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 71 focal events and 14 molecular subtypes across 579 patients, 267 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p34.3 cnv correlated to 'CN_CNMF'.
amp_1q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_1q42.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_2p23.2 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_2q31.2 cnv correlated to 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CNMF'.
amp_3q26.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'METHLYATION_CNMF'.
amp_4p16.3 cnv correlated to 'MIR_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_4q13.3 cnv correlated to 'CN_CNMF'.
amp_5p15.33 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
amp_6p22.3 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'METHLYATION_CNMF'.
amp_7q36.3 cnv correlated to 'CN_CNMF'.
amp_8p11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CNMF'.
amp_8q24.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_10p15.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
amp_11q14.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_12p13.33 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_12p12.1 cnv correlated to 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12q15 cnv correlated to 'MRNA_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_14q11.2 cnv correlated to 'MRNA_CNMF' and 'MIR_CHIERARCHICAL'.
amp_14q32.33 cnv correlated to 'MIR_CHIERARCHICAL' and 'CN_CNMF'.
amp_15q26.3 cnv correlated to 'CN_CNMF'.
amp_17q25.3 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.
amp_18q11.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_19p13.12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.
amp_19q12 cnv correlated to 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CNMF'.
amp_19q13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_20p13 cnv correlated to 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_20q11.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_20q13.33 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_22q12.2 cnv correlated to 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_xp11.23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_xq28 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
del_1p36.11 cnv correlated to 'MIR_CNMF', 'CN_CNMF', and 'RPPA_CNMF'.
del_1q41 cnv correlated to 'CN_CNMF'.
del_2q22.1 cnv correlated to 'MIR_CHIERARCHICAL'.
del_2q37.3 cnv correlated to 'MRNA_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_3p26.2 cnv correlated to 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_3q13.31 cnv correlated to 'RPPA_CHIERARCHICAL' and 'MRNASEQ_CNMF'.
del_4q22.1 cnv correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.
del_4q34.3 cnv correlated to 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_5q12.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_5q13.2 cnv correlated to 'CN_CNMF'.
del_6q27 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_7p22.1 cnv correlated to 'CN_CNMF'.
del_8p23.3 cnv correlated to 'MRNA_CNMF', 'MIR_CHIERARCHICAL', and 'CN_CNMF'.
del_8p21.2 cnv correlated to 'MRNA_CNMF', 'MIR_CHIERARCHICAL', and 'CN_CNMF'.
del_9p24.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
del_9q34.13 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_10q24.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_11p15.5 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_12q24.33 cnv correlated to 'MRNA_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_13q14.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_14q23.3 cnv correlated to 'CN_CNMF'.
del_15q11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_15q15.1 cnv correlated to 'MRNA_CNMF', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_16p13.3 cnv correlated to 'MIR_CHIERARCHICAL' and 'RPPA_CNMF'.
del_16q22.1 cnv correlated to 'MIR_CNMF', 'CN_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_16q23.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
del_17q11.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_18q23 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CNMF'.
del_19q13.33 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_19q13.43 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_21q22.3 cnv correlated to 'MRNA_CHIERARCHICAL'.
del_22q13.32 cnv correlated to 'MIR_CNMF', 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_xp21.1 cnv correlated to 'METHLYATION_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 71 focal events and 14 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 267 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	MIR CNMF	MIR CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
amp 20q13 33	402 (69%)	177	0.0104 (0.0657)	0.00074 (0.00826)	0.684 (0.838)	0.0014 (0.0143)	1e-05 (0.000226)	1e-05 (0.000226)	0.347 (0.604)	0.966 (1.00)	0.0254 (0.122)	0.00248 (0.0226)	0.476 (0.722)	0.0495 (0.185)	0.624 (0.82)	0.0143 (0.0838)
del 13q14 2	364 (63%)	215	0.00956 (0.0605)	0.0161 (0.0903)	0.609 (0.816)	0.0418 (0.169)	0.00024 (0.00331)	4e-05 (0.00075)	0.00114 (0.0119)	0.00293 (0.0245)	0.0198 (0.102)	0.0441 (0.173)	0.376 (0.63)	0.368 (0.627)	0.675 (0.833)	0.251 (0.501)
del 15q11 2	299 (52%)	280	0.00613 (0.0426)	0.0369 (0.153)	0.0108 (0.0673)	0.00593 (0.0415)	1e-05 (0.000226)	4e-05 (0.00075)	0.144 (0.361)	0.499 (0.743)	0.00052 (0.00654)	0.192 (0.424)	0.0251 (0.122)	0.00956 (0.0605)	1 (1.00)	0.372 (0.628)
del 19q13 33	299 (52%)	280	0.00019 (0.00278)	0.00223 (0.0211)	0.0469 (0.179)	0.0205 (0.105)	0.0141 (0.0828)	0.00239 (0.0222)	0.0759 (0.246)	0.0323 (0.141)	0.0155 (0.0885)	0.0164 (0.0903)	0.321 (0.574)	0.129 (0.329)	0.391 (0.641)	0.114 (0.307)
amp 19p13 12	315 (54%)	264	0.0002 (0.00284)	0.00021 (0.00294)	0.039 (0.161)	0.251 (0.501)	1e-05 (0.000226)	1e-05 (0.000226)	8e-05 (0.00128)	0.00143 (0.0145)	0.0419 (0.169)	0.186 (0.414)	0.589 (0.806)	0.0974 (0.284)	1 (1.00)	0.476 (0.722)
amp 20q11 21	348 (60%)	231	0.00255 (0.0226)	0.00308 (0.0252)	0.112 (0.303)	0.00324 (0.026)	1e-05 (0.000226)	1e-05 (0.000226)	0.0853 (0.266)	0.177 (0.4)	0.00332 (0.0264)	0.00259 (0.0226)	0.288 (0.536)	0.0007 (0.008)	1 (1.00)	0.333 (0.584)
del 12q24 33	220 (38%)	359	0.00116 (0.012)	0.0986 (0.285)	0.163 (0.383)	0.014 (0.0828)	1e-05 (0.000226)	0.0192 (0.0997)	0.147 (0.364)	0.403 (0.654)	0.0492 (0.185)	0.0262 (0.125)	0.0156 (0.0889)	0.005 (0.0365)	0.646 (0.832)	1 (1.00)
amp 8q24 21	461 (80%)	118	1e-05 (0.000226)	1e-05 (0.000226)	0.25 (0.501)	0.00283 (0.024)	1e-05 (0.000226)	0.00445 (0.0335)	0.667 (0.833)	0.0765 (0.246)	1e-05 (0.000226)	1e-05 (0.000226)	0.162 (0.383)	0.0983 (0.285)	0.571 (0.798)	0.573 (0.798)
amp 12p12 1	313 (54%)	266	0.126 (0.326)	0.307 (0.559)	0.9 (0.987)	0.0411 (0.168)	1e-05 (0.000226)	5e-05 (0.000857)	0.176 (0.4)	0.606 (0.816)	0.00489 (0.036)	0.00419 (0.0318)	0.448 (0.7)	0.00532 (0.0383)	0.391 (0.641)	0.0441 (0.173)
amp 20p13	317 (55%)	262	0.188 (0.417)	0.00538 (0.0385)	0.208 (0.445)	0.0333 (0.142)	1e-05 (0.000226)	1e-05 (0.000226)	0.567 (0.794)	0.361 (0.621)	0.015 (0.087)	0.0448 (0.174)	0.249 (0.501)	0.00068 (0.00786)	1 (1.00)	0.936 (1.00)
del 3p26 2	209 (36%)	370	0.155 (0.374)	0.00062 (0.00742)	0.00624 (0.0431)	0.00472 (0.035)	5e-05 (0.000857)	0.00058 (0.00712)	0.384 (0.636)	0.105 (0.294)	0.00085 (0.00908)	0.00093 (0.00983)	0.632 (0.822)	0.124 (0.324)	0.415 (0.666)	0.94 (1.00)
del 9q34 13	342 (59%)	237	0.0174 (0.0939)	0.00082 (0.00886)	0.698 (0.846)	0.407 (0.657)	1e-05 (0.000226)	0.0176 (0.0943)	0.684 (0.838)	0.0463 (0.178)	0.0999 (0.285)	0.00871 (0.0565)	0.0496 (0.185)	0.102 (0.289)	1 (1.00)	0.789 (0.915)
del 10q24 2	251 (43%)	328	0.00315 (0.0255)	0.00232 (0.0218)	0.00689 (0.0466)	0.235 (0.482)	5e-05 (0.000857)	0.002 (0.0191)	0.297 (0.55)	0.0326 (0.141)	0.783 (0.911)	0.668 (0.833)	0.00159 (0.0158)	0.365 (0.625)	1 (1.00)	0.782 (0.911)
del 15q15 1	363 (63%)	216	0.0258 (0.123)	0.0594 (0.206)	0.0218 (0.11)	0.00252 (0.0226)	1e-05 (0.000226)	1e-05 (0.000226)	0.059 (0.206)	0.22 (0.462)	0.0164 (0.0903)	0.374 (0.63)	0.394 (0.643)	0.00184 (0.0179)	0.204 (0.443)	0.145 (0.363)
amp 1q42 2	322 (56%)	257	0.0239 (0.118)	0.0268 (0.125)	0.885 (0.978)	0.0082 (0.0536)	1e-05 (0.000226)	7e-05 (0.00114)	0.107 (0.296)	0.805 (0.927)	0.0858 (0.266)	0.064 (0.217)	0.266 (0.517)	0.00287 (0.0242)	1 (1.00)	0.512 (0.75)
amp 11q14 1	257 (44%)	322	0.00521 (0.0378)	0.00375 (0.0291)	0.774 (0.909)	0.307 (0.559)	2e-05 (0.000432)	0.00257 (0.0226)	0.426 (0.672)	0.619 (0.82)	0.308 (0.559)	0.0187 (0.098)	0.131 (0.336)	0.921 (0.994)	0.0427 (0.169)	0.435 (0.682)
amp 12p13 33	330 (57%)	249	0.0239 (0.118)	0.00309 (0.0252)	0.264 (0.516)	0.0545 (0.196)	1e-05 (0.000226)	0.0002 (0.00284)	0.125 (0.325)	0.301 (0.553)	0.0187 (0.098)	0.148 (0.365)	0.534 (0.764)	0.00778 (0.0514)	0.378 (0.631)	0.528 (0.761)
amp 12q15	222 (38%)	357	0.0027 (0.0231)	0.244 (0.495)	0.577 (0.8)	0.00251 (0.0226)	1e-05 (0.000226)	5e-05 (0.000857)	0.0677 (0.225)	0.62 (0.82)	0.0111 (0.0688)	0.00247 (0.0226)	0.969 (1.00)	0.102 (0.289)	0.231 (0.475)	0.269 (0.518)
amp 1q21 3	367 (63%)	212	0.268 (0.517)	0.163 (0.383)	0.641 (0.831)	0.398 (0.647)	1e-05 (0.000226)	0.00014 (0.00214)	0.0265 (0.125)	0.0137 (0.0814)	0.567 (0.794)	0.117 (0.313)	0.843 (0.95)	0.00587 (0.0414)	0.652 (0.833)	0.693 (0.844)
amp 2p23 2	252 (44%)	327	0.33 (0.581)	0.0128 (0.0775)	0.759 (0.898)	0.171 (0.391)	1e-05 (0.000226)	0.00452 (0.0338)	0.159 (0.378)	0.477 (0.722)	0.034 (0.144)	0.00053 (0.00659)	0.92 (0.994)	0.202 (0.441)	1 (1.00)	0.67 (0.833)
amp 2q31 2	262 (45%)	317	0.115 (0.308)	0.171 (0.391)	0.0332 (0.142)	0.0292 (0.131)	1e-05 (0.000226)	0.00765 (0.051)	0.0282 (0.129)	0.92 (0.994)	0.171 (0.391)	0.12 (0.317)	0.289 (0.537)	0.0855 (0.266)	0.67 (0.833)	0.889 (0.981)
amp 19q12	322 (56%)	257	0.122 (0.322)	0.00656 (0.045)	0.0286 (0.129)	0.513 (0.75)	1e-05 (0.000226)	1e-05 (0.000226)	0.0118 (0.0724)	0.803 (0.926)	0.607 (0.816)	0.232 (0.477)	0.347 (0.604)	0.0584 (0.205)	1 (1.00)	0.781 (0.911)
amp 22q12 2	91 (16%)	488	0.624 (0.82)	0.155 (0.374)	0.0716 (0.235)	0.0342 (0.145)	0.00762 (0.051)	0.00081 (0.00885)	0.675 (0.833)	0.00154 (0.0155)	0.156 (0.375)	0.0762 (0.246)	0.109 (0.3)	0.0147 (0.0855)	1 (1.00)	0.0865 (0.266)
del 2q37 3	175 (30%)	404	0.0162 (0.0903)	0.462 (0.714)	0.631 (0.822)	0.0274 (0.127)	4e-05 (0.00075)	0.0875 (0.266)	0.91 (0.991)	0.38 (0.633)	0.125 (0.325)	0.355 (0.613)	0.0239 (0.118)	0.0193 (0.1)	0.323 (0.574)	0.965 (1.00)
