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, 250 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', and 'MIRSEQ_CHIERARCHICAL'.
amp_1q44 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_2p24.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_2q33.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_3q26.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3q28 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', 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_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_9p24.1 cnv correlated to 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.
amp_11q13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_11q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_13q22.1 cnv correlated to 'METHLYATION_CNMF'.
amp_13q34 cnv correlated to 'CN_CNMF'.
amp_17q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q25.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
amp_19p13.3 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_19q13.13 cnv correlated to 'CN_CNMF'.
amp_20q11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_xq28 cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_MATURE_CNMF'.
del_1p36.23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p13.2 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q22.1 cnv correlated to 'MRNASEQ_CNMF'.
del_2q37.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', '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_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', and 'MRNASEQ_CHIERARCHICAL'.
del_5q12.1 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q35.2 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
del_6p24.2 cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CHIERARCHICAL'.
del_6q26 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_7q34 cnv correlated to 'CN_CNMF'.
del_8p23.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_8p23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_10q23.31 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_11p15.1 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_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', 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 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_15q21.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_16q11.2 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q23.1 cnv correlated to 'CN_CNMF', '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 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q21.2 cnv correlated to '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', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19q13.33 cnv correlated to 'METHLYATION_CNMF'.
del_20p12.1 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
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 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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, 250 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	0.00032 (0.00305)	5e-05 (0.000716)	0.00896 (0.0367)	1e-05 (0.000233)	2e-05 (0.00036)	1e-05 (0.000233)	0.00071 (0.00532)	1e-05 (0.000233)	0.0701 (0.165)	0.0031 (0.017)
amp 17q12	55 (19%)	240	0.00529 (0.0244)	0.00357 (0.0186)	0.682 (0.785)	0.0377 (0.102)	0.00372 (0.0192)	0.00355 (0.0186)	0.0298 (0.0865)	0.0326 (0.0915)	0.019 (0.0624)	0.044 (0.116)
del 3p14 2	134 (45%)	161	1e-05 (0.000233)	2e-05 (0.00036)	0.109 (0.223)	0.0471 (0.12)	0.002 (0.0119)	5e-05 (0.000716)	0.00982 (0.0389)	0.00053 (0.00439)	0.00223 (0.013)	0.00014 (0.00173)
del 16q23 1	55 (19%)	240	0.013 (0.0477)	0.0008 (0.00593)	0.424 (0.57)	0.186 (0.322)	0.00046 (0.00392)	0.00035 (0.00329)	0.0261 (0.079)	0.00058 (0.00463)	0.0496 (0.125)	0.00319 (0.0173)
del 19p13 3	105 (36%)	190	1e-05 (0.000233)	1e-05 (0.000233)	0.521 (0.659)	0.0853 (0.189)	0.00023 (0.00241)	1e-05 (0.000233)	0.0132 (0.0481)	2e-05 (0.00036)	0.0469 (0.12)	0.048 (0.121)
amp 3q28	224 (76%)	71	1e-05 (0.000233)	1e-05 (0.000233)	0.735 (0.82)	0.856 (0.9)	0.00184 (0.0111)	1e-05 (0.000233)	0.301 (0.45)	2e-05 (0.00036)	0.0342 (0.0944)	0.00019 (0.0021)
amp 5p15 33	138 (47%)	157	1e-05 (0.000233)	0.0053 (0.0244)	0.109 (0.223)	0.372 (0.52)	0.00391 (0.0196)	0.00538 (0.0244)	0.00528 (0.0244)	0.00101 (0.00692)	0.191 (0.328)	0.0153 (0.0526)
amp 7p11 2	52 (18%)	243	0.00015 (0.00182)	0.00045 (0.00388)	0.173 (0.31)	0.00815 (0.034)	0.0152 (0.0526)	0.0659 (0.158)	0.00021 (0.00224)	0.0895 (0.194)	0.0274 (0.0815)	0.0158 (0.0538)
amp 11q13 3	41 (14%)	254	0.00036 (0.00329)	0.024 (0.0742)	0.196 (0.333)	0.0313 (0.0893)	0.0136 (0.0488)	7e-05 (0.000919)	0.0166 (0.0561)	2e-05 (0.00036)	0.371 (0.52)	0.32 (0.471)
del 2q37 1	129 (44%)	166	0.00392 (0.0196)	0.00044 (0.00385)	0.32 (0.471)	0.107 (0.22)	3e-05 (0.000472)	1e-05 (0.000233)	0.0151 (0.0526)	0.00124 (0.00789)	0.0876 (0.191)	1e-05 (0.000233)
del 13q12 11	98 (33%)	197	0.00262 (0.0149)	0.00082 (0.00601)	0.33 (0.48)	0.0925 (0.196)	0.012 (0.0444)	0.00027 (0.0027)	0.00171 (0.0105)	0.0048 (0.0231)	0.248 (0.394)	0.00242 (0.0139)
del 13q14 2	118 (40%)	177	0.00405 (0.0201)	0.00109 (0.00723)	0.803 (0.869)	0.624 (0.74)	0.00117 (0.0076)	0.00219 (0.0129)	0.0145 (0.051)	0.00056 (0.00452)	0.0809 (0.183)	0.00352 (0.0186)
del 18q21 2	82 (28%)	213	0.137 (0.262)	0.00011 (0.00139)	0.559 (0.692)	0.0553 (0.136)	1e-05 (0.000233)	2e-05 (0.00036)	0.0158 (0.0538)	3e-05 (0.000472)	0.0384 (0.103)	0.00269 (0.0151)
amp 3q26 31	227 (77%)	68	1e-05 (0.000233)	6e-05 (0.000822)	0.832 (0.889)	0.886 (0.918)	0.00042 (0.00373)	1e-05 (0.000233)	0.309 (0.459)	1e-05 (0.000233)	0.0518 (0.129)	0.00032 (0.00305)
del 1p36 23	40 (14%)	255	0.00068 (0.00529)	0.00477 (0.0231)	0.881 (0.917)	0.0954 (0.2)	0.00042 (0.00373)	2e-05 (0.00036)	0.172 (0.309)	0.00021 (0.00224)	0.126 (0.246)	0.0237 (0.0741)
del 8p23 3	104 (35%)	191	1e-05 (0.000233)	0.0302 (0.0873)	0.186 (0.322)	0.092 (0.196)	0.00049 (0.00412)	0.0256 (0.0787)	0.0741 (0.172)	0.0176 (0.0586)	0.0317 (0.0901)	0.194 (0.332)
del 8p23 1	97 (33%)	198	4e-05 (6e-04)	0.0166 (0.0561)	0.435 (0.578)	0.0926 (0.196)	0.00347 (0.0185)	0.159 (0.292)	0.023 (0.0724)	0.0224 (0.0712)	0.00912 (0.0371)	0.0823 (0.185)
del 16q11 2	53 (18%)	242	0.2 (0.337)	0.00199 (0.0119)	0.168 (0.304)	0.157 (0.292)	0.0366 (0.0994)	0.0105 (0.0412)	0.0113 (0.0427)	0.0107 (0.0413)	0.2 (0.337)	0.0136 (0.0488)
del 17q25 3	51 (17%)	244	0.333 (0.481)	0.00016 (0.0019)	0.457 (0.597)	0.953 (0.97)	3e-05 (0.000472)	0.00101 (0.00692)	0.00336 (0.0181)	0.00088 (0.0063)	0.418 (0.564)	0.0057 (0.0256)
amp 1q44	152 (52%)	143	1e-05 (0.000233)	0.251 (0.396)	0.814 (0.877)	0.317 (0.469)	0.00831 (0.0344)	0.00638 (0.0283)	0.85 (0.899)	0.00145 (0.00913)	0.433 (0.578)	0.0208 (0.0671)
amp 20q11 21	135 (46%)	160	0.00036 (0.00329)	0.0259 (0.079)	0.664 (0.769)	0.00375 (0.0192)	0.0632 (0.153)	0.0364 (0.0993)	0.182 (0.319)	0.0354 (0.097)	0.679 (0.785)	0.186 (0.322)
del 11p15 1	102 (35%)	193	0.00115 (0.00755)	0.171 (0.307)	0.0374 (0.101)	0.00941 (0.0378)	0.0286 (0.0846)	0.0185 (0.0611)	0.264 (0.409)	0.0763 (0.175)	0.987 (0.996)	0.144 (0.274)
del 11q23 3	162 (55%)	133	1e-05 (0.000233)	0.148 (0.277)	0.385 (0.532)	0.131 (0.253)	0.0437 (0.115)	0.00384 (0.0195)	0.814 (0.877)	0.00232 (0.0134)	0.117 (0.235)	0.00624 (0.0279)
del 11q25	160 (54%)	135	1e-05 (0.000233)	0.163 (0.297)	0.63 (0.744)	0.188 (0.324)	0.0336 (0.0933)	0.0051 (0.0242)	0.533 (0.671)	0.00534 (0.0244)	0.0757 (0.175)	0.00809 (0.034)
del 14q32 31	50 (17%)	245	7e-05 (0.000919)	0.0701 (0.165)	0.228 (0.372)	0.00771 (0.0326)	0.0134 (0.0486)	0.00955 (0.0381)	0.236 (0.381)	0.0265 (0.0791)	0.0909 (0.195)	0.13 (0.251)
del 15q21 1	70 (24%)	225	9e-05 (0.00116)	0.243 (0.388)	0.737 (0.82)	0.552 (0.688)	0.113 (0.229)	0.047 (0.12)	0.0103 (0.0406)	0.033 (0.0919)	0.0196 (0.0637)	0.0508 (0.128)
del xp11 3	72 (24%)	223	0.00071 (0.00532)	0.00032 (0.00305)	0.682 (0.785)	0.654 (0.763)	0.0925 (0.196)	0.243 (0.388)	0.00027 (0.0027)	0.0321 (0.0906)	0.00308 (0.017)	0.159 (0.292)
amp 1p31 3	96 (33%)	199	0.00068 (0.00529)	0.258 (0.402)	0.454 (0.595)	0.712 (0.806)	0.0304 (0.0876)	0.00154 (0.00961)	0.341 (0.491)	0.0012 (0.00771)	0.545 (0.684)	0.288 (0.437)
amp 1q21 3	158 (54%)	137	1e-05 (0.000233)	0.568 (0.699)	0.34 (0.49)	0.246 (0.392)	0.0479 (0.121)	0.0107 (0.0413)	0.989 (0.996)	0.00098 (0.00692)	0.793 (0.864)	0.0555 (0.136)
amp 2p24 3	79 (27%)	216	2e-05 (0.00036)	0.00646 (0.0285)	0.308 (0.458)	0.0532 (0.132)	0.135 (0.258)	0.0436 (0.115)	0.0693 (0.164)	4e-05 (6e-04)	0.11 (0.224)	0.114 (0.229)
amp 2q33 1	41 (14%)	254	6e-05 (0.000822)	0.0451 (0.117)	0.203 (0.339)	0.442 (0.584)	0.00019 (0.0021)	0.0553 (0.136)	0.307 (0.458)	0.00695 (0.0301)	0.326 (0.477)	0.82 (0.881)
del 1p13 2	34 (12%)	261	0.0579 (0.142)	0.00451 (0.0222)	0.166 (0.301)	0.26 (0.404)	3e-05 (0.000472)	0.071 (0.166)	0.0107 (0.0413)	0.178 (0.316)	0.636 (0.747)	0.0262 (0.079)
del 4q22 1	100 (34%)	195	1e-05 (0.000233)	0.235 (0.38)	0.773 (0.846)	0.871 (0.911)	0.0229 (0.0724)	0.0113 (0.0427)	0.633 (0.744)	0.0444 (0.116)	0.229 (0.373)	0.412 (0.561)
del 5q12 1	76 (26%)	219	3e-05 (0.000472)	0.926 (0.953)	0.059 (0.144)	0.0293 (0.0863)	0.417 (0.564)	0.94 (0.964)	0.0209 (0.0673)	0.345 (0.492)	0.816 (0.878)	0.0313 (0.0893)
amp 6p21 33	82 (28%)	213	0.00026 (0.00269)	0.12 (0.237)	0.695 (0.792)	0.0615 (0.15)	0.0219 (0.0701)	0.16 (0.292)	0.724 (0.814)	0.0145 (0.051)	0.418 (0.564)	0.69 (0.792)
amp 8q24 21	127 (43%)	168	0.254 (0.398)	0.128 (0.248)	0.289 (0.437)	0.146 (0.275)	0.452 (0.594)	0.0393 (0.104)	0.0864 (0.19)	0.0981 (0.202)	0.0195 (0.0636)	0.00084 (0.00608)
amp 9p24 1	63 (21%)	232	0.344 (0.492)	0.141 (0.269)	0.0153 (0.0526)	0.0121 (0.0448)	0.299 (0.45)	0.0327 (0.0915)	0.646 (0.755)	0.0694 (0.164)	0.118 (0.235)	0.182 (0.319)
amp 17q25 1	74 (25%)	221	0.001 (0.00692)	0.0179 (0.0593)	0.0964 (0.201)	0.0796 (0.181)	0.0119 (0.0444)	0.509 (0.648)	0.156 (0.291)	0.943 (0.965)	0.264 (0.409)	0.776 (0.847)
amp 19p13 3	39 (13%)	256	0.356 (0.505)	0.024 (0.0742)	0.094 (0.197)	0.588 (0.711)	0.179 (0.318)	0.00105 (0.00711)	0.516 (0.656)	0.0175 (0.0586)	0.44 (0.583)	0.157 (0.291)
del 4q21 3	103 (35%)	192	1e-05 (0.000233)	0.39 (0.536)	0.863 (0.904)	0.802 (0.869)	0.0114 (0.0427)	0.00527 (0.0244)	0.493 (0.63)	0.233 (0.378)	0.563 (0.694)	0.329 (0.479)
del 4q35 2	114 (39%)	181	1e-05 (0.000233)	0.208 (0.345)	1 (1.00)	0.998 (1.00)	0.0087 (0.0358)	0.00271 (0.0151)	0.383 (0.53)	0.125 (0.245)	0.416 (0.564)	0.0865 (0.19)
del 21q11 2	58 (20%)	237	0.00019 (0.0021)	0.202 (0.338)	0.414 (0.564)	0.00493 (0.0235)	0.0833 (0.187)	0.00922 (0.0372)	0.476 (0.612)	0.233 (0.378)	0.435 (0.578)	1 (1.00)
amp xq28	75 (25%)	220	0.625 (0.74)	0.575 (0.704)	0.834 (0.889)	0.908 (0.937)	0.753 (0.832)	0.559 (0.692)	0.00107 (0.00717)	0.165 (0.301)	0.0234 (0.0733)	0.0714 (0.167)
del 5q35 2	71 (24%)	224	0.00019 (0.0021)	0.961 (0.975)	0.374 (0.521)	0.546 (0.684)	0.846 (0.897)	0.84 (0.893)	0.0297 (0.0865)	0.555 (0.69)	0.486 (0.622)	0.126 (0.246)
del 6p24 2	46 (16%)	249	0.286 (0.435)	0.0875 (0.191)	0.35 (0.496)	0.184 (0.321)	0.118 (0.235)	0.0388 (0.104)	0.286 (0.435)	0.0265 (0.0791)	0.174 (0.311)	0.0902 (0.195)
del 6q26	100 (34%)	195	1e-05 (0.000233)	0.00166 (0.0103)	0.549 (0.686)	0.748 (0.828)	0.273 (0.42)	0.084 (0.187)	0.318 (0.47)	0.321 (0.471)	0.181 (0.319)	0.227 (0.371)
del 10q23 31	86 (29%)	209	0.00767 (0.0326)	0.509 (0.648)	0.224 (0.368)	0.763 (0.84)	0.0466 (0.12)	0.33 (0.48)	0.947 (0.967)	0.24 (0.385)	0.853 (0.899)	0.586 (0.71)
del 20p12 1	36 (12%)	259	0.581 (0.71)	0.026 (0.079)	0.633 (0.744)	0.122 (0.241)	0.00731 (0.0313)	0.126 (0.246)	0.0766 (0.176)	0.144 (0.273)	0.0911 (0.195)	0.363 (0.511)
del 22q13 32	88 (30%)	207	0.0048 (0.0231)	0.46 (0.599)	0.094 (0.197)	0.705 (0.8)	0.349 (0.496)	0.0294 (0.0863)	0.974 (0.985)	0.659 (0.765)	1 (1.00)	0.907 (0.937)
amp 4q12	21 (7%)	274	0.88 (0.917)	0.198 (0.336)	0.00698 (0.0301)	0.431 (0.577)	0.689 (0.792)	0.891 (0.922)	1 (1.00)	0.369 (0.518)	0.397 (0.543)	0.11 (0.224)
amp 13q22 1	65 (22%)	230	0.194 (0.332)	0.00697 (0.0301)	0.345 (0.492)	0.519 (0.658)	0.315 (0.467)	0.744 (0.825)	0.757 (0.835)	0.425 (0.57)	0.358 (0.506)	0.64 (0.75)
amp 13q34	69 (23%)	226	0.0343 (0.0944)	0.0979 (0.202)	0.42 (0.565)	0.586 (0.71)	0.607 (0.726)	0.616 (0.734)	0.765 (0.841)	0.771 (0.846)	0.583 (0.71)	0.468 (0.606)
amp 19q13 13	93 (32%)	202	1e-05 (0.000233)	0.208 (0.345)	0.956 (0.971)	0.253 (0.398)	0.386 (0.533)	0.436 (0.578)	0.657 (0.765)	0.273 (0.42)	0.881 (0.917)	0.848 (0.897)
del 2q22 1	65 (22%)	230	0.585 (0.71)	0.398 (0.544)	0.726 (0.814)	0.723 (0.814)	0.0143 (0.0509)	0.118 (0.235)	0.967 (0.979)	0.181 (0.319)	0.603 (0.723)	0.077 (0.176)
del 7q34	60 (20%)	235	0.00069 (0.0053)	0.274 (0.42)	0.342 (0.492)	0.461 (0.599)	0.829 (0.888)	0.695 (0.792)	0.691 (0.792)	0.469 (0.606)	0.739 (0.821)	0.599 (0.72)
del 17p12	109 (37%)	186	0.00056 (0.00452)	0.084 (0.187)	0.153 (0.286)	0.726 (0.814)	0.145 (0.274)	0.272 (0.42)	0.198 (0.336)	0.202 (0.338)	0.624 (0.74)	0.774 (0.846)
del 19q13 33	38 (13%)	257	0.63 (0.744)	0.047 (0.12)	0.29 (0.438)	0.593 (0.715)	0.145 (0.274)	0.182 (0.319)	0.0971 (0.201)	0.166 (0.301)	0.0728 (0.169)	0.159 (0.292)
del xq21 33	60 (20%)	235	0.128 (0.248)	0.0656 (0.158)	0.252 (0.397)	0.0111 (0.0425)	0.941 (0.964)	0.731 (0.816)	0.25 (0.395)	0.953 (0.97)	0.0865 (0.19)	0.703 (0.8)
amp 11p12	23 (8%)	272	0.528 (0.666)	0.255 (0.398)	0.728 (0.814)	0.862 (0.904)	0.365 (0.513)	0.301 (0.45)	0.454 (0.595)	0.0681 (0.163)	0.561 (0.693)	0.707 (0.801)
amp 15q26 1	76 (26%)	219	0.089 (0.193)	0.377 (0.524)	0.479 (0.615)	0.332 (0.48)	0.714 (0.806)	0.594 (0.715)	0.55 (0.686)	0.605 (0.725)	0.472 (0.608)	0.392 (0.538)
amp 16p13 13	65 (22%)	230	0.242 (0.388)	0.546 (0.684)	0.841 (0.893)	0.886 (0.918)	0.209 (0.346)	0.379 (0.525)	0.299 (0.45)	0.22 (0.363)	0.616 (0.734)	0.459 (0.599)
amp 19p13 2	43 (15%)	252	0.794 (0.864)	0.185 (0.322)	0.205 (0.342)	0.585 (0.71)	0.66 (0.765)	0.0806 (0.183)	0.693 (0.792)	0.0968 (0.201)	0.927 (0.953)	0.278 (0.426)
amp 21q22 13	48 (16%)	247	0.223 (0.367)	0.574 (0.704)	0.853 (0.899)	0.801 (0.869)	0.0629 (0.152)	0.444 (0.586)	0.882 (0.917)	0.834 (0.889)	0.804 (0.869)	0.469 (0.606)

