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 55 focal events and 10 molecular subtypes across 366 patients, 154 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p12 cnv correlated to 'CN_CNMF'.
amp_1q21.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_1q44 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_4q12 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
amp_5p15.33 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
amp_5q35.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.
amp_6p24.3 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_6q12 cnv correlated to 'MIRSEQ_CHIERARCHICAL'.
amp_7p22.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
amp_7q34 cnv correlated to 'CN_CNMF'.
amp_8q11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
amp_12q14.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
amp_13q31.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_15q26.2 cnv correlated to 'CN_CNMF'.
amp_17q25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_19p13.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
amp_20q13.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
amp_22q13.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_1p36.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
del_1p22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_2q37.3 cnv correlated to 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_4p16.3 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
del_4q34.3 cnv correlated to 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q12.1 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
del_5q31.3 cnv correlated to 'METHLYATION_CNMF'.
del_6q22.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
del_6q26 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_8p23.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_9p23 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_10p15.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_10q21.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_10q26.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_11p15.5 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_11q23.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12q23.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_13q34 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_14q23.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q32.31 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q13.3 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_16p13.3 cnv correlated to 'RPPA_CNMF' and 'MIRSEQ_MATURE_CNMF'.
del_16q12.1 cnv correlated to 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q24.3 cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p13.3 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_xp21.1 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 55 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, 154 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 6p24 3	210 (57%)	156	1e-05 (0.000239)	1e-05 (0.000239)	0.151 (0.345)	0.0164 (0.0868)	0.0342 (0.145)	0.00822 (0.0532)	0.0172 (0.0883)	5e-05 (0.000917)	0.00209 (0.0213)	0.00056 (0.00751)
amp 1q44	201 (55%)	165	1e-05 (0.000239)	0.00939 (0.0574)	0.378 (0.57)	0.143 (0.333)	0.00881 (0.0551)	0.369 (0.563)	0.00434 (0.0348)	0.00258 (0.024)	0.029 (0.131)	0.00479 (0.0361)
del xp21 1	87 (24%)	279	0.12 (0.299)	1e-05 (0.000239)	0.0224 (0.106)	0.111 (0.284)	0.00436 (0.0348)	0.00221 (0.0221)	5e-05 (0.000917)	0.0129 (0.073)	0.00727 (0.0485)	0.401 (0.595)
del 2q37 3	93 (25%)	273	0.423 (0.615)	0.0968 (0.267)	0.0394 (0.156)	0.0196 (0.0958)	0.00543 (0.0398)	0.0185 (0.0925)	0.0142 (0.0778)	0.0349 (0.145)	0.202 (0.414)	0.238 (0.447)
del 11q23 3	202 (55%)	164	1e-05 (0.000239)	0.334 (0.525)	0.719 (0.807)	0.261 (0.462)	0.0437 (0.164)	0.00062 (0.00812)	0.293 (0.488)	0.0415 (0.161)	0.0239 (0.11)	0.00725 (0.0485)
del 9p21 3	278 (76%)	88	2e-05 (0.00044)	0.00732 (0.0485)	0.708 (0.807)	0.703 (0.807)	2e-05 (0.00044)	0.00717 (0.0485)	0.0143 (0.0778)	0.542 (0.696)	0.688 (0.8)	0.227 (0.433)
del 14q23 3	120 (33%)	246	1e-05 (0.000239)	0.78 (0.85)	0.19 (0.396)	0.246 (0.455)	0.00563 (0.0407)	0.0355 (0.146)	0.0478 (0.172)	0.564 (0.706)	0.11 (0.284)	0.0283 (0.129)
del 16q24 3	133 (36%)	233	0.112 (0.285)	0.621 (0.747)	0.181 (0.383)	0.906 (0.932)	0.0088 (0.0551)	0.00238 (0.0234)	0.043 (0.163)	0.0904 (0.255)	0.0152 (0.0811)	0.0339 (0.145)
amp 1q21 3	203 (55%)	163	1e-05 (0.000239)	0.0757 (0.233)	0.612 (0.745)	0.523 (0.692)	0.00425 (0.0348)	0.472 (0.652)	0.00262 (0.024)	0.0207 (0.0996)	0.172 (0.371)	0.0795 (0.237)
amp 5q35 3	59 (16%)	307	0.00019 (0.00307)	0.00049 (0.00674)	0.0552 (0.19)	0.0344 (0.145)	0.015 (0.081)	0.525 (0.692)	0.787 (0.852)	0.149 (0.343)	0.25 (0.458)	0.64 (0.762)
amp 8q11 21	163 (45%)	203	1e-05 (0.000239)	0.0015 (0.0159)	0.674 (0.794)	0.246 (0.455)	0.0177 (0.0901)	0.0106 (0.0619)	0.94 (0.949)	0.288 (0.486)	0.532 (0.694)	0.928 (0.945)
amp 13q31 3	104 (28%)	262	1e-05 (0.000239)	1e-05 (0.000239)	0.51 (0.68)	0.27 (0.471)	0.0004 (0.00579)	0.00103 (0.0118)	0.453 (0.638)	0.559 (0.705)	0.131 (0.32)	0.935 (0.949)
del 1p22 1	97 (27%)	269	0.00087 (0.0102)	1e-05 (0.000239)	0.431 (0.622)	0.211 (0.422)	0.00015 (0.00266)	0.0224 (0.106)	0.103 (0.279)	0.63 (0.753)	0.164 (0.357)	0.492 (0.664)
del 6q26	221 (60%)	145	1e-05 (0.000239)	0.00979 (0.0585)	0.782 (0.85)	0.54 (0.696)	0.00018 (0.003)	0.047 (0.172)	0.0953 (0.265)	0.204 (0.416)	0.68 (0.794)	0.547 (0.7)
del 10p15 3	199 (54%)	167	1e-05 (0.000239)	0.0428 (0.163)	0.79 (0.852)	0.219 (0.427)	0.00066 (0.00844)	0.00078 (0.00953)	0.216 (0.426)	0.214 (0.423)	0.616 (0.747)	0.32 (0.513)
del 14q32 31	117 (32%)	249	1e-05 (0.000239)	0.62 (0.747)	0.371 (0.563)	0.183 (0.386)	0.00456 (0.0348)	0.0348 (0.145)	0.173 (0.371)	0.605 (0.745)	0.511 (0.68)	0.0477 (0.172)
del 19p13 3	104 (28%)	262	0.0208 (0.0996)	0.704 (0.807)	0.00157 (0.0163)	0.0636 (0.211)	0.00078 (0.00953)	0.00134 (0.0145)	0.764 (0.839)	0.0839 (0.246)	0.433 (0.624)	0.0789 (0.237)
amp 8q24 21	191 (52%)	175	1e-05 (0.000239)	0.00358 (0.0303)	0.737 (0.822)	0.938 (0.949)	0.0097 (0.0585)	0.314 (0.505)	0.801 (0.86)	0.126 (0.311)	0.492 (0.664)	0.92 (0.94)
