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 52 focal events and 12 molecular subtypes across 513 patients, 338 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
amp_1q32.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_2p24.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_3q26.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_4q12 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7p11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7q31.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7q32.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q24.13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_9q34.3 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
amp_10p15.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_11q24.1 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12p13.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_12q14.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_13q34 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_15q26.3 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
amp_19p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_xp11.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_xp11.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.32 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p32.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1q43 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_2q37.3 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_3p21.31 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_3q13.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_3q29 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_4q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5p15.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_5q34 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_6p25.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_6q22.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q24.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_7p22.3 cnv correlated to 'CN_CNMF'.
del_8q24.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q26.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p15.5 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_11p15.1 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_12q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_13q14.2 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_13q14.2 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_13q34 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_14q24.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q23 cnv correlated to 'METHLYATION_CNMF'.
del_19q13.41 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19q13.42 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_22q13.31 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xq21.1 cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 52 focal events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 338 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA 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
del 1p36 32	206 (40%)	307	0.0006 (0.00192)	0.00028 (0.000955)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.00071 (0.00223)	0.845 (0.933)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	1e-05 (4.55e-05)
del 1p32 3	196 (38%)	317	0.0279 (0.0566)	0.00019 (0.000674)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.00055 (0.00179)	0.614 (0.718)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	1e-05 (4.55e-05)
del 19q13 41	267 (52%)	246	0.0342 (0.0673)	0.0103 (0.0232)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.00091 (0.00269)	0.183 (0.266)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	1e-05 (4.55e-05)
del 19q13 42	278 (54%)	235	0.0352 (0.0686)	0.0207 (0.0437)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.00213 (0.00578)	0.575 (0.689)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	1e-05 (4.55e-05)
del 22q13 31	77 (15%)	436	0.251 (0.348)	0.0422 (0.0795)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.00021 (0.000736)	0.0113 (0.0255)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.0354 (0.0688)	1e-05 (4.55e-05)	0.00159 (0.00439)	3e-05 (0.000123)
amp 7p11 2	128 (25%)	385	0.764 (0.852)	0.403 (0.514)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	2e-05 (8.55e-05)	0.0116 (0.0258)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.00037 (0.00125)	1e-05 (4.55e-05)	6e-05 (0.000233)	1e-05 (4.55e-05)
del 10q26 3	151 (29%)	362	0.0839 (0.144)	0.707 (0.805)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.00026 (0.000891)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	2e-05 (8.55e-05)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	1e-05 (4.55e-05)
del 14q24 3	121 (24%)	392	0.301 (0.403)	0.0978 (0.164)	0.00458 (0.0112)	0.012 (0.0265)	0.00158 (0.00438)	0.0374 (0.0726)	0.00088 (0.00261)	0.0007 (0.00221)	0.00038 (0.00127)	0.00497 (0.0121)	0.00176 (0.00484)	0.00111 (0.00319)
amp 4q12	30 (6%)	483	1 (1.00)	0.0431 (0.0805)	0.00023 (0.000797)	0.0002 (0.000705)	0.0092 (0.0212)	0.279 (0.38)	0.00017 (0.00061)	1e-05 (4.55e-05)	0.00309 (0.00803)	0.0001 (0.000376)	0.944 (1.00)	0.0039 (0.00985)
amp 7q31 2	174 (34%)	339	1 (1.00)	0.812 (0.9)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.004 (0.01)	0.185 (0.268)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.0102 (0.023)	1e-05 (4.55e-05)	0.00892 (0.0206)	1e-05 (4.55e-05)
amp 12q14 1	37 (7%)	476			1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.0146 (0.0317)	0.731 (0.824)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.00306 (0.00799)	1e-05 (4.55e-05)	0.0422 (0.0795)	1e-05 (4.55e-05)
del 9p21 3	176 (34%)	337	0.332 (0.438)	0.0636 (0.112)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	3e-05 (0.000123)	2e-05 (8.55e-05)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.249 (0.347)	1e-05 (4.55e-05)	0.00088 (0.00261)	1e-05 (4.55e-05)
del 11p15 1	72 (14%)	441	1 (1.00)	0.0316 (0.063)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.0123 (0.0272)	0.792 (0.881)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	2e-05 (8.55e-05)	6e-05 (0.000233)	0.872 (0.954)	0.0328 (0.0652)
amp 7q32 3	182 (35%)	331	0.695 (0.795)	1 (1.00)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.00681 (0.0161)	0.165 (0.247)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.0571 (0.102)	1e-05 (4.55e-05)	0.0221 (0.0464)	1e-05 (4.55e-05)
amp 8q24 13	100 (19%)	413	0.37 (0.474)	0.235 (0.33)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.0422 (0.0795)	0.487 (0.602)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.0288 (0.0582)	0.00088 (0.00261)	0.109 (0.18)	3e-05 (0.000123)
del 2q37 3	77 (15%)	436	0.372 (0.476)	0.013 (0.0284)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.00453 (0.0112)	0.0195 (0.0413)	0.00078 (0.00241)	1e-05 (4.55e-05)	0.0147 (0.0317)	0.14 (0.222)	0.102 (0.168)	0.0811 (0.139)
del 3p21 31	49 (10%)	464	1 (1.00)	0.00712 (0.0166)	0.0001 (0.000376)	0.00217 (0.00586)	0.00206 (0.00561)	0.261 (0.359)	0.0418 (0.0795)	0.00105 (0.00308)	0.00052 (0.00171)	0.00235 (0.00624)	0.726 (0.82)	0.0508 (0.0931)
del 4q34 3	138 (27%)	375	1 (1.00)	0.358 (0.463)	0.0135 (0.0294)	1e-05 (4.55e-05)	0.165 (0.247)	0.223 (0.315)	0.0239 (0.0498)	0.00015 (0.000547)	0.0295 (0.0592)	0.0388 (0.0749)	0.00111 (0.00319)	0.00548 (0.0133)
del 13q14 2	142 (28%)	371	0.18 (0.263)	5e-05 (2e-04)	1e-05 (4.55e-05)	3e-05 (0.000123)	0.0345 (0.0677)	0.606 (0.715)	0.00706 (0.0166)	1e-05 (4.55e-05)	0.0182 (0.0389)	0.00608 (0.0146)	0.475 (0.588)	0.416 (0.525)
del 13q14 2	144 (28%)	369	0.181 (0.264)	9e-05 (0.000342)	1e-05 (4.55e-05)	3e-05 (0.000123)	0.0337 (0.0665)	0.713 (0.811)	0.00397 (0.00999)	1e-05 (4.55e-05)	0.0175 (0.0376)	0.00345 (0.00882)	0.437 (0.55)	0.36 (0.463)
amp 1q32 1	43 (8%)	470			1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.165 (0.247)	0.353 (0.458)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.251 (0.348)	2e-05 (8.55e-05)	0.00117 (0.00335)	2e-05 (8.55e-05)
amp 3q26 33	21 (4%)	492	1 (1.00)	0.581 (0.693)	1e-05 (4.55e-05)	0.00097 (0.00286)	0.144 (0.226)	0.852 (0.939)	0.00058 (0.00187)	0.00108 (0.00315)	0.00125 (0.00355)	0.0182 (0.0389)	0.0527 (0.0953)	0.00389 (0.00985)
amp 10p15 3	71 (14%)	442	0.526 (0.64)	0.0843 (0.144)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.0289 (0.0582)	0.135 (0.215)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.00076 (0.00237)	0.0765 (0.132)	0.334 (0.438)	0.00019 (0.000674)
amp 12p13 32	72 (14%)	441	0.866 (0.949)	0.0972 (0.163)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.115 (0.187)	0.189 (0.273)	0.00135 (0.00379)	1e-05 (4.55e-05)	0.00953 (0.0219)	0.00671 (0.0159)	0.024 (0.0498)	0.0854 (0.145)
amp 19p13 3	129 (25%)	384	0.0745 (0.13)	0.15 (0.233)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.885 (0.96)	0.579 (0.692)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.00014 (0.000514)	0.154 (0.235)	0.0452 (0.0835)	0.00083 (0.00251)
amp 19p13 2	122 (24%)	391	0.0755 (0.131)	0.151 (0.233)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.279 (0.38)	0.203 (0.289)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.00017 (0.00061)	0.141 (0.223)	0.0414 (0.079)	0.00049 (0.00163)
amp xp11 22	63 (12%)	450	0.649 (0.75)	1 (1.00)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.0268 (0.0547)	0.387 (0.494)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.00048 (0.0016)	0.352 (0.458)	0.076 (0.131)	0.00979 (0.0224)
del 6q22 31	78 (15%)	435	0.618 (0.72)	0.582 (0.693)	0.00011 (0.000411)	1e-05 (4.55e-05)	0.116 (0.188)	0.507 (0.619)	0.00449 (0.0111)	0.00109 (0.00316)	0.0008 (0.00245)	0.119 (0.192)	0.00634 (0.0152)	2e-05 (8.55e-05)
del 6q24 3	82 (16%)	431	0.17 (0.253)	0.279 (0.38)	0.00026 (0.000891)	1e-05 (4.55e-05)	0.0986 (0.164)	0.616 (0.72)	0.00138 (0.00386)	0.0003 (0.00102)	0.00014 (0.000514)	0.161 (0.243)	0.0209 (0.044)	4e-05 (0.000163)
del 8q24 3	29 (6%)	484			1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.929 (0.994)	0.459 (0.569)	0.00331 (0.0085)	0.00658 (0.0157)	0.0043 (0.0107)	0.00328 (0.00846)	0.167 (0.249)	0.0304 (0.0609)
del 9p23	150 (29%)	363	0.448 (0.559)	0.655 (0.755)	1e-05 (4.55e-05)	2e-05 (8.55e-05)	0.0389 (0.0749)	0.00228 (0.00611)	0.0222 (0.0465)	0.00022 (0.000767)	0.918 (0.988)	0.112 (0.184)	0.411 (0.52)	0.00326 (0.00844)
del 11p15 5	104 (20%)	409	0.642 (0.744)	0.00051 (0.00168)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.145 (0.226)	0.63 (0.731)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	6e-05 (0.000233)	0.00457 (0.0112)	0.99 (1.00)	0.887 (0.961)
del 13q34	110 (21%)	403	0.508 (0.619)	0.15 (0.233)	6e-05 (0.000233)	0.0115 (0.0257)	0.085 (0.145)	0.76 (0.851)	0.0432 (0.0805)	0.00079 (0.00243)	0.0263 (0.054)	0.00242 (0.0064)	0.309 (0.412)	0.175 (0.258)
del 3q29	47 (9%)	466	0.175 (0.258)	0.883 (0.96)	1e-05 (4.55e-05)	0.00063 (0.00201)	0.405 (0.515)	0.923 (0.991)	0.0161 (0.0347)	8e-05 (0.000308)	0.13 (0.208)	0.00469 (0.0114)	0.689 (0.79)	0.172 (0.255)
del 5p15 33	50 (10%)	463	1 (1.00)	0.0668 (0.118)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.865 (0.949)	0.584 (0.693)	0.00082 (0.0025)	6e-05 (0.000233)	0.00202 (0.00553)	0.206 (0.294)	0.948 (1.00)	0.442 (0.554)
del 5q34	64 (12%)	449	0.448 (0.559)	0.237 (0.332)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.162 (0.244)	1 (1.00)	2e-05 (8.55e-05)	1e-05 (4.55e-05)	5e-05 (2e-04)	0.145 (0.226)	0.612 (0.718)	0.666 (0.765)
del 12p13 1	38 (7%)	475			0.00069 (0.00219)	0.00218 (0.00586)	0.152 (0.234)	1 (1.00)	0.0102 (0.023)	0.00701 (0.0165)	0.0563 (0.101)	0.044 (0.0815)	0.955 (1.00)	0.255 (0.351)
del 12q12	72 (14%)	441	1 (1.00)	0.151 (0.233)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.911 (0.982)	0.281 (0.382)	0.0023 (0.00613)	1e-05 (4.55e-05)	0.0129 (0.0284)	0.494 (0.608)	0.911 (0.982)	0.962 (1.00)
amp 2p24 3	24 (5%)	489	0.619 (0.72)	0.583 (0.693)	0.00248 (0.00653)	0.0336 (0.0665)	0.49 (0.604)	1 (1.00)	0.177 (0.26)	0.00277 (0.00726)	0.721 (0.816)	0.035 (0.0685)	0.443 (0.555)	0.116 (0.188)
amp 13q34	22 (4%)	491			0.00141 (0.00393)	0.0013 (0.00367)	0.188 (0.272)	0.719 (0.816)	0.0401 (0.0767)	0.0228 (0.0476)	0.295 (0.396)	0.691 (0.791)	0.962 (1.00)	0.0502 (0.0922)
amp 15q26 3	19 (4%)	494	1 (1.00)	0.0427 (0.08)	5e-05 (2e-04)	0.00078 (0.00241)	0.222 (0.315)	0.607 (0.715)	0.0265 (0.0543)	0.0626 (0.111)	0.497 (0.61)	0.285 (0.385)	0.59 (0.699)	0.192 (0.276)
amp xp11 22	48 (9%)	465	0.651 (0.751)	1 (1.00)	1e-05 (4.55e-05)	1e-05 (4.55e-05)	0.317 (0.421)	0.731 (0.824)	0.00122 (0.00348)	3e-05 (0.000123)	0.0554 (0.0994)	0.6 (0.709)	0.333 (0.438)	0.109 (0.18)
del 3q13 31	39 (8%)	474	0.174 (0.257)	0.882 (0.96)	9e-05 (0.000342)	0.00416 (0.0104)	0.341 (0.446)	0.174 (0.257)	0.149 (0.233)	0.0132 (0.0288)	0.157 (0.239)	0.00058 (0.00187)	0.575 (0.689)	0.117 (0.189)
amp 1q22	42 (8%)	471			0.00053 (0.00173)	0.00755 (0.0176)	0.25 (0.348)	0.884 (0.96)	0.00559 (0.0135)	0.0572 (0.102)	0.57 (0.685)	0.0897 (0.151)	0.154 (0.235)	0.317 (0.421)
amp 11q24 1	87 (17%)	426	0.0702 (0.123)	0.121 (0.195)	0.611 (0.718)	0.0118 (0.0262)	0.0533 (0.0961)	0.0285 (0.0578)	0.0996 (0.165)	0.157 (0.239)	0.765 (0.852)	0.115 (0.187)	0.853 (0.939)	0.0438 (0.0814)
del 1q43	31 (6%)	482			0.317 (0.421)	0.0101 (0.023)	0.1 (0.166)	0.532 (0.645)	0.0252 (0.052)	0.0396 (0.0761)	0.231 (0.326)	0.756 (0.849)	0.796 (0.884)	0.3 (0.402)
del xq21 1	78 (15%)	435	0.84 (0.929)	0.264 (0.363)	0.193 (0.277)	0.0525 (0.0952)	0.0522 (0.0952)	0.153 (0.234)	0.00851 (0.0197)	1e-05 (4.55e-05)	0.00088 (0.00261)	0.36 (0.463)	0.121 (0.195)	0.157 (0.239)
del 6p25 3	50 (10%)	463			0.00012 (0.000446)	0.0423 (0.0795)	0.232 (0.327)	0.928 (0.994)	0.181 (0.264)	0.0733 (0.128)	0.411 (0.52)	0.251 (0.348)	0.144 (0.226)	0.0865 (0.147)
amp 9q34 3	46 (9%)	467	0.507 (0.619)	0.882 (0.96)	0.0949 (0.16)	0.0502 (0.0922)	0.21 (0.299)	0.762 (0.852)	0.0707 (0.124)	0.00017 (0.00061)	0.203 (0.289)	0.0871 (0.147)	0.283 (0.383)	0.287 (0.386)
del 7p22 3	23 (4%)	490			0.0254 (0.0523)	0.123 (0.197)	0.252 (0.349)	0.355 (0.46)	0.558 (0.675)	0.706 (0.805)	0.503 (0.617)	0.0981 (0.164)	0.734 (0.825)	0.352 (0.458)
del 18q23	78 (15%)	435	0.325 (0.43)	0.329 (0.435)	0.459 (0.569)	0.00353 (0.00899)	0.457 (0.569)	0.0751 (0.13)	0.282 (0.382)	0.227 (0.321)	0.347 (0.453)	0.62 (0.72)	0.531 (0.644)	0.898 (0.972)
amp 17q25 1	44 (9%)	469			0.055 (0.099)	0.359 (0.463)	0.333 (0.438)	0.439 (0.552)	0.14 (0.222)	0.0524 (0.0952)	0.151 (0.233)	0.565 (0.681)	0.188 (0.272)	0.561 (0.677)

