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

Overview

Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 62 focal events and 8 molecular subtypes across 370 patients, 288 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_1q22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_1q42.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_2p24.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_2q33.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_3q26.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_4p14 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', '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', and 'MRNASEQ_CHIERARCHICAL'.
amp_6p21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
amp_6q12 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_6q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_7q31.2 cnv correlated to 'METHLYATION_CNMF'.
amp_8q13.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_9q34.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_11q13.3 cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_13q32.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_13q33.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_15q26.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_17p11.2 cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_CNMF'.
amp_17q25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19p13.12 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19q12 cnv correlated to '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', and 'MIRSEQ_MATURE_CNMF'.
amp_20q13.33 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_xq28 cnv correlated to 'CN_CNMF', 'METHLYATION_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_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 'MRNASEQ_CNMF'.
del_2q37.3 cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p13 cnv correlated to 'CN_CNMF', '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', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q35.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q27 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_8p23.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_8p12 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9q31.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', '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_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q14.1 cnv correlated to 'CN_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q24.2 cnv correlated to 'CN_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12p12.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_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', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q23.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 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_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_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_20p12.1 cnv correlated to 'CN_CNMF'.
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 62 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, 288 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 17q25 3	145 (39%)	225	3e-05 (0.000216)	0.021 (0.0431)	0.00106 (0.00392)	0.0104 (0.0242)	0.00103 (0.00384)	0.0014 (0.00489)	0.0255 (0.0508)	0.015 (0.0324)
amp xq28	85 (23%)	285	9e-05 (0.000519)	0.0294 (0.0574)	0.0409 (0.0732)	0.0161 (0.0342)	0.00924 (0.0221)	0.00492 (0.0133)	0.0473 (0.0823)	0.00034 (0.00148)
del 1p36 11	142 (38%)	228	4e-05 (0.000268)	1e-05 (9.54e-05)	1e-05 (9.54e-05)	1e-05 (9.54e-05)	0.00167 (0.00559)	5e-05 (0.000314)	0.00023 (0.00113)	0.00037 (0.00157)
del 3p13	73 (20%)	297	0.0054 (0.0145)	0.0458 (0.0803)	7e-05 (0.000418)	1e-05 (9.54e-05)	0.00167 (0.00559)	0.0339 (0.0635)	0.00028 (0.00131)	0.00202 (0.00638)
del 10q23 31	97 (26%)	273	0.0306 (0.0583)	0.0139 (0.0306)	1e-05 (9.54e-05)	1e-05 (9.54e-05)	0.0312 (0.0592)	1e-05 (9.54e-05)	0.0481 (0.0832)	1e-05 (9.54e-05)
amp 3q26 31	77 (21%)	293	0.0003 (0.00133)	0.0318 (0.06)	0.00671 (0.0176)	0.0196 (0.0407)	0.0757 (0.119)	0.0045 (0.0124)	0.0402 (0.0725)	0.0227 (0.046)
amp 8q24 21	231 (62%)	139	1e-05 (9.54e-05)	0.00752 (0.0191)	2e-05 (0.00015)	1e-05 (9.54e-05)	0.0153 (0.033)	0.00718 (0.0185)	0.0821 (0.127)	2e-05 (0.00015)
amp 19p13 12	69 (19%)	301	0.081 (0.126)	0.00017 (0.000888)	8e-05 (0.000467)	0.00054 (0.00216)	4e-05 (0.000268)	0.00246 (0.00753)	0.0006 (0.00238)	0.00129 (0.0046)
amp 19q12	78 (21%)	292	0.0549 (0.0924)	0.00239 (0.00736)	0.00154 (0.00523)	0.00138 (0.00485)	0.00111 (0.00408)	0.0111 (0.0256)	0.00027 (0.00129)	0.002 (0.00636)
amp 19q13 11	91 (25%)	279	0.0299 (0.0578)	0.0733 (0.116)	0.00099 (0.00372)	0.00062 (0.00244)	0.00701 (0.0182)	0.00178 (0.00577)	3e-05 (0.000216)	0.00046 (0.00189)
del 1p36 31	162 (44%)	208	0.00149 (0.00513)	1e-05 (9.54e-05)	1e-05 (9.54e-05)	2e-05 (0.00015)	0.0545 (0.0919)	0.00127 (0.00456)	0.0127 (0.0284)	0.00971 (0.023)
del 4q21 3	171 (46%)	199	1e-05 (9.54e-05)	0.00281 (0.00835)	1e-05 (9.54e-05)	0.0003 (0.00133)	0.189 (0.249)	0.00174 (0.00568)	2e-05 (0.00015)	0.00041 (0.00169)
del 4q22 3	172 (46%)	198	1e-05 (9.54e-05)	0.00341 (0.00989)	1e-05 (9.54e-05)	0.00022 (0.0011)	0.209 (0.265)	0.00121 (0.00438)	0.00011 (6e-04)	0.00052 (0.0021)
del 4q35 1	172 (46%)	198	1e-05 (9.54e-05)	0.00028 (0.00131)	1e-05 (9.54e-05)	0.00067 (0.00262)	0.153 (0.212)	0.00595 (0.0159)	0.0003 (0.00133)	0.00453 (0.0124)
del 9p21 3	150 (41%)	220	3e-05 (0.000216)	0.00787 (0.0198)	2e-05 (0.00015)	0.00199 (0.00636)	0.265 (0.322)	0.00206 (0.00647)	0.0192 (0.04)	0.00773 (0.0196)
del 16q23 1	162 (44%)	208	1e-05 (9.54e-05)	1e-05 (9.54e-05)	1e-05 (9.54e-05)	1e-05 (9.54e-05)	0.712 (0.748)	1e-05 (9.54e-05)	2e-05 (0.00015)	4e-05 (0.000268)
del 17p13 1	226 (61%)	144	1e-05 (9.54e-05)	0.0214 (0.0436)	2e-05 (0.00015)	0.0001 (0.000564)	0.00172 (0.00568)	5e-05 (0.000314)	0.627 (0.677)	1e-05 (9.54e-05)
amp 4p14	54 (15%)	316	0.00364 (0.0104)	0.027 (0.0534)	0.00011 (6e-04)	0.00112 (0.00408)	0.185 (0.245)	0.0566 (0.0948)	0.01 (0.0235)	0.0159 (0.0341)
amp 8q13 3	207 (56%)	163	1e-05 (9.54e-05)	0.148 (0.207)	6e-05 (0.000367)	1e-05 (9.54e-05)	0.0991 (0.149)	0.00219 (0.00679)	0.0394 (0.0718)	2e-05 (0.00015)