'amp_1p31.3' versus 'CN_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.0053

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
AMP PEAK 1(1P31.3) MUTATED	28	26	42
AMP PEAK 1(1P31.3) WILD-TYPE	101	47	51

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 = 0.0304 (Fisher's exact test), Q value = 0.088

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
AMP PEAK 1(1P31.3) MUTATED	21	41	17	16
AMP PEAK 1(1P31.3) WILD-TYPE	33	59	52	53

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 = 0.00154 (Fisher's exact test), Q value = 0.0096

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 = 0.0012 (Fisher's exact test), Q value = 0.0077

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 = 0.00023

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
AMP PEAK 2(1Q21.3) MUTATED	49	42	67
AMP PEAK 2(1Q21.3) WILD-TYPE	80	31	26

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 = 0.0479 (Fisher's exact test), Q value = 0.12

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
AMP PEAK 2(1Q21.3) MUTATED	29	64	32	31
AMP PEAK 2(1Q21.3) WILD-TYPE	25	36	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 = 0.0107 (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 = 0.00098 (Fisher's exact test), Q value = 0.0069

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_1q44' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S9. Gene #3: 'amp_1q44' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
AMP PEAK 3(1Q44) MUTATED	46	41	65
AMP PEAK 3(1Q44) WILD-TYPE	83	32	28

Figure S9. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q44' versus 'MRNASEQ_CNMF'

P value = 0.00831 (Fisher's exact test), Q value = 0.034

Table S10. Gene #3: 'amp_1q44' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
AMP PEAK 3(1Q44) MUTATED	30	63	30	27
AMP PEAK 3(1Q44) WILD-TYPE	24	37	39	42

Figure S10. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q44' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00638 (Fisher's exact test), Q value = 0.028

Table S11. Gene #3: 'amp_1q44' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
AMP PEAK 3(1Q44) MUTATED	27	108	15
AMP PEAK 3(1Q44) WILD-TYPE	45	77	20

Figure S11. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1q44' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00145 (Fisher's exact test), Q value = 0.0091

Table S12. Gene #3: 'amp_1q44' 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(1Q44) MUTATED	21	58	43	15	15
AMP PEAK 3(1Q44) WILD-TYPE	39	37	29	10	28

Figure S12. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1q44' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0208 (Fisher's exact test), Q value = 0.067

Table S13. Gene #3: 'amp_1q44' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	50	26	142
AMP PEAK 3(1Q44) MUTATED	24	30	18	72
AMP PEAK 3(1Q44) WILD-TYPE	40	20	8	70

Figure S13. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_2p24.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00036

Table S14. Gene #4: 'amp_2p24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
AMP PEAK 4(2P24.3) MUTATED	21	35	23
AMP PEAK 4(2P24.3) WILD-TYPE	108	38	70

Figure S14. Get High-res Image Gene #4: 'amp_2p24.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2p24.3' versus 'METHLYATION_CNMF'

