Correlation between copy number variation genes (focal events) and molecular subtypes

Liver Hepatocellular Carcinoma (Primary solid tumor)

28 January 2016 | analyses__2016_01_28

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1K936ZM

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 61 focal events and 8 molecular subtypes across 370 patients, 289 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_1q42.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_2p24.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_2q33.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_3q26.31 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_4p14 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5p15.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_5q35.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_6p25.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
amp_6p21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
amp_6q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
amp_6q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_7q31.2 cnv correlated to 'METHLYATION_CNMF'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_9q34.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_10p15.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_11q13.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_13q32.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_13q33.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_15q26.3 cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
amp_17p11.2 cnv correlated to 'METHLYATION_CNMF'.
amp_17q25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19p13.12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19q13.11 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20q13.13 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20q13.33 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_xq28 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q22.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_2q37.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p13 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4p16.3 cnv correlated to 'CN_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q24 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q35.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q27 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_7q36.3 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p23.2 cnv correlated to 'CN_CNMF'.
del_8p12 cnv correlated to 'CN_CNMF'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9q31.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q26.13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q14.1 cnv correlated to 'CN_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q23.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12p12.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12q24.33 cnv correlated to 'CN_CNMF'.
del_13q14.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q23.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_14q32.33 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q26.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_16q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p13.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p11.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q21.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_22q12.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_22q13.32 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_xq26.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 61 focal events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 289 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	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
amp 19p13 12	69 (19%)	301	0.013 (0.0279)	0.00118 (0.0042)	0.00065 (0.00254)	0.00055 (0.0022)	0.00321 (0.00932)	0.00223 (0.00676)	0.00247 (0.00739)	0.00129 (0.00453)
del 1p36 31	162 (44%)	208	1e-05 (7.39e-05)	1e-05 (7.39e-05)	1e-05 (7.39e-05)	1e-05 (7.39e-05)	0.00149 (0.00505)	0.00113 (0.00408)	0.00398 (0.0111)	0.00469 (0.0127)
del 1p36 11	142 (38%)	228	1e-05 (7.39e-05)	1e-05 (7.39e-05)	1e-05 (7.39e-05)	1e-05 (7.39e-05)	2e-05 (0.000137)	7e-05 (0.00038)	0.00054 (0.00218)	0.00026 (0.00117)
del 4q21 3	171 (46%)	199	1e-05 (7.39e-05)	0.00095 (0.00351)	1e-05 (7.39e-05)	0.00021 (0.000976)	0.00133 (0.0046)	0.00154 (0.00515)	6e-05 (0.000337)	6e-05 (0.000337)
del 4q24	173 (47%)	197	1e-05 (7.39e-05)	0.00081 (0.00309)	1e-05 (7.39e-05)	5e-05 (0.000298)	0.00183 (0.0058)	0.00021 (0.000976)	2e-05 (0.000137)	4e-05 (0.000257)
del 4q35 1	172 (46%)	198	1e-05 (7.39e-05)	0.00036 (0.00153)	1e-05 (7.39e-05)	0.00072 (0.00277)	0.00188 (0.00592)	0.00597 (0.0153)	9e-05 (0.000453)	0.00148 (0.00505)
del 9p21 3	150 (41%)	220	1e-05 (7.39e-05)	0.0242 (0.0469)	1e-05 (7.39e-05)	0.00175 (0.00566)	4e-05 (0.000257)	0.00215 (0.0066)	0.0208 (0.0409)	0.00478 (0.0127)
del 10q23 31	97 (26%)	273	1e-05 (7.39e-05)	0.015 (0.0314)	1e-05 (7.39e-05)	1e-05 (7.39e-05)	1e-05 (7.39e-05)	1e-05 (7.39e-05)	0.0156 (0.0324)	1e-05 (7.39e-05)
del 16q23 1	162 (44%)	208	1e-05 (7.39e-05)	1e-05 (7.39e-05)	1e-05 (7.39e-05)	1e-05 (7.39e-05)	5e-05 (0.000298)	1e-05 (7.39e-05)	1e-05 (7.39e-05)	5e-05 (0.000298)
amp 17q25 3	145 (39%)	225	1e-05 (7.39e-05)	0.0478 (0.0809)	0.0113 (0.0251)	0.0106 (0.0239)	0.00748 (0.0183)	0.00131 (0.00457)	0.0548 (0.0906)	0.011 (0.0246)
amp 19q13 11	91 (25%)	279	0.0164 (0.0336)	0.0926 (0.137)	0.00041 (0.00171)	0.00066 (0.00256)	0.0325 (0.0598)	0.0018 (0.00574)	1e-05 (7.39e-05)	0.00027 (0.00121)
amp xq28	87 (24%)	283	0.00178 (0.00571)	0.0503 (0.0846)	0.0275 (0.0521)	0.00997 (0.0225)	0.00011 (0.000537)	0.00335 (0.00962)	0.0158 (0.0326)	0.00034 (0.00147)
del 3p13	73 (20%)	297	0.0751 (0.115)	0.00882 (0.0208)	0.00011 (0.000537)	1e-05 (7.39e-05)	5e-05 (0.000298)	0.0335 (0.0608)	0.00993 (0.0225)	0.00163 (0.00534)
del 9q31 3	119 (32%)	251	1e-05 (7.39e-05)	0.00897 (0.021)	0.00115 (0.00413)	0.00032 (0.00139)	0.027 (0.0513)	0.00696 (0.0173)	0.251 (0.307)	0.00022 (0.00101)
del 10q26 13	105 (28%)	265	1e-05 (7.39e-05)	0.0242 (0.0469)	1e-05 (7.39e-05)	1e-05 (7.39e-05)	3e-05 (0.000201)	1e-05 (7.39e-05)	0.0728 (0.112)	1e-05 (7.39e-05)
del 13q14 2	179 (48%)	191	1e-05 (7.39e-05)	0.134 (0.184)	0.00028 (0.00124)	1e-05 (7.39e-05)	0.00175 (0.00566)	0.00064 (0.00252)	0.0179 (0.0359)	8e-05 (0.00042)
amp 4p14	54 (15%)	316	0.0636 (0.102)	0.0188 (0.0376)	4e-05 (0.000257)	0.00122 (0.00431)	0.0331 (0.0603)	0.0555 (0.0912)	0.00764 (0.0186)	0.0123 (0.0268)
amp 8q24 21	231 (62%)	139	1e-05 (7.39e-05)	0.0474 (0.0808)	0.0005 (0.00207)	1e-05 (7.39e-05)	0.0804 (0.122)	0.00625 (0.0157)	0.376 (0.44)	7e-05 (0.00038)
amp 11q13 3	57 (15%)	313	0.04 (0.0709)	0.494 (0.546)	0.00459 (0.0125)	0.0177 (0.0358)	0.0128 (0.0276)	0.00331 (0.00956)	0.181 (0.234)	0.0001 (0.000498)
amp 20q13 13	124 (34%)	246	1e-05 (7.39e-05)	0.579 (0.62)	0.0168 (0.0343)	0.00035 (0.0015)	0.377 (0.44)	0.0108 (0.0241)	5e-05 (0.000298)	0.0477 (0.0809)
del 17p13 1	226 (61%)	144	1e-05 (7.39e-05)	0.0682 (0.108)	2e-05 (0.000137)	6e-05 (0.000337)	1e-05 (7.39e-05)	8e-05 (0.00042)	0.187 (0.241)	1e-05 (7.39e-05)
del 17p11 2	195 (53%)	175	1e-05 (7.39e-05)	0.326 (0.384)	0.00016 (0.000765)	0.00839 (0.02)	0.0009 (0.00338)	0.00024 (0.00109)	0.231 (0.289)	0.00039 (0.00164)
amp 1q21 3	271 (73%)	99	1e-05 (7.39e-05)	9e-05 (0.000453)	3e-05 (0.000201)	0.00398 (0.0111)	0.136 (0.186)	0.0299 (0.0557)	0.106 (0.152)	0.385 (0.448)
amp 1q42 2	268 (72%)	102	1e-05 (7.39e-05)	0.0021 (0.00653)	1e-05 (7.39e-05)	7e-05 (0.00038)	0.249 (0.306)	0.00852 (0.0202)	0.0575 (0.0942)	0.406 (0.466)
amp 3q26 31	77 (21%)	293	1e-05 (7.39e-05)	0.0995 (0.145)	0.0206 (0.0409)	0.0203 (0.0405)	0.0703 (0.11)	0.00491 (0.013)	0.255 (0.31)	0.0482 (0.0814)
amp 6p25 2	159 (43%)	211	1e-05 (7.39e-05)	0.00017 (0.000805)	0.0434 (0.0745)	0.0245 (0.0471)	0.015 (0.0314)	0.0634 (0.102)	0.709 (0.741)	0.426 (0.482)
amp 10p15 1	72 (19%)	298	0.00415 (0.0115)	0.902 (0.914)	0.0359 (0.0644)	0.00356 (0.0101)	0.408 (0.468)	0.243 (0.3)	0.008 (0.0193)	0.0236 (0.0463)
amp 13q32 3	67 (18%)	303	1e-05 (7.39e-05)	0.101 (0.146)	0.00938 (0.0219)	0.08 (0.121)	0.0126 (0.0272)	0.198 (0.253)	0.0062 (0.0157)	0.0351 (0.0634)
amp 13q33 3	67 (18%)	303	1e-05 (7.39e-05)	0.0464 (0.0795)	0.00162 (0.00534)	0.25 (0.306)	0.00949 (0.0221)	0.18 (0.234)	0.00617 (0.0157)	0.084 (0.125)
del 2q37 3	62 (17%)	308	5e-05 (0.000298)	0.535 (0.585)	1e-05 (7.39e-05)	0.00091 (0.00339)	0.0507 (0.0847)	0.00994 (0.0225)	0.307 (0.365)	0.00148 (0.00505)
del 14q23 3	131 (35%)	239	1e-05 (7.39e-05)	0.499 (0.55)	0.00214 (0.0066)	6e-05 (0.000337)	0.012 (0.0263)	0.0976 (0.143)	0.00416 (0.0115)	0.0504 (0.0846)
del 14q32 33	133 (36%)	237	1e-05 (7.39e-05)	0.143 (0.193)	0.00474 (0.0127)	0.00012 (0.00058)	0.083 (0.125)	0.175 (0.228)	0.0125 (0.0271)	0.015 (0.0314)
del 19p13 3	87 (24%)	283	1e-05 (7.39e-05)	0.424 (0.482)	0.00498 (0.0131)	0.0026 (0.00769)	0.111 (0.159)	0.132 (0.181)	0.00217 (0.00662)	0.00099 (0.00363)
amp 2p24 1	65 (18%)	305	0.0354 (0.0638)	1 (1.00)	0.112 (0.159)	0.00399 (0.0111)	0.0173 (0.0351)	0.0423 (0.073)	0.0687 (0.108)	0.173 (0.227)
amp 2q33 1	64 (17%)	306	0.0277 (0.0522)	0.938 (0.946)	0.0515 (0.0858)	0.0114 (0.0253)	0.00157 (0.00521)	0.121 (0.171)	0.00596 (0.0153)	0.192 (0.246)
amp 6q12	109 (29%)	261	1e-05 (7.39e-05)	0.0417 (0.0725)	0.0318 (0.0588)	0.108 (0.154)	0.041 (0.0717)	0.618 (0.659)	0.235 (0.292)	0.159 (0.211)
amp 6q12	83 (22%)	287	2e-05 (0.000137)	0.00725 (0.018)	0.00813 (0.0195)	0.00967 (0.0224)	0.319 (0.378)	0.549 (0.595)	0.0836 (0.125)	0.0872 (0.13)
amp 9q34 2	47 (13%)	323	0.029 (0.0542)	0.404 (0.464)	0.0258 (0.0494)	0.0927 (0.137)	0.242 (0.3)	0.0122 (0.0268)	0.4 (0.461)	0.0208 (0.0409)
amp 20q13 33	128 (35%)	242	1e-05 (7.39e-05)	0.149 (0.198)	0.00482 (0.0128)	6e-05 (0.000337)	0.231 (0.289)	0.0622 (0.101)	1e-05 (7.39e-05)	0.13 (0.18)
del 6q27	136 (37%)	234	0.00152 (0.00512)	0.0054 (0.0141)	0.471 (0.526)	0.48 (0.534)	0.0289 (0.0542)	0.0391 (0.07)	0.559 (0.603)	0.309 (0.367)
del 7q36 3	34 (9%)	336	0.231 (0.289)	0.0408 (0.0716)	0.0414 (0.0722)	0.131 (0.181)	0.901 (0.914)	0.0706 (0.11)	0.00032 (0.00139)	0.00772 (0.0187)
del 11q23 3	93 (25%)	277	0.00054 (0.00218)	0.488 (0.541)	0.0587 (0.0955)	0.0406 (0.0716)	0.0761 (0.116)	0.136 (0.186)	0.0138 (0.0295)	0.0021 (0.00653)
del 12p12 1	78 (21%)	292	0.00084 (0.00318)	0.453 (0.507)	0.00254 (0.00756)	0.229 (0.289)	0.0641 (0.103)	0.031 (0.0575)	0.181 (0.234)	0.0326 (0.0598)
del 15q26 3	79 (21%)	291	0.00052 (0.00213)	0.436 (0.491)	0.00834 (0.02)	0.00971 (0.0224)	0.0793 (0.12)	0.121 (0.171)	0.00225 (0.00678)	0.0649 (0.103)
amp 5p15 33	163 (44%)	207	1e-05 (7.39e-05)	0.0331 (0.0603)	0.199 (0.253)	0.607 (0.648)	0.141 (0.191)	0.0174 (0.0353)	0.143 (0.193)	0.127 (0.177)
amp 6p21 1	158 (43%)	212	1e-05 (7.39e-05)	0.00109 (0.00397)	0.0141 (0.03)	0.0655 (0.104)	0.054 (0.0896)	0.0623 (0.101)	0.174 (0.228)	0.529 (0.581)
del 4p16 3	85 (23%)	285	1e-05 (7.39e-05)	0.148 (0.198)	0.105 (0.15)	0.101 (0.146)	0.0982 (0.144)	0.027 (0.0513)	0.0578 (0.0943)	0.00557 (0.0145)
del 11q14 1	77 (21%)	293	0.0161 (0.0331)	0.357 (0.418)	0.122 (0.172)	0.144 (0.194)	0.13 (0.18)	0.263 (0.319)	0.00743 (0.0183)	0.0153 (0.0319)
del 18q21 2	94 (25%)	276	0.0241 (0.0469)	9e-05 (0.000453)	0.0709 (0.11)	2e-05 (0.000137)	0.821 (0.837)	0.538 (0.587)	0.417 (0.474)	0.299 (0.356)
del 22q13 32	83 (22%)	287	0.00056 (0.00222)	0.0819 (0.123)	9e-05 (0.000453)	0.00992 (0.0225)	0.0552 (0.0911)	0.264 (0.32)	0.718 (0.746)	0.285 (0.34)
amp 5q35 3	135 (36%)	235	1e-05 (7.39e-05)	0.0403 (0.0713)	0.73 (0.754)	0.957 (0.963)	0.436 (0.491)	0.999 (1.00)	0.688 (0.725)	0.62 (0.659)
amp 15q26 3	54 (15%)	316	0.0741 (0.114)	0.445 (0.5)	0.0243 (0.0469)	0.0395 (0.0703)	0.415 (0.473)	0.181 (0.234)	0.497 (0.548)	0.576 (0.619)
del 2q22 1	52 (14%)	318	0.00308 (0.009)	0.394 (0.455)	0.00471 (0.0127)	0.0659 (0.104)	0.275 (0.332)	0.167 (0.221)	0.777 (0.793)	0.0778 (0.119)
del 22q12 1	79 (21%)	291	0.00622 (0.0157)	0.323 (0.382)	0.00288 (0.00847)	0.106 (0.152)	0.635 (0.673)	0.194 (0.248)	0.714 (0.744)	0.771 (0.791)
del xq26 2	67 (18%)	303	8e-05 (0.00042)	0.00695 (0.0173)	0.145 (0.195)	0.392 (0.454)	0.281 (0.339)	0.695 (0.731)	0.285 (0.34)	0.701 (0.734)
amp 7q31 2	120 (32%)	250	0.225 (0.285)	0.00454 (0.0124)	0.637 (0.674)	0.897 (0.911)	0.171 (0.225)	0.432 (0.489)	0.722 (0.748)	0.604 (0.647)
amp 17p11 2	46 (12%)	324	0.188 (0.242)	0.042 (0.0727)	0.472 (0.526)	0.231 (0.289)	0.144 (0.194)	0.252 (0.307)	0.387 (0.45)	0.244 (0.3)
del 8p23 2	247 (67%)	123	1e-05 (7.39e-05)	0.127 (0.178)	0.0974 (0.143)	0.652 (0.688)	0.696 (0.731)	0.17 (0.224)	0.17 (0.225)	0.0691 (0.108)
del 8p12	242 (65%)	128	1e-05 (7.39e-05)	0.128 (0.178)	0.0725 (0.112)	0.562 (0.606)	0.34 (0.4)	0.1 (0.145)	0.129 (0.18)	0.0884 (0.131)
del 12q24 33	59 (16%)	311	0.00345 (0.00985)	1 (1.00)	0.544 (0.593)	0.916 (0.925)	0.502 (0.552)	0.717 (0.746)	0.776 (0.793)	0.283 (0.34)
del 20p12 1	29 (8%)	341	0.234 (0.292)	0.548 (0.595)	0.734 (0.758)	0.549 (0.595)	0.206 (0.261)	0.737 (0.759)	0.76 (0.781)	0.409 (0.468)