del 9q31 3	119 (32%)	251	0.00199 (0.00636)	0.0142 (0.0311)	0.00284 (0.00838)	0.00032 (0.0014)	0.157 (0.216)	0.00661 (0.0175)	0.0652 (0.106)	0.0002 (0.00102)
del 10q26 13	105 (28%)	265	0.00831 (0.0205)	0.048 (0.0832)	1e-05 (9.54e-05)	1e-05 (9.54e-05)	0.135 (0.193)	2e-05 (0.00015)	0.203 (0.261)	1e-05 (9.54e-05)
del 13q14 2	179 (48%)	191	1e-05 (9.54e-05)	0.0773 (0.121)	0.00029 (0.00132)	1e-05 (9.54e-05)	0.00271 (0.00815)	0.00071 (0.00275)	0.0989 (0.149)	8e-05 (0.000467)
del 17p11 2	195 (53%)	175	1e-05 (9.54e-05)	0.153 (0.212)	0.00145 (0.00503)	0.00828 (0.0205)	0.0001 (0.000564)	0.00029 (0.00132)	0.275 (0.334)	0.00022 (0.0011)
amp 1q22	283 (76%)	87	1e-05 (9.54e-05)	1e-05 (9.54e-05)	5e-05 (0.000314)	0.0035 (0.01)	0.829 (0.857)	0.0124 (0.028)	0.209 (0.265)	0.304 (0.362)
amp 1q42 3	270 (73%)	100	1e-05 (9.54e-05)	0.00012 (0.00064)	2e-05 (0.00015)	0.0009 (0.00341)	0.495 (0.556)	0.0375 (0.0689)	0.387 (0.448)	0.557 (0.611)
amp 6q12	83 (22%)	287	2e-05 (0.00015)	0.00722 (0.0185)	0.00811 (0.0202)	0.00931 (0.0222)	0.881 (0.901)	0.551 (0.606)	0.00423 (0.0119)	0.07 (0.113)
amp 11q13 3	57 (15%)	313	0.308 (0.366)	0.616 (0.668)	0.0079 (0.0198)	0.0175 (0.0369)	0.00853 (0.0208)	0.00334 (0.00974)	0.215 (0.272)	0.00018 (0.00093)
amp 20q13 13	124 (34%)	246	1e-05 (9.54e-05)	0.365 (0.427)	0.0311 (0.0591)	0.00039 (0.00164)	0.109 (0.161)	0.0118 (0.0268)	1e-05 (9.54e-05)	0.0609 (0.101)
del 2q37 3	62 (17%)	308	0.104 (0.156)	0.706 (0.743)	4e-05 (0.000268)	0.00081 (0.00309)	0.04 (0.0725)	0.0098 (0.0231)	0.236 (0.295)	0.00151 (0.00517)
del 14q32 33	132 (36%)	238	1e-05 (9.54e-05)	0.114 (0.168)	0.00024 (0.00117)	7e-05 (0.000418)	0.753 (0.784)	0.243 (0.303)	0.0147 (0.032)	0.0304 (0.0581)
del 19p13 3	87 (24%)	283	1e-05 (9.54e-05)	0.428 (0.486)	0.00027 (0.00129)	0.00295 (0.00866)	0.405 (0.463)	0.131 (0.187)	0.0212 (0.0433)	0.00251 (0.00764)
amp 1p22 3	89 (24%)	281	1e-05 (9.54e-05)	0.00279 (0.00834)	0.0534 (0.0909)	0.0458 (0.0803)	0.522 (0.579)	0.945 (0.953)	0.00899 (0.0216)	0.149 (0.208)
amp 6p25 2	159 (43%)	211	1e-05 (9.54e-05)	0.00015 (0.000791)	0.0177 (0.0372)	0.0245 (0.0492)	0.667 (0.711)	0.0625 (0.103)	0.209 (0.265)	0.4 (0.46)
amp 9q34 2	47 (13%)	323	0.03 (0.0578)	0.168 (0.227)	0.0334 (0.0628)	0.0925 (0.142)	0.0591 (0.098)	0.0134 (0.0295)	0.329 (0.389)	0.0128 (0.0284)
amp 13q32 3	67 (18%)	303	1e-05 (9.54e-05)	0.0537 (0.0909)	0.016 (0.0342)	0.0801 (0.125)	0.166 (0.225)	0.2 (0.258)	0.0129 (0.0285)	0.0183 (0.0382)
amp 13q33 3	67 (18%)	303	1e-05 (9.54e-05)	0.0199 (0.0411)	0.00436 (0.0121)	0.25 (0.308)	0.154 (0.213)	0.179 (0.239)	0.0714 (0.114)	0.0491 (0.0845)
amp 20q13 33	128 (35%)	242	1e-05 (9.54e-05)	0.0717 (0.114)	0.00713 (0.0184)	6e-05 (0.000367)	0.191 (0.25)	0.061 (0.101)	2e-05 (0.00015)	0.125 (0.179)
del 4p16 3	85 (23%)	285	2e-05 (0.00015)	0.105 (0.157)	0.198 (0.257)	0.102 (0.153)	0.704 (0.743)	0.0273 (0.0536)	0.0453 (0.08)	0.0068 (0.0178)
del 14q23 3	131 (35%)	239	1e-05 (9.54e-05)	0.374 (0.436)	0.00012 (0.00064)	4e-05 (0.000268)	0.875 (0.897)	0.0975 (0.148)	0.00665 (0.0175)	0.0585 (0.0974)
del 15q26 3	79 (21%)	291	0.0349 (0.0648)	0.25 (0.308)	0.0045 (0.0124)	0.00839 (0.0206)	0.356 (0.417)	0.121 (0.175)	0.00173 (0.00568)	0.0708 (0.114)
amp 2p24 1	65 (18%)	305	0.00475 (0.0129)	0.54 (0.597)	0.144 (0.204)	0.00403 (0.0114)	0.481 (0.542)	0.043 (0.0768)	0.141 (0.2)	0.0923 (0.142)
amp 2q33 1	64 (17%)	306	0.00344 (0.00992)	0.583 (0.636)	0.0522 (0.0892)	0.0112 (0.0256)	0.281 (0.338)	0.121 (0.175)	0.00023 (0.00113)	0.173 (0.232)
amp 5p15 33	163 (44%)	207	1e-05 (9.54e-05)	0.0374 (0.0689)	0.221 (0.278)	0.607 (0.66)	0.0756 (0.119)	0.0172 (0.0364)	0.0919 (0.142)	0.165 (0.225)
amp 6p21 1	158 (43%)	212	1e-05 (9.54e-05)	0.00035 (0.00151)	0.0112 (0.0256)	0.0645 (0.105)	0.117 (0.17)	0.0643 (0.105)	0.277 (0.335)	0.5 (0.561)
amp 6q12	109 (29%)	261	1e-05 (9.54e-05)	0.0536 (0.0909)	0.0367 (0.0679)	0.107 (0.159)	0.458 (0.519)	0.619 (0.671)	0.00993 (0.0233)	0.153 (0.212)
amp 15q26 3	54 (15%)	316	0.0258 (0.0512)	0.2 (0.258)	0.0405 (0.0729)	0.0389 (0.0712)	0.838 (0.864)	0.181 (0.24)	0.299 (0.358)	0.419 (0.479)
del 6q27	136 (37%)	234	0.00878 (0.0212)	0.0272 (0.0535)	0.685 (0.728)	0.481 (0.542)	0.647 (0.695)	0.0397 (0.0721)	0.353 (0.415)	0.159 (0.218)
del 11q14 1	77 (21%)	293	0.0115 (0.0263)	0.652 (0.697)	0.11 (0.162)	0.144 (0.204)	0.802 (0.834)	0.261 (0.319)	0.00037 (0.00157)	0.0125 (0.0282)
del 11q24 2	95 (26%)	275	0.00428 (0.012)	0.296 (0.355)	0.124 (0.178)	0.0511 (0.0878)	0.318 (0.377)	0.257 (0.314)	0.00077 (0.00296)	0.0004 (0.00167)
del 12p12 1	78 (21%)	292	0.00047 (0.00191)	0.161 (0.22)	0.00211 (0.00658)	0.227 (0.286)	0.216 (0.273)	0.0301 (0.0578)	0.506 (0.565)	0.0716 (0.114)
del 18q21 2	94 (25%)	276	0.00138 (0.00485)	0.00029 (0.00132)	0.205 (0.263)	1e-05 (9.54e-05)	0.115 (0.168)	0.539 (0.596)	0.172 (0.231)	0.248 (0.308)
del 22q13 32	83 (22%)	287	0.0049 (0.0133)	0.0581 (0.0971)	5e-05 (0.000314)	0.0104 (0.0242)	0.093 (0.142)	0.263 (0.321)	0.181 (0.24)	0.122 (0.175)
amp 5q35 3	135 (36%)	235	5e-05 (0.000314)	0.0347 (0.0646)	0.574 (0.627)	0.959 (0.962)	0.937 (0.947)	0.999 (0.999)	0.852 (0.875)	0.635 (0.684)
amp 17p11 2	46 (12%)	324	0.2 (0.258)	0.0209 (0.043)	0.391 (0.451)	0.231 (0.288)	0.0253 (0.0507)	0.252 (0.309)	0.0796 (0.125)	0.0872 (0.135)
del 8p23 2	247 (67%)	123	1e-05 (9.54e-05)	0.0443 (0.0785)	0.157 (0.216)	0.649 (0.695)	0.249 (0.308)	0.167 (0.227)	0.334 (0.394)	0.145 (0.204)
del 8p12	242 (65%)	128	1e-05 (9.54e-05)	0.0239 (0.0482)	0.145 (0.204)	0.562 (0.615)	0.191 (0.25)	0.101 (0.152)	0.278 (0.336)	0.0964 (0.147)
del 22q12 1	79 (21%)	291	0.0296 (0.0576)	0.189 (0.249)	0.00168 (0.00559)	0.105 (0.157)	0.229 (0.287)	0.196 (0.255)	0.181 (0.24)	0.503 (0.563)
del xq26 2	67 (18%)	303	2e-05 (0.00015)	0.0469 (0.0819)	0.341 (0.401)	0.392 (0.452)	0.905 (0.92)	0.697 (0.737)	0.313 (0.372)	0.894 (0.912)
amp 7q31 2	120 (32%)	250	0.196 (0.256)	0.00875 (0.0212)	0.98 (0.982)	0.896 (0.912)	0.522 (0.579)	0.434 (0.493)	0.697 (0.737)	0.422 (0.481)
del 2q22 1	52 (14%)	318	0.0689 (0.111)	0.509 (0.567)	0.00254 (0.00768)	0.0651 (0.106)	0.208 (0.265)	0.169 (0.227)	0.636 (0.684)	0.116 (0.169)
del 12q24 33	59 (16%)	311	0.00011 (6e-04)	0.841 (0.865)	0.748 (0.781)	0.914 (0.928)	0.815 (0.846)	0.715 (0.75)	0.819 (0.849)	0.291 (0.349)
del 20p12 1	29 (8%)	341	0.0437 (0.0777)	0.684 (0.728)	0.954 (0.96)	0.547 (0.602)	0.377 (0.438)	0.735 (0.77)	0.923 (0.934)	0.378 (0.438)