del 6q27	380 (66%)	199	0.318 (0.573)	0.0618 (0.212)	0.273 (0.518)	0.103 (0.292)	1e-05 (0.000226)	5e-05 (0.000857)	0.915 (0.994)	0.9 (0.987)	0.00076 (0.00839)	0.00181 (0.0178)	0.562 (0.79)	0.0242 (0.118)	0.691 (0.844)	0.431 (0.68)
del 9p24 3	261 (45%)	318	0.00025 (0.00336)	4e-05 (0.00075)	0.619 (0.82)	0.0134 (0.0802)	0.0619 (0.212)	6e-05 (0.000994)	0.454 (0.705)	0.167 (0.385)	0.0234 (0.117)	0.232 (0.477)	0.087 (0.266)	0.125 (0.325)	1 (1.00)	0.512 (0.75)
del 19q13 43	285 (49%)	294	0.0163 (0.0903)	0.082 (0.26)	0.0794 (0.253)	0.387 (0.64)	0.00011 (0.00171)	3e-05 (0.000609)	0.177 (0.4)	0.398 (0.647)	0.545 (0.771)	0.0601 (0.208)	0.518 (0.753)	0.119 (0.315)	0.0427 (0.169)	0.0215 (0.109)
del 22q13 32	503 (87%)	76	0.206 (0.445)	0.124 (0.324)	0.0334 (0.142)	0.287 (0.535)	0.0173 (0.0939)	0.159 (0.378)	0.038 (0.157)	0.0427 (0.169)	0.0903 (0.27)	0.0785 (0.251)	0.0366 (0.153)	0.576 (0.8)
amp 3q26 2	485 (84%)	94	0.00897 (0.0575)	0.0254 (0.122)	0.817 (0.935)	0.278 (0.522)	1e-05 (0.000226)	0.0361 (0.152)	0.898 (0.987)	0.0547 (0.196)	0.148 (0.365)	0.441 (0.69)	0.124 (0.324)	0.067 (0.224)	1 (1.00)	0.578 (0.8)
amp 4p16 3	160 (28%)	419	1 (1.00)	0.32 (0.574)	0.029 (0.13)	0.48 (0.724)	0.0004 (0.0051)	0.0269 (0.125)	0.238 (0.485)	0.475 (0.722)	0.367 (0.626)	0.693 (0.844)	0.627 (0.82)	0.0181 (0.0961)	0.652 (0.833)	0.578 (0.8)
del 4q34 3	421 (73%)	158	0.0533 (0.194)	0.00071 (0.00802)	0.0622 (0.212)	0.0283 (0.129)	0.185 (0.413)	0.58 (0.8)	0.838 (0.948)	0.167 (0.385)	0.0295 (0.132)	0.0461 (0.178)	0.42 (0.67)	0.53 (0.762)	1 (1.00)	0.561 (0.79)
amp 5p15 33	309 (53%)	270	1 (1.00)	0.0546 (0.196)	0.628 (0.821)	0.25 (0.501)	1e-05 (0.000226)	0.0976 (0.284)	0.518 (0.753)	0.156 (0.375)	0.781 (0.911)	0.028 (0.129)	0.0242 (0.118)	0.146 (0.364)	0.231 (0.475)	0.27 (0.518)
amp 6p22 3	306 (53%)	273	0.173 (0.395)	0.0321 (0.14)	0.276 (0.52)	0.0745 (0.242)	1e-05 (0.000226)	0.0124 (0.0757)	0.215 (0.457)	0.582 (0.8)	0.239 (0.487)	0.147 (0.364)	0.374 (0.63)	0.613 (0.817)	1 (1.00)	0.255 (0.505)
amp 8p11 21	211 (36%)	368	0.11 (0.3)	0.352 (0.609)	0.0997 (0.285)	0.531 (0.763)	3e-05 (0.000609)	0.0158 (0.0891)	0.0494 (0.185)	0.353 (0.609)	0.143 (0.361)	0.274 (0.518)	0.768 (0.905)	0.326 (0.575)	0.231 (0.475)	0.858 (0.963)
amp 10p15 3	252 (44%)	327	0.823 (0.939)	0.0995 (0.285)	0.0544 (0.196)	0.165 (0.384)	1e-05 (0.000226)	0.0006 (0.00727)	0.412 (0.663)	0.986 (1.00)	0.0286 (0.129)	0.097 (0.284)	0.377 (0.63)	0.0667 (0.223)	1 (1.00)	0.61 (0.816)
amp 17q25 3	215 (37%)	364	0.472 (0.722)	0.057 (0.202)	0.981 (1.00)	0.665 (0.833)	0.00398 (0.0307)	0.773 (0.909)	0.468 (0.719)	0.0129 (0.0775)	0.0268 (0.125)	0.363 (0.623)	0.324 (0.574)	0.128 (0.328)	1 (1.00)	0.711 (0.856)
amp 19q13 2	245 (42%)	334	0.945 (1.00)	0.542 (0.771)	0.661 (0.833)	0.391 (0.641)	1e-05 (0.000226)	9e-05 (0.00142)	0.0532 (0.194)	0.466 (0.717)	0.544 (0.771)	0.0268 (0.125)	0.978 (1.00)	0.549 (0.775)	0.675 (0.833)	0.614 (0.817)
amp xp11 23	159 (27%)	420	0.663 (0.833)	0.866 (0.969)	0.418 (0.669)	0.631 (0.822)	1e-05 (0.000226)	0.00191 (0.0184)	0.583 (0.801)	0.451 (0.703)	0.663 (0.833)	0.682 (0.838)	0.275 (0.519)	0.0312 (0.137)	0.675 (0.833)	0.632 (0.822)
del 1p36 11	269 (46%)	310	0.738 (0.877)	0.069 (0.228)	0.03 (0.133)	0.115 (0.308)	6e-05 (0.000994)	0.0878 (0.266)	0.0495 (0.185)	0.207 (0.445)	0.132 (0.337)	0.195 (0.429)	0.221 (0.462)	0.167 (0.385)	0.675 (0.833)	0.978 (1.00)
del 8p23 3	388 (67%)	191	0.0444 (0.173)	0.15 (0.367)	0.58 (0.8)	0.0113 (0.0699)	1e-05 (0.000226)	0.0511 (0.189)	0.842 (0.95)	0.115 (0.308)	0.738 (0.877)	0.903 (0.987)	0.249 (0.501)	0.25 (0.501)	1 (1.00)
del 8p21 2	406 (70%)	173	0.0412 (0.168)	0.0908 (0.271)	0.18 (0.404)	0.00554 (0.0393)	1e-05 (0.000226)	0.149 (0.365)	0.782 (0.911)	0.702 (0.85)	0.246 (0.498)	0.683 (0.838)	0.579 (0.8)	0.513 (0.75)	1 (1.00)
del 11p15 5	346 (60%)	233	0.111 (0.3)	0.972 (1.00)	0.619 (0.82)	0.0873 (0.266)	1e-05 (0.000226)	0.00781 (0.0514)	0.0815 (0.259)	0.66 (0.833)	0.892 (0.983)	0.488 (0.732)	0.107 (0.296)	0.00875 (0.0565)	0.204 (0.443)	0.928 (0.996)
del 16q22 1	461 (80%)	118	0.497 (0.742)	0.703 (0.85)	0.0329 (0.142)	0.453 (0.705)	0.00064 (0.00748)	0.644 (0.832)	0.342 (0.597)	0.0502 (0.186)	0.281 (0.526)	0.911 (0.991)	0.31 (0.562)	0.0472 (0.18)	1 (1.00)	0.384 (0.636)
del 19p13 3	512 (88%)	67	0.16 (0.379)	0.091 (0.271)	0.837 (0.948)	0.545 (0.771)	0.00036 (0.00465)	0.0178 (0.0951)	0.0041 (0.0313)	0.16 (0.38)	0.47 (0.719)	0.0549 (0.196)	0.476 (0.722)	0.729 (0.871)	1 (1.00)
amp 14q11 2	148 (26%)	431	0.0167 (0.0915)	0.0594 (0.206)	0.29 (0.537)	0.00679 (0.0462)	0.069 (0.228)	0.191 (0.424)	0.974 (1.00)	0.204 (0.443)	0.208 (0.445)	0.274 (0.518)	0.3 (0.551)	0.822 (0.938)	0.323 (0.574)	0.278 (0.522)
amp 14q32 33	156 (27%)	423	0.438 (0.687)	0.653 (0.833)	0.197 (0.431)	0.0183 (0.0968)	0.00015 (0.00223)	0.29 (0.537)	0.91 (0.991)	0.811 (0.931)	0.178 (0.401)	0.0916 (0.272)	0.374 (0.63)	0.423 (0.672)	0.0964 (0.283)	0.139 (0.353)
amp 18q11 2	143 (25%)	436	0.82 (0.938)	0.78 (0.911)	0.952 (1.00)	0.219 (0.462)	1e-05 (0.000226)	0.00375 (0.0291)	0.145 (0.363)	0.882 (0.978)	0.538 (0.768)	0.614 (0.817)	0.147 (0.364)	0.513 (0.75)	0.381 (0.633)	0.0925 (0.274)
amp xq28	220 (38%)	359	0.247 (0.499)	0.847 (0.952)	0.556 (0.784)	0.121 (0.319)	0.00035 (0.00458)	0.177 (0.4)	0.534 (0.764)	0.424 (0.672)	0.601 (0.812)	0.375 (0.63)	0.88 (0.978)	0.808 (0.928)	0.0427 (0.169)	0.623 (0.82)
del 3q13 31	84 (15%)	495	0.325 (0.575)	0.228 (0.474)	0.567 (0.794)	0.627 (0.82)	0.109 (0.3)	0.0824 (0.26)	0.235 (0.482)	0.0368 (0.153)	0.0438 (0.173)	0.0879 (0.266)	0.521 (0.756)	0.525 (0.76)	1 (1.00)
del 4q22 1	394 (68%)	185	0.0522 (0.192)	0.0233 (0.117)	1 (1.00)	0.164 (0.384)	0.0154 (0.0885)	0.224 (0.467)	0.0628 (0.214)	0.917 (0.994)	0.67 (0.833)	0.723 (0.867)	0.308 (0.559)	0.253 (0.502)	0.675 (0.833)	0.411 (0.663)
del 5q12 1	355 (61%)	224	0.884 (0.978)	0.872 (0.974)	0.582 (0.8)	0.0557 (0.198)	1e-05 (0.000226)	0.00025 (0.00336)	0.761 (0.898)	0.793 (0.918)	0.203 (0.443)	0.31 (0.562)	0.161 (0.381)	0.255 (0.505)	1 (1.00)	0.265 (0.516)
del 16p13 3	313 (54%)	266	0.604 (0.815)	0.0709 (0.234)	0.273 (0.518)	0.0298 (0.132)	0.107 (0.296)	0.421 (0.671)	0.0422 (0.169)	0.452 (0.704)	0.827 (0.941)	0.989 (1.00)	0.222 (0.464)	0.485 (0.73)	0.675 (0.833)	0.785 (0.912)
del 16q23 1	452 (78%)	127	0.11 (0.3)	0.245 (0.498)	0.102 (0.289)	0.0613 (0.212)	0.00015 (0.00223)	0.536 (0.765)	0.479 (0.724)	0.371 (0.628)	0.0968 (0.284)	0.41 (0.662)	0.0573 (0.202)	0.0497 (0.185)	1 (1.00)	0.903 (0.987)
del 17q11 2	472 (82%)	107	0.922 (0.994)	0.192 (0.424)	0.734 (0.877)	0.217 (0.459)	0.00064 (0.00748)	0.00302 (0.025)	0.67 (0.833)	0.512 (0.75)	0.527 (0.76)	0.517 (0.753)	0.149 (0.366)	0.164 (0.383)	1 (1.00)	0.339 (0.594)
del 18q23	381 (66%)	198	0.885 (0.978)	0.853 (0.958)	0.371 (0.628)	0.956 (1.00)	0.00262 (0.0226)	0.588 (0.806)	0.22 (0.462)	0.275 (0.519)	0.544 (0.771)	0.0466 (0.179)	0.663 (0.833)	0.492 (0.736)	0.646 (0.832)	0.793 (0.918)
amp 1p34 3	292 (50%)	287	0.433 (0.681)	0.0832 (0.262)	0.127 (0.328)	0.0856 (0.266)	1e-05 (0.000226)	0.192 (0.424)	0.273 (0.518)	0.366 (0.626)	0.587 (0.805)	0.758 (0.897)	0.0878 (0.266)	0.165 (0.384)	0.0743 (0.242)	0.927 (0.996)
amp 4q13 3	113 (20%)	466	0.905 (0.988)	0.459 (0.71)	0.387 (0.639)	0.986 (1.00)	0.00026 (0.00345)	0.52 (0.754)	0.885 (0.978)	0.883 (0.978)	0.752 (0.892)	0.591 (0.806)	0.965 (1.00)	0.694 (0.844)	0.323 (0.574)	0.694 (0.844)
amp 7q36 3	320 (55%)	259	0.105 (0.294)	0.178 (0.4)	0.357 (0.615)	0.989 (1.00)	2e-05 (0.000432)	0.457 (0.707)	0.216 (0.459)	0.115 (0.308)	0.882 (0.978)	0.654 (0.833)	0.213 (0.454)	0.503 (0.748)	0.198 (0.434)	0.264 (0.516)
amp 15q26 3	163 (28%)	416	0.085 (0.266)	0.424 (0.672)	0.508 (0.75)	0.428 (0.675)	1e-05 (0.000226)	0.805 (0.927)	0.968 (1.00)	0.738 (0.877)	0.313 (0.566)	0.94 (1.00)	0.154 (0.374)	0.0664 (0.223)	0.675 (0.833)	0.786 (0.913)
del 1q41	97 (17%)	482	0.0896 (0.27)	0.624 (0.82)	0.3 (0.551)	0.839 (0.949)	1e-05 (0.000226)	0.133 (0.338)	0.395 (0.645)	0.545 (0.771)	0.609 (0.816)	0.928 (0.996)	0.92 (0.994)	0.969 (1.00)	0.455 (0.705)
del 2q22 1	137 (24%)	442	0.108 (0.297)	0.271 (0.518)	0.572 (0.798)	0.0036 (0.0284)	0.0746 (0.242)	0.664 (0.833)	0.964 (1.00)	0.922 (0.994)	0.466 (0.717)	0.831 (0.943)	0.479 (0.724)	0.601 (0.812)	1 (1.00)	0.265 (0.516)
del 5q13 2	419 (72%)	160	0.746 (0.886)	0.624 (0.82)	0.898 (0.987)	0.26 (0.512)	1e-05 (0.000226)	0.105 (0.294)	0.502 (0.746)	0.969 (1.00)	0.323 (0.574)	0.0903 (0.27)	0.154 (0.374)	0.107 (0.296)	1 (1.00)	0.724 (0.869)
del 7p22 1	253 (44%)	326	0.389 (0.641)	0.515 (0.751)	0.771 (0.908)	0.0641 (0.217)	1e-05 (0.000226)	0.625 (0.82)	0.923 (0.994)	0.812 (0.931)	0.298 (0.55)	0.686 (0.84)	0.348 (0.605)	0.903 (0.987)	0.231 (0.475)	0.781 (0.911)
del 14q23 3	305 (53%)	274	0.065 (0.219)	0.505 (0.749)	0.654 (0.833)	0.61 (0.816)	3e-05 (0.000609)	0.736 (0.877)	0.657 (0.833)	0.316 (0.57)	0.265 (0.516)	0.513 (0.75)	0.898 (0.987)	0.595 (0.806)	0.666 (0.833)	0.142 (0.359)
del 21q22 3	227 (39%)	352	0.37 (0.628)	0.0406 (0.167)	0.696 (0.844)	0.205 (0.443)	0.796 (0.92)	0.264 (0.516)	0.611 (0.816)	0.593 (0.806)	0.651 (0.833)	0.486 (0.73)	0.821 (0.938)	0.728 (0.871)	0.162 (0.382)	0.929 (0.996)
del xp21 1	355 (61%)	224	0.404 (0.654)	0.645 (0.832)	0.0989 (0.285)	0.8 (0.924)	0.166 (0.385)	0.0208 (0.106)	0.681 (0.838)	0.0563 (0.2)	0.513 (0.75)	0.474 (0.722)	0.977 (1.00)	0.716 (0.861)	0.594 (0.806)	0.282 (0.528)
amp 10q22 3	184 (32%)	395	0.369 (0.628)	0.267 (0.517)	0.608 (0.816)	0.949 (1.00)	0.0782 (0.251)	0.845 (0.952)	0.865 (0.969)	0.841 (0.95)	0.532 (0.763)	0.571 (0.798)	0.228 (0.474)	0.647 (0.832)	0.67 (0.833)	0.302 (0.553)
del 2p25 3	120 (21%)	459	0.881 (0.978)	0.27 (0.518)	0.42 (0.67)	0.156 (0.375)	0.406 (0.657)	0.636 (0.825)	0.526 (0.76)	0.831 (0.943)	0.118 (0.314)	0.662 (0.833)	0.877 (0.978)	0.951 (1.00)	0.381 (0.633)	0.425 (0.672)
del 10p15 3	120 (21%)	459	0.181 (0.404)	0.71 (0.856)	0.089 (0.269)	0.321 (0.574)	0.0964 (0.283)	0.349 (0.605)	0.329 (0.58)	0.49 (0.735)	0.829 (0.942)	0.982 (1.00)	0.254 (0.503)	0.263 (0.516)	0.594 (0.806)	0.106 (0.295)
del 11q25	201 (35%)	378	0.625 (0.82)	0.657 (0.833)	0.208 (0.445)	0.0519 (0.191)	0.271 (0.518)	0.418 (0.669)	0.494 (0.738)	0.39 (0.641)	0.756 (0.896)	0.158 (0.378)	0.707 (0.854)	0.27 (0.518)	1 (1.00)	0.772 (0.908)
del 17p12	491 (85%)	88	0.145 (0.363)	0.335 (0.587)	0.59 (0.806)	0.691 (0.844)	0.71 (0.856)	0.323 (0.574)	0.867 (0.969)	0.661 (0.833)	0.647 (0.832)	0.463 (0.714)	0.508 (0.75)	0.209 (0.446)	1 (1.00)