'amp_1q22' versus 'CN_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.0017

Table S1. Gene #1: 'amp_1q22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
AMP PEAK 1(1Q22) MUTATED	15	19	8
AMP PEAK 1(1Q22) WILD-TYPE	157	101	213

Figure S1. Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q22' versus 'METHLYATION_CNMF'

P value = 0.00755 (Fisher's exact test), Q value = 0.018

Table S2. Gene #1: 'amp_1q22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
AMP PEAK 1(1Q22) MUTATED	19	14	8	1
AMP PEAK 1(1Q22) WILD-TYPE	206	67	159	39

Figure S2. Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q22' versus 'MRNASEQ_CNMF'

P value = 0.00559 (Fisher's exact test), Q value = 0.013

Table S3. Gene #1: 'amp_1q22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
AMP PEAK 1(1Q22) MUTATED	8	19	4	9	2
AMP PEAK 1(1Q22) WILD-TYPE	126	90	104	123	28

Figure S3. Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q32.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S4. Gene #2: 'amp_1q32.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
AMP PEAK 2(1Q32.1) MUTATED	10	28	5
AMP PEAK 2(1Q32.1) WILD-TYPE	162	92	216

Figure S4. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q32.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S5. Gene #2: 'amp_1q32.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
AMP PEAK 2(1Q32.1) MUTATED	12	24	6	1
AMP PEAK 2(1Q32.1) WILD-TYPE	213	57	161	39

Figure S5. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q32.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S6. Gene #2: 'amp_1q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
AMP PEAK 2(1Q32.1) MUTATED	2	25	2	12	2
AMP PEAK 2(1Q32.1) WILD-TYPE	132	84	106	120	28

Figure S6. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q32.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S7. Gene #2: 'amp_1q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 2(1Q32.1) MUTATED	3	20	3	6	2	4	5
AMP PEAK 2(1Q32.1) WILD-TYPE	132	51	33	62	88	37	67

Figure S7. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q32.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8.5e-05

Table S8. Gene #2: 'amp_1q32.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 2(1Q32.1) MUTATED	8	13	22
AMP PEAK 2(1Q32.1) WILD-TYPE	214	171	81

Figure S8. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q32.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00117 (Fisher's exact test), Q value = 0.0033

Table S9. Gene #2: 'amp_1q32.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
AMP PEAK 2(1Q32.1) MUTATED	23	4	16
AMP PEAK 2(1Q32.1) WILD-TYPE	162	157	143

Figure S9. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_1q32.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8.5e-05

Table S10. Gene #2: 'amp_1q32.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 2(1Q32.1) MUTATED	5	3	14	21
AMP PEAK 2(1Q32.1) WILD-TYPE	86	134	174	68

Figure S10. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_2p24.3' versus 'CN_CNMF'

P value = 0.00248 (Fisher's exact test), Q value = 0.0065

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
AMP PEAK 3(2P24.3) MUTATED	6	13	5
AMP PEAK 3(2P24.3) WILD-TYPE	166	107	216

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

'amp_2p24.3' versus 'METHLYATION_CNMF'

P value = 0.0336 (Fisher's exact test), Q value = 0.066

Table S12. Gene #3: 'amp_2p24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
AMP PEAK 3(2P24.3) MUTATED	10	9	4	1
AMP PEAK 3(2P24.3) WILD-TYPE	215	72	163	39

Figure S12. Get High-res Image Gene #3: 'amp_2p24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2p24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00277 (Fisher's exact test), Q value = 0.0073

Table S13. Gene #3: 'amp_2p24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 3(2P24.3) MUTATED	3	7	1	6	2	5	0
AMP PEAK 3(2P24.3) WILD-TYPE	132	64	35	62	88	36	72

Figure S13. Get High-res Image Gene #3: 'amp_2p24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_2p24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.035 (Fisher's exact test), Q value = 0.069

Table S14. Gene #3: 'amp_2p24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 3(2P24.3) MUTATED	9	5	10
AMP PEAK 3(2P24.3) WILD-TYPE	213	179	93

Figure S14. Get High-res Image Gene #3: 'amp_2p24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S15. Gene #4: 'amp_3q26.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
AMP PEAK 4(3Q26.33) MUTATED	1	17	3
AMP PEAK 4(3Q26.33) WILD-TYPE	171	103	218

Figure S15. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.33' versus 'METHLYATION_CNMF'

P value = 0.00097 (Fisher's exact test), Q value = 0.0029

Table S16. Gene #4: 'amp_3q26.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
AMP PEAK 4(3Q26.33) MUTATED	9	10	2	0
AMP PEAK 4(3Q26.33) WILD-TYPE	216	71	165	40

Figure S16. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.33' versus 'MRNASEQ_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.0019

Table S17. Gene #4: 'amp_3q26.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
AMP PEAK 4(3Q26.33) MUTATED	5	13	2	1	0
AMP PEAK 4(3Q26.33) WILD-TYPE	129	96	106	131	30

Figure S17. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00108 (Fisher's exact test), Q value = 0.0031

Table S18. Gene #4: 'amp_3q26.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 4(3Q26.33) MUTATED	4	9	1	2	0	4	1
AMP PEAK 4(3Q26.33) WILD-TYPE	131	62	35	66	90	37	71

Figure S18. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'MIRSEQ_CNMF'

P value = 0.00125 (Fisher's exact test), Q value = 0.0035

Table S19. Gene #4: 'amp_3q26.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
AMP PEAK 4(3Q26.33) MUTATED	11	7	1	2
AMP PEAK 4(3Q26.33) WILD-TYPE	126	100	182	80

Figure S19. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0182 (Fisher's exact test), Q value = 0.039

Table S20. Gene #4: 'amp_3q26.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 4(3Q26.33) MUTATED	9	3	9
AMP PEAK 4(3Q26.33) WILD-TYPE	213	181	94

Figure S20. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00389 (Fisher's exact test), Q value = 0.0099

Table S21. Gene #4: 'amp_3q26.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 4(3Q26.33) MUTATED	6	2	4	9
AMP PEAK 4(3Q26.33) WILD-TYPE	85	135	184	80

Figure S21. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.0431 (Fisher's exact test), Q value = 0.081

Table S22. Gene #5: 'amp_4q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
AMP PEAK 5(4Q12) MUTATED	0	3	0	0
AMP PEAK 5(4Q12) WILD-TYPE	7	4	7	6

Figure S22. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_4q12' versus 'CN_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 8e-04

Table S23. Gene #5: 'amp_4q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
AMP PEAK 5(4Q12) MUTATED	17	10	3
AMP PEAK 5(4Q12) WILD-TYPE	155	110	218

Figure S23. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_4q12' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.00071

Table S24. Gene #5: 'amp_4q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
AMP PEAK 5(4Q12) MUTATED	19	9	1	1
AMP PEAK 5(4Q12) WILD-TYPE	206	72	166	39

Figure S24. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_4q12' versus 'RPPA_CNMF'

P value = 0.0092 (Fisher's exact test), Q value = 0.021

Table S25. Gene #5: 'amp_4q12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
AMP PEAK 5(4Q12) MUTATED	2	8	0	5
AMP PEAK 5(4Q12) WILD-TYPE	50	54	68	69

Figure S25. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_4q12' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00061

Table S26. Gene #5: 'amp_4q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
AMP PEAK 5(4Q12) MUTATED	5	17	1	6	1
AMP PEAK 5(4Q12) WILD-TYPE	129	92	107	126	29

Figure S26. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_4q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S27. Gene #5: 'amp_4q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 5(4Q12) MUTATED	5	8	0	2	0	11	4
AMP PEAK 5(4Q12) WILD-TYPE	130	63	36	66	90	30	68

Figure S27. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_4q12' versus 'MIRSEQ_CNMF'

P value = 0.00309 (Fisher's exact test), Q value = 0.008

Table S28. Gene #5: 'amp_4q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
AMP PEAK 5(4Q12) MUTATED	6	15	7	2
AMP PEAK 5(4Q12) WILD-TYPE	131	92	176	80

Figure S28. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_4q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00038

Table S29. Gene #5: 'amp_4q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 5(4Q12) MUTATED	7	7	16
AMP PEAK 5(4Q12) WILD-TYPE	215	177	87

Figure S29. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_4q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0039 (Fisher's exact test), Q value = 0.0099

Table S30. Gene #5: 'amp_4q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 5(4Q12) MUTATED	3	8	6	13
AMP PEAK 5(4Q12) WILD-TYPE	88	129	182	76

Figure S30. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S31. Gene #6: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
AMP PEAK 6(7P11.2) MUTATED	21	98	9
AMP PEAK 6(7P11.2) WILD-TYPE	151	22	212

Figure S31. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S32. Gene #6: 'amp_7p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
AMP PEAK 6(7P11.2) MUTATED	40	64	15	9
AMP PEAK 6(7P11.2) WILD-TYPE	185	17	152	31

Figure S32. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.5e-05

Table S33. Gene #6: 'amp_7p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
AMP PEAK 6(7P11.2) MUTATED	13	31	12	12
AMP PEAK 6(7P11.2) WILD-TYPE	39	31	56	62

Figure S33. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_7p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0116 (Fisher's exact test), Q value = 0.026

Table S34. Gene #6: 'amp_7p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	131	58
AMP PEAK 6(7P11.2) MUTATED	14	45	9
AMP PEAK 6(7P11.2) WILD-TYPE	53	86	49

Figure S34. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S35. Gene #6: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
AMP PEAK 6(7P11.2) MUTATED	23	64	11	25	5
AMP PEAK 6(7P11.2) WILD-TYPE	111	45	97	107	25

Figure S35. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S36. Gene #6: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 6(7P11.2) MUTATED	19	57	3	27	7	9	6
AMP PEAK 6(7P11.2) WILD-TYPE	116	14	33	41	83	32	66

Figure S36. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0012

Table S37. Gene #6: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
AMP PEAK 6(7P11.2) MUTATED	44	37	32	13
AMP PEAK 6(7P11.2) WILD-TYPE	93	70	151	69

Figure S37. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S38. Gene #6: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 6(7P11.2) MUTATED	37	28	61
AMP PEAK 6(7P11.2) WILD-TYPE	185	156	42

Figure S38. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00023

Table S39. Gene #6: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
AMP PEAK 6(7P11.2) MUTATED	66	26	33
AMP PEAK 6(7P11.2) WILD-TYPE	119	135	126

Figure S39. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S40. Gene #6: 'amp_7p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 6(7P11.2) MUTATED	13	22	32	58
AMP PEAK 6(7P11.2) WILD-TYPE	78	115	156	31