'amp_1p22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S1. Gene #1: 'amp_1p22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
AMP PEAK 1(1P22.3) MUTATED	22	49	18
AMP PEAK 1(1P22.3) WILD-TYPE	87	75	119

Figure S1. Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1p22.3' versus 'METHLYATION_CNMF'

P value = 0.00279 (Fisher's exact test), Q value = 0.0083

Table S2. Gene #1: 'amp_1p22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
AMP PEAK 1(1P22.3) MUTATED	11	40	38
AMP PEAK 1(1P22.3) WILD-TYPE	77	127	77

Figure S2. Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1p22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0458 (Fisher's exact test), Q value = 0.08

Table S3. Gene #1: 'amp_1p22.3' 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(1P22.3) MUTATED	16	8	27	28	9
AMP PEAK 1(1P22.3) WILD-TYPE	38	48	87	56	47

Figure S3. Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_1p22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00899 (Fisher's exact test), Q value = 0.022

Table S4. Gene #1: 'amp_1p22.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
AMP PEAK 1(1P22.3) MUTATED	32	18	19	13
AMP PEAK 1(1P22.3) WILD-TYPE	60	69	100	29

Figure S4. Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_1q22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S5. Gene #2: 'amp_1q22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
AMP PEAK 2(1Q22) MUTATED	93	111	79
AMP PEAK 2(1Q22) WILD-TYPE	16	13	58

Figure S5. Get High-res Image Gene #2: 'amp_1q22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q22' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S6. Gene #2: 'amp_1q22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
AMP PEAK 2(1Q22) MUTATED	47	135	101
AMP PEAK 2(1Q22) WILD-TYPE	41	32	14

Figure S6. Get High-res Image Gene #2: 'amp_1q22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q22' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00031

Table S7. Gene #2: 'amp_1q22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
AMP PEAK 2(1Q22) MUTATED	45	65	64	46	58
AMP PEAK 2(1Q22) WILD-TYPE	16	32	4	23	11

Figure S7. Get High-res Image Gene #2: 'amp_1q22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_1q22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0035 (Fisher's exact test), Q value = 0.01

Table S8. Gene #2: 'amp_1q22' 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(1Q22) MUTATED	36	39	81	73	49
AMP PEAK 2(1Q22) WILD-TYPE	18	17	33	11	7

Figure S8. Get High-res Image Gene #2: 'amp_1q22' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_1q22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0124 (Fisher's exact test), Q value = 0.028

Table S9. Gene #2: 'amp_1q22' 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(1Q22) MUTATED	39	65	47	87	41
AMP PEAK 2(1Q22) WILD-TYPE	5	30	9	35	7

Figure S9. Get High-res Image Gene #2: 'amp_1q22' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_1q42.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S10. Gene #3: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
AMP PEAK 3(1Q42.3) MUTATED	90	103	77
AMP PEAK 3(1Q42.3) WILD-TYPE	19	21	60

Figure S10. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q42.3' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00064

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
AMP PEAK 3(1Q42.3) MUTATED	48	130	92
AMP PEAK 3(1Q42.3) WILD-TYPE	40	37	23

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

'amp_1q42.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S12. Gene #3: 'amp_1q42.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
AMP PEAK 3(1Q42.3) MUTATED	43	57	63	46	56
AMP PEAK 3(1Q42.3) WILD-TYPE	18	40	5	23	13

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

'amp_1q42.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-04 (Fisher's exact test), Q value = 0.0034

Table S13. Gene #3: 'amp_1q42.3' 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 3(1Q42.3) MUTATED	34	39	73	72	47
AMP PEAK 3(1Q42.3) WILD-TYPE	20	17	41	12	9

Figure S13. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_1q42.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0375 (Fisher's exact test), Q value = 0.069

Table S14. Gene #3: 'amp_1q42.3' 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 3(1Q42.3) MUTATED	32	61	44	87	42
AMP PEAK 3(1Q42.3) WILD-TYPE	12	34	12	35	6

Figure S14. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_2p24.1' versus 'CN_CNMF'

P value = 0.00475 (Fisher's exact test), Q value = 0.013

Table S15. Gene #4: 'amp_2p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
AMP PEAK 4(2P24.1) MUTATED	12	33	20
AMP PEAK 4(2P24.1) WILD-TYPE	97	91	117

Figure S15. Get High-res Image Gene #4: 'amp_2p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2p24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00403 (Fisher's exact test), Q value = 0.011

Table S16. Gene #4: '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 4(2P24.1) MUTATED	17	3	21	16	6
AMP PEAK 4(2P24.1) WILD-TYPE	37	53	93	68	50

Figure S16. Get High-res Image Gene #4: 'amp_2p24.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_2p24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.043 (Fisher's exact test), Q value = 0.077

Table S17. Gene #4: '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 4(2P24.1) MUTATED	14	20	9	16	5
AMP PEAK 4(2P24.1) WILD-TYPE	30	75	47	106	43

Figure S17. Get High-res Image Gene #4: 'amp_2p24.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_2q33.1' versus 'CN_CNMF'

P value = 0.00344 (Fisher's exact test), Q value = 0.0099

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
AMP PEAK 5(2Q33.1) MUTATED	16	33	15
AMP PEAK 5(2Q33.1) WILD-TYPE	93	91	122

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

'amp_2q33.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 0.026

Table S19. Gene #5: '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 5(2Q33.1) MUTATED	15	4	14	20	9
AMP PEAK 5(2Q33.1) WILD-TYPE	39	52	100	64	47

Figure S19. Get High-res Image Gene #5: 'amp_2q33.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_2q33.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0011

Table S20. Gene #5: 'amp_2q33.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
AMP PEAK 5(2Q33.1) MUTATED	29	9	13	10
AMP PEAK 5(2Q33.1) WILD-TYPE	63	78	106	32

Figure S20. Get High-res Image Gene #5: 'amp_2q33.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.31' versus 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0013

Table S21. Gene #6: 'amp_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
AMP PEAK 6(3Q26.31) MUTATED	15	41	21
AMP PEAK 6(3Q26.31) WILD-TYPE	94	83	116

Figure S21. Get High-res Image Gene #6: 'amp_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.31' versus 'METHLYATION_CNMF'

P value = 0.0318 (Fisher's exact test), Q value = 0.06

Table S22. Gene #6: 'amp_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
AMP PEAK 6(3Q26.31) MUTATED	13	45	19
AMP PEAK 6(3Q26.31) WILD-TYPE	75	122	96

Figure S22. Get High-res Image Gene #6: 'amp_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q26.31' versus 'MRNASEQ_CNMF'

P value = 0.00671 (Fisher's exact test), Q value = 0.018

Table S23. Gene #6: 'amp_3q26.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
AMP PEAK 6(3Q26.31) MUTATED	22	25	11	10	9
AMP PEAK 6(3Q26.31) WILD-TYPE	39	72	57	59	60

Figure S23. Get High-res Image Gene #6: 'amp_3q26.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_3q26.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0196 (Fisher's exact test), Q value = 0.041

Table S24. Gene #6: '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 6(3Q26.31) MUTATED	17	5	30	16	9
AMP PEAK 6(3Q26.31) WILD-TYPE	37	51	84	68	47

Figure S24. Get High-res Image Gene #6: 'amp_3q26.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0045 (Fisher's exact test), Q value = 0.012

Table S25. Gene #6: '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 6(3Q26.31) MUTATED	17	24	9	22	4
AMP PEAK 6(3Q26.31) WILD-TYPE	27	71	47	100	44

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

'amp_3q26.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0402 (Fisher's exact test), Q value = 0.073

Table S26. Gene #6: 'amp_3q26.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
AMP PEAK 6(3Q26.31) MUTATED	21	12	23	15
AMP PEAK 6(3Q26.31) WILD-TYPE	71	75	96	27

Figure S26. Get High-res Image Gene #6: 'amp_3q26.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0227 (Fisher's exact test), Q value = 0.046

Table S27. Gene #6: 'amp_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
AMP PEAK 6(3Q26.31) MUTATED	13	22	18	13	5
AMP PEAK 6(3Q26.31) WILD-TYPE	54	64	81	22	48

Figure S27. Get High-res Image Gene #6: 'amp_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4p14' versus 'CN_CNMF'

P value = 0.00364 (Fisher's exact test), Q value = 0.01

Table S28. Gene #7: 'amp_4p14' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
AMP PEAK 7(4P14) MUTATED	13	29	12
AMP PEAK 7(4P14) WILD-TYPE	96	95	125

Figure S28. Get High-res Image Gene #7: 'amp_4p14' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4p14' versus 'METHLYATION_CNMF'

P value = 0.027 (Fisher's exact test), Q value = 0.053

Table S29. Gene #7: 'amp_4p14' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
AMP PEAK 7(4P14) MUTATED	12	17	25
AMP PEAK 7(4P14) WILD-TYPE	76	150	90

Figure S29. Get High-res Image Gene #7: 'amp_4p14' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_4p14' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 6e-04

Table S30. Gene #7: 'amp_4p14' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
AMP PEAK 7(4P14) MUTATED	10	14	20	8	1
AMP PEAK 7(4P14) WILD-TYPE	51	83	48	61	68