P value = 0.00646 (Fisher's exact test), Q value = 0.028

Table S15. Gene #4: 'amp_2p24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	54	57	59	9	45
AMP PEAK 4(2P24.3) MUTATED	26	14	6	21	3	9
AMP PEAK 4(2P24.3) WILD-TYPE	45	40	51	38	6	36

Figure S15. Get High-res Image Gene #4: 'amp_2p24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_2p24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0436 (Fisher's exact test), Q value = 0.12

Table S16. Gene #4: 'amp_2p24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
AMP PEAK 4(2P24.3) MUTATED	25	41	13
AMP PEAK 4(2P24.3) WILD-TYPE	47	144	22

Figure S16. Get High-res Image Gene #4: 'amp_2p24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_2p24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 6e-04

Table S17. Gene #4: '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 4(2P24.3) MUTATED	21	26	6	13	13
AMP PEAK 4(2P24.3) WILD-TYPE	39	69	66	12	30

Figure S17. Get High-res Image Gene #4: 'amp_2p24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_2q33.1' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00082

Table S18. Gene #5: 'amp_2q33.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
AMP PEAK 5(2Q33.1) MUTATED	7	21	13
AMP PEAK 5(2Q33.1) WILD-TYPE	122	52	80

Figure S18. Get High-res Image Gene #5: 'amp_2q33.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2q33.1' versus 'METHLYATION_CNMF'

P value = 0.0451 (Fisher's exact test), Q value = 0.12

Table S19. Gene #5: 'amp_2q33.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	54	57	59	9	45
AMP PEAK 5(2Q33.1) MUTATED	14	4	3	13	1	6
AMP PEAK 5(2Q33.1) WILD-TYPE	57	50	54	46	8	39

Figure S19. Get High-res Image Gene #5: 'amp_2q33.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_2q33.1' versus 'MRNASEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0021

Table S20. Gene #5: 'amp_2q33.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
AMP PEAK 5(2Q33.1) MUTATED	12	3	10	15
AMP PEAK 5(2Q33.1) WILD-TYPE	42	97	59	54

Figure S20. Get High-res Image Gene #5: 'amp_2q33.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_2q33.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00695 (Fisher's exact test), Q value = 0.03

Table S21. Gene #5: '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 5(2Q33.1) MUTATED	12	10	4	3	12
AMP PEAK 5(2Q33.1) WILD-TYPE	48	85	68	22	31

Figure S21. Get High-res Image Gene #5: '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 = 0.00023

Table S22. Gene #6: 'amp_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
AMP PEAK 6(3Q26.31) MUTATED	77	57	93
AMP PEAK 6(3Q26.31) WILD-TYPE	52	16	0

Figure S22. Get High-res Image Gene #6: 'amp_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.31' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00082

Table S23. Gene #6: 'amp_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	54	57	59	9	45
AMP PEAK 6(3Q26.31) MUTATED	45	46	45	39	8	44
AMP PEAK 6(3Q26.31) WILD-TYPE	26	8	12	20	1	1

Figure S23. Get High-res Image Gene #6: 'amp_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q26.31' versus 'MRNASEQ_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0037

Table S24. Gene #6: 'amp_3q26.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
AMP PEAK 6(3Q26.31) MUTATED	45	88	46	45
AMP PEAK 6(3Q26.31) WILD-TYPE	9	12	23	24

Figure S24. Get High-res Image Gene #6: '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 = 0.00023

Table S25. Gene #6: 'amp_3q26.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
AMP PEAK 6(3Q26.31) MUTATED	43	160	21
AMP PEAK 6(3Q26.31) WILD-TYPE	29	25	14

Figure S25. Get High-res Image Gene #6: 'amp_3q26.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S26. Gene #6: '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 6(3Q26.31) MUTATED	34	81	65	20	27
AMP PEAK 6(3Q26.31) WILD-TYPE	26	14	7	5	16

Figure S26. Get High-res Image Gene #6: 'amp_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.0031

Table S27. Gene #6: 'amp_3q26.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	50	26	142
AMP PEAK 6(3Q26.31) MUTATED	38	45	24	109
AMP PEAK 6(3Q26.31) WILD-TYPE	26	5	2	33

Figure S27. Get High-res Image Gene #6: 'amp_3q26.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q28' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S28. Gene #7: 'amp_3q28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
AMP PEAK 7(3Q28) MUTATED	77	54	93
AMP PEAK 7(3Q28) WILD-TYPE	52	19	0

Figure S28. Get High-res Image Gene #7: 'amp_3q28' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q28' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S29. Gene #7: 'amp_3q28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	54	57	59	9	45
AMP PEAK 7(3Q28) MUTATED	43	45	44	39	9	44
AMP PEAK 7(3Q28) WILD-TYPE	28	9	13	20	0	1

Figure S29. Get High-res Image Gene #7: 'amp_3q28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q28' versus 'MRNASEQ_CNMF'

P value = 0.00184 (Fisher's exact test), Q value = 0.011

Table S30. Gene #7: 'amp_3q28' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
AMP PEAK 7(3Q28) MUTATED	43	87	45	46
AMP PEAK 7(3Q28) WILD-TYPE	11	13	24	23

Figure S30. Get High-res Image Gene #7: 'amp_3q28' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3q28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S31. Gene #7: 'amp_3q28' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
AMP PEAK 7(3Q28) MUTATED	41	158	22
AMP PEAK 7(3Q28) WILD-TYPE	31	27	13

Figure S31. Get High-res Image Gene #7: 'amp_3q28' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3q28' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00036

Table S32. Gene #7: 'amp_3q28' 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(3Q28) MUTATED	33	80	65	19	27
AMP PEAK 7(3Q28) WILD-TYPE	27	15	7	6	16

Figure S32. Get High-res Image Gene #7: 'amp_3q28' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3q28' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0342 (Fisher's exact test), Q value = 0.094

Table S33. Gene #7: 'amp_3q28' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	77	80
AMP PEAK 7(3Q28) MUTATED	85	62	66
AMP PEAK 7(3Q28) WILD-TYPE	40	15	14

Figure S33. Get High-res Image Gene #7: 'amp_3q28' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_3q28' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.0021

Table S34. Gene #7: 'amp_3q28' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	50	26	142
AMP PEAK 7(3Q28) MUTATED	36	44	24	109
AMP PEAK 7(3Q28) WILD-TYPE	28	6	2	33

Figure S34. Get High-res Image Gene #7: 'amp_3q28' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q12' versus 'RPPA_CNMF'

P value = 0.00698 (Fisher's exact test), Q value = 0.03

Table S35. Gene #8: 'amp_4q12' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	42	69
AMP PEAK 8(4Q12) MUTATED	3	0	11
AMP PEAK 8(4Q12) WILD-TYPE	50	42	58

Figure S35. Get High-res Image Gene #8: 'amp_4q12' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S36. Gene #9: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
AMP PEAK 9(5P15.33) MUTATED	34	60	44
AMP PEAK 9(5P15.33) WILD-TYPE	95	13	49

Figure S36. Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 0.0053 (Fisher's exact test), Q value = 0.024

Table S37. Gene #9: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	54	57	59	9	45
AMP PEAK 9(5P15.33) MUTATED	24	27	27	39	5	16
AMP PEAK 9(5P15.33) WILD-TYPE	47	27	30	20	4	29

Figure S37. Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 0.00391 (Fisher's exact test), Q value = 0.02

Table S38. Gene #9: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
AMP PEAK 9(5P15.33) MUTATED	21	49	23	43
AMP PEAK 9(5P15.33) WILD-TYPE	33	51	46	26

Figure S38. Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00538 (Fisher's exact test), Q value = 0.024

Table S39. Gene #9: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
AMP PEAK 9(5P15.33) MUTATED	24	89	23
AMP PEAK 9(5P15.33) WILD-TYPE	48	96	12

Figure S39. Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 0.00528 (Fisher's exact test), Q value = 0.024

Table S40. Gene #9: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	77	119
AMP PEAK 9(5P15.33) MUTATED	41	28	69
AMP PEAK 9(5P15.33) WILD-TYPE	58	49	50

Figure S40. Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S41. Gene #9: '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 9(5P15.33) MUTATED	17	50	28	16	27
AMP PEAK 9(5P15.33) WILD-TYPE	43	45	44	9	16

Figure S41. Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0153 (Fisher's exact test), Q value = 0.053

Table S42. Gene #9: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	50	26	142
AMP PEAK 9(5P15.33) MUTATED	21	23	9	78
AMP PEAK 9(5P15.33) WILD-TYPE	43	27	17	64

Figure S42. Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6p21.33' versus 'CN_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0027

Table S43. Gene #10: 'amp_6p21.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
AMP PEAK 10(6P21.33) MUTATED	26	34	22
AMP PEAK 10(6P21.33) WILD-TYPE	103	39	71

Figure S43. Get High-res Image Gene #10: 'amp_6p21.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p21.33' versus 'MRNASEQ_CNMF'

P value = 0.0219 (Fisher's exact test), Q value = 0.07

Table S44. Gene #10: 'amp_6p21.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
AMP PEAK 10(6P21.33) MUTATED	16	18	21	27
AMP PEAK 10(6P21.33) WILD-TYPE	38	82	48	42

Figure S44. Get High-res Image Gene #10: 'amp_6p21.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6p21.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0145 (Fisher's exact test), Q value = 0.051

Table S45. Gene #10: '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 10(6P21.33) MUTATED	17	21	15	8	21
AMP PEAK 10(6P21.33) WILD-TYPE	43	74	57	17	22

Figure S45. Get High-res Image Gene #10: 'amp_6p21.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0018

Table S46. Gene #11: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
AMP PEAK 11(7P11.2) MUTATED	13	25	14
AMP PEAK 11(7P11.2) WILD-TYPE	116	48	79

Figure S46. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

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

Table S47. Gene #11: 'amp_7p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	54	57	59	9	45
AMP PEAK 11(7P11.2) MUTATED	5	14	11	18	2	2
AMP PEAK 11(7P11.2) WILD-TYPE	66	40	46	41	7	43

Figure S47. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00815 (Fisher's exact test), Q value = 0.034

Table S48. Gene #11: '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 11(7P11.2) MUTATED	5	4	7	10	1
AMP PEAK 11(7P11.2) WILD-TYPE	27	43	38	13	16

Figure S48. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.053

Table S49. Gene #11: 'amp_7p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
AMP PEAK 11(7P11.2) MUTATED	7	17	7	21
AMP PEAK 11(7P11.2) WILD-TYPE	47	83	62	48

Figure S49. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0022

Table S50. Gene #11: 'amp_7p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	77	119
AMP PEAK 11(7P11.2) MUTATED	12	6	34
AMP PEAK 11(7P11.2) WILD-TYPE	87	71	85

Figure S50. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CNMF'

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

Table S51. Gene #11: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	77	80
AMP PEAK 11(7P11.2) MUTATED	22	7	20
AMP PEAK 11(7P11.2) WILD-TYPE	103	70	60

Figure S51. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0158 (Fisher's exact test), Q value = 0.054

Table S52. Gene #11: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	50	26	142
AMP PEAK 11(7P11.2) MUTATED	6	4	5	34
AMP PEAK 11(7P11.2) WILD-TYPE	58	46	21	108

Figure S52. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0393 (Fisher's exact test), Q value = 0.1

Table S53. Gene #12: 'amp_8q24.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
AMP PEAK 12(8Q24.21) MUTATED	23	90	13
AMP PEAK 12(8Q24.21) WILD-TYPE	49	95	22

Figure S53. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0195 (Fisher's exact test), Q value = 0.064

Table S54. Gene #12: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	77	80
AMP PEAK 12(8Q24.21) MUTATED	61	23	38
AMP PEAK 12(8Q24.21) WILD-TYPE	64	54	42