Figure S40. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S41. Gene #7: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
AMP PEAK 7(7Q31.2) MUTATED	46	105	23
AMP PEAK 7(7Q31.2) WILD-TYPE	126	15	198

Figure S41. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q31.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S42. Gene #7: 'amp_7q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
AMP PEAK 7(7Q31.2) MUTATED	77	59	29	9
AMP PEAK 7(7Q31.2) WILD-TYPE	148	22	138	31

Figure S42. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7q31.2' versus 'RPPA_CNMF'

P value = 0.004 (Fisher's exact test), Q value = 0.01

Table S43. Gene #7: 'amp_7q31.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
AMP PEAK 7(7Q31.2) MUTATED	19	33	17	21
AMP PEAK 7(7Q31.2) WILD-TYPE	33	29	51	53

Figure S43. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S44. Gene #7: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
AMP PEAK 7(7Q31.2) MUTATED	49	61	17	39	8
AMP PEAK 7(7Q31.2) WILD-TYPE	85	48	91	93	22

Figure S44. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S45. Gene #7: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 7(7Q31.2) MUTATED	44	53	6	33	14	9	15
AMP PEAK 7(7Q31.2) WILD-TYPE	91	18	30	35	76	32	57

Figure S45. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.023

Table S46. Gene #7: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
AMP PEAK 7(7Q31.2) MUTATED	56	44	52	20
AMP PEAK 7(7Q31.2) WILD-TYPE	81	63	131	62

Figure S46. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S47. Gene #7: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 7(7Q31.2) MUTATED	65	48	59
AMP PEAK 7(7Q31.2) WILD-TYPE	157	136	44

Figure S47. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00892 (Fisher's exact test), Q value = 0.021

Table S48. Gene #7: 'amp_7q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
AMP PEAK 7(7Q31.2) MUTATED	76	41	54
AMP PEAK 7(7Q31.2) WILD-TYPE	109	120	105

Figure S48. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S49. Gene #7: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 7(7Q31.2) MUTATED	24	35	57	55
AMP PEAK 7(7Q31.2) WILD-TYPE	67	102	131	34

Figure S49. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q32.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S50. Gene #8: 'amp_7q32.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
AMP PEAK 8(7Q32.3) MUTATED	49	108	25
AMP PEAK 8(7Q32.3) WILD-TYPE	123	12	196

Figure S50. Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q32.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S51. Gene #8: 'amp_7q32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
AMP PEAK 8(7Q32.3) MUTATED	82	60	30	10
AMP PEAK 8(7Q32.3) WILD-TYPE	143	21	137	30

Figure S51. Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7q32.3' versus 'RPPA_CNMF'

P value = 0.00681 (Fisher's exact test), Q value = 0.016

Table S52. Gene #8: 'amp_7q32.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
AMP PEAK 8(7Q32.3) MUTATED	20	34	19	22
AMP PEAK 8(7Q32.3) WILD-TYPE	32	28	49	52

Figure S52. Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_7q32.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S53. Gene #8: 'amp_7q32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
AMP PEAK 8(7Q32.3) MUTATED	53	61	18	42	8
AMP PEAK 8(7Q32.3) WILD-TYPE	81	48	90	90	22

Figure S53. Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q32.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S54. Gene #8: 'amp_7q32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 8(7Q32.3) MUTATED	47	53	6	37	15	9	15
AMP PEAK 8(7Q32.3) WILD-TYPE	88	18	30	31	75	32	57

Figure S54. Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q32.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S55. Gene #8: 'amp_7q32.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 8(7Q32.3) MUTATED	68	52	60
AMP PEAK 8(7Q32.3) WILD-TYPE	154	132	43

Figure S55. Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7q32.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.046

Table S56. Gene #8: 'amp_7q32.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
AMP PEAK 8(7Q32.3) MUTATED	78	45	56
AMP PEAK 8(7Q32.3) WILD-TYPE	107	116	103

Figure S56. Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7q32.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S57. Gene #8: 'amp_7q32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 8(7Q32.3) MUTATED	28	37	59	55
AMP PEAK 8(7Q32.3) WILD-TYPE	63	100	129	34

Figure S57. Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S58. Gene #9: 'amp_8q24.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
AMP PEAK 9(8Q24.13) MUTATED	66	19	15
AMP PEAK 9(8Q24.13) WILD-TYPE	106	101	206

Figure S58. Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S59. Gene #9: 'amp_8q24.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
AMP PEAK 9(8Q24.13) MUTATED	82	4	10	4
AMP PEAK 9(8Q24.13) WILD-TYPE	143	77	157	36

Figure S59. Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.13' versus 'RPPA_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.079

Table S60. Gene #9: 'amp_8q24.13' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
AMP PEAK 9(8Q24.13) MUTATED	14	13	19	8
AMP PEAK 9(8Q24.13) WILD-TYPE	38	49	49	66

Figure S60. Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_8q24.13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S61. Gene #9: 'amp_8q24.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
AMP PEAK 9(8Q24.13) MUTATED	50	11	6	26	7
AMP PEAK 9(8Q24.13) WILD-TYPE	84	98	102	106	23

Figure S61. Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S62. Gene #9: 'amp_8q24.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 9(8Q24.13) MUTATED	52	3	2	20	5	9	9
AMP PEAK 9(8Q24.13) WILD-TYPE	83	68	34	48	85	32	63

Figure S62. Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.13' versus 'MIRSEQ_CNMF'

P value = 0.0288 (Fisher's exact test), Q value = 0.058

Table S63. Gene #9: 'amp_8q24.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
AMP PEAK 9(8Q24.13) MUTATED	33	22	36	7
AMP PEAK 9(8Q24.13) WILD-TYPE	104	85	147	75

Figure S63. Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00088 (Fisher's exact test), Q value = 0.0026

Table S64. Gene #9: 'amp_8q24.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 9(8Q24.13) MUTATED	58	30	10
AMP PEAK 9(8Q24.13) WILD-TYPE	164	154	93

Figure S64. Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

Table S65. Gene #9: 'amp_8q24.13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 9(8Q24.13) MUTATED	34	21	35	8
AMP PEAK 9(8Q24.13) WILD-TYPE	57	116	153	81

Figure S65. Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00061

Table S66. Gene #10: 'amp_9q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 10(9Q34.3) MUTATED	8	6	3	9	4	13	3
AMP PEAK 10(9Q34.3) WILD-TYPE	127	65	33	59	86	28	69

Figure S66. Get High-res Image Gene #10: 'amp_9q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S67. Gene #11: 'amp_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
AMP PEAK 11(10P15.3) MUTATED	58	9	4
AMP PEAK 11(10P15.3) WILD-TYPE	114	111	217

Figure S67. Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_10p15.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S68. Gene #11: 'amp_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
AMP PEAK 11(10P15.3) MUTATED	65	3	0	3
AMP PEAK 11(10P15.3) WILD-TYPE	160	78	167	37

Figure S68. Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_10p15.3' versus 'RPPA_CNMF'

P value = 0.0289 (Fisher's exact test), Q value = 0.058

Table S69. Gene #11: 'amp_10p15.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
AMP PEAK 11(10P15.3) MUTATED	13	9	13	5
AMP PEAK 11(10P15.3) WILD-TYPE	39	53	55	69

Figure S69. Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_10p15.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S70. Gene #11: 'amp_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
AMP PEAK 11(10P15.3) MUTATED	41	11	1	16	2
AMP PEAK 11(10P15.3) WILD-TYPE	93	98	107	116	28

Figure S70. Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S71. Gene #11: 'amp_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 11(10P15.3) MUTATED	40	1	0	14	0	12	4
AMP PEAK 11(10P15.3) WILD-TYPE	95	70	36	54	90	29	68

Figure S71. Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10p15.3' versus 'MIRSEQ_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0024

Table S72. Gene #11: 'amp_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
AMP PEAK 11(10P15.3) MUTATED	20	26	20	4
AMP PEAK 11(10P15.3) WILD-TYPE	117	81	163	78

Figure S72. Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_10p15.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00067

Table S73. Gene #11: 'amp_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 11(10P15.3) MUTATED	27	16	21	6
AMP PEAK 11(10P15.3) WILD-TYPE	64	121	167	83

Figure S73. Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q24.1' versus 'METHLYATION_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.026

Table S74. Gene #12: 'amp_11q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
AMP PEAK 12(11Q24.1) MUTATED	50	7	27	3
AMP PEAK 12(11Q24.1) WILD-TYPE	175	74	140	37

Figure S74. Get High-res Image Gene #12: 'amp_11q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q24.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0285 (Fisher's exact test), Q value = 0.058

Table S75. Gene #12: 'amp_11q24.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	131	58
AMP PEAK 12(11Q24.1) MUTATED	5	29	10
AMP PEAK 12(11Q24.1) WILD-TYPE	62	102	48

Figure S75. Get High-res Image Gene #12: 'amp_11q24.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_11q24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0438 (Fisher's exact test), Q value = 0.081

Table S76. Gene #12: 'amp_11q24.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 12(11Q24.1) MUTATED	20	24	36	7
AMP PEAK 12(11Q24.1) WILD-TYPE	71	113	152	82

Figure S76. Get High-res Image Gene #12: 'amp_11q24.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S77. Gene #13: 'amp_12p13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
AMP PEAK 13(12P13.32) MUTATED	46	17	9
AMP PEAK 13(12P13.32) WILD-TYPE	126	103	212

Figure S77. Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12p13.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S78. Gene #13: 'amp_12p13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
AMP PEAK 13(12P13.32) MUTATED	55	9	5	3
AMP PEAK 13(12P13.32) WILD-TYPE	170	72	162	37

Figure S78. Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12p13.32' versus 'MRNASEQ_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.0038

Table S79. Gene #13: 'amp_12p13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
AMP PEAK 13(12P13.32) MUTATED	30	19	6	13	4
AMP PEAK 13(12P13.32) WILD-TYPE	104	90	102	119	26

Figure S79. Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12p13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S80. Gene #13: 'amp_12p13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 13(12P13.32) MUTATED	32	8	1	14	4	12	1
AMP PEAK 13(12P13.32) WILD-TYPE	103	63	35	54	86	29	71

Figure S80. Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12p13.32' versus 'MIRSEQ_CNMF'

P value = 0.00953 (Fisher's exact test), Q value = 0.022

Table S81. Gene #13: 'amp_12p13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
AMP PEAK 13(12P13.32) MUTATED	17	26	18	11
AMP PEAK 13(12P13.32) WILD-TYPE	120	81	165	71

Figure S81. Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12p13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00671 (Fisher's exact test), Q value = 0.016

Table S82. Gene #13: 'amp_12p13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 13(12P13.32) MUTATED	36	15	21
AMP PEAK 13(12P13.32) WILD-TYPE	186	169	82

Figure S82. Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12p13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.024 (Fisher's exact test), Q value = 0.05

Table S83. Gene #13: 'amp_12p13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
AMP PEAK 13(12P13.32) MUTATED	31	28	13
AMP PEAK 13(12P13.32) WILD-TYPE	154	133	146

Figure S83. Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S84. Gene #14: 'amp_12q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
AMP PEAK 14(12Q14.1) MUTATED	10	22	5
AMP PEAK 14(12Q14.1) WILD-TYPE	162	98	216

Figure S84. Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q14.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S85. Gene #14: 'amp_12q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
AMP PEAK 14(12Q14.1) MUTATED	13	19	4	1
AMP PEAK 14(12Q14.1) WILD-TYPE	212	62	163	39

Figure S85. Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q14.1' versus 'RPPA_CNMF'

P value = 0.0146 (Fisher's exact test), Q value = 0.032

Table S86. Gene #14: 'amp_12q14.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
AMP PEAK 14(12Q14.1) MUTATED	2	9	1	3
AMP PEAK 14(12Q14.1) WILD-TYPE	50	53	67	71

Figure S86. Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S87. Gene #14: 'amp_12q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
AMP PEAK 14(12Q14.1) MUTATED	4	25	4	3	1
AMP PEAK 14(12Q14.1) WILD-TYPE	130	84	104	129	29

Figure S87. Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S88. Gene #14: 'amp_12q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 14(12Q14.1) MUTATED	3	18	1	4	3	8	0
AMP PEAK 14(12Q14.1) WILD-TYPE	132	53	35	64	87	33	72

Figure S88. Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'MIRSEQ_CNMF'

P value = 0.00306 (Fisher's exact test), Q value = 0.008

Table S89. Gene #14: 'amp_12q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
AMP PEAK 14(12Q14.1) MUTATED	13	15	6	3
AMP PEAK 14(12Q14.1) WILD-TYPE	124	92	177	79

Figure S89. Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S90. Gene #14: 'amp_12q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 14(12Q14.1) MUTATED	10	5	22
AMP PEAK 14(12Q14.1) WILD-TYPE	212	179	81

Figure S90. Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.079

Table S91. Gene #14: 'amp_12q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
AMP PEAK 14(12Q14.1) MUTATED	21	8	8
AMP PEAK 14(12Q14.1) WILD-TYPE	164	153	151

Figure S91. Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S92. Gene #14: 'amp_12q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 14(12Q14.1) MUTATED	6	5	7	19
AMP PEAK 14(12Q14.1) WILD-TYPE	85	132	181	70

Figure S92. Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q34' versus 'CN_CNMF'

P value = 0.00141 (Fisher's exact test), Q value = 0.0039

Table S93. Gene #15: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
AMP PEAK 15(13Q34) MUTATED	12	8	2
AMP PEAK 15(13Q34) WILD-TYPE	160	112	219

Figure S93. Get High-res Image Gene #15: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q34' versus 'METHLYATION_CNMF'