Figure S30. Get High-res Image Gene #7: 'amp_4p14' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_4p14' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00112 (Fisher's exact test), Q value = 0.0041

Table S31. Gene #7: '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 7(4P14) MUTATED	10	8	13	21	1
AMP PEAK 7(4P14) WILD-TYPE	44	48	101	63	55

Figure S31. Get High-res Image Gene #7: 'amp_4p14' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_4p14' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.01 (Fisher's exact test), Q value = 0.023

Table S32. Gene #7: 'amp_4p14' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
AMP PEAK 7(4P14) MUTATED	18	14	10	12
AMP PEAK 7(4P14) WILD-TYPE	74	73	109	30

Figure S32. Get High-res Image Gene #7: 'amp_4p14' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_4p14' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0159 (Fisher's exact test), Q value = 0.034

Table S33. Gene #7: 'amp_4p14' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
AMP PEAK 7(4P14) MUTATED	12	17	18	6	1
AMP PEAK 7(4P14) WILD-TYPE	55	69	81	29	52

Figure S33. Get High-res Image Gene #7: '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 = 9.5e-05

Table S34. Gene #8: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
AMP PEAK 8(5P15.33) MUTATED	54	72	37
AMP PEAK 8(5P15.33) WILD-TYPE	55	52	100

Figure S34. Get High-res Image Gene #8: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 0.0374 (Fisher's exact test), Q value = 0.069

Table S35. Gene #8: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
AMP PEAK 8(5P15.33) MUTATED	29	83	51
AMP PEAK 8(5P15.33) WILD-TYPE	59	84	64

Figure S35. Get High-res Image Gene #8: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0172 (Fisher's exact test), Q value = 0.036

Table S36. Gene #8: '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 8(5P15.33) MUTATED	26	47	28	43	16
AMP PEAK 8(5P15.33) WILD-TYPE	18	48	28	79	32

Figure S36. Get High-res Image Gene #8: 'amp_5p15.33' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_5q35.3' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00031

Table S37. Gene #9: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
AMP PEAK 9(5Q35.3) MUTATED	56	46	33
AMP PEAK 9(5Q35.3) WILD-TYPE	53	78	104

Figure S37. Get High-res Image Gene #9: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q35.3' versus 'METHLYATION_CNMF'

P value = 0.0347 (Fisher's exact test), Q value = 0.065

Table S38. Gene #9: 'amp_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
AMP PEAK 9(5Q35.3) MUTATED	22	66	47
AMP PEAK 9(5Q35.3) WILD-TYPE	66	101	68

Figure S38. Get High-res Image Gene #9: '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 = 9.5e-05

Table S39. Gene #10: 'amp_6p25.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
AMP PEAK 10(6P25.2) MUTATED	50	79	30
AMP PEAK 10(6P25.2) WILD-TYPE	59	45	107

Figure S39. Get High-res Image Gene #10: 'amp_6p25.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p25.2' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00079

Table S40. Gene #10: 'amp_6p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
AMP PEAK 10(6P25.2) MUTATED	21	82	56
AMP PEAK 10(6P25.2) WILD-TYPE	67	85	59

Figure S40. Get High-res Image Gene #10: 'amp_6p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p25.2' versus 'MRNASEQ_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.037

Table S41. Gene #10: 'amp_6p25.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
AMP PEAK 10(6P25.2) MUTATED	30	36	37	21	35
AMP PEAK 10(6P25.2) WILD-TYPE	31	61	31	48	34

Figure S41. Get High-res Image Gene #10: '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 = 0.049

Table S42. Gene #10: '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 10(6P25.2) MUTATED	24	16	45	46	28
AMP PEAK 10(6P25.2) WILD-TYPE	30	40	69	38	28

Figure S42. Get High-res Image Gene #10: 'amp_6p25.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S43. Gene #11: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
AMP PEAK 11(6P21.1) MUTATED	47	73	38
AMP PEAK 11(6P21.1) WILD-TYPE	62	51	99

Figure S43. Get High-res Image Gene #11: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p21.1' versus 'METHLYATION_CNMF'

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

Table S44. Gene #11: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
AMP PEAK 11(6P21.1) MUTATED	22	84	52
AMP PEAK 11(6P21.1) WILD-TYPE	66	83	63

Figure S44. Get High-res Image Gene #11: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.026

Table S45. Gene #11: 'amp_6p21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
AMP PEAK 11(6P21.1) MUTATED	25	44	36	18	35
AMP PEAK 11(6P21.1) WILD-TYPE	36	53	32	51	34

Figure S45. Get High-res Image Gene #11: 'amp_6p21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_6q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S46. Gene #12: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
AMP PEAK 12(6Q12) MUTATED	33	55	21
AMP PEAK 12(6Q12) WILD-TYPE	76	69	116

Figure S46. Get High-res Image Gene #12: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q12' versus 'MRNASEQ_CNMF'

P value = 0.0367 (Fisher's exact test), Q value = 0.068

Table S47. Gene #12: 'amp_6q12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
AMP PEAK 12(6Q12) MUTATED	22	25	29	14	19
AMP PEAK 12(6Q12) WILD-TYPE	39	72	39	55	50

Figure S47. Get High-res Image Gene #12: 'amp_6q12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_6q12' versus 'MIRSEQ_MATURE_CNMF'

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

Table S48. Gene #12: 'amp_6q12' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
AMP PEAK 12(6Q12) MUTATED	35	21	26	18
AMP PEAK 12(6Q12) WILD-TYPE	57	66	93	24

Figure S48. Get High-res Image Gene #12: 'amp_6q12' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_6q12' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S49. Gene #13: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
AMP PEAK 13(6Q12) MUTATED	25	45	13
AMP PEAK 13(6Q12) WILD-TYPE	84	79	124

Figure S49. Get High-res Image Gene #13: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q12' versus 'METHLYATION_CNMF'

P value = 0.00722 (Fisher's exact test), Q value = 0.018

Table S50. Gene #13: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
AMP PEAK 13(6Q12) MUTATED	10	40	33
AMP PEAK 13(6Q12) WILD-TYPE	78	127	82

Figure S50. Get High-res Image Gene #13: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q12' versus 'MRNASEQ_CNMF'

P value = 0.00811 (Fisher's exact test), Q value = 0.02

Table S51. Gene #13: 'amp_6q12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
AMP PEAK 13(6Q12) MUTATED	16	14	26	13	14
AMP PEAK 13(6Q12) WILD-TYPE	45	83	42	56	55

Figure S51. Get High-res Image Gene #13: 'amp_6q12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_6q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00931 (Fisher's exact test), Q value = 0.022

Table S52. Gene #13: '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 13(6Q12) MUTATED	15	10	17	30	11
AMP PEAK 13(6Q12) WILD-TYPE	39	46	97	54	45

Figure S52. Get High-res Image Gene #13: 'amp_6q12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_6q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00423 (Fisher's exact test), Q value = 0.012

Table S53. Gene #13: 'amp_6q12' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
AMP PEAK 13(6Q12) MUTATED	27	17	17	16
AMP PEAK 13(6Q12) WILD-TYPE	65	70	102	26

Figure S53. Get High-res Image Gene #13: 'amp_6q12' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_7q31.2' versus 'METHLYATION_CNMF'

P value = 0.00875 (Fisher's exact test), Q value = 0.021

Table S54. Gene #14: 'amp_7q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
AMP PEAK 14(7Q31.2) MUTATED	22	68	30
AMP PEAK 14(7Q31.2) WILD-TYPE	66	99	85

Figure S54. Get High-res Image Gene #14: 'amp_7q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S55. Gene #15: 'amp_8q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
AMP PEAK 15(8Q13.3) MUTATED	105	68	34
AMP PEAK 15(8Q13.3) WILD-TYPE	4	56	103

Figure S55. Get High-res Image Gene #15: 'amp_8q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q13.3' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00037

Table S56. Gene #15: 'amp_8q13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
AMP PEAK 15(8Q13.3) MUTATED	40	33	45	40	44
AMP PEAK 15(8Q13.3) WILD-TYPE	21	64	23	29	25

Figure S56. Get High-res Image Gene #15: 'amp_8q13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_8q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S57. Gene #15: 'amp_8q13.3' 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 15(8Q13.3) MUTATED	33	36	41	56	36
AMP PEAK 15(8Q13.3) WILD-TYPE	21	20	73	28	20

Figure S57. Get High-res Image Gene #15: 'amp_8q13.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_8q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00219 (Fisher's exact test), Q value = 0.0068

Table S58. Gene #15: 'amp_8q13.3' 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 15(8Q13.3) MUTATED	23	37	34	77	32
AMP PEAK 15(8Q13.3) WILD-TYPE	21	58	22	45	16

Figure S58. Get High-res Image Gene #15: 'amp_8q13.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_8q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0394 (Fisher's exact test), Q value = 0.072

Table S59. Gene #15: 'amp_8q13.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
AMP PEAK 15(8Q13.3) MUTATED	59	50	57	29
AMP PEAK 15(8Q13.3) WILD-TYPE	33	37	62	13