amp 17q25 3	122 (33%)	244	0.00018 (0.003)	0.041 (0.16)	0.0566 (0.192)	0.0742 (0.23)	0.43 (0.622)	0.00719 (0.0485)	0.786 (0.852)	0.0695 (0.222)	0.411 (0.602)	0.109 (0.284)
amp 20q13 33	187 (51%)	179	1e-05 (0.000239)	0.00131 (0.0144)	0.774 (0.848)	0.989 (0.99)	0.00581 (0.0415)	0.0746 (0.23)	0.38 (0.572)	0.65 (0.769)	0.748 (0.83)	0.478 (0.657)
del 1p36 31	81 (22%)	285	0.0359 (0.146)	1e-05 (0.000239)	0.257 (0.461)	0.208 (0.42)	0.0326 (0.143)	0.0899 (0.255)	0.118 (0.296)	0.141 (0.329)	0.513 (0.68)	0.462 (0.643)
del 4q34 3	110 (30%)	256	0.264 (0.463)	0.0653 (0.215)	0.34 (0.529)	0.552 (0.701)	0.0763 (0.233)	0.011 (0.063)	0.837 (0.878)	0.00294 (0.0265)	0.11 (0.284)	0.00305 (0.0269)
del 6q22 31	215 (59%)	151	1e-05 (0.000239)	0.00527 (0.0392)	0.922 (0.94)	0.445 (0.634)	0.00033 (0.00491)	0.166 (0.361)	0.339 (0.529)	0.257 (0.461)	0.484 (0.663)	0.454 (0.638)
del 9p23	249 (68%)	117	1e-05 (0.000239)	0.101 (0.276)	0.691 (0.802)	0.612 (0.745)	0.00894 (0.0552)	0.157 (0.352)	0.0329 (0.143)	0.0888 (0.255)	0.893 (0.92)	0.298 (0.493)
del 10q21 1	217 (59%)	149	1e-05 (0.000239)	0.466 (0.647)	0.629 (0.753)	0.147 (0.34)	0.0137 (0.0763)	0.0318 (0.141)	0.062 (0.207)	0.158 (0.352)	0.353 (0.545)	0.827 (0.871)
del 10q23 31	230 (63%)	136	1e-05 (0.000239)	0.127 (0.312)	0.849 (0.884)	0.209 (0.42)	0.00386 (0.0322)	0.0168 (0.088)	0.0807 (0.239)	0.291 (0.487)	0.407 (0.601)	0.719 (0.807)
del 10q26 3	236 (64%)	130	1e-05 (0.000239)	0.396 (0.592)	0.819 (0.868)	0.311 (0.503)	0.00022 (0.00346)	0.00449 (0.0348)	0.05 (0.176)	0.213 (0.423)	0.28 (0.48)	0.597 (0.738)
del 11p15 5	114 (31%)	252	0.0197 (0.0958)	0.0489 (0.175)	0.571 (0.713)	0.714 (0.807)	0.534 (0.694)	0.259 (0.462)	0.264 (0.463)	0.0854 (0.247)	0.0346 (0.145)	0.0796 (0.237)
del 13q34	85 (23%)	281	0.951 (0.958)	0.0103 (0.0609)	0.044 (0.164)	0.743 (0.826)	0.815 (0.868)	0.00718 (0.0485)	0.718 (0.807)	0.352 (0.545)	0.151 (0.345)	0.781 (0.85)
del 16q12 1	117 (32%)	249	0.263 (0.463)	0.307 (0.502)	0.0503 (0.176)	0.682 (0.794)	0.037 (0.147)	0.07 (0.222)	0.153 (0.347)	0.044 (0.164)	0.184 (0.386)	0.0472 (0.172)
amp 4q12	65 (18%)	301	0.00308 (0.0269)	0.219 (0.427)	0.133 (0.32)	0.536 (0.694)	0.757 (0.836)	0.101 (0.276)	0.0682 (0.221)	0.00107 (0.012)	0.45 (0.638)	0.369 (0.563)
amp 5p15 33	110 (30%)	256	3e-05 (0.000589)	0.133 (0.32)	0.872 (0.903)	0.738 (0.822)	0.0606 (0.205)	0.563 (0.706)	0.00446 (0.0348)	0.247 (0.456)	0.288 (0.486)	0.079 (0.237)
amp 7p22 1	208 (57%)	158	1e-05 (0.000239)	0.814 (0.868)	0.645 (0.766)	0.214 (0.423)	0.0239 (0.11)	0.132 (0.32)	0.527 (0.693)	0.399 (0.594)	0.868 (0.9)	0.138 (0.326)
amp 12q14 1	58 (16%)	308	0.00318 (0.0273)	0.332 (0.525)	0.89 (0.918)	0.287 (0.486)	0.0449 (0.166)	0.488 (0.664)	0.595 (0.737)	0.225 (0.432)	0.274 (0.474)	0.68 (0.794)
amp 19p13 2	69 (19%)	297	0.00087 (0.0102)	0.0937 (0.262)	0.532 (0.694)	0.958 (0.963)	0.00248 (0.0235)	0.137 (0.326)	0.974 (0.977)	0.387 (0.58)	0.243 (0.454)	0.839 (0.878)
amp 22q13 2	151 (41%)	215	3e-05 (0.000589)	0.0418 (0.161)	0.92 (0.94)	0.718 (0.807)	0.235 (0.443)	0.134 (0.32)	0.556 (0.705)	0.104 (0.279)	0.261 (0.462)	0.191 (0.396)
del 8p23 3	89 (24%)	277	0.0087 (0.0551)	0.106 (0.283)	0.199 (0.411)	0.16 (0.352)	0.0397 (0.156)	0.278 (0.477)	0.211 (0.422)	0.41 (0.602)	0.435 (0.624)	0.236 (0.444)
del 12q23 3	92 (25%)	274	0.0134 (0.0751)	0.036 (0.146)	0.79 (0.852)	0.818 (0.868)	0.301 (0.495)	0.368 (0.563)	0.22 (0.427)	0.11 (0.284)	0.791 (0.852)	0.611 (0.745)
del 15q13 3	84 (23%)	282	0.0501 (0.176)	0.0107 (0.0619)	0.133 (0.32)	0.305 (0.501)	0.401 (0.595)	0.0185 (0.0925)	0.332 (0.525)	0.846 (0.882)	0.056 (0.191)	0.726 (0.814)
del 16p13 3	62 (17%)	304	0.56 (0.705)	0.0898 (0.255)	0.00799 (0.0523)	0.336 (0.526)	0.16 (0.352)	0.108 (0.284)	0.311 (0.503)	0.355 (0.547)	0.0238 (0.11)	0.145 (0.337)
del 17p13 3	135 (37%)	231	0.253 (0.459)	0.00023 (0.00351)	0.289 (0.486)	0.637 (0.76)	0.0913 (0.256)	0.0187 (0.0925)	0.714 (0.807)	0.31 (0.503)	0.697 (0.806)	0.173 (0.371)
amp 1p12	121 (33%)	245	0.0363 (0.146)	0.91 (0.934)	0.701 (0.807)	0.882 (0.912)	0.368 (0.563)	0.251 (0.458)	0.14 (0.328)	0.537 (0.694)	0.761 (0.837)	0.68 (0.794)
amp 6q12	80 (22%)	286	0.549 (0.701)	0.561 (0.705)	0.323 (0.516)	0.0816 (0.24)	0.457 (0.638)	0.0698 (0.222)	0.0672 (0.22)	0.0316 (0.141)	0.5 (0.67)	0.153 (0.347)
amp 7q34	224 (61%)	142	3e-05 (0.000589)	0.482 (0.66)	0.287 (0.486)	0.94 (0.949)	0.159 (0.352)	0.253 (0.459)	0.59 (0.732)	0.223 (0.43)	0.0713 (0.225)	0.49 (0.664)
amp 15q26 2	119 (33%)	247	0.00044 (0.00621)	0.205 (0.417)	0.932 (0.947)	0.81 (0.867)	0.158 (0.352)	0.457 (0.638)	0.676 (0.794)	0.486 (0.663)	0.104 (0.279)	0.714 (0.807)
del 4p16 3	91 (25%)	275	0.543 (0.696)	0.109 (0.284)	0.678 (0.794)	0.705 (0.807)	0.177 (0.376)	0.0171 (0.0883)	0.99 (0.99)	0.203 (0.414)	0.619 (0.747)	0.445 (0.634)
del 5q12 1	97 (27%)	269	0.234 (0.443)	0.22 (0.427)	0.156 (0.352)	0.114 (0.29)	0.492 (0.664)	0.0353 (0.146)	0.562 (0.706)	0.588 (0.732)	0.718 (0.807)	0.778 (0.85)
del 5q31 3	131 (36%)	235	0.275 (0.474)	0.00245 (0.0235)	0.325 (0.518)	0.301 (0.495)	0.737 (0.822)	0.176 (0.375)	0.701 (0.807)	0.609 (0.745)	0.513 (0.68)	0.61 (0.745)
amp 3p13	103 (28%)	263	0.122 (0.304)	0.537 (0.694)	0.257 (0.461)	0.0528 (0.184)	0.603 (0.743)	0.294 (0.488)	0.696 (0.806)	0.111 (0.284)	0.761 (0.837)	0.835 (0.878)
amp 11q13 3	69 (19%)	297	0.126 (0.311)	0.0852 (0.247)	0.862 (0.897)	0.84 (0.878)	0.283 (0.484)	0.453 (0.638)	0.421 (0.614)	0.0684 (0.221)	0.805 (0.863)	0.274 (0.474)
amp 12q15	59 (16%)	307	0.0725 (0.227)	0.227 (0.433)	0.827 (0.871)	0.426 (0.618)	0.0971 (0.267)	0.186 (0.39)	0.314 (0.505)	0.31 (0.503)	0.496 (0.667)	0.138 (0.326)
del 3p25 1	71 (19%)	295	0.173 (0.371)	0.239 (0.447)	0.375 (0.568)	0.218 (0.427)	0.529 (0.694)	0.751 (0.831)	0.334 (0.525)	0.255 (0.461)	0.476 (0.656)	0.436 (0.624)
del 3q13 31	62 (17%)	304	0.162 (0.355)	0.0898 (0.255)	0.268 (0.467)	0.118 (0.296)	0.0544 (0.188)	0.551 (0.701)	0.334 (0.525)	0.0619 (0.207)	0.228 (0.433)	0.62 (0.747)
del 5p15 31	79 (22%)	287	0.649 (0.769)	0.377 (0.57)	0.248 (0.457)	0.536 (0.694)	0.818 (0.868)	0.0724 (0.227)	0.622 (0.747)	0.411 (0.602)	0.2 (0.412)	0.449 (0.638)
del 15q21 1	91 (25%)	275	0.0777 (0.236)	0.105 (0.281)	0.472 (0.652)	0.339 (0.529)	0.501 (0.67)	0.29 (0.487)	0.457 (0.638)	0.41 (0.602)	0.26 (0.462)	0.825 (0.871)