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S1. Gene #1: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
AMP PEAK 1(1Q21.3) MUTATED	42	116	113
AMP PEAK 1(1Q21.3) WILD-TYPE	51	35	13

Figure S1. Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00045

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
AMP PEAK 1(1Q21.3) MUTATED	54	119	98
AMP PEAK 1(1Q21.3) WILD-TYPE	39	42	18

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

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 2e-04

Table S3. Gene #1: 'amp_1q21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
AMP PEAK 1(1Q21.3) MUTATED	49	51	66	46	54
AMP PEAK 1(1Q21.3) WILD-TYPE	18	35	5	25	15

Figure S3. Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00398 (Fisher's exact test), Q value = 0.011

Table S4. Gene #1: 'amp_1q21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
AMP PEAK 1(1Q21.3) MUTATED	36	38	74	72	46
AMP PEAK 1(1Q21.3) WILD-TYPE	18	18	40	12	10

Figure S4. Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0299 (Fisher's exact test), Q value = 0.056

Table S5. Gene #1: 'amp_1q21.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
AMP PEAK 1(1Q21.3) MUTATED	37	60	45	86	39
AMP PEAK 1(1Q21.3) WILD-TYPE	7	35	11	36	9

Figure S5. Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_1q42.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S6. Gene #2: 'amp_1q42.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
AMP PEAK 2(1Q42.2) MUTATED	50	105	113
AMP PEAK 2(1Q42.2) WILD-TYPE	43	46	13

Figure S6. Get High-res Image Gene #2: 'amp_1q42.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q42.2' versus 'METHLYATION_CNMF'

P value = 0.0021 (Fisher's exact test), Q value = 0.0065

Table S7. Gene #2: 'amp_1q42.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
AMP PEAK 2(1Q42.2) MUTATED	55	119	94
AMP PEAK 2(1Q42.2) WILD-TYPE	38	42	22

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

'amp_1q42.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
AMP PEAK 2(1Q42.2) MUTATED	46	46	67	49	55
AMP PEAK 2(1Q42.2) WILD-TYPE	21	40	4	22	14

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

'amp_1q42.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00038

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
AMP PEAK 2(1Q42.2) MUTATED	33	39	71	73	47
AMP PEAK 2(1Q42.2) WILD-TYPE	21	17	43	11	9

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

'amp_1q42.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00852 (Fisher's exact test), Q value = 0.02

Table S10. Gene #2: 'amp_1q42.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
AMP PEAK 2(1Q42.2) MUTATED	32	58	45	87	42
AMP PEAK 2(1Q42.2) WILD-TYPE	12	37	11	35	6

Figure S10. Get High-res Image Gene #2: 'amp_1q42.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_2p24.1' versus 'CN_CNMF'

P value = 0.0354 (Fisher's exact test), Q value = 0.064

Table S11. Gene #3: 'amp_2p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
AMP PEAK 3(2P24.1) MUTATED	9	34	22
AMP PEAK 3(2P24.1) WILD-TYPE	84	117	104

Figure S11. Get High-res Image Gene #3: 'amp_2p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2p24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00399 (Fisher's exact test), Q value = 0.011

Table S12. Gene #3: 'amp_2p24.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
AMP PEAK 3(2P24.1) MUTATED	17	3	21	16	6
AMP PEAK 3(2P24.1) WILD-TYPE	37	53	93	68	50

Figure S12. Get High-res Image Gene #3: 'amp_2p24.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_2p24.1' versus 'MIRSEQ_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 0.035

Table S13. Gene #3: 'amp_2p24.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
AMP PEAK 3(2P24.1) MUTATED	12	15	8	13	6	10
AMP PEAK 3(2P24.1) WILD-TYPE	28	48	84	71	40	30

Figure S13. Get High-res Image Gene #3: 'amp_2p24.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_2p24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0423 (Fisher's exact test), Q value = 0.073

Table S14. Gene #3: 'amp_2p24.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
AMP PEAK 3(2P24.1) MUTATED	14	20	9	16	5
AMP PEAK 3(2P24.1) WILD-TYPE	30	75	47	106	43

Figure S14. Get High-res Image Gene #3: 'amp_2p24.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_2q33.1' versus 'CN_CNMF'

P value = 0.0277 (Fisher's exact test), Q value = 0.052

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
AMP PEAK 4(2Q33.1) MUTATED	8	30	26
AMP PEAK 4(2Q33.1) WILD-TYPE	85	121	100

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

'amp_2q33.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0114 (Fisher's exact test), Q value = 0.025

Table S16. Gene #4: 'amp_2q33.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
AMP PEAK 4(2Q33.1) MUTATED	15	4	14	20	9
AMP PEAK 4(2Q33.1) WILD-TYPE	39	52	100	64	47

Figure S16. Get High-res Image Gene #4: 'amp_2q33.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_2q33.1' versus 'MIRSEQ_CNMF'

P value = 0.00157 (Fisher's exact test), Q value = 0.0052

Table S17. Gene #4: 'amp_2q33.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
AMP PEAK 4(2Q33.1) MUTATED	9	17	6	10	10	11
AMP PEAK 4(2Q33.1) WILD-TYPE	31	46	86	74	36	29

Figure S17. Get High-res Image Gene #4: 'amp_2q33.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_2q33.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00596 (Fisher's exact test), Q value = 0.015

Table S18. Gene #4: 'amp_2q33.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
AMP PEAK 4(2Q33.1) MUTATED	30	10	11	10
AMP PEAK 4(2Q33.1) WILD-TYPE	77	71	91	40

Figure S18. Get High-res Image Gene #4: 'amp_2q33.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S19. Gene #5: 'amp_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
AMP PEAK 5(3Q26.31) MUTATED	7	51	19
AMP PEAK 5(3Q26.31) WILD-TYPE	86	100	107

Figure S19. Get High-res Image Gene #5: 'amp_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.31' versus 'MRNASEQ_CNMF'

P value = 0.0206 (Fisher's exact test), Q value = 0.041

Table S20. Gene #5: 'amp_3q26.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
AMP PEAK 5(3Q26.31) MUTATED	22	23	12	11	9
AMP PEAK 5(3Q26.31) WILD-TYPE	45	63	59	60	60

Figure S20. Get High-res Image Gene #5: 'amp_3q26.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_3q26.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0203 (Fisher's exact test), Q value = 0.041

Table S21. Gene #5: 'amp_3q26.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
AMP PEAK 5(3Q26.31) MUTATED	17	5	30	16	9
AMP PEAK 5(3Q26.31) WILD-TYPE	37	51	84	68	47

Figure S21. Get High-res Image Gene #5: 'amp_3q26.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00491 (Fisher's exact test), Q value = 0.013

Table S22. Gene #5: 'amp_3q26.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
AMP PEAK 5(3Q26.31) MUTATED	17	24	9	22	4
AMP PEAK 5(3Q26.31) WILD-TYPE	27	71	47	100	44

Figure S22. Get High-res Image Gene #5: 'amp_3q26.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0482 (Fisher's exact test), Q value = 0.081

Table S23. Gene #5: 'amp_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
AMP PEAK 5(3Q26.31) MUTATED	14	20	20	12	5
AMP PEAK 5(3Q26.31) WILD-TYPE	56	62	80	22	49

Figure S23. Get High-res Image Gene #5: 'amp_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4p14' versus 'METHLYATION_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.038

Table S24. Gene #6: 'amp_4p14' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
AMP PEAK 6(4P14) MUTATED	11	17	26
AMP PEAK 6(4P14) WILD-TYPE	82	144	90

Figure S24. Get High-res Image Gene #6: 'amp_4p14' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_4p14' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00026

Table S25. Gene #6: 'amp_4p14' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
AMP PEAK 6(4P14) MUTATED	12	11	21	8	1
AMP PEAK 6(4P14) WILD-TYPE	55	75	50	63	68

Figure S25. Get High-res Image Gene #6: 'amp_4p14' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_4p14' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00122 (Fisher's exact test), Q value = 0.0043

Table S26. Gene #6: 'amp_4p14' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
AMP PEAK 6(4P14) MUTATED	10	8	13	21	1
AMP PEAK 6(4P14) WILD-TYPE	44	48	101	63	55

Figure S26. Get High-res Image Gene #6: 'amp_4p14' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_4p14' versus 'MIRSEQ_CNMF'

P value = 0.0331 (Fisher's exact test), Q value = 0.06

Table S27. Gene #6: 'amp_4p14' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
AMP PEAK 6(4P14) MUTATED	7	14	9	6	10	8
AMP PEAK 6(4P14) WILD-TYPE	33	49	83	78	36	32

Figure S27. Get High-res Image Gene #6: 'amp_4p14' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_4p14' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00764 (Fisher's exact test), Q value = 0.019

Table S28. Gene #6: 'amp_4p14' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
AMP PEAK 6(4P14) MUTATED	18	16	7	13
AMP PEAK 6(4P14) WILD-TYPE	89	65	95	37

Figure S28. Get High-res Image Gene #6: 'amp_4p14' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_4p14' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0123 (Fisher's exact test), Q value = 0.027

Table S29. Gene #6: 'amp_4p14' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
AMP PEAK 6(4P14) MUTATED	14	16	18	5	1
AMP PEAK 6(4P14) WILD-TYPE	56	66	82	29	53

Figure S29. Get High-res Image Gene #6: 'amp_4p14' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S30. Gene #7: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
AMP PEAK 7(5P15.33) MUTATED	16	80	67
AMP PEAK 7(5P15.33) WILD-TYPE	77	71	59

Figure S30. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 0.0331 (Fisher's exact test), Q value = 0.06

Table S31. Gene #7: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
AMP PEAK 7(5P15.33) MUTATED	32	82	49
AMP PEAK 7(5P15.33) WILD-TYPE	61	79	67

Figure S31. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0174 (Fisher's exact test), Q value = 0.035