Figure S59. Get High-res Image Gene #15: 'amp_8q13.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_8q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S60. Gene #15: 'amp_8q13.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
AMP PEAK 15(8Q13.3) MUTATED	49	32	61	16	37
AMP PEAK 15(8Q13.3) WILD-TYPE	18	54	38	19	16

Figure S60. Get High-res Image Gene #15: 'amp_8q13.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S61. Gene #16: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
AMP PEAK 16(8Q24.21) MUTATED	105	80	46
AMP PEAK 16(8Q24.21) WILD-TYPE	4	44	91

Figure S61. Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 0.00752 (Fisher's exact test), Q value = 0.019

Table S62. Gene #16: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
AMP PEAK 16(8Q24.21) MUTATED	51	95	85
AMP PEAK 16(8Q24.21) WILD-TYPE	37	72	30

Figure S62. Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S63. Gene #16: 'amp_8q24.21' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
AMP PEAK 16(8Q24.21) MUTATED	42	39	48	47	50
AMP PEAK 16(8Q24.21) WILD-TYPE	19	58	20	22	19

Figure S63. Get High-res Image Gene #16: '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 = 9.5e-05

Table S64. Gene #16: '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 16(8Q24.21) MUTATED	39	40	45	61	41
AMP PEAK 16(8Q24.21) WILD-TYPE	15	16	69	23	15

Figure S64. Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.033

Table S65. Gene #16: 'amp_8q24.21' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	127	49	124
AMP PEAK 16(8Q24.21) MUTATED	29	83	31	84
AMP PEAK 16(8Q24.21) WILD-TYPE	36	44	18	40

Figure S65. Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00718 (Fisher's exact test), Q value = 0.018

Table S66. Gene #16: '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 16(8Q24.21) MUTATED	24	46	37	85	35
AMP PEAK 16(8Q24.21) WILD-TYPE	20	49	19	37	13

Figure S66. Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S67. Gene #16: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
AMP PEAK 16(8Q24.21) MUTATED	51	37	70	18	41
AMP PEAK 16(8Q24.21) WILD-TYPE	16	49	29	17	12

Figure S67. Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9q34.2' versus 'CN_CNMF'

P value = 0.03 (Fisher's exact test), Q value = 0.058

Table S68. Gene #17: 'amp_9q34.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
AMP PEAK 17(9Q34.2) MUTATED	11	24	12
AMP PEAK 17(9Q34.2) WILD-TYPE	98	100	125

Figure S68. Get High-res Image Gene #17: 'amp_9q34.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9q34.2' versus 'MRNASEQ_CNMF'

P value = 0.0334 (Fisher's exact test), Q value = 0.063

Table S69. Gene #17: 'amp_9q34.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
AMP PEAK 17(9Q34.2) MUTATED	10	16	12	5	3
AMP PEAK 17(9Q34.2) WILD-TYPE	51	81	56	64	66

Figure S69. Get High-res Image Gene #17: 'amp_9q34.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_9q34.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.029

Table S70. Gene #17: '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 17(9Q34.2) MUTATED	11	15	9	10	2
AMP PEAK 17(9Q34.2) WILD-TYPE	33	80	47	112	46

Figure S70. Get High-res Image Gene #17: 'amp_9q34.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_9q34.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S71. Gene #17: 'amp_9q34.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
AMP PEAK 17(9Q34.2) MUTATED	11	18	8	6	2
AMP PEAK 17(9Q34.2) WILD-TYPE	56	68	91	29	51

Figure S71. Get High-res Image Gene #17: 'amp_9q34.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

P value = 0.0079 (Fisher's exact test), Q value = 0.02

Table S72. Gene #18: 'amp_11q13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
AMP PEAK 18(11Q13.3) MUTATED	15	20	10	6	4
AMP PEAK 18(11Q13.3) WILD-TYPE	46	77	58	63	65

Figure S72. Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0175 (Fisher's exact test), Q value = 0.037

Table S73. Gene #18: '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 18(11Q13.3) MUTATED	10	7	25	11	2
AMP PEAK 18(11Q13.3) WILD-TYPE	44	49	89	73	54

Figure S73. Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

P value = 0.00853 (Fisher's exact test), Q value = 0.021

Table S74. Gene #18: 'amp_11q13.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	127	49	124
AMP PEAK 18(11Q13.3) MUTATED	18	12	10	17
AMP PEAK 18(11Q13.3) WILD-TYPE	47	115	39	107

Figure S74. Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00334 (Fisher's exact test), Q value = 0.0097

Table S75. Gene #18: '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 18(11Q13.3) MUTATED	11	23	5	16	2
AMP PEAK 18(11Q13.3) WILD-TYPE	33	72	51	106	46

Figure S75. Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00093

Table S76. Gene #18: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
AMP PEAK 18(11Q13.3) MUTATED	12	19	13	10	0
AMP PEAK 18(11Q13.3) WILD-TYPE	55	67	86	25	53

Figure S76. Get High-res Image Gene #18: '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 = 9.5e-05

Table S77. Gene #19: 'amp_13q32.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
AMP PEAK 19(13Q32.3) MUTATED	11	47	9
AMP PEAK 19(13Q32.3) WILD-TYPE	98	77	128

Figure S77. Get High-res Image Gene #19: 'amp_13q32.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q32.3' versus 'MRNASEQ_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.034

Table S78. Gene #19: 'amp_13q32.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
AMP PEAK 19(13Q32.3) MUTATED	14	15	21	8	8
AMP PEAK 19(13Q32.3) WILD-TYPE	47	82	47	61	61

Figure S78. Get High-res Image Gene #19: 'amp_13q32.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_13q32.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.029

Table S79. Gene #19: 'amp_13q32.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
AMP PEAK 19(13Q32.3) MUTATED	26	13	14	10
AMP PEAK 19(13Q32.3) WILD-TYPE	66	74	105	32

Figure S79. Get High-res Image Gene #19: 'amp_13q32.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_13q32.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0183 (Fisher's exact test), Q value = 0.038

Table S80. Gene #19: 'amp_13q32.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
AMP PEAK 19(13Q32.3) MUTATED	19	13	17	10	4
AMP PEAK 19(13Q32.3) WILD-TYPE	48	73	82	25	49

Figure S80. Get High-res Image Gene #19: '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 = 9.5e-05

Table S81. Gene #20: 'amp_13q33.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
AMP PEAK 20(13Q33.3) MUTATED	14	44	9
AMP PEAK 20(13Q33.3) WILD-TYPE	95	80	128

Figure S81. Get High-res Image Gene #20: 'amp_13q33.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q33.3' versus 'METHLYATION_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.041

Table S82. Gene #20: 'amp_13q33.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
AMP PEAK 20(13Q33.3) MUTATED	9	29	29
AMP PEAK 20(13Q33.3) WILD-TYPE	79	138	86

Figure S82. Get High-res Image Gene #20: 'amp_13q33.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q33.3' versus 'MRNASEQ_CNMF'

P value = 0.00436 (Fisher's exact test), Q value = 0.012

Table S83. Gene #20: 'amp_13q33.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
AMP PEAK 20(13Q33.3) MUTATED	13	12	23	8	10
AMP PEAK 20(13Q33.3) WILD-TYPE	48	85	45	61	59

Figure S83. Get High-res Image Gene #20: 'amp_13q33.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_13q33.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0491 (Fisher's exact test), Q value = 0.085

Table S84. Gene #20: 'amp_13q33.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
AMP PEAK 20(13Q33.3) MUTATED	18	12	18	10	5
AMP PEAK 20(13Q33.3) WILD-TYPE	49	74	81	25	48

Figure S84. Get High-res Image Gene #20: 'amp_13q33.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_15q26.3' versus 'CN_CNMF'

P value = 0.0258 (Fisher's exact test), Q value = 0.051

Table S85. Gene #21: 'amp_15q26.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
AMP PEAK 21(15Q26.3) MUTATED	12	27	15
AMP PEAK 21(15Q26.3) WILD-TYPE	97	97	122

Figure S85. Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CNMF'

P value = 0.0405 (Fisher's exact test), Q value = 0.073

Table S86. Gene #21: 'amp_15q26.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
AMP PEAK 21(15Q26.3) MUTATED	8	16	17	7	5
AMP PEAK 21(15Q26.3) WILD-TYPE	53	81	51	62	64

Figure S86. Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0389 (Fisher's exact test), Q value = 0.071

Table S87. Gene #21: '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 21(15Q26.3) MUTATED	9	7	17	18	2
AMP PEAK 21(15Q26.3) WILD-TYPE	45	49	97	66	54

Figure S87. Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_17p11.2' versus 'METHLYATION_CNMF'

P value = 0.0209 (Fisher's exact test), Q value = 0.043

Table S88. Gene #22: 'amp_17p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
AMP PEAK 22(17P11.2) MUTATED	4	23	19
AMP PEAK 22(17P11.2) WILD-TYPE	84	144	96

Figure S88. Get High-res Image Gene #22: 'amp_17p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17p11.2' versus 'MIRSEQ_CNMF'