P value = 0.0013 (Fisher's exact test), Q value = 0.0037

Table S94. Gene #15: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
AMP PEAK 15(13Q34) MUTATED	18	3	1	0
AMP PEAK 15(13Q34) WILD-TYPE	207	78	166	40

Figure S94. Get High-res Image Gene #15: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q34' versus 'MRNASEQ_CNMF'

P value = 0.0401 (Fisher's exact test), Q value = 0.077

Table S95. Gene #15: 'amp_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
AMP PEAK 15(13Q34) MUTATED	7	8	0	6	1
AMP PEAK 15(13Q34) WILD-TYPE	127	101	108	126	29

Figure S95. Get High-res Image Gene #15: 'amp_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0228 (Fisher's exact test), Q value = 0.048

Table S96. Gene #15: 'amp_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 15(13Q34) MUTATED	8	3	0	4	0	5	2
AMP PEAK 15(13Q34) WILD-TYPE	127	68	36	64	90	36	70

Figure S96. Get High-res Image Gene #15: 'amp_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0427 (Fisher's exact test), Q value = 0.08

Table S97. Gene #16: 'amp_15q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
AMP PEAK 16(15Q26.3) MUTATED	0	3	0	0
AMP PEAK 16(15Q26.3) WILD-TYPE	7	4	7	6

Figure S97. Get High-res Image Gene #16: 'amp_15q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_15q26.3' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 2e-04

Table S98. Gene #16: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
AMP PEAK 16(15Q26.3) MUTATED	12	7	0
AMP PEAK 16(15Q26.3) WILD-TYPE	160	113	221

Figure S98. Get High-res Image Gene #16: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_15q26.3' versus 'METHLYATION_CNMF'

P value = 0.00078 (Fisher's exact test), Q value = 0.0024

Table S99. Gene #16: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
AMP PEAK 16(15Q26.3) MUTATED	14	5	0	0
AMP PEAK 16(15Q26.3) WILD-TYPE	211	76	167	40

Figure S99. Get High-res Image Gene #16: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CNMF'

P value = 0.0265 (Fisher's exact test), Q value = 0.054

Table S100. Gene #16: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
AMP PEAK 16(15Q26.3) MUTATED	5	8	0	4	2
AMP PEAK 16(15Q26.3) WILD-TYPE	129	101	108	128	28

Figure S100. Get High-res Image Gene #16: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S101. Gene #18: 'amp_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
AMP PEAK 18(19P13.3) MUTATED	9	40	80
AMP PEAK 18(19P13.3) WILD-TYPE	163	80	141

Figure S101. Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S102. Gene #18: 'amp_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
AMP PEAK 18(19P13.3) MUTATED	19	27	80	3
AMP PEAK 18(19P13.3) WILD-TYPE	206	54	87	37

Figure S102. Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S103. Gene #18: 'amp_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
AMP PEAK 18(19P13.3) MUTATED	10	29	54	34	2
AMP PEAK 18(19P13.3) WILD-TYPE	124	80	54	98	28

Figure S103. Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S104. Gene #18: 'amp_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 18(19P13.3) MUTATED	8	25	18	10	40	6	22
AMP PEAK 18(19P13.3) WILD-TYPE	127	46	18	58	50	35	50

Figure S104. Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.3' versus 'MIRSEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00051

Table S105. Gene #18: 'amp_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
AMP PEAK 18(19P13.3) MUTATED	24	23	45	37
AMP PEAK 18(19P13.3) WILD-TYPE	113	84	138	45

Figure S105. Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0452 (Fisher's exact test), Q value = 0.083

Table S106. Gene #18: 'amp_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
AMP PEAK 18(19P13.3) MUTATED	37	51	41
AMP PEAK 18(19P13.3) WILD-TYPE	148	110	118

Figure S106. Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00083 (Fisher's exact test), Q value = 0.0025

Table S107. Gene #18: 'amp_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 18(19P13.3) MUTATED	10	46	47	26
AMP PEAK 18(19P13.3) WILD-TYPE	81	91	141	63

Figure S107. Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S108. Gene #19: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
AMP PEAK 19(19P13.2) MUTATED	6	42	74
AMP PEAK 19(19P13.2) WILD-TYPE	166	78	147

Figure S108. Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S109. Gene #19: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
AMP PEAK 19(19P13.2) MUTATED	12	30	77	3
AMP PEAK 19(19P13.2) WILD-TYPE	213	51	90	37

Figure S109. Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S110. Gene #19: 'amp_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
AMP PEAK 19(19P13.2) MUTATED	6	33	53	27	3
AMP PEAK 19(19P13.2) WILD-TYPE	128	76	55	105	27

Figure S110. Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S111. Gene #19: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 19(19P13.2) MUTATED	6	28	18	7	39	5	19
AMP PEAK 19(19P13.2) WILD-TYPE	129	43	18	61	51	36	53

Figure S111. Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'MIRSEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00061

Table S112. Gene #19: 'amp_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
AMP PEAK 19(19P13.2) MUTATED	26	21	39	36
AMP PEAK 19(19P13.2) WILD-TYPE	111	86	144	46

Figure S112. Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0414 (Fisher's exact test), Q value = 0.079

Table S113. Gene #19: 'amp_19p13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
AMP PEAK 19(19P13.2) MUTATED	36	50	36
AMP PEAK 19(19P13.2) WILD-TYPE	149	111	123

Figure S113. Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.0016

Table S114. Gene #19: 'amp_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 19(19P13.2) MUTATED	9	41	43	29
AMP PEAK 19(19P13.2) WILD-TYPE	82	96	145	60

Figure S114. Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xp11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S115. Gene #20: 'amp_xp11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
AMP PEAK 20(XP11.22) MUTATED	33	8	7
AMP PEAK 20(XP11.22) WILD-TYPE	139	112	214

Figure S115. Get High-res Image Gene #20: 'amp_xp11.22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xp11.22' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S116. Gene #20: 'amp_xp11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
AMP PEAK 20(XP11.22) MUTATED	41	5	1	1
AMP PEAK 20(XP11.22) WILD-TYPE	184	76	166	39

Figure S116. Get High-res Image Gene #20: 'amp_xp11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xp11.22' versus 'MRNASEQ_CNMF'

P value = 0.00122 (Fisher's exact test), Q value = 0.0035

Table S117. Gene #20: 'amp_xp11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
AMP PEAK 20(XP11.22) MUTATED	20	11	1	13	3
AMP PEAK 20(XP11.22) WILD-TYPE	114	98	107	119	27

Figure S117. Get High-res Image Gene #20: 'amp_xp11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xp11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

Table S118. Gene #20: 'amp_xp11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 20(XP11.22) MUTATED	22	3	0	9	1	8	5
AMP PEAK 20(XP11.22) WILD-TYPE	113	68	36	59	89	33	67

Figure S118. Get High-res Image Gene #20: 'amp_xp11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S119. Gene #21: 'amp_xp11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
AMP PEAK 21(XP11.22) MUTATED	47	7	9
AMP PEAK 21(XP11.22) WILD-TYPE	125	113	212

Figure S119. Get High-res Image Gene #21: 'amp_xp11.22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xp11.22' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S120. Gene #21: 'amp_xp11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
AMP PEAK 21(XP11.22) MUTATED	54	6	1	2
AMP PEAK 21(XP11.22) WILD-TYPE	171	75	166	38

Figure S120. Get High-res Image Gene #21: 'amp_xp11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xp11.22' versus 'RPPA_CNMF'

P value = 0.0268 (Fisher's exact test), Q value = 0.055

Table S121. Gene #21: 'amp_xp11.22' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
AMP PEAK 21(XP11.22) MUTATED	5	14	13	5
AMP PEAK 21(XP11.22) WILD-TYPE	47	48	55	69

Figure S121. Get High-res Image Gene #21: 'amp_xp11.22' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_xp11.22' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S122. Gene #21: 'amp_xp11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
AMP PEAK 21(XP11.22) MUTATED	27	16	1	15	4
AMP PEAK 21(XP11.22) WILD-TYPE	107	93	107	117	26

Figure S122. Get High-res Image Gene #21: 'amp_xp11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xp11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S123. Gene #21: 'amp_xp11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 21(XP11.22) MUTATED	30	5	0	12	1	11	4
AMP PEAK 21(XP11.22) WILD-TYPE	105	66	36	56	89	30	68

Figure S123. Get High-res Image Gene #21: 'amp_xp11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.22' versus 'MIRSEQ_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.0016

Table S124. Gene #21: 'amp_xp11.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
AMP PEAK 21(XP11.22) MUTATED	22	19	20	1
AMP PEAK 21(XP11.22) WILD-TYPE	115	88	163	81

Figure S124. Get High-res Image Gene #21: 'amp_xp11.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_xp11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00979 (Fisher's exact test), Q value = 0.022

Table S125. Gene #21: 'amp_xp11.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 21(XP11.22) MUTATED	21	11	21	9
AMP PEAK 21(XP11.22) WILD-TYPE	70	126	167	80

Figure S125. Get High-res Image Gene #21: 'amp_xp11.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.32' versus 'MRNA_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0019

Table S126. Gene #22: 'del_1p36.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	10	8
DEL PEAK 1(1P36.32) MUTATED	0	8	2
DEL PEAK 1(1P36.32) WILD-TYPE	9	2	6

Figure S126. Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.32' versus 'MRNA_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.00095

Table S127. Gene #22: 'del_1p36.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
DEL PEAK 1(1P36.32) MUTATED	0	1	7	2
DEL PEAK 1(1P36.32) WILD-TYPE	7	6	0	4

Figure S127. Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p36.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S128. Gene #22: 'del_1p36.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
DEL PEAK 1(1P36.32) MUTATED	10	29	167
DEL PEAK 1(1P36.32) WILD-TYPE	162	91	54

Figure S128. Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S129. Gene #22: 'del_1p36.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
DEL PEAK 1(1P36.32) MUTATED	11	19	166	10
DEL PEAK 1(1P36.32) WILD-TYPE	214	62	1	30

Figure S129. Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.32' versus 'RPPA_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0022

Table S130. Gene #22: 'del_1p36.32' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
DEL PEAK 1(1P36.32) MUTATED	8	20	29	36
DEL PEAK 1(1P36.32) WILD-TYPE	44	42	39	38

Figure S130. Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p36.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S131. Gene #22: 'del_1p36.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
DEL PEAK 1(1P36.32) MUTATED	5	20	106	61	14
DEL PEAK 1(1P36.32) WILD-TYPE	129	89	2	71	16

Figure S131. Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S132. Gene #22: 'del_1p36.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 1(1P36.32) MUTATED	7	19	36	5	88	1	50
DEL PEAK 1(1P36.32) WILD-TYPE	128	52	0	63	2	40	22

Figure S132. Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S133. Gene #22: 'del_1p36.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 1(1P36.32) MUTATED	33	13	92	68
DEL PEAK 1(1P36.32) WILD-TYPE	104	94	91	14

Figure S133. Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S134. Gene #22: 'del_1p36.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 1(1P36.32) MUTATED	84	101	21
DEL PEAK 1(1P36.32) WILD-TYPE	138	83	82

Figure S134. Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S135. Gene #22: 'del_1p36.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 1(1P36.32) MUTATED	44	83	79
DEL PEAK 1(1P36.32) WILD-TYPE	141	78	80

Figure S135. Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S136. Gene #22: 'del_1p36.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 1(1P36.32) MUTATED	7	83	95	21
DEL PEAK 1(1P36.32) WILD-TYPE	84	54	93	68

Figure S136. Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p32.3' versus 'MRNA_CNMF'

P value = 0.0279 (Fisher's exact test), Q value = 0.057

Table S137. Gene #23: 'del_1p32.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	10	8
DEL PEAK 2(1P32.3) MUTATED	1	7	2
DEL PEAK 2(1P32.3) WILD-TYPE	8	3	6

Figure S137. Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p32.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00067

Table S138. Gene #23: 'del_1p32.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
DEL PEAK 2(1P32.3) MUTATED	0	1	7	2
DEL PEAK 2(1P32.3) WILD-TYPE	7	6	0	4

Figure S138. Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p32.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S139. Gene #23: 'del_1p32.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
DEL PEAK 2(1P32.3) MUTATED	6	24	166
DEL PEAK 2(1P32.3) WILD-TYPE	166	96	55

Figure S139. Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p32.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S140. Gene #23: 'del_1p32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
DEL PEAK 2(1P32.3) MUTATED	5	15	166	10
DEL PEAK 2(1P32.3) WILD-TYPE	220	66	1	30

Figure S140. Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p32.3' versus 'RPPA_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0018

Table S141. Gene #23: 'del_1p32.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
DEL PEAK 2(1P32.3) MUTATED	8	16	28	35
DEL PEAK 2(1P32.3) WILD-TYPE	44	46	40	39

Figure S141. Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p32.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S142. Gene #23: 'del_1p32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
DEL PEAK 2(1P32.3) MUTATED	4	15	106	58	13
DEL PEAK 2(1P32.3) WILD-TYPE	130	94	2	74	17

Figure S142. Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p32.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S143. Gene #23: 'del_1p32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 2(1P32.3) MUTATED	5	16	36	2	88	0	49
DEL PEAK 2(1P32.3) WILD-TYPE	130	55	0	66	2	41	23

Figure S143. Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p32.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S144. Gene #23: 'del_1p32.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 2(1P32.3) MUTATED	33	10	86	67
DEL PEAK 2(1P32.3) WILD-TYPE	104	97	97	15

Figure S144. Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p32.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S145. Gene #23: 'del_1p32.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 2(1P32.3) MUTATED	82	96	18
DEL PEAK 2(1P32.3) WILD-TYPE	140	88	85