Figure S54. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00084 (Fisher's exact test), Q value = 0.0061

Table S55. Gene #12: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	50	26	142
AMP PEAK 12(8Q24.21) MUTATED	17	16	15	74
AMP PEAK 12(8Q24.21) WILD-TYPE	47	34	11	68

Figure S55. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9p24.1' versus 'RPPA_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.053

Table S56. Gene #13: 'amp_9p24.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	42	69
AMP PEAK 13(9P24.1) MUTATED	5	9	21
AMP PEAK 13(9P24.1) WILD-TYPE	48	33	48

Figure S56. Get High-res Image Gene #13: 'amp_9p24.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_9p24.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0121 (Fisher's exact test), Q value = 0.045

Table S57. Gene #13: '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 13(9P24.1) MUTATED	3	12	15	5	0
AMP PEAK 13(9P24.1) WILD-TYPE	29	35	30	18	17

Figure S57. Get High-res Image Gene #13: 'amp_9p24.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_9p24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0327 (Fisher's exact test), Q value = 0.092

Table S58. Gene #13: 'amp_9p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
AMP PEAK 13(9P24.1) MUTATED	9	42	12
AMP PEAK 13(9P24.1) WILD-TYPE	63	143	23

Figure S58. Get High-res Image Gene #13: 'amp_9p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0033

Table S59. Gene #15: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
AMP PEAK 15(11Q13.3) MUTATED	11	21	9
AMP PEAK 15(11Q13.3) WILD-TYPE	118	52	84

Figure S59. Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

P value = 0.024 (Fisher's exact test), Q value = 0.074

Table S60. Gene #15: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	54	57	59	9	45
AMP PEAK 15(11Q13.3) MUTATED	7	11	4	15	0	4
AMP PEAK 15(11Q13.3) WILD-TYPE	64	43	53	44	9	41

Figure S60. Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0313 (Fisher's exact test), Q value = 0.089

Table S61. Gene #15: '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 15(11Q13.3) MUTATED	6	5	6	8	0
AMP PEAK 15(11Q13.3) WILD-TYPE	26	42	39	15	17

Figure S61. Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.049

Table S62. Gene #15: 'amp_11q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
AMP PEAK 15(11Q13.3) MUTATED	6	10	6	18
AMP PEAK 15(11Q13.3) WILD-TYPE	48	90	63	51

Figure S62. Get High-res Image Gene #15: '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 = 0.00092

Table S63. Gene #15: 'amp_11q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
AMP PEAK 15(11Q13.3) MUTATED	6	20	14
AMP PEAK 15(11Q13.3) WILD-TYPE	66	165	21

Figure S63. Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.056

Table S64. Gene #15: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	77	119
AMP PEAK 15(11Q13.3) MUTATED	10	6	25
AMP PEAK 15(11Q13.3) WILD-TYPE	89	71	94

Figure S64. Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00036

Table S65. Gene #15: '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 15(11Q13.3) MUTATED	3	10	5	6	17
AMP PEAK 15(11Q13.3) WILD-TYPE	57	85	67	19	26

Figure S65. Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11q22.1' versus 'CN_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0031

Table S66. Gene #16: 'amp_11q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
AMP PEAK 16(11Q22.1) MUTATED	15	23	9
AMP PEAK 16(11Q22.1) WILD-TYPE	114	50	84

Figure S66. Get High-res Image Gene #16: 'amp_11q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q22.1' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00072

Table S67. Gene #16: 'amp_11q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	54	57	59	9	45
AMP PEAK 16(11Q22.1) MUTATED	5	5	9	23	1	4
AMP PEAK 16(11Q22.1) WILD-TYPE	66	49	48	36	8	41

Figure S67. Get High-res Image Gene #16: 'amp_11q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11q22.1' versus 'RPPA_CNMF'

P value = 0.00896 (Fisher's exact test), Q value = 0.037

Table S68. Gene #16: 'amp_11q22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	42	69
AMP PEAK 16(11Q22.1) MUTATED	17	4	9
AMP PEAK 16(11Q22.1) WILD-TYPE	36	38	60

Figure S68. Get High-res Image Gene #16: '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 = 0.00023

Table S69. Gene #16: '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 16(11Q22.1) MUTATED	9	5	3	13	0
AMP PEAK 16(11Q22.1) WILD-TYPE	23	42	42	10	17

Figure S69. Get High-res Image Gene #16: '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 = 0.00036

Table S70. Gene #16: 'amp_11q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
AMP PEAK 16(11Q22.1) MUTATED	4	9	7	26
AMP PEAK 16(11Q22.1) WILD-TYPE	50	91	62	43

Figure S70. Get High-res Image Gene #16: '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 = 0.00023

Table S71. Gene #16: 'amp_11q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
AMP PEAK 16(11Q22.1) MUTATED	4	22	20
AMP PEAK 16(11Q22.1) WILD-TYPE	68	163	15

Figure S71. Get High-res Image Gene #16: 'amp_11q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11q22.1' versus 'MIRSEQ_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0053

Table S72. Gene #16: 'amp_11q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	77	119
AMP PEAK 16(11Q22.1) MUTATED	8	8	31
AMP PEAK 16(11Q22.1) WILD-TYPE	91	69	88

Figure S72. Get High-res Image Gene #16: '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 = 0.00023

Table S73. Gene #16: '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 16(11Q22.1) MUTATED	2	8	11	3	23
AMP PEAK 16(11Q22.1) WILD-TYPE	58	87	61	22	20

Figure S73. Get High-res Image Gene #16: 'amp_11q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0031 (Fisher's exact test), Q value = 0.017

Table S74. Gene #16: 'amp_11q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	50	26	142
AMP PEAK 16(11Q22.1) MUTATED	3	5	7	30
AMP PEAK 16(11Q22.1) WILD-TYPE	61	45	19	112

Figure S74. Get High-res Image Gene #16: 'amp_11q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q22.1' versus 'METHLYATION_CNMF'

P value = 0.00697 (Fisher's exact test), Q value = 0.03

Table S75. Gene #17: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	54	57	59	9	45
AMP PEAK 17(13Q22.1) MUTATED	14	18	10	19	1	3
AMP PEAK 17(13Q22.1) WILD-TYPE	57	36	47	40	8	42

Figure S75. Get High-res Image Gene #17: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q34' versus 'CN_CNMF'

P value = 0.0343 (Fisher's exact test), Q value = 0.094

Table S76. Gene #18: 'amp_13q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
AMP PEAK 18(13Q34) MUTATED	23	25	21
AMP PEAK 18(13Q34) WILD-TYPE	106	48	72

Figure S76. Get High-res Image Gene #18: 'amp_13q34' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q12' versus 'CN_CNMF'

P value = 0.00529 (Fisher's exact test), Q value = 0.024

Table S77. Gene #21: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
AMP PEAK 21(17Q12) MUTATED	15	22	18
AMP PEAK 21(17Q12) WILD-TYPE	114	51	75

Figure S77. Get High-res Image Gene #21: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 0.00357 (Fisher's exact test), Q value = 0.019

Table S78. Gene #21: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	54	57	59	9	45
AMP PEAK 21(17Q12) MUTATED	22	8	9	4	4	8
AMP PEAK 21(17Q12) WILD-TYPE	49	46	48	55	5	37

Figure S78. Get High-res Image Gene #21: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.0377 (Fisher's exact test), Q value = 0.1

Table S79. Gene #21: '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 21(17Q12) MUTATED	2	11	12	2	6
AMP PEAK 21(17Q12) WILD-TYPE	30	36	33	21	11

Figure S79. Get High-res Image Gene #21: 'amp_17q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 0.00372 (Fisher's exact test), Q value = 0.019

Table S80. Gene #21: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
AMP PEAK 21(17Q12) MUTATED	10	13	23	8
AMP PEAK 21(17Q12) WILD-TYPE	44	87	46	61

Figure S80. Get High-res Image Gene #21: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00355 (Fisher's exact test), Q value = 0.019

Table S81. Gene #21: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
AMP PEAK 21(17Q12) MUTATED	23	28	3
AMP PEAK 21(17Q12) WILD-TYPE	49	157	32

Figure S81. Get High-res Image Gene #21: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.087

Table S82. Gene #21: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	77	119
AMP PEAK 21(17Q12) MUTATED	25	16	14
AMP PEAK 21(17Q12) WILD-TYPE	74	61	105

Figure S82. Get High-res Image Gene #21: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0326 (Fisher's exact test), Q value = 0.092

Table S83. Gene #21: '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 21(17Q12) MUTATED	20	17	9	3	6
AMP PEAK 21(17Q12) WILD-TYPE	40	78	63	22	37

Figure S83. Get High-res Image Gene #21: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.019 (Fisher's exact test), Q value = 0.062

Table S84. Gene #21: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	77	80
AMP PEAK 21(17Q12) MUTATED	32	14	8
AMP PEAK 21(17Q12) WILD-TYPE	93	63	72

Figure S84. Get High-res Image Gene #21: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.044 (Fisher's exact test), Q value = 0.12

Table S85. Gene #21: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	50	26	142
AMP PEAK 21(17Q12) MUTATED	20	9	5	20
AMP PEAK 21(17Q12) WILD-TYPE	44	41	21	122

Figure S85. Get High-res Image Gene #21: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q25.1' versus 'CN_CNMF'

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

Table S86. Gene #22: 'amp_17q25.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
AMP PEAK 22(17Q25.1) MUTATED	19	26	29
AMP PEAK 22(17Q25.1) WILD-TYPE	110	47	64

Figure S86. Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q25.1' versus 'METHLYATION_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.059

Table S87. Gene #22: 'amp_17q25.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	54	57	59	9	45
AMP PEAK 22(17Q25.1) MUTATED	22	13	8	12	6	13
AMP PEAK 22(17Q25.1) WILD-TYPE	49	41	49	47	3	32

Figure S87. Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q25.1' versus 'MRNASEQ_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.044

Table S88. Gene #22: 'amp_17q25.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
AMP PEAK 22(17Q25.1) MUTATED	21	16	20	15
AMP PEAK 22(17Q25.1) WILD-TYPE	33	84	49	54

Figure S88. Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19p13.3' versus 'METHLYATION_CNMF'

P value = 0.024 (Fisher's exact test), Q value = 0.074

Table S89. Gene #23: 'amp_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	54	57	59	9	45
AMP PEAK 23(19P13.3) MUTATED	5	10	9	3	1	11
AMP PEAK 23(19P13.3) WILD-TYPE	66	44	48	56	8	34

Figure S89. Get High-res Image Gene #23: 'amp_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00105 (Fisher's exact test), Q value = 0.0071

Table S90. Gene #23: 'amp_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
AMP PEAK 23(19P13.3) MUTATED	5	34	0
AMP PEAK 23(19P13.3) WILD-TYPE	67	151	35

Figure S90. Get High-res Image Gene #23: 'amp_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0175 (Fisher's exact test), Q value = 0.059

Table S91. Gene #23: '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 23(19P13.3) MUTATED	5	12	18	1	3
AMP PEAK 23(19P13.3) WILD-TYPE	55	83	54	24	40

Figure S91. Get High-res Image Gene #23: 'amp_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_19q13.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S92. Gene #25: 'amp_19q13.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
AMP PEAK 25(19Q13.13) MUTATED	21	46	26
AMP PEAK 25(19Q13.13) WILD-TYPE	108	27	67

Figure S92. Get High-res Image Gene #25: 'amp_19q13.13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q11.21' versus 'CN_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0033

Table S93. Gene #26: 'amp_20q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
AMP PEAK 26(20Q11.21) MUTATED	43	44	48
AMP PEAK 26(20Q11.21) WILD-TYPE	86	29	45