P value = 0.0253 (Fisher's exact test), Q value = 0.051

Table S89. Gene #22: 'amp_17p11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	127	49	124
AMP PEAK 22(17P11.2) MUTATED	6	25	6	9
AMP PEAK 22(17P11.2) WILD-TYPE	59	102	43	115

Figure S89. Get High-res Image Gene #22: 'amp_17p11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_17q25.3' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00022

Table S90. Gene #23: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
AMP PEAK 23(17Q25.3) MUTATED	35	70	40
AMP PEAK 23(17Q25.3) WILD-TYPE	74	54	97

Figure S90. Get High-res Image Gene #23: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q25.3' versus 'METHLYATION_CNMF'

P value = 0.021 (Fisher's exact test), Q value = 0.043

Table S91. Gene #23: 'amp_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
AMP PEAK 23(17Q25.3) MUTATED	25	77	43
AMP PEAK 23(17Q25.3) WILD-TYPE	63	90	72

Figure S91. Get High-res Image Gene #23: 'amp_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q25.3' versus 'MRNASEQ_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.0039

Table S92. Gene #23: 'amp_17q25.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
AMP PEAK 23(17Q25.3) MUTATED	33	40	22	15	32
AMP PEAK 23(17Q25.3) WILD-TYPE	28	57	46	54	37

Figure S92. Get High-res Image Gene #23: 'amp_17q25.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_17q25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.024

Table S93. Gene #23: '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 23(17Q25.3) MUTATED	28	12	49	29	24
AMP PEAK 23(17Q25.3) WILD-TYPE	26	44	65	55	32

Figure S93. Get High-res Image Gene #23: 'amp_17q25.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_17q25.3' versus 'MIRSEQ_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.0038

Table S94. Gene #23: 'amp_17q25.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	127	49	124
AMP PEAK 23(17Q25.3) MUTATED	29	65	15	35
AMP PEAK 23(17Q25.3) WILD-TYPE	36	62	34	89

Figure S94. Get High-res Image Gene #23: 'amp_17q25.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_17q25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0014 (Fisher's exact test), Q value = 0.0049

Table S95. Gene #23: '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 23(17Q25.3) MUTATED	26	40	24	32	22
AMP PEAK 23(17Q25.3) WILD-TYPE	18	55	32	90	26

Figure S95. Get High-res Image Gene #23: 'amp_17q25.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_17q25.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0255 (Fisher's exact test), Q value = 0.051

Table S96. Gene #23: 'amp_17q25.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
AMP PEAK 23(17Q25.3) MUTATED	46	26	51	13
AMP PEAK 23(17Q25.3) WILD-TYPE	46	61	68	29

Figure S96. Get High-res Image Gene #23: 'amp_17q25.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_17q25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.015 (Fisher's exact test), Q value = 0.032

Table S97. Gene #23: 'amp_17q25.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
AMP PEAK 23(17Q25.3) MUTATED	32	37	26	18	23
AMP PEAK 23(17Q25.3) WILD-TYPE	35	49	73	17	30

Figure S97. Get High-res Image Gene #23: 'amp_17q25.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.12' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00089

Table S98. Gene #24: 'amp_19p13.12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
AMP PEAK 24(19P13.12) MUTATED	14	19	36
AMP PEAK 24(19P13.12) WILD-TYPE	74	148	79

Figure S98. Get High-res Image Gene #24: 'amp_19p13.12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19p13.12' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00047

Table S99. Gene #24: 'amp_19p13.12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
AMP PEAK 24(19P13.12) MUTATED	12	11	20	21	4
AMP PEAK 24(19P13.12) WILD-TYPE	49	86	48	48	65

Figure S99. Get High-res Image Gene #24: 'amp_19p13.12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_19p13.12' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S100. Gene #24: '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 24(19P13.12) MUTATED	16	13	12	23	4
AMP PEAK 24(19P13.12) WILD-TYPE	38	43	102	61	52

Figure S100. Get High-res Image Gene #24: 'amp_19p13.12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.12' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00027

Table S101. Gene #24: 'amp_19p13.12' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	127	49	124
AMP PEAK 24(19P13.12) MUTATED	7	13	9	39
AMP PEAK 24(19P13.12) WILD-TYPE	58	114	40	85

Figure S101. Get High-res Image Gene #24: 'amp_19p13.12' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_19p13.12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00246 (Fisher's exact test), Q value = 0.0075

Table S102. Gene #24: '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 24(19P13.12) MUTATED	3	20	14	29	2
AMP PEAK 24(19P13.12) WILD-TYPE	41	75	42	93	46

Figure S102. Get High-res Image Gene #24: 'amp_19p13.12' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_19p13.12' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0024

Table S103. Gene #24: 'amp_19p13.12' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
AMP PEAK 24(19P13.12) MUTATED	23	23	9	9
AMP PEAK 24(19P13.12) WILD-TYPE	69	64	110	33

Figure S103. Get High-res Image Gene #24: '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 = 0.0046

Table S104. Gene #24: 'amp_19p13.12' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
AMP PEAK 24(19P13.12) MUTATED	17	15	27	2	3
AMP PEAK 24(19P13.12) WILD-TYPE	50	71	72	33	50

Figure S104. Get High-res Image Gene #24: 'amp_19p13.12' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 0.00239 (Fisher's exact test), Q value = 0.0074

Table S105. Gene #25: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
AMP PEAK 25(19Q12) MUTATED	16	25	37
AMP PEAK 25(19Q12) WILD-TYPE	72	142	78

Figure S105. Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 0.00154 (Fisher's exact test), Q value = 0.0052

Table S106. Gene #25: 'amp_19q12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
AMP PEAK 25(19Q12) MUTATED	13	17	21	21	5
AMP PEAK 25(19Q12) WILD-TYPE	48	80	47	48	64

Figure S106. Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00138 (Fisher's exact test), Q value = 0.0049

Table S107. Gene #25: 'amp_19q12' 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(19Q12) MUTATED	14	16	17	26	4
AMP PEAK 25(19Q12) WILD-TYPE	40	40	97	58	52

Figure S107. Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0041

Table S108. Gene #25: 'amp_19q12' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	127	49	124
AMP PEAK 25(19Q12) MUTATED	14	14	10	39
AMP PEAK 25(19Q12) WILD-TYPE	51	113	39	85

Figure S108. Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0111 (Fisher's exact test), Q value = 0.026

Table S109. Gene #25: 'amp_19q12' 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(19Q12) MUTATED	10	19	14	32	2
AMP PEAK 25(19Q12) WILD-TYPE	34	76	42	90	46

Figure S109. Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0013

Table S110. Gene #25: 'amp_19q12' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
AMP PEAK 25(19Q12) MUTATED	24	27	11	10
AMP PEAK 25(19Q12) WILD-TYPE	68	60	108	32

Figure S110. Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.002 (Fisher's exact test), Q value = 0.0064

Table S111. Gene #25: 'amp_19q12' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
AMP PEAK 25(19Q12) MUTATED	16	17	29	8	2
AMP PEAK 25(19Q12) WILD-TYPE	51	69	70	27	51

Figure S111. Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q13.11' versus 'CN_CNMF'

P value = 0.0299 (Fisher's exact test), Q value = 0.058

Table S112. Gene #26: 'amp_19q13.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
AMP PEAK 26(19Q13.11) MUTATED	23	41	27
AMP PEAK 26(19Q13.11) WILD-TYPE	86	83	110

Figure S112. Get High-res Image Gene #26: 'amp_19q13.11' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q13.11' versus 'MRNASEQ_CNMF'

P value = 0.00099 (Fisher's exact test), Q value = 0.0037

Table S113. Gene #26: 'amp_19q13.11' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
AMP PEAK 26(19Q13.11) MUTATED	20	20	23	21	6
AMP PEAK 26(19Q13.11) WILD-TYPE	41	77	45	48	63

Figure S113. Get High-res Image Gene #26: 'amp_19q13.11' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_19q13.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0024

Table S114. Gene #26: '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 26(19Q13.11) MUTATED	16	17	21	31	5
AMP PEAK 26(19Q13.11) WILD-TYPE	38	39	93	53	51

Figure S114. Get High-res Image Gene #26: 'amp_19q13.11' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_19q13.11' versus 'MIRSEQ_CNMF'

P value = 0.00701 (Fisher's exact test), Q value = 0.018

Table S115. Gene #26: 'amp_19q13.11' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	127	49	124
AMP PEAK 26(19Q13.11) MUTATED	16	19	14	41
AMP PEAK 26(19Q13.11) WILD-TYPE	49	108	35	83

Figure S115. Get High-res Image Gene #26: 'amp_19q13.11' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_19q13.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00178 (Fisher's exact test), Q value = 0.0058

Table S116. Gene #26: '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 26(19Q13.11) MUTATED	14	23	18	33	2
AMP PEAK 26(19Q13.11) WILD-TYPE	30	72	38	89	46

Figure S116. Get High-res Image Gene #26: 'amp_19q13.11' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_19q13.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00022

Table S117. Gene #26: 'amp_19q13.11' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
AMP PEAK 26(19Q13.11) MUTATED	32	27	11	15
AMP PEAK 26(19Q13.11) WILD-TYPE	60	60	108	27

