 7(5P15.33) WILD-TYPE	55	53	43

Figure S30. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0148 (Fisher's exact test), Q value = 0.05

Table S31. Gene #7: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	79	99	42	33
AMP PEAK 7(5P15.33) MUTATED	12	32	47	29	11
AMP PEAK 7(5P15.33) WILD-TYPE	17	47	52	13	22

Figure S31. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6p21.33' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0032

Table S32. Gene #8: 'amp_6p21.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
AMP PEAK 8(6P21.33) MUTATED	1	48	10	13	10
AMP PEAK 8(6P21.33) WILD-TYPE	14	64	46	46	43

Figure S32. Get High-res Image Gene #8: 'amp_6p21.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p21.33' versus 'MRNASEQ_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.059

Table S33. Gene #8: 'amp_6p21.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
AMP PEAK 8(6P21.33) MUTATED	18	17	21	26
AMP PEAK 8(6P21.33) WILD-TYPE	39	81	48	42

Figure S33. Get High-res Image Gene #8: 'amp_6p21.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6p21.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0147 (Fisher's exact test), Q value = 0.05

Table S34. Gene #8: 'amp_6p21.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
AMP PEAK 8(6P21.33) MUTATED	17	21	15	8	21
AMP PEAK 8(6P21.33) WILD-TYPE	43	74	57	17	22

Figure S34. Get High-res Image Gene #8: 'amp_6p21.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 5e-04

Table S35. Gene #9: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
AMP PEAK 9(7P11.2) MUTATED	3	29	10	0	10
AMP PEAK 9(7P11.2) WILD-TYPE	12	83	46	59	43

Figure S35. Get High-res Image Gene #9: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.05

Table S36. Gene #9: 'amp_7p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	115	108
AMP PEAK 9(7P11.2) MUTATED	5	23	24
AMP PEAK 9(7P11.2) WILD-TYPE	67	92	84

Figure S36. Get High-res Image Gene #9: 'amp_7p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'RPPA_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.082

Table S37. Gene #9: 'amp_7p11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	41	64
AMP PEAK 9(7P11.2) MUTATED	16	4	7
AMP PEAK 9(7P11.2) WILD-TYPE	43	37	57

Figure S37. Get High-res Image Gene #9: 'amp_7p11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_7p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00841 (Fisher's exact test), Q value = 0.034

Table S38. Gene #9: 'amp_7p11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	47	45	23	17
AMP PEAK 9(7P11.2) MUTATED	5	4	7	10	1
AMP PEAK 9(7P11.2) WILD-TYPE	27	43	38	13	16

Figure S38. Get High-res Image Gene #9: 'amp_7p11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 0.0316 (Fisher's exact test), Q value = 0.085

Table S39. Gene #9: 'amp_7p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
AMP PEAK 9(7P11.2) MUTATED	9	16	7	20
AMP PEAK 9(7P11.2) WILD-TYPE	48	82	62	48

Figure S39. Get High-res Image Gene #9: 'amp_7p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0025

Table S40. Gene #9: 'amp_7p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	75	115
AMP PEAK 9(7P11.2) MUTATED	13	6	33
AMP PEAK 9(7P11.2) WILD-TYPE	92	69	82

Figure S40. Get High-res Image Gene #9: 'amp_7p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 8e-04

Table S41. Gene #9: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	79	102
AMP PEAK 9(7P11.2) MUTATED	12	6	31
AMP PEAK 9(7P11.2) WILD-TYPE	89	73	71

Figure S41. Get High-res Image Gene #9: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 0.00113 (Fisher's exact test), Q value = 0.0076

Table S42. Gene #10: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	115	108
AMP PEAK 10(8Q24.21) MUTATED	20	63	44
AMP PEAK 10(8Q24.21) WILD-TYPE	52	52	64

Figure S42. Get High-res Image Gene #10: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0395 (Fisher's exact test), Q value = 0.1

Table S43. Gene #10: 'amp_8q24.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
AMP PEAK 10(8Q24.21) MUTATED	23	90	13
AMP PEAK 10(8Q24.21) WILD-TYPE	49	95	22

Figure S43. Get High-res Image Gene #10: 'amp_8q24.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 0.048

Table S44. Gene #10: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	79	99	42	33
AMP PEAK 10(8Q24.21) MUTATED	9	29	54	21	9
AMP PEAK 10(8Q24.21) WILD-TYPE	20	50	45	21	24

Figure S44. Get High-res Image Gene #10: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9p24.1' versus 'CN_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.0038

Table S45. Gene #11: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
AMP PEAK 11(9P24.1) MUTATED	1	26	23	6	7
AMP PEAK 11(9P24.1) WILD-TYPE	14	86	33	53	46

Figure S45. Get High-res Image Gene #11: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p24.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0119 (Fisher's exact test), Q value = 0.042

Table S46. Gene #11: 'amp_9p24.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	47	45	23	17
AMP PEAK 11(9P24.1) MUTATED	3	12	15	5	0
AMP PEAK 11(9P24.1) WILD-TYPE	29	35	30	18	17

Figure S46. Get High-res Image Gene #11: 'amp_9p24.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_9p24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0333 (Fisher's exact test), Q value = 0.088

Table S47. Gene #11: 'amp_9p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
AMP PEAK 11(9P24.1) MUTATED	9	42	12
AMP PEAK 11(9P24.1) WILD-TYPE	63	143	23

Figure S47. Get High-res Image Gene #11: 'amp_9p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 8e-04

Table S48. Gene #13: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
AMP PEAK 13(11Q13.3) MUTATED	0	29	2	3	7
AMP PEAK 13(11Q13.3) WILD-TYPE	15	83	54	56	46

Figure S48. Get High-res Image Gene #13: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.031 (Fisher's exact test), Q value = 0.084

Table S49. Gene #13: 'amp_11q13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	47	45	23	17
AMP PEAK 13(11Q13.3) MUTATED	6	5	6	8	0
AMP PEAK 13(11Q13.3) WILD-TYPE	26	42	39	15	17

Figure S49. Get High-res Image Gene #13: 'amp_11q13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 0.082

Table S50. Gene #13: 'amp_11q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
AMP PEAK 13(11Q13.3) MUTATED	7	10	6	17
AMP PEAK 13(11Q13.3) WILD-TYPE	50	88	63	51

Figure S50. Get High-res Image Gene #13: 'amp_11q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 8e-04

Table S51. Gene #13: 'amp_11q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
AMP PEAK 13(11Q13.3) MUTATED	6	20	14
AMP PEAK 13(11Q13.3) WILD-TYPE	66	165	21

Figure S51. Get High-res Image Gene #13: 'amp_11q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S52. Gene #13: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
AMP PEAK 13(11Q13.3) MUTATED	3	10	5	6	17
AMP PEAK 13(11Q13.3) WILD-TYPE	57	85	67	19	26

Figure S52. Get High-res Image Gene #13: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0039

Table S53. Gene #13: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	79	102
AMP PEAK 13(11Q13.3) MUTATED	10	4	25
AMP PEAK 13(11Q13.3) WILD-TYPE	91	75	77

Figure S53. Get High-res Image Gene #13: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_11q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S54. Gene #14: 'amp_11q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
AMP PEAK 14(11Q22.1) MUTATED	0	34	0	4	9
AMP PEAK 14(11Q22.1) WILD-TYPE	15	78	56	55	44

Figure S54. Get High-res Image Gene #14: 'amp_11q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q22.1' versus 'METHLYATION_CNMF'

P value = 0.00137 (Fisher's exact test), Q value = 0.0087

Table S55. Gene #14: 'amp_11q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	115	108
AMP PEAK 14(11Q22.1) MUTATED	4	16	27
AMP PEAK 14(11Q22.1) WILD-TYPE	68	99	81

Figure S55. Get High-res Image Gene #14: 'amp_11q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11q22.1' versus 'RPPA_CNMF'

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

Table S56. Gene #14: 'amp_11q22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	41	64
AMP PEAK 14(11Q22.1) MUTATED	19	3	8
AMP PEAK 14(11Q22.1) WILD-TYPE	40	38	56

Figure S56. Get High-res Image Gene #14: 'amp_11q22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_11q22.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S57. Gene #14: 'amp_11q22.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	47	45	23	17
AMP PEAK 14(11Q22.1) MUTATED	9	5	3	13	0
AMP PEAK 14(11Q22.1) WILD-TYPE	23	42	42	10	17

Figure S57. Get High-res Image Gene #14: 'amp_11q22.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_11q22.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S58. Gene #14: 'amp_11q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
AMP PEAK 14(11Q22.1) MUTATED	5	9	7	25
AMP PEAK 14(11Q22.1) WILD-TYPE	52	89	62	43

Figure S58. Get High-res Image Gene #14: 'amp_11q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_11q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S59. Gene #14: 'amp_11q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
AMP PEAK 14(11Q22.1) MUTATED	4	22	20
AMP PEAK 14(11Q22.1) WILD-TYPE	68	163	15

Figure S59. Get High-res Image Gene #14: 'amp_11q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11q22.1' versus 'MIRSEQ_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.0055

Table S60. Gene #14: 'amp_11q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	75	115
AMP PEAK 14(11Q22.1) MUTATED	8	9	30
AMP PEAK 14(11Q22.1) WILD-TYPE	97	66	85