Figure S93. Get High-res Image Gene #26: 'amp_20q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q11.21' versus 'METHLYATION_CNMF'

P value = 0.0259 (Fisher's exact test), Q value = 0.079

Table S94. Gene #26: 'amp_20q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	54	57	59	9	45
AMP PEAK 26(20Q11.21) MUTATED	40	30	20	19	5	21
AMP PEAK 26(20Q11.21) WILD-TYPE	31	24	37	40	4	24

Figure S94. Get High-res Image Gene #26: 'amp_20q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.00375 (Fisher's exact test), Q value = 0.019

Table S95. Gene #26: '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 26(20Q11.21) MUTATED	13	17	22	9	15
AMP PEAK 26(20Q11.21) WILD-TYPE	19	30	23	14	2

Figure S95. Get High-res Image Gene #26: 'amp_20q11.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0364 (Fisher's exact test), Q value = 0.099

Table S96. Gene #26: 'amp_20q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
AMP PEAK 26(20Q11.21) MUTATED	42	81	12
AMP PEAK 26(20Q11.21) WILD-TYPE	30	104	23

Figure S96. Get High-res Image Gene #26: 'amp_20q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0354 (Fisher's exact test), Q value = 0.097

Table S97. Gene #26: '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 26(20Q11.21) MUTATED	35	37	31	16	16
AMP PEAK 26(20Q11.21) WILD-TYPE	25	58	41	9	27

Figure S97. Get High-res Image Gene #26: 'amp_20q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_CNMF'

P value = 0.00107 (Fisher's exact test), Q value = 0.0072

Table S98. Gene #28: 'amp_xq28' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	77	119
AMP PEAK 28(XQ28) MUTATED	29	8	38
AMP PEAK 28(XQ28) WILD-TYPE	70	69	81

Figure S98. Get High-res Image Gene #28: 'amp_xq28' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_xq28' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0234 (Fisher's exact test), Q value = 0.073

Table S99. Gene #28: 'amp_xq28' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	77	80
AMP PEAK 28(XQ28) MUTATED	33	11	26
AMP PEAK 28(XQ28) WILD-TYPE	92	66	54

Figure S99. Get High-res Image Gene #28: 'amp_xq28' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p36.23' versus 'CN_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.0053

Table S100. Gene #29: 'del_1p36.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 1(1P36.23) MUTATED	10	20	10
DEL PEAK 1(1P36.23) WILD-TYPE	119	53	83

Figure S100. Get High-res Image Gene #29: 'del_1p36.23' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.23' versus 'METHLYATION_CNMF'

P value = 0.00477 (Fisher's exact test), Q value = 0.023

Table S101. Gene #29: 'del_1p36.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	54	57	59	9	45
DEL PEAK 1(1P36.23) MUTATED	17	5	2	12	1	3
DEL PEAK 1(1P36.23) WILD-TYPE	54	49	55	47	8	42

Figure S101. Get High-res Image Gene #29: 'del_1p36.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.23' versus 'MRNASEQ_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0037

Table S102. Gene #29: 'del_1p36.23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
DEL PEAK 1(1P36.23) MUTATED	10	3	14	13
DEL PEAK 1(1P36.23) WILD-TYPE	44	97	55	56

Figure S102. Get High-res Image Gene #29: '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 = 0.00036

Table S103. Gene #29: '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 S103. Get High-res Image Gene #29: 'del_1p36.23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.0022

Table S104. Gene #29: '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 S104. Get High-res Image Gene #29: 'del_1p36.23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0237 (Fisher's exact test), Q value = 0.074

Table S105. Gene #29: 'del_1p36.23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	50	26	142
DEL PEAK 1(1P36.23) MUTATED	16	3	2	18
DEL PEAK 1(1P36.23) WILD-TYPE	48	47	24	124

Figure S105. Get High-res Image Gene #29: 'del_1p36.23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p13.2' versus 'METHLYATION_CNMF'

P value = 0.00451 (Fisher's exact test), Q value = 0.022

Table S106. Gene #30: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	54	57	59	9	45
DEL PEAK 2(1P13.2) MUTATED	4	5	3	16	1	5
DEL PEAK 2(1P13.2) WILD-TYPE	67	49	54	43	8	40

Figure S106. Get High-res Image Gene #30: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p13.2' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00047

Table S107. Gene #30: 'del_1p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
DEL PEAK 2(1P13.2) MUTATED	7	5	3	19
DEL PEAK 2(1P13.2) WILD-TYPE	47	95	66	50

Figure S107. Get High-res Image Gene #30: 'del_1p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p13.2' versus 'MIRSEQ_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.041

Table S108. Gene #30: 'del_1p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	77	119
DEL PEAK 2(1P13.2) MUTATED	6	6	22
DEL PEAK 2(1P13.2) WILD-TYPE	93	71	97

Figure S108. Get High-res Image Gene #30: 'del_1p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0262 (Fisher's exact test), Q value = 0.079

Table S109. Gene #30: 'del_1p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	50	26	142
DEL PEAK 2(1P13.2) MUTATED	3	5	1	25
DEL PEAK 2(1P13.2) WILD-TYPE	61	45	25	117

Figure S109. Get High-res Image Gene #30: 'del_1p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 0.0143 (Fisher's exact test), Q value = 0.051

Table S110. Gene #31: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
DEL PEAK 3(2Q22.1) MUTATED	7	29	9	20
DEL PEAK 3(2Q22.1) WILD-TYPE	47	71	60	49

Figure S110. Get High-res Image Gene #31: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q37.1' versus 'CN_CNMF'

P value = 0.00392 (Fisher's exact test), Q value = 0.02

Table S111. Gene #32: 'del_2q37.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 4(2Q37.1) MUTATED	47	44	38
DEL PEAK 4(2Q37.1) WILD-TYPE	82	29	55

Figure S111. Get High-res Image Gene #32: 'del_2q37.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.1' versus 'METHLYATION_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0038

Table S112. Gene #32: 'del_2q37.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	54	57	59	9	45
DEL PEAK 4(2Q37.1) MUTATED	16	26	27	36	3	21
DEL PEAK 4(2Q37.1) WILD-TYPE	55	28	30	23	6	24

Figure S112. Get High-res Image Gene #32: '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 = 0.00047

Table S113. Gene #32: 'del_2q37.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
DEL PEAK 4(2Q37.1) MUTATED	13	52	21	42
DEL PEAK 4(2Q37.1) WILD-TYPE	41	48	48	27

Figure S113. Get High-res Image Gene #32: '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 = 0.00023

Table S114. Gene #32: '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 S114. Get High-res Image Gene #32: 'del_2q37.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.1' versus 'MIRSEQ_CNMF'

P value = 0.0151 (Fisher's exact test), Q value = 0.053

Table S115. Gene #32: 'del_2q37.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	77	119
DEL PEAK 4(2Q37.1) MUTATED	35	30	64
DEL PEAK 4(2Q37.1) WILD-TYPE	64	47	55

Figure S115. Get High-res Image Gene #32: '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 = 0.0079

Table S116. Gene #32: '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 S116. Get High-res Image Gene #32: 'del_2q37.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S117. Gene #32: 'del_2q37.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	50	26	142
DEL PEAK 4(2Q37.1) MUTATED	13	20	9	81
DEL PEAK 4(2Q37.1) WILD-TYPE	51	30	17	61

Figure S117. Get High-res Image Gene #32: 'del_2q37.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S118. Gene #33: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 5(3P14.2) MUTATED	40	47	47
DEL PEAK 5(3P14.2) WILD-TYPE	89	26	46

Figure S118. Get High-res Image Gene #33: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00036

Table S119. Gene #33: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	54	57	59	9	45
DEL PEAK 5(3P14.2) MUTATED	18	32	19	35	7	23
DEL PEAK 5(3P14.2) WILD-TYPE	53	22	38	24	2	22

Figure S119. Get High-res Image Gene #33: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p14.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0471 (Fisher's exact test), Q value = 0.12

Table S120. Gene #33: '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 5(3P14.2) MUTATED	11	12	24	12	8
DEL PEAK 5(3P14.2) WILD-TYPE	21	35	21	11	9

Figure S120. Get High-res Image Gene #33: 'del_3p14.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_3p14.2' versus 'MRNASEQ_CNMF'

P value = 0.002 (Fisher's exact test), Q value = 0.012

Table S121. Gene #33: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
DEL PEAK 5(3P14.2) MUTATED	30	47	18	37
DEL PEAK 5(3P14.2) WILD-TYPE	24	53	51	32

Figure S121. Get High-res Image Gene #33: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00072

Table S122. Gene #33: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 5(3P14.2) MUTATED	17	102	13
DEL PEAK 5(3P14.2) WILD-TYPE	55	83	22

Figure S122. Get High-res Image Gene #33: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_CNMF'

P value = 0.00982 (Fisher's exact test), Q value = 0.039

Table S123. Gene #33: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	77	119
DEL PEAK 5(3P14.2) MUTATED	33	37	64
DEL PEAK 5(3P14.2) WILD-TYPE	66	40	55

Figure S123. Get High-res Image Gene #33: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.0044

Table S124. Gene #33: '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 5(3P14.2) MUTATED	13	54	34	13	20
DEL PEAK 5(3P14.2) WILD-TYPE	47	41	38	12	23

Figure S124. Get High-res Image Gene #33: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00223 (Fisher's exact test), Q value = 0.013

Table S125. Gene #33: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	77	80
DEL PEAK 5(3P14.2) MUTATED	44	35	48
DEL PEAK 5(3P14.2) WILD-TYPE	81	42	32

Figure S125. Get High-res Image Gene #33: '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 = 0.0017

Table S126. Gene #33: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	50	26	142
DEL PEAK 5(3P14.2) MUTATED	14	30	14	69
DEL PEAK 5(3P14.2) WILD-TYPE	50	20	12	73

Figure S126. Get High-res Image Gene #33: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S127. Gene #34: 'del_4q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 6(4Q21.3) MUTATED	21	48	34
DEL PEAK 6(4Q21.3) WILD-TYPE	108	25	59

Figure S127. Get High-res Image Gene #34: 'del_4q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q21.3' versus 'MRNASEQ_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.043

Table S128. Gene #34: 'del_4q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
DEL PEAK 6(4Q21.3) MUTATED	22	30	17	34
DEL PEAK 6(4Q21.3) WILD-TYPE	32	70	52	35

Figure S128. Get High-res Image Gene #34: 'del_4q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00527 (Fisher's exact test), Q value = 0.024

Table S129. Gene #34: 'del_4q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 6(4Q21.3) MUTATED	21	61	21
DEL PEAK 6(4Q21.3) WILD-TYPE	51	124	14

Figure S129. 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 = 0.00023

Table S130. Gene #35: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 7(4Q22.1) MUTATED	17	51	32
DEL PEAK 7(4Q22.1) WILD-TYPE	112	22	61

Figure S130. Get High-res Image Gene #35: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 0.0229 (Fisher's exact test), Q value = 0.072

Table S131. Gene #35: 'del_4q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
DEL PEAK 7(4Q22.1) MUTATED	22	29	17	32
DEL PEAK 7(4Q22.1) WILD-TYPE	32	71	52	37

Figure S131. Get High-res Image Gene #35: 'del_4q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.043

Table S132. Gene #35: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 7(4Q22.1) MUTATED	21	59	20
DEL PEAK 7(4Q22.1) WILD-TYPE	51	126	15

Figure S132. Get High-res Image Gene #35: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0444 (Fisher's exact test), Q value = 0.12

Table S133. 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 7(4Q22.1) MUTATED	16	33	22	6	23
DEL PEAK 7(4Q22.1) WILD-TYPE	44	62	50	19	20

Figure S133. 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 = 0.00023

Table S134. Gene #36: 'del_4q35.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 8(4Q35.2) MUTATED	25	52	37
DEL PEAK 8(4Q35.2) WILD-TYPE	104	21	56