'amp_1p34.3' versus 'CN_CNMF'

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

Table S1. Gene #1: 'amp_1p34.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 1(1P34.3) MUTATED	58	114	120
AMP PEAK 1(1P34.3) WILD-TYPE	113	92	82

Figure S1. Get High-res Image Gene #1: 'amp_1p34.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_1q21.3' versus 'CN_CNMF'

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

Table S2. Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 2(1Q21.3) MUTATED	86	114	167
AMP PEAK 2(1Q21.3) WILD-TYPE	85	92	35

Figure S2. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0021

Table S3. Gene #2: 'amp_1q21.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 2(1Q21.3) MUTATED	128	92	141
AMP PEAK 2(1Q21.3) WILD-TYPE	44	83	80

Figure S3. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_1q21.3' versus 'RPPA_CNMF'

P value = 0.0265 (Fisher's exact test), Q value = 0.13

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	189	76
AMP PEAK 2(1Q21.3) MUTATED	85	132	42
AMP PEAK 2(1Q21.3) WILD-TYPE	61	57	34

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

'amp_1q21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 0.081

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	54	60	154
AMP PEAK 2(1Q21.3) MUTATED	79	43	40	97
AMP PEAK 2(1Q21.3) WILD-TYPE	64	11	20	57

Figure S5. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00587 (Fisher's exact test), Q value = 0.041

Table S6. Gene #2: 'amp_1q21.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	71	165	106
AMP PEAK 2(1Q21.3) MUTATED	54	42	119	68
AMP PEAK 2(1Q21.3) WILD-TYPE	51	29	46	38

Figure S6. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_1q42.2' versus 'MRNA_CNMF'

P value = 0.0239 (Fisher's exact test), Q value = 0.12

Table S7. Gene #3: 'amp_1q42.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	216	126
AMP PEAK 3(1Q42.2) MUTATED	133	106	66
AMP PEAK 3(1Q42.2) WILD-TYPE	82	110	60

Figure S7. Get High-res Image Gene #3: 'amp_1q42.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1q42.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0268 (Fisher's exact test), Q value = 0.13

Table S8. Gene #3: 'amp_1q42.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	310	158	89
AMP PEAK 3(1Q42.2) MUTATED	174	74	57
AMP PEAK 3(1Q42.2) WILD-TYPE	136	84	32

Figure S8. Get High-res Image Gene #3: 'amp_1q42.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_1q42.2' versus 'MIR_CHIERARCHICAL'

P value = 0.0082 (Fisher's exact test), Q value = 0.054

Table S9. Gene #3: 'amp_1q42.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	85	57	58	82	34	75	34	36	52	42
AMP PEAK 3(1Q42.2) MUTATED	45	30	36	43	13	44	21	22	37	13
AMP PEAK 3(1Q42.2) WILD-TYPE	40	27	22	39	21	31	13	14	15	29

Figure S9. Get High-res Image Gene #3: 'amp_1q42.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_1q42.2' versus 'CN_CNMF'

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

Table S10. Gene #3: 'amp_1q42.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 3(1Q42.2) MUTATED	88	87	147
AMP PEAK 3(1Q42.2) WILD-TYPE	83	119	55

Figure S10. Get High-res Image Gene #3: 'amp_1q42.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_1q42.2' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.0011

Table S11. Gene #3: 'amp_1q42.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 3(1Q42.2) MUTATED	119	87	108
AMP PEAK 3(1Q42.2) WILD-TYPE	53	88	113

Figure S11. Get High-res Image Gene #3: 'amp_1q42.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_1q42.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00287 (Fisher's exact test), Q value = 0.024

Table S12. Gene #3: 'amp_1q42.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	71	165	106
AMP PEAK 3(1Q42.2) MUTATED	41	43	101	59
AMP PEAK 3(1Q42.2) WILD-TYPE	64	28	64	47

Figure S12. Get High-res Image Gene #3: 'amp_1q42.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_2p23.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0128 (Fisher's exact test), Q value = 0.077

Table S13. Gene #4: 'amp_2p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	310	158	89
AMP PEAK 4(2P23.2) MUTATED	123	67	51
AMP PEAK 4(2P23.2) WILD-TYPE	187	91	38

Figure S13. Get High-res Image Gene #4: 'amp_2p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_2p23.2' versus 'CN_CNMF'

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

Table S14. Gene #4: 'amp_2p23.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 4(2P23.2) MUTATED	47	87	118
AMP PEAK 4(2P23.2) WILD-TYPE	124	119	84

Figure S14. Get High-res Image Gene #4: 'amp_2p23.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_2p23.2' versus 'METHLYATION_CNMF'

P value = 0.00452 (Fisher's exact test), Q value = 0.034

Table S15. Gene #4: 'amp_2p23.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 4(2P23.2) MUTATED	90	61	93
AMP PEAK 4(2P23.2) WILD-TYPE	82	114	128

Figure S15. Get High-res Image Gene #4: 'amp_2p23.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_2p23.2' versus 'MRNASEQ_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 0.14

Table S16. Gene #4: 'amp_2p23.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	108	113
AMP PEAK 4(2P23.2) MUTATED	27	57	55
AMP PEAK 4(2P23.2) WILD-TYPE	52	51	58

Figure S16. Get High-res Image Gene #4: 'amp_2p23.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_2p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.0066

Table S17. Gene #4: 'amp_2p23.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	59	95
AMP PEAK 4(2P23.2) MUTATED	55	40	44
AMP PEAK 4(2P23.2) WILD-TYPE	91	19	51

Figure S17. Get High-res Image Gene #4: 'amp_2p23.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_2q31.2' versus 'MIR_CNMF'

P value = 0.0332 (Fisher's exact test), Q value = 0.14

Table S18. Gene #5: 'amp_2q31.2' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	164	232
AMP PEAK 5(2Q31.2) MUTATED	73	61	117
AMP PEAK 5(2Q31.2) WILD-TYPE	86	103	115

Figure S18. Get High-res Image Gene #5: 'amp_2q31.2' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_2q31.2' versus 'MIR_CHIERARCHICAL'

P value = 0.0292 (Fisher's exact test), Q value = 0.13

Table S19. Gene #5: 'amp_2q31.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	85	57	58	82	34	75	34	36	52	42
AMP PEAK 5(2Q31.2) MUTATED	30	20	32	42	14	36	18	15	31	13
AMP PEAK 5(2Q31.2) WILD-TYPE	55	37	26	40	20	39	16	21	21	29

Figure S19. Get High-res Image Gene #5: 'amp_2q31.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_2q31.2' versus 'CN_CNMF'

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

Table S20. Gene #5: 'amp_2q31.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 5(2Q31.2) MUTATED	46	102	114
AMP PEAK 5(2Q31.2) WILD-TYPE	125	104	88

Figure S20. Get High-res Image Gene #5: 'amp_2q31.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_2q31.2' versus 'METHLYATION_CNMF'

P value = 0.00765 (Fisher's exact test), Q value = 0.051

Table S21. Gene #5: 'amp_2q31.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 5(2Q31.2) MUTATED	95	70	93
AMP PEAK 5(2Q31.2) WILD-TYPE	77	105	128

Figure S21. Get High-res Image Gene #5: 'amp_2q31.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_2q31.2' versus 'RPPA_CNMF'

P value = 0.0282 (Fisher's exact test), Q value = 0.13

Table S22. Gene #5: 'amp_2q31.2' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	189	76
AMP PEAK 5(2Q31.2) MUTATED	64	96	25
AMP PEAK 5(2Q31.2) WILD-TYPE	82	93	51

Figure S22. Get High-res Image Gene #5: 'amp_2q31.2' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_3q26.2' versus 'MRNA_CNMF'

P value = 0.00897 (Fisher's exact test), Q value = 0.058

Table S23. Gene #6: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	216	126
AMP PEAK 6(3Q26.2) MUTATED	167	191	108
AMP PEAK 6(3Q26.2) WILD-TYPE	48	25	18

Figure S23. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0254 (Fisher's exact test), Q value = 0.12

Table S24. Gene #6: 'amp_3q26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	310	158	89
AMP PEAK 6(3Q26.2) MUTATED	257	141	68
AMP PEAK 6(3Q26.2) WILD-TYPE	53	17	21

Figure S24. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_3q26.2' versus 'CN_CNMF'

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

Table S25. Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 6(3Q26.2) MUTATED	113	181	191
AMP PEAK 6(3Q26.2) WILD-TYPE	58	25	11

Figure S25. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 0.0361 (Fisher's exact test), Q value = 0.15

Table S26. Gene #6: 'amp_3q26.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 6(3Q26.2) MUTATED	151	136	188
AMP PEAK 6(3Q26.2) WILD-TYPE	21	39	33

Figure S26. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_4p16.3' versus 'MIR_CNMF'

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

Table S27. Gene #7: 'amp_4p16.3' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	164	232
AMP PEAK 7(4P16.3) MUTATED	41	35	77
AMP PEAK 7(4P16.3) WILD-TYPE	118	129	155

Figure S27. Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_4p16.3' versus 'CN_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0051

Table S28. Gene #7: 'amp_4p16.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 7(4P16.3) MUTATED	32	76	52
AMP PEAK 7(4P16.3) WILD-TYPE	139	130	150

Figure S28. Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_4p16.3' versus 'METHLYATION_CNMF'

P value = 0.0269 (Fisher's exact test), Q value = 0.13

Table S29. Gene #7: 'amp_4p16.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 7(4P16.3) MUTATED	55	54	47
AMP PEAK 7(4P16.3) WILD-TYPE	117	121	174

Figure S29. Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0181 (Fisher's exact test), Q value = 0.096

Table S30. Gene #7: 'amp_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	71	165	106
AMP PEAK 7(4P16.3) MUTATED	22	24	57	22
AMP PEAK 7(4P16.3) WILD-TYPE	83	47	108	84

Figure S30. Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_4q13.3' versus 'CN_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0034

Table S31. Gene #8: 'amp_4q13.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 8(4Q13.3) MUTATED	17	54	42
AMP PEAK 8(4Q13.3) WILD-TYPE	154	152	160

Figure S31. Get High-res Image Gene #8: 'amp_4q13.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

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

Table S32. Gene #9: 'amp_5p15.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 9(5P15.33) MUTATED	60	123	126
AMP PEAK 9(5P15.33) WILD-TYPE	111	83	76

Figure S32. Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.028 (Fisher's exact test), Q value = 0.13

Table S33. Gene #9: 'amp_5p15.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	59	95
AMP PEAK 9(5P15.33) MUTATED	91	26	47
AMP PEAK 9(5P15.33) WILD-TYPE	55	33	48

Figure S33. Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 0.0242 (Fisher's exact test), Q value = 0.12

Table S34. Gene #9: 'amp_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	182	144
AMP PEAK 9(5P15.33) MUTATED	61	115	72
AMP PEAK 9(5P15.33) WILD-TYPE	60	67	72

Figure S34. Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_6p22.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0321 (Fisher's exact test), Q value = 0.14

Table S35. Gene #10: 'amp_6p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	310	158	89
AMP PEAK 10(6P22.3) MUTATED	167	71	55
AMP PEAK 10(6P22.3) WILD-TYPE	143	87	34

Figure S35. Get High-res Image Gene #10: 'amp_6p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_6p22.3' versus 'CN_CNMF'

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

Table S36. Gene #10: 'amp_6p22.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 10(6P22.3) MUTATED	59	124	123
AMP PEAK 10(6P22.3) WILD-TYPE	112	82	79

Figure S36. Get High-res Image Gene #10: 'amp_6p22.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_6p22.3' versus 'METHLYATION_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.076

Table S37. Gene #10: 'amp_6p22.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 10(6P22.3) MUTATED	104	78	117
AMP PEAK 10(6P22.3) WILD-TYPE	68	97	104

Figure S37. Get High-res Image Gene #10: 'amp_6p22.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_7q36.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00043

Table S38. Gene #11: 'amp_7q36.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 11(7Q36.3) MUTATED	69	124	127
AMP PEAK 11(7Q36.3) WILD-TYPE	102	82	75

Figure S38. Get High-res Image Gene #11: 'amp_7q36.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_8p11.21' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00061

Table S39. Gene #12: 'amp_8p11.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 12(8P11.21) MUTATED	42	70	99
AMP PEAK 12(8P11.21) WILD-TYPE	129	136	103

Figure S39. Get High-res Image Gene #12: 'amp_8p11.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_8p11.21' versus 'METHLYATION_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.089

Table S40. Gene #12: 'amp_8p11.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 12(8P11.21) MUTATED	78	57	72
AMP PEAK 12(8P11.21) WILD-TYPE	94	118	149

Figure S40. Get High-res Image Gene #12: 'amp_8p11.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_8p11.21' versus 'RPPA_CNMF'

P value = 0.0494 (Fisher's exact test), Q value = 0.18

Table S41. Gene #12: 'amp_8p11.21' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	189	76
AMP PEAK 12(8P11.21) MUTATED	41	77	29
AMP PEAK 12(8P11.21) WILD-TYPE	105	112	47

Figure S41. Get High-res Image Gene #12: 'amp_8p11.21' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_8q24.21' versus 'MRNA_CNMF'

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

Table S42. Gene #13: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	216	126
AMP PEAK 13(8Q24.21) MUTATED	144	188	110
AMP PEAK 13(8Q24.21) WILD-TYPE	71	28	16

Figure S42. Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8q24.21' versus 'MRNA_CHIERARCHICAL'

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

Table S43. Gene #13: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	310	158	89
AMP PEAK 13(8Q24.21) MUTATED	245	144	53
AMP PEAK 13(8Q24.21) WILD-TYPE	65	14	36

Figure S43. Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8q24.21' versus 'MIR_CHIERARCHICAL'

P value = 0.00283 (Fisher's exact test), Q value = 0.024

Table S44. Gene #13: 'amp_8q24.21' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	85	57	58	82	34	75	34	36	52	42
AMP PEAK 13(8Q24.21) MUTATED	71	46	43	67	31	64	24	27	30	38
AMP PEAK 13(8Q24.21) WILD-TYPE	14	11	15	15	3	11	10	9	22	4

Figure S44. Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

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

Table S45. Gene #13: 'amp_8q24.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 13(8Q24.21) MUTATED	113	200	148
AMP PEAK 13(8Q24.21) WILD-TYPE	58	6	54

Figure S45. Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 0.00445 (Fisher's exact test), Q value = 0.034

Table S46. Gene #13: 'amp_8q24.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 13(8Q24.21) MUTATED	124	137	189
AMP PEAK 13(8Q24.21) WILD-TYPE	48	38	32