Figure S60. Get High-res Image Gene #14: 'amp_11q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_11q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S61. Gene #14: 'amp_11q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
AMP PEAK 14(11Q22.1) MUTATED	2	8	11	3	23
AMP PEAK 14(11Q22.1) WILD-TYPE	58	87	61	22	20

Figure S61. Get High-res Image Gene #14: 'amp_11q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00039

Table S62. Gene #14: 'amp_11q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	79	102
AMP PEAK 14(11Q22.1) MUTATED	7	8	30
AMP PEAK 14(11Q22.1) WILD-TYPE	94	71	72

Figure S62. Get High-res Image Gene #14: 'amp_11q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_11q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.0023

Table S63. Gene #14: 'amp_11q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	79	99	42	33
AMP PEAK 14(11Q22.1) MUTATED	1	12	13	17	2
AMP PEAK 14(11Q22.1) WILD-TYPE	28	67	86	25	31

Figure S63. Get High-res Image Gene #14: 'amp_11q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_15q26.1' versus 'CN_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.041

Table S64. Gene #17: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
AMP PEAK 17(15Q26.1) MUTATED	4	40	14	7	11
AMP PEAK 17(15Q26.1) WILD-TYPE	11	72	42	52	42

Figure S64. Get High-res Image Gene #17: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q12' versus 'CN_CNMF'

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

Table S65. Gene #19: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
AMP PEAK 19(17Q12) MUTATED	0	34	6	7	8
AMP PEAK 19(17Q12) WILD-TYPE	15	78	50	52	45

Figure S65. Get High-res Image Gene #19: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 0.00391 (Fisher's exact test), Q value = 0.019

Table S66. Gene #19: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	115	108
AMP PEAK 19(17Q12) MUTATED	23	19	13
AMP PEAK 19(17Q12) WILD-TYPE	49	96	95

Figure S66. Get High-res Image Gene #19: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.0377 (Fisher's exact test), Q value = 0.095

Table S67. Gene #19: 'amp_17q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	47	45	23	17
AMP PEAK 19(17Q12) MUTATED	2	11	12	2	6
AMP PEAK 19(17Q12) WILD-TYPE	30	36	33	21	11

Figure S67. Get High-res Image Gene #19: 'amp_17q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 0.00496 (Fisher's exact test), Q value = 0.023

Table S68. Gene #19: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
AMP PEAK 19(17Q12) MUTATED	10	13	23	8
AMP PEAK 19(17Q12) WILD-TYPE	47	85	46	60

Figure S68. Get High-res Image Gene #19: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00343 (Fisher's exact test), Q value = 0.018

Table S69. Gene #19: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
AMP PEAK 19(17Q12) MUTATED	23	28	3
AMP PEAK 19(17Q12) WILD-TYPE	49	157	32

Figure S69. Get High-res Image Gene #19: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0325 (Fisher's exact test), Q value = 0.087

Table S70. Gene #19: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
AMP PEAK 19(17Q12) MUTATED	20	17	9	3	6
AMP PEAK 19(17Q12) WILD-TYPE	40	78	63	22	37

Figure S70. Get High-res Image Gene #19: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.052

Table S71. Gene #19: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	79	102
AMP PEAK 19(17Q12) MUTATED	28	14	12
AMP PEAK 19(17Q12) WILD-TYPE	73	65	90

Figure S71. Get High-res Image Gene #19: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_17q25.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S72. Gene #20: 'amp_17q25.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
AMP PEAK 20(17Q25.1) MUTATED	2	44	7	4	17
AMP PEAK 20(17Q25.1) WILD-TYPE	13	68	49	55	36

Figure S72. Get High-res Image Gene #20: 'amp_17q25.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q25.1' versus 'METHLYATION_CNMF'

P value = 0.00595 (Fisher's exact test), Q value = 0.025

Table S73. Gene #20: 'amp_17q25.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	115	108
AMP PEAK 20(17Q25.1) MUTATED	23	35	16
AMP PEAK 20(17Q25.1) WILD-TYPE	49	80	92

Figure S73. Get High-res Image Gene #20: 'amp_17q25.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q25.1' versus 'MRNASEQ_CNMF'

P value = 0.027 (Fisher's exact test), Q value = 0.077

Table S74. Gene #20: 'amp_17q25.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
AMP PEAK 20(17Q25.1) MUTATED	21	16	20	15
AMP PEAK 20(17Q25.1) WILD-TYPE	36	82	49	53

Figure S74. Get High-res Image Gene #20: 'amp_17q25.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19p13.3' versus 'CN_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.044

Table S75. Gene #21: 'amp_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
AMP PEAK 21(19P13.3) MUTATED	1	17	14	5	2
AMP PEAK 21(19P13.3) WILD-TYPE	14	95	42	54	51

Figure S75. Get High-res Image Gene #21: 'amp_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00122 (Fisher's exact test), Q value = 0.008

Table S76. Gene #21: 'amp_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
AMP PEAK 21(19P13.3) MUTATED	5	34	0
AMP PEAK 21(19P13.3) WILD-TYPE	67	151	35

Figure S76. Get High-res Image Gene #21: 'amp_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0184 (Fisher's exact test), Q value = 0.059

Table S77. Gene #21: 'amp_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
AMP PEAK 21(19P13.3) MUTATED	5	12	18	1	3
AMP PEAK 21(19P13.3) WILD-TYPE	55	83	54	24	40

Figure S77. Get High-res Image Gene #21: 'amp_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

P value = 0.0329 (Fisher's exact test), Q value = 0.087

Table S78. Gene #22: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
AMP PEAK 22(19P13.2) MUTATED	1	15	16	5	6
AMP PEAK 22(19P13.2) WILD-TYPE	14	97	40	54	47

Figure S78. Get High-res Image Gene #22: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q13.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S79. Gene #23: 'amp_19q13.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
AMP PEAK 23(19Q13.13) MUTATED	4	63	19	5	2
AMP PEAK 23(19Q13.13) WILD-TYPE	11	49	37	54	51

Figure S79. Get High-res Image Gene #23: 'amp_19q13.13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S80. Gene #24: 'amp_20q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
AMP PEAK 24(20Q11.21) MUTATED	1	65	31	12	26
AMP PEAK 24(20Q11.21) WILD-TYPE	14	47	25	47	27

Figure S80. Get High-res Image Gene #24: 'amp_20q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q11.21' versus 'METHLYATION_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.047

Table S81. Gene #24: 'amp_20q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	115	108
AMP PEAK 24(20Q11.21) MUTATED	42	54	39
AMP PEAK 24(20Q11.21) WILD-TYPE	30	61	69

Figure S81. Get High-res Image Gene #24: 'amp_20q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.00361 (Fisher's exact test), Q value = 0.019

Table S82. Gene #24: 'amp_20q11.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	47	45	23	17
AMP PEAK 24(20Q11.21) MUTATED	13	17	22	9	15
AMP PEAK 24(20Q11.21) WILD-TYPE	19	30	23	14	2

Figure S82. Get High-res Image Gene #24: 'amp_20q11.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNASEQ_CNMF'

P value = 0.0419 (Fisher's exact test), Q value = 0.1

Table S83. Gene #24: 'amp_20q11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
AMP PEAK 24(20Q11.21) MUTATED	32	43	37	23
AMP PEAK 24(20Q11.21) WILD-TYPE	25	55	32	45

Figure S83. Get High-res Image Gene #24: 'amp_20q11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0373 (Fisher's exact test), Q value = 0.095

Table S84. Gene #24: 'amp_20q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
AMP PEAK 24(20Q11.21) MUTATED	42	81	12
AMP PEAK 24(20Q11.21) WILD-TYPE	30	104	23

Figure S84. Get High-res Image Gene #24: 'amp_20q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0345 (Fisher's exact test), Q value = 0.09

Table S85. Gene #24: 'amp_20q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
AMP PEAK 24(20Q11.21) MUTATED	35	37	31	16	16
AMP PEAK 24(20Q11.21) WILD-TYPE	25	58	41	9	27

Figure S85. Get High-res Image Gene #24: 'amp_20q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0475 (Fisher's exact test), Q value = 0.12

Table S86. Gene #24: 'amp_20q11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	79	102
AMP PEAK 24(20Q11.21) MUTATED	56	35	39
AMP PEAK 24(20Q11.21) WILD-TYPE	45	44	63

Figure S86. Get High-res Image Gene #24: 'amp_20q11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_xq28' versus 'METHLYATION_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.059

Table S87. Gene #26: 'amp_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	115	108
AMP PEAK 26(XQ28) MUTATED	17	39	19
AMP PEAK 26(XQ28) WILD-TYPE	55	76	89

Figure S87. Get High-res Image Gene #26: 'amp_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xq28' versus 'MIRSEQ_CNMF'

P value = 0.00132 (Fisher's exact test), Q value = 0.0085

Table S88. Gene #26: 'amp_xq28' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	75	115
AMP PEAK 26(XQ28) MUTATED	29	8	38
AMP PEAK 26(XQ28) WILD-TYPE	76	67	77

Figure S88. Get High-res Image Gene #26: 'amp_xq28' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_xq28' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0233 (Fisher's exact test), Q value = 0.069