Figure S134. Get High-res Image Gene #36: 'del_4q35.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q35.2' versus 'MRNASEQ_CNMF'

P value = 0.0087 (Fisher's exact test), Q value = 0.036

Table S135. Gene #36: 'del_4q35.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
DEL PEAK 8(4Q35.2) MUTATED	26	31	21	36
DEL PEAK 8(4Q35.2) WILD-TYPE	28	69	48	33

Figure S135. Get High-res Image Gene #36: 'del_4q35.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q35.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00271 (Fisher's exact test), Q value = 0.015

Table S136. Gene #36: 'del_4q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 8(4Q35.2) MUTATED	24	67	23
DEL PEAK 8(4Q35.2) WILD-TYPE	48	118	12

Figure S136. Get High-res Image Gene #36: 'del_4q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00047

Table S137. Gene #37: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 9(5Q12.1) MUTATED	19	33	24
DEL PEAK 9(5Q12.1) WILD-TYPE	110	40	69

Figure S137. Get High-res Image Gene #37: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q12.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0293 (Fisher's exact test), Q value = 0.086

Table S138. 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 9(5Q12.1) MUTATED	12	6	12	10	6
DEL PEAK 9(5Q12.1) WILD-TYPE	20	41	33	13	11

Figure S138. Get High-res Image Gene #37: 'del_5q12.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_CNMF'

P value = 0.0209 (Fisher's exact test), Q value = 0.067

Table S139. Gene #37: 'del_5q12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	77	119
DEL PEAK 9(5Q12.1) MUTATED	19	16	41
DEL PEAK 9(5Q12.1) WILD-TYPE	80	61	78

Figure S139. Get High-res Image Gene #37: 'del_5q12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5q12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0313 (Fisher's exact test), Q value = 0.089

Table S140. Gene #37: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	50	26	142
DEL PEAK 9(5Q12.1) MUTATED	14	15	13	32
DEL PEAK 9(5Q12.1) WILD-TYPE	50	35	13	110

Figure S140. Get High-res Image Gene #37: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q35.2' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0021

Table S141. Gene #38: 'del_5q35.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 10(5Q35.2) MUTATED	19	30	22
DEL PEAK 10(5Q35.2) WILD-TYPE	110	43	71

Figure S141. Get High-res Image Gene #38: 'del_5q35.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q35.2' versus 'MIRSEQ_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.087

Table S142. Gene #38: 'del_5q35.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	77	119
DEL PEAK 10(5Q35.2) MUTATED	17	16	38
DEL PEAK 10(5Q35.2) WILD-TYPE	82	61	81

Figure S142. Get High-res Image Gene #38: 'del_5q35.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6p24.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0388 (Fisher's exact test), Q value = 0.1

Table S143. Gene #39: 'del_6p24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 11(6P24.2) MUTATED	5	36	5
DEL PEAK 11(6P24.2) WILD-TYPE	67	149	30

Figure S143. Get High-res Image Gene #39: 'del_6p24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6p24.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0265 (Fisher's exact test), Q value = 0.079

Table S144. 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 11(6P24.2) MUTATED	4	22	12	5	3
DEL PEAK 11(6P24.2) WILD-TYPE	56	73	60	20	40

Figure S144. Get High-res Image Gene #39: 'del_6p24.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S145. Gene #40: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 12(6Q26) MUTATED	39	43	18
DEL PEAK 12(6Q26) WILD-TYPE	90	30	75

Figure S145. Get High-res Image Gene #40: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 0.00166 (Fisher's exact test), Q value = 0.01

Table S146. Gene #40: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	54	57	59	9	45
DEL PEAK 12(6Q26) MUTATED	18	27	16	27	4	8
DEL PEAK 12(6Q26) WILD-TYPE	53	27	41	32	5	37

Figure S146. Get High-res Image Gene #40: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q34' versus 'CN_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0053

Table S147. Gene #41: 'del_7q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 13(7Q34) MUTATED	14	23	23
DEL PEAK 13(7Q34) WILD-TYPE	115	50	70

Figure S147. Get High-res Image Gene #41: 'del_7q34' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S148. Gene #42: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 14(8P23.3) MUTATED	28	42	34
DEL PEAK 14(8P23.3) WILD-TYPE	101	31	59

Figure S148. Get High-res Image Gene #42: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.3' versus 'METHLYATION_CNMF'

P value = 0.0302 (Fisher's exact test), Q value = 0.087

Table S149. Gene #42: 'del_8p23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	54	57	59	9	45
DEL PEAK 14(8P23.3) MUTATED	27	15	12	29	4	17
DEL PEAK 14(8P23.3) WILD-TYPE	44	39	45	30	5	28

Figure S149. Get High-res Image Gene #42: 'del_8p23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.3' versus 'MRNASEQ_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0041

Table S150. Gene #42: 'del_8p23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
DEL PEAK 14(8P23.3) MUTATED	23	22	23	36
DEL PEAK 14(8P23.3) WILD-TYPE	31	78	46	33

Figure S150. 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 = 0.079

Table S151. Gene #42: 'del_8p23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 14(8P23.3) MUTATED	28	57	19
DEL PEAK 14(8P23.3) WILD-TYPE	44	128	16

Figure S151. Get High-res Image Gene #42: 'del_8p23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0176 (Fisher's exact test), Q value = 0.059

Table S152. 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 14(8P23.3) MUTATED	24	26	20	11	23
DEL PEAK 14(8P23.3) WILD-TYPE	36	69	52	14	20

Figure S152. Get High-res Image Gene #42: 'del_8p23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0317 (Fisher's exact test), Q value = 0.09

Table S153. Gene #42: 'del_8p23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	77	80
DEL PEAK 14(8P23.3) MUTATED	48	19	35
DEL PEAK 14(8P23.3) WILD-TYPE	77	58	45

Figure S153. Get High-res Image Gene #42: 'del_8p23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8p23.1' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 6e-04

Table S154. Gene #43: 'del_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 15(8P23.1) MUTATED	28	39	30
DEL PEAK 15(8P23.1) WILD-TYPE	101	34	63

Figure S154. Get High-res Image Gene #43: 'del_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.1' versus 'METHLYATION_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.056

Table S155. Gene #43: 'del_8p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	54	57	59	9	45
DEL PEAK 15(8P23.1) MUTATED	25	14	10	26	5	17
DEL PEAK 15(8P23.1) WILD-TYPE	46	40	47	33	4	28

Figure S155. Get High-res Image Gene #43: 'del_8p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.1' versus 'MRNASEQ_CNMF'

P value = 0.00347 (Fisher's exact test), Q value = 0.019

Table S156. Gene #43: 'del_8p23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
DEL PEAK 15(8P23.1) MUTATED	22	21	22	32
DEL PEAK 15(8P23.1) WILD-TYPE	32	79	47	37

Figure S156. Get High-res Image Gene #43: 'del_8p23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p23.1' versus 'MIRSEQ_CNMF'

P value = 0.023 (Fisher's exact test), Q value = 0.072

Table S157. Gene #43: 'del_8p23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	77	119
DEL PEAK 15(8P23.1) MUTATED	35	16	46
DEL PEAK 15(8P23.1) WILD-TYPE	64	61	73

Figure S157. Get High-res Image Gene #43: 'del_8p23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0224 (Fisher's exact test), Q value = 0.071

Table S158. 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 15(8P23.1) MUTATED	22	26	17	10	22
DEL PEAK 15(8P23.1) WILD-TYPE	38	69	55	15	21

Figure S158. Get High-res Image Gene #43: 'del_8p23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00912 (Fisher's exact test), Q value = 0.037

Table S159. Gene #43: 'del_8p23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	77	80
DEL PEAK 15(8P23.1) MUTATED	43	17	36
DEL PEAK 15(8P23.1) WILD-TYPE	82	60	44

Figure S159. Get High-res Image Gene #43: 'del_8p23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'CN_CNMF'

P value = 0.00767 (Fisher's exact test), Q value = 0.033

Table S160. Gene #44: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 16(10Q23.31) MUTATED	30	32	24
DEL PEAK 16(10Q23.31) WILD-TYPE	99	41	69

Figure S160. Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 0.0466 (Fisher's exact test), Q value = 0.12

Table S161. Gene #44: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
DEL PEAK 16(10Q23.31) MUTATED	24	23	18	21
DEL PEAK 16(10Q23.31) WILD-TYPE	30	77	51	48

Figure S161. Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11p15.1' versus 'CN_CNMF'

P value = 0.00115 (Fisher's exact test), Q value = 0.0075

Table S162. Gene #45: 'del_11p15.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 17(11P15.1) MUTATED	30	34	38
DEL PEAK 17(11P15.1) WILD-TYPE	99	39	55

Figure S162. Get High-res Image Gene #45: 'del_11p15.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.1' versus 'RPPA_CNMF'

P value = 0.0374 (Fisher's exact test), Q value = 0.1

Table S163. Gene #45: 'del_11p15.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	42	69
DEL PEAK 17(11P15.1) MUTATED	11	19	20
DEL PEAK 17(11P15.1) WILD-TYPE	42	23	49

Figure S163. Get High-res Image Gene #45: 'del_11p15.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_11p15.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00941 (Fisher's exact test), Q value = 0.038

Table S164. 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 17(11P15.1) MUTATED	5	9	19	8	9
DEL PEAK 17(11P15.1) WILD-TYPE	27	38	26	15	8

Figure S164. Get High-res Image Gene #45: 'del_11p15.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_11p15.1' versus 'MRNASEQ_CNMF'

P value = 0.0286 (Fisher's exact test), Q value = 0.085

Table S165. Gene #45: 'del_11p15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
DEL PEAK 17(11P15.1) MUTATED	21	40	14	27
DEL PEAK 17(11P15.1) WILD-TYPE	33	60	55	42

Figure S165. Get High-res Image Gene #45: 'del_11p15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11p15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0185 (Fisher's exact test), Q value = 0.061

Table S166. Gene #45: 'del_11p15.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 17(11P15.1) MUTATED	16	75	11
DEL PEAK 17(11P15.1) WILD-TYPE	56	110	24

Figure S166. Get High-res Image Gene #45: 'del_11p15.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S167. Gene #46: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 18(11Q23.3) MUTATED	49	42	71
DEL PEAK 18(11Q23.3) WILD-TYPE	80	31	22

Figure S167. Get High-res Image Gene #46: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q23.3' versus 'MRNASEQ_CNMF'

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

Table S168. Gene #46: 'del_11q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
DEL PEAK 18(11Q23.3) MUTATED	34	60	28	37
DEL PEAK 18(11Q23.3) WILD-TYPE	20	40	41	32

Figure S168. Get High-res Image Gene #46: 'del_11q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00384 (Fisher's exact test), Q value = 0.02

Table S169. Gene #46: 'del_11q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 18(11Q23.3) MUTATED	27	112	20
DEL PEAK 18(11Q23.3) WILD-TYPE	45	73	15

Figure S169. Get High-res Image Gene #46: 'del_11q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00232 (Fisher's exact test), Q value = 0.013

Table S170. 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 18(11Q23.3) MUTATED	21	63	43	11	24
DEL PEAK 18(11Q23.3) WILD-TYPE	39	32	29	14	19

Figure S170. Get High-res Image Gene #46: 'del_11q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00624 (Fisher's exact test), Q value = 0.028

Table S171. Gene #46: 'del_11q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	50	26	142
DEL PEAK 18(11Q23.3) MUTATED	25	29	20	82
DEL PEAK 18(11Q23.3) WILD-TYPE	39	21	6	60

Figure S171. 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 = 0.00023

Table S172. Gene #47: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 19(11Q25) MUTATED	45	45	70
DEL PEAK 19(11Q25) WILD-TYPE	84	28	23