Figure S46. Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

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

Table S47. Gene #13: 'amp_8q24.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	108	113
AMP PEAK 13(8Q24.21) MUTATED	70	72	106
AMP PEAK 13(8Q24.21) WILD-TYPE	9	36	7

Figure S47. Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S48. Gene #13: 'amp_8q24.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	59	95
AMP PEAK 13(8Q24.21) MUTATED	120	38	90
AMP PEAK 13(8Q24.21) WILD-TYPE	26	21	5

Figure S48. Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_10p15.3' versus 'CN_CNMF'

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

Table S49. Gene #14: 'amp_10p15.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 14(10P15.3) MUTATED	45	81	126
AMP PEAK 14(10P15.3) WILD-TYPE	126	125	76

Figure S49. Get High-res Image Gene #14: 'amp_10p15.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_10p15.3' versus 'METHLYATION_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0073

Table S50. Gene #14: 'amp_10p15.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 14(10P15.3) MUTATED	95	63	87
AMP PEAK 14(10P15.3) WILD-TYPE	77	112	134

Figure S50. Get High-res Image Gene #14: 'amp_10p15.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_10p15.3' versus 'MRNASEQ_CNMF'

P value = 0.0286 (Fisher's exact test), Q value = 0.13

Table S51. Gene #14: 'amp_10p15.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	108	113
AMP PEAK 14(10P15.3) MUTATED	25	55	45
AMP PEAK 14(10P15.3) WILD-TYPE	54	53	68

Figure S51. Get High-res Image Gene #14: 'amp_10p15.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_11q14.1' versus 'MRNA_CNMF'

P value = 0.00521 (Fisher's exact test), Q value = 0.038

Table S52. Gene #16: 'amp_11q14.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	216	126
AMP PEAK 16(11Q14.1) MUTATED	81	114	52
AMP PEAK 16(11Q14.1) WILD-TYPE	134	102	74

Figure S52. Get High-res Image Gene #16: 'amp_11q14.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11q14.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00375 (Fisher's exact test), Q value = 0.029

Table S53. Gene #16: 'amp_11q14.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	310	158	89
AMP PEAK 16(11Q14.1) MUTATED	154	66	27
AMP PEAK 16(11Q14.1) WILD-TYPE	156	92	62

Figure S53. Get High-res Image Gene #16: 'amp_11q14.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11q14.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00043

Table S54. Gene #16: 'amp_11q14.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 16(11Q14.1) MUTATED	54	117	86
AMP PEAK 16(11Q14.1) WILD-TYPE	117	89	116

Figure S54. Get High-res Image Gene #16: 'amp_11q14.1' versus Molecular Subtype #5: 'CN_CNMF'

'amp_11q14.1' versus 'METHLYATION_CNMF'

P value = 0.00257 (Fisher's exact test), Q value = 0.023

Table S55. Gene #16: 'amp_11q14.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 16(11Q14.1) MUTATED	82	59	111
AMP PEAK 16(11Q14.1) WILD-TYPE	90	116	110

Figure S55. Get High-res Image Gene #16: 'amp_11q14.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_11q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0187 (Fisher's exact test), Q value = 0.098

Table S56. Gene #16: 'amp_11q14.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	59	95
AMP PEAK 16(11Q14.1) MUTATED	75	18	47
AMP PEAK 16(11Q14.1) WILD-TYPE	71	41	48

Figure S56. Get High-res Image Gene #16: 'amp_11q14.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_11q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0427 (Fisher's exact test), Q value = 0.17

Table S57. Gene #16: 'amp_11q14.1' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2
ALL	12	10
AMP PEAK 16(11Q14.1) MUTATED	8	2
AMP PEAK 16(11Q14.1) WILD-TYPE	4	8

Figure S57. Get High-res Image Gene #16: 'amp_11q14.1' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_12p13.33' versus 'MRNA_CNMF'

P value = 0.0239 (Fisher's exact test), Q value = 0.12

Table S58. Gene #17: 'amp_12p13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	216	126
AMP PEAK 17(12P13.33) MUTATED	137	114	64
AMP PEAK 17(12P13.33) WILD-TYPE	78	102	62

Figure S58. Get High-res Image Gene #17: 'amp_12p13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_12p13.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.00309 (Fisher's exact test), Q value = 0.025

Table S59. Gene #17: 'amp_12p13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	310	158	89
AMP PEAK 17(12P13.33) MUTATED	175	77	63
AMP PEAK 17(12P13.33) WILD-TYPE	135	81	26

Figure S59. Get High-res Image Gene #17: 'amp_12p13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_12p13.33' versus 'CN_CNMF'

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

Table S60. Gene #17: 'amp_12p13.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 17(12P13.33) MUTATED	71	111	148
AMP PEAK 17(12P13.33) WILD-TYPE	100	95	54

Figure S60. Get High-res Image Gene #17: 'amp_12p13.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_12p13.33' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0028

Table S61. Gene #17: 'amp_12p13.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 17(12P13.33) MUTATED	119	96	108
AMP PEAK 17(12P13.33) WILD-TYPE	53	79	113

Figure S61. Get High-res Image Gene #17: 'amp_12p13.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_12p13.33' versus 'MRNASEQ_CNMF'

P value = 0.0187 (Fisher's exact test), Q value = 0.098

Table S62. Gene #17: 'amp_12p13.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	108	113
AMP PEAK 17(12P13.33) MUTATED	38	71	56
AMP PEAK 17(12P13.33) WILD-TYPE	41	37	57

Figure S62. Get High-res Image Gene #17: 'amp_12p13.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_12p13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00778 (Fisher's exact test), Q value = 0.051

Table S63. Gene #17: 'amp_12p13.33' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	71	165	106
AMP PEAK 17(12P13.33) MUTATED	45	45	103	57
AMP PEAK 17(12P13.33) WILD-TYPE	60	26	62	49

Figure S63. Get High-res Image Gene #17: 'amp_12p13.33' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIR_CHIERARCHICAL'

P value = 0.0411 (Fisher's exact test), Q value = 0.17

Table S64. Gene #18: 'amp_12p12.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	85	57	58	82	34	75	34	36	52	42
AMP PEAK 18(12P12.1) MUTATED	41	27	31	47	20	37	21	17	39	17
AMP PEAK 18(12P12.1) WILD-TYPE	44	30	27	35	14	38	13	19	13	25

Figure S64. Get High-res Image Gene #18: 'amp_12p12.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_12p12.1' versus 'CN_CNMF'

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

Table S65. Gene #18: 'amp_12p12.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 18(12P12.1) MUTATED	66	98	149
AMP PEAK 18(12P12.1) WILD-TYPE	105	108	53

Figure S65. Get High-res Image Gene #18: 'amp_12p12.1' versus Molecular Subtype #5: 'CN_CNMF'

'amp_12p12.1' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00086

Table S66. Gene #18: 'amp_12p12.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 18(12P12.1) MUTATED	117	87	102
AMP PEAK 18(12P12.1) WILD-TYPE	55	88	119

Figure S66. Get High-res Image Gene #18: 'amp_12p12.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CNMF'

P value = 0.00489 (Fisher's exact test), Q value = 0.036

Table S67. Gene #18: 'amp_12p12.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	108	113
AMP PEAK 18(12P12.1) MUTATED	32	70	63
AMP PEAK 18(12P12.1) WILD-TYPE	47	38	50

Figure S67. Get High-res Image Gene #18: 'amp_12p12.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00419 (Fisher's exact test), Q value = 0.032

Table S68. Gene #18: 'amp_12p12.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	59	95
AMP PEAK 18(12P12.1) MUTATED	68	42	55
AMP PEAK 18(12P12.1) WILD-TYPE	78	17	40

Figure S68. Get High-res Image Gene #18: 'amp_12p12.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00532 (Fisher's exact test), Q value = 0.038

Table S69. Gene #18: 'amp_12p12.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	71	165	106
AMP PEAK 18(12P12.1) MUTATED	43	44	100	52
AMP PEAK 18(12P12.1) WILD-TYPE	62	27	65	54

Figure S69. Get High-res Image Gene #18: 'amp_12p12.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0441 (Fisher's exact test), Q value = 0.17

Table S70. Gene #18: 'amp_12p12.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	6	2	2	6	4	2
AMP PEAK 18(12P12.1) MUTATED	4	0	0	2	4	2
AMP PEAK 18(12P12.1) WILD-TYPE	2	2	2	4	0	0

Figure S70. Get High-res Image Gene #18: 'amp_12p12.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q15' versus 'MRNA_CNMF'

P value = 0.0027 (Fisher's exact test), Q value = 0.023

Table S71. Gene #19: 'amp_12q15' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	216	126
AMP PEAK 19(12Q15) MUTATED	99	65	47
AMP PEAK 19(12Q15) WILD-TYPE	116	151	79

Figure S71. Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_12q15' versus 'MIR_CHIERARCHICAL'

P value = 0.00251 (Fisher's exact test), Q value = 0.023

Table S72. Gene #19: 'amp_12q15' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	85	57	58	82	34	75	34	36	52	42
AMP PEAK 19(12Q15) MUTATED	31	13	23	29	15	24	15	16	33	11
AMP PEAK 19(12Q15) WILD-TYPE	54	44	35	53	19	51	19	20	19	31

Figure S72. Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

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

Table S73. Gene #19: 'amp_12q15' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 19(12Q15) MUTATED	52	58	112
AMP PEAK 19(12Q15) WILD-TYPE	119	148	90

Figure S73. Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #5: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00086

Table S74. Gene #19: 'amp_12q15' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 19(12Q15) MUTATED	90	62	65
AMP PEAK 19(12Q15) WILD-TYPE	82	113	156

Figure S74. Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_12q15' versus 'MRNASEQ_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.069

Table S75. Gene #19: 'amp_12q15' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	108	113
AMP PEAK 19(12Q15) MUTATED	25	55	39
AMP PEAK 19(12Q15) WILD-TYPE	54	53	74

Figure S75. Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00247 (Fisher's exact test), Q value = 0.023

Table S76. Gene #19: 'amp_12q15' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	59	95
AMP PEAK 19(12Q15) MUTATED	53	35	31
AMP PEAK 19(12Q15) WILD-TYPE	93	24	64

Figure S76. Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_14q11.2' versus 'MRNA_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.091

Table S77. Gene #20: 'amp_14q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	216	126
AMP PEAK 20(14Q11.2) MUTATED	70	48	26
AMP PEAK 20(14Q11.2) WILD-TYPE	145	168	100

Figure S77. Get High-res Image Gene #20: 'amp_14q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_14q11.2' versus 'MIR_CHIERARCHICAL'

P value = 0.00679 (Fisher's exact test), Q value = 0.046

Table S78. Gene #20: 'amp_14q11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	85	57	58	82	34	75	34	36	52	42
AMP PEAK 20(14Q11.2) MUTATED	26	16	15	21	10	8	10	11	21	5
AMP PEAK 20(14Q11.2) WILD-TYPE	59	41	43	61	24	67	24	25	31	37

Figure S78. Get High-res Image Gene #20: 'amp_14q11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_14q32.33' versus 'MIR_CHIERARCHICAL'

P value = 0.0183 (Fisher's exact test), Q value = 0.097

Table S79. Gene #21: 'amp_14q32.33' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	85	57	58	82	34	75	34	36	52	42
AMP PEAK 21(14Q32.33) MUTATED	25	12	12	26	11	11	5	15	17	16
AMP PEAK 21(14Q32.33) WILD-TYPE	60	45	46	56	23	64	29	21	35	26

Figure S79. Get High-res Image Gene #21: 'amp_14q32.33' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_14q32.33' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0022

Table S80. Gene #21: 'amp_14q32.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 21(14Q32.33) MUTATED	41	77	38
AMP PEAK 21(14Q32.33) WILD-TYPE	130	129	164

Figure S80. Get High-res Image Gene #21: 'amp_14q32.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_15q26.3' versus 'CN_CNMF'

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

Table S81. Gene #22: 'amp_15q26.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 22(15Q26.3) MUTATED	34	90	39
AMP PEAK 22(15Q26.3) WILD-TYPE	137	116	163

Figure S81. Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_17q25.3' versus 'CN_CNMF'

P value = 0.00398 (Fisher's exact test), Q value = 0.031

Table S82. Gene #23: 'amp_17q25.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 23(17Q25.3) MUTATED	53	95	67
AMP PEAK 23(17Q25.3) WILD-TYPE	118	111	135

Figure S82. Get High-res Image Gene #23: 'amp_17q25.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_17q25.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0129 (Fisher's exact test), Q value = 0.078

Table S83. Gene #23: 'amp_17q25.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	54	60	154
AMP PEAK 23(17Q25.3) MUTATED	62	24	27	43
AMP PEAK 23(17Q25.3) WILD-TYPE	81	30	33	111

Figure S83. Get High-res Image Gene #23: 'amp_17q25.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_17q25.3' versus 'MRNASEQ_CNMF'

P value = 0.0268 (Fisher's exact test), Q value = 0.13

Table S84. Gene #23: 'amp_17q25.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	108	113
AMP PEAK 23(17Q25.3) MUTATED	36	31	49
AMP PEAK 23(17Q25.3) WILD-TYPE	43	77	64

Figure S84. Get High-res Image Gene #23: 'amp_17q25.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_18q11.2' versus 'CN_CNMF'

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

Table S85. Gene #24: 'amp_18q11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 24(18Q11.2) MUTATED	25	44	74
AMP PEAK 24(18Q11.2) WILD-TYPE	146	162	128

Figure S85. Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 0.00375 (Fisher's exact test), Q value = 0.029

Table S86. Gene #24: 'amp_18q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 24(18Q11.2) MUTATED	56	30	56
AMP PEAK 24(18Q11.2) WILD-TYPE	116	145	165

Figure S86. Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_19p13.12' versus 'MRNA_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0028

Table S87. Gene #25: 'amp_19p13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	216	126
AMP PEAK 25(19P13.12) MUTATED	136	115	51
AMP PEAK 25(19P13.12) WILD-TYPE	79	101	75

Figure S87. Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19p13.12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.0029

Table S88. Gene #25: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	310	158	89
AMP PEAK 25(19P13.12) MUTATED	186	64	52
AMP PEAK 25(19P13.12) WILD-TYPE	124	94	37

Figure S88. Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19p13.12' versus 'MIR_CNMF'

P value = 0.039 (Fisher's exact test), Q value = 0.16

Table S89. Gene #25: 'amp_19p13.12' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	164	232
AMP PEAK 25(19P13.12) MUTATED	85	77	139
AMP PEAK 25(19P13.12) WILD-TYPE	74	87	93

Figure S89. Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_19p13.12' versus 'CN_CNMF'

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

Table S90. Gene #25: 'amp_19p13.12' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 25(19P13.12) MUTATED	72	92	151
AMP PEAK 25(19P13.12) WILD-TYPE	99	114	51

Figure S90. Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19p13.12' versus 'METHLYATION_CNMF'

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

Table S91. Gene #25: 'amp_19p13.12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 25(19P13.12) MUTATED	118	73	116
AMP PEAK 25(19P13.12) WILD-TYPE	54	102	105

Figure S91. Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_19p13.12' versus 'RPPA_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0013

Table S92. Gene #25: 'amp_19p13.12' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	189	76
AMP PEAK 25(19P13.12) MUTATED	70	126	30
AMP PEAK 25(19P13.12) WILD-TYPE	76	63	46