'amp_1p12' versus 'CN_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.15

Table S1. Gene #1: 'amp_1p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 1(1P12) MUTATED	43	37	41
AMP PEAK 1(1P12) WILD-TYPE	58	102	85

Figure S1. Get High-res Image Gene #1: 'amp_1p12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S2. Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 2(1Q21.3) MUTATED	92	51	60
AMP PEAK 2(1Q21.3) WILD-TYPE	9	88	66

Figure S2. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 0.00425 (Fisher's exact test), Q value = 0.035

Table S3. Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
AMP PEAK 2(1Q21.3) MUTATED	87	44	72
AMP PEAK 2(1Q21.3) WILD-TYPE	50	60	53

Figure S3. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CNMF'

P value = 0.00262 (Fisher's exact test), Q value = 0.024

Table S4. Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	73	94	118	21	44
AMP PEAK 2(1Q21.3) MUTATED	34	51	72	5	31
AMP PEAK 2(1Q21.3) WILD-TYPE	39	43	46	16	13

Figure S4. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0207 (Fisher's exact test), Q value = 0.1

Table S5. Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	132	93	87	38
AMP PEAK 2(1Q21.3) MUTATED	80	40	47	26
AMP PEAK 2(1Q21.3) WILD-TYPE	52	53	40	12

Figure S5. 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 = 0.00024

Table S6. Gene #3: 'amp_1q44' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 3(1Q44) MUTATED	90	50	61
AMP PEAK 3(1Q44) WILD-TYPE	11	89	65

Figure S6. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q44' versus 'METHLYATION_CNMF'

P value = 0.00939 (Fisher's exact test), Q value = 0.057

Table S7. Gene #3: 'amp_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
AMP PEAK 3(1Q44) MUTATED	74	66	61
AMP PEAK 3(1Q44) WILD-TYPE	55	78	32

Figure S7. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q44' versus 'MRNASEQ_CNMF'

P value = 0.00881 (Fisher's exact test), Q value = 0.055

Table S8. Gene #3: 'amp_1q44' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
AMP PEAK 3(1Q44) MUTATED	83	44	74
AMP PEAK 3(1Q44) WILD-TYPE	54	60	51

Figure S8. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q44' versus 'MIRSEQ_CNMF'

P value = 0.00434 (Fisher's exact test), Q value = 0.035

Table S9. Gene #3: 'amp_1q44' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	73	94	118	21	44
AMP PEAK 3(1Q44) MUTATED	31	48	71	9	33
AMP PEAK 3(1Q44) WILD-TYPE	42	46	47	12	11

Figure S9. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q44' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00258 (Fisher's exact test), Q value = 0.024

Table S10. Gene #3: 'amp_1q44' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	132	93	87	38
AMP PEAK 3(1Q44) MUTATED	77	39	47	29
AMP PEAK 3(1Q44) WILD-TYPE	55	54	40	9

Figure S10. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1q44' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.029 (Fisher's exact test), Q value = 0.13

Table S11. Gene #3: 'amp_1q44' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	108	134
AMP PEAK 3(1Q44) MUTATED	43	58	85
AMP PEAK 3(1Q44) WILD-TYPE	51	50	49

Figure S11. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_1q44' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00479 (Fisher's exact test), Q value = 0.036

Table S12. Gene #3: 'amp_1q44' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	160	70	76	30
AMP PEAK 3(1Q44) MUTATED	89	37	35	25
AMP PEAK 3(1Q44) WILD-TYPE	71	33	41	5

Figure S12. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q12' versus 'CN_CNMF'

P value = 0.00308 (Fisher's exact test), Q value = 0.027

Table S13. Gene #5: 'amp_4q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 5(4Q12) MUTATED	22	13	30
AMP PEAK 5(4Q12) WILD-TYPE	79	126	96

Figure S13. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00107 (Fisher's exact test), Q value = 0.012

Table S14. Gene #5: 'amp_4q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	132	93	87	38
AMP PEAK 5(4Q12) MUTATED	38	8	14	5
AMP PEAK 5(4Q12) WILD-TYPE	94	85	73	33

Figure S14. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00059

Table S15. Gene #6: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 6(5P15.33) MUTATED	31	24	55
AMP PEAK 6(5P15.33) WILD-TYPE	70	115	71

Figure S15. Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 0.00446 (Fisher's exact test), Q value = 0.035

Table S16. Gene #6: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	73	94	118	21	44
AMP PEAK 6(5P15.33) MUTATED	22	15	41	10	16
AMP PEAK 6(5P15.33) WILD-TYPE	51	79	77	11	28

Figure S16. Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5q35.3' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0031

Table S17. Gene #7: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 7(5Q35.3) MUTATED	21	9	29
AMP PEAK 7(5Q35.3) WILD-TYPE	80	130	97

Figure S17. Get High-res Image Gene #7: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q35.3' versus 'METHLYATION_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0067

Table S18. Gene #7: 'amp_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
AMP PEAK 7(5Q35.3) MUTATED	19	13	27
AMP PEAK 7(5Q35.3) WILD-TYPE	110	131	66

Figure S18. Get High-res Image Gene #7: 'amp_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5q35.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0344 (Fisher's exact test), Q value = 0.15

Table S19. Gene #7: 'amp_5q35.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	58	35	49
AMP PEAK 7(5Q35.3) MUTATED	3	4	7	13
AMP PEAK 7(5Q35.3) WILD-TYPE	24	54	28	36

Figure S19. Get High-res Image Gene #7: 'amp_5q35.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_5q35.3' versus 'MRNASEQ_CNMF'

P value = 0.015 (Fisher's exact test), Q value = 0.081

Table S20. Gene #7: 'amp_5q35.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
AMP PEAK 7(5Q35.3) MUTATED	26	8	25
AMP PEAK 7(5Q35.3) WILD-TYPE	111	96	100

Figure S20. Get High-res Image Gene #7: 'amp_5q35.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6p24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S21. Gene #8: 'amp_6p24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 8(6P24.3) MUTATED	78	57	75
AMP PEAK 8(6P24.3) WILD-TYPE	23	82	51