Table S32. Gene #7: 'amp_5p15.33' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
AMP PEAK 7(5P15.33) MUTATED	26	47	28	43	16
AMP PEAK 7(5P15.33) WILD-TYPE	18	48	28	79	32

Figure S32. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_5q35.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S33. Gene #8: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
AMP PEAK 8(5Q35.3) MUTATED	20	49	66
AMP PEAK 8(5Q35.3) WILD-TYPE	73	102	60

Figure S33. Get High-res Image Gene #8: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q35.3' versus 'METHLYATION_CNMF'

P value = 0.0403 (Fisher's exact test), Q value = 0.071

Table S34. Gene #8: 'amp_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
AMP PEAK 8(5Q35.3) MUTATED	24	66	45
AMP PEAK 8(5Q35.3) WILD-TYPE	69	95	71

Figure S34. Get High-res Image Gene #8: 'amp_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S35. Gene #9: 'amp_6p25.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
AMP PEAK 9(6P25.2) MUTATED	15	79	65
AMP PEAK 9(6P25.2) WILD-TYPE	78	72	61

Figure S35. Get High-res Image Gene #9: 'amp_6p25.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p25.2' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00081

Table S36. Gene #9: 'amp_6p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
AMP PEAK 9(6P25.2) MUTATED	23	79	57
AMP PEAK 9(6P25.2) WILD-TYPE	70	82	59

Figure S36. Get High-res Image Gene #9: 'amp_6p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p25.2' versus 'MRNASEQ_CNMF'

P value = 0.0434 (Fisher's exact test), Q value = 0.075

Table S37. Gene #9: 'amp_6p25.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
AMP PEAK 9(6P25.2) MUTATED	32	33	38	22	34
AMP PEAK 9(6P25.2) WILD-TYPE	35	53	33	49	35

Figure S37. Get High-res Image Gene #9: 'amp_6p25.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_6p25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0245 (Fisher's exact test), Q value = 0.047

Table S38. Gene #9: 'amp_6p25.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
AMP PEAK 9(6P25.2) MUTATED	24	16	45	46	28
AMP PEAK 9(6P25.2) WILD-TYPE	30	40	69	38	28

Figure S38. Get High-res Image Gene #9: 'amp_6p25.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_6p25.2' versus 'MIRSEQ_CNMF'

P value = 0.015 (Fisher's exact test), Q value = 0.031

Table S39. Gene #9: 'amp_6p25.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
AMP PEAK 9(6P25.2) MUTATED	24	27	26	37	21	20
AMP PEAK 9(6P25.2) WILD-TYPE	16	36	66	47	25	20

Figure S39. Get High-res Image Gene #9: 'amp_6p25.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_6p21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S40. Gene #10: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
AMP PEAK 10(6P21.1) MUTATED	17	79	62
AMP PEAK 10(6P21.1) WILD-TYPE	76	72	64

Figure S40. Get High-res Image Gene #10: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p21.1' versus 'METHLYATION_CNMF'

P value = 0.00109 (Fisher's exact test), Q value = 0.004

Table S41. Gene #10: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
AMP PEAK 10(6P21.1) MUTATED	25	80	53
AMP PEAK 10(6P21.1) WILD-TYPE	68	81	63

Figure S41. Get High-res Image Gene #10: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.03

Table S42. Gene #10: 'amp_6p21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
AMP PEAK 10(6P21.1) MUTATED	27	40	37	19	35
AMP PEAK 10(6P21.1) WILD-TYPE	40	46	34	52	34

Figure S42. Get High-res Image Gene #10: 'amp_6p21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_6q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S43. Gene #11: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
AMP PEAK 11(6Q12) MUTATED	9	62	38
AMP PEAK 11(6Q12) WILD-TYPE	84	89	88

Figure S43. Get High-res Image Gene #11: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q12' versus 'METHLYATION_CNMF'

P value = 0.0417 (Fisher's exact test), Q value = 0.073

Table S44. Gene #11: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
AMP PEAK 11(6Q12) MUTATED	18	52	39
AMP PEAK 11(6Q12) WILD-TYPE	75	109	77

Figure S44. Get High-res Image Gene #11: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q12' versus 'MRNASEQ_CNMF'

P value = 0.0318 (Fisher's exact test), Q value = 0.059

Table S45. Gene #11: 'amp_6q12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
AMP PEAK 11(6Q12) MUTATED	24	22	30	14	19
AMP PEAK 11(6Q12) WILD-TYPE	43	64	41	57	50

Figure S45. Get High-res Image Gene #11: 'amp_6q12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_6q12' versus 'MIRSEQ_CNMF'

P value = 0.041 (Fisher's exact test), Q value = 0.072

Table S46. Gene #11: 'amp_6q12' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
AMP PEAK 11(6Q12) MUTATED	17	18	18	22	18	15
AMP PEAK 11(6Q12) WILD-TYPE	23	45	74	62	28	25

Figure S46. Get High-res Image Gene #11: 'amp_6q12' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_6q12' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S47. Gene #12: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
AMP PEAK 12(6Q12) MUTATED	5	47	31
AMP PEAK 12(6Q12) WILD-TYPE	88	104	95

Figure S47. Get High-res Image Gene #12: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q12' versus 'METHLYATION_CNMF'

P value = 0.00725 (Fisher's exact test), Q value = 0.018

Table S48. Gene #12: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
AMP PEAK 12(6Q12) MUTATED	11	38	34
AMP PEAK 12(6Q12) WILD-TYPE	82	123	82

Figure S48. Get High-res Image Gene #12: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q12' versus 'MRNASEQ_CNMF'

P value = 0.00813 (Fisher's exact test), Q value = 0.02

Table S49. Gene #12: 'amp_6q12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
AMP PEAK 12(6Q12) MUTATED	17	12	27	13	14
AMP PEAK 12(6Q12) WILD-TYPE	50	74	44	58	55

Figure S49. Get High-res Image Gene #12: 'amp_6q12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_6q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00967 (Fisher's exact test), Q value = 0.022

Table S50. Gene #12: 'amp_6q12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
AMP PEAK 12(6Q12) MUTATED	15	10	17	30	11
AMP PEAK 12(6Q12) WILD-TYPE	39	46	97	54	45

Figure S50. Get High-res Image Gene #12: 'amp_6q12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'METHLYATION_CNMF'

P value = 0.00454 (Fisher's exact test), Q value = 0.012

Table S51. Gene #13: 'amp_7q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
AMP PEAK 13(7Q31.2) MUTATED	24	67	29
AMP PEAK 13(7Q31.2) WILD-TYPE	69	94	87

Figure S51. Get High-res Image Gene #13: 'amp_7q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S52. Gene #14: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
AMP PEAK 14(8Q24.21) MUTATED	45	79	107
AMP PEAK 14(8Q24.21) WILD-TYPE	48	72	19

Figure S52. Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 0.0474 (Fisher's exact test), Q value = 0.081

Table S53. Gene #14: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
AMP PEAK 14(8Q24.21) MUTATED	55	93	83
AMP PEAK 14(8Q24.21) WILD-TYPE	38	68	33

Figure S53. Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0021

Table S54. Gene #14: 'amp_8q24.21' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
AMP PEAK 14(8Q24.21) MUTATED	44	36	50	47	49
AMP PEAK 14(8Q24.21) WILD-TYPE	23	50	21	24	20

Figure S54. Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S55. Gene #14: 'amp_8q24.21' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
AMP PEAK 14(8Q24.21) MUTATED	39	40	45	61	41
AMP PEAK 14(8Q24.21) WILD-TYPE	15	16	69	23	15

Figure S55. Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00625 (Fisher's exact test), Q value = 0.016

Table S56. Gene #14: 'amp_8q24.21' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
AMP PEAK 14(8Q24.21) MUTATED	24	46	37	85	35
AMP PEAK 14(8Q24.21) WILD-TYPE	20	49	19	37	13

Figure S56. Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00038

Table S57. Gene #14: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
AMP PEAK 14(8Q24.21) MUTATED	52	36	70	18	41
AMP PEAK 14(8Q24.21) WILD-TYPE	18	46	30	16	13

Figure S57. Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9q34.2' versus 'CN_CNMF'

P value = 0.029 (Fisher's exact test), Q value = 0.054

Table S58. Gene #15: 'amp_9q34.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
AMP PEAK 15(9Q34.2) MUTATED	5	25	17
AMP PEAK 15(9Q34.2) WILD-TYPE	88	126	109

Figure S58. Get High-res Image Gene #15: 'amp_9q34.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9q34.2' versus 'MRNASEQ_CNMF'

P value = 0.0258 (Fisher's exact test), Q value = 0.049

Table S59. Gene #15: 'amp_9q34.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
AMP PEAK 15(9Q34.2) MUTATED	11	15	12	5	3
AMP PEAK 15(9Q34.2) WILD-TYPE	56	71	59	66	66

Figure S59. Get High-res Image Gene #15: 'amp_9q34.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_9q34.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0122 (Fisher's exact test), Q value = 0.027

Table S60. Gene #15: 'amp_9q34.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
AMP PEAK 15(9Q34.2) MUTATED	11	15	9	10	2
AMP PEAK 15(9Q34.2) WILD-TYPE	33	80	47	112	46

Figure S60. Get High-res Image Gene #15: 'amp_9q34.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_9q34.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0208 (Fisher's exact test), Q value = 0.041

Table S61. Gene #15: 'amp_9q34.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
AMP PEAK 15(9Q34.2) MUTATED	12	17	9	5	2
AMP PEAK 15(9Q34.2) WILD-TYPE	58	65	91	29	52

Figure S61. Get High-res Image Gene #15: 'amp_9q34.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10p15.1' versus 'CN_CNMF'

P value = 0.00415 (Fisher's exact test), Q value = 0.011

Table S62. Gene #16: 'amp_10p15.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
AMP PEAK 16(10P15.1) MUTATED	8	38	26
AMP PEAK 16(10P15.1) WILD-TYPE	85	113	100

Figure S62. Get High-res Image Gene #16: 'amp_10p15.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10p15.1' versus 'MRNASEQ_CNMF'

P value = 0.0359 (Fisher's exact test), Q value = 0.064

Table S63. Gene #16: 'amp_10p15.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
AMP PEAK 16(10P15.1) MUTATED	20	10	18	11	12
AMP PEAK 16(10P15.1) WILD-TYPE	47	76	53	60	57

Figure S63. Get High-res Image Gene #16: 'amp_10p15.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_10p15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00356 (Fisher's exact test), Q value = 0.01

Table S64. Gene #16: 'amp_10p15.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
AMP PEAK 16(10P15.1) MUTATED	19	8	14	22	8
AMP PEAK 16(10P15.1) WILD-TYPE	35	48	100	62	48

Figure S64. Get High-res Image Gene #16: 'amp_10p15.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_10p15.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.008 (Fisher's exact test), Q value = 0.019

Table S65. Gene #16: 'amp_10p15.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
AMP PEAK 16(10P15.1) MUTATED	30	18	10	10
AMP PEAK 16(10P15.1) WILD-TYPE	77	63	92	40

Figure S65. Get High-res Image Gene #16: 'amp_10p15.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_10p15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0236 (Fisher's exact test), Q value = 0.046

Table S66. Gene #16: 'amp_10p15.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
AMP PEAK 16(10P15.1) MUTATED	22	11	20	9	6
AMP PEAK 16(10P15.1) WILD-TYPE	48	71	80	25	48

Figure S66. Get High-res Image Gene #16: 'amp_10p15.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

P value = 0.04 (Fisher's exact test), Q value = 0.071

Table S67. Gene #17: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
AMP PEAK 17(11Q13.3) MUTATED	14	31	12
AMP PEAK 17(11Q13.3) WILD-TYPE	79	120	114

Figure S67. Get High-res Image Gene #17: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

P value = 0.00459 (Fisher's exact test), Q value = 0.013

Table S68. Gene #17: 'amp_11q13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
AMP PEAK 17(11Q13.3) MUTATED	17	18	10	6	4
AMP PEAK 17(11Q13.3) WILD-TYPE	50	68	61	65	65

Figure S68. Get High-res Image Gene #17: 'amp_11q13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0177 (Fisher's exact test), Q value = 0.036

Table S69. Gene #17: 'amp_11q13.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
AMP PEAK 17(11Q13.3) MUTATED	10	7	25	11	2
AMP PEAK 17(11Q13.3) WILD-TYPE	44	49	89	73	54

Figure S69. Get High-res Image Gene #17: 'amp_11q13.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.028

Table S70. Gene #17: 'amp_11q13.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
AMP PEAK 17(11Q13.3) MUTATED	10	16	13	5	6	7
AMP PEAK 17(11Q13.3) WILD-TYPE	30	47	79	79	40	33

Figure S70. Get High-res Image Gene #17: 'amp_11q13.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00331 (Fisher's exact test), Q value = 0.0096

Table S71. Gene #17: 'amp_11q13.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
AMP PEAK 17(11Q13.3) MUTATED	11	23	5	16	2
AMP PEAK 17(11Q13.3) WILD-TYPE	33	72	51	106	46

Figure S71. Get High-res Image Gene #17: 'amp_11q13.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 5e-04

Table S72. Gene #17: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
AMP PEAK 17(11Q13.3) MUTATED	13	18	13	10	0
AMP PEAK 17(11Q13.3) WILD-TYPE	57	64	87	24	54

Figure S72. Get High-res Image Gene #17: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q32.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S73. Gene #18: 'amp_13q32.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
AMP PEAK 18(13Q32.3) MUTATED	1	42	24
AMP PEAK 18(13Q32.3) WILD-TYPE	92	109	102

Figure S73. Get High-res Image Gene #18: 'amp_13q32.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q32.3' versus 'MRNASEQ_CNMF'

P value = 0.00938 (Fisher's exact test), Q value = 0.022

Table S74. Gene #18: 'amp_13q32.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
AMP PEAK 18(13Q32.3) MUTATED	14	12	23	9	8
AMP PEAK 18(13Q32.3) WILD-TYPE	53	74	48	62	61