Figure S145. Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p32.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S146. Gene #23: 'del_1p32.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 2(1P32.3) MUTATED	39	82	75
DEL PEAK 2(1P32.3) WILD-TYPE	146	79	84

Figure S146. Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p32.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S147. Gene #23: 'del_1p32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 2(1P32.3) MUTATED	7	82	90	17
DEL PEAK 2(1P32.3) WILD-TYPE	84	55	98	72

Figure S147. Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1q43' versus 'METHLYATION_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.023

Table S148. Gene #24: 'del_1q43' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
DEL PEAK 3(1Q43) MUTATED	20	4	3	4
DEL PEAK 3(1Q43) WILD-TYPE	205	77	164	36

Figure S148. Get High-res Image Gene #24: 'del_1q43' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1q43' versus 'MRNASEQ_CNMF'

P value = 0.0252 (Fisher's exact test), Q value = 0.052

Table S149. Gene #24: 'del_1q43' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
DEL PEAK 3(1Q43) MUTATED	14	7	1	8	1
DEL PEAK 3(1Q43) WILD-TYPE	120	102	107	124	29

Figure S149. Get High-res Image Gene #24: 'del_1q43' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1q43' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0396 (Fisher's exact test), Q value = 0.076

Table S150. Gene #24: 'del_1q43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 3(1Q43) MUTATED	15	3	1	2	1	3	6
DEL PEAK 3(1Q43) WILD-TYPE	120	68	35	66	89	38	66

Figure S150. Get High-res Image Gene #24: 'del_1q43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.013 (Fisher's exact test), Q value = 0.028

Table S151. Gene #25: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
DEL PEAK 4(2Q37.3) MUTATED	0	4	0	2
DEL PEAK 4(2Q37.3) WILD-TYPE	7	3	7	4

Figure S151. Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S152. Gene #25: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
DEL PEAK 4(2Q37.3) MUTATED	44	22	11
DEL PEAK 4(2Q37.3) WILD-TYPE	128	98	210

Figure S152. Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S153. Gene #25: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
DEL PEAK 4(2Q37.3) MUTATED	64	4	6	3
DEL PEAK 4(2Q37.3) WILD-TYPE	161	77	161	37

Figure S153. Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q37.3' versus 'RPPA_CNMF'

P value = 0.00453 (Fisher's exact test), Q value = 0.011

Table S154. Gene #25: 'del_2q37.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
DEL PEAK 4(2Q37.3) MUTATED	8	17	10	4
DEL PEAK 4(2Q37.3) WILD-TYPE	44	45	58	70

Figure S154. Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_2q37.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0195 (Fisher's exact test), Q value = 0.041

Table S155. Gene #25: 'del_2q37.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	131	58
DEL PEAK 4(2Q37.3) MUTATED	5	28	6
DEL PEAK 4(2Q37.3) WILD-TYPE	62	103	52

Figure S155. Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 0.00078 (Fisher's exact test), Q value = 0.0024

Table S156. Gene #25: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
DEL PEAK 4(2Q37.3) MUTATED	33	20	8	13	3
DEL PEAK 4(2Q37.3) WILD-TYPE	101	89	100	119	27

Figure S156. Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S157. Gene #25: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 4(2Q37.3) MUTATED	31	2	1	16	5	21	1
DEL PEAK 4(2Q37.3) WILD-TYPE	104	69	35	52	85	20	71

Figure S157. Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.032

Table S158. Gene #25: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 4(2Q37.3) MUTATED	25	24	19	8
DEL PEAK 4(2Q37.3) WILD-TYPE	112	83	164	74

Figure S158. Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p21.31' versus 'MRNA_CHIERARCHICAL'

P value = 0.00712 (Fisher's exact test), Q value = 0.017

Table S159. Gene #26: 'del_3p21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
DEL PEAK 5(3P21.31) MUTATED	0	4	0	0
DEL PEAK 5(3P21.31) WILD-TYPE	7	3	7	6

Figure S159. Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p21.31' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00038

Table S160. Gene #26: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
DEL PEAK 5(3P21.31) MUTATED	26	15	8
DEL PEAK 5(3P21.31) WILD-TYPE	146	105	213

Figure S160. Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p21.31' versus 'METHLYATION_CNMF'

P value = 0.00217 (Fisher's exact test), Q value = 0.0059

Table S161. Gene #26: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
DEL PEAK 5(3P21.31) MUTATED	32	9	6	2
DEL PEAK 5(3P21.31) WILD-TYPE	193	72	161	38

Figure S161. Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p21.31' versus 'RPPA_CNMF'

P value = 0.00206 (Fisher's exact test), Q value = 0.0056

Table S162. Gene #26: 'del_3p21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
DEL PEAK 5(3P21.31) MUTATED	3	14	3	4
DEL PEAK 5(3P21.31) WILD-TYPE	49	48	65	70

Figure S162. Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p21.31' versus 'MRNASEQ_CNMF'

P value = 0.0418 (Fisher's exact test), Q value = 0.079

Table S163. Gene #26: 'del_3p21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
DEL PEAK 5(3P21.31) MUTATED	16	16	6	11	0
DEL PEAK 5(3P21.31) WILD-TYPE	118	93	102	121	30

Figure S163. Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00105 (Fisher's exact test), Q value = 0.0031

Table S164. Gene #26: 'del_3p21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 5(3P21.31) MUTATED	15	7	2	7	3	12	3
DEL PEAK 5(3P21.31) WILD-TYPE	120	64	34	61	87	29	69

Figure S164. Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0017

Table S165. Gene #26: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 5(3P21.31) MUTATED	12	21	8	8
DEL PEAK 5(3P21.31) WILD-TYPE	125	86	175	74

Figure S165. Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00235 (Fisher's exact test), Q value = 0.0062

Table S166. Gene #26: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 5(3P21.31) MUTATED	24	8	17
DEL PEAK 5(3P21.31) WILD-TYPE	198	176	86

Figure S166. Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3q13.31' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00034

Table S167. Gene #27: 'del_3q13.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
DEL PEAK 6(3Q13.31) MUTATED	25	8	6
DEL PEAK 6(3Q13.31) WILD-TYPE	147	112	215

Figure S167. Get High-res Image Gene #27: 'del_3q13.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q13.31' versus 'METHLYATION_CNMF'

P value = 0.00416 (Fisher's exact test), Q value = 0.01

Table S168. Gene #27: 'del_3q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
DEL PEAK 6(3Q13.31) MUTATED	26	7	4	2
DEL PEAK 6(3Q13.31) WILD-TYPE	199	74	163	38

Figure S168. Get High-res Image Gene #27: 'del_3q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0132 (Fisher's exact test), Q value = 0.029

Table S169. Gene #27: 'del_3q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 6(3Q13.31) MUTATED	14	4	1	7	2	8	3
DEL PEAK 6(3Q13.31) WILD-TYPE	121	67	35	61	88	33	69

Figure S169. Get High-res Image Gene #27: 'del_3q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.0019

Table S170. Gene #27: 'del_3q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 6(3Q13.31) MUTATED	16	6	17
DEL PEAK 6(3Q13.31) WILD-TYPE	206	178	86

Figure S170. Get High-res Image Gene #27: 'del_3q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3q29' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S171. Gene #28: 'del_3q29' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
DEL PEAK 7(3Q29) MUTATED	33	10	4
DEL PEAK 7(3Q29) WILD-TYPE	139	110	217

Figure S171. Get High-res Image Gene #28: 'del_3q29' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q29' versus 'METHLYATION_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.002

Table S172. Gene #28: 'del_3q29' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
DEL PEAK 7(3Q29) MUTATED	31	8	4	4
DEL PEAK 7(3Q29) WILD-TYPE	194	73	163	36

Figure S172. Get High-res Image Gene #28: 'del_3q29' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3q29' versus 'MRNASEQ_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.035

Table S173. Gene #28: 'del_3q29' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
DEL PEAK 7(3Q29) MUTATED	17	15	3	11	1
DEL PEAK 7(3Q29) WILD-TYPE	117	94	105	121	29

Figure S173. Get High-res Image Gene #28: 'del_3q29' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3q29' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00031

Table S174. Gene #28: 'del_3q29' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 7(3Q29) MUTATED	16	5	1	6	2	13	4
DEL PEAK 7(3Q29) WILD-TYPE	119	66	35	62	88	28	68

Figure S174. Get High-res Image Gene #28: 'del_3q29' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3q29' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00469 (Fisher's exact test), Q value = 0.011

Table S175. Gene #28: 'del_3q29' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 7(3Q29) MUTATED	19	10	18
DEL PEAK 7(3Q29) WILD-TYPE	203	174	85

Figure S175. Get High-res Image Gene #28: 'del_3q29' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.029

Table S176. Gene #29: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
DEL PEAK 8(4Q34.3) MUTATED	58	22	58
DEL PEAK 8(4Q34.3) WILD-TYPE	114	98	163

Figure S176. Get High-res Image Gene #29: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S177. Gene #29: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
DEL PEAK 8(4Q34.3) MUTATED	78	5	51	4
DEL PEAK 8(4Q34.3) WILD-TYPE	147	76	116	36

Figure S177. Get High-res Image Gene #29: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 0.0239 (Fisher's exact test), Q value = 0.05

Table S178. Gene #29: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
DEL PEAK 8(4Q34.3) MUTATED	39	19	35	41	4
DEL PEAK 8(4Q34.3) WILD-TYPE	95	90	73	91	26

Figure S178. Get High-res Image Gene #29: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00055

Table S179. Gene #29: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 8(4Q34.3) MUTATED	36	5	17	18	25	16	21
DEL PEAK 8(4Q34.3) WILD-TYPE	99	66	19	50	65	25	51

Figure S179. Get High-res Image Gene #29: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CNMF'

P value = 0.0295 (Fisher's exact test), Q value = 0.059

Table S180. Gene #29: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 8(4Q34.3) MUTATED	25	31	52	29
DEL PEAK 8(4Q34.3) WILD-TYPE	112	76	131	53

Figure S180. Get High-res Image Gene #29: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0388 (Fisher's exact test), Q value = 0.075

Table S181. Gene #29: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 8(4Q34.3) MUTATED	62	57	18
DEL PEAK 8(4Q34.3) WILD-TYPE	160	127	85

Figure S181. Get High-res Image Gene #29: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0032

Table S182. Gene #29: 'del_4q34.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 8(4Q34.3) MUTATED	33	55	49
DEL PEAK 8(4Q34.3) WILD-TYPE	152	106	110

Figure S182. Get High-res Image Gene #29: 'del_4q34.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00548 (Fisher's exact test), Q value = 0.013

Table S183. Gene #29: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 8(4Q34.3) MUTATED	24	46	55	12
DEL PEAK 8(4Q34.3) WILD-TYPE	67	91	133	77

Figure S183. Get High-res Image Gene #29: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S184. Gene #30: 'del_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
DEL PEAK 9(5P15.33) MUTATED	33	12	5
DEL PEAK 9(5P15.33) WILD-TYPE	139	108	216

Figure S184. Get High-res Image Gene #30: 'del_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_5p15.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S185. Gene #30: 'del_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
DEL PEAK 9(5P15.33) MUTATED	37	9	3	1
DEL PEAK 9(5P15.33) WILD-TYPE	188	72	164	39

Figure S185. Get High-res Image Gene #30: 'del_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5p15.33' versus 'MRNASEQ_CNMF'

P value = 0.00082 (Fisher's exact test), Q value = 0.0025

Table S186. Gene #30: 'del_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
DEL PEAK 9(5P15.33) MUTATED	15	17	1	13	4
DEL PEAK 9(5P15.33) WILD-TYPE	119	92	107	119	26

Figure S186. Get High-res Image Gene #30: 'del_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00023

Table S187. Gene #30: 'del_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 9(5P15.33) MUTATED	17	4	0	9	2	12	6
DEL PEAK 9(5P15.33) WILD-TYPE	118	67	36	59	88	29	66

Figure S187. Get High-res Image Gene #30: 'del_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5p15.33' versus 'MIRSEQ_CNMF'

P value = 0.00202 (Fisher's exact test), Q value = 0.0055

Table S188. Gene #30: 'del_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 9(5P15.33) MUTATED	11	20	17	2
DEL PEAK 9(5P15.33) WILD-TYPE	126	87	166	80

Figure S188. Get High-res Image Gene #30: 'del_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S189. Gene #31: 'del_5q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
DEL PEAK 10(5Q34) MUTATED	49	7	8
DEL PEAK 10(5Q34) WILD-TYPE	123	113	213

Figure S189. Get High-res Image Gene #31: 'del_5q34' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q34' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S190. Gene #31: 'del_5q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
DEL PEAK 10(5Q34) MUTATED	52	7	2	3
DEL PEAK 10(5Q34) WILD-TYPE	173	74	165	37

Figure S190. Get High-res Image Gene #31: 'del_5q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q34' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.5e-05

Table S191. Gene #31: 'del_5q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
DEL PEAK 10(5Q34) MUTATED	20	23	1	15	5
DEL PEAK 10(5Q34) WILD-TYPE	114	86	107	117	25

Figure S191. Get High-res Image Gene #31: 'del_5q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S192. Gene #31: 'del_5q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 10(5Q34) MUTATED	20	3	0	12	2	22	5
DEL PEAK 10(5Q34) WILD-TYPE	115	68	36	56	88	19	67

Figure S192. Get High-res Image Gene #31: 'del_5q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q34' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 2e-04

Table S193. Gene #31: 'del_5q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 10(5Q34) MUTATED	15	28	18	3
DEL PEAK 10(5Q34) WILD-TYPE	122	79	165	79

Figure S193. Get High-res Image Gene #31: 'del_5q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6p25.3' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00045