Figure S21. Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p24.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S22. Gene #8: 'amp_6p24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
AMP PEAK 8(6P24.3) MUTATED	79	61	70
AMP PEAK 8(6P24.3) WILD-TYPE	50	83	23

Figure S22. Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p24.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 0.087

Table S23. Gene #8: 'amp_6p24.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	58	35	49
AMP PEAK 8(6P24.3) MUTATED	12	38	13	32
AMP PEAK 8(6P24.3) WILD-TYPE	15	20	22	17

Figure S23. Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_6p24.3' versus 'MRNASEQ_CNMF'

P value = 0.0342 (Fisher's exact test), Q value = 0.15

Table S24. Gene #8: 'amp_6p24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
AMP PEAK 8(6P24.3) MUTATED	87	49	74
AMP PEAK 8(6P24.3) WILD-TYPE	50	55	51

Figure S24. Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6p24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00822 (Fisher's exact test), Q value = 0.053

Table S25. Gene #8: 'amp_6p24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
AMP PEAK 8(6P24.3) MUTATED	71	65	42	32
AMP PEAK 8(6P24.3) WILD-TYPE	36	40	54	26

Figure S25. Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6p24.3' versus 'MIRSEQ_CNMF'

P value = 0.0172 (Fisher's exact test), Q value = 0.088

Table S26. Gene #8: 'amp_6p24.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	73	94	118	21	44
AMP PEAK 8(6P24.3) MUTATED	39	47	81	8	26
AMP PEAK 8(6P24.3) WILD-TYPE	34	47	37	13	18

Figure S26. Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6p24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00092

Table S27. Gene #8: 'amp_6p24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	132	93	87	38
AMP PEAK 8(6P24.3) MUTATED	91	35	54	21
AMP PEAK 8(6P24.3) WILD-TYPE	41	58	33	17

Figure S27. Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6p24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00209 (Fisher's exact test), Q value = 0.021

Table S28. Gene #8: 'amp_6p24.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	108	134
AMP PEAK 8(6P24.3) MUTATED	45	55	92
AMP PEAK 8(6P24.3) WILD-TYPE	49	53	42

Figure S28. Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_6p24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0075

Table S29. Gene #8: 'amp_6p24.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	160	70	76	30
AMP PEAK 8(6P24.3) MUTATED	105	42	28	17
AMP PEAK 8(6P24.3) WILD-TYPE	55	28	48	13

Figure S29. Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0316 (Fisher's exact test), Q value = 0.14

Table S30. Gene #9: 'amp_6q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	132	93	87	38
AMP PEAK 9(6Q12) MUTATED	35	14	24	4
AMP PEAK 9(6Q12) WILD-TYPE	97	79	63	34

Figure S30. Get High-res Image Gene #9: 'amp_6q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7p22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S31. Gene #10: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 10(7P22.1) MUTATED	62	55	91
AMP PEAK 10(7P22.1) WILD-TYPE	39	84	35

Figure S31. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p22.1' versus 'MRNASEQ_CNMF'

P value = 0.0239 (Fisher's exact test), Q value = 0.11

Table S32. Gene #10: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
AMP PEAK 10(7P22.1) MUTATED	73	52	83
AMP PEAK 10(7P22.1) WILD-TYPE	64	52	42

Figure S32. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7q34' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00059

Table S33. Gene #11: 'amp_7q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 11(7Q34) MUTATED	64	66	94
AMP PEAK 11(7Q34) WILD-TYPE	37	73	32

Figure S33. Get High-res Image Gene #11: 'amp_7q34' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S34. Gene #12: 'amp_8q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 12(8Q11.21) MUTATED	35	39	89
AMP PEAK 12(8Q11.21) WILD-TYPE	66	100	37

Figure S34. Get High-res Image Gene #12: 'amp_8q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q11.21' versus 'METHLYATION_CNMF'

P value = 0.0015 (Fisher's exact test), Q value = 0.016

Table S35. Gene #12: 'amp_8q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
AMP PEAK 12(8Q11.21) MUTATED	47	60	56
AMP PEAK 12(8Q11.21) WILD-TYPE	82	84	37

Figure S35. Get High-res Image Gene #12: 'amp_8q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q11.21' versus 'MRNASEQ_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.09

Table S36. Gene #12: 'amp_8q11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
AMP PEAK 12(8Q11.21) MUTATED	57	38	68
AMP PEAK 12(8Q11.21) WILD-TYPE	80	66	57

Figure S36. Get High-res Image Gene #12: 'amp_8q11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0106 (Fisher's exact test), Q value = 0.062

Table S37. Gene #12: 'amp_8q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
AMP PEAK 12(8Q11.21) MUTATED	56	43	48	16
AMP PEAK 12(8Q11.21) WILD-TYPE	51	62	48	42

Figure S37. Get High-res Image Gene #12: 'amp_8q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S38. Gene #13: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 13(8Q24.21) MUTATED	47	48	96
AMP PEAK 13(8Q24.21) WILD-TYPE	54	91	30

Figure S38. Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 0.00358 (Fisher's exact test), Q value = 0.03

Table S39. Gene #13: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
AMP PEAK 13(8Q24.21) MUTATED	58	71	62
AMP PEAK 13(8Q24.21) WILD-TYPE	71	73	31

Figure S39. Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 0.0097 (Fisher's exact test), Q value = 0.059

Table S40. Gene #13: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
AMP PEAK 13(8Q24.21) MUTATED	71	43	77
AMP PEAK 13(8Q24.21) WILD-TYPE	66	61	48

Figure S40. Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_12q14.1' versus 'CN_CNMF'

P value = 0.00318 (Fisher's exact test), Q value = 0.027

Table S41. Gene #15: 'amp_12q14.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 15(12Q14.1) MUTATED	16	12	30
AMP PEAK 15(12Q14.1) WILD-TYPE	85	127	96

Figure S41. Get High-res Image Gene #15: 'amp_12q14.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CNMF'

P value = 0.0449 (Fisher's exact test), Q value = 0.17

Table S42. Gene #15: 'amp_12q14.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
AMP PEAK 15(12Q14.1) MUTATED	25	9	24
AMP PEAK 15(12Q14.1) WILD-TYPE	112	95	101

Figure S42. Get High-res Image Gene #15: 'amp_12q14.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_13q31.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S43. Gene #17: 'amp_13q31.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 17(13Q31.3) MUTATED	34	19	51
AMP PEAK 17(13Q31.3) WILD-TYPE	67	120	75

Figure S43. Get High-res Image Gene #17: 'amp_13q31.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q31.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S44. Gene #17: 'amp_13q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
AMP PEAK 17(13Q31.3) MUTATED	37	23	44
AMP PEAK 17(13Q31.3) WILD-TYPE	92	121	49

Figure S44. Get High-res Image Gene #17: 'amp_13q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q31.3' versus 'MRNASEQ_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0058

Table S45. Gene #17: 'amp_13q31.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
AMP PEAK 17(13Q31.3) MUTATED	31	21	52
AMP PEAK 17(13Q31.3) WILD-TYPE	106	83	73

Figure S45. Get High-res Image Gene #17: 'amp_13q31.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_13q31.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00103 (Fisher's exact test), Q value = 0.012

Table S46. Gene #17: 'amp_13q31.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
AMP PEAK 17(13Q31.3) MUTATED	35	31	33	5
AMP PEAK 17(13Q31.3) WILD-TYPE	72	74	63	53

Figure S46. Get High-res Image Gene #17: 'amp_13q31.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.2' versus 'CN_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0062

Table S47. Gene #18: 'amp_15q26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 18(15Q26.2) MUTATED	30	32	57
AMP PEAK 18(15Q26.2) WILD-TYPE	71	107	69

Figure S47. Get High-res Image Gene #18: 'amp_15q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q25.3' versus 'CN_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.003

Table S48. Gene #19: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 19(17Q25.3) MUTATED	50	33	39
AMP PEAK 19(17Q25.3) WILD-TYPE	51	106	87