Figure S92. Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_19p13.12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00143 (Fisher's exact test), Q value = 0.015

Table S93. Gene #25: 'amp_19p13.12' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	54	60	154
AMP PEAK 25(19P13.12) MUTATED	64	26	43	93
AMP PEAK 25(19P13.12) WILD-TYPE	79	28	17	61

Figure S93. Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_19p13.12' versus 'MRNASEQ_CNMF'

P value = 0.0419 (Fisher's exact test), Q value = 0.17

Table S94. Gene #25: 'amp_19p13.12' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	108	113
AMP PEAK 25(19P13.12) MUTATED	37	68	55
AMP PEAK 25(19P13.12) WILD-TYPE	42	40	58

Figure S94. Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00656 (Fisher's exact test), Q value = 0.045

Table S95. Gene #26: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	310	158	89
AMP PEAK 26(19Q12) MUTATED	186	72	55
AMP PEAK 26(19Q12) WILD-TYPE	124	86	34

Figure S95. Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q12' versus 'MIR_CNMF'

P value = 0.0286 (Fisher's exact test), Q value = 0.13

Table S96. Gene #26: 'amp_19q12' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	164	232
AMP PEAK 26(19Q12) MUTATED	92	78	141
AMP PEAK 26(19Q12) WILD-TYPE	67	86	91

Figure S96. Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_19q12' versus 'CN_CNMF'

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

Table S97. Gene #26: 'amp_19q12' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 26(19Q12) MUTATED	67	83	172
AMP PEAK 26(19Q12) WILD-TYPE	104	123	30

Figure S97. Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

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

Table S98. Gene #26: 'amp_19q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 26(19Q12) MUTATED	128	70	121
AMP PEAK 26(19Q12) WILD-TYPE	44	105	100

Figure S98. Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_19q12' versus 'RPPA_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.072

Table S99. Gene #26: 'amp_19q12' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	189	76
AMP PEAK 26(19Q12) MUTATED	70	117	35
AMP PEAK 26(19Q12) WILD-TYPE	76	72	41

Figure S99. Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_19q13.2' versus 'CN_CNMF'

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

Table S100. Gene #27: 'amp_19q13.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 27(19Q13.2) MUTATED	51	71	123
AMP PEAK 27(19Q13.2) WILD-TYPE	120	135	79

Figure S100. Get High-res Image Gene #27: 'amp_19q13.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19q13.2' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.0014

Table S101. Gene #27: 'amp_19q13.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 27(19Q13.2) MUTATED	94	56	91
AMP PEAK 27(19Q13.2) WILD-TYPE	78	119	130

Figure S101. Get High-res Image Gene #27: 'amp_19q13.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_19q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0268 (Fisher's exact test), Q value = 0.13

Table S102. Gene #27: 'amp_19q13.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	59	95
AMP PEAK 27(19Q13.2) MUTATED	55	34	37
AMP PEAK 27(19Q13.2) WILD-TYPE	91	25	58

Figure S102. Get High-res Image Gene #27: 'amp_19q13.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_20p13' versus 'MRNA_CHIERARCHICAL'

P value = 0.00538 (Fisher's exact test), Q value = 0.038

Table S103. Gene #28: 'amp_20p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	310	158	89
AMP PEAK 28(20P13) MUTATED	161	79	62
AMP PEAK 28(20P13) WILD-TYPE	149	79	27

Figure S103. Get High-res Image Gene #28: 'amp_20p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20p13' versus 'MIR_CHIERARCHICAL'

P value = 0.0333 (Fisher's exact test), Q value = 0.14

Table S104. Gene #28: 'amp_20p13' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	85	57	58	82	34	75	34	36	52	42
AMP PEAK 28(20P13) MUTATED	41	28	36	44	19	44	23	19	34	13
AMP PEAK 28(20P13) WILD-TYPE	44	29	22	38	15	31	11	17	18	29

Figure S104. Get High-res Image Gene #28: 'amp_20p13' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_20p13' versus 'CN_CNMF'

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

Table S105. Gene #28: 'amp_20p13' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 28(20P13) MUTATED	69	97	151
AMP PEAK 28(20P13) WILD-TYPE	102	109	51

Figure S105. Get High-res Image Gene #28: 'amp_20p13' versus Molecular Subtype #5: 'CN_CNMF'

'amp_20p13' versus 'METHLYATION_CNMF'

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

Table S106. Gene #28: 'amp_20p13' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 28(20P13) MUTATED	123	81	103
AMP PEAK 28(20P13) WILD-TYPE	49	94	118

Figure S106. Get High-res Image Gene #28: 'amp_20p13' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_20p13' versus 'MRNASEQ_CNMF'

P value = 0.015 (Fisher's exact test), Q value = 0.087

Table S107. Gene #28: 'amp_20p13' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	108	113
AMP PEAK 28(20P13) MUTATED	36	71	59
AMP PEAK 28(20P13) WILD-TYPE	43	37	54

Figure S107. Get High-res Image Gene #28: 'amp_20p13' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_20p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0448 (Fisher's exact test), Q value = 0.17

Table S108. Gene #28: 'amp_20p13' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	59	95
AMP PEAK 28(20P13) MUTATED	74	41	51
AMP PEAK 28(20P13) WILD-TYPE	72	18	44

Figure S108. Get High-res Image Gene #28: 'amp_20p13' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_20p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00068 (Fisher's exact test), Q value = 0.0079

Table S109. Gene #28: 'amp_20p13' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	71	165	106
AMP PEAK 28(20P13) MUTATED	44	44	106	50
AMP PEAK 28(20P13) WILD-TYPE	61	27	59	56

Figure S109. Get High-res Image Gene #28: 'amp_20p13' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNA_CNMF'

P value = 0.00255 (Fisher's exact test), Q value = 0.023

Table S110. Gene #29: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	216	126
AMP PEAK 29(20Q11.21) MUTATED	144	110	78
AMP PEAK 29(20Q11.21) WILD-TYPE	71	106	48

Figure S110. Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q11.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.00308 (Fisher's exact test), Q value = 0.025

Table S111. Gene #29: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	310	158	89
AMP PEAK 29(20Q11.21) MUTATED	178	87	67
AMP PEAK 29(20Q11.21) WILD-TYPE	132	71	22

Figure S111. Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q11.21' versus 'MIR_CHIERARCHICAL'

P value = 0.00324 (Fisher's exact test), Q value = 0.026

Table S112. Gene #29: 'amp_20q11.21' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	85	57	58	82	34	75	34	36	52	42
AMP PEAK 29(20Q11.21) MUTATED	45	33	36	44	20	45	29	22	40	18
AMP PEAK 29(20Q11.21) WILD-TYPE	40	24	22	38	14	30	5	14	12	24

Figure S112. Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_20q11.21' versus 'CN_CNMF'

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

Table S113. Gene #29: 'amp_20q11.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 29(20Q11.21) MUTATED	79	95	174
AMP PEAK 29(20Q11.21) WILD-TYPE	92	111	28

Figure S113. Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_20q11.21' versus 'METHLYATION_CNMF'

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

Table S114. Gene #29: 'amp_20q11.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 29(20Q11.21) MUTATED	140	91	109
AMP PEAK 29(20Q11.21) WILD-TYPE	32	84	112

Figure S114. Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CNMF'

P value = 0.00332 (Fisher's exact test), Q value = 0.026

Table S115. Gene #29: 'amp_20q11.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	108	113
AMP PEAK 29(20Q11.21) MUTATED	37	77	69
AMP PEAK 29(20Q11.21) WILD-TYPE	42	31	44

Figure S115. Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00259 (Fisher's exact test), Q value = 0.023

Table S116. Gene #29: 'amp_20q11.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	59	95
AMP PEAK 29(20Q11.21) MUTATED	80	47	56
AMP PEAK 29(20Q11.21) WILD-TYPE	66	12	39

Figure S116. Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.008

Table S117. Gene #29: 'amp_20q11.21' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	71	165	106
AMP PEAK 29(20Q11.21) MUTATED	52	46	119	57
AMP PEAK 29(20Q11.21) WILD-TYPE	53	25	46	49

Figure S117. Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MRNA_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.066

Table S118. Gene #30: 'amp_20q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	216	126
AMP PEAK 30(20Q13.33) MUTATED	164	136	86
AMP PEAK 30(20Q13.33) WILD-TYPE	51	80	40

Figure S118. Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q13.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.00074 (Fisher's exact test), Q value = 0.0083

Table S119. Gene #30: 'amp_20q13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	310	158	89
AMP PEAK 30(20Q13.33) MUTATED	207	103	76
AMP PEAK 30(20Q13.33) WILD-TYPE	103	55	13

Figure S119. Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q13.33' versus 'MIR_CHIERARCHICAL'

P value = 0.0014 (Fisher's exact test), Q value = 0.014

Table S120. Gene #30: 'amp_20q13.33' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	85	57	58	82	34	75	34	36	52	42
AMP PEAK 30(20Q13.33) MUTATED	49	35	41	52	29	54	29	26	45	25
AMP PEAK 30(20Q13.33) WILD-TYPE	36	22	17	30	5	21	5	10	7	17

Figure S120. Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_20q13.33' versus 'CN_CNMF'

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

Table S121. Gene #30: 'amp_20q13.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 30(20Q13.33) MUTATED	87	132	183
AMP PEAK 30(20Q13.33) WILD-TYPE	84	74	19

Figure S121. Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_20q13.33' versus 'METHLYATION_CNMF'

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

Table S122. Gene #30: 'amp_20q13.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 30(20Q13.33) MUTATED	144	109	140
AMP PEAK 30(20Q13.33) WILD-TYPE	28	66	81

Figure S122. Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CNMF'

P value = 0.0254 (Fisher's exact test), Q value = 0.12

Table S123. Gene #30: 'amp_20q13.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	108	113
AMP PEAK 30(20Q13.33) MUTATED	49	86	78
AMP PEAK 30(20Q13.33) WILD-TYPE	30	22	35

Figure S123. Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00248 (Fisher's exact test), Q value = 0.023

Table S124. Gene #30: 'amp_20q13.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	59	95
AMP PEAK 30(20Q13.33) MUTATED	95	52	66
AMP PEAK 30(20Q13.33) WILD-TYPE	51	7	29

Figure S124. Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0495 (Fisher's exact test), Q value = 0.18

Table S125. Gene #30: 'amp_20q13.33' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	71	165	106
AMP PEAK 30(20Q13.33) MUTATED	69	53	128	68
AMP PEAK 30(20Q13.33) WILD-TYPE	36	18	37	38

Figure S125. Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.084

Table S126. Gene #30: 'amp_20q13.33' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	6	2	2	6	4	2
AMP PEAK 30(20Q13.33) MUTATED	6	2	0	3	4	2
AMP PEAK 30(20Q13.33) WILD-TYPE	0	0	2	3	0	0

Figure S126. Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_22q12.2' versus 'MIR_CHIERARCHICAL'

P value = 0.0342 (Fisher's exact test), Q value = 0.14

Table S127. Gene #31: 'amp_22q12.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	85	57	58	82	34	75	34	36	52	42
AMP PEAK 31(22Q12.2) MUTATED	11	7	15	16	4	16	5	8	3	2
AMP PEAK 31(22Q12.2) WILD-TYPE	74	50	43	66	30	59	29	28	49	40

Figure S127. Get High-res Image Gene #31: 'amp_22q12.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_22q12.2' versus 'CN_CNMF'

P value = 0.00762 (Fisher's exact test), Q value = 0.051

Table S128. Gene #31: 'amp_22q12.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 31(22Q12.2) MUTATED	15	40	36
AMP PEAK 31(22Q12.2) WILD-TYPE	156	166	166

Figure S128. Get High-res Image Gene #31: 'amp_22q12.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_22q12.2' versus 'METHLYATION_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.0088

Table S129. Gene #31: 'amp_22q12.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 31(22Q12.2) MUTATED	27	14	48
AMP PEAK 31(22Q12.2) WILD-TYPE	145	161	173

Figure S129. Get High-res Image Gene #31: 'amp_22q12.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_22q12.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00154 (Fisher's exact test), Q value = 0.015

Table S130. Gene #31: 'amp_22q12.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	54	60	154
AMP PEAK 31(22Q12.2) MUTATED	22	18	13	16
AMP PEAK 31(22Q12.2) WILD-TYPE	121	36	47	138

Figure S130. Get High-res Image Gene #31: 'amp_22q12.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_22q12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0147 (Fisher's exact test), Q value = 0.086

Table S131. Gene #31: 'amp_22q12.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	71	165	106
AMP PEAK 31(22Q12.2) MUTATED	15	8	38	10
AMP PEAK 31(22Q12.2) WILD-TYPE	90	63	127	96

Figure S131. Get High-res Image Gene #31: 'amp_22q12.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_xp11.23' versus 'CN_CNMF'

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

Table S132. Gene #32: 'amp_xp11.23' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 32(XP11.23) MUTATED	25	55	79
AMP PEAK 32(XP11.23) WILD-TYPE	146	151	123

Figure S132. Get High-res Image Gene #32: 'amp_xp11.23' versus Molecular Subtype #5: 'CN_CNMF'

'amp_xp11.23' versus 'METHLYATION_CNMF'

P value = 0.00191 (Fisher's exact test), Q value = 0.018

Table S133. Gene #32: 'amp_xp11.23' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 32(XP11.23) MUTATED	64	37	53
AMP PEAK 32(XP11.23) WILD-TYPE	108	138	168

Figure S133. Get High-res Image Gene #32: 'amp_xp11.23' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_xp11.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0312 (Fisher's exact test), Q value = 0.14

Table S134. Gene #32: 'amp_xp11.23' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	71	165	106
AMP PEAK 32(XP11.23) MUTATED	23	27	53	23
AMP PEAK 32(XP11.23) WILD-TYPE	82	44	112	83

Figure S134. Get High-res Image Gene #32: 'amp_xp11.23' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_xq28' versus 'CN_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0046

Table S135. Gene #33: 'amp_xq28' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
AMP PEAK 33(XQ28) MUTATED	46	96	78
AMP PEAK 33(XQ28) WILD-TYPE	125	110	124

Figure S135. Get High-res Image Gene #33: 'amp_xq28' versus Molecular Subtype #5: 'CN_CNMF'

'amp_xq28' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0427 (Fisher's exact test), Q value = 0.17

Table S136. Gene #33: 'amp_xq28' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2
ALL	12	10
AMP PEAK 33(XQ28) MUTATED	8	2
AMP PEAK 33(XQ28) WILD-TYPE	4	8

Figure S136. Get High-res Image Gene #33: 'amp_xq28' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'MIR_CNMF'

P value = 0.03 (Fisher's exact test), Q value = 0.13

Table S137. Gene #34: 'del_1p36.11' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	164	232
DEL PEAK 1(1P36.11) MUTATED	74	92	99
DEL PEAK 1(1P36.11) WILD-TYPE	85	72	133

Figure S137. Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #3: 'MIR_CNMF'

'del_1p36.11' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00099

Table S138. Gene #34: 'del_1p36.11' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 1(1P36.11) MUTATED	87	113	69
DEL PEAK 1(1P36.11) WILD-TYPE	84	93	133

Figure S138. Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #5: 'CN_CNMF'

'del_1p36.11' versus 'RPPA_CNMF'