Table S89. Gene #26: 'amp_xq28' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	79	102
AMP PEAK 26(XQ28) MUTATED	28	11	31
AMP PEAK 26(XQ28) WILD-TYPE	73	68	71

Figure S89. Get High-res Image Gene #26: 'amp_xq28' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_xq28' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0339 (Fisher's exact test), Q value = 0.089

Table S90. Gene #26: 'amp_xq28' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	79	99	42	33
AMP PEAK 26(XQ28) MUTATED	11	13	32	9	5
AMP PEAK 26(XQ28) WILD-TYPE	18	66	67	33	28

Figure S90. Get High-res Image Gene #26: 'amp_xq28' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.23' versus 'METHLYATION_CNMF'

P value = 0.022 (Fisher's exact test), Q value = 0.066

Table S91. Gene #27: 'del_1p36.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	115	108
DEL PEAK 1(1P36.23) MUTATED	17	13	10
DEL PEAK 1(1P36.23) WILD-TYPE	55	102	98

Figure S91. Get High-res Image Gene #27: 'del_1p36.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.23' versus 'MRNASEQ_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.005

Table S92. Gene #27: 'del_1p36.23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
DEL PEAK 1(1P36.23) MUTATED	10	3	14	13
DEL PEAK 1(1P36.23) WILD-TYPE	47	95	55	55

Figure S92. Get High-res Image Gene #27: 'del_1p36.23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p36.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S93. Gene #27: 'del_1p36.23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 1(1P36.23) MUTATED	18	12	10
DEL PEAK 1(1P36.23) WILD-TYPE	54	173	25

Figure S93. Get High-res Image Gene #27: 'del_1p36.23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.0011

Table S94. Gene #27: 'del_1p36.23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
DEL PEAK 1(1P36.23) MUTATED	16	11	1	5	7
DEL PEAK 1(1P36.23) WILD-TYPE	44	84	71	20	36

Figure S94. Get High-res Image Gene #27: 'del_1p36.23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00505 (Fisher's exact test), Q value = 0.023

Table S95. Gene #27: 'del_1p36.23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	79	99	42	33
DEL PEAK 1(1P36.23) MUTATED	6	4	12	7	10
DEL PEAK 1(1P36.23) WILD-TYPE	23	75	87	35	23

Figure S95. Get High-res Image Gene #27: 'del_1p36.23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p13.2' versus 'CN_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.052

Table S96. Gene #28: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
DEL PEAK 2(1P13.2) MUTATED	0	18	4	2	10
DEL PEAK 2(1P13.2) WILD-TYPE	15	94	52	57	43

Figure S96. Get High-res Image Gene #28: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p13.2' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00061

Table S97. Gene #28: 'del_1p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
DEL PEAK 2(1P13.2) MUTATED	7	5	3	19
DEL PEAK 2(1P13.2) WILD-TYPE	50	93	66	49

Figure S97. Get High-res Image Gene #28: 'del_1p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p13.2' versus 'MIRSEQ_CNMF'

P value = 0.00551 (Fisher's exact test), Q value = 0.024

Table S98. Gene #28: 'del_1p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	75	115
DEL PEAK 2(1P13.2) MUTATED	6	6	22
DEL PEAK 2(1P13.2) WILD-TYPE	99	69	93

Figure S98. Get High-res Image Gene #28: 'del_1p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00958 (Fisher's exact test), Q value = 0.037

Table S99. Gene #28: 'del_1p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	79	102
DEL PEAK 2(1P13.2) MUTATED	6	8	20
DEL PEAK 2(1P13.2) WILD-TYPE	95	71	82

Figure S99. Get High-res Image Gene #28: 'del_1p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_2q22.1' versus 'CN_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.052

Table S100. Gene #29: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
DEL PEAK 3(2Q22.1) MUTATED	3	21	22	8	11
DEL PEAK 3(2Q22.1) WILD-TYPE	12	91	34	51	42

Figure S100. Get High-res Image Gene #29: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.058

Table S101. Gene #29: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
DEL PEAK 3(2Q22.1) MUTATED	8	29	9	19
DEL PEAK 3(2Q22.1) WILD-TYPE	49	69	60	49

Figure S101. Get High-res Image Gene #29: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q37.1' versus 'CN_CNMF'

P value = 0.00155 (Fisher's exact test), Q value = 0.0096

Table S102. Gene #30: 'del_2q37.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
DEL PEAK 4(2Q37.1) MUTATED	3	61	25	15	25
DEL PEAK 4(2Q37.1) WILD-TYPE	12	51	31	44	28

Figure S102. Get High-res Image Gene #30: 'del_2q37.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.1' versus 'METHLYATION_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.0038

Table S103. Gene #30: 'del_2q37.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	115	108
DEL PEAK 4(2Q37.1) MUTATED	17	57	55
DEL PEAK 4(2Q37.1) WILD-TYPE	55	58	53

Figure S103. Get High-res Image Gene #30: 'del_2q37.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.1' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00039

Table S104. Gene #30: 'del_2q37.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
DEL PEAK 4(2Q37.1) MUTATED	14	51	21	42
DEL PEAK 4(2Q37.1) WILD-TYPE	43	47	48	26

Figure S104. Get High-res Image Gene #30: 'del_2q37.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q37.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S105. Gene #30: 'del_2q37.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 4(2Q37.1) MUTATED	14	93	21
DEL PEAK 4(2Q37.1) WILD-TYPE	58	92	14

Figure S105. Get High-res Image Gene #30: 'del_2q37.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.1' versus 'MIRSEQ_CNMF'

P value = 0.00676 (Fisher's exact test), Q value = 0.028

Table S106. Gene #30: 'del_2q37.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	75	115
DEL PEAK 4(2Q37.1) MUTATED	36	30	63
DEL PEAK 4(2Q37.1) WILD-TYPE	69	45	52

Figure S106. Get High-res Image Gene #30: 'del_2q37.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q37.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00124 (Fisher's exact test), Q value = 0.0081

Table S107. Gene #30: 'del_2q37.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
DEL PEAK 4(2Q37.1) MUTATED	13	48	32	11	25
DEL PEAK 4(2Q37.1) WILD-TYPE	47	47	40	14	18

Figure S107. Get High-res Image Gene #30: 'del_2q37.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00763 (Fisher's exact test), Q value = 0.031

Table S108. Gene #30: 'del_2q37.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	79	102
DEL PEAK 4(2Q37.1) MUTATED	36	30	57
DEL PEAK 4(2Q37.1) WILD-TYPE	65	49	45

Figure S108. Get High-res Image Gene #30: 'del_2q37.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_2q37.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00098

Table S109. Gene #30: 'del_2q37.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	79	99	42	33
DEL PEAK 4(2Q37.1) MUTATED	3	33	53	24	10
DEL PEAK 4(2Q37.1) WILD-TYPE	26	46	46	18	23

Figure S109. Get High-res Image Gene #30: 'del_2q37.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S110. Gene #31: 'del_3p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
DEL PEAK 5(3P22.1) MUTATED	10	46	25	0	32
DEL PEAK 5(3P22.1) WILD-TYPE	5	66	31	59	21

Figure S110. Get High-res Image Gene #31: 'del_3p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p22.1' versus 'METHLYATION_CNMF'

P value = 0.00393 (Fisher's exact test), Q value = 0.019

Table S111. Gene #31: 'del_3p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	115	108
DEL PEAK 5(3P22.1) MUTATED	19	57	37
DEL PEAK 5(3P22.1) WILD-TYPE	53	58	71

Figure S111. Get High-res Image Gene #31: 'del_3p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p22.1' versus 'RPPA_CNMF'

P value = 0.0368 (Fisher's exact test), Q value = 0.094

Table S112. Gene #31: 'del_3p22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	41	64
DEL PEAK 5(3P22.1) MUTATED	15	20	18
DEL PEAK 5(3P22.1) WILD-TYPE	44	21	46

Figure S112. Get High-res Image Gene #31: 'del_3p22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_3p22.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00139 (Fisher's exact test), Q value = 0.0088

Table S113. Gene #31: 'del_3p22.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	47	45	23	17
DEL PEAK 5(3P22.1) MUTATED	8	6	20	12	7
DEL PEAK 5(3P22.1) WILD-TYPE	24	41	25	11	10

Figure S113. Get High-res Image Gene #31: 'del_3p22.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_3p22.1' versus 'MRNASEQ_CNMF'

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

Table S114. Gene #31: 'del_3p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
DEL PEAK 5(3P22.1) MUTATED	28	40	15	29
DEL PEAK 5(3P22.1) WILD-TYPE	29	58	54	39

Figure S114. Get High-res Image Gene #31: 'del_3p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00039

Table S115. Gene #31: 'del_3p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 5(3P22.1) MUTATED	14	88	10
DEL PEAK 5(3P22.1) WILD-TYPE	58	97	25

Figure S115. Get High-res Image Gene #31: 'del_3p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.005

Table S116. Gene #31: 'del_3p22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
DEL PEAK 5(3P22.1) MUTATED	10	48	30	10	15
DEL PEAK 5(3P22.1) WILD-TYPE	50	47	42	15	28

Figure S116. Get High-res Image Gene #31: 'del_3p22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00093 (Fisher's exact test), Q value = 0.0067