Figure S48. Get High-res Image Gene #19: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q25.3' versus 'METHLYATION_CNMF'

P value = 0.041 (Fisher's exact test), Q value = 0.16

Table S49. Gene #19: 'amp_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
AMP PEAK 19(17Q25.3) MUTATED	43	39	40
AMP PEAK 19(17Q25.3) WILD-TYPE	86	105	53

Figure S49. Get High-res Image Gene #19: 'amp_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00719 (Fisher's exact test), Q value = 0.049

Table S50. Gene #19: 'amp_17q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
AMP PEAK 19(17Q25.3) MUTATED	32	40	22	28
AMP PEAK 19(17Q25.3) WILD-TYPE	75	65	74	30

Figure S50. Get High-res Image Gene #19: 'amp_17q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.01

Table S51. Gene #20: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 20(19P13.2) MUTATED	16	16	37
AMP PEAK 20(19P13.2) WILD-TYPE	85	123	89

Figure S51. Get High-res Image Gene #20: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CNMF'

P value = 0.00248 (Fisher's exact test), Q value = 0.024

Table S52. Gene #20: 'amp_19p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
AMP PEAK 20(19P13.2) MUTATED	25	10	34
AMP PEAK 20(19P13.2) WILD-TYPE	112	94	91

Figure S52. Get High-res Image Gene #20: 'amp_19p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_20q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S53. Gene #21: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 21(20Q13.33) MUTATED	64	41	82
AMP PEAK 21(20Q13.33) WILD-TYPE	37	98	44

Figure S53. Get High-res Image Gene #21: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.33' versus 'METHLYATION_CNMF'

P value = 0.00131 (Fisher's exact test), Q value = 0.014

Table S54. Gene #21: 'amp_20q13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
AMP PEAK 21(20Q13.33) MUTATED	63	62	62
AMP PEAK 21(20Q13.33) WILD-TYPE	66	82	31

Figure S54. Get High-res Image Gene #21: 'amp_20q13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CNMF'

P value = 0.00581 (Fisher's exact test), Q value = 0.041

Table S55. Gene #21: 'amp_20q13.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
AMP PEAK 21(20Q13.33) MUTATED	65	44	78
AMP PEAK 21(20Q13.33) WILD-TYPE	72	60	47

Figure S55. Get High-res Image Gene #21: 'amp_20q13.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_22q13.2' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00059

Table S56. Gene #22: 'amp_22q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 22(22Q13.2) MUTATED	54	37	60
AMP PEAK 22(22Q13.2) WILD-TYPE	47	102	66

Figure S56. Get High-res Image Gene #22: 'amp_22q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_22q13.2' versus 'METHLYATION_CNMF'

P value = 0.0418 (Fisher's exact test), Q value = 0.16

Table S57. Gene #22: 'amp_22q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
AMP PEAK 22(22Q13.2) MUTATED	58	48	45
AMP PEAK 22(22Q13.2) WILD-TYPE	71	96	48

Figure S57. Get High-res Image Gene #22: 'amp_22q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.31' versus 'CN_CNMF'

P value = 0.0359 (Fisher's exact test), Q value = 0.15

Table S58. Gene #23: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 1(1P36.31) MUTATED	30	22	29
DEL PEAK 1(1P36.31) WILD-TYPE	71	117	97

Figure S58. Get High-res Image Gene #23: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S59. Gene #23: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
DEL PEAK 1(1P36.31) MUTATED	20	22	39
DEL PEAK 1(1P36.31) WILD-TYPE	109	122	54

Figure S59. Get High-res Image Gene #23: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.31' versus 'MRNASEQ_CNMF'

P value = 0.0326 (Fisher's exact test), Q value = 0.14

Table S60. Gene #23: 'del_1p36.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 1(1P36.31) MUTATED	30	15	36
DEL PEAK 1(1P36.31) WILD-TYPE	107	89	89

Figure S60. Get High-res Image Gene #23: 'del_1p36.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p22.1' versus 'CN_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.01

Table S61. Gene #24: 'del_1p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 2(1P22.1) MUTATED	32	22	43
DEL PEAK 2(1P22.1) WILD-TYPE	69	117	83

Figure S61. Get High-res Image Gene #24: 'del_1p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S62. Gene #24: 'del_1p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
DEL PEAK 2(1P22.1) MUTATED	22	31	44
DEL PEAK 2(1P22.1) WILD-TYPE	107	113	49

Figure S62. Get High-res Image Gene #24: 'del_1p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p22.1' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0027

Table S63. Gene #24: 'del_1p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 2(1P22.1) MUTATED	36	14	47
DEL PEAK 2(1P22.1) WILD-TYPE	101	90	78

Figure S63. Get High-res Image Gene #24: 'del_1p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0224 (Fisher's exact test), Q value = 0.11

Table S64. Gene #24: 'del_1p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 2(1P22.1) MUTATED	26	22	37	12
DEL PEAK 2(1P22.1) WILD-TYPE	81	83	59	46

Figure S64. Get High-res Image Gene #24: 'del_1p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'RPPA_CNMF'

P value = 0.0394 (Fisher's exact test), Q value = 0.16

Table S65. Gene #25: 'del_2q37.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	50	51	42	26
DEL PEAK 3(2Q37.3) MUTATED	10	19	6	9
DEL PEAK 3(2Q37.3) WILD-TYPE	40	32	36	17

Figure S65. Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_2q37.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0196 (Fisher's exact test), Q value = 0.096

Table S66. Gene #25: 'del_2q37.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	58	35	49
DEL PEAK 3(2Q37.3) MUTATED	4	11	8	21
DEL PEAK 3(2Q37.3) WILD-TYPE	23	47	27	28

Figure S66. Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 0.00543 (Fisher's exact test), Q value = 0.04

Table S67. Gene #25: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 3(2Q37.3) MUTATED	48	19	26
DEL PEAK 3(2Q37.3) WILD-TYPE	89	85	99

Figure S67. Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0185 (Fisher's exact test), Q value = 0.092

Table S68. Gene #25: 'del_2q37.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 3(2Q37.3) MUTATED	37	28	15	13
DEL PEAK 3(2Q37.3) WILD-TYPE	70	77	81	45

Figure S68. Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.078

Table S69. Gene #25: 'del_2q37.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	73	94	118	21	44
DEL PEAK 3(2Q37.3) MUTATED	13	20	44	3	11
DEL PEAK 3(2Q37.3) WILD-TYPE	60	74	74	18	33

Figure S69. Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0349 (Fisher's exact test), Q value = 0.15

Table S70. Gene #25: 'del_2q37.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	132	93	87	38
DEL PEAK 3(2Q37.3) MUTATED	44	15	23	9
DEL PEAK 3(2Q37.3) WILD-TYPE	88	78	64	29

Figure S70. Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0171 (Fisher's exact test), Q value = 0.088

Table S71. Gene #28: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 6(4P16.3) MUTATED	33	16	30	12
DEL PEAK 6(4P16.3) WILD-TYPE	74	89	66	46

Figure S71. Get High-res Image Gene #28: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.063

Table S72. Gene #29: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 7(4Q34.3) MUTATED	27	26	42	15
DEL PEAK 7(4Q34.3) WILD-TYPE	80	79	54	43

Figure S72. Get High-res Image Gene #29: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00294 (Fisher's exact test), Q value = 0.027

Table S73. Gene #29: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	132	93	87	38
DEL PEAK 7(4Q34.3) MUTATED	26	38	28	15
DEL PEAK 7(4Q34.3) WILD-TYPE	106	55	59	23

Figure S73. Get High-res Image Gene #29: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00305 (Fisher's exact test), Q value = 0.027

Table S74. Gene #29: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	160	70	76	30
DEL PEAK 7(4Q34.3) MUTATED	42	15	36	10
DEL PEAK 7(4Q34.3) WILD-TYPE	118	55	40	20

Figure S74. Get High-res Image Gene #29: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0353 (Fisher's exact test), Q value = 0.15