Table S194. Gene #32: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
DEL PEAK 11(6P25.3) MUTATED	25	17	8
DEL PEAK 11(6P25.3) WILD-TYPE	147	103	213

Figure S194. Get High-res Image Gene #32: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 0.0423 (Fisher's exact test), Q value = 0.079

Table S195. Gene #32: 'del_6p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
DEL PEAK 11(6P25.3) MUTATED	27	11	8	4
DEL PEAK 11(6P25.3) WILD-TYPE	198	70	159	36

Figure S195. Get High-res Image Gene #32: 'del_6p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q22.31' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00041

Table S196. Gene #33: 'del_6q22.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
DEL PEAK 12(6Q22.31) MUTATED	29	31	18
DEL PEAK 12(6Q22.31) WILD-TYPE	143	89	203

Figure S196. Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q22.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S197. Gene #33: 'del_6q22.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
DEL PEAK 12(6Q22.31) MUTATED	49	16	8	5
DEL PEAK 12(6Q22.31) WILD-TYPE	176	65	159	35

Figure S197. Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q22.31' versus 'MRNASEQ_CNMF'

P value = 0.00449 (Fisher's exact test), Q value = 0.011

Table S198. Gene #33: 'del_6q22.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
DEL PEAK 12(6Q22.31) MUTATED	26	25	7	16	4
DEL PEAK 12(6Q22.31) WILD-TYPE	108	84	101	116	26

Figure S198. Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q22.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00109 (Fisher's exact test), Q value = 0.0032

Table S199. Gene #33: 'del_6q22.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 12(6Q22.31) MUTATED	27	16	1	12	6	10	6
DEL PEAK 12(6Q22.31) WILD-TYPE	108	55	35	56	84	31	66

Figure S199. Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q22.31' versus 'MIRSEQ_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0024

Table S200. Gene #33: 'del_6q22.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 12(6Q22.31) MUTATED	34	18	19	6
DEL PEAK 12(6Q22.31) WILD-TYPE	103	89	164	76

Figure S200. Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6q22.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00634 (Fisher's exact test), Q value = 0.015

Table S201. Gene #33: 'del_6q22.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 12(6Q22.31) MUTATED	40	18	17
DEL PEAK 12(6Q22.31) WILD-TYPE	145	143	142

Figure S201. Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6q22.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8.5e-05

Table S202. Gene #33: 'del_6q22.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 12(6Q22.31) MUTATED	24	11	18	22
DEL PEAK 12(6Q22.31) WILD-TYPE	67	126	170	67

Figure S202. Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q24.3' versus 'CN_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.00089

Table S203. Gene #34: 'del_6q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
DEL PEAK 13(6Q24.3) MUTATED	32	30	20
DEL PEAK 13(6Q24.3) WILD-TYPE	140	90	201

Figure S203. Get High-res Image Gene #34: 'del_6q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q24.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S204. Gene #34: 'del_6q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
DEL PEAK 13(6Q24.3) MUTATED	53	16	8	5
DEL PEAK 13(6Q24.3) WILD-TYPE	172	65	159	35

Figure S204. Get High-res Image Gene #34: 'del_6q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q24.3' versus 'MRNASEQ_CNMF'

P value = 0.00138 (Fisher's exact test), Q value = 0.0039

Table S205. Gene #34: 'del_6q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
DEL PEAK 13(6Q24.3) MUTATED	30	25	7	16	4
DEL PEAK 13(6Q24.3) WILD-TYPE	104	84	101	116	26

Figure S205. Get High-res Image Gene #34: 'del_6q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.001

Table S206. Gene #34: 'del_6q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 13(6Q24.3) MUTATED	31	15	1	12	6	11	6
DEL PEAK 13(6Q24.3) WILD-TYPE	104	56	35	56	84	30	66

Figure S206. Get High-res Image Gene #34: 'del_6q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q24.3' versus 'MIRSEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00051

Table S207. Gene #34: 'del_6q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 13(6Q24.3) MUTATED	36	20	20	5
DEL PEAK 13(6Q24.3) WILD-TYPE	101	87	163	77

Figure S207. Get High-res Image Gene #34: 'del_6q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6q24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0209 (Fisher's exact test), Q value = 0.044

Table S208. Gene #34: 'del_6q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 13(6Q24.3) MUTATED	40	21	18
DEL PEAK 13(6Q24.3) WILD-TYPE	145	140	141

Figure S208. Get High-res Image Gene #34: 'del_6q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00016

Table S209. Gene #34: 'del_6q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 13(6Q24.3) MUTATED	27	12	19	21
DEL PEAK 13(6Q24.3) WILD-TYPE	64	125	169	68

Figure S209. Get High-res Image Gene #34: 'del_6q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7p22.3' versus 'CN_CNMF'

P value = 0.0254 (Fisher's exact test), Q value = 0.052

Table S210. Gene #35: 'del_7p22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
DEL PEAK 14(7P22.3) MUTATED	14	3	6
DEL PEAK 14(7P22.3) WILD-TYPE	158	117	215

Figure S210. Get High-res Image Gene #35: 'del_7p22.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_8q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S211. Gene #36: 'del_8q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
DEL PEAK 15(8Q24.3) MUTATED	15	13	1
DEL PEAK 15(8Q24.3) WILD-TYPE	157	107	220

Figure S211. Get High-res Image Gene #36: 'del_8q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_8q24.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S212. Gene #36: 'del_8q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
DEL PEAK 15(8Q24.3) MUTATED	17	11	0	1
DEL PEAK 15(8Q24.3) WILD-TYPE	208	70	167	39

Figure S212. Get High-res Image Gene #36: 'del_8q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8q24.3' versus 'MRNASEQ_CNMF'

P value = 0.00331 (Fisher's exact test), Q value = 0.0085

Table S213. Gene #36: 'del_8q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
DEL PEAK 15(8Q24.3) MUTATED	11	11	0	6	1
DEL PEAK 15(8Q24.3) WILD-TYPE	123	98	108	126	29

Figure S213. Get High-res Image Gene #36: 'del_8q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00658 (Fisher's exact test), Q value = 0.016

Table S214. Gene #36: 'del_8q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 15(8Q24.3) MUTATED	10	9	0	4	0	3	3
DEL PEAK 15(8Q24.3) WILD-TYPE	125	62	36	64	90	38	69

Figure S214. Get High-res Image Gene #36: 'del_8q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8q24.3' versus 'MIRSEQ_CNMF'

P value = 0.0043 (Fisher's exact test), Q value = 0.011

Table S215. Gene #36: 'del_8q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 15(8Q24.3) MUTATED	13	9	7	0
DEL PEAK 15(8Q24.3) WILD-TYPE	124	98	176	82

Figure S215. Get High-res Image Gene #36: 'del_8q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00328 (Fisher's exact test), Q value = 0.0085

Table S216. Gene #36: 'del_8q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 15(8Q24.3) MUTATED	11	5	13
DEL PEAK 15(8Q24.3) WILD-TYPE	211	179	90

Figure S216. Get High-res Image Gene #36: 'del_8q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0304 (Fisher's exact test), Q value = 0.061

Table S217. Gene #36: 'del_8q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 15(8Q24.3) MUTATED	8	6	5	9
DEL PEAK 15(8Q24.3) WILD-TYPE	83	131	183	80

Figure S217. Get High-res Image Gene #36: 'del_8q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S218. Gene #37: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
DEL PEAK 16(9P23) MUTATED	55	57	38
DEL PEAK 16(9P23) WILD-TYPE	117	63	183

Figure S218. Get High-res Image Gene #37: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.5e-05

Table S219. Gene #37: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
DEL PEAK 16(9P23) MUTATED	79	35	28	8
DEL PEAK 16(9P23) WILD-TYPE	146	46	139	32

Figure S219. Get High-res Image Gene #37: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p23' versus 'RPPA_CNMF'

P value = 0.0389 (Fisher's exact test), Q value = 0.075

Table S220. Gene #37: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
DEL PEAK 16(9P23) MUTATED	11	27	22	18
DEL PEAK 16(9P23) WILD-TYPE	41	35	46	56

Figure S220. Get High-res Image Gene #37: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p23' versus 'RPPA_CHIERARCHICAL'

P value = 0.00228 (Fisher's exact test), Q value = 0.0061

Table S221. Gene #37: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	131	58
DEL PEAK 16(9P23) MUTATED	10	50	18
DEL PEAK 16(9P23) WILD-TYPE	57	81	40

Figure S221. Get High-res Image Gene #37: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 0.047

Table S222. Gene #37: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
DEL PEAK 16(9P23) MUTATED	35	42	21	44	8
DEL PEAK 16(9P23) WILD-TYPE	99	67	87	88	22

Figure S222. Get High-res Image Gene #37: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.00077

Table S223. Gene #37: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 16(9P23) MUTATED	39	27	10	31	15	16	12
DEL PEAK 16(9P23) WILD-TYPE	96	44	26	37	75	25	60

Figure S223. Get High-res Image Gene #37: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00326 (Fisher's exact test), Q value = 0.0084

Table S224. Gene #37: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 16(9P23) MUTATED	28	27	55	38
DEL PEAK 16(9P23) WILD-TYPE	63	110	133	51

Figure S224. Get High-res Image Gene #37: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S225. Gene #38: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
DEL PEAK 17(9P21.3) MUTATED	63	77	36
DEL PEAK 17(9P21.3) WILD-TYPE	109	43	185

Figure S225. Get High-res Image Gene #38: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S226. Gene #38: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
DEL PEAK 17(9P21.3) MUTATED	82	59	27	8
DEL PEAK 17(9P21.3) WILD-TYPE	143	22	140	32

Figure S226. Get High-res Image Gene #38: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

Table S227. Gene #38: 'del_9p21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
DEL PEAK 17(9P21.3) MUTATED	12	38	26	18
DEL PEAK 17(9P21.3) WILD-TYPE	40	24	42	56

Figure S227. Get High-res Image Gene #38: 'del_9p21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8.5e-05

Table S228. Gene #38: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	131	58
DEL PEAK 17(9P21.3) MUTATED	11	65	18
DEL PEAK 17(9P21.3) WILD-TYPE	56	66	40

Figure S228. Get High-res Image Gene #38: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S229. Gene #38: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
DEL PEAK 17(9P21.3) MUTATED	40	64	19	45	8
DEL PEAK 17(9P21.3) WILD-TYPE	94	45	89	87	22

Figure S229. Get High-res Image Gene #38: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S230. Gene #38: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 17(9P21.3) MUTATED	44	47	10	31	13	18	13
DEL PEAK 17(9P21.3) WILD-TYPE	91	24	26	37	77	23	59

Figure S230. Get High-res Image Gene #38: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S231. Gene #38: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 17(9P21.3) MUTATED	59	56	60
DEL PEAK 17(9P21.3) WILD-TYPE	163	128	43

Figure S231. Get High-res Image Gene #38: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00088 (Fisher's exact test), Q value = 0.0026

Table S232. Gene #38: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 17(9P21.3) MUTATED	82	41	51
DEL PEAK 17(9P21.3) WILD-TYPE	103	120	108

Figure S232. Get High-res Image Gene #38: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S233. Gene #38: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 17(9P21.3) MUTATED	31	28	54	61
DEL PEAK 17(9P21.3) WILD-TYPE	60	109	134	28

Figure S233. Get High-res Image Gene #38: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S234. Gene #39: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
DEL PEAK 18(10Q26.3) MUTATED	53	85	13
DEL PEAK 18(10Q26.3) WILD-TYPE	119	35	208

Figure S234. Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q26.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S235. Gene #39: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
DEL PEAK 18(10Q26.3) MUTATED	64	72	8	7
DEL PEAK 18(10Q26.3) WILD-TYPE	161	9	159	33

Figure S235. Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q26.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S236. Gene #39: 'del_10q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
DEL PEAK 18(10Q26.3) MUTATED	13	35	14	11
DEL PEAK 18(10Q26.3) WILD-TYPE	39	27	54	63

Figure S236. Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_10q26.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.00089

Table S237. Gene #39: 'del_10q26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	131	58
DEL PEAK 18(10Q26.3) MUTATED	11	52	10
DEL PEAK 18(10Q26.3) WILD-TYPE	56	79	48

Figure S237. Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S238. Gene #39: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
DEL PEAK 18(10Q26.3) MUTATED	33	79	6	26	7
DEL PEAK 18(10Q26.3) WILD-TYPE	101	30	102	106	23

Figure S238. Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S239. Gene #39: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 18(10Q26.3) MUTATED	34	60	3	24	5	22	3
DEL PEAK 18(10Q26.3) WILD-TYPE	101	11	33	44	85	19	69

Figure S239. Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.5e-05

Table S240. Gene #39: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 18(10Q26.3) MUTATED	55	46	39	11
DEL PEAK 18(10Q26.3) WILD-TYPE	82	61	144	71

Figure S240. Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S241. Gene #39: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 18(10Q26.3) MUTATED	49	28	74
DEL PEAK 18(10Q26.3) WILD-TYPE	173	156	29

Figure S241. Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S242. Gene #39: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 18(10Q26.3) MUTATED	94	22	35
DEL PEAK 18(10Q26.3) WILD-TYPE	91	139	124

Figure S242. Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S243. Gene #39: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 18(10Q26.3) MUTATED	28	18	33	72
DEL PEAK 18(10Q26.3) WILD-TYPE	63	119	155	17

Figure S243. Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'MRNA_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.0017

Table S244. Gene #40: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
DEL PEAK 19(11P15.5) MUTATED	1	6	0	0
DEL PEAK 19(11P15.5) WILD-TYPE	6	1	7	6