P value = 0.0495 (Fisher's exact test), Q value = 0.18

Table S139. Gene #34: 'del_1p36.11' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	189	76
DEL PEAK 1(1P36.11) MUTATED	76	75	39
DEL PEAK 1(1P36.11) WILD-TYPE	70	114	37

Figure S139. Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_1q41' versus 'CN_CNMF'

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

Table S140. Gene #35: 'del_1q41' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 2(1Q41) MUTATED	14	60	23
DEL PEAK 2(1Q41) WILD-TYPE	157	146	179

Figure S140. Get High-res Image Gene #35: 'del_1q41' versus Molecular Subtype #5: 'CN_CNMF'

'del_2q22.1' versus 'MIR_CHIERARCHICAL'

P value = 0.0036 (Fisher's exact test), Q value = 0.028

Table S141. Gene #37: 'del_2q22.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	85	57	58	82	34	75	34	36	52	42
DEL PEAK 4(2Q22.1) MUTATED	22	8	8	20	14	18	4	17	12	10
DEL PEAK 4(2Q22.1) WILD-TYPE	63	49	50	62	20	57	30	19	40	32

Figure S141. Get High-res Image Gene #37: 'del_2q22.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_2q37.3' versus 'MRNA_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.09

Table S142. Gene #38: 'del_2q37.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	216	126
DEL PEAK 5(2Q37.3) MUTATED	51	78	41
DEL PEAK 5(2Q37.3) WILD-TYPE	164	138	85

Figure S142. Get High-res Image Gene #38: 'del_2q37.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_2q37.3' versus 'MIR_CHIERARCHICAL'

P value = 0.0274 (Fisher's exact test), Q value = 0.13

Table S143. Gene #38: 'del_2q37.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	85	57	58	82	34	75	34	36	52	42
DEL PEAK 5(2Q37.3) MUTATED	23	12	16	31	9	24	6	20	14	15
DEL PEAK 5(2Q37.3) WILD-TYPE	62	45	42	51	25	51	28	16	38	27

Figure S143. Get High-res Image Gene #38: 'del_2q37.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00075

Table S144. Gene #38: 'del_2q37.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 5(2Q37.3) MUTATED	35	86	54
DEL PEAK 5(2Q37.3) WILD-TYPE	136	120	148

Figure S144. Get High-res Image Gene #38: 'del_2q37.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 0.0239 (Fisher's exact test), Q value = 0.12

Table S145. Gene #38: 'del_2q37.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	182	144
DEL PEAK 5(2Q37.3) MUTATED	42	66	33
DEL PEAK 5(2Q37.3) WILD-TYPE	79	116	111

Figure S145. Get High-res Image Gene #38: 'del_2q37.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0193 (Fisher's exact test), Q value = 0.1

Table S146. Gene #38: 'del_2q37.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	71	165	106
DEL PEAK 5(2Q37.3) MUTATED	45	19	52	25
DEL PEAK 5(2Q37.3) WILD-TYPE	60	52	113	81

Figure S146. Get High-res Image Gene #38: 'del_2q37.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0074

Table S147. Gene #39: 'del_3p26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	310	158	89
DEL PEAK 6(3P26.2) MUTATED	101	54	49
DEL PEAK 6(3P26.2) WILD-TYPE	209	104	40

Figure S147. Get High-res Image Gene #39: 'del_3p26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p26.2' versus 'MIR_CNMF'

P value = 0.00624 (Fisher's exact test), Q value = 0.043

Table S148. Gene #39: 'del_3p26.2' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	164	232
DEL PEAK 6(3P26.2) MUTATED	54	47	102
DEL PEAK 6(3P26.2) WILD-TYPE	105	117	130

Figure S148. Get High-res Image Gene #39: 'del_3p26.2' versus Molecular Subtype #3: 'MIR_CNMF'

'del_3p26.2' versus 'MIR_CHIERARCHICAL'

P value = 0.00472 (Fisher's exact test), Q value = 0.035

Table S149. Gene #39: 'del_3p26.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	85	57	58	82	34	75	34	36	52	42
DEL PEAK 6(3P26.2) MUTATED	29	20	12	34	13	26	17	16	28	8
DEL PEAK 6(3P26.2) WILD-TYPE	56	37	46	48	21	49	17	20	24	34

Figure S149. Get High-res Image Gene #39: 'del_3p26.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_3p26.2' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00086

Table S150. Gene #39: 'del_3p26.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 6(3P26.2) MUTATED	47	66	96
DEL PEAK 6(3P26.2) WILD-TYPE	124	140	106

Figure S150. Get High-res Image Gene #39: 'del_3p26.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_3p26.2' versus 'METHLYATION_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.0071

Table S151. Gene #39: 'del_3p26.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
DEL PEAK 6(3P26.2) MUTATED	83	51	74
DEL PEAK 6(3P26.2) WILD-TYPE	89	124	147

Figure S151. Get High-res Image Gene #39: 'del_3p26.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_3p26.2' versus 'MRNASEQ_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.0091

Table S152. Gene #39: 'del_3p26.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	108	113
DEL PEAK 6(3P26.2) MUTATED	16	46	50
DEL PEAK 6(3P26.2) WILD-TYPE	63	62	63

Figure S152. Get High-res Image Gene #39: 'del_3p26.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_3p26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00093 (Fisher's exact test), Q value = 0.0098

Table S153. Gene #39: 'del_3p26.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	59	95
DEL PEAK 6(3P26.2) MUTATED	39	29	44
DEL PEAK 6(3P26.2) WILD-TYPE	107	30	51

Figure S153. Get High-res Image Gene #39: 'del_3p26.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_3q13.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0368 (Fisher's exact test), Q value = 0.15

Table S154. Gene #40: 'del_3q13.31' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	54	60	154
DEL PEAK 7(3Q13.31) MUTATED	27	7	14	15
DEL PEAK 7(3Q13.31) WILD-TYPE	116	47	46	139

Figure S154. Get High-res Image Gene #40: 'del_3q13.31' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_3q13.31' versus 'MRNASEQ_CNMF'

P value = 0.0438 (Fisher's exact test), Q value = 0.17

Table S155. Gene #40: 'del_3q13.31' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	108	113
DEL PEAK 7(3Q13.31) MUTATED	5	16	21
DEL PEAK 7(3Q13.31) WILD-TYPE	74	92	92

Figure S155. Get High-res Image Gene #40: 'del_3q13.31' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0233 (Fisher's exact test), Q value = 0.12

Table S156. Gene #41: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	310	158	89
DEL PEAK 8(4Q22.1) MUTATED	212	96	69
DEL PEAK 8(4Q22.1) WILD-TYPE	98	62	20

Figure S156. Get High-res Image Gene #41: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.088

Table S157. Gene #41: 'del_4q22.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 8(4Q22.1) MUTATED	114	128	152
DEL PEAK 8(4Q22.1) WILD-TYPE	57	78	50

Figure S157. Get High-res Image Gene #41: 'del_4q22.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_4q34.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00071 (Fisher's exact test), Q value = 0.008

Table S158. Gene #42: 'del_4q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	310	158	89
DEL PEAK 9(4Q34.3) MUTATED	226	102	77
DEL PEAK 9(4Q34.3) WILD-TYPE	84	56	12

Figure S158. Get High-res Image Gene #42: 'del_4q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q34.3' versus 'MIR_CHIERARCHICAL'

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

Table S159. Gene #42: 'del_4q34.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	85	57	58	82	34	75	34	36	52	42
DEL PEAK 9(4Q34.3) MUTATED	66	42	41	65	22	49	29	24	43	23
DEL PEAK 9(4Q34.3) WILD-TYPE	19	15	17	17	12	26	5	12	9	19

Figure S159. Get High-res Image Gene #42: 'del_4q34.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 0.0295 (Fisher's exact test), Q value = 0.13

Table S160. Gene #42: 'del_4q34.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	108	113
DEL PEAK 9(4Q34.3) MUTATED	64	79	72
DEL PEAK 9(4Q34.3) WILD-TYPE	15	29	41

Figure S160. Get High-res Image Gene #42: 'del_4q34.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0461 (Fisher's exact test), Q value = 0.18

Table S161. Gene #42: 'del_4q34.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	59	95
DEL PEAK 9(4Q34.3) MUTATED	110	46	59
DEL PEAK 9(4Q34.3) WILD-TYPE	36	13	36

Figure S161. Get High-res Image Gene #42: 'del_4q34.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

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

Table S162. Gene #43: 'del_5q12.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 10(5Q12.1) MUTATED	73	145	137
DEL PEAK 10(5Q12.1) WILD-TYPE	98	61	65

Figure S162. Get High-res Image Gene #43: 'del_5q12.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0034

Table S163. Gene #43: 'del_5q12.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
DEL PEAK 10(5Q12.1) MUTATED	117	85	146
DEL PEAK 10(5Q12.1) WILD-TYPE	55	90	75

Figure S163. Get High-res Image Gene #43: 'del_5q12.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_5q13.2' versus 'CN_CNMF'

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

Table S164. Gene #44: 'del_5q13.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 11(5Q13.2) MUTATED	92	180	147
DEL PEAK 11(5Q13.2) WILD-TYPE	79	26	55

Figure S164. Get High-res Image Gene #44: 'del_5q13.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_6q27' versus 'CN_CNMF'

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

Table S165. Gene #45: 'del_6q27' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 12(6Q27) MUTATED	121	162	97
DEL PEAK 12(6Q27) WILD-TYPE	50	44	105

Figure S165. Get High-res Image Gene #45: 'del_6q27' versus Molecular Subtype #5: 'CN_CNMF'

'del_6q27' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00086

Table S166. Gene #45: 'del_6q27' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
DEL PEAK 12(6Q27) MUTATED	91	132	152
DEL PEAK 12(6Q27) WILD-TYPE	81	43	69

Figure S166. Get High-res Image Gene #45: 'del_6q27' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_6q27' versus 'MRNASEQ_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0084

Table S167. Gene #45: 'del_6q27' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	108	113
DEL PEAK 12(6Q27) MUTATED	56	52	79
DEL PEAK 12(6Q27) WILD-TYPE	23	56	34

Figure S167. Get High-res Image Gene #45: 'del_6q27' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_6q27' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00181 (Fisher's exact test), Q value = 0.018

Table S168. Gene #45: 'del_6q27' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	59	95
DEL PEAK 12(6Q27) MUTATED	92	26	69
DEL PEAK 12(6Q27) WILD-TYPE	54	33	26

Figure S168. Get High-res Image Gene #45: 'del_6q27' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_6q27' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0242 (Fisher's exact test), Q value = 0.12

Table S169. Gene #45: 'del_6q27' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	71	165	106
DEL PEAK 12(6Q27) MUTATED	79	43	96	72
DEL PEAK 12(6Q27) WILD-TYPE	26	28	69	34

Figure S169. Get High-res Image Gene #45: 'del_6q27' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_7p22.1' versus 'CN_CNMF'

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

Table S170. Gene #46: 'del_7p22.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 13(7P22.1) MUTATED	48	135	70
DEL PEAK 13(7P22.1) WILD-TYPE	123	71	132

Figure S170. Get High-res Image Gene #46: 'del_7p22.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_8p23.3' versus 'MRNA_CNMF'

P value = 0.0444 (Fisher's exact test), Q value = 0.17

Table S171. Gene #47: 'del_8p23.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	216	126
DEL PEAK 14(8P23.3) MUTATED	132	157	85
DEL PEAK 14(8P23.3) WILD-TYPE	83	59	41

Figure S171. Get High-res Image Gene #47: 'del_8p23.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p23.3' versus 'MIR_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.07

Table S172. Gene #47: 'del_8p23.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	85	57	58	82	34	75	34	36	52	42
DEL PEAK 14(8P23.3) MUTATED	57	36	34	61	30	53	15	27	33	29
DEL PEAK 14(8P23.3) WILD-TYPE	28	21	24	21	4	22	19	9	19	13

Figure S172. Get High-res Image Gene #47: 'del_8p23.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_8p23.3' versus 'CN_CNMF'

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

Table S173. Gene #47: 'del_8p23.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 14(8P23.3) MUTATED	78	162	148
DEL PEAK 14(8P23.3) WILD-TYPE	93	44	54

Figure S173. Get High-res Image Gene #47: 'del_8p23.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_8p21.2' versus 'MRNA_CNMF'

P value = 0.0412 (Fisher's exact test), Q value = 0.17

Table S174. Gene #48: 'del_8p21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	216	126
DEL PEAK 15(8P21.2) MUTATED	138	160	94
DEL PEAK 15(8P21.2) WILD-TYPE	77	56	32

Figure S174. Get High-res Image Gene #48: 'del_8p21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p21.2' versus 'MIR_CHIERARCHICAL'

P value = 0.00554 (Fisher's exact test), Q value = 0.039

Table S175. Gene #48: 'del_8p21.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	85	57	58	82	34	75	34	36	52	42
DEL PEAK 15(8P21.2) MUTATED	66	35	39	56	30	51	16	30	36	33
DEL PEAK 15(8P21.2) WILD-TYPE	19	22	19	26	4	24	18	6	16	9

Figure S175. Get High-res Image Gene #48: 'del_8p21.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_8p21.2' versus 'CN_CNMF'

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

Table S176. Gene #48: 'del_8p21.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 15(8P21.2) MUTATED	88	166	152
DEL PEAK 15(8P21.2) WILD-TYPE	83	40	50

Figure S176. Get High-res Image Gene #48: 'del_8p21.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_9p24.3' versus 'MRNA_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0034

Table S177. Gene #49: 'del_9p24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	216	126
DEL PEAK 16(9P24.3) MUTATED	109	73	66
DEL PEAK 16(9P24.3) WILD-TYPE	106	143	60

Figure S177. Get High-res Image Gene #49: 'del_9p24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p24.3' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00075

Table S178. Gene #49: 'del_9p24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	310	158	89
DEL PEAK 16(9P24.3) MUTATED	120	69	59
DEL PEAK 16(9P24.3) WILD-TYPE	190	89	30

Figure S178. Get High-res Image Gene #49: 'del_9p24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p24.3' versus 'MIR_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.08

Table S179. Gene #49: 'del_9p24.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	85	57	58	82	34	75	34	36	52	42
DEL PEAK 16(9P24.3) MUTATED	34	21	28	30	18	27	16	16	36	20
DEL PEAK 16(9P24.3) WILD-TYPE	51	36	30	52	16	48	18	20	16	22

Figure S179. Get High-res Image Gene #49: 'del_9p24.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_9p24.3' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00099

Table S180. Gene #49: 'del_9p24.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
DEL PEAK 16(9P24.3) MUTATED	92	90	75
DEL PEAK 16(9P24.3) WILD-TYPE	80	85	146

Figure S180. Get High-res Image Gene #49: 'del_9p24.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_9p24.3' versus 'MRNASEQ_CNMF'

P value = 0.0234 (Fisher's exact test), Q value = 0.12

Table S181. Gene #49: 'del_9p24.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	108	113
DEL PEAK 16(9P24.3) MUTATED	26	57	53
DEL PEAK 16(9P24.3) WILD-TYPE	53	51	60

Figure S181. Get High-res Image Gene #49: 'del_9p24.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_9q34.13' versus 'MRNA_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.094

Table S182. Gene #50: 'del_9q34.13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	216	126
DEL PEAK 17(9Q34.13) MUTATED	143	121	66
DEL PEAK 17(9Q34.13) WILD-TYPE	72	95	60