Table S75. Gene #31: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 9(5Q12.1) MUTATED	32	17	30	18
DEL PEAK 9(5Q12.1) WILD-TYPE	75	88	66	40

Figure S75. Get High-res Image Gene #31: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q31.3' versus 'METHLYATION_CNMF'

P value = 0.00245 (Fisher's exact test), Q value = 0.024

Table S76. Gene #32: 'del_5q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
DEL PEAK 10(5Q31.3) MUTATED	58	52	21
DEL PEAK 10(5Q31.3) WILD-TYPE	71	92	72

Figure S76. Get High-res Image Gene #32: 'del_5q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q22.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S77. Gene #33: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 11(6Q22.31) MUTATED	81	47	87
DEL PEAK 11(6Q22.31) WILD-TYPE	20	92	39

Figure S77. Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q22.31' versus 'METHLYATION_CNMF'

P value = 0.00527 (Fisher's exact test), Q value = 0.039

Table S78. Gene #33: 'del_6q22.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
DEL PEAK 11(6Q22.31) MUTATED	87	70	58
DEL PEAK 11(6Q22.31) WILD-TYPE	42	74	35

Figure S78. Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q22.31' versus 'MRNASEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0049

Table S79. Gene #33: 'del_6q22.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 11(6Q22.31) MUTATED	87	44	84
DEL PEAK 11(6Q22.31) WILD-TYPE	50	60	41

Figure S79. Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S80. Gene #34: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 12(6Q26) MUTATED	82	50	89
DEL PEAK 12(6Q26) WILD-TYPE	19	89	37

Figure S80. Get High-res Image Gene #34: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 0.00979 (Fisher's exact test), Q value = 0.059

Table S81. Gene #34: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
DEL PEAK 12(6Q26) MUTATED	87	73	61
DEL PEAK 12(6Q26) WILD-TYPE	42	71	32

Figure S81. Get High-res Image Gene #34: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.003

Table S82. Gene #34: 'del_6q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 12(6Q26) MUTATED	90	45	86
DEL PEAK 12(6Q26) WILD-TYPE	47	59	39

Figure S82. Get High-res Image Gene #34: 'del_6q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.047 (Fisher's exact test), Q value = 0.17

Table S83. Gene #34: 'del_6q26' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 12(6Q26) MUTATED	72	52	62	35
DEL PEAK 12(6Q26) WILD-TYPE	35	53	34	23

Figure S83. Get High-res Image Gene #34: 'del_6q26' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.3' versus 'CN_CNMF'

P value = 0.0087 (Fisher's exact test), Q value = 0.055

Table S84. Gene #35: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 13(8P23.3) MUTATED	35	24	30
DEL PEAK 13(8P23.3) WILD-TYPE	66	115	96

Figure S84. Get High-res Image Gene #35: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.3' versus 'MRNASEQ_CNMF'

P value = 0.0397 (Fisher's exact test), Q value = 0.16

Table S85. Gene #35: 'del_8p23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 13(8P23.3) MUTATED	38	16	35
DEL PEAK 13(8P23.3) WILD-TYPE	99	88	90

Figure S85. Get High-res Image Gene #35: 'del_8p23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S86. Gene #36: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 14(9P23) MUTATED	63	80	106
DEL PEAK 14(9P23) WILD-TYPE	38	59	20

Figure S86. Get High-res Image Gene #36: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 0.00894 (Fisher's exact test), Q value = 0.055

Table S87. Gene #36: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 14(9P23) MUTATED	93	60	96
DEL PEAK 14(9P23) WILD-TYPE	44	44	29

Figure S87. Get High-res Image Gene #36: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 0.0329 (Fisher's exact test), Q value = 0.14

Table S88. Gene #36: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	73	94	118	21	44
DEL PEAK 14(9P23) MUTATED	41	69	82	18	26
DEL PEAK 14(9P23) WILD-TYPE	32	25	36	3	18

Figure S88. Get High-res Image Gene #36: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00044

Table S89. Gene #37: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 15(9P21.3) MUTATED	77	86	115
DEL PEAK 15(9P21.3) WILD-TYPE	24	53	11

Figure S89. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 0.00732 (Fisher's exact test), Q value = 0.049

Table S90. Gene #37: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
DEL PEAK 15(9P21.3) MUTATED	107	97	74
DEL PEAK 15(9P21.3) WILD-TYPE	22	47	19

Figure S90. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00044

Table S91. Gene #37: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 15(9P21.3) MUTATED	102	65	111
DEL PEAK 15(9P21.3) WILD-TYPE	35	39	14

Figure S91. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00717 (Fisher's exact test), Q value = 0.049

Table S92. Gene #37: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 15(9P21.3) MUTATED	83	75	83	37
DEL PEAK 15(9P21.3) WILD-TYPE	24	30	13	21

Figure S92. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 0.0143 (Fisher's exact test), Q value = 0.078

Table S93. Gene #37: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	73	94	118	21	44
DEL PEAK 15(9P21.3) MUTATED	46	76	90	20	32
DEL PEAK 15(9P21.3) WILD-TYPE	27	18	28	1	12

Figure S93. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S94. Gene #38: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 16(10P15.3) MUTATED	54	48	97
DEL PEAK 16(10P15.3) WILD-TYPE	47	91	29

Figure S94. Get High-res Image Gene #38: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 0.0428 (Fisher's exact test), Q value = 0.16

Table S95. Gene #38: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
DEL PEAK 16(10P15.3) MUTATED	70	69	60
DEL PEAK 16(10P15.3) WILD-TYPE	59	75	33

Figure S95. Get High-res Image Gene #38: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0084

Table S96. Gene #38: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 16(10P15.3) MUTATED	66	48	85
DEL PEAK 16(10P15.3) WILD-TYPE	71	56	40

Figure S96. Get High-res Image Gene #38: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.0095

Table S97. Gene #38: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 16(10P15.3) MUTATED	57	50	68	24
DEL PEAK 16(10P15.3) WILD-TYPE	50	55	28	34

Figure S97. Get High-res Image Gene #38: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S98. Gene #39: 'del_10q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 17(10Q21.1) MUTATED	48	61	108
DEL PEAK 17(10Q21.1) WILD-TYPE	53	78	18

Figure S98. Get High-res Image Gene #39: 'del_10q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q21.1' versus 'MRNASEQ_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.076

Table S99. Gene #39: 'del_10q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 17(10Q21.1) MUTATED	75	55	87
DEL PEAK 17(10Q21.1) WILD-TYPE	62	49	38

Figure S99. Get High-res Image Gene #39: 'del_10q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0318 (Fisher's exact test), Q value = 0.14

Table S100. Gene #39: 'del_10q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 17(10Q21.1) MUTATED	59	58	69	31
DEL PEAK 17(10Q21.1) WILD-TYPE	48	47	27	27

Figure S100. Get High-res Image Gene #39: 'del_10q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S101. Gene #40: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 18(10Q23.31) MUTATED	53	66	111
DEL PEAK 18(10Q23.31) WILD-TYPE	48	73	15

Figure S101. Get High-res Image Gene #40: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 0.00386 (Fisher's exact test), Q value = 0.032

Table S102. Gene #40: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 18(10Q23.31) MUTATED	79	58	93
DEL PEAK 18(10Q23.31) WILD-TYPE	58	46	32

Figure S102. Get High-res Image Gene #40: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.088

Table S103. Gene #40: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 18(10Q23.31) MUTATED	63	60	73	34
DEL PEAK 18(10Q23.31) WILD-TYPE	44	45	23	24

Figure S103. Get High-res Image Gene #40: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S104. Gene #41: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 19(10Q26.3) MUTATED	51	71	114
DEL PEAK 19(10Q26.3) WILD-TYPE	50	68	12

Figure S104. Get High-res Image Gene #41: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0035

Table S105. Gene #41: 'del_10q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 19(10Q26.3) MUTATED	78	60	98
DEL PEAK 19(10Q26.3) WILD-TYPE	59	44	27