Table S117. Gene #31: 'del_3p22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	79	99	42	33
DEL PEAK 5(3P22.1) MUTATED	8	32	44	20	3
DEL PEAK 5(3P22.1) WILD-TYPE	21	47	55	22	30

Figure S117. Get High-res Image Gene #31: 'del_3p22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S118. Gene #32: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
DEL PEAK 6(3P14.2) MUTATED	10	61	26	1	36
DEL PEAK 6(3P14.2) WILD-TYPE	5	51	30	58	17

Figure S118. Get High-res Image Gene #32: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.2' versus 'METHLYATION_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.005

Table S119. Gene #32: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	115	108
DEL PEAK 6(3P14.2) MUTATED	21	66	47
DEL PEAK 6(3P14.2) WILD-TYPE	51	49	61

Figure S119. Get High-res Image Gene #32: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p14.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0466 (Fisher's exact test), Q value = 0.11

Table S120. Gene #32: 'del_3p14.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	47	45	23	17
DEL PEAK 6(3P14.2) MUTATED	11	12	24	12	8
DEL PEAK 6(3P14.2) WILD-TYPE	21	35	21	11	9

Figure S120. Get High-res Image Gene #32: 'del_3p14.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_3p14.2' versus 'MRNASEQ_CNMF'

P value = 0.00161 (Fisher's exact test), Q value = 0.0097

Table S121. Gene #32: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
DEL PEAK 6(3P14.2) MUTATED	32	46	18	36
DEL PEAK 6(3P14.2) WILD-TYPE	25	52	51	32

Figure S121. Get High-res Image Gene #32: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S122. Gene #32: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 6(3P14.2) MUTATED	17	102	13
DEL PEAK 6(3P14.2) WILD-TYPE	55	83	22

Figure S122. Get High-res Image Gene #32: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_CNMF'

P value = 0.0039 (Fisher's exact test), Q value = 0.019

Table S123. Gene #32: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	75	115
DEL PEAK 6(3P14.2) MUTATED	35	35	64
DEL PEAK 6(3P14.2) WILD-TYPE	70	40	51

Figure S123. Get High-res Image Gene #32: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.0039

Table S124. Gene #32: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
DEL PEAK 6(3P14.2) MUTATED	13	54	34	13	20
DEL PEAK 6(3P14.2) WILD-TYPE	47	41	38	12	23

Figure S124. Get High-res Image Gene #32: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 0.061

Table S125. Gene #32: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	79	102
DEL PEAK 6(3P14.2) MUTATED	35	37	55
DEL PEAK 6(3P14.2) WILD-TYPE	66	42	47

Figure S125. Get High-res Image Gene #32: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.0015

Table S126. Gene #32: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	79	99	42	33
DEL PEAK 6(3P14.2) MUTATED	9	39	54	21	4
DEL PEAK 6(3P14.2) WILD-TYPE	20	40	45	21	29

Figure S126. Get High-res Image Gene #32: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4p16.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S127. Gene #33: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
DEL PEAK 7(4P16.3) MUTATED	6	72	28	7	14
DEL PEAK 7(4P16.3) WILD-TYPE	9	40	28	52	39

Figure S127. Get High-res Image Gene #33: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4p16.3' versus 'METHLYATION_CNMF'

P value = 0.0214 (Fisher's exact test), Q value = 0.064

Table S128. Gene #33: 'del_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	115	108
DEL PEAK 7(4P16.3) MUTATED	22	59	46
DEL PEAK 7(4P16.3) WILD-TYPE	50	56	62

Figure S128. Get High-res Image Gene #33: 'del_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4p16.3' versus 'MRNASEQ_CNMF'

P value = 0.00466 (Fisher's exact test), Q value = 0.022

Table S129. Gene #33: 'del_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
DEL PEAK 7(4P16.3) MUTATED	28	49	17	31
DEL PEAK 7(4P16.3) WILD-TYPE	29	49	52	37

Figure S129. Get High-res Image Gene #33: 'del_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.001 (Fisher's exact test), Q value = 0.0069

Table S130. Gene #33: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 7(4P16.3) MUTATED	18	87	20
DEL PEAK 7(4P16.3) WILD-TYPE	54	98	15

Figure S130. Get High-res Image Gene #33: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.0035

Table S131. Gene #33: 'del_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
DEL PEAK 7(4P16.3) MUTATED	12	52	30	13	20
DEL PEAK 7(4P16.3) WILD-TYPE	48	43	42	12	23

Figure S131. Get High-res Image Gene #33: 'del_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00491 (Fisher's exact test), Q value = 0.023

Table S132. Gene #33: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	79	99	42	33
DEL PEAK 7(4P16.3) MUTATED	9	34	53	18	6
DEL PEAK 7(4P16.3) WILD-TYPE	20	45	46	24	27

Figure S132. Get High-res Image Gene #33: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S133. Gene #34: 'del_4q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
DEL PEAK 8(4Q21.3) MUTATED	4	68	26	2	3
DEL PEAK 8(4Q21.3) WILD-TYPE	11	44	30	57	50

Figure S133. Get High-res Image Gene #34: 'del_4q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q21.3' versus 'MRNASEQ_CNMF'

P value = 0.00852 (Fisher's exact test), Q value = 0.034

Table S134. Gene #34: 'del_4q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
DEL PEAK 8(4Q21.3) MUTATED	23	29	17	34
DEL PEAK 8(4Q21.3) WILD-TYPE	34	69	52	34

Figure S134. Get High-res Image Gene #34: 'del_4q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00537 (Fisher's exact test), Q value = 0.024

Table S135. Gene #34: 'del_4q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 8(4Q21.3) MUTATED	21	61	21
DEL PEAK 8(4Q21.3) WILD-TYPE	51	124	14

Figure S135. Get High-res Image Gene #34: 'del_4q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S136. Gene #35: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
DEL PEAK 9(4Q22.1) MUTATED	4	71	25	0	0
DEL PEAK 9(4Q22.1) WILD-TYPE	11	41	31	59	53

Figure S136. Get High-res Image Gene #35: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 0.0172 (Fisher's exact test), Q value = 0.056

Table S137. Gene #35: 'del_4q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
DEL PEAK 9(4Q22.1) MUTATED	23	28	17	32
DEL PEAK 9(4Q22.1) WILD-TYPE	34	70	52	36

Figure S137. Get High-res Image Gene #35: 'del_4q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0114 (Fisher's exact test), Q value = 0.041

Table S138. Gene #35: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 9(4Q22.1) MUTATED	21	59	20
DEL PEAK 9(4Q22.1) WILD-TYPE	51	126	15

Figure S138. Get High-res Image Gene #35: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0442 (Fisher's exact test), Q value = 0.11

Table S139. Gene #35: 'del_4q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
DEL PEAK 9(4Q22.1) MUTATED	16	33	22	6	23
DEL PEAK 9(4Q22.1) WILD-TYPE	44	62	50	19	20

Figure S139. Get High-res Image Gene #35: 'del_4q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q35.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S140. Gene #36: 'del_4q35.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
DEL PEAK 10(4Q35.2) MUTATED	4	77	25	6	2
DEL PEAK 10(4Q35.2) WILD-TYPE	11	35	31	53	51

Figure S140. Get High-res Image Gene #36: 'del_4q35.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q35.2' versus 'MRNASEQ_CNMF'

P value = 0.00675 (Fisher's exact test), Q value = 0.028

Table S141. Gene #36: 'del_4q35.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
DEL PEAK 10(4Q35.2) MUTATED	27	30	21	36
DEL PEAK 10(4Q35.2) WILD-TYPE	30	68	48	32

Figure S141. Get High-res Image Gene #36: 'del_4q35.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q35.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00272 (Fisher's exact test), Q value = 0.015

Table S142. Gene #36: 'del_4q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 10(4Q35.2) MUTATED	24	67	23
DEL PEAK 10(4Q35.2) WILD-TYPE	48	118	12

Figure S142. Get High-res Image Gene #36: 'del_4q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00546 (Fisher's exact test), Q value = 0.024

Table S143. Gene #36: 'del_4q35.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	79	99	42	33
DEL PEAK 10(4Q35.2) MUTATED	12	32	31	26	8
DEL PEAK 10(4Q35.2) WILD-TYPE	17	47	68	16	25

Figure S143. Get High-res Image Gene #36: 'del_4q35.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S144. Gene #37: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
DEL PEAK 11(5Q12.1) MUTATED	2	51	8	7	8
DEL PEAK 11(5Q12.1) WILD-TYPE	13	61	48	52	45

Figure S144. Get High-res Image Gene #37: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q12.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.03 (Fisher's exact test), Q value = 0.082

Table S145. Gene #37: 'del_5q12.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	47	45	23	17
DEL PEAK 11(5Q12.1) MUTATED	12	6	12	10	6
DEL PEAK 11(5Q12.1) WILD-TYPE	20	41	33	13	11

Figure S145. Get High-res Image Gene #37: 'del_5q12.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_CNMF'

P value = 0.0349 (Fisher's exact test), Q value = 0.091

Table S146. Gene #37: 'del_5q12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	75	115
DEL PEAK 11(5Q12.1) MUTATED	20	17	39
DEL PEAK 11(5Q12.1) WILD-TYPE	85	58	76