Figure S172. Get High-res Image Gene #47: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q25' versus 'MRNASEQ_CNMF'

P value = 0.0336 (Fisher's exact test), Q value = 0.093

Table S173. Gene #47: 'del_11q25' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
DEL PEAK 19(11Q25) MUTATED	32	61	27	38
DEL PEAK 19(11Q25) WILD-TYPE	22	39	42	31

Figure S173. Get High-res Image Gene #47: 'del_11q25' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q25' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0051 (Fisher's exact test), Q value = 0.024

Table S174. Gene #47: 'del_11q25' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 19(11Q25) MUTATED	27	110	21
DEL PEAK 19(11Q25) WILD-TYPE	45	75	14

Figure S174. Get High-res Image Gene #47: 'del_11q25' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q25' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S175. 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 19(11Q25) MUTATED	21	61	42	11	25
DEL PEAK 19(11Q25) WILD-TYPE	39	34	30	14	18

Figure S175. Get High-res Image Gene #47: 'del_11q25' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11q25' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00809 (Fisher's exact test), Q value = 0.034

Table S176. Gene #47: 'del_11q25' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	50	26	142
DEL PEAK 19(11Q25) MUTATED	25	28	20	80
DEL PEAK 19(11Q25) WILD-TYPE	39	22	6	62

Figure S176. Get High-res Image Gene #47: 'del_11q25' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q12.11' versus 'CN_CNMF'

P value = 0.00262 (Fisher's exact test), Q value = 0.015

Table S177. Gene #48: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 20(13Q12.11) MUTATED	31	35	32
DEL PEAK 20(13Q12.11) WILD-TYPE	98	38	61

Figure S177. Get High-res Image Gene #48: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q12.11' versus 'METHLYATION_CNMF'

P value = 0.00082 (Fisher's exact test), Q value = 0.006

Table S178. Gene #48: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	54	57	59	9	45
DEL PEAK 20(13Q12.11) MUTATED	11	22	20	28	5	12
DEL PEAK 20(13Q12.11) WILD-TYPE	60	32	37	31	4	33

Figure S178. Get High-res Image Gene #48: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q12.11' versus 'MRNASEQ_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.044

Table S179. Gene #48: 'del_13q12.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
DEL PEAK 20(13Q12.11) MUTATED	16	32	15	33
DEL PEAK 20(13Q12.11) WILD-TYPE	38	68	54	36

Figure S179. Get High-res Image Gene #48: 'del_13q12.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q12.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.0027

Table S180. Gene #48: 'del_13q12.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 20(13Q12.11) MUTATED	11	68	17
DEL PEAK 20(13Q12.11) WILD-TYPE	61	117	18

Figure S180. Get High-res Image Gene #48: 'del_13q12.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q12.11' versus 'MIRSEQ_CNMF'

P value = 0.00171 (Fisher's exact test), Q value = 0.01

Table S181. Gene #48: 'del_13q12.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	77	119
DEL PEAK 20(13Q12.11) MUTATED	21	25	52
DEL PEAK 20(13Q12.11) WILD-TYPE	78	52	67

Figure S181. Get High-res Image Gene #48: 'del_13q12.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_13q12.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0048 (Fisher's exact test), Q value = 0.023

Table S182. 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 20(13Q12.11) MUTATED	9	33	25	11	20
DEL PEAK 20(13Q12.11) WILD-TYPE	51	62	47	14	23

Figure S182. Get High-res Image Gene #48: 'del_13q12.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q12.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00242 (Fisher's exact test), Q value = 0.014

Table S183. Gene #48: 'del_13q12.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	50	26	142
DEL PEAK 20(13Q12.11) MUTATED	9	18	10	55
DEL PEAK 20(13Q12.11) WILD-TYPE	55	32	16	87

Figure S183. Get High-res Image Gene #48: 'del_13q12.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 0.00405 (Fisher's exact test), Q value = 0.02

Table S184. Gene #49: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 21(13Q14.2) MUTATED	39	39	40
DEL PEAK 21(13Q14.2) WILD-TYPE	90	34	53

Figure S184. Get High-res Image Gene #49: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 0.00109 (Fisher's exact test), Q value = 0.0072

Table S185. Gene #49: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	54	57	59	9	45
DEL PEAK 21(13Q14.2) MUTATED	16	26	24	30	7	15
DEL PEAK 21(13Q14.2) WILD-TYPE	55	28	33	29	2	30

Figure S185. Get High-res Image Gene #49: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 0.00117 (Fisher's exact test), Q value = 0.0076

Table S186. Gene #49: 'del_13q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
DEL PEAK 21(13Q14.2) MUTATED	27	38	15	35
DEL PEAK 21(13Q14.2) WILD-TYPE	27	62	54	34

Figure S186. Get High-res Image Gene #49: 'del_13q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00219 (Fisher's exact test), Q value = 0.013

Table S187. Gene #49: 'del_13q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 21(13Q14.2) MUTATED	16	83	16
DEL PEAK 21(13Q14.2) WILD-TYPE	56	102	19

Figure S187. Get High-res Image Gene #49: 'del_13q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.051

Table S188. Gene #49: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	77	119
DEL PEAK 21(13Q14.2) MUTATED	30	29	59
DEL PEAK 21(13Q14.2) WILD-TYPE	69	48	60

Figure S188. Get High-res Image Gene #49: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0045

Table S189. 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 21(13Q14.2) MUTATED	11	43	27	13	24
DEL PEAK 21(13Q14.2) WILD-TYPE	49	52	45	12	19

Figure S189. Get High-res Image Gene #49: 'del_13q14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00352 (Fisher's exact test), Q value = 0.019

Table S190. Gene #49: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	50	26	142
DEL PEAK 21(13Q14.2) MUTATED	14	19	10	69
DEL PEAK 21(13Q14.2) WILD-TYPE	50	31	16	73

Figure S190. Get High-res Image Gene #49: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q32.31' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00092

Table S191. Gene #50: 'del_14q32.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 22(14Q32.31) MUTATED	17	25	8
DEL PEAK 22(14Q32.31) WILD-TYPE	112	48	85

Figure S191. Get High-res Image Gene #50: 'del_14q32.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00771 (Fisher's exact test), Q value = 0.033

Table S192. 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 22(14Q32.31) MUTATED	1	12	5	6	6
DEL PEAK 22(14Q32.31) WILD-TYPE	31	35	40	17	11

Figure S192. Get High-res Image Gene #50: 'del_14q32.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_14q32.31' versus 'MRNASEQ_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.049

Table S193. Gene #50: 'del_14q32.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
DEL PEAK 22(14Q32.31) MUTATED	7	10	20	12
DEL PEAK 22(14Q32.31) WILD-TYPE	47	90	49	57

Figure S193. Get High-res Image Gene #50: 'del_14q32.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q32.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00955 (Fisher's exact test), Q value = 0.038

Table S194. Gene #50: 'del_14q32.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S194. Get High-res Image Gene #50: 'del_14q32.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0265 (Fisher's exact test), Q value = 0.079

Table S195. 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 22(14Q32.31) MUTATED	13	19	4	4	10
DEL PEAK 22(14Q32.31) WILD-TYPE	47	76	68	21	33

Figure S195. Get High-res Image Gene #50: 'del_14q32.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q21.1' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.0012

Table S196. Gene #51: 'del_15q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 23(15Q21.1) MUTATED	20	31	19
DEL PEAK 23(15Q21.1) WILD-TYPE	109	42	74

Figure S196. Get High-res Image Gene #51: 'del_15q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.047 (Fisher's exact test), Q value = 0.12

Table S197. Gene #51: 'del_15q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 23(15Q21.1) MUTATED	24	36	10
DEL PEAK 23(15Q21.1) WILD-TYPE	48	149	25

Figure S197. Get High-res Image Gene #51: 'del_15q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q21.1' versus 'MIRSEQ_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.041

Table S198. Gene #51: 'del_15q21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	77	119
DEL PEAK 23(15Q21.1) MUTATED	27	9	34
DEL PEAK 23(15Q21.1) WILD-TYPE	72	68	85

Figure S198. Get High-res Image Gene #51: 'del_15q21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_15q21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.033 (Fisher's exact test), Q value = 0.092

Table S199. 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 23(15Q21.1) MUTATED	20	21	9	6	14
DEL PEAK 23(15Q21.1) WILD-TYPE	40	74	63	19	29

Figure S199. Get High-res Image Gene #51: 'del_15q21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.064

Table S200. Gene #51: 'del_15q21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	77	80
DEL PEAK 23(15Q21.1) MUTATED	40	12	16
DEL PEAK 23(15Q21.1) WILD-TYPE	85	65	64

Figure S200. Get High-res Image Gene #51: 'del_15q21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q11.2' versus 'METHLYATION_CNMF'

P value = 0.00199 (Fisher's exact test), Q value = 0.012

Table S201. Gene #52: 'del_16q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	54	57	59	9	45
DEL PEAK 24(16Q11.2) MUTATED	22	8	2	10	2	9
DEL PEAK 24(16Q11.2) WILD-TYPE	49	46	55	49	7	36

Figure S201. Get High-res Image Gene #52: 'del_16q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q11.2' versus 'MRNASEQ_CNMF'

P value = 0.0366 (Fisher's exact test), Q value = 0.099

Table S202. Gene #52: 'del_16q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
DEL PEAK 24(16Q11.2) MUTATED	11	12	20	10
DEL PEAK 24(16Q11.2) WILD-TYPE	43	88	49	59

Figure S202. Get High-res Image Gene #52: 'del_16q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.041

Table S203. Gene #52: 'del_16q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 24(16Q11.2) MUTATED	22	26	5
DEL PEAK 24(16Q11.2) WILD-TYPE	50	159	30

Figure S203. Get High-res Image Gene #52: 'del_16q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q11.2' versus 'MIRSEQ_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.043

Table S204. Gene #52: 'del_16q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	77	119
DEL PEAK 24(16Q11.2) MUTATED	27	12	14
DEL PEAK 24(16Q11.2) WILD-TYPE	72	65	105

Figure S204. Get High-res Image Gene #52: 'del_16q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0107 (Fisher's exact test), Q value = 0.041

Table S205. 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 24(16Q11.2) MUTATED	18	14	6	7	8
DEL PEAK 24(16Q11.2) WILD-TYPE	42	81	66	18	35

Figure S205. Get High-res Image Gene #52: 'del_16q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.049

Table S206. Gene #52: 'del_16q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	50	26	142
DEL PEAK 24(16Q11.2) MUTATED	20	5	6	21
DEL PEAK 24(16Q11.2) WILD-TYPE	44	45	20	121

Figure S206. Get High-res Image Gene #52: 'del_16q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.048

Table S207. Gene #53: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 25(16Q23.1) MUTATED	17	22	16
DEL PEAK 25(16Q23.1) WILD-TYPE	112	51	77

Figure S207. Get High-res Image Gene #53: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0059

Table S208. Gene #53: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	54	57	59	9	45
DEL PEAK 25(16Q23.1) MUTATED	24	7	4	10	4	6
DEL PEAK 25(16Q23.1) WILD-TYPE	47	47	53	49	5	39

Figure S208. Get High-res Image Gene #53: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

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

Table S209. Gene #53: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
DEL PEAK 25(16Q23.1) MUTATED	14	8	22	11
DEL PEAK 25(16Q23.1) WILD-TYPE	40	92	47	58

Figure S209. Get High-res Image Gene #53: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.0033

Table S210. Gene #53: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 25(16Q23.1) MUTATED	25	23	7
DEL PEAK 25(16Q23.1) WILD-TYPE	47	162	28

Figure S210. Get High-res Image Gene #53: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 0.0261 (Fisher's exact test), Q value = 0.079