Figure S74. Get High-res Image Gene #18: 'amp_13q32.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_13q32.3' versus 'MIRSEQ_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.027

Table S75. Gene #18: 'amp_13q32.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
AMP PEAK 18(13Q32.3) MUTATED	13	11	13	8	13	9
AMP PEAK 18(13Q32.3) WILD-TYPE	27	52	79	76	33	31

Figure S75. Get High-res Image Gene #18: 'amp_13q32.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_13q32.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0062 (Fisher's exact test), Q value = 0.016

Table S76. Gene #18: 'amp_13q32.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
AMP PEAK 18(13Q32.3) MUTATED	29	12	10	12
AMP PEAK 18(13Q32.3) WILD-TYPE	78	69	92	38

Figure S76. Get High-res Image Gene #18: 'amp_13q32.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_13q32.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0351 (Fisher's exact test), Q value = 0.063

Table S77. Gene #18: 'amp_13q32.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
AMP PEAK 18(13Q32.3) MUTATED	18	13	18	10	4
AMP PEAK 18(13Q32.3) WILD-TYPE	52	69	82	24	50

Figure S77. Get High-res Image Gene #18: 'amp_13q32.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q33.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S78. Gene #19: 'amp_13q33.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
AMP PEAK 19(13Q33.3) MUTATED	3	39	25
AMP PEAK 19(13Q33.3) WILD-TYPE	90	112	101

Figure S78. Get High-res Image Gene #19: 'amp_13q33.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q33.3' versus 'METHLYATION_CNMF'

P value = 0.0464 (Fisher's exact test), Q value = 0.08

Table S79. Gene #19: 'amp_13q33.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
AMP PEAK 19(13Q33.3) MUTATED	11	27	29
AMP PEAK 19(13Q33.3) WILD-TYPE	82	134	87

Figure S79. Get High-res Image Gene #19: 'amp_13q33.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q33.3' versus 'MRNASEQ_CNMF'

P value = 0.00162 (Fisher's exact test), Q value = 0.0053

Table S80. Gene #19: 'amp_13q33.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
AMP PEAK 19(13Q33.3) MUTATED	13	10	25	8	10
AMP PEAK 19(13Q33.3) WILD-TYPE	54	76	46	63	59

Figure S80. Get High-res Image Gene #19: 'amp_13q33.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_13q33.3' versus 'MIRSEQ_CNMF'

P value = 0.00949 (Fisher's exact test), Q value = 0.022

Table S81. Gene #19: 'amp_13q33.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
AMP PEAK 19(13Q33.3) MUTATED	12	8	14	9	15	9
AMP PEAK 19(13Q33.3) WILD-TYPE	28	55	78	75	31	31

Figure S81. Get High-res Image Gene #19: 'amp_13q33.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_13q33.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00617 (Fisher's exact test), Q value = 0.016

Table S82. Gene #19: 'amp_13q33.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
AMP PEAK 19(13Q33.3) MUTATED	28	12	10	13
AMP PEAK 19(13Q33.3) WILD-TYPE	79	69	92	37

Figure S82. Get High-res Image Gene #19: 'amp_13q33.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CNMF'

P value = 0.0243 (Fisher's exact test), Q value = 0.047

Table S83. Gene #20: 'amp_15q26.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
AMP PEAK 20(15Q26.3) MUTATED	8	15	18	7	5
AMP PEAK 20(15Q26.3) WILD-TYPE	59	71	53	64	64

Figure S83. Get High-res Image Gene #20: 'amp_15q26.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0395 (Fisher's exact test), Q value = 0.07

Table S84. Gene #20: 'amp_15q26.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
AMP PEAK 20(15Q26.3) MUTATED	9	7	17	18	2
AMP PEAK 20(15Q26.3) WILD-TYPE	45	49	97	66	54

Figure S84. Get High-res Image Gene #20: 'amp_15q26.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_17p11.2' versus 'METHLYATION_CNMF'

P value = 0.042 (Fisher's exact test), Q value = 0.073

Table S85. Gene #21: 'amp_17p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
AMP PEAK 21(17P11.2) MUTATED	5	23	18
AMP PEAK 21(17P11.2) WILD-TYPE	88	138	98

Figure S85. Get High-res Image Gene #21: 'amp_17p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q25.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S86. Gene #22: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
AMP PEAK 22(17Q25.3) MUTATED	18	82	45
AMP PEAK 22(17Q25.3) WILD-TYPE	75	69	81

Figure S86. Get High-res Image Gene #22: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q25.3' versus 'METHLYATION_CNMF'

P value = 0.0478 (Fisher's exact test), Q value = 0.081

Table S87. Gene #22: 'amp_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
AMP PEAK 22(17Q25.3) MUTATED	29	74	42
AMP PEAK 22(17Q25.3) WILD-TYPE	64	87	74

Figure S87. Get High-res Image Gene #22: 'amp_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q25.3' versus 'MRNASEQ_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.025

Table S88. Gene #22: 'amp_17q25.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
AMP PEAK 22(17Q25.3) MUTATED	34	36	24	17	31
AMP PEAK 22(17Q25.3) WILD-TYPE	33	50	47	54	38

Figure S88. Get High-res Image Gene #22: 'amp_17q25.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_17q25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0106 (Fisher's exact test), Q value = 0.024

Table S89. Gene #22: 'amp_17q25.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
AMP PEAK 22(17Q25.3) MUTATED	28	12	49	29	24
AMP PEAK 22(17Q25.3) WILD-TYPE	26	44	65	55	32

Figure S89. Get High-res Image Gene #22: 'amp_17q25.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_17q25.3' versus 'MIRSEQ_CNMF'

P value = 0.00748 (Fisher's exact test), Q value = 0.018

Table S90. Gene #22: 'amp_17q25.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
AMP PEAK 22(17Q25.3) MUTATED	22	30	29	38	10	15
AMP PEAK 22(17Q25.3) WILD-TYPE	18	33	63	46	36	25

Figure S90. Get High-res Image Gene #22: 'amp_17q25.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_17q25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00131 (Fisher's exact test), Q value = 0.0046

Table S91. Gene #22: 'amp_17q25.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
AMP PEAK 22(17Q25.3) MUTATED	26	40	24	32	22
AMP PEAK 22(17Q25.3) WILD-TYPE	18	55	32	90	26

Figure S91. Get High-res Image Gene #22: 'amp_17q25.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_17q25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.025

Table S92. Gene #22: 'amp_17q25.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
AMP PEAK 22(17Q25.3) MUTATED	33	35	26	18	24
AMP PEAK 22(17Q25.3) WILD-TYPE	37	47	74	16	30

Figure S92. Get High-res Image Gene #22: 'amp_17q25.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.12' versus 'CN_CNMF'

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

Table S93. Gene #23: 'amp_19p13.12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
AMP PEAK 23(19P13.12) MUTATED	10	26	33
AMP PEAK 23(19P13.12) WILD-TYPE	83	125	93

Figure S93. Get High-res Image Gene #23: 'amp_19p13.12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19p13.12' versus 'METHLYATION_CNMF'

P value = 0.00118 (Fisher's exact test), Q value = 0.0042

Table S94. Gene #23: 'amp_19p13.12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
AMP PEAK 23(19P13.12) MUTATED	16	19	34
AMP PEAK 23(19P13.12) WILD-TYPE	77	142	82

Figure S94. Get High-res Image Gene #23: 'amp_19p13.12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19p13.12' versus 'MRNASEQ_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.0025

Table S95. Gene #23: 'amp_19p13.12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
AMP PEAK 23(19P13.12) MUTATED	15	10	20	19	4
AMP PEAK 23(19P13.12) WILD-TYPE	52	76	51	52	65

Figure S95. Get High-res Image Gene #23: 'amp_19p13.12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_19p13.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.0022

Table S96. Gene #23: 'amp_19p13.12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
AMP PEAK 23(19P13.12) MUTATED	16	13	12	23	4
AMP PEAK 23(19P13.12) WILD-TYPE	38	43	102	61	52

Figure S96. Get High-res Image Gene #23: 'amp_19p13.12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.12' versus 'MIRSEQ_CNMF'

P value = 0.00321 (Fisher's exact test), Q value = 0.0093

Table S97. Gene #23: 'amp_19p13.12' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
AMP PEAK 23(19P13.12) MUTATED	4	8	23	9	9	15
AMP PEAK 23(19P13.12) WILD-TYPE	36	55	69	75	37	25

Figure S97. Get High-res Image Gene #23: 'amp_19p13.12' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_19p13.12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00223 (Fisher's exact test), Q value = 0.0068

Table S98. Gene #23: 'amp_19p13.12' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
AMP PEAK 23(19P13.12) MUTATED	3	20	14	29	2
AMP PEAK 23(19P13.12) WILD-TYPE	41	75	42	93	46

Figure S98. Get High-res Image Gene #23: 'amp_19p13.12' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_19p13.12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00247 (Fisher's exact test), Q value = 0.0074

Table S99. Gene #23: 'amp_19p13.12' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
AMP PEAK 23(19P13.12) MUTATED	24	22	8	10
AMP PEAK 23(19P13.12) WILD-TYPE	83	59	94	40

Figure S99. Get High-res Image Gene #23: 'amp_19p13.12' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_19p13.12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00129 (Fisher's exact test), Q value = 0.0045

Table S100. Gene #23: 'amp_19p13.12' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
AMP PEAK 23(19P13.12) MUTATED	18	14	27	2	3
AMP PEAK 23(19P13.12) WILD-TYPE	52	68	73	32	51

Figure S100. Get High-res Image Gene #23: 'amp_19p13.12' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q13.11' versus 'CN_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.034

Table S101. Gene #24: 'amp_19q13.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
AMP PEAK 24(19Q13.11) MUTATED	14	47	30
AMP PEAK 24(19Q13.11) WILD-TYPE	79	104	96

Figure S101. Get High-res Image Gene #24: 'amp_19q13.11' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q13.11' versus 'MRNASEQ_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0017

Table S102. Gene #24: 'amp_19q13.11' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
AMP PEAK 24(19Q13.11) MUTATED	22	16	25	21	6
AMP PEAK 24(19Q13.11) WILD-TYPE	45	70	46	50	63

Figure S102. Get High-res Image Gene #24: 'amp_19q13.11' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_19q13.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.0026

Table S103. Gene #24: 'amp_19q13.11' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
AMP PEAK 24(19Q13.11) MUTATED	16	17	21	31	5
AMP PEAK 24(19Q13.11) WILD-TYPE	38	39	93	53	51

Figure S103. Get High-res Image Gene #24: 'amp_19q13.11' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_19q13.11' versus 'MIRSEQ_CNMF'

P value = 0.0325 (Fisher's exact test), Q value = 0.06

Table S104. Gene #24: 'amp_19q13.11' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
AMP PEAK 24(19Q13.11) MUTATED	12	15	28	10	12	13
AMP PEAK 24(19Q13.11) WILD-TYPE	28	48	64	74	34	27

Figure S104. Get High-res Image Gene #24: 'amp_19q13.11' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_19q13.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0018 (Fisher's exact test), Q value = 0.0057

Table S105. Gene #24: 'amp_19q13.11' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
AMP PEAK 24(19Q13.11) MUTATED	14	23	18	33	2
AMP PEAK 24(19Q13.11) WILD-TYPE	30	72	38	89	46

Figure S105. Get High-res Image Gene #24: 'amp_19q13.11' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_19q13.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S106. Gene #24: 'amp_19q13.11' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
AMP PEAK 24(19Q13.11) MUTATED	36	23	7	19
AMP PEAK 24(19Q13.11) WILD-TYPE	71	58	95	31

Figure S106. Get High-res Image Gene #24: 'amp_19q13.11' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_19q13.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.0012

Table S107. Gene #24: 'amp_19q13.11' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
AMP PEAK 24(19Q13.11) MUTATED	24	20	29	10	2
AMP PEAK 24(19Q13.11) WILD-TYPE	46	62	71	24	52

Figure S107. Get High-res Image Gene #24: 'amp_19q13.11' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S108. Gene #25: 'amp_20q13.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
AMP PEAK 25(20Q13.13) MUTATED	11	69	44
AMP PEAK 25(20Q13.13) WILD-TYPE	82	82	82

Figure S108. Get High-res Image Gene #25: 'amp_20q13.13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.13' versus 'MRNASEQ_CNMF'

P value = 0.0168 (Fisher's exact test), Q value = 0.034

Table S109. Gene #25: 'amp_20q13.13' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
AMP PEAK 25(20Q13.13) MUTATED	26	29	32	23	13
AMP PEAK 25(20Q13.13) WILD-TYPE	41	57	39	48	56

Figure S109. Get High-res Image Gene #25: 'amp_20q13.13' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_20q13.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.0015

Table S110. Gene #25: 'amp_20q13.13' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
AMP PEAK 25(20Q13.13) MUTATED	19	19	37	41	7
AMP PEAK 25(20Q13.13) WILD-TYPE	35	37	77	43	49

Figure S110. Get High-res Image Gene #25: 'amp_20q13.13' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0108 (Fisher's exact test), Q value = 0.024

Table S111. Gene #25: 'amp_20q13.13' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
AMP PEAK 25(20Q13.13) MUTATED	21	29	24	41	8
AMP PEAK 25(20Q13.13) WILD-TYPE	23	66	32	81	40

Figure S111. Get High-res Image Gene #25: 'amp_20q13.13' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 3e-04

Table S112. Gene #25: 'amp_20q13.13' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
AMP PEAK 25(20Q13.13) MUTATED	45	25	19	27
AMP PEAK 25(20Q13.13) WILD-TYPE	62	56	83	23