Figure S146. Get High-res Image Gene #37: 'del_5q12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5q35.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S147. Gene #38: 'del_5q35.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
DEL PEAK 12(5Q35.2) MUTATED	1	48	8	6	8
DEL PEAK 12(5Q35.2) WILD-TYPE	14	64	48	53	45

Figure S147. Get High-res Image Gene #38: 'del_5q35.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q35.2' versus 'MIRSEQ_CNMF'

P value = 0.0287 (Fisher's exact test), Q value = 0.08

Table S148. Gene #38: 'del_5q35.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	75	115
DEL PEAK 12(5Q35.2) MUTATED	18	16	37
DEL PEAK 12(5Q35.2) WILD-TYPE	87	59	78

Figure S148. Get High-res Image Gene #38: 'del_5q35.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6p24.2' versus 'CN_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.052

Table S149. Gene #39: 'del_6p24.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
DEL PEAK 13(6P24.2) MUTATED	1	14	13	4	14
DEL PEAK 13(6P24.2) WILD-TYPE	14	98	43	55	39

Figure S149. Get High-res Image Gene #39: 'del_6p24.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p24.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0401 (Fisher's exact test), Q value = 0.1

Table S150. Gene #39: 'del_6p24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 13(6P24.2) MUTATED	5	36	5
DEL PEAK 13(6P24.2) WILD-TYPE	67	149	30

Figure S150. Get High-res Image Gene #39: 'del_6p24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6p24.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0261 (Fisher's exact test), Q value = 0.074

Table S151. Gene #39: 'del_6p24.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
DEL PEAK 13(6P24.2) MUTATED	4	22	12	5	3
DEL PEAK 13(6P24.2) WILD-TYPE	56	73	60	20	40

Figure S151. Get High-res Image Gene #39: 'del_6p24.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'CN_CNMF'

P value = 0.00279 (Fisher's exact test), Q value = 0.015

Table S152. Gene #40: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
DEL PEAK 14(6Q26) MUTATED	5	46	19	8	22
DEL PEAK 14(6Q26) WILD-TYPE	10	66	37	51	31

Figure S152. Get High-res Image Gene #40: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S153. Gene #42: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
DEL PEAK 16(8P23.3) MUTATED	1	64	6	16	17
DEL PEAK 16(8P23.3) WILD-TYPE	14	48	50	43	36

Figure S153. Get High-res Image Gene #42: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.3' versus 'MRNASEQ_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0042

Table S154. Gene #42: 'del_8p23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
DEL PEAK 16(8P23.3) MUTATED	25	21	23	35
DEL PEAK 16(8P23.3) WILD-TYPE	32	77	46	33

Figure S154. Get High-res Image Gene #42: 'del_8p23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0256 (Fisher's exact test), Q value = 0.073

Table S155. Gene #42: 'del_8p23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 16(8P23.3) MUTATED	28	57	19
DEL PEAK 16(8P23.3) WILD-TYPE	44	128	16

Figure S155. Get High-res Image Gene #42: 'del_8p23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0173 (Fisher's exact test), Q value = 0.056

Table S156. Gene #42: 'del_8p23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
DEL PEAK 16(8P23.3) MUTATED	24	26	20	11	23
DEL PEAK 16(8P23.3) WILD-TYPE	36	69	52	14	20

Figure S156. Get High-res Image Gene #42: 'del_8p23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.041

Table S157. Gene #42: 'del_8p23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	79	102
DEL PEAK 16(8P23.3) MUTATED	40	18	44
DEL PEAK 16(8P23.3) WILD-TYPE	61	61	58

Figure S157. Get High-res Image Gene #42: 'del_8p23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8p23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S158. Gene #43: 'del_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
DEL PEAK 17(8P23.1) MUTATED	1	60	4	15	17
DEL PEAK 17(8P23.1) WILD-TYPE	14	52	52	44	36

Figure S158. Get High-res Image Gene #43: 'del_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.1' versus 'MRNASEQ_CNMF'

P value = 0.0022 (Fisher's exact test), Q value = 0.012

Table S159. Gene #43: 'del_8p23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
DEL PEAK 17(8P23.1) MUTATED	24	20	22	31
DEL PEAK 17(8P23.1) WILD-TYPE	33	78	47	37

Figure S159. Get High-res Image Gene #43: 'del_8p23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p23.1' versus 'MIRSEQ_CNMF'

P value = 0.0249 (Fisher's exact test), Q value = 0.072

Table S160. Gene #43: 'del_8p23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	75	115
DEL PEAK 17(8P23.1) MUTATED	35	16	46
DEL PEAK 17(8P23.1) WILD-TYPE	70	59	69

Figure S160. Get High-res Image Gene #43: 'del_8p23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0211 (Fisher's exact test), Q value = 0.064

Table S161. Gene #43: 'del_8p23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
DEL PEAK 17(8P23.1) MUTATED	22	26	17	10	22
DEL PEAK 17(8P23.1) WILD-TYPE	38	69	55	15	21

Figure S161. Get High-res Image Gene #43: 'del_8p23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00442 (Fisher's exact test), Q value = 0.021

Table S162. Gene #43: 'del_8p23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	79	102
DEL PEAK 17(8P23.1) MUTATED	36	16	44
DEL PEAK 17(8P23.1) WILD-TYPE	65	63	58

Figure S162. Get High-res Image Gene #43: 'del_8p23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'CN_CNMF'

P value = 0.00534 (Fisher's exact test), Q value = 0.024

Table S163. Gene #44: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
DEL PEAK 18(10Q23.31) MUTATED	2	45	18	10	11
DEL PEAK 18(10Q23.31) WILD-TYPE	13	67	38	49	42

Figure S163. Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S164. Gene #45: 'del_11p15.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
DEL PEAK 19(11P15.1) MUTATED	1	48	26	7	20
DEL PEAK 19(11P15.1) WILD-TYPE	14	64	30	52	33

Figure S164. Get High-res Image Gene #45: 'del_11p15.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.1' versus 'RPPA_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.038

Table S165. Gene #45: 'del_11p15.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	41	64
DEL PEAK 19(11P15.1) MUTATED	12	20	18
DEL PEAK 19(11P15.1) WILD-TYPE	47	21	46

Figure S165. Get High-res Image Gene #45: 'del_11p15.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_11p15.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00932 (Fisher's exact test), Q value = 0.036

Table S166. Gene #45: 'del_11p15.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	47	45	23	17
DEL PEAK 19(11P15.1) MUTATED	5	9	19	8	9
DEL PEAK 19(11P15.1) WILD-TYPE	27	38	26	15	8

Figure S166. Get High-res Image Gene #45: 'del_11p15.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_11p15.1' versus 'MRNASEQ_CNMF'

P value = 0.029 (Fisher's exact test), Q value = 0.081

Table S167. Gene #45: 'del_11p15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
DEL PEAK 19(11P15.1) MUTATED	22	39	14	27
DEL PEAK 19(11P15.1) WILD-TYPE	35	59	55	41

Figure S167. Get High-res Image Gene #45: 'del_11p15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11p15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0194 (Fisher's exact test), Q value = 0.06

Table S168. Gene #45: 'del_11p15.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 19(11P15.1) MUTATED	16	75	11
DEL PEAK 19(11P15.1) WILD-TYPE	56	110	24

Figure S168. Get High-res Image Gene #45: 'del_11p15.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0354 (Fisher's exact test), Q value = 0.091

Table S169. Gene #45: 'del_11p15.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	79	99	42	33
DEL PEAK 19(11P15.1) MUTATED	7	29	44	12	6
DEL PEAK 19(11P15.1) WILD-TYPE	22	50	55	30	27

Figure S169. Get High-res Image Gene #45: 'del_11p15.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S170. Gene #46: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
DEL PEAK 20(11Q23.3) MUTATED	1	66	41	20	34
DEL PEAK 20(11Q23.3) WILD-TYPE	14	46	15	39	19

Figure S170. Get High-res Image Gene #46: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q23.3' versus 'MRNASEQ_CNMF'

P value = 0.041 (Fisher's exact test), Q value = 0.1

Table S171. Gene #46: 'del_11q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
DEL PEAK 20(11Q23.3) MUTATED	35	60	28	36
DEL PEAK 20(11Q23.3) WILD-TYPE	22	38	41	32

Figure S171. Get High-res Image Gene #46: 'del_11q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00373 (Fisher's exact test), Q value = 0.019

Table S172. Gene #46: 'del_11q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 20(11Q23.3) MUTATED	27	112	20
DEL PEAK 20(11Q23.3) WILD-TYPE	45	73	15

Figure S172. Get High-res Image Gene #46: 'del_11q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00237 (Fisher's exact test), Q value = 0.013

Table S173. Gene #46: 'del_11q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
DEL PEAK 20(11Q23.3) MUTATED	21	63	43	11	24
DEL PEAK 20(11Q23.3) WILD-TYPE	39	32	29	14	19

Figure S173. Get High-res Image Gene #46: 'del_11q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0114 (Fisher's exact test), Q value = 0.041

Table S174. Gene #46: 'del_11q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	79	99	42	33
DEL PEAK 20(11Q23.3) MUTATED	10	48	62	24	12
DEL PEAK 20(11Q23.3) WILD-TYPE	19	31	37	18	21