Figure S117. Get High-res Image Gene #26: 'amp_19q13.11' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_19q13.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.0019

Table S118. Gene #26: 'amp_19q13.11' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
AMP PEAK 26(19Q13.11) MUTATED	21	22	29	11	2
AMP PEAK 26(19Q13.11) WILD-TYPE	46	64	70	24	51

Figure S118. Get High-res Image Gene #26: '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 = 9.5e-05

Table S119. Gene #27: 'amp_20q13.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
AMP PEAK 27(20Q13.13) MUTATED	34	65	25
AMP PEAK 27(20Q13.13) WILD-TYPE	75	59	112

Figure S119. Get High-res Image Gene #27: 'amp_20q13.13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.13' versus 'MRNASEQ_CNMF'

P value = 0.0311 (Fisher's exact test), Q value = 0.059

Table S120. Gene #27: 'amp_20q13.13' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
AMP PEAK 27(20Q13.13) MUTATED	23	33	31	22	14
AMP PEAK 27(20Q13.13) WILD-TYPE	38	64	37	47	55

Figure S120. Get High-res Image Gene #27: 'amp_20q13.13' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_20q13.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0016

Table S121. Gene #27: '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 27(20Q13.13) MUTATED	19	19	37	41	7
AMP PEAK 27(20Q13.13) WILD-TYPE	35	37	77	43	49

Figure S121. Get High-res Image Gene #27: 'amp_20q13.13' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0118 (Fisher's exact test), Q value = 0.027

Table S122. Gene #27: '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 27(20Q13.13) MUTATED	21	29	24	41	8
AMP PEAK 27(20Q13.13) WILD-TYPE	23	66	32	81	40

Figure S122. Get High-res Image Gene #27: 'amp_20q13.13' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S123. Gene #27: 'amp_20q13.13' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
AMP PEAK 27(20Q13.13) MUTATED	41	27	23	25
AMP PEAK 27(20Q13.13) WILD-TYPE	51	60	96	17

Figure S123. Get High-res Image Gene #27: 'amp_20q13.13' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S124. Gene #28: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
AMP PEAK 28(20Q13.33) MUTATED	35	66	27
AMP PEAK 28(20Q13.33) WILD-TYPE	74	58	110

Figure S124. Get High-res Image Gene #28: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CNMF'

P value = 0.00713 (Fisher's exact test), Q value = 0.018

Table S125. Gene #28: 'amp_20q13.33' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
AMP PEAK 28(20Q13.33) MUTATED	22	34	35	21	15
AMP PEAK 28(20Q13.33) WILD-TYPE	39	63	33	48	54

Figure S125. Get High-res Image Gene #28: '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 = 0.00037

Table S126. Gene #28: '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 28(20Q13.33) MUTATED	21	17	39	43	7
AMP PEAK 28(20Q13.33) WILD-TYPE	33	39	75	41	49

Figure S126. Get High-res Image Gene #28: 'amp_20q13.33' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S127. Gene #28: 'amp_20q13.33' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
AMP PEAK 28(20Q13.33) MUTATED	42	27	26	25
AMP PEAK 28(20Q13.33) WILD-TYPE	50	60	93	17

Figure S127. Get High-res Image Gene #28: 'amp_20q13.33' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_xq28' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00052

Table S128. Gene #29: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
AMP PEAK 29(XQ28) MUTATED	41	25	19
AMP PEAK 29(XQ28) WILD-TYPE	68	99	118

Figure S128. Get High-res Image Gene #29: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq28' versus 'METHLYATION_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 0.057

Table S129. Gene #29: 'amp_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
AMP PEAK 29(XQ28) MUTATED	12	47	26
AMP PEAK 29(XQ28) WILD-TYPE	76	120	89

Figure S129. Get High-res Image Gene #29: 'amp_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xq28' versus 'MRNASEQ_CNMF'

P value = 0.0409 (Fisher's exact test), Q value = 0.073

Table S130. Gene #29: 'amp_xq28' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
AMP PEAK 29(XQ28) MUTATED	12	25	11	12	25
AMP PEAK 29(XQ28) WILD-TYPE	49	72	57	57	44

Figure S130. Get High-res Image Gene #29: 'amp_xq28' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_xq28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0161 (Fisher's exact test), Q value = 0.034

Table S131. Gene #29: '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 29(XQ28) MUTATED	12	11	30	11	21
AMP PEAK 29(XQ28) WILD-TYPE	42	45	84	73	35

Figure S131. Get High-res Image Gene #29: 'amp_xq28' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_CNMF'

P value = 0.00924 (Fisher's exact test), Q value = 0.022

Table S132. Gene #29: 'amp_xq28' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	127	49	124
AMP PEAK 29(XQ28) MUTATED	10	42	7	25
AMP PEAK 29(XQ28) WILD-TYPE	55	85	42	99

Figure S132. Get High-res Image Gene #29: 'amp_xq28' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_xq28' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00492 (Fisher's exact test), Q value = 0.013

Table S133. Gene #29: '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 29(XQ28) MUTATED	5	24	14	21	20
AMP PEAK 29(XQ28) WILD-TYPE	39	71	42	101	28

Figure S133. Get High-res Image Gene #29: 'amp_xq28' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0473 (Fisher's exact test), Q value = 0.082

Table S134. Gene #29: 'amp_xq28' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
AMP PEAK 29(XQ28) MUTATED	21	15	36	5
AMP PEAK 29(XQ28) WILD-TYPE	71	72	83	37

Figure S134. Get High-res Image Gene #29: '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 S135. Gene #29: 'amp_xq28' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
AMP PEAK 29(XQ28) MUTATED	16	20	16	2	23
AMP PEAK 29(XQ28) WILD-TYPE	51	66	83	33	30

Figure S135. Get High-res Image Gene #29: 'amp_xq28' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.31' versus 'CN_CNMF'

P value = 0.00149 (Fisher's exact test), Q value = 0.0051

Table S136. Gene #30: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 1(1P36.31) MUTATED	47	69	46
DEL PEAK 1(1P36.31) WILD-TYPE	62	55	91

Figure S136. Get High-res Image Gene #30: '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 = 9.5e-05

Table S137. Gene #30: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
DEL PEAK 1(1P36.31) MUTATED	25	64	73
DEL PEAK 1(1P36.31) WILD-TYPE	63	103	42

Figure S137. Get High-res Image Gene #30: '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 = 9.5e-05

Table S138. Gene #30: 'del_1p36.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
DEL PEAK 1(1P36.31) MUTATED	17	35	57	31	19
DEL PEAK 1(1P36.31) WILD-TYPE	44	62	11	38	50

Figure S138. Get High-res Image Gene #30: 'del_1p36.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_1p36.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S139. Gene #30: '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 S139. Get High-res Image Gene #30: 'del_1p36.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00127 (Fisher's exact test), Q value = 0.0046

Table S140. Gene #30: '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 S140. Get High-res Image Gene #30: 'del_1p36.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.028

Table S141. Gene #30: 'del_1p36.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
DEL PEAK 1(1P36.31) MUTATED	48	40	39	23
DEL PEAK 1(1P36.31) WILD-TYPE	44	47	80	19

Figure S141. Get High-res Image Gene #30: 'del_1p36.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_1p36.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00971 (Fisher's exact test), Q value = 0.023

Table S142. Gene #30: 'del_1p36.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
DEL PEAK 1(1P36.31) MUTATED	31	36	56	12	15
DEL PEAK 1(1P36.31) WILD-TYPE	36	50	43	23	38

Figure S142. Get High-res Image Gene #30: 'del_1p36.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.11' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00027

Table S143. Gene #31: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 2(1P36.11) MUTATED	40	66	36
DEL PEAK 2(1P36.11) WILD-TYPE	69	58	101

Figure S143. Get High-res Image Gene #31: '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 = 9.5e-05

Table S144. Gene #31: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
DEL PEAK 2(1P36.11) MUTATED	22	49	71
DEL PEAK 2(1P36.11) WILD-TYPE	66	118	44

Figure S144. Get High-res Image Gene #31: '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 = 9.5e-05

Table S145. Gene #31: 'del_1p36.11' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
DEL PEAK 2(1P36.11) MUTATED	16	26	56	24	18
DEL PEAK 2(1P36.11) WILD-TYPE	45	71	12	45	51

Figure S145. Get High-res Image Gene #31: '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 = 9.5e-05

Table S146. Gene #31: '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 S146. Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CNMF'

P value = 0.00167 (Fisher's exact test), Q value = 0.0056

Table S147. Gene #31: 'del_1p36.11' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	127	49	124
DEL PEAK 2(1P36.11) MUTATED	13	46	21	59
DEL PEAK 2(1P36.11) WILD-TYPE	52	81	28	65

Figure S147. Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_1p36.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00031

Table S148. Gene #31: '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 S148. Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0011

Table S149. Gene #31: 'del_1p36.11' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
DEL PEAK 2(1P36.11) MUTATED	46	37	28	21
DEL PEAK 2(1P36.11) WILD-TYPE	46	50	91	21