Figure S182. Get High-res Image Gene #50: 'del_9q34.13' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9q34.13' versus 'MRNA_CHIERARCHICAL'

P value = 0.00082 (Fisher's exact test), Q value = 0.0089

Table S183. Gene #50: 'del_9q34.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	310	158	89
DEL PEAK 17(9Q34.13) MUTATED	185	79	66
DEL PEAK 17(9Q34.13) WILD-TYPE	125	79	23

Figure S183. Get High-res Image Gene #50: 'del_9q34.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9q34.13' versus 'CN_CNMF'

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

Table S184. Gene #50: 'del_9q34.13' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 17(9Q34.13) MUTATED	93	98	151
DEL PEAK 17(9Q34.13) WILD-TYPE	78	108	51

Figure S184. Get High-res Image Gene #50: 'del_9q34.13' versus Molecular Subtype #5: 'CN_CNMF'

'del_9q34.13' versus 'METHLYATION_CNMF'

P value = 0.0176 (Fisher's exact test), Q value = 0.094

Table S185. Gene #50: 'del_9q34.13' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
DEL PEAK 17(9Q34.13) MUTATED	115	91	132
DEL PEAK 17(9Q34.13) WILD-TYPE	57	84	89

Figure S185. Get High-res Image Gene #50: 'del_9q34.13' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_9q34.13' versus 'RPPA_CHIERARCHICAL'

P value = 0.0463 (Fisher's exact test), Q value = 0.18

Table S186. Gene #50: 'del_9q34.13' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	54	60	154
DEL PEAK 17(9Q34.13) MUTATED	70	34	31	98
DEL PEAK 17(9Q34.13) WILD-TYPE	73	20	29	56

Figure S186. Get High-res Image Gene #50: 'del_9q34.13' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_9q34.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00871 (Fisher's exact test), Q value = 0.056

Table S187. Gene #50: 'del_9q34.13' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	59	95
DEL PEAK 17(9Q34.13) MUTATED	82	46	54
DEL PEAK 17(9Q34.13) WILD-TYPE	64	13	41

Figure S187. Get High-res Image Gene #50: 'del_9q34.13' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_9q34.13' versus 'MIRSEQ_CNMF'

P value = 0.0496 (Fisher's exact test), Q value = 0.18

Table S188. Gene #50: 'del_9q34.13' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	182	144
DEL PEAK 17(9Q34.13) MUTATED	65	107	98
DEL PEAK 17(9Q34.13) WILD-TYPE	56	75	46

Figure S188. Get High-res Image Gene #50: 'del_9q34.13' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_10q24.2' versus 'MRNA_CNMF'

P value = 0.00315 (Fisher's exact test), Q value = 0.025

Table S189. Gene #52: 'del_10q24.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	216	126
DEL PEAK 19(10Q24.2) MUTATED	87	112	43
DEL PEAK 19(10Q24.2) WILD-TYPE	128	104	83

Figure S189. Get High-res Image Gene #52: 'del_10q24.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q24.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00232 (Fisher's exact test), Q value = 0.022

Table S190. Gene #52: 'del_10q24.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	310	158	89
DEL PEAK 19(10Q24.2) MUTATED	152	64	26
DEL PEAK 19(10Q24.2) WILD-TYPE	158	94	63

Figure S190. Get High-res Image Gene #52: 'del_10q24.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q24.2' versus 'MIR_CNMF'

P value = 0.00689 (Fisher's exact test), Q value = 0.047

Table S191. Gene #52: 'del_10q24.2' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	164	232
DEL PEAK 19(10Q24.2) MUTATED	70	56	116
DEL PEAK 19(10Q24.2) WILD-TYPE	89	108	116

Figure S191. Get High-res Image Gene #52: 'del_10q24.2' versus Molecular Subtype #3: 'MIR_CNMF'

'del_10q24.2' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00086

Table S192. Gene #52: 'del_10q24.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 19(10Q24.2) MUTATED	53	111	87
DEL PEAK 19(10Q24.2) WILD-TYPE	118	95	115

Figure S192. Get High-res Image Gene #52: 'del_10q24.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_10q24.2' versus 'METHLYATION_CNMF'

P value = 0.002 (Fisher's exact test), Q value = 0.019

Table S193. Gene #52: 'del_10q24.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
DEL PEAK 19(10Q24.2) MUTATED	79	58	111
DEL PEAK 19(10Q24.2) WILD-TYPE	93	117	110

Figure S193. Get High-res Image Gene #52: 'del_10q24.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_10q24.2' versus 'RPPA_CHIERARCHICAL'

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

Table S194. Gene #52: 'del_10q24.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	54	60	154
DEL PEAK 19(10Q24.2) MUTATED	52	32	27	71
DEL PEAK 19(10Q24.2) WILD-TYPE	91	22	33	83

Figure S194. Get High-res Image Gene #52: 'del_10q24.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_10q24.2' versus 'MIRSEQ_CNMF'

P value = 0.00159 (Fisher's exact test), Q value = 0.016

Table S195. Gene #52: 'del_10q24.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	182	144
DEL PEAK 19(10Q24.2) MUTATED	48	102	55
DEL PEAK 19(10Q24.2) WILD-TYPE	73	80	89

Figure S195. Get High-res Image Gene #52: 'del_10q24.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'CN_CNMF'

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

Table S196. Gene #53: 'del_11p15.5' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 20(11P15.5) MUTATED	77	163	106
DEL PEAK 20(11P15.5) WILD-TYPE	94	43	96

Figure S196. Get High-res Image Gene #53: 'del_11p15.5' versus Molecular Subtype #5: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 0.00781 (Fisher's exact test), Q value = 0.051

Table S197. Gene #53: 'del_11p15.5' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
DEL PEAK 20(11P15.5) MUTATED	89	100	148
DEL PEAK 20(11P15.5) WILD-TYPE	83	75	73

Figure S197. Get High-res Image Gene #53: 'del_11p15.5' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00875 (Fisher's exact test), Q value = 0.056

Table S198. Gene #53: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	71	165	106
DEL PEAK 20(11P15.5) MUTATED	76	38	91	56
DEL PEAK 20(11P15.5) WILD-TYPE	29	33	74	50

Figure S198. Get High-res Image Gene #53: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_12q24.33' versus 'MRNA_CNMF'

P value = 0.00116 (Fisher's exact test), Q value = 0.012

Table S199. Gene #55: 'del_12q24.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	216	126
DEL PEAK 22(12Q24.33) MUTATED	62	99	51
DEL PEAK 22(12Q24.33) WILD-TYPE	153	117	75

Figure S199. Get High-res Image Gene #55: 'del_12q24.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12q24.33' versus 'MIR_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 0.083

Table S200. Gene #55: 'del_12q24.33' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	85	57	58	82	34	75	34	36	52	42
DEL PEAK 22(12Q24.33) MUTATED	34	21	19	35	11	34	7	19	11	21
DEL PEAK 22(12Q24.33) WILD-TYPE	51	36	39	47	23	41	27	17	41	21

Figure S200. Get High-res Image Gene #55: 'del_12q24.33' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_12q24.33' versus 'CN_CNMF'

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

Table S201. Gene #55: 'del_12q24.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 22(12Q24.33) MUTATED	56	113	51
DEL PEAK 22(12Q24.33) WILD-TYPE	115	93	151

Figure S201. Get High-res Image Gene #55: 'del_12q24.33' versus Molecular Subtype #5: 'CN_CNMF'

'del_12q24.33' versus 'METHLYATION_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.1

Table S202. Gene #55: 'del_12q24.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
DEL PEAK 22(12Q24.33) MUTATED	51	75	91
DEL PEAK 22(12Q24.33) WILD-TYPE	121	100	130

Figure S202. Get High-res Image Gene #55: 'del_12q24.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_12q24.33' versus 'MRNASEQ_CNMF'

P value = 0.0492 (Fisher's exact test), Q value = 0.18

Table S203. Gene #55: 'del_12q24.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	108	113
DEL PEAK 22(12Q24.33) MUTATED	33	29	45
DEL PEAK 22(12Q24.33) WILD-TYPE	46	79	68

Figure S203. Get High-res Image Gene #55: 'del_12q24.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_12q24.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0262 (Fisher's exact test), Q value = 0.12

Table S204. Gene #55: 'del_12q24.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	59	95
DEL PEAK 22(12Q24.33) MUTATED	53	13	41
DEL PEAK 22(12Q24.33) WILD-TYPE	93	46	54

Figure S204. Get High-res Image Gene #55: 'del_12q24.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_12q24.33' versus 'MIRSEQ_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.089

Table S205. Gene #55: 'del_12q24.33' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	182	144
DEL PEAK 22(12Q24.33) MUTATED	42	82	43
DEL PEAK 22(12Q24.33) WILD-TYPE	79	100	101

Figure S205. Get High-res Image Gene #55: 'del_12q24.33' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_12q24.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.005 (Fisher's exact test), Q value = 0.037

Table S206. Gene #55: 'del_12q24.33' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	71	165	106
DEL PEAK 22(12Q24.33) MUTATED	54	20	60	33
DEL PEAK 22(12Q24.33) WILD-TYPE	51	51	105	73

Figure S206. Get High-res Image Gene #55: 'del_12q24.33' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MRNA_CNMF'

P value = 0.00956 (Fisher's exact test), Q value = 0.061

Table S207. Gene #56: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	216	126
DEL PEAK 23(13Q14.2) MUTATED	133	150	67
DEL PEAK 23(13Q14.2) WILD-TYPE	82	66	59

Figure S207. Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q14.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0161 (Fisher's exact test), Q value = 0.09

Table S208. Gene #56: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	310	158	89
DEL PEAK 23(13Q14.2) MUTATED	211	88	51
DEL PEAK 23(13Q14.2) WILD-TYPE	99	70	38

Figure S208. Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q14.2' versus 'MIR_CHIERARCHICAL'

P value = 0.0418 (Fisher's exact test), Q value = 0.17

Table S209. Gene #56: 'del_13q14.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	85	57	58	82	34	75	34	36	52	42
DEL PEAK 23(13Q14.2) MUTATED	52	37	42	52	26	37	16	27	32	29
DEL PEAK 23(13Q14.2) WILD-TYPE	33	20	16	30	8	38	18	9	20	13

Figure S209. Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0033

Table S210. Gene #56: 'del_13q14.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 23(13Q14.2) MUTATED	90	150	124
DEL PEAK 23(13Q14.2) WILD-TYPE	81	56	78

Figure S210. Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00075

Table S211. Gene #56: 'del_13q14.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
DEL PEAK 23(13Q14.2) MUTATED	109	88	161
DEL PEAK 23(13Q14.2) WILD-TYPE	63	87	60

Figure S211. Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_13q14.2' versus 'RPPA_CNMF'

P value = 0.00114 (Fisher's exact test), Q value = 0.012

Table S212. Gene #56: 'del_13q14.2' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	189	76
DEL PEAK 23(13Q14.2) MUTATED	76	135	45
DEL PEAK 23(13Q14.2) WILD-TYPE	70	54	31

Figure S212. Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_13q14.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00293 (Fisher's exact test), Q value = 0.024

Table S213. Gene #56: 'del_13q14.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	54	60	154
DEL PEAK 23(13Q14.2) MUTATED	73	32	42	109
DEL PEAK 23(13Q14.2) WILD-TYPE	70	22	18	45

Figure S213. Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 0.0198 (Fisher's exact test), Q value = 0.1

Table S214. Gene #56: 'del_13q14.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	108	113
DEL PEAK 23(13Q14.2) MUTATED	54	77	61
DEL PEAK 23(13Q14.2) WILD-TYPE	25	31	52

Figure S214. Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0441 (Fisher's exact test), Q value = 0.17

Table S215. Gene #56: 'del_13q14.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	59	95
DEL PEAK 23(13Q14.2) MUTATED	101	40	51
DEL PEAK 23(13Q14.2) WILD-TYPE	45	19	44

Figure S215. Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_14q23.3' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00061

Table S216. Gene #57: 'del_14q23.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 24(14Q23.3) MUTATED	70	104	131
DEL PEAK 24(14Q23.3) WILD-TYPE	101	102	71

Figure S216. Get High-res Image Gene #57: 'del_14q23.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_15q11.2' versus 'MRNA_CNMF'

P value = 0.00613 (Fisher's exact test), Q value = 0.043

Table S217. Gene #58: 'del_15q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	216	126
DEL PEAK 25(15Q11.2) MUTATED	130	98	62
DEL PEAK 25(15Q11.2) WILD-TYPE	85	118	64

Figure S217. Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0369 (Fisher's exact test), Q value = 0.15

Table S218. Gene #58: 'del_15q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	310	158	89
DEL PEAK 25(15Q11.2) MUTATED	164	71	55
DEL PEAK 25(15Q11.2) WILD-TYPE	146	87	34

Figure S218. Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q11.2' versus 'MIR_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.067

Table S219. Gene #58: 'del_15q11.2' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	164	232
DEL PEAK 25(15Q11.2) MUTATED	77	74	138
DEL PEAK 25(15Q11.2) WILD-TYPE	82	90	94

Figure S219. Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #3: 'MIR_CNMF'

'del_15q11.2' versus 'MIR_CHIERARCHICAL'

P value = 0.00593 (Fisher's exact test), Q value = 0.042

Table S220. Gene #58: 'del_15q11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	85	57	58	82	34	75	34	36	52	42
DEL PEAK 25(15Q11.2) MUTATED	35	28	36	40	19	43	23	21	32	12
DEL PEAK 25(15Q11.2) WILD-TYPE	50	29	22	42	15	32	11	15	20	30

Figure S220. Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_15q11.2' versus 'CN_CNMF'

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

Table S221. Gene #58: 'del_15q11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 25(15Q11.2) MUTATED	68	76	155
DEL PEAK 25(15Q11.2) WILD-TYPE	103	130	47

Figure S221. Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_15q11.2' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00075

Table S222. Gene #58: 'del_15q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
DEL PEAK 25(15Q11.2) MUTATED	114	82	100
DEL PEAK 25(15Q11.2) WILD-TYPE	58	93	121

Figure S222. Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_15q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0065

Table S223. Gene #58: 'del_15q11.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	108	113
DEL PEAK 25(15Q11.2) MUTATED	29	70	54
DEL PEAK 25(15Q11.2) WILD-TYPE	50	38	59

Figure S223. Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_15q11.2' versus 'MIRSEQ_CNMF'

P value = 0.0251 (Fisher's exact test), Q value = 0.12

Table S224. Gene #58: 'del_15q11.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	182	144
DEL PEAK 25(15Q11.2) MUTATED	54	110	79
DEL PEAK 25(15Q11.2) WILD-TYPE	67	72	65

Figure S224. Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_15q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00956 (Fisher's exact test), Q value = 0.061

Table S225. Gene #58: 'del_15q11.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	71	165	106
DEL PEAK 25(15Q11.2) MUTATED	43	40	102	58
DEL PEAK 25(15Q11.2) WILD-TYPE	62	31	63	48

Figure S225. Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MRNA_CNMF'

P value = 0.0258 (Fisher's exact test), Q value = 0.12

Table S226. Gene #59: 'del_15q15.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	216	126
DEL PEAK 26(15Q15.1) MUTATED	150	124	78
DEL PEAK 26(15Q15.1) WILD-TYPE	65	92	48

Figure S226. Get High-res Image Gene #59: 'del_15q15.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q15.1' versus 'MIR_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.11