Figure S105. Get High-res Image Gene #41: 'del_10q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00449 (Fisher's exact test), Q value = 0.035

Table S106. Gene #41: 'del_10q26.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 19(10Q26.3) MUTATED	63	64	76	33
DEL PEAK 19(10Q26.3) WILD-TYPE	44	41	20	25

Figure S106. Get High-res Image Gene #41: 'del_10q26.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 0.0197 (Fisher's exact test), Q value = 0.096

Table S107. Gene #42: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 20(11P15.5) MUTATED	41	33	40
DEL PEAK 20(11P15.5) WILD-TYPE	60	106	86

Figure S107. Get High-res Image Gene #42: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 0.0489 (Fisher's exact test), Q value = 0.17

Table S108. Gene #42: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
DEL PEAK 20(11P15.5) MUTATED	43	35	36
DEL PEAK 20(11P15.5) WILD-TYPE	86	109	57

Figure S108. Get High-res Image Gene #42: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0346 (Fisher's exact test), Q value = 0.15

Table S109. Gene #42: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	108	134
DEL PEAK 20(11P15.5) MUTATED	23	30	53
DEL PEAK 20(11P15.5) WILD-TYPE	71	78	81

Figure S109. Get High-res Image Gene #42: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S110. Gene #43: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 21(11Q23.3) MUTATED	77	63	62
DEL PEAK 21(11Q23.3) WILD-TYPE	24	76	64

Figure S110. Get High-res Image Gene #43: '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 = 0.16

Table S111. Gene #43: 'del_11q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 21(11Q23.3) MUTATED	87	51	64
DEL PEAK 21(11Q23.3) WILD-TYPE	50	53	61

Figure S111. Get High-res Image Gene #43: 'del_11q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0081

Table S112. Gene #43: 'del_11q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 21(11Q23.3) MUTATED	62	49	46	45
DEL PEAK 21(11Q23.3) WILD-TYPE	45	56	50	13

Figure S112. Get High-res Image Gene #43: 'del_11q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0415 (Fisher's exact test), Q value = 0.16

Table S113. Gene #43: 'del_11q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	132	93	87	38
DEL PEAK 21(11Q23.3) MUTATED	82	41	53	21
DEL PEAK 21(11Q23.3) WILD-TYPE	50	52	34	17

Figure S113. Get High-res Image Gene #43: 'del_11q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0239 (Fisher's exact test), Q value = 0.11

Table S114. Gene #43: 'del_11q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	108	134
DEL PEAK 21(11Q23.3) MUTATED	50	53	88
DEL PEAK 21(11Q23.3) WILD-TYPE	44	55	46

Figure S114. Get High-res Image Gene #43: 'del_11q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00725 (Fisher's exact test), Q value = 0.049

Table S115. Gene #43: 'del_11q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	160	70	76	30
DEL PEAK 21(11Q23.3) MUTATED	100	43	30	18
DEL PEAK 21(11Q23.3) WILD-TYPE	60	27	46	12

Figure S115. Get High-res Image Gene #43: 'del_11q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q23.3' versus 'CN_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.075

Table S116. Gene #44: 'del_12q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 22(12Q23.3) MUTATED	23	26	43
DEL PEAK 22(12Q23.3) WILD-TYPE	78	113	83

Figure S116. Get High-res Image Gene #44: 'del_12q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q23.3' versus 'METHLYATION_CNMF'

P value = 0.036 (Fisher's exact test), Q value = 0.15

Table S117. Gene #44: 'del_12q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
DEL PEAK 22(12Q23.3) MUTATED	40	26	26
DEL PEAK 22(12Q23.3) WILD-TYPE	89	118	67

Figure S117. Get High-res Image Gene #44: 'del_12q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q34' versus 'METHLYATION_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.061

Table S118. Gene #45: 'del_13q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
DEL PEAK 23(13Q34) MUTATED	28	44	13
DEL PEAK 23(13Q34) WILD-TYPE	101	100	80

Figure S118. Get High-res Image Gene #45: 'del_13q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q34' versus 'RPPA_CNMF'

P value = 0.044 (Fisher's exact test), Q value = 0.16

Table S119. Gene #45: 'del_13q34' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	50	51	42	26
DEL PEAK 23(13Q34) MUTATED	14	5	13	5
DEL PEAK 23(13Q34) WILD-TYPE	36	46	29	21

Figure S119. Get High-res Image Gene #45: 'del_13q34' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00718 (Fisher's exact test), Q value = 0.049

Table S120. Gene #45: 'del_13q34' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 23(13Q34) MUTATED	21	16	26	22
DEL PEAK 23(13Q34) WILD-TYPE	86	89	70	36

Figure S120. Get High-res Image Gene #45: 'del_13q34' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S121. Gene #46: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 24(14Q23.3) MUTATED	30	29	61
DEL PEAK 24(14Q23.3) WILD-TYPE	71	110	65

Figure S121. Get High-res Image Gene #46: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q23.3' versus 'MRNASEQ_CNMF'

P value = 0.00563 (Fisher's exact test), Q value = 0.041

Table S122. Gene #46: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 24(14Q23.3) MUTATED	32	36	52
DEL PEAK 24(14Q23.3) WILD-TYPE	105	68	73

Figure S122. Get High-res Image Gene #46: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0355 (Fisher's exact test), Q value = 0.15

Table S123. Gene #46: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 24(14Q23.3) MUTATED	32	35	41	12
DEL PEAK 24(14Q23.3) WILD-TYPE	75	70	55	46

Figure S123. Get High-res Image Gene #46: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q23.3' versus 'MIRSEQ_CNMF'

P value = 0.0478 (Fisher's exact test), Q value = 0.17

Table S124. Gene #46: 'del_14q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	73	94	118	21	44
DEL PEAK 24(14Q23.3) MUTATED	23	37	26	9	16
DEL PEAK 24(14Q23.3) WILD-TYPE	50	57	92	12	28

Figure S124. Get High-res Image Gene #46: 'del_14q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_14q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0283 (Fisher's exact test), Q value = 0.13

Table S125. Gene #46: 'del_14q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	160	70	76	30
DEL PEAK 24(14Q23.3) MUTATED	41	21	34	11
DEL PEAK 24(14Q23.3) WILD-TYPE	119	49	42	19

Figure S125. Get High-res Image Gene #46: 'del_14q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q32.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S126. Gene #47: 'del_14q32.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 25(14Q32.31) MUTATED	28	27	62
DEL PEAK 25(14Q32.31) WILD-TYPE	73	112	64

Figure S126. Get High-res Image Gene #47: 'del_14q32.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.31' versus 'MRNASEQ_CNMF'

P value = 0.00456 (Fisher's exact test), Q value = 0.035

Table S127. Gene #47: 'del_14q32.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 25(14Q32.31) MUTATED	31	34	52
DEL PEAK 25(14Q32.31) WILD-TYPE	106	70	73

Figure S127. Get High-res Image Gene #47: 'del_14q32.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q32.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0348 (Fisher's exact test), Q value = 0.15

Table S128. Gene #47: 'del_14q32.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 25(14Q32.31) MUTATED	32	32	41	12
DEL PEAK 25(14Q32.31) WILD-TYPE	75	73	55	46

Figure S128. Get High-res Image Gene #47: 'del_14q32.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0477 (Fisher's exact test), Q value = 0.17

Table S129. Gene #47: 'del_14q32.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	160	70	76	30
DEL PEAK 25(14Q32.31) MUTATED	42	19	33	11
DEL PEAK 25(14Q32.31) WILD-TYPE	118	51	43	19

Figure S129. Get High-res Image Gene #47: 'del_14q32.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q13.3' versus 'METHLYATION_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.062

Table S130. Gene #48: 'del_15q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
DEL PEAK 26(15Q13.3) MUTATED	33	22	29
DEL PEAK 26(15Q13.3) WILD-TYPE	96	122	64

Figure S130. Get High-res Image Gene #48: 'del_15q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0185 (Fisher's exact test), Q value = 0.092