Figure S112. Get High-res Image Gene #25: 'amp_20q13.13' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0477 (Fisher's exact test), Q value = 0.081

Table S113. Gene #25: 'amp_20q13.13' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
AMP PEAK 25(20Q13.13) MUTATED	28	24	37	16	11
AMP PEAK 25(20Q13.13) WILD-TYPE	42	58	63	18	43

Figure S113. Get High-res Image Gene #25: 'amp_20q13.13' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S114. Gene #26: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
AMP PEAK 26(20Q13.33) MUTATED	10	69	49
AMP PEAK 26(20Q13.33) WILD-TYPE	83	82	77

Figure S114. Get High-res Image Gene #26: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CNMF'

P value = 0.00482 (Fisher's exact test), Q value = 0.013

Table S115. Gene #26: 'amp_20q13.33' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
AMP PEAK 26(20Q13.33) MUTATED	25	30	36	22	14
AMP PEAK 26(20Q13.33) WILD-TYPE	42	56	35	49	55

Figure S115. Get High-res Image Gene #26: 'amp_20q13.33' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00034

Table S116. Gene #26: 'amp_20q13.33' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
AMP PEAK 26(20Q13.33) MUTATED	21	17	39	43	7
AMP PEAK 26(20Q13.33) WILD-TYPE	33	39	75	41	49

Figure S116. Get High-res Image Gene #26: 'amp_20q13.33' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S117. Gene #26: 'amp_20q13.33' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
AMP PEAK 26(20Q13.33) MUTATED	48	25	20	27
AMP PEAK 26(20Q13.33) WILD-TYPE	59	56	82	23

Figure S117. Get High-res Image Gene #26: 'amp_20q13.33' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_xq28' versus 'CN_CNMF'

P value = 0.00178 (Fisher's exact test), Q value = 0.0057

Table S118. Gene #27: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
AMP PEAK 27(XQ28) MUTATED	22	23	42
AMP PEAK 27(XQ28) WILD-TYPE	71	128	84

Figure S118. Get High-res Image Gene #27: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq28' versus 'MRNASEQ_CNMF'

P value = 0.0275 (Fisher's exact test), Q value = 0.052

Table S119. Gene #27: 'amp_xq28' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
AMP PEAK 27(XQ28) MUTATED	14	22	12	12	26
AMP PEAK 27(XQ28) WILD-TYPE	53	64	59	59	43

Figure S119. Get High-res Image Gene #27: 'amp_xq28' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_xq28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00997 (Fisher's exact test), Q value = 0.023

Table S120. Gene #27: 'amp_xq28' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
AMP PEAK 27(XQ28) MUTATED	13	11	29	11	22
AMP PEAK 27(XQ28) WILD-TYPE	41	45	85	73	34

Figure S120. Get High-res Image Gene #27: 'amp_xq28' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00054

Table S121. Gene #27: 'amp_xq28' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
AMP PEAK 27(XQ28) MUTATED	4	17	15	35	5	9
AMP PEAK 27(XQ28) WILD-TYPE	36	46	77	49	41	31

Figure S121. Get High-res Image Gene #27: 'amp_xq28' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_xq28' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00335 (Fisher's exact test), Q value = 0.0096

Table S122. Gene #27: 'amp_xq28' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
AMP PEAK 27(XQ28) MUTATED	5	23	14	22	21
AMP PEAK 27(XQ28) WILD-TYPE	39	72	42	100	27

Figure S122. Get High-res Image Gene #27: 'amp_xq28' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.033

Table S123. Gene #27: 'amp_xq28' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
AMP PEAK 27(XQ28) MUTATED	23	15	34	6
AMP PEAK 27(XQ28) WILD-TYPE	84	66	68	44

Figure S123. Get High-res Image Gene #27: 'amp_xq28' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_xq28' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.0015

Table S124. Gene #27: 'amp_xq28' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
AMP PEAK 27(XQ28) MUTATED	16	19	17	2	24
AMP PEAK 27(XQ28) WILD-TYPE	54	63	83	32	30

Figure S124. Get High-res Image Gene #27: 'amp_xq28' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S125. Gene #28: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 1(1P36.31) MUTATED	18	62	82
DEL PEAK 1(1P36.31) WILD-TYPE	75	89	44

Figure S125. Get High-res Image Gene #28: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S126. Gene #28: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
DEL PEAK 1(1P36.31) MUTATED	28	61	73
DEL PEAK 1(1P36.31) WILD-TYPE	65	100	43

Figure S126. Get High-res Image Gene #28: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S127. Gene #28: 'del_1p36.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
DEL PEAK 1(1P36.31) MUTATED	17	33	59	32	18
DEL PEAK 1(1P36.31) WILD-TYPE	50	53	12	39	51

Figure S127. Get High-res Image Gene #28: 'del_1p36.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_1p36.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S128. Gene #28: 'del_1p36.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
DEL PEAK 1(1P36.31) MUTATED	24	24	40	57	14
DEL PEAK 1(1P36.31) WILD-TYPE	30	32	74	27	42

Figure S128. Get High-res Image Gene #28: 'del_1p36.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.31' versus 'MIRSEQ_CNMF'

P value = 0.00149 (Fisher's exact test), Q value = 0.005

Table S129. Gene #28: 'del_1p36.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
DEL PEAK 1(1P36.31) MUTATED	12	26	39	30	23	29
DEL PEAK 1(1P36.31) WILD-TYPE	28	37	53	54	23	11

Figure S129. Get High-res Image Gene #28: 'del_1p36.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_1p36.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00113 (Fisher's exact test), Q value = 0.0041

Table S130. Gene #28: 'del_1p36.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
DEL PEAK 1(1P36.31) MUTATED	14	37	31	65	12
DEL PEAK 1(1P36.31) WILD-TYPE	30	58	25	57	36

Figure S130. Get High-res Image Gene #28: 'del_1p36.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00398 (Fisher's exact test), Q value = 0.011

Table S131. Gene #28: 'del_1p36.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
DEL PEAK 1(1P36.31) MUTATED	56	39	30	25
DEL PEAK 1(1P36.31) WILD-TYPE	51	42	72	25

Figure S131. Get High-res Image Gene #28: 'del_1p36.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_1p36.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00469 (Fisher's exact test), Q value = 0.013

Table S132. Gene #28: 'del_1p36.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
DEL PEAK 1(1P36.31) MUTATED	33	34	57	11	15
DEL PEAK 1(1P36.31) WILD-TYPE	37	48	43	23	39

Figure S132. Get High-res Image Gene #28: 'del_1p36.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S133. Gene #29: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 2(1P36.11) MUTATED	11	56	75
DEL PEAK 2(1P36.11) WILD-TYPE	82	95	51

Figure S133. Get High-res Image Gene #29: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S134. Gene #29: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
DEL PEAK 2(1P36.11) MUTATED	24	48	70
DEL PEAK 2(1P36.11) WILD-TYPE	69	113	46

Figure S134. Get High-res Image Gene #29: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S135. Gene #29: 'del_1p36.11' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
DEL PEAK 2(1P36.11) MUTATED	17	23	58	25	17
DEL PEAK 2(1P36.11) WILD-TYPE	50	63	13	46	52

Figure S135. Get High-res Image Gene #29: 'del_1p36.11' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S136. Gene #29: 'del_1p36.11' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
DEL PEAK 2(1P36.11) MUTATED	22	19	31	54	14
DEL PEAK 2(1P36.11) WILD-TYPE	32	37	83	30	42

Figure S136. Get High-res Image Gene #29: 'del_1p36.11' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S137. Gene #29: 'del_1p36.11' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
DEL PEAK 2(1P36.11) MUTATED	8	18	33	28	25	27
DEL PEAK 2(1P36.11) WILD-TYPE	32	45	59	56	21	13

Figure S137. Get High-res Image Gene #29: 'del_1p36.11' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_1p36.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00038

Table S138. Gene #29: 'del_1p36.11' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
DEL PEAK 2(1P36.11) MUTATED	9	30	25	64	11
DEL PEAK 2(1P36.11) WILD-TYPE	35	65	31	58	37

Figure S138. Get High-res Image Gene #29: 'del_1p36.11' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.0022

Table S139. Gene #29: 'del_1p36.11' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
DEL PEAK 2(1P36.11) MUTATED	52	34	23	23
DEL PEAK 2(1P36.11) WILD-TYPE	55	47	79	27

Figure S139. Get High-res Image Gene #29: 'del_1p36.11' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.0012

Table S140. Gene #29: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
DEL PEAK 2(1P36.11) MUTATED	30	26	55	7	14
DEL PEAK 2(1P36.11) WILD-TYPE	40	56	45	27	40

Figure S140. Get High-res Image Gene #29: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q22.1' versus 'CN_CNMF'

P value = 0.00308 (Fisher's exact test), Q value = 0.009

Table S141. Gene #30: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 3(2Q22.1) MUTATED	6	32	14
DEL PEAK 3(2Q22.1) WILD-TYPE	87	119	112

Figure S141. Get High-res Image Gene #30: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00471 (Fisher's exact test), Q value = 0.013

Table S142. Gene #30: 'del_2q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
DEL PEAK 3(2Q22.1) MUTATED	14	16	13	7	2
DEL PEAK 3(2Q22.1) WILD-TYPE	53	70	58	64	67

Figure S142. Get High-res Image Gene #30: 'del_2q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 3e-04

Table S143. Gene #31: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 4(2Q37.3) MUTATED	5	39	18
DEL PEAK 4(2Q37.3) WILD-TYPE	88	112	108

Figure S143. Get High-res Image Gene #31: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S144. Gene #31: 'del_2q37.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
DEL PEAK 4(2Q37.3) MUTATED	18	22	14	8	0
DEL PEAK 4(2Q37.3) WILD-TYPE	49	64	57	63	69

Figure S144. Get High-res Image Gene #31: 'del_2q37.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00091 (Fisher's exact test), Q value = 0.0034

Table S145. Gene #31: 'del_2q37.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
DEL PEAK 4(2Q37.3) MUTATED	12	9	28	12	1
DEL PEAK 4(2Q37.3) WILD-TYPE	42	47	86	72	55

Figure S145. Get High-res Image Gene #31: 'del_2q37.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00994 (Fisher's exact test), Q value = 0.023

Table S146. Gene #31: 'del_2q37.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
DEL PEAK 4(2Q37.3) MUTATED	11	16	16	15	3
DEL PEAK 4(2Q37.3) WILD-TYPE	33	79	40	107	45

Figure S146. Get High-res Image Gene #31: 'del_2q37.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00148 (Fisher's exact test), Q value = 0.005

Table S147. Gene #31: 'del_2q37.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
DEL PEAK 4(2Q37.3) MUTATED	21	14	10	9	4
DEL PEAK 4(2Q37.3) WILD-TYPE	49	68	90	25	50

Figure S147. Get High-res Image Gene #31: 'del_2q37.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p13' versus 'METHLYATION_CNMF'

P value = 0.00882 (Fisher's exact test), Q value = 0.021

Table S148. Gene #32: 'del_3p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
DEL PEAK 5(3P13) MUTATED	20	21	32
DEL PEAK 5(3P13) WILD-TYPE	73	140	84

Figure S148. Get High-res Image Gene #32: 'del_3p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p13' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00054

Table S149. Gene #32: 'del_3p13' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
DEL PEAK 5(3P13) MUTATED	13	10	26	18	5
DEL PEAK 5(3P13) WILD-TYPE	54	76	45	53	64

Figure S149. Get High-res Image Gene #32: 'del_3p13' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S150. Gene #32: 'del_3p13' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
DEL PEAK 5(3P13) MUTATED	23	5	15	24	5
DEL PEAK 5(3P13) WILD-TYPE	31	51	99	60	51

Figure S150. Get High-res Image Gene #32: 'del_3p13' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p13' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 3e-04

Table S151. Gene #32: 'del_3p13' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
DEL PEAK 5(3P13) MUTATED	5	8	20	9	9	20
DEL PEAK 5(3P13) WILD-TYPE	35	55	72	75	37	20

Figure S151. Get High-res Image Gene #32: 'del_3p13' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0335 (Fisher's exact test), Q value = 0.061

Table S152. Gene #32: 'del_3p13' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
DEL PEAK 5(3P13) MUTATED	5	17	12	33	4
DEL PEAK 5(3P13) WILD-TYPE	39	78	44	89	44

Figure S152. Get High-res Image Gene #32: 'del_3p13' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00993 (Fisher's exact test), Q value = 0.023

Table S153. Gene #32: 'del_3p13' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
DEL PEAK 5(3P13) MUTATED	29	19	10	9
DEL PEAK 5(3P13) WILD-TYPE	78	62	92	41

Figure S153. Get High-res Image Gene #32: 'del_3p13' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00163 (Fisher's exact test), Q value = 0.0053

Table S154. Gene #32: 'del_3p13' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
DEL PEAK 5(3P13) MUTATED	20	12	28	3	4
DEL PEAK 5(3P13) WILD-TYPE	50	70	72	31	50

Figure S154. Get High-res Image Gene #32: 'del_3p13' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4p16.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S155. Gene #33: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 6(4P16.3) MUTATED	4	51	30
DEL PEAK 6(4P16.3) WILD-TYPE	89	100	96

Figure S155. Get High-res Image Gene #33: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.027 (Fisher's exact test), Q value = 0.051

Table S156. Gene #33: 'del_4p16.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
DEL PEAK 6(4P16.3) MUTATED	6	20	20	32	6
DEL PEAK 6(4P16.3) WILD-TYPE	38	75	36	90	42

Figure S156. Get High-res Image Gene #33: 'del_4p16.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00557 (Fisher's exact test), Q value = 0.014

Table S157. Gene #33: 'del_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
DEL PEAK 6(4P16.3) MUTATED	26	20	22	4	6
DEL PEAK 6(4P16.3) WILD-TYPE	44	62	78	30	48