Figure S244. Get High-res Image Gene #40: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S245. Gene #40: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
DEL PEAK 19(11P15.5) MUTATED	74	20	10
DEL PEAK 19(11P15.5) WILD-TYPE	98	100	211

Figure S245. Get High-res Image Gene #40: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S246. Gene #40: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
DEL PEAK 19(11P15.5) MUTATED	85	14	0	5
DEL PEAK 19(11P15.5) WILD-TYPE	140	67	167	35

Figure S246. Get High-res Image Gene #40: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S247. Gene #40: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
DEL PEAK 19(11P15.5) MUTATED	38	34	1	24	7
DEL PEAK 19(11P15.5) WILD-TYPE	96	75	107	108	23

Figure S247. Get High-res Image Gene #40: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S248. Gene #40: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 19(11P15.5) MUTATED	38	9	0	18	0	29	10
DEL PEAK 19(11P15.5) WILD-TYPE	97	62	36	50	90	12	62

Figure S248. Get High-res Image Gene #40: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00023

Table S249. Gene #40: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 19(11P15.5) MUTATED	23	40	33	8
DEL PEAK 19(11P15.5) WILD-TYPE	114	67	150	74

Figure S249. Get High-res Image Gene #40: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00457 (Fisher's exact test), Q value = 0.011

Table S250. Gene #40: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 19(11P15.5) MUTATED	42	29	33
DEL PEAK 19(11P15.5) WILD-TYPE	180	155	70

Figure S250. Get High-res Image Gene #40: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0316 (Fisher's exact test), Q value = 0.063

Table S251. Gene #41: 'del_11p15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
DEL PEAK 20(11P15.1) MUTATED	1	4	0	0
DEL PEAK 20(11P15.1) WILD-TYPE	6	3	7	6

Figure S251. Get High-res Image Gene #41: 'del_11p15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11p15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S252. Gene #41: 'del_11p15.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
DEL PEAK 20(11P15.1) MUTATED	52	15	5
DEL PEAK 20(11P15.1) WILD-TYPE	120	105	216

Figure S252. Get High-res Image Gene #41: 'del_11p15.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_11p15.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S253. Gene #41: 'del_11p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
DEL PEAK 20(11P15.1) MUTATED	52	14	1	5
DEL PEAK 20(11P15.1) WILD-TYPE	173	67	166	35

Figure S253. Get High-res Image Gene #41: 'del_11p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11p15.1' versus 'RPPA_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.027

Table S254. Gene #41: 'del_11p15.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
DEL PEAK 20(11P15.1) MUTATED	10	17	5	9
DEL PEAK 20(11P15.1) WILD-TYPE	42	45	63	65

Figure S254. Get High-res Image Gene #41: 'del_11p15.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_11p15.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S255. Gene #41: 'del_11p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
DEL PEAK 20(11P15.1) MUTATED	17	34	2	13	6
DEL PEAK 20(11P15.1) WILD-TYPE	117	75	106	119	24

Figure S255. Get High-res Image Gene #41: 'del_11p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11p15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S256. Gene #41: 'del_11p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 20(11P15.1) MUTATED	20	9	0	6	1	29	7
DEL PEAK 20(11P15.1) WILD-TYPE	115	62	36	62	89	12	65

Figure S256. Get High-res Image Gene #41: 'del_11p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.1' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.5e-05

Table S257. Gene #41: 'del_11p15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 20(11P15.1) MUTATED	16	32	19	5
DEL PEAK 20(11P15.1) WILD-TYPE	121	75	164	77

Figure S257. Get High-res Image Gene #41: 'del_11p15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11p15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00023

Table S258. Gene #41: 'del_11p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 20(11P15.1) MUTATED	27	16	29
DEL PEAK 20(11P15.1) WILD-TYPE	195	168	74

Figure S258. Get High-res Image Gene #41: 'del_11p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0328 (Fisher's exact test), Q value = 0.065

Table S259. Gene #41: 'del_11p15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 20(11P15.1) MUTATED	13	18	19	21
DEL PEAK 20(11P15.1) WILD-TYPE	78	119	169	68

Figure S259. Get High-res Image Gene #41: 'del_11p15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12p13.1' versus 'CN_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0022

Table S260. Gene #42: 'del_12p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
DEL PEAK 21(12P13.1) MUTATED	23	8	7
DEL PEAK 21(12P13.1) WILD-TYPE	149	112	214

Figure S260. Get High-res Image Gene #42: 'del_12p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

P value = 0.00218 (Fisher's exact test), Q value = 0.0059

Table S261. Gene #42: 'del_12p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
DEL PEAK 21(12P13.1) MUTATED	26	7	5	0
DEL PEAK 21(12P13.1) WILD-TYPE	199	74	162	40

Figure S261. Get High-res Image Gene #42: 'del_12p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12p13.1' versus 'MRNASEQ_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.023

Table S262. Gene #42: 'del_12p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
DEL PEAK 21(12P13.1) MUTATED	15	12	2	9	0
DEL PEAK 21(12P13.1) WILD-TYPE	119	97	106	123	30

Figure S262. Get High-res Image Gene #42: 'del_12p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00701 (Fisher's exact test), Q value = 0.017

Table S263. Gene #42: 'del_12p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 21(12P13.1) MUTATED	15	4	1	3	3	9	3
DEL PEAK 21(12P13.1) WILD-TYPE	120	67	35	65	87	32	69

Figure S263. Get High-res Image Gene #42: 'del_12p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.044 (Fisher's exact test), Q value = 0.082

Table S264. Gene #42: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 21(12P13.1) MUTATED	13	11	14
DEL PEAK 21(12P13.1) WILD-TYPE	209	173	89

Figure S264. Get High-res Image Gene #42: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S265. Gene #43: 'del_12q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
DEL PEAK 22(12Q12) MUTATED	53	7	12
DEL PEAK 22(12Q12) WILD-TYPE	119	113	209

Figure S265. Get High-res Image Gene #43: 'del_12q12' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S266. Gene #43: 'del_12q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
DEL PEAK 22(12Q12) MUTATED	57	5	8	2
DEL PEAK 22(12Q12) WILD-TYPE	168	76	159	38

Figure S266. Get High-res Image Gene #43: 'del_12q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12q12' versus 'MRNASEQ_CNMF'

P value = 0.0023 (Fisher's exact test), Q value = 0.0061

Table S267. Gene #43: 'del_12q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
DEL PEAK 22(12Q12) MUTATED	24	21	4	18	5
DEL PEAK 22(12Q12) WILD-TYPE	110	88	104	114	25

Figure S267. Get High-res Image Gene #43: 'del_12q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S268. Gene #43: 'del_12q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 22(12Q12) MUTATED	25	4	3	11	4	18	7
DEL PEAK 22(12Q12) WILD-TYPE	110	67	33	57	86	23	65

Figure S268. Get High-res Image Gene #43: 'del_12q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q12' versus 'MIRSEQ_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.028

Table S269. Gene #43: 'del_12q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 22(12Q12) MUTATED	14	26	23	9
DEL PEAK 22(12Q12) WILD-TYPE	123	81	160	73

Figure S269. Get High-res Image Gene #43: 'del_12q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 2e-04

Table S270. Gene #44: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
DEL PEAK 23(13Q14.2) MUTATED	2	7	0	0
DEL PEAK 23(13Q14.2) WILD-TYPE	5	0	7	6

Figure S270. Get High-res Image Gene #44: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S271. Gene #44: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
DEL PEAK 23(13Q14.2) MUTATED	73	36	33
DEL PEAK 23(13Q14.2) WILD-TYPE	99	84	188

Figure S271. Get High-res Image Gene #44: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

Table S272. Gene #44: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
DEL PEAK 23(13Q14.2) MUTATED	80	28	27	7
DEL PEAK 23(13Q14.2) WILD-TYPE	145	53	140	33

Figure S272. Get High-res Image Gene #44: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'RPPA_CNMF'

P value = 0.0345 (Fisher's exact test), Q value = 0.068

Table S273. Gene #44: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
DEL PEAK 23(13Q14.2) MUTATED	9	26	18	20
DEL PEAK 23(13Q14.2) WILD-TYPE	43	36	50	54

Figure S273. Get High-res Image Gene #44: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 0.00706 (Fisher's exact test), Q value = 0.017

Table S274. Gene #44: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
DEL PEAK 23(13Q14.2) MUTATED	40	43	19	32	8
DEL PEAK 23(13Q14.2) WILD-TYPE	94	66	89	100	22

Figure S274. Get High-res Image Gene #44: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S275. Gene #44: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 23(13Q14.2) MUTATED	43	21	2	17	18	25	16
DEL PEAK 23(13Q14.2) WILD-TYPE	92	50	34	51	72	16	56

Figure S275. Get High-res Image Gene #44: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.039

Table S276. Gene #44: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 23(13Q14.2) MUTATED	38	42	40	21
DEL PEAK 23(13Q14.2) WILD-TYPE	99	65	143	61

Figure S276. Get High-res Image Gene #44: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00608 (Fisher's exact test), Q value = 0.015

Table S277. Gene #44: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 23(13Q14.2) MUTATED	66	37	38
DEL PEAK 23(13Q14.2) WILD-TYPE	156	147	65

Figure S277. Get High-res Image Gene #44: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MRNA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00034

Table S278. Gene #45: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
DEL PEAK 24(13Q14.2) MUTATED	2	7	0	0
DEL PEAK 24(13Q14.2) WILD-TYPE	5	0	7	6

Figure S278. Get High-res Image Gene #45: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S279. Gene #45: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
DEL PEAK 24(13Q14.2) MUTATED	74	37	33
DEL PEAK 24(13Q14.2) WILD-TYPE	98	83	188

Figure S279. Get High-res Image Gene #45: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

Table S280. Gene #45: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
DEL PEAK 24(13Q14.2) MUTATED	81	29	27	7
DEL PEAK 24(13Q14.2) WILD-TYPE	144	52	140	33

Figure S280. Get High-res Image Gene #45: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'RPPA_CNMF'

P value = 0.0337 (Fisher's exact test), Q value = 0.066

Table S281. Gene #45: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
DEL PEAK 24(13Q14.2) MUTATED	10	27	18	20
DEL PEAK 24(13Q14.2) WILD-TYPE	42	35	50	54

Figure S281. Get High-res Image Gene #45: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 0.00397 (Fisher's exact test), Q value = 0.01

Table S282. Gene #45: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
DEL PEAK 24(13Q14.2) MUTATED	41	44	19	32	8
DEL PEAK 24(13Q14.2) WILD-TYPE	93	65	89	100	22

Figure S282. Get High-res Image Gene #45: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S283. Gene #45: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 24(13Q14.2) MUTATED	44	22	2	17	18	25	16
DEL PEAK 24(13Q14.2) WILD-TYPE	91	49	34	51	72	16	56

Figure S283. Get High-res Image Gene #45: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 0.038

Table S284. Gene #45: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 24(13Q14.2) MUTATED	40	42	40	21
DEL PEAK 24(13Q14.2) WILD-TYPE	97	65	143	61

Figure S284. Get High-res Image Gene #45: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00345 (Fisher's exact test), Q value = 0.0088

Table S285. Gene #45: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 24(13Q14.2) MUTATED	67	37	39
DEL PEAK 24(13Q14.2) WILD-TYPE	155	147	64

Figure S285. Get High-res Image Gene #45: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q34' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00023

Table S286. Gene #46: 'del_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
DEL PEAK 25(13Q34) MUTATED	52	30	28
DEL PEAK 25(13Q34) WILD-TYPE	120	90	193

Figure S286. Get High-res Image Gene #46: 'del_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q34' versus 'METHLYATION_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.026

Table S287. Gene #46: 'del_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
DEL PEAK 25(13Q34) MUTATED	51	27	26	6
DEL PEAK 25(13Q34) WILD-TYPE	174	54	141	34

Figure S287. Get High-res Image Gene #46: 'del_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q34' versus 'MRNASEQ_CNMF'

P value = 0.0432 (Fisher's exact test), Q value = 0.081

Table S288. Gene #46: 'del_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
DEL PEAK 25(13Q34) MUTATED	29	35	18	23	5
DEL PEAK 25(13Q34) WILD-TYPE	105	74	90	109	25

Figure S288. Get High-res Image Gene #46: 'del_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.0024

Table S289. Gene #46: 'del_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 25(13Q34) MUTATED	31	20	2	9	17	18	13
DEL PEAK 25(13Q34) WILD-TYPE	104	51	34	59	73	23	59

Figure S289. Get High-res Image Gene #46: 'del_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q34' versus 'MIRSEQ_CNMF'

P value = 0.0263 (Fisher's exact test), Q value = 0.054

Table S290. Gene #46: 'del_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 25(13Q34) MUTATED	28	34	30	17
DEL PEAK 25(13Q34) WILD-TYPE	109	73	153	65

Figure S290. Get High-res Image Gene #46: 'del_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00242 (Fisher's exact test), Q value = 0.0064

Table S291. Gene #46: 'del_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 25(13Q34) MUTATED	49	27	33
DEL PEAK 25(13Q34) WILD-TYPE	173	157	70

Figure S291. Get High-res Image Gene #46: 'del_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q24.3' versus 'CN_CNMF'

P value = 0.00458 (Fisher's exact test), Q value = 0.011

Table S292. Gene #47: 'del_14q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
DEL PEAK 26(14Q24.3) MUTATED	36	42	43
DEL PEAK 26(14Q24.3) WILD-TYPE	136	78	178

Figure S292. Get High-res Image Gene #47: 'del_14q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q24.3' versus 'METHLYATION_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.027