Table S131. Gene #48: 'del_15q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 26(15Q13.3) MUTATED	35	21	21	7
DEL PEAK 26(15Q13.3) WILD-TYPE	72	84	75	51

Figure S131. Get High-res Image Gene #48: 'del_15q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16p13.3' versus 'RPPA_CNMF'

P value = 0.00799 (Fisher's exact test), Q value = 0.052

Table S132. Gene #50: 'del_16p13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	50	51	42	26
DEL PEAK 28(16P13.3) MUTATED	9	15	9	0
DEL PEAK 28(16P13.3) WILD-TYPE	41	36	33	26

Figure S132. Get High-res Image Gene #50: 'del_16p13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0238 (Fisher's exact test), Q value = 0.11

Table S133. Gene #50: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	108	134
DEL PEAK 28(16P13.3) MUTATED	18	11	31
DEL PEAK 28(16P13.3) WILD-TYPE	76	97	103

Figure S133. Get High-res Image Gene #50: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q12.1' versus 'MRNASEQ_CNMF'

P value = 0.037 (Fisher's exact test), Q value = 0.15

Table S134. Gene #51: 'del_16q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 29(16Q12.1) MUTATED	55	29	33
DEL PEAK 29(16Q12.1) WILD-TYPE	82	75	92

Figure S134. Get High-res Image Gene #51: 'del_16q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.044 (Fisher's exact test), Q value = 0.16

Table S135. Gene #51: 'del_16q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	132	93	87	38
DEL PEAK 29(16Q12.1) MUTATED	43	24	37	8
DEL PEAK 29(16Q12.1) WILD-TYPE	89	69	50	30

Figure S135. Get High-res Image Gene #51: 'del_16q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0472 (Fisher's exact test), Q value = 0.17

Table S136. Gene #51: 'del_16q12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	160	70	76	30
DEL PEAK 29(16Q12.1) MUTATED	61	22	17	6
DEL PEAK 29(16Q12.1) WILD-TYPE	99	48	59	24

Figure S136. Get High-res Image Gene #51: 'del_16q12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q24.3' versus 'MRNASEQ_CNMF'

P value = 0.0088 (Fisher's exact test), Q value = 0.055

Table S137. Gene #52: 'del_16q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 30(16Q24.3) MUTATED	63	35	35
DEL PEAK 30(16Q24.3) WILD-TYPE	74	69	90

Figure S137. Get High-res Image Gene #52: 'del_16q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00238 (Fisher's exact test), Q value = 0.023

Table S138. Gene #52: 'del_16q24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 30(16Q24.3) MUTATED	41	36	24	32
DEL PEAK 30(16Q24.3) WILD-TYPE	66	69	72	26

Figure S138. Get High-res Image Gene #52: 'del_16q24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q24.3' versus 'MIRSEQ_CNMF'

P value = 0.043 (Fisher's exact test), Q value = 0.16

Table S139. Gene #52: 'del_16q24.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	73	94	118	21	44
DEL PEAK 30(16Q24.3) MUTATED	23	27	56	6	15
DEL PEAK 30(16Q24.3) WILD-TYPE	50	67	62	15	29

Figure S139. Get High-res Image Gene #52: 'del_16q24.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.081

Table S140. Gene #52: 'del_16q24.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	108	134
DEL PEAK 30(16Q24.3) MUTATED	40	27	53
DEL PEAK 30(16Q24.3) WILD-TYPE	54	81	81

Figure S140. Get High-res Image Gene #52: 'del_16q24.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0339 (Fisher's exact test), Q value = 0.15

Table S141. Gene #52: 'del_16q24.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	160	70	76	30
DEL PEAK 30(16Q24.3) MUTATED	67	27	19	7
DEL PEAK 30(16Q24.3) WILD-TYPE	93	43	57	23

Figure S141. Get High-res Image Gene #52: 'del_16q24.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p13.3' versus 'METHLYATION_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0035

Table S142. Gene #53: 'del_17p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
DEL PEAK 31(17P13.3) MUTATED	59	57	19
DEL PEAK 31(17P13.3) WILD-TYPE	70	87	74

Figure S142. Get High-res Image Gene #53: 'del_17p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0187 (Fisher's exact test), Q value = 0.092

Table S143. Gene #53: 'del_17p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 31(17P13.3) MUTATED	44	33	28	30
DEL PEAK 31(17P13.3) WILD-TYPE	63	72	68	28

Figure S143. Get High-res Image Gene #53: 'del_17p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 0.0208 (Fisher's exact test), Q value = 0.1

Table S144. Gene #54: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 32(19P13.3) MUTATED	39	31	34
DEL PEAK 32(19P13.3) WILD-TYPE	62	108	92

Figure S144. Get High-res Image Gene #54: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'RPPA_CNMF'

P value = 0.00157 (Fisher's exact test), Q value = 0.016

Table S145. Gene #54: 'del_19p13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	50	51	42	26
DEL PEAK 32(19P13.3) MUTATED	16	9	11	16
DEL PEAK 32(19P13.3) WILD-TYPE	34	42	31	10

Figure S145. Get High-res Image Gene #54: 'del_19p13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00078 (Fisher's exact test), Q value = 0.0095

Table S146. Gene #54: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 32(19P13.3) MUTATED	55	22	27
DEL PEAK 32(19P13.3) WILD-TYPE	82	82	98

Figure S146. Get High-res Image Gene #54: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00134 (Fisher's exact test), Q value = 0.014

Table S147. Gene #54: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 32(19P13.3) MUTATED	37	21	20	26
DEL PEAK 32(19P13.3) WILD-TYPE	70	84	76	32

Figure S147. Get High-res Image Gene #54: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S148. Gene #55: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
DEL PEAK 33(XP21.1) MUTATED	47	16	24
DEL PEAK 33(XP21.1) WILD-TYPE	82	128	69

Figure S148. Get High-res Image Gene #55: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp21.1' versus 'RPPA_CNMF'

P value = 0.0224 (Fisher's exact test), Q value = 0.11

Table S149. Gene #55: 'del_xp21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	50	51	42	26
DEL PEAK 33(XP21.1) MUTATED	4	15	9	8
DEL PEAK 33(XP21.1) WILD-TYPE	46	36	33	18

Figure S149. Get High-res Image Gene #55: 'del_xp21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_xp21.1' versus 'MRNASEQ_CNMF'

P value = 0.00436 (Fisher's exact test), Q value = 0.035

Table S150. Gene #55: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 33(XP21.1) MUTATED	39	13	35
DEL PEAK 33(XP21.1) WILD-TYPE	98	91	90

Figure S150. Get High-res Image Gene #55: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00221 (Fisher's exact test), Q value = 0.022

Table S151. Gene #55: 'del_xp21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 33(XP21.1) MUTATED	36	13	26	12
DEL PEAK 33(XP21.1) WILD-TYPE	71	92	70	46

Figure S151. Get High-res Image Gene #55: 'del_xp21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00092

Table S152. Gene #55: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	73	94	118	21	44
DEL PEAK 33(XP21.1) MUTATED	10	15	41	11	6
DEL PEAK 33(XP21.1) WILD-TYPE	63	79	77	10	38

Figure S152. Get High-res Image Gene #55: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xp21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0129 (Fisher's exact test), Q value = 0.073

Table S153. Gene #55: 'del_xp21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	132	93	87	38
DEL PEAK 33(XP21.1) MUTATED	40	15	24	4
DEL PEAK 33(XP21.1) WILD-TYPE	92	78	63	34

Figure S153. Get High-res Image Gene #55: 'del_xp21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00727 (Fisher's exact test), Q value = 0.049

Table S154. Gene #55: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	108	134
DEL PEAK 33(XP21.1) MUTATED	18	17	43
DEL PEAK 33(XP21.1) WILD-TYPE	76	91	91

Figure S154. Get High-res Image Gene #55: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SKCM-TM/19784514/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/SKCM-TM/20140641/SKCM-TM.transferedmergedcluster.txt
Number of patients = 366
Number of significantly focal cnvs = 55
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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