Table S211. Gene #53: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	77	119
DEL PEAK 25(16Q23.1) MUTATED	27	12	16
DEL PEAK 25(16Q23.1) WILD-TYPE	72	65	103

Figure S211. Get High-res Image Gene #53: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.0046

Table S212. 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 25(16Q23.1) MUTATED	20	16	4	7	8
DEL PEAK 25(16Q23.1) WILD-TYPE	40	79	68	18	35

Figure S212. Get High-res Image Gene #53: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0496 (Fisher's exact test), Q value = 0.13

Table S213. Gene #53: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	77	80
DEL PEAK 25(16Q23.1) MUTATED	32	12	10
DEL PEAK 25(16Q23.1) WILD-TYPE	93	65	70

Figure S213. 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 = 0.00319 (Fisher's exact test), Q value = 0.017

Table S214. Gene #53: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	50	26	142
DEL PEAK 25(16Q23.1) MUTATED	22	4	4	24
DEL PEAK 25(16Q23.1) WILD-TYPE	42	46	22	118

Figure S214. Get High-res Image Gene #53: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0045

Table S215. Gene #54: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 26(17P12) MUTATED	34	39	36
DEL PEAK 26(17P12) WILD-TYPE	95	34	57

Figure S215. Get High-res Image Gene #54: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q25.3' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0019

Table S216. Gene #55: 'del_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	54	57	59	9	45
DEL PEAK 27(17Q25.3) MUTATED	3	19	8	14	1	6
DEL PEAK 27(17Q25.3) WILD-TYPE	68	35	49	45	8	39

Figure S216. Get High-res Image Gene #55: 'del_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q25.3' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00047

Table S217. Gene #55: 'del_17q25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
DEL PEAK 27(17Q25.3) MUTATED	5	21	2	22
DEL PEAK 27(17Q25.3) WILD-TYPE	49	79	67	47

Figure S217. Get High-res Image Gene #55: 'del_17q25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17q25.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S218. Gene #55: 'del_17q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 27(17Q25.3) MUTATED	3	39	8
DEL PEAK 27(17Q25.3) WILD-TYPE	69	146	27

Figure S218. Get High-res Image Gene #55: 'del_17q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17q25.3' versus 'MIRSEQ_CNMF'

P value = 0.00336 (Fisher's exact test), Q value = 0.018

Table S219. Gene #55: 'del_17q25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	77	119
DEL PEAK 27(17Q25.3) MUTATED	9	11	31
DEL PEAK 27(17Q25.3) WILD-TYPE	90	66	88

Figure S219. Get High-res Image Gene #55: 'del_17q25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17q25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00088 (Fisher's exact test), Q value = 0.0063

Table S220. 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 27(17Q25.3) MUTATED	1	23	12	6	9
DEL PEAK 27(17Q25.3) WILD-TYPE	59	72	60	19	34

Figure S220. Get High-res Image Gene #55: 'del_17q25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17q25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0057 (Fisher's exact test), Q value = 0.026

Table S221. Gene #55: 'del_17q25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	50	26	142
DEL PEAK 27(17Q25.3) MUTATED	3	8	3	33
DEL PEAK 27(17Q25.3) WILD-TYPE	61	42	23	109

Figure S221. Get High-res Image Gene #55: 'del_17q25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0014

Table S222. Gene #56: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	54	57	59	9	45
DEL PEAK 28(18Q21.2) MUTATED	31	9	10	25	1	6
DEL PEAK 28(18Q21.2) WILD-TYPE	40	45	47	34	8	39

Figure S222. 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 = 0.00023

Table S223. Gene #56: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
DEL PEAK 28(18Q21.2) MUTATED	12	9	31	30
DEL PEAK 28(18Q21.2) WILD-TYPE	42	91	38	39

Figure S223. Get High-res Image Gene #56: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00036

Table S224. Gene #56: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 28(18Q21.2) MUTATED	32	35	15
DEL PEAK 28(18Q21.2) WILD-TYPE	40	150	20

Figure S224. Get High-res Image Gene #56: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.054

Table S225. Gene #56: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	77	119
DEL PEAK 28(18Q21.2) MUTATED	31	12	39
DEL PEAK 28(18Q21.2) WILD-TYPE	68	65	80

Figure S225. Get High-res Image Gene #56: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00047

Table S226. 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 28(18Q21.2) MUTATED	29	18	11	4	20
DEL PEAK 28(18Q21.2) WILD-TYPE	31	77	61	21	23

Figure S226. Get High-res Image Gene #56: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0384 (Fisher's exact test), Q value = 0.1

Table S227. Gene #56: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	77	80
DEL PEAK 28(18Q21.2) MUTATED	45	15	22
DEL PEAK 28(18Q21.2) WILD-TYPE	80	62	58

Figure S227. 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 = 0.00269 (Fisher's exact test), Q value = 0.015

Table S228. Gene #56: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	50	26	142
DEL PEAK 28(18Q21.2) MUTATED	29	7	6	40
DEL PEAK 28(18Q21.2) WILD-TYPE	35	43	20	102

Figure S228. 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 = 0.00023

Table S229. Gene #57: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 29(19P13.3) MUTATED	24	52	29
DEL PEAK 29(19P13.3) WILD-TYPE	105	21	64

Figure S229. Get High-res Image Gene #57: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S230. Gene #57: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	54	57	59	9	45
DEL PEAK 29(19P13.3) MUTATED	25	16	9	39	2	14
DEL PEAK 29(19P13.3) WILD-TYPE	46	38	48	20	7	31

Figure S230. Get High-res Image Gene #57: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0024

Table S231. Gene #57: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
DEL PEAK 29(19P13.3) MUTATED	17	23	25	39
DEL PEAK 29(19P13.3) WILD-TYPE	37	77	44	30

Figure S231. 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 = 0.00023

Table S232. Gene #57: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 29(19P13.3) MUTATED	25	53	26
DEL PEAK 29(19P13.3) WILD-TYPE	47	132	9

Figure S232. Get High-res Image Gene #57: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 0.0132 (Fisher's exact test), Q value = 0.048

Table S233. Gene #57: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	77	119
DEL PEAK 29(19P13.3) MUTATED	40	17	48
DEL PEAK 29(19P13.3) WILD-TYPE	59	60	71

Figure S233. Get High-res Image Gene #57: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00036

Table S234. 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 29(19P13.3) MUTATED	17	36	13	13	26
DEL PEAK 29(19P13.3) WILD-TYPE	43	59	59	12	17

Figure S234. Get High-res Image Gene #57: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0469 (Fisher's exact test), Q value = 0.12

Table S235. Gene #57: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	77	80
DEL PEAK 29(19P13.3) MUTATED	52	19	30
DEL PEAK 29(19P13.3) WILD-TYPE	73	58	50

Figure S235. 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 = 0.048 (Fisher's exact test), Q value = 0.12

Table S236. Gene #57: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	50	26	142
DEL PEAK 29(19P13.3) MUTATED	20	11	9	61
DEL PEAK 29(19P13.3) WILD-TYPE	44	39	17	81

Figure S236. Get High-res Image Gene #57: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.33' versus 'METHLYATION_CNMF'

P value = 0.047 (Fisher's exact test), Q value = 0.12

Table S237. Gene #58: 'del_19q13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	54	57	59	9	45
DEL PEAK 30(19Q13.33) MUTATED	13	7	1	9	1	7
DEL PEAK 30(19Q13.33) WILD-TYPE	58	47	56	50	8	38

Figure S237. Get High-res Image Gene #58: 'del_19q13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_20p12.1' versus 'METHLYATION_CNMF'

P value = 0.026 (Fisher's exact test), Q value = 0.079

Table S238. Gene #59: 'del_20p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	54	57	59	9	45
DEL PEAK 31(20P12.1) MUTATED	10	3	3	14	0	6
DEL PEAK 31(20P12.1) WILD-TYPE	61	51	54	45	9	39

Figure S238. Get High-res Image Gene #59: 'del_20p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_20p12.1' versus 'MRNASEQ_CNMF'

P value = 0.00731 (Fisher's exact test), Q value = 0.031

Table S239. Gene #59: 'del_20p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	100	69	69
DEL PEAK 31(20P12.1) MUTATED	2	8	11	15
DEL PEAK 31(20P12.1) WILD-TYPE	52	92	58	54

Figure S239. Get High-res Image Gene #59: 'del_20p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_21q11.2' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0021

Table S240. Gene #60: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 32(21Q11.2) MUTATED	13	24	21
DEL PEAK 32(21Q11.2) WILD-TYPE	116	49	72

Figure S240. Get High-res Image Gene #60: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00493 (Fisher's exact test), Q value = 0.024

Table S241. 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 32(21Q11.2) MUTATED	6	7	2	8	6
DEL PEAK 32(21Q11.2) WILD-TYPE	26	40	43	15	11

Figure S241. Get High-res Image Gene #60: 'del_21q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_21q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00922 (Fisher's exact test), Q value = 0.037

Table S242. Gene #60: 'del_21q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 32(21Q11.2) MUTATED	14	30	14
DEL PEAK 32(21Q11.2) WILD-TYPE	58	155	21

Figure S242. Get High-res Image Gene #60: 'del_21q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 0.0048 (Fisher's exact test), Q value = 0.023

Table S243. Gene #61: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 33(22Q13.32) MUTATED	28	32	28
DEL PEAK 33(22Q13.32) WILD-TYPE	101	41	65

Figure S243. Get High-res Image Gene #61: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0294 (Fisher's exact test), Q value = 0.086

Table S244. Gene #61: 'del_22q13.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	185	35
DEL PEAK 33(22Q13.32) MUTATED	23	48	17
DEL PEAK 33(22Q13.32) WILD-TYPE	49	137	18

Figure S244. Get High-res Image Gene #61: 'del_22q13.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp11.3' versus 'CN_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0053

Table S245. Gene #62: 'del_xp11.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 34(XP11.3) MUTATED	22	30	20
DEL PEAK 34(XP11.3) WILD-TYPE	107	43	73

Figure S245. Get High-res Image Gene #62: 'del_xp11.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp11.3' versus 'METHLYATION_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0031

Table S246. Gene #62: 'del_xp11.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	71	54	57	59	9	45
DEL PEAK 34(XP11.3) MUTATED	12	18	6	24	4	8
DEL PEAK 34(XP11.3) WILD-TYPE	59	36	51	35	5	37

Figure S246. Get High-res Image Gene #62: 'del_xp11.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp11.3' versus 'MIRSEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0027

Table S247. Gene #62: 'del_xp11.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	77	119
DEL PEAK 34(XP11.3) MUTATED	22	8	42
DEL PEAK 34(XP11.3) WILD-TYPE	77	69	77

Figure S247. Get High-res Image Gene #62: 'del_xp11.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xp11.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0321 (Fisher's exact test), Q value = 0.091

Table S248. 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 34(XP11.3) MUTATED	11	28	10	9	14
DEL PEAK 34(XP11.3) WILD-TYPE	49	67	62	16	29

Figure S248. Get High-res Image Gene #62: 'del_xp11.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xp11.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00308 (Fisher's exact test), Q value = 0.017

Table S249. Gene #62: 'del_xp11.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	77	80
DEL PEAK 34(XP11.3) MUTATED	29	10	29
DEL PEAK 34(XP11.3) WILD-TYPE	96	67	51

Figure S249. Get High-res Image Gene #62: 'del_xp11.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xq21.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.0111 (Fisher's exact test), Q value = 0.042

Table S250. 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 35(XQ21.33) MUTATED	2	9	14	5	0
DEL PEAK 35(XQ21.33) WILD-TYPE	30	38	31	18	17

Figure S250. 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/15082576/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/CESC-TP/15095897/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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