Figure S174. Get High-res Image Gene #46: 'del_11q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q25' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S175. Gene #47: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
DEL PEAK 21(11Q25) MUTATED	0	68	38	20	34
DEL PEAK 21(11Q25) WILD-TYPE	15	44	18	39	19

Figure S175. Get High-res Image Gene #47: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q25' versus 'MRNASEQ_CNMF'

P value = 0.0271 (Fisher's exact test), Q value = 0.077

Table S176. Gene #47: 'del_11q25' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
DEL PEAK 21(11Q25) MUTATED	33	61	27	37
DEL PEAK 21(11Q25) WILD-TYPE	24	37	42	31

Figure S176. Get High-res Image Gene #47: 'del_11q25' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q25' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00549 (Fisher's exact test), Q value = 0.024

Table S177. Gene #47: 'del_11q25' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 21(11Q25) MUTATED	27	110	21
DEL PEAK 21(11Q25) WILD-TYPE	45	75	14

Figure S177. Get High-res Image Gene #47: 'del_11q25' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q25' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00576 (Fisher's exact test), Q value = 0.025

Table S178. Gene #47: 'del_11q25' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
DEL PEAK 21(11Q25) MUTATED	21	61	42	11	25
DEL PEAK 21(11Q25) WILD-TYPE	39	34	30	14	18

Figure S178. Get High-res Image Gene #47: 'del_11q25' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11q25' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0196 (Fisher's exact test), Q value = 0.061

Table S179. Gene #47: 'del_11q25' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	79	99	42	33
DEL PEAK 21(11Q25) MUTATED	10	47	61	23	12
DEL PEAK 21(11Q25) WILD-TYPE	19	32	38	19	21

Figure S179. Get High-res Image Gene #47: 'del_11q25' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q12.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S180. Gene #48: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
DEL PEAK 22(13Q12.11) MUTATED	4	52	18	5	19
DEL PEAK 22(13Q12.11) WILD-TYPE	11	60	38	54	34

Figure S180. Get High-res Image Gene #48: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q12.11' versus 'METHLYATION_CNMF'

P value = 0.00173 (Fisher's exact test), Q value = 0.01

Table S181. Gene #48: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	115	108
DEL PEAK 22(13Q12.11) MUTATED	12	43	43
DEL PEAK 22(13Q12.11) WILD-TYPE	60	72	65

Figure S181. Get High-res Image Gene #48: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q12.11' versus 'MRNASEQ_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.059

Table S182. Gene #48: 'del_13q12.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
DEL PEAK 22(13Q12.11) MUTATED	18	31	15	32
DEL PEAK 22(13Q12.11) WILD-TYPE	39	67	54	36

Figure S182. Get High-res Image Gene #48: 'del_13q12.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q12.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.0032

Table S183. Gene #48: 'del_13q12.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 22(13Q12.11) MUTATED	11	68	17
DEL PEAK 22(13Q12.11) WILD-TYPE	61	117	18

Figure S183. Get High-res Image Gene #48: 'del_13q12.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q12.11' versus 'MIRSEQ_CNMF'

P value = 0.00187 (Fisher's exact test), Q value = 0.011

Table S184. Gene #48: 'del_13q12.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	75	115
DEL PEAK 22(13Q12.11) MUTATED	23	24	51
DEL PEAK 22(13Q12.11) WILD-TYPE	82	51	64

Figure S184. Get High-res Image Gene #48: 'del_13q12.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_13q12.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00483 (Fisher's exact test), Q value = 0.023

Table S185. Gene #48: 'del_13q12.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
DEL PEAK 22(13Q12.11) MUTATED	9	33	25	11	20
DEL PEAK 22(13Q12.11) WILD-TYPE	51	62	47	14	23

Figure S185. Get High-res Image Gene #48: 'del_13q12.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q12.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0351 (Fisher's exact test), Q value = 0.091

Table S186. Gene #48: 'del_13q12.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	79	102
DEL PEAK 22(13Q12.11) MUTATED	26	23	43
DEL PEAK 22(13Q12.11) WILD-TYPE	75	56	59

Figure S186. Get High-res Image Gene #48: 'del_13q12.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_13q12.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00545 (Fisher's exact test), Q value = 0.024

Table S187. Gene #48: 'del_13q12.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	79	99	42	33
DEL PEAK 22(13Q12.11) MUTATED	6	29	36	18	3
DEL PEAK 22(13Q12.11) WILD-TYPE	23	50	63	24	30

Figure S187. Get High-res Image Gene #48: 'del_13q12.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S188. Gene #49: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
DEL PEAK 23(13Q14.2) MUTATED	6	57	24	7	24
DEL PEAK 23(13Q14.2) WILD-TYPE	9	55	32	52	29

Figure S188. Get High-res Image Gene #49: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

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

Table S189. Gene #49: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	115	108
DEL PEAK 23(13Q14.2) MUTATED	19	53	46
DEL PEAK 23(13Q14.2) WILD-TYPE	53	62	62

Figure S189. Get High-res Image Gene #49: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 0.00122 (Fisher's exact test), Q value = 0.008

Table S190. Gene #49: 'del_13q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
DEL PEAK 23(13Q14.2) MUTATED	29	37	15	34
DEL PEAK 23(13Q14.2) WILD-TYPE	28	61	54	34

Figure S190. Get High-res Image Gene #49: 'del_13q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00216 (Fisher's exact test), Q value = 0.012

Table S191. Gene #49: 'del_13q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 23(13Q14.2) MUTATED	16	83	16
DEL PEAK 23(13Q14.2) WILD-TYPE	56	102	19

Figure S191. Get High-res Image Gene #49: 'del_13q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 0.00507 (Fisher's exact test), Q value = 0.023

Table S192. Gene #49: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	75	115
DEL PEAK 23(13Q14.2) MUTATED	32	27	59
DEL PEAK 23(13Q14.2) WILD-TYPE	73	48	56

Figure S192. Get High-res Image Gene #49: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00059 (Fisher's exact test), Q value = 0.0049

Table S193. Gene #49: 'del_13q14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
DEL PEAK 23(13Q14.2) MUTATED	11	43	27	13	24
DEL PEAK 23(13Q14.2) WILD-TYPE	49	52	45	12	19

Figure S193. Get High-res Image Gene #49: 'del_13q14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00998 (Fisher's exact test), Q value = 0.038

Table S194. Gene #49: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	79	99	42	33
DEL PEAK 23(13Q14.2) MUTATED	9	32	45	21	5
DEL PEAK 23(13Q14.2) WILD-TYPE	20	47	54	21	28

Figure S194. Get High-res Image Gene #49: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q32.31' versus 'METHLYATION_CNMF'

P value = 0.00677 (Fisher's exact test), Q value = 0.028

Table S195. Gene #50: 'del_14q32.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	115	108
DEL PEAK 24(14Q32.31) MUTATED	17	10	23
DEL PEAK 24(14Q32.31) WILD-TYPE	55	105	85

Figure S195. Get High-res Image Gene #50: 'del_14q32.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q32.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00808 (Fisher's exact test), Q value = 0.032

Table S196. Gene #50: 'del_14q32.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	47	45	23	17
DEL PEAK 24(14Q32.31) MUTATED	1	12	5	6	6
DEL PEAK 24(14Q32.31) WILD-TYPE	31	35	40	17	11

Figure S196. Get High-res Image Gene #50: 'del_14q32.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_14q32.31' versus 'MRNASEQ_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.041

Table S197. Gene #50: 'del_14q32.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
DEL PEAK 24(14Q32.31) MUTATED	9	9	20	11
DEL PEAK 24(14Q32.31) WILD-TYPE	48	89	49	57

Figure S197. Get High-res Image Gene #50: 'del_14q32.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q32.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00922 (Fisher's exact test), Q value = 0.036

Table S198. Gene #50: 'del_14q32.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 24(14Q32.31) MUTATED	17	22	10
DEL PEAK 24(14Q32.31) WILD-TYPE	55	163	25

Figure S198. Get High-res Image Gene #50: 'del_14q32.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0255 (Fisher's exact test), Q value = 0.073

Table S199. Gene #50: 'del_14q32.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
DEL PEAK 24(14Q32.31) MUTATED	13	19	4	4	10
DEL PEAK 24(14Q32.31) WILD-TYPE	47	76	68	21	33

Figure S199. Get High-res Image Gene #50: 'del_14q32.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_14q32.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0242 (Fisher's exact test), Q value = 0.071

Table S200. Gene #50: 'del_14q32.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	79	99	42	33
DEL PEAK 24(14Q32.31) MUTATED	7	8	13	12	9
DEL PEAK 24(14Q32.31) WILD-TYPE	22	71	86	30	24

Figure S200. Get High-res Image Gene #50: 'del_14q32.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q21.1' versus 'CN_CNMF'

P value = 0.0249 (Fisher's exact test), Q value = 0.072

Table S201. Gene #51: 'del_15q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
DEL PEAK 25(15Q21.1) MUTATED	1	37	14	9	9
DEL PEAK 25(15Q21.1) WILD-TYPE	14	75	42	50	44

Figure S201. Get High-res Image Gene #51: 'del_15q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0472 (Fisher's exact test), Q value = 0.11

Table S202. Gene #51: 'del_15q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 25(15Q21.1) MUTATED	24	36	10
DEL PEAK 25(15Q21.1) WILD-TYPE	48	149	25