Figure S157. Get High-res Image Gene #33: 'del_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S158. Gene #34: 'del_4q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 7(4Q21.3) MUTATED	7	108	56
DEL PEAK 7(4Q21.3) WILD-TYPE	86	43	70

Figure S158. Get High-res Image Gene #34: 'del_4q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q21.3' versus 'METHLYATION_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.0035

Table S159. Gene #34: 'del_4q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
DEL PEAK 7(4Q21.3) MUTATED	35	66	70
DEL PEAK 7(4Q21.3) WILD-TYPE	58	95	46

Figure S159. Get High-res Image Gene #34: 'del_4q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S160. Gene #34: 'del_4q21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
DEL PEAK 7(4Q21.3) MUTATED	39	43	52	20	15
DEL PEAK 7(4Q21.3) WILD-TYPE	28	43	19	51	54

Figure S160. Get High-res Image Gene #34: 'del_4q21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_4q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00098

Table S161. Gene #34: 'del_4q21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
DEL PEAK 7(4Q21.3) MUTATED	28	22	55	51	13
DEL PEAK 7(4Q21.3) WILD-TYPE	26	34	59	33	43

Figure S161. Get High-res Image Gene #34: 'del_4q21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_4q21.3' versus 'MIRSEQ_CNMF'

P value = 0.00133 (Fisher's exact test), Q value = 0.0046

Table S162. Gene #34: 'del_4q21.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
DEL PEAK 7(4Q21.3) MUTATED	20	28	39	27	30	26
DEL PEAK 7(4Q21.3) WILD-TYPE	20	35	53	57	16	14

Figure S162. Get High-res Image Gene #34: 'del_4q21.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_4q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00154 (Fisher's exact test), Q value = 0.0051

Table S163. Gene #34: 'del_4q21.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
DEL PEAK 7(4Q21.3) MUTATED	20	45	32	63	10
DEL PEAK 7(4Q21.3) WILD-TYPE	24	50	24	59	38

Figure S163. Get High-res Image Gene #34: 'del_4q21.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_4q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00034

Table S164. Gene #34: 'del_4q21.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
DEL PEAK 7(4Q21.3) MUTATED	62	33	34	34
DEL PEAK 7(4Q21.3) WILD-TYPE	45	48	68	16

Figure S164. Get High-res Image Gene #34: 'del_4q21.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_4q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00034

Table S165. Gene #34: 'del_4q21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
DEL PEAK 7(4Q21.3) MUTATED	45	42	50	14	12
DEL PEAK 7(4Q21.3) WILD-TYPE	25	40	50	20	42

Figure S165. Get High-res Image Gene #34: 'del_4q21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q24' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S166. Gene #35: 'del_4q24' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 8(4Q24) MUTATED	5	111	57
DEL PEAK 8(4Q24) WILD-TYPE	88	40	69

Figure S166. Get High-res Image Gene #35: 'del_4q24' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q24' versus 'METHLYATION_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.0031

Table S167. Gene #35: 'del_4q24' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
DEL PEAK 8(4Q24) MUTATED	36	66	71
DEL PEAK 8(4Q24) WILD-TYPE	57	95	45

Figure S167. Get High-res Image Gene #35: 'del_4q24' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q24' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S168. Gene #35: 'del_4q24' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
DEL PEAK 8(4Q24) MUTATED	38	43	52	22	15
DEL PEAK 8(4Q24) WILD-TYPE	29	43	19	49	54

Figure S168. Get High-res Image Gene #35: 'del_4q24' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_4q24' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 3e-04

Table S169. Gene #35: 'del_4q24' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
DEL PEAK 8(4Q24) MUTATED	29	23	54	52	12
DEL PEAK 8(4Q24) WILD-TYPE	25	33	60	32	44

Figure S169. Get High-res Image Gene #35: 'del_4q24' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_4q24' versus 'MIRSEQ_CNMF'

P value = 0.00183 (Fisher's exact test), Q value = 0.0058

Table S170. Gene #35: 'del_4q24' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
DEL PEAK 8(4Q24) MUTATED	21	27	40	28	30	26
DEL PEAK 8(4Q24) WILD-TYPE	19	36	52	56	16	14

Figure S170. Get High-res Image Gene #35: 'del_4q24' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_4q24' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00098

Table S171. Gene #35: 'del_4q24' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
DEL PEAK 8(4Q24) MUTATED	23	43	33	64	9
DEL PEAK 8(4Q24) WILD-TYPE	21	52	23	58	39

Figure S171. Get High-res Image Gene #35: 'del_4q24' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_4q24' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S172. Gene #35: 'del_4q24' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
DEL PEAK 8(4Q24) MUTATED	61	34	34	36
DEL PEAK 8(4Q24) WILD-TYPE	46	47	68	14

Figure S172. Get High-res Image Gene #35: 'del_4q24' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_4q24' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00026

Table S173. Gene #35: 'del_4q24' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
DEL PEAK 8(4Q24) MUTATED	45	42	50	17	11
DEL PEAK 8(4Q24) WILD-TYPE	25	40	50	17	43

Figure S173. Get High-res Image Gene #35: 'del_4q24' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q35.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S174. Gene #36: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 9(4Q35.1) MUTATED	9	102	61
DEL PEAK 9(4Q35.1) WILD-TYPE	84	49	65

Figure S174. Get High-res Image Gene #36: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q35.1' versus 'METHLYATION_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0015

Table S175. Gene #36: 'del_4q35.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
DEL PEAK 9(4Q35.1) MUTATED	33	68	71
DEL PEAK 9(4Q35.1) WILD-TYPE	60	93	45

Figure S175. Get High-res Image Gene #36: 'del_4q35.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q35.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S176. Gene #36: 'del_4q35.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
DEL PEAK 9(4Q35.1) MUTATED	39	39	50	21	20
DEL PEAK 9(4Q35.1) WILD-TYPE	28	47	21	50	49

Figure S176. Get High-res Image Gene #36: 'del_4q35.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_4q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00072 (Fisher's exact test), Q value = 0.0028

Table S177. Gene #36: 'del_4q35.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
DEL PEAK 9(4Q35.1) MUTATED	28	22	48	54	17
DEL PEAK 9(4Q35.1) WILD-TYPE	26	34	66	30	39

Figure S177. Get High-res Image Gene #36: 'del_4q35.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MIRSEQ_CNMF'

P value = 0.00188 (Fisher's exact test), Q value = 0.0059

Table S178. Gene #36: 'del_4q35.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
DEL PEAK 9(4Q35.1) MUTATED	22	26	36	31	29	27
DEL PEAK 9(4Q35.1) WILD-TYPE	18	37	56	53	17	13

Figure S178. Get High-res Image Gene #36: 'del_4q35.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_4q35.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00597 (Fisher's exact test), Q value = 0.015

Table S179. Gene #36: 'del_4q35.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
DEL PEAK 9(4Q35.1) MUTATED	21	41	32	65	12
DEL PEAK 9(4Q35.1) WILD-TYPE	23	54	24	57	36

Figure S179. Get High-res Image Gene #36: 'del_4q35.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00045

Table S180. Gene #36: 'del_4q35.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
DEL PEAK 9(4Q35.1) MUTATED	60	36	32	33
DEL PEAK 9(4Q35.1) WILD-TYPE	47	45	70	17

Figure S180. Get High-res Image Gene #36: 'del_4q35.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_4q35.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00148 (Fisher's exact test), Q value = 0.005

Table S181. Gene #36: 'del_4q35.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
DEL PEAK 9(4Q35.1) MUTATED	42	39	51	16	13
DEL PEAK 9(4Q35.1) WILD-TYPE	28	43	49	18	41

Figure S181. Get High-res Image Gene #36: 'del_4q35.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q27' versus 'CN_CNMF'

P value = 0.00152 (Fisher's exact test), Q value = 0.0051

Table S182. Gene #37: 'del_6q27' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 10(6Q27) MUTATED	20	64	52
DEL PEAK 10(6Q27) WILD-TYPE	73	87	74

Figure S182. Get High-res Image Gene #37: 'del_6q27' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q27' versus 'METHLYATION_CNMF'

P value = 0.0054 (Fisher's exact test), Q value = 0.014

Table S183. Gene #37: 'del_6q27' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
DEL PEAK 10(6Q27) MUTATED	23	72	41
DEL PEAK 10(6Q27) WILD-TYPE	70	89	75

Figure S183. Get High-res Image Gene #37: 'del_6q27' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q27' versus 'MIRSEQ_CNMF'

P value = 0.0289 (Fisher's exact test), Q value = 0.054

Table S184. Gene #37: 'del_6q27' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
DEL PEAK 10(6Q27) MUTATED	19	20	23	35	15	20
DEL PEAK 10(6Q27) WILD-TYPE	21	43	69	49	31	20

Figure S184. Get High-res Image Gene #37: 'del_6q27' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_6q27' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0391 (Fisher's exact test), Q value = 0.07

Table S185. Gene #37: 'del_6q27' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
DEL PEAK 10(6Q27) MUTATED	20	25	18	45	24
DEL PEAK 10(6Q27) WILD-TYPE	24	70	38	77	24

Figure S185. Get High-res Image Gene #37: 'del_6q27' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_7q36.3' versus 'METHLYATION_CNMF'

P value = 0.0408 (Fisher's exact test), Q value = 0.072

Table S186. Gene #38: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
DEL PEAK 11(7Q36.3) MUTATED	8	9	17
DEL PEAK 11(7Q36.3) WILD-TYPE	85	152	99

Figure S186. Get High-res Image Gene #38: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q36.3' versus 'MRNASEQ_CNMF'

P value = 0.0414 (Fisher's exact test), Q value = 0.072

Table S187. Gene #38: 'del_7q36.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
DEL PEAK 11(7Q36.3) MUTATED	10	4	11	6	3
DEL PEAK 11(7Q36.3) WILD-TYPE	57	82	60	65	66

Figure S187. Get High-res Image Gene #38: 'del_7q36.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_7q36.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0014

Table S188. Gene #38: 'del_7q36.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
DEL PEAK 11(7Q36.3) MUTATED	19	5	2	7
DEL PEAK 11(7Q36.3) WILD-TYPE	88	76	100	43

Figure S188. Get High-res Image Gene #38: 'del_7q36.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_7q36.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00772 (Fisher's exact test), Q value = 0.019

Table S189. Gene #38: 'del_7q36.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
DEL PEAK 11(7Q36.3) MUTATED	11	8	8	6	0
DEL PEAK 11(7Q36.3) WILD-TYPE	59	74	92	28	54

Figure S189. Get High-res Image Gene #38: 'del_7q36.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S190. Gene #39: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 12(8P23.2) MUTATED	46	96	105
DEL PEAK 12(8P23.2) WILD-TYPE	47	55	21

Figure S190. Get High-res Image Gene #39: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S191. Gene #40: 'del_8p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 13(8P12) MUTATED	44	91	107
DEL PEAK 13(8P12) WILD-TYPE	49	60	19

Figure S191. Get High-res Image Gene #40: 'del_8p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S192. Gene #41: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 14(9P21.3) MUTATED	13	76	61
DEL PEAK 14(9P21.3) WILD-TYPE	80	75	65

Figure S192. Get High-res Image Gene #41: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 0.0242 (Fisher's exact test), Q value = 0.047

Table S193. Gene #41: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
DEL PEAK 14(9P21.3) MUTATED	34	57	59
DEL PEAK 14(9P21.3) WILD-TYPE	59	104	57

Figure S193. Get High-res Image Gene #41: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S194. Gene #41: 'del_9p21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
DEL PEAK 14(9P21.3) MUTATED	31	29	45	27	15
DEL PEAK 14(9P21.3) WILD-TYPE	36	57	26	44	54

Figure S194. Get High-res Image Gene #41: 'del_9p21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00175 (Fisher's exact test), Q value = 0.0057

Table S195. Gene #41: 'del_9p21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
DEL PEAK 14(9P21.3) MUTATED	28	20	38	46	15
DEL PEAK 14(9P21.3) WILD-TYPE	26	36	76	38	41

Figure S195. Get High-res Image Gene #41: 'del_9p21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00026

Table S196. Gene #41: 'del_9p21.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
DEL PEAK 14(9P21.3) MUTATED	20	16	35	26	31	21
DEL PEAK 14(9P21.3) WILD-TYPE	20	47	57	58	15	19

Figure S196. Get High-res Image Gene #41: 'del_9p21.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00215 (Fisher's exact test), Q value = 0.0066

Table S197. Gene #41: 'del_9p21.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
DEL PEAK 14(9P21.3) MUTATED	20	31	29	59	10
DEL PEAK 14(9P21.3) WILD-TYPE	24	64	27	63	38

Figure S197. Get High-res Image Gene #41: 'del_9p21.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0208 (Fisher's exact test), Q value = 0.041

Table S198. Gene #41: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
DEL PEAK 14(9P21.3) MUTATED	49	30	34	29
DEL PEAK 14(9P21.3) WILD-TYPE	58	51	68	21

Figure S198. Get High-res Image Gene #41: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00478 (Fisher's exact test), Q value = 0.013

Table S199. Gene #41: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
DEL PEAK 14(9P21.3) MUTATED	40	28	45	15	14
DEL PEAK 14(9P21.3) WILD-TYPE	30	54	55	19	40

Figure S199. Get High-res Image Gene #41: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q31.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S200. Gene #42: 'del_9q31.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 15(9Q31.3) MUTATED	10	66	43
DEL PEAK 15(9Q31.3) WILD-TYPE	83	85	83

Figure S200. Get High-res Image Gene #42: 'del_9q31.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q31.3' versus 'METHLYATION_CNMF'

P value = 0.00897 (Fisher's exact test), Q value = 0.021

Table S201. Gene #42: 'del_9q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
DEL PEAK 15(9Q31.3) MUTATED	23	46	50
DEL PEAK 15(9Q31.3) WILD-TYPE	70	115	66