Table S293. Gene #47: 'del_14q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
DEL PEAK 26(14Q24.3) MUTATED	53	30	32	6
DEL PEAK 26(14Q24.3) WILD-TYPE	172	51	135	34

Figure S293. Get High-res Image Gene #47: 'del_14q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q24.3' versus 'RPPA_CNMF'

P value = 0.00158 (Fisher's exact test), Q value = 0.0044

Table S294. Gene #47: 'del_14q24.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
DEL PEAK 26(14Q24.3) MUTATED	6	24	18	11
DEL PEAK 26(14Q24.3) WILD-TYPE	46	38	50	63

Figure S294. Get High-res Image Gene #47: 'del_14q24.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_14q24.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0374 (Fisher's exact test), Q value = 0.073

Table S295. Gene #47: 'del_14q24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	131	58
DEL PEAK 26(14Q24.3) MUTATED	10	39	10
DEL PEAK 26(14Q24.3) WILD-TYPE	57	92	48

Figure S295. Get High-res Image Gene #47: 'del_14q24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_14q24.3' versus 'MRNASEQ_CNMF'

P value = 0.00088 (Fisher's exact test), Q value = 0.0026

Table S296. Gene #47: 'del_14q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
DEL PEAK 26(14Q24.3) MUTATED	25	42	25	21	8
DEL PEAK 26(14Q24.3) WILD-TYPE	109	67	83	111	22

Figure S296. Get High-res Image Gene #47: 'del_14q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.0022

Table S297. Gene #47: 'del_14q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 26(14Q24.3) MUTATED	32	27	8	12	17	17	8
DEL PEAK 26(14Q24.3) WILD-TYPE	103	44	28	56	73	24	64

Figure S297. Get High-res Image Gene #47: 'del_14q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q24.3' versus 'MIRSEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0013

Table S298. Gene #47: 'del_14q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 26(14Q24.3) MUTATED	51	21	32	16
DEL PEAK 26(14Q24.3) WILD-TYPE	86	86	151	66

Figure S298. Get High-res Image Gene #47: 'del_14q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_14q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00497 (Fisher's exact test), Q value = 0.012

Table S299. Gene #47: 'del_14q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 26(14Q24.3) MUTATED	54	31	35
DEL PEAK 26(14Q24.3) WILD-TYPE	168	153	68

Figure S299. Get High-res Image Gene #47: 'del_14q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00176 (Fisher's exact test), Q value = 0.0048

Table S300. Gene #47: 'del_14q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 26(14Q24.3) MUTATED	58	38	24
DEL PEAK 26(14Q24.3) WILD-TYPE	127	123	135

Figure S300. Get High-res Image Gene #47: 'del_14q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_14q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00111 (Fisher's exact test), Q value = 0.0032

Table S301. Gene #47: 'del_14q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 26(14Q24.3) MUTATED	26	33	29	32
DEL PEAK 26(14Q24.3) WILD-TYPE	65	104	159	57

Figure S301. Get High-res Image Gene #47: 'del_14q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q23' versus 'METHLYATION_CNMF'

P value = 0.00353 (Fisher's exact test), Q value = 0.009

Table S302. Gene #48: 'del_18q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
DEL PEAK 27(18Q23) MUTATED	31	13	34	0
DEL PEAK 27(18Q23) WILD-TYPE	194	68	133	40

Figure S302. Get High-res Image Gene #48: 'del_18q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q13.41' versus 'MRNA_CNMF'

P value = 0.0342 (Fisher's exact test), Q value = 0.067

Table S303. Gene #49: 'del_19q13.41' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	10	8
DEL PEAK 28(19Q13.41) MUTATED	6	10	4
DEL PEAK 28(19Q13.41) WILD-TYPE	3	0	4

Figure S303. Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19q13.41' versus 'MRNA_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.023

Table S304. Gene #49: 'del_19q13.41' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
DEL PEAK 28(19Q13.41) MUTATED	3	7	7	3
DEL PEAK 28(19Q13.41) WILD-TYPE	4	0	0	3

Figure S304. Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19q13.41' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S305. Gene #49: 'del_19q13.41' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
DEL PEAK 28(19Q13.41) MUTATED	40	35	192
DEL PEAK 28(19Q13.41) WILD-TYPE	132	85	29

Figure S305. Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q13.41' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S306. Gene #49: 'del_19q13.41' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
DEL PEAK 28(19Q13.41) MUTATED	78	12	167	10
DEL PEAK 28(19Q13.41) WILD-TYPE	147	69	0	30

Figure S306. Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q13.41' versus 'RPPA_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.0027

Table S307. Gene #49: 'del_19q13.41' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
DEL PEAK 28(19Q13.41) MUTATED	16	28	36	49
DEL PEAK 28(19Q13.41) WILD-TYPE	36	34	32	25

Figure S307. Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19q13.41' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S308. Gene #49: 'del_19q13.41' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
DEL PEAK 28(19Q13.41) MUTATED	41	30	107	77	12
DEL PEAK 28(19Q13.41) WILD-TYPE	93	79	1	55	18

Figure S308. Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19q13.41' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S309. Gene #49: 'del_19q13.41' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 28(19Q13.41) MUTATED	39	7	36	19	89	23	54
DEL PEAK 28(19Q13.41) WILD-TYPE	96	64	0	49	1	18	18

Figure S309. Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.41' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S310. Gene #49: 'del_19q13.41' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 28(19Q13.41) MUTATED	50	36	107	74
DEL PEAK 28(19Q13.41) WILD-TYPE	87	71	76	8

Figure S310. Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19q13.41' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S311. Gene #49: 'del_19q13.41' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 28(19Q13.41) MUTATED	129	118	20
DEL PEAK 28(19Q13.41) WILD-TYPE	93	66	83

Figure S311. Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.41' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S312. Gene #49: 'del_19q13.41' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 28(19Q13.41) MUTATED	61	110	95
DEL PEAK 28(19Q13.41) WILD-TYPE	124	51	64

Figure S312. Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19q13.41' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S313. Gene #49: 'del_19q13.41' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 28(19Q13.41) MUTATED	32	105	113	16
DEL PEAK 28(19Q13.41) WILD-TYPE	59	32	75	73

Figure S313. Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.42' versus 'MRNA_CNMF'

P value = 0.0352 (Fisher's exact test), Q value = 0.069

Table S314. Gene #50: 'del_19q13.42' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	10	8
DEL PEAK 29(19Q13.42) MUTATED	7	10	4
DEL PEAK 29(19Q13.42) WILD-TYPE	2	0	4

Figure S314. Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19q13.42' versus 'MRNA_CHIERARCHICAL'

P value = 0.0207 (Fisher's exact test), Q value = 0.044

Table S315. Gene #50: 'del_19q13.42' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
DEL PEAK 29(19Q13.42) MUTATED	4	7	7	3
DEL PEAK 29(19Q13.42) WILD-TYPE	3	0	0	3

Figure S315. Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19q13.42' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S316. Gene #50: 'del_19q13.42' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
DEL PEAK 29(19Q13.42) MUTATED	42	38	198
DEL PEAK 29(19Q13.42) WILD-TYPE	130	82	23

Figure S316. Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q13.42' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S317. Gene #50: 'del_19q13.42' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
DEL PEAK 29(19Q13.42) MUTATED	88	13	167	10
DEL PEAK 29(19Q13.42) WILD-TYPE	137	68	0	30

Figure S317. Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q13.42' versus 'RPPA_CNMF'

P value = 0.00213 (Fisher's exact test), Q value = 0.0058

Table S318. Gene #50: 'del_19q13.42' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
DEL PEAK 29(19Q13.42) MUTATED	17	29	40	48
DEL PEAK 29(19Q13.42) WILD-TYPE	35	33	28	26

Figure S318. Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19q13.42' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S319. Gene #50: 'del_19q13.42' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
DEL PEAK 29(19Q13.42) MUTATED	50	32	107	77	12
DEL PEAK 29(19Q13.42) WILD-TYPE	84	77	1	55	18

Figure S319. Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19q13.42' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S320. Gene #50: 'del_19q13.42' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 29(19Q13.42) MUTATED	46	9	36	21	89	23	54
DEL PEAK 29(19Q13.42) WILD-TYPE	89	62	0	47	1	18	18

Figure S320. Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.42' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S321. Gene #50: 'del_19q13.42' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 29(19Q13.42) MUTATED	56	40	106	76
DEL PEAK 29(19Q13.42) WILD-TYPE	81	67	77	6

Figure S321. Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19q13.42' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S322. Gene #50: 'del_19q13.42' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 29(19Q13.42) MUTATED	137	119	22
DEL PEAK 29(19Q13.42) WILD-TYPE	85	65	81

Figure S322. Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.42' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S323. Gene #50: 'del_19q13.42' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 29(19Q13.42) MUTATED	69	113	95
DEL PEAK 29(19Q13.42) WILD-TYPE	116	48	64

Figure S323. Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19q13.42' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S324. Gene #50: 'del_19q13.42' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 29(19Q13.42) MUTATED	36	109	115	17
DEL PEAK 29(19Q13.42) WILD-TYPE	55	28	73	72

Figure S324. Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.31' versus 'MRNA_CHIERARCHICAL'

P value = 0.0422 (Fisher's exact test), Q value = 0.079

Table S325. Gene #51: 'del_22q13.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
DEL PEAK 30(22Q13.31) MUTATED	2	4	0	0
DEL PEAK 30(22Q13.31) WILD-TYPE	5	3	7	6

Figure S325. Get High-res Image Gene #51: 'del_22q13.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_22q13.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S326. Gene #51: 'del_22q13.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
DEL PEAK 30(22Q13.31) MUTATED	34	35	8
DEL PEAK 30(22Q13.31) WILD-TYPE	138	85	213

Figure S326. Get High-res Image Gene #51: 'del_22q13.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S327. Gene #51: 'del_22q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
DEL PEAK 30(22Q13.31) MUTATED	39	29	4	5
DEL PEAK 30(22Q13.31) WILD-TYPE	186	52	163	35

Figure S327. Get High-res Image Gene #51: 'del_22q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q13.31' versus 'RPPA_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00074

Table S328. Gene #51: 'del_22q13.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
DEL PEAK 30(22Q13.31) MUTATED	4	21	8	6
DEL PEAK 30(22Q13.31) WILD-TYPE	48	41	60	68

Figure S328. Get High-res Image Gene #51: 'del_22q13.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_22q13.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.025

Table S329. Gene #51: 'del_22q13.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	131	58
DEL PEAK 30(22Q13.31) MUTATED	4	28	7
DEL PEAK 30(22Q13.31) WILD-TYPE	63	103	51

Figure S329. Get High-res Image Gene #51: 'del_22q13.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_22q13.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S330. Gene #51: 'del_22q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
DEL PEAK 30(22Q13.31) MUTATED	14	39	4	14	6
DEL PEAK 30(22Q13.31) WILD-TYPE	120	70	104	118	24

Figure S330. Get High-res Image Gene #51: 'del_22q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S331. Gene #51: 'del_22q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 30(22Q13.31) MUTATED	17	26	2	14	2	14	2
DEL PEAK 30(22Q13.31) WILD-TYPE	118	45	34	54	88	27	70

Figure S331. Get High-res Image Gene #51: 'del_22q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_CNMF'

P value = 0.0354 (Fisher's exact test), Q value = 0.069

Table S332. Gene #51: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 30(22Q13.31) MUTATED	25	23	22	7
DEL PEAK 30(22Q13.31) WILD-TYPE	112	84	161	75

Figure S332. Get High-res Image Gene #51: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_22q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S333. Gene #51: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 30(22Q13.31) MUTATED	27	18	32
DEL PEAK 30(22Q13.31) WILD-TYPE	195	166	71

Figure S333. Get High-res Image Gene #51: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00159 (Fisher's exact test), Q value = 0.0044

Table S334. Gene #51: 'del_22q13.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 30(22Q13.31) MUTATED	42	18	16
DEL PEAK 30(22Q13.31) WILD-TYPE	143	143	143

Figure S334. Get High-res Image Gene #51: 'del_22q13.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_22q13.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

Table S335. Gene #51: 'del_22q13.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 30(22Q13.31) MUTATED	11	18	18	29
DEL PEAK 30(22Q13.31) WILD-TYPE	80	119	170	60

Figure S335. Get High-res Image Gene #51: 'del_22q13.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xq21.1' versus 'MRNASEQ_CNMF'

P value = 0.00851 (Fisher's exact test), Q value = 0.02

Table S336. Gene #52: 'del_xq21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
DEL PEAK 31(XQ21.1) MUTATED	14	23	24	16	1
DEL PEAK 31(XQ21.1) WILD-TYPE	120	86	84	116	29

Figure S336. Get High-res Image Gene #52: 'del_xq21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_xq21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.6e-05

Table S337. Gene #52: 'del_xq21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 31(XQ21.1) MUTATED	13	8	9	8	20	16	4
DEL PEAK 31(XQ21.1) WILD-TYPE	122	63	27	60	70	25	68

Figure S337. Get High-res Image Gene #52: 'del_xq21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_xq21.1' versus 'MIRSEQ_CNMF'

P value = 0.00088 (Fisher's exact test), Q value = 0.0026

Table S338. Gene #52: 'del_xq21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 31(XQ21.1) MUTATED	14	19	21	24
DEL PEAK 31(XQ21.1) WILD-TYPE	123	88	162	58

Figure S338. Get High-res Image Gene #52: 'del_xq21.1' versus Molecular Subtype #9: 'MIRSEQ_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/LGG-TP/15087635/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LGG-TP/15115118/LGG-TP.transferedmergedcluster.txt
Number of patients = 513
Number of significantly focal cnvs = 52
Number of molecular subtypes = 12
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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