Figure S202. Get High-res Image Gene #51: 'del_15q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q21.1' versus 'MIRSEQ_CNMF'

P value = 0.00492 (Fisher's exact test), Q value = 0.023

Table S203. Gene #51: 'del_15q21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	75	115
DEL PEAK 25(15Q21.1) MUTATED	28	8	34
DEL PEAK 25(15Q21.1) WILD-TYPE	77	67	81

Figure S203. Get High-res Image Gene #51: 'del_15q21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_15q21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0317 (Fisher's exact test), Q value = 0.085

Table S204. Gene #51: 'del_15q21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
DEL PEAK 25(15Q21.1) MUTATED	20	21	9	6	14
DEL PEAK 25(15Q21.1) WILD-TYPE	40	74	63	19	29

Figure S204. Get High-res Image Gene #51: 'del_15q21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.06

Table S205. Gene #51: 'del_15q21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	79	102
DEL PEAK 25(15Q21.1) MUTATED	32	11	25
DEL PEAK 25(15Q21.1) WILD-TYPE	69	68	77

Figure S205. Get High-res Image Gene #51: 'del_15q21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_15q21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00885 (Fisher's exact test), Q value = 0.035

Table S206. Gene #51: 'del_15q21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	79	99	42	33
DEL PEAK 25(15Q21.1) MUTATED	11	9	24	13	11
DEL PEAK 25(15Q21.1) WILD-TYPE	18	70	75	29	22

Figure S206. Get High-res Image Gene #51: 'del_15q21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q11.2' versus 'CN_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.082

Table S207. Gene #52: 'del_16q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
DEL PEAK 26(16Q11.2) MUTATED	0	25	5	15	8
DEL PEAK 26(16Q11.2) WILD-TYPE	15	87	51	44	45

Figure S207. Get High-res Image Gene #52: 'del_16q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q11.2' versus 'METHLYATION_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0033

Table S208. Gene #52: 'del_16q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	115	108
DEL PEAK 26(16Q11.2) MUTATED	24	18	11
DEL PEAK 26(16Q11.2) WILD-TYPE	48	97	97

Figure S208. Get High-res Image Gene #52: 'del_16q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q11.2' versus 'MRNASEQ_CNMF'

P value = 0.0472 (Fisher's exact test), Q value = 0.11

Table S209. Gene #52: 'del_16q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
DEL PEAK 26(16Q11.2) MUTATED	11	12	20	10
DEL PEAK 26(16Q11.2) WILD-TYPE	46	86	49	58

Figure S209. Get High-res Image Gene #52: 'del_16q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00979 (Fisher's exact test), Q value = 0.037

Table S210. Gene #52: 'del_16q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 26(16Q11.2) MUTATED	22	26	5
DEL PEAK 26(16Q11.2) WILD-TYPE	50	159	30

Figure S210. Get High-res Image Gene #52: 'del_16q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q11.2' versus 'MIRSEQ_CNMF'

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

Table S211. Gene #52: 'del_16q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	75	115
DEL PEAK 26(16Q11.2) MUTATED	28	11	14
DEL PEAK 26(16Q11.2) WILD-TYPE	77	64	101

Figure S211. Get High-res Image Gene #52: 'del_16q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q11.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S212. Gene #52: 'del_16q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
DEL PEAK 26(16Q11.2) MUTATED	18	14	6	7	8
DEL PEAK 26(16Q11.2) WILD-TYPE	42	81	66	18	35

Figure S212. Get High-res Image Gene #52: 'del_16q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.0033

Table S213. Gene #52: 'del_16q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	79	99	42	33
DEL PEAK 26(16Q11.2) MUTATED	4	8	18	6	16
DEL PEAK 26(16Q11.2) WILD-TYPE	25	71	81	36	17

Figure S213. Get High-res Image Gene #52: 'del_16q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 0.00642 (Fisher's exact test), Q value = 0.027

Table S214. Gene #53: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	115	108
DEL PEAK 27(16Q23.1) MUTATED	23	17	15
DEL PEAK 27(16Q23.1) WILD-TYPE	49	98	93

Figure S214. Get High-res Image Gene #53: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.005

Table S215. Gene #53: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
DEL PEAK 27(16Q23.1) MUTATED	14	8	22	11
DEL PEAK 27(16Q23.1) WILD-TYPE	43	90	47	57

Figure S215. Get High-res Image Gene #53: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.0033

Table S216. Gene #53: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 27(16Q23.1) MUTATED	25	23	7
DEL PEAK 27(16Q23.1) WILD-TYPE	47	162	28

Figure S216. Get High-res Image Gene #53: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 0.0374 (Fisher's exact test), Q value = 0.095

Table S217. Gene #53: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	75	115
DEL PEAK 27(16Q23.1) MUTATED	28	11	16
DEL PEAK 27(16Q23.1) WILD-TYPE	77	64	99

Figure S217. Get High-res Image Gene #53: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.0049

Table S218. Gene #53: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
DEL PEAK 27(16Q23.1) MUTATED	20	16	4	7	8
DEL PEAK 27(16Q23.1) WILD-TYPE	40	79	68	18	35

Figure S218. Get High-res Image Gene #53: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 0.068

Table S219. Gene #53: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	79	102
DEL PEAK 27(16Q23.1) MUTATED	28	13	13
DEL PEAK 27(16Q23.1) WILD-TYPE	73	66	89

Figure S219. Get High-res Image Gene #53: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00098

Table S220. Gene #53: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	79	99	42	33
DEL PEAK 27(16Q23.1) MUTATED	6	8	17	6	17
DEL PEAK 27(16Q23.1) WILD-TYPE	23	71	82	36	16

Figure S220. Get High-res Image Gene #53: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.0055

Table S221. Gene #54: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
DEL PEAK 28(17P12) MUTATED	4	56	22	11	16
DEL PEAK 28(17P12) WILD-TYPE	11	56	34	48	37

Figure S221. Get High-res Image Gene #54: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q25.3' versus 'CN_CNMF'

P value = 0.00948 (Fisher's exact test), Q value = 0.036

Table S222. Gene #55: 'del_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
DEL PEAK 29(17Q25.3) MUTATED	2	22	13	2	12
DEL PEAK 29(17Q25.3) WILD-TYPE	13	90	43	57	41

Figure S222. Get High-res Image Gene #55: 'del_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q25.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S223. Gene #55: 'del_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	115	108
DEL PEAK 29(17Q25.3) MUTATED	4	35	12
DEL PEAK 29(17Q25.3) WILD-TYPE	68	80	96

Figure S223. Get High-res Image Gene #55: 'del_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q25.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S224. Gene #55: 'del_17q25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
DEL PEAK 29(17Q25.3) MUTATED	4	22	2	22
DEL PEAK 29(17Q25.3) WILD-TYPE	53	76	67	46

Figure S224. Get High-res Image Gene #55: 'del_17q25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17q25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00094 (Fisher's exact test), Q value = 0.0067

Table S225. Gene #55: 'del_17q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 29(17Q25.3) MUTATED	3	39	8
DEL PEAK 29(17Q25.3) WILD-TYPE	69	146	27

Figure S225. Get High-res Image Gene #55: 'del_17q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17q25.3' versus 'MIRSEQ_CNMF'

P value = 0.00189 (Fisher's exact test), Q value = 0.011

Table S226. Gene #55: 'del_17q25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	75	115
DEL PEAK 29(17Q25.3) MUTATED	10	10	31
DEL PEAK 29(17Q25.3) WILD-TYPE	95	65	84

Figure S226. Get High-res Image Gene #55: 'del_17q25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17q25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00086 (Fisher's exact test), Q value = 0.0063

Table S227. Gene #55: 'del_17q25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
DEL PEAK 29(17Q25.3) MUTATED	1	23	12	6	9
DEL PEAK 29(17Q25.3) WILD-TYPE	59	72	60	19	34

Figure S227. Get High-res Image Gene #55: 'del_17q25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17q25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0286 (Fisher's exact test), Q value = 0.08

Table S228. Gene #55: 'del_17q25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	79	99	42	33
DEL PEAK 29(17Q25.3) MUTATED	2	12	22	10	1
DEL PEAK 29(17Q25.3) WILD-TYPE	27	67	77	32	32

Figure S228. Get High-res Image Gene #55: 'del_17q25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q21.2' versus 'CN_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.005

Table S229. Gene #56: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
DEL PEAK 30(18Q21.2) MUTATED	1	44	6	17	14
DEL PEAK 30(18Q21.2) WILD-TYPE	14	68	50	42	39

Figure S229. Get High-res Image Gene #56: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 0.00113 (Fisher's exact test), Q value = 0.0076

Table S230. Gene #56: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	115	108
DEL PEAK 30(18Q21.2) MUTATED	31	21	30
DEL PEAK 30(18Q21.2) WILD-TYPE	41	94	78

Figure S230. Get High-res Image Gene #56: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S231. Gene #56: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
DEL PEAK 30(18Q21.2) MUTATED	13	9	31	29
DEL PEAK 30(18Q21.2) WILD-TYPE	44	89	38	39

Figure S231. Get High-res Image Gene #56: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00039