Figure S201. Get High-res Image Gene #42: 'del_9q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9q31.3' versus 'MRNASEQ_CNMF'

P value = 0.00115 (Fisher's exact test), Q value = 0.0041

Table S202. Gene #42: 'del_9q31.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
DEL PEAK 15(9Q31.3) MUTATED	25	29	31	24	9
DEL PEAK 15(9Q31.3) WILD-TYPE	42	57	40	47	60

Figure S202. Get High-res Image Gene #42: 'del_9q31.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_9q31.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.0014

Table S203. Gene #42: 'del_9q31.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
DEL PEAK 15(9Q31.3) MUTATED	21	16	38	37	6
DEL PEAK 15(9Q31.3) WILD-TYPE	33	40	76	47	50

Figure S203. Get High-res Image Gene #42: 'del_9q31.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_9q31.3' versus 'MIRSEQ_CNMF'

P value = 0.027 (Fisher's exact test), Q value = 0.051

Table S204. Gene #42: 'del_9q31.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
DEL PEAK 15(9Q31.3) MUTATED	17	19	29	16	17	18
DEL PEAK 15(9Q31.3) WILD-TYPE	23	44	63	68	29	22

Figure S204. Get High-res Image Gene #42: 'del_9q31.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_9q31.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00696 (Fisher's exact test), Q value = 0.017

Table S205. Gene #42: 'del_9q31.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
DEL PEAK 15(9Q31.3) MUTATED	17	30	21	43	5
DEL PEAK 15(9Q31.3) WILD-TYPE	27	65	35	79	43

Figure S205. Get High-res Image Gene #42: 'del_9q31.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_9q31.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.001

Table S206. Gene #42: 'del_9q31.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
DEL PEAK 15(9Q31.3) MUTATED	29	25	36	16	5
DEL PEAK 15(9Q31.3) WILD-TYPE	41	57	64	18	49

Figure S206. Get High-res Image Gene #42: 'del_9q31.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S207. Gene #43: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 16(10Q23.31) MUTATED	11	71	15
DEL PEAK 16(10Q23.31) WILD-TYPE	82	80	111

Figure S207. Get High-res Image Gene #43: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 0.015 (Fisher's exact test), Q value = 0.031

Table S208. Gene #43: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
DEL PEAK 16(10Q23.31) MUTATED	32	45	20
DEL PEAK 16(10Q23.31) WILD-TYPE	61	116	96

Figure S208. Get High-res Image Gene #43: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S209. Gene #43: 'del_10q23.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
DEL PEAK 16(10Q23.31) MUTATED	38	29	6	16	5
DEL PEAK 16(10Q23.31) WILD-TYPE	29	57	65	55	64

Figure S209. Get High-res Image Gene #43: 'del_10q23.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S210. Gene #43: 'del_10q23.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
DEL PEAK 16(10Q23.31) MUTATED	27	9	41	11	6
DEL PEAK 16(10Q23.31) WILD-TYPE	27	47	73	73	50

Figure S210. Get High-res Image Gene #43: 'del_10q23.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S211. Gene #43: 'del_10q23.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
DEL PEAK 16(10Q23.31) MUTATED	15	33	15	11	9	14
DEL PEAK 16(10Q23.31) WILD-TYPE	25	30	77	73	37	26

Figure S211. Get High-res Image Gene #43: 'del_10q23.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S212. Gene #43: 'del_10q23.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
DEL PEAK 16(10Q23.31) MUTATED	15	41	13	25	3
DEL PEAK 16(10Q23.31) WILD-TYPE	29	54	43	97	45

Figure S212. Get High-res Image Gene #43: 'del_10q23.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.032

Table S213. Gene #43: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
DEL PEAK 16(10Q23.31) MUTATED	42	19	21	12
DEL PEAK 16(10Q23.31) WILD-TYPE	65	62	81	38

Figure S213. Get High-res Image Gene #43: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S214. Gene #43: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
DEL PEAK 16(10Q23.31) MUTATED	21	38	20	13	2
DEL PEAK 16(10Q23.31) WILD-TYPE	49	44	80	21	52

Figure S214. Get High-res Image Gene #43: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q26.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S215. Gene #44: 'del_10q26.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 17(10Q26.13) MUTATED	15	75	15
DEL PEAK 17(10Q26.13) WILD-TYPE	78	76	111

Figure S215. Get High-res Image Gene #44: 'del_10q26.13' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q26.13' versus 'METHLYATION_CNMF'

P value = 0.0242 (Fisher's exact test), Q value = 0.047

Table S216. Gene #44: 'del_10q26.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
DEL PEAK 17(10Q26.13) MUTATED	36	44	25
DEL PEAK 17(10Q26.13) WILD-TYPE	57	117	91

Figure S216. Get High-res Image Gene #44: 'del_10q26.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q26.13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S217. Gene #44: 'del_10q26.13' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
DEL PEAK 17(10Q26.13) MUTATED	37	32	10	18	5
DEL PEAK 17(10Q26.13) WILD-TYPE	30	54	61	53	64

Figure S217. Get High-res Image Gene #44: 'del_10q26.13' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_10q26.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S218. Gene #44: 'del_10q26.13' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
DEL PEAK 17(10Q26.13) MUTATED	30	11	41	14	6
DEL PEAK 17(10Q26.13) WILD-TYPE	24	45	73	70	50

Figure S218. Get High-res Image Gene #44: 'del_10q26.13' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.13' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 2e-04

Table S219. Gene #44: 'del_10q26.13' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
DEL PEAK 17(10Q26.13) MUTATED	13	32	19	13	11	17
DEL PEAK 17(10Q26.13) WILD-TYPE	27	31	73	71	35	23

Figure S219. Get High-res Image Gene #44: 'del_10q26.13' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_10q26.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S220. Gene #44: 'del_10q26.13' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
DEL PEAK 17(10Q26.13) MUTATED	14	45	12	31	3
DEL PEAK 17(10Q26.13) WILD-TYPE	30	50	44	91	45

Figure S220. Get High-res Image Gene #44: 'del_10q26.13' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_10q26.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S221. Gene #44: 'del_10q26.13' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
DEL PEAK 17(10Q26.13) MUTATED	22	40	25	13	2
DEL PEAK 17(10Q26.13) WILD-TYPE	48	42	75	21	52

Figure S221. Get High-res Image Gene #44: 'del_10q26.13' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q14.1' versus 'CN_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.033

Table S222. Gene #45: 'del_11q14.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 18(11Q14.1) MUTATED	10	37	30
DEL PEAK 18(11Q14.1) WILD-TYPE	83	114	96

Figure S222. Get High-res Image Gene #45: 'del_11q14.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00743 (Fisher's exact test), Q value = 0.018

Table S223. Gene #45: 'del_11q14.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
DEL PEAK 18(11Q14.1) MUTATED	33	13	13	12
DEL PEAK 18(11Q14.1) WILD-TYPE	74	68	89	38

Figure S223. Get High-res Image Gene #45: 'del_11q14.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_11q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0153 (Fisher's exact test), Q value = 0.032

Table S224. Gene #45: 'del_11q14.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
DEL PEAK 18(11Q14.1) MUTATED	23	21	15	6	6
DEL PEAK 18(11Q14.1) WILD-TYPE	47	61	85	28	48

Figure S224. Get High-res Image Gene #45: 'del_11q14.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q23.3' versus 'CN_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.0022

Table S225. Gene #46: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 19(11Q23.3) MUTATED	10	45	38
DEL PEAK 19(11Q23.3) WILD-TYPE	83	106	88

Figure S225. Get High-res Image Gene #46: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0406 (Fisher's exact test), Q value = 0.072

Table S226. Gene #46: 'del_11q23.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
DEL PEAK 19(11Q23.3) MUTATED	16	8	31	28	9
DEL PEAK 19(11Q23.3) WILD-TYPE	38	48	83	56	47

Figure S226. Get High-res Image Gene #46: 'del_11q23.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0138 (Fisher's exact test), Q value = 0.03

Table S227. Gene #46: 'del_11q23.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
DEL PEAK 19(11Q23.3) MUTATED	39	17	18	12
DEL PEAK 19(11Q23.3) WILD-TYPE	68	64	84	38

Figure S227. Get High-res Image Gene #46: 'del_11q23.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_11q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0021 (Fisher's exact test), Q value = 0.0065

Table S228. Gene #46: 'del_11q23.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
DEL PEAK 19(11Q23.3) MUTATED	27	27	20	5	7
DEL PEAK 19(11Q23.3) WILD-TYPE	43	55	80	29	47

Figure S228. Get High-res Image Gene #46: 'del_11q23.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12p12.1' versus 'CN_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.0032

Table S229. Gene #47: 'del_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 20(12P12.1) MUTATED	9	44	25
DEL PEAK 20(12P12.1) WILD-TYPE	84	107	101

Figure S229. Get High-res Image Gene #47: 'del_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p12.1' versus 'MRNASEQ_CNMF'

P value = 0.00254 (Fisher's exact test), Q value = 0.0076

Table S230. Gene #47: 'del_12p12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
DEL PEAK 20(12P12.1) MUTATED	24	24	10	11	9
DEL PEAK 20(12P12.1) WILD-TYPE	43	62	61	60	60

Figure S230. Get High-res Image Gene #47: 'del_12p12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_12p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.031 (Fisher's exact test), Q value = 0.058

Table S231. Gene #47: 'del_12p12.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
DEL PEAK 20(12P12.1) MUTATED	14	27	8	21	6
DEL PEAK 20(12P12.1) WILD-TYPE	30	68	48	101	42

Figure S231. Get High-res Image Gene #47: 'del_12p12.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_12p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0326 (Fisher's exact test), Q value = 0.06

Table S232. Gene #47: 'del_12p12.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
DEL PEAK 20(12P12.1) MUTATED	11	26	16	11	10
DEL PEAK 20(12P12.1) WILD-TYPE	59	56	84	23	44

Figure S232. Get High-res Image Gene #47: 'del_12p12.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q24.33' versus 'CN_CNMF'

P value = 0.00345 (Fisher's exact test), Q value = 0.0098

Table S233. Gene #48: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 21(12Q24.33) MUTATED	7	35	17
DEL PEAK 21(12Q24.33) WILD-TYPE	86	116	109

Figure S233. Get High-res Image Gene #48: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S234. Gene #49: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 22(13Q14.2) MUTATED	21	109	49
DEL PEAK 22(13Q14.2) WILD-TYPE	72	42	77

Figure S234. Get High-res Image Gene #49: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0012

Table S235. Gene #49: 'del_13q14.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
DEL PEAK 22(13Q14.2) MUTATED	41	45	41	30	19
DEL PEAK 22(13Q14.2) WILD-TYPE	26	41	30	41	50

Figure S235. Get High-res Image Gene #49: 'del_13q14.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S236. Gene #49: 'del_13q14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
DEL PEAK 22(13Q14.2) MUTATED	34	15	67	46	14
DEL PEAK 22(13Q14.2) WILD-TYPE	20	41	47	38	42

Figure S236. Get High-res Image Gene #49: 'del_13q14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 0.00175 (Fisher's exact test), Q value = 0.0057

Table S237. Gene #49: 'del_13q14.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
DEL PEAK 22(13Q14.2) MUTATED	26	36	45	26	20	24
DEL PEAK 22(13Q14.2) WILD-TYPE	14	27	47	58	26	16

Figure S237. Get High-res Image Gene #49: 'del_13q14.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00064 (Fisher's exact test), Q value = 0.0025

Table S238. Gene #49: 'del_13q14.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
DEL PEAK 22(13Q14.2) MUTATED	28	53	26	59	11
DEL PEAK 22(13Q14.2) WILD-TYPE	16	42	30	63	37

Figure S238. Get High-res Image Gene #49: 'del_13q14.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.036

Table S239. Gene #49: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
DEL PEAK 22(13Q14.2) MUTATED	63	42	38	25
DEL PEAK 22(13Q14.2) WILD-TYPE	44	39	64	25

Figure S239. Get High-res Image Gene #49: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00042

Table S240. Gene #49: 'del_13q14.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
DEL PEAK 22(13Q14.2) MUTATED	37	48	49	22	12
DEL PEAK 22(13Q14.2) WILD-TYPE	33	34	51	12	42

Figure S240. Get High-res Image Gene #49: 'del_13q14.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S241. Gene #50: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 23(14Q23.3) MUTATED	9	83	39
DEL PEAK 23(14Q23.3) WILD-TYPE	84	68	87

Figure S241. Get High-res Image Gene #50: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q23.3' versus 'MRNASEQ_CNMF'

P value = 0.00214 (Fisher's exact test), Q value = 0.0066

Table S242. Gene #50: 'del_14q23.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
DEL PEAK 23(14Q23.3) MUTATED	36	23	29	24	17
DEL PEAK 23(14Q23.3) WILD-TYPE	31	63	42	47	52

Figure S242. Get High-res Image Gene #50: 'del_14q23.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_14q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00034

Table S243. Gene #50: 'del_14q23.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
DEL PEAK 23(14Q23.3) MUTATED	34	12	38	32	13
DEL PEAK 23(14Q23.3) WILD-TYPE	20	44	76	52	43

Figure S243. Get High-res Image Gene #50: 'del_14q23.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_14q23.3' versus 'MIRSEQ_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.026

Table S244. Gene #50: 'del_14q23.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
DEL PEAK 23(14Q23.3) MUTATED	21	26	26	21	17	19
DEL PEAK 23(14Q23.3) WILD-TYPE	19	37	66	63	29	21

Figure S244. Get High-res Image Gene #50: 'del_14q23.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_14q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00416 (Fisher's exact test), Q value = 0.011