Table S227. Gene #59: 'del_15q15.1' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	164	232
DEL PEAK 26(15Q15.1) MUTATED	95	94	162
DEL PEAK 26(15Q15.1) WILD-TYPE	64	70	70

Figure S227. Get High-res Image Gene #59: 'del_15q15.1' versus Molecular Subtype #3: 'MIR_CNMF'

'del_15q15.1' versus 'MIR_CHIERARCHICAL'

P value = 0.00252 (Fisher's exact test), Q value = 0.023

Table S228. Gene #59: 'del_15q15.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	85	57	58	82	34	75	34	36	52	42
DEL PEAK 26(15Q15.1) MUTATED	43	32	42	51	23	52	23	26	41	18
DEL PEAK 26(15Q15.1) WILD-TYPE	42	25	16	31	11	23	11	10	11	24

Figure S228. Get High-res Image Gene #59: 'del_15q15.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_15q15.1' versus 'CN_CNMF'

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

Table S229. Gene #59: 'del_15q15.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 26(15Q15.1) MUTATED	81	115	167
DEL PEAK 26(15Q15.1) WILD-TYPE	90	91	35

Figure S229. Get High-res Image Gene #59: 'del_15q15.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_15q15.1' versus 'METHLYATION_CNMF'

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

Table S230. Gene #59: 'del_15q15.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
DEL PEAK 26(15Q15.1) MUTATED	134	97	129
DEL PEAK 26(15Q15.1) WILD-TYPE	38	78	92

Figure S230. Get High-res Image Gene #59: 'del_15q15.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_15q15.1' versus 'MRNASEQ_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.09

Table S231. Gene #59: 'del_15q15.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	108	113
DEL PEAK 26(15Q15.1) MUTATED	42	79	70
DEL PEAK 26(15Q15.1) WILD-TYPE	37	29	43

Figure S231. Get High-res Image Gene #59: 'del_15q15.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_15q15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00184 (Fisher's exact test), Q value = 0.018

Table S232. Gene #59: 'del_15q15.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	71	165	106
DEL PEAK 26(15Q15.1) MUTATED	58	48	124	61
DEL PEAK 26(15Q15.1) WILD-TYPE	47	23	41	45

Figure S232. Get High-res Image Gene #59: 'del_15q15.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIR_CHIERARCHICAL'

P value = 0.0298 (Fisher's exact test), Q value = 0.13

Table S233. Gene #60: 'del_16p13.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	85	57	58	82	34	75	34	36	52	42
DEL PEAK 27(16P13.3) MUTATED	42	29	25	45	21	43	21	29	25	19
DEL PEAK 27(16P13.3) WILD-TYPE	43	28	33	37	13	32	13	7	27	23

Figure S233. Get High-res Image Gene #60: 'del_16p13.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_16p13.3' versus 'RPPA_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.17

Table S234. Gene #60: 'del_16p13.3' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	189	76
DEL PEAK 27(16P13.3) MUTATED	85	104	31
DEL PEAK 27(16P13.3) WILD-TYPE	61	85	45

Figure S234. Get High-res Image Gene #60: 'del_16p13.3' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_16q22.1' versus 'MIR_CNMF'

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

Table S235. Gene #61: 'del_16q22.1' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	164	232
DEL PEAK 28(16Q22.1) MUTATED	127	120	195
DEL PEAK 28(16Q22.1) WILD-TYPE	32	44	37

Figure S235. Get High-res Image Gene #61: 'del_16q22.1' versus Molecular Subtype #3: 'MIR_CNMF'

'del_16q22.1' versus 'CN_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.0075

Table S236. Gene #61: 'del_16q22.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 28(16Q22.1) MUTATED	119	171	171
DEL PEAK 28(16Q22.1) WILD-TYPE	52	35	31

Figure S236. Get High-res Image Gene #61: 'del_16q22.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_16q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0472 (Fisher's exact test), Q value = 0.18

Table S237. Gene #61: 'del_16q22.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	71	165	106
DEL PEAK 28(16Q22.1) MUTATED	89	50	140	83
DEL PEAK 28(16Q22.1) WILD-TYPE	16	21	25	23

Figure S237. Get High-res Image Gene #61: 'del_16q22.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0022

Table S238. Gene #62: 'del_16q23.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 29(16Q23.1) MUTATED	114	168	170
DEL PEAK 29(16Q23.1) WILD-TYPE	57	38	32

Figure S238. Get High-res Image Gene #62: 'del_16q23.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0497 (Fisher's exact test), Q value = 0.18

Table S239. Gene #62: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	71	165	106
DEL PEAK 29(16Q23.1) MUTATED	87	51	140	79
DEL PEAK 29(16Q23.1) WILD-TYPE	18	20	25	27

Figure S239. Get High-res Image Gene #62: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_17q11.2' versus 'CN_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.0075

Table S240. Gene #64: 'del_17q11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 31(17Q11.2) MUTATED	136	184	152
DEL PEAK 31(17Q11.2) WILD-TYPE	35	22	50

Figure S240. Get High-res Image Gene #64: 'del_17q11.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_17q11.2' versus 'METHLYATION_CNMF'

P value = 0.00302 (Fisher's exact test), Q value = 0.025

Table S241. Gene #64: 'del_17q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
DEL PEAK 31(17Q11.2) MUTATED	127	145	193
DEL PEAK 31(17Q11.2) WILD-TYPE	45	30	28

Figure S241. Get High-res Image Gene #64: 'del_17q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_18q23' versus 'CN_CNMF'

P value = 0.00262 (Fisher's exact test), Q value = 0.023

Table S242. Gene #65: 'del_18q23' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 32(18Q23) MUTATED	103	154	124
DEL PEAK 32(18Q23) WILD-TYPE	68	52	78

Figure S242. Get High-res Image Gene #65: 'del_18q23' versus Molecular Subtype #5: 'CN_CNMF'

'del_18q23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0466 (Fisher's exact test), Q value = 0.18

Table S243. Gene #65: 'del_18q23' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	59	95
DEL PEAK 32(18Q23) MUTATED	86	45	65
DEL PEAK 32(18Q23) WILD-TYPE	60	14	30

Figure S243. Get High-res Image Gene #65: 'del_18q23' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0046

Table S244. Gene #66: 'del_19p13.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 33(19P13.3) MUTATED	142	178	192
DEL PEAK 33(19P13.3) WILD-TYPE	29	28	10

Figure S244. Get High-res Image Gene #66: 'del_19p13.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 0.0178 (Fisher's exact test), Q value = 0.095

Table S245. Gene #66: 'del_19p13.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
DEL PEAK 33(19P13.3) MUTATED	161	153	187
DEL PEAK 33(19P13.3) WILD-TYPE	11	22	34

Figure S245. Get High-res Image Gene #66: 'del_19p13.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_19p13.3' versus 'RPPA_CNMF'

P value = 0.0041 (Fisher's exact test), Q value = 0.031

Table S246. Gene #66: 'del_19p13.3' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	189	76
DEL PEAK 33(19P13.3) MUTATED	129	175	59
DEL PEAK 33(19P13.3) WILD-TYPE	17	14	17

Figure S246. Get High-res Image Gene #66: 'del_19p13.3' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_19q13.33' versus 'MRNA_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0028

Table S247. Gene #67: 'del_19q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	216	126
DEL PEAK 34(19Q13.33) MUTATED	127	117	46
DEL PEAK 34(19Q13.33) WILD-TYPE	88	99	80

Figure S247. Get High-res Image Gene #67: 'del_19q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19q13.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.00223 (Fisher's exact test), Q value = 0.021

Table S248. Gene #67: 'del_19q13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	310	158	89
DEL PEAK 34(19Q13.33) MUTATED	178	64	48
DEL PEAK 34(19Q13.33) WILD-TYPE	132	94	41

Figure S248. Get High-res Image Gene #67: 'del_19q13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19q13.33' versus 'MIR_CNMF'

P value = 0.0469 (Fisher's exact test), Q value = 0.18

Table S249. Gene #67: 'del_19q13.33' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	164	232
DEL PEAK 34(19Q13.33) MUTATED	78	76	135
DEL PEAK 34(19Q13.33) WILD-TYPE	81	88	97

Figure S249. Get High-res Image Gene #67: 'del_19q13.33' versus Molecular Subtype #3: 'MIR_CNMF'

'del_19q13.33' versus 'MIR_CHIERARCHICAL'

P value = 0.0205 (Fisher's exact test), Q value = 0.11

Table S250. Gene #67: 'del_19q13.33' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	85	57	58	82	34	75	34	36	52	42
DEL PEAK 34(19Q13.33) MUTATED	44	35	36	50	10	32	18	16	23	25
DEL PEAK 34(19Q13.33) WILD-TYPE	41	22	22	32	24	43	16	20	29	17

Figure S250. Get High-res Image Gene #67: 'del_19q13.33' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_19q13.33' versus 'CN_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.083

Table S251. Gene #67: 'del_19q13.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 34(19Q13.33) MUTATED	86	93	120
DEL PEAK 34(19Q13.33) WILD-TYPE	85	113	82

Figure S251. Get High-res Image Gene #67: 'del_19q13.33' versus Molecular Subtype #5: 'CN_CNMF'

'del_19q13.33' versus 'METHLYATION_CNMF'

P value = 0.00239 (Fisher's exact test), Q value = 0.022

Table S252. Gene #67: 'del_19q13.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
DEL PEAK 34(19Q13.33) MUTATED	103	73	118
DEL PEAK 34(19Q13.33) WILD-TYPE	69	102	103

Figure S252. Get High-res Image Gene #67: 'del_19q13.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_19q13.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.0323 (Fisher's exact test), Q value = 0.14

Table S253. Gene #67: 'del_19q13.33' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	54	60	154
DEL PEAK 34(19Q13.33) MUTATED	59	33	35	74
DEL PEAK 34(19Q13.33) WILD-TYPE	84	21	25	80

Figure S253. Get High-res Image Gene #67: 'del_19q13.33' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_19q13.33' versus 'MRNASEQ_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 0.088

Table S254. Gene #67: 'del_19q13.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	108	113
DEL PEAK 34(19Q13.33) MUTATED	38	63	44
DEL PEAK 34(19Q13.33) WILD-TYPE	41	45	69

Figure S254. Get High-res Image Gene #67: 'del_19q13.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_19q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 0.09

Table S255. Gene #67: 'del_19q13.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	59	95
DEL PEAK 34(19Q13.33) MUTATED	71	37	37
DEL PEAK 34(19Q13.33) WILD-TYPE	75	22	58

Figure S255. Get High-res Image Gene #67: 'del_19q13.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.43' versus 'MRNA_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 0.09

Table S256. Gene #68: 'del_19q13.43' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	216	126
DEL PEAK 35(19Q13.43) MUTATED	121	104	51
DEL PEAK 35(19Q13.43) WILD-TYPE	94	112	75

Figure S256. Get High-res Image Gene #68: 'del_19q13.43' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19q13.43' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0017

Table S257. Gene #68: 'del_19q13.43' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 35(19Q13.43) MUTATED	84	80	121
DEL PEAK 35(19Q13.43) WILD-TYPE	87	126	81

Figure S257. Get High-res Image Gene #68: 'del_19q13.43' versus Molecular Subtype #5: 'CN_CNMF'

'del_19q13.43' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00061

Table S258. Gene #68: 'del_19q13.43' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
DEL PEAK 35(19Q13.43) MUTATED	105	64	111
DEL PEAK 35(19Q13.43) WILD-TYPE	67	111	110

Figure S258. Get High-res Image Gene #68: 'del_19q13.43' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_19q13.43' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0427 (Fisher's exact test), Q value = 0.17

Table S259. Gene #68: 'del_19q13.43' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2
ALL	12	10
DEL PEAK 35(19Q13.43) MUTATED	8	2
DEL PEAK 35(19Q13.43) WILD-TYPE	4	8

Figure S259. Get High-res Image Gene #68: 'del_19q13.43' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_19q13.43' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0215 (Fisher's exact test), Q value = 0.11

Table S260. Gene #68: 'del_19q13.43' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	6	2	2	6	4	2
DEL PEAK 35(19Q13.43) MUTATED	3	2	2	1	0	2
DEL PEAK 35(19Q13.43) WILD-TYPE	3	0	0	5	4	0

Figure S260. Get High-res Image Gene #68: 'del_19q13.43' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q22.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0406 (Fisher's exact test), Q value = 0.17

Table S261. Gene #69: 'del_21q22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	310	158	89
DEL PEAK 36(21Q22.3) MUTATED	117	58	46
DEL PEAK 36(21Q22.3) WILD-TYPE	193	100	43

Figure S261. Get High-res Image Gene #69: 'del_21q22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_22q13.32' versus 'MIR_CNMF'

P value = 0.0334 (Fisher's exact test), Q value = 0.14

Table S262. Gene #70: 'del_22q13.32' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	164	232
DEL PEAK 37(22Q13.32) MUTATED	136	135	211
DEL PEAK 37(22Q13.32) WILD-TYPE	23	29	21

Figure S262. Get High-res Image Gene #70: 'del_22q13.32' versus Molecular Subtype #3: 'MIR_CNMF'

'del_22q13.32' versus 'CN_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 0.094

Table S263. Gene #70: 'del_22q13.32' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	206	202
DEL PEAK 37(22Q13.32) MUTATED	138	182	183
DEL PEAK 37(22Q13.32) WILD-TYPE	33	24	19

Figure S263. Get High-res Image Gene #70: 'del_22q13.32' versus Molecular Subtype #5: 'CN_CNMF'

'del_22q13.32' versus 'RPPA_CNMF'

P value = 0.038 (Fisher's exact test), Q value = 0.16

Table S264. Gene #70: 'del_22q13.32' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	189	76
DEL PEAK 37(22Q13.32) MUTATED	124	171	60
DEL PEAK 37(22Q13.32) WILD-TYPE	22	18	16

Figure S264. Get High-res Image Gene #70: 'del_22q13.32' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_22q13.32' versus 'RPPA_CHIERARCHICAL'

P value = 0.0427 (Fisher's exact test), Q value = 0.17

Table S265. Gene #70: 'del_22q13.32' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	54	60	154
DEL PEAK 37(22Q13.32) MUTATED	115	46	53	141
DEL PEAK 37(22Q13.32) WILD-TYPE	28	8	7	13

Figure S265. Get High-res Image Gene #70: 'del_22q13.32' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_CNMF'

P value = 0.0366 (Fisher's exact test), Q value = 0.15

Table S266. Gene #70: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	182	144
DEL PEAK 37(22Q13.32) MUTATED	97	164	128
DEL PEAK 37(22Q13.32) WILD-TYPE	24	18	16

Figure S266. Get High-res Image Gene #70: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 0.0208 (Fisher's exact test), Q value = 0.11

Table S267. Gene #71: 'del_xp21.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
DEL PEAK 38(XP21.1) MUTATED	93	107	150
DEL PEAK 38(XP21.1) WILD-TYPE	79	68	71

Figure S267. Get High-res Image Gene #71: 'del_xp21.1' versus Molecular Subtype #6: 'METHLYATION_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/OV-TP/19783383/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/OV-TP/20141012/OV-TP.transferedmergedcluster.txt
Number of patients = 579
Number of significantly focal cnvs = 71
Number of molecular subtypes = 14
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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