Table S232. Gene #56: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 30(18Q21.2) MUTATED	32	35	15
DEL PEAK 30(18Q21.2) WILD-TYPE	40	150	20

Figure S232. Get High-res Image Gene #56: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_CNMF'

P value = 0.0231 (Fisher's exact test), Q value = 0.069

Table S233. Gene #56: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	75	115
DEL PEAK 30(18Q21.2) MUTATED	32	12	38
DEL PEAK 30(18Q21.2) WILD-TYPE	73	63	77

Figure S233. Get High-res Image Gene #56: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S234. Gene #56: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
DEL PEAK 30(18Q21.2) MUTATED	29	18	11	4	20
DEL PEAK 30(18Q21.2) WILD-TYPE	31	77	61	21	23

Figure S234. Get High-res Image Gene #56: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0029 (Fisher's exact test), Q value = 0.015

Table S235. Gene #56: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	79	102
DEL PEAK 30(18Q21.2) MUTATED	38	12	32
DEL PEAK 30(18Q21.2) WILD-TYPE	63	67	70

Figure S235. Get High-res Image Gene #56: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_18q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S236. Gene #56: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	79	99	42	33
DEL PEAK 30(18Q21.2) MUTATED	6	11	25	19	21
DEL PEAK 30(18Q21.2) WILD-TYPE	23	68	74	23	12

Figure S236. Get High-res Image Gene #56: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S237. Gene #57: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
DEL PEAK 31(19P13.3) MUTATED	3	63	13	4	22
DEL PEAK 31(19P13.3) WILD-TYPE	12	49	43	55	31

Figure S237. Get High-res Image Gene #57: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 9e-04

Table S238. Gene #57: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
DEL PEAK 31(19P13.3) MUTATED	18	22	25	39
DEL PEAK 31(19P13.3) WILD-TYPE	39	76	44	29

Figure S238. Get High-res Image Gene #57: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S239. Gene #57: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 31(19P13.3) MUTATED	25	53	26
DEL PEAK 31(19P13.3) WILD-TYPE	47	132	9

Figure S239. Get High-res Image Gene #57: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 0.0194 (Fisher's exact test), Q value = 0.06

Table S240. Gene #57: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	75	115
DEL PEAK 31(19P13.3) MUTATED	40	17	48
DEL PEAK 31(19P13.3) WILD-TYPE	65	58	67

Figure S240. Get High-res Image Gene #57: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00061

Table S241. Gene #57: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
DEL PEAK 31(19P13.3) MUTATED	17	36	13	13	26
DEL PEAK 31(19P13.3) WILD-TYPE	43	59	59	12	17

Figure S241. Get High-res Image Gene #57: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.052

Table S242. Gene #57: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	79	102
DEL PEAK 31(19P13.3) MUTATED	40	18	43
DEL PEAK 31(19P13.3) WILD-TYPE	61	61	59

Figure S242. Get High-res Image Gene #57: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00096 (Fisher's exact test), Q value = 0.0067

Table S243. Gene #57: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	79	99	42	33
DEL PEAK 31(19P13.3) MUTATED	10	18	37	26	10
DEL PEAK 31(19P13.3) WILD-TYPE	19	61	62	16	23

Figure S243. Get High-res Image Gene #57: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.33' versus 'CN_CNMF'

P value = 0.0197 (Fisher's exact test), Q value = 0.061

Table S244. Gene #58: 'del_19q13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
DEL PEAK 32(19Q13.33) MUTATED	1	18	2	5	12
DEL PEAK 32(19Q13.33) WILD-TYPE	14	94	54	54	41

Figure S244. Get High-res Image Gene #58: 'del_19q13.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.33' versus 'METHLYATION_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 0.082

Table S245. Gene #58: 'del_19q13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	115	108
DEL PEAK 32(19Q13.33) MUTATED	13	18	7
DEL PEAK 32(19Q13.33) WILD-TYPE	59	97	101

Figure S245. Get High-res Image Gene #58: 'del_19q13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19q13.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0122 (Fisher's exact test), Q value = 0.043

Table S246. Gene #58: 'del_19q13.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	79	99	42	33
DEL PEAK 32(19Q13.33) MUTATED	4	5	19	2	8
DEL PEAK 32(19Q13.33) WILD-TYPE	25	74	80	40	25

Figure S246. Get High-res Image Gene #58: 'del_19q13.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20p12.1' versus 'MRNASEQ_CNMF'

P value = 0.00535 (Fisher's exact test), Q value = 0.024

Table S247. Gene #59: 'del_20p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	98	69	68
DEL PEAK 33(20P12.1) MUTATED	2	8	11	15
DEL PEAK 33(20P12.1) WILD-TYPE	55	90	58	53

Figure S247. Get High-res Image Gene #59: 'del_20p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_20p12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00152 (Fisher's exact test), Q value = 0.0095

Table S248. Gene #59: 'del_20p12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	79	102
DEL PEAK 33(20P12.1) MUTATED	6	6	22
DEL PEAK 33(20P12.1) WILD-TYPE	95	73	80

Figure S248. Get High-res Image Gene #59: 'del_20p12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_20p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00162 (Fisher's exact test), Q value = 0.0097

Table S249. Gene #59: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	79	99	42	33
DEL PEAK 33(20P12.1) MUTATED	1	7	7	12	7
DEL PEAK 33(20P12.1) WILD-TYPE	28	72	92	30	26

Figure S249. Get High-res Image Gene #59: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q11.2' versus 'CN_CNMF'

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

Table S250. Gene #60: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
DEL PEAK 34(21Q11.2) MUTATED	2	35	9	7	5
DEL PEAK 34(21Q11.2) WILD-TYPE	13	77	47	52	48

Figure S250. Get High-res Image Gene #60: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00449 (Fisher's exact test), Q value = 0.022

Table S251. Gene #60: 'del_21q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	47	45	23	17
DEL PEAK 34(21Q11.2) MUTATED	6	7	2	8	6
DEL PEAK 34(21Q11.2) WILD-TYPE	26	40	43	15	11

Figure S251. Get High-res Image Gene #60: 'del_21q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_21q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00872 (Fisher's exact test), Q value = 0.034

Table S252. Gene #60: 'del_21q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 34(21Q11.2) MUTATED	14	30	14
DEL PEAK 34(21Q11.2) WILD-TYPE	58	155	21

Figure S252. Get High-res Image Gene #60: 'del_21q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 0.00406 (Fisher's exact test), Q value = 0.02

Table S253. Gene #61: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	112	56	59	53
DEL PEAK 35(22Q13.32) MUTATED	4	46	15	8	14
DEL PEAK 35(22Q13.32) WILD-TYPE	11	66	41	51	39

Figure S253. Get High-res Image Gene #61: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0236 (Fisher's exact test), Q value = 0.069

Table S254. Gene #61: 'del_22q13.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 35(22Q13.32) MUTATED	23	47	17
DEL PEAK 35(22Q13.32) WILD-TYPE	49	138	18

Figure S254. Get High-res Image Gene #61: 'del_22q13.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp11.3' versus 'METHLYATION_CNMF'

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

Table S255. Gene #62: 'del_xp11.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	115	108
DEL PEAK 36(XP11.3) MUTATED	14	39	19
DEL PEAK 36(XP11.3) WILD-TYPE	58	76	89

Figure S255. Get High-res Image Gene #62: 'del_xp11.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp11.3' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S256. Gene #62: 'del_xp11.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	75	115
DEL PEAK 36(XP11.3) MUTATED	21	7	44
DEL PEAK 36(XP11.3) WILD-TYPE	84	68	71

Figure S256. Get High-res Image Gene #62: 'del_xp11.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xp11.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.032 (Fisher's exact test), Q value = 0.085

Table S257. Gene #62: 'del_xp11.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
DEL PEAK 36(XP11.3) MUTATED	11	28	10	9	14
DEL PEAK 36(XP11.3) WILD-TYPE	49	67	62	16	29

Figure S257. Get High-res Image Gene #62: 'del_xp11.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xp11.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00275 (Fisher's exact test), Q value = 0.015

Table S258. Gene #62: 'del_xp11.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	79	102
DEL PEAK 36(XP11.3) MUTATED	23	10	35
DEL PEAK 36(XP11.3) WILD-TYPE	78	69	67

Figure S258. Get High-res Image Gene #62: 'del_xp11.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xp11.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0145 (Fisher's exact test), Q value = 0.05

Table S259. Gene #62: 'del_xp11.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	79	99	42	33
DEL PEAK 36(XP11.3) MUTATED	8	11	31	14	4
DEL PEAK 36(XP11.3) WILD-TYPE	21	68	68	28	29

Figure S259. Get High-res Image Gene #62: 'del_xp11.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xq21.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.0114 (Fisher's exact test), Q value = 0.041

Table S260. Gene #63: 'del_xq21.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	47	45	23	17
DEL PEAK 37(XQ21.33) MUTATED	2	9	14	5	0
DEL PEAK 37(XQ21.33) WILD-TYPE	30	38	31	18	17

Figure S260. Get High-res Image Gene #63: 'del_xq21.33' versus Molecular Subtype #4: 'RPPA_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/CESC-TP/22507940/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/CESC-TP/22541064/CESC-TP.transferedmergedcluster.txt
Number of patients = 295
Number of significantly focal cnvs = 63
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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