Table S245. Gene #50: 'del_14q23.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
DEL PEAK 23(14Q23.3) MUTATED	52	29	25	19
DEL PEAK 23(14Q23.3) WILD-TYPE	55	52	77	31

Figure S245. Get High-res Image Gene #50: 'del_14q23.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_14q32.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S246. Gene #51: 'del_14q32.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 24(14Q32.33) MUTATED	10	83	40
DEL PEAK 24(14Q32.33) WILD-TYPE	83	68	86

Figure S246. Get High-res Image Gene #51: 'del_14q32.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.33' versus 'MRNASEQ_CNMF'

P value = 0.00474 (Fisher's exact test), Q value = 0.013

Table S247. Gene #51: 'del_14q32.33' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
DEL PEAK 24(14Q32.33) MUTATED	35	24	30	25	17
DEL PEAK 24(14Q32.33) WILD-TYPE	32	62	41	46	52

Figure S247. Get High-res Image Gene #51: 'del_14q32.33' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_14q32.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00058

Table S248. Gene #51: 'del_14q32.33' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
DEL PEAK 24(14Q32.33) MUTATED	33	12	37	35	14
DEL PEAK 24(14Q32.33) WILD-TYPE	21	44	77	49	42

Figure S248. Get High-res Image Gene #51: 'del_14q32.33' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.027

Table S249. Gene #51: 'del_14q32.33' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
DEL PEAK 24(14Q32.33) MUTATED	48	32	25	21
DEL PEAK 24(14Q32.33) WILD-TYPE	59	49	77	29

Figure S249. Get High-res Image Gene #51: 'del_14q32.33' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_14q32.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.015 (Fisher's exact test), Q value = 0.031

Table S250. Gene #51: 'del_14q32.33' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
DEL PEAK 24(14Q32.33) MUTATED	32	23	41	17	13
DEL PEAK 24(14Q32.33) WILD-TYPE	38	59	59	17	41

Figure S250. Get High-res Image Gene #51: 'del_14q32.33' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q26.3' versus 'CN_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0021

Table S251. Gene #52: 'del_15q26.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 25(15Q26.3) MUTATED	11	47	21
DEL PEAK 25(15Q26.3) WILD-TYPE	82	104	105

Figure S251. Get High-res Image Gene #52: 'del_15q26.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q26.3' versus 'MRNASEQ_CNMF'

P value = 0.00834 (Fisher's exact test), Q value = 0.02

Table S252. Gene #52: 'del_15q26.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
DEL PEAK 25(15Q26.3) MUTATED	25	17	16	11	9
DEL PEAK 25(15Q26.3) WILD-TYPE	42	69	55	60	60

Figure S252. Get High-res Image Gene #52: 'del_15q26.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_15q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00971 (Fisher's exact test), Q value = 0.022

Table S253. Gene #52: 'del_15q26.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
DEL PEAK 25(15Q26.3) MUTATED	21	6	22	19	10
DEL PEAK 25(15Q26.3) WILD-TYPE	33	50	92	65	46

Figure S253. Get High-res Image Gene #52: 'del_15q26.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_15q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00225 (Fisher's exact test), Q value = 0.0068

Table S254. Gene #52: 'del_15q26.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
DEL PEAK 25(15Q26.3) MUTATED	32	11	15	17
DEL PEAK 25(15Q26.3) WILD-TYPE	75	70	87	33

Figure S254. Get High-res Image Gene #52: 'del_15q26.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S255. Gene #53: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 26(16Q23.1) MUTATED	8	86	68
DEL PEAK 26(16Q23.1) WILD-TYPE	85	65	58

Figure S255. Get High-res Image Gene #53: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S256. Gene #53: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
DEL PEAK 26(16Q23.1) MUTATED	30	56	76
DEL PEAK 26(16Q23.1) WILD-TYPE	63	105	40

Figure S256. Get High-res Image Gene #53: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S257. Gene #53: 'del_16q23.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
DEL PEAK 26(16Q23.1) MUTATED	36	34	60	20	10
DEL PEAK 26(16Q23.1) WILD-TYPE	31	52	11	51	59

Figure S257. Get High-res Image Gene #53: 'del_16q23.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S258. Gene #53: 'del_16q23.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
DEL PEAK 26(16Q23.1) MUTATED	25	18	52	57	8
DEL PEAK 26(16Q23.1) WILD-TYPE	29	38	62	27	48

Figure S258. Get High-res Image Gene #53: 'del_16q23.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 3e-04

Table S259. Gene #53: 'del_16q23.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
DEL PEAK 26(16Q23.1) MUTATED	19	28	32	24	32	25
DEL PEAK 26(16Q23.1) WILD-TYPE	21	35	60	60	14	15

Figure S259. Get High-res Image Gene #53: 'del_16q23.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S260. Gene #53: 'del_16q23.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
DEL PEAK 26(16Q23.1) MUTATED	19	40	33	62	6
DEL PEAK 26(16Q23.1) WILD-TYPE	25	55	23	60	42

Figure S260. Get High-res Image Gene #53: 'del_16q23.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S261. Gene #53: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
DEL PEAK 26(16Q23.1) MUTATED	61	33	28	32
DEL PEAK 26(16Q23.1) WILD-TYPE	46	48	74	18

Figure S261. Get High-res Image Gene #53: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 3e-04

Table S262. Gene #53: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
DEL PEAK 26(16Q23.1) MUTATED	44	36	50	14	10
DEL PEAK 26(16Q23.1) WILD-TYPE	26	46	50	20	44

Figure S262. Get High-res Image Gene #53: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S263. Gene #54: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 27(17P13.1) MUTATED	37	137	52
DEL PEAK 27(17P13.1) WILD-TYPE	56	14	74

Figure S263. Get High-res Image Gene #54: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S264. Gene #54: 'del_17p13.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
DEL PEAK 27(17P13.1) MUTATED	53	63	37	35	33
DEL PEAK 27(17P13.1) WILD-TYPE	14	23	34	36	36

Figure S264. Get High-res Image Gene #54: 'del_17p13.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_17p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00034

Table S265. Gene #54: 'del_17p13.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
DEL PEAK 27(17P13.1) MUTATED	40	28	85	42	26
DEL PEAK 27(17P13.1) WILD-TYPE	14	28	29	42	30

Figure S265. Get High-res Image Gene #54: 'del_17p13.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S266. Gene #54: 'del_17p13.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
DEL PEAK 27(17P13.1) MUTATED	35	49	48	40	27	25
DEL PEAK 27(17P13.1) WILD-TYPE	5	14	44	44	19	15

Figure S266. Get High-res Image Gene #54: 'del_17p13.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_17p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00042

Table S267. Gene #54: 'del_17p13.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
DEL PEAK 27(17P13.1) MUTATED	38	67	30	66	23
DEL PEAK 27(17P13.1) WILD-TYPE	6	28	26	56	25

Figure S267. Get High-res Image Gene #54: 'del_17p13.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_17p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S268. Gene #54: 'del_17p13.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
DEL PEAK 27(17P13.1) MUTATED	39	65	55	30	25
DEL PEAK 27(17P13.1) WILD-TYPE	31	17	45	4	29

Figure S268. Get High-res Image Gene #54: 'del_17p13.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S269. Gene #55: 'del_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 28(17P11.2) MUTATED	32	119	44
DEL PEAK 28(17P11.2) WILD-TYPE	61	32	82

Figure S269. Get High-res Image Gene #55: 'del_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p11.2' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00077

Table S270. Gene #55: 'del_17p11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
DEL PEAK 28(17P11.2) MUTATED	49	52	32	32	27
DEL PEAK 28(17P11.2) WILD-TYPE	18	34	39	39	42

Figure S270. Get High-res Image Gene #55: 'del_17p11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_17p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00839 (Fisher's exact test), Q value = 0.02

Table S271. Gene #55: 'del_17p11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
DEL PEAK 28(17P11.2) MUTATED	37	27	68	37	23
DEL PEAK 28(17P11.2) WILD-TYPE	17	29	46	47	33

Figure S271. Get High-res Image Gene #55: 'del_17p11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_17p11.2' versus 'MIRSEQ_CNMF'

P value = 9e-04 (Fisher's exact test), Q value = 0.0034

Table S272. Gene #55: 'del_17p11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
DEL PEAK 28(17P11.2) MUTATED	32	39	41	36	23	22
DEL PEAK 28(17P11.2) WILD-TYPE	8	24	51	48	23	18

Figure S272. Get High-res Image Gene #55: 'del_17p11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_17p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0011

Table S273. Gene #55: 'del_17p11.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
DEL PEAK 28(17P11.2) MUTATED	36	54	25	56	22
DEL PEAK 28(17P11.2) WILD-TYPE	8	41	31	66	26

Figure S273. Get High-res Image Gene #55: 'del_17p11.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_17p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0016

Table S274. Gene #55: 'del_17p11.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
DEL PEAK 28(17P11.2) MUTATED	34	52	48	28	22
DEL PEAK 28(17P11.2) WILD-TYPE	36	30	52	6	32

Figure S274. Get High-res Image Gene #55: 'del_17p11.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q21.2' versus 'CN_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.047

Table S275. Gene #56: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 29(18Q21.2) MUTATED	14	45	35
DEL PEAK 29(18Q21.2) WILD-TYPE	79	106	91

Figure S275. Get High-res Image Gene #56: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00045

Table S276. Gene #56: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
DEL PEAK 29(18Q21.2) MUTATED	14	34	46
DEL PEAK 29(18Q21.2) WILD-TYPE	79	127	70

Figure S276. Get High-res Image Gene #56: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S277. Gene #56: 'del_18q21.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
DEL PEAK 29(18Q21.2) MUTATED	9	5	28	39	13
DEL PEAK 29(18Q21.2) WILD-TYPE	45	51	86	45	43

Figure S277. Get High-res Image Gene #56: 'del_18q21.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S278. Gene #57: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 30(19P13.3) MUTATED	6	61	20
DEL PEAK 30(19P13.3) WILD-TYPE	87	90	106

Figure S278. Get High-res Image Gene #57: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00498 (Fisher's exact test), Q value = 0.013

Table S279. Gene #57: 'del_19p13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
DEL PEAK 30(19P13.3) MUTATED	28	17	17	12	12
DEL PEAK 30(19P13.3) WILD-TYPE	39	69	54	59	57

Figure S279. Get High-res Image Gene #57: 'del_19p13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0026 (Fisher's exact test), Q value = 0.0077

Table S280. Gene #57: 'del_19p13.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
DEL PEAK 30(19P13.3) MUTATED	22	9	23	25	7
DEL PEAK 30(19P13.3) WILD-TYPE	32	47	91	59	49

Figure S280. Get High-res Image Gene #57: 'del_19p13.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00217 (Fisher's exact test), Q value = 0.0066

Table S281. Gene #57: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
DEL PEAK 30(19P13.3) MUTATED	38	15	15	15
DEL PEAK 30(19P13.3) WILD-TYPE	69	66	87	35

Figure S281. Get High-res Image Gene #57: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00099 (Fisher's exact test), Q value = 0.0036

Table S282. Gene #57: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
DEL PEAK 30(19P13.3) MUTATED	26	21	17	13	6
DEL PEAK 30(19P13.3) WILD-TYPE	44	61	83	21	48

Figure S282. Get High-res Image Gene #57: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q12.1' versus 'CN_CNMF'

P value = 0.00622 (Fisher's exact test), Q value = 0.016

Table S283. Gene #59: 'del_22q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 32(22Q12.1) MUTATED	18	44	17
DEL PEAK 32(22Q12.1) WILD-TYPE	75	107	109

Figure S283. Get High-res Image Gene #59: 'del_22q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q12.1' versus 'MRNASEQ_CNMF'

P value = 0.00288 (Fisher's exact test), Q value = 0.0085

Table S284. Gene #59: 'del_22q12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
DEL PEAK 32(22Q12.1) MUTATED	26	19	9	15	10
DEL PEAK 32(22Q12.1) WILD-TYPE	41	67	62	56	59

Figure S284. Get High-res Image Gene #59: 'del_22q12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'CN_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0022

Table S285. Gene #60: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 33(22Q13.32) MUTATED	19	48	16
DEL PEAK 33(22Q13.32) WILD-TYPE	74	103	110

Figure S285. Get High-res Image Gene #60: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00045

Table S286. Gene #60: 'del_22q13.32' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
DEL PEAK 33(22Q13.32) MUTATED	28	24	7	14	10
DEL PEAK 33(22Q13.32) WILD-TYPE	39	62	64	57	59

Figure S286. Get High-res Image Gene #60: 'del_22q13.32' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00992 (Fisher's exact test), Q value = 0.023

Table S287. Gene #60: 'del_22q13.32' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
DEL PEAK 33(22Q13.32) MUTATED	16	6	36	16	9
DEL PEAK 33(22Q13.32) WILD-TYPE	38	50	78	68	47

Figure S287. Get High-res Image Gene #60: 'del_22q13.32' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_xq26.2' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00042

Table S288. Gene #61: 'del_xq26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
DEL PEAK 34(XQ26.2) MUTATED	6	42	19
DEL PEAK 34(XQ26.2) WILD-TYPE	87	109	107

Figure S288. Get High-res Image Gene #61: 'del_xq26.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq26.2' versus 'METHLYATION_CNMF'

P value = 0.00695 (Fisher's exact test), Q value = 0.017

Table S289. Gene #61: 'del_xq26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
DEL PEAK 34(XQ26.2) MUTATED	8	30	29
DEL PEAK 34(XQ26.2) WILD-TYPE	85	131	87

Figure S289. Get High-res Image Gene #61: 'del_xq26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LIHC-TP/22531241/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LIHC-TP/22542932/LIHC-TP.transferedmergedcluster.txt
Number of patients = 370
Number of significantly focal cnvs = 61
Number of molecular subtypes = 8
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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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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