Figure S149. Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.0016

Table S150. Gene #31: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
DEL PEAK 2(1P36.11) MUTATED	28	27	55	8	14
DEL PEAK 2(1P36.11) WILD-TYPE	39	59	44	27	39

Figure S150. Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00254 (Fisher's exact test), Q value = 0.0077

Table S151. Gene #32: 'del_2q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
DEL PEAK 3(2Q22.1) MUTATED	15	16	12	7	2
DEL PEAK 3(2Q22.1) WILD-TYPE	46	81	56	62	67

Figure S151. Get High-res Image Gene #32: 'del_2q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00027

Table S152. Gene #33: 'del_2q37.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
DEL PEAK 4(2Q37.3) MUTATED	18	23	12	8	1
DEL PEAK 4(2Q37.3) WILD-TYPE	43	74	56	61	68

Figure S152. Get High-res Image Gene #33: 'del_2q37.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S153. Gene #33: '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 S153. Get High-res Image Gene #33: 'del_2q37.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 0.04 (Fisher's exact test), Q value = 0.072

Table S154. Gene #33: 'del_2q37.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	127	49	124
DEL PEAK 4(2Q37.3) MUTATED	15	26	3	17
DEL PEAK 4(2Q37.3) WILD-TYPE	50	101	46	107

Figure S154. Get High-res Image Gene #33: 'del_2q37.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0098 (Fisher's exact test), Q value = 0.023

Table S155. Gene #33: '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 S155. Get High-res Image Gene #33: 'del_2q37.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00151 (Fisher's exact test), Q value = 0.0052

Table S156. Gene #33: 'del_2q37.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
DEL PEAK 4(2Q37.3) MUTATED	20	14	10	10	4
DEL PEAK 4(2Q37.3) WILD-TYPE	47	72	89	25	49

Figure S156. Get High-res Image Gene #33: 'del_2q37.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p13' versus 'CN_CNMF'

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

Table S157. Gene #34: 'del_3p13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 5(3P13) MUTATED	14	36	23
DEL PEAK 5(3P13) WILD-TYPE	95	88	114

Figure S157. Get High-res Image Gene #34: 'del_3p13' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p13' versus 'METHLYATION_CNMF'

P value = 0.0458 (Fisher's exact test), Q value = 0.08

Table S158. Gene #34: 'del_3p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
DEL PEAK 5(3P13) MUTATED	17	25	31
DEL PEAK 5(3P13) WILD-TYPE	71	142	84

Figure S158. Get High-res Image Gene #34: 'del_3p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p13' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00042

Table S159. Gene #34: 'del_3p13' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
DEL PEAK 5(3P13) MUTATED	14	11	24	18	5
DEL PEAK 5(3P13) WILD-TYPE	47	86	44	51	64

Figure S159. Get High-res Image Gene #34: 'del_3p13' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S160. Gene #34: '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 S160. Get High-res Image Gene #34: 'del_3p13' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p13' versus 'MIRSEQ_CNMF'

P value = 0.00167 (Fisher's exact test), Q value = 0.0056

Table S161. Gene #34: 'del_3p13' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	127	49	124
DEL PEAK 5(3P13) MUTATED	5	20	9	37
DEL PEAK 5(3P13) WILD-TYPE	60	107	40	87

Figure S161. Get High-res Image Gene #34: 'del_3p13' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0339 (Fisher's exact test), Q value = 0.064

Table S162. Gene #34: '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 S162. Get High-res Image Gene #34: 'del_3p13' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0013

Table S163. Gene #34: 'del_3p13' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
DEL PEAK 5(3P13) MUTATED	29	21	11	6
DEL PEAK 5(3P13) WILD-TYPE	63	66	108	36

Figure S163. Get High-res Image Gene #34: 'del_3p13' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00202 (Fisher's exact test), Q value = 0.0064

Table S164. Gene #34: 'del_3p13' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
DEL PEAK 5(3P13) MUTATED	20	13	27	3	4
DEL PEAK 5(3P13) WILD-TYPE	47	73	72	32	49

Figure S164. Get High-res Image Gene #34: 'del_3p13' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4p16.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S165. Gene #35: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 6(4P16.3) MUTATED	21	48	16
DEL PEAK 6(4P16.3) WILD-TYPE	88	76	121

Figure S165. Get High-res Image Gene #35: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0273 (Fisher's exact test), Q value = 0.054

Table S166. Gene #35: '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 S166. Get High-res Image Gene #35: 'del_4p16.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0453 (Fisher's exact test), Q value = 0.08

Table S167. Gene #35: 'del_4p16.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
DEL PEAK 6(4P16.3) MUTATED	30	20	19	9
DEL PEAK 6(4P16.3) WILD-TYPE	62	67	100	33

Figure S167. Get High-res Image Gene #35: 'del_4p16.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0068 (Fisher's exact test), Q value = 0.018

Table S168. Gene #35: 'del_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
DEL PEAK 6(4P16.3) MUTATED	25	20	23	4	6
DEL PEAK 6(4P16.3) WILD-TYPE	42	66	76	31	47

Figure S168. Get High-res Image Gene #35: '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 = 9.5e-05

Table S169. Gene #36: 'del_4q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 7(4Q21.3) MUTATED	38	93	40
DEL PEAK 7(4Q21.3) WILD-TYPE	71	31	97

Figure S169. Get High-res Image Gene #36: 'del_4q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q21.3' versus 'METHLYATION_CNMF'

P value = 0.00281 (Fisher's exact test), Q value = 0.0083

Table S170. Gene #36: 'del_4q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
DEL PEAK 7(4Q21.3) MUTATED	33	70	68
DEL PEAK 7(4Q21.3) WILD-TYPE	55	97	47

Figure S170. Get High-res Image Gene #36: '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 = 9.5e-05

Table S171. Gene #36: 'del_4q21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
DEL PEAK 7(4Q21.3) MUTATED	37	44	51	21	16
DEL PEAK 7(4Q21.3) WILD-TYPE	24	53	17	48	53

Figure S171. Get High-res Image Gene #36: 'del_4q21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_4q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0013

Table S172. Gene #36: '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 S172. Get High-res Image Gene #36: 'del_4q21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_4q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00174 (Fisher's exact test), Q value = 0.0057

Table S173. Gene #36: '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 S173. Get High-res Image Gene #36: 'del_4q21.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_4q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S174. Gene #36: 'del_4q21.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
DEL PEAK 7(4Q21.3) MUTATED	56	38	40	29
DEL PEAK 7(4Q21.3) WILD-TYPE	36	49	79	13

Figure S174. Get High-res Image Gene #36: 'del_4q21.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_4q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S175. Gene #36: 'del_4q21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
DEL PEAK 7(4Q21.3) MUTATED	41	43	52	15	12
DEL PEAK 7(4Q21.3) WILD-TYPE	26	43	47	20	41

Figure S175. Get High-res Image Gene #36: 'del_4q21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S176. Gene #37: 'del_4q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 8(4Q22.3) MUTATED	39	94	39
DEL PEAK 8(4Q22.3) WILD-TYPE	70	30	98

Figure S176. Get High-res Image Gene #37: 'del_4q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q22.3' versus 'METHLYATION_CNMF'

P value = 0.00341 (Fisher's exact test), Q value = 0.0099

Table S177. Gene #37: 'del_4q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
DEL PEAK 8(4Q22.3) MUTATED	33	71	68
DEL PEAK 8(4Q22.3) WILD-TYPE	55	96	47

Figure S177. Get High-res Image Gene #37: 'del_4q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S178. Gene #37: 'del_4q22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
DEL PEAK 8(4Q22.3) MUTATED	36	44	51	21	17
DEL PEAK 8(4Q22.3) WILD-TYPE	25	53	17	48	52

Figure S178. Get High-res Image Gene #37: 'del_4q22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_4q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.0011

Table S179. Gene #37: 'del_4q22.3' 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 8(4Q22.3) MUTATED	28	22	54	52	13
DEL PEAK 8(4Q22.3) WILD-TYPE	26	34	60	32	43

Figure S179. Get High-res Image Gene #37: 'del_4q22.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00121 (Fisher's exact test), Q value = 0.0044

Table S180. Gene #37: 'del_4q22.3' 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 8(4Q22.3) MUTATED	22	43	32	64	10
DEL PEAK 8(4Q22.3) WILD-TYPE	22	52	24	58	38

Figure S180. Get High-res Image Gene #37: 'del_4q22.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_4q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 6e-04

Table S181. Gene #37: 'del_4q22.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
DEL PEAK 8(4Q22.3) MUTATED	55	38	42	29
DEL PEAK 8(4Q22.3) WILD-TYPE	37	49	77	13

Figure S181. Get High-res Image Gene #37: 'del_4q22.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_4q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.0021

Table S182. Gene #37: 'del_4q22.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
DEL PEAK 8(4Q22.3) MUTATED	41	42	52	17	12
DEL PEAK 8(4Q22.3) WILD-TYPE	26	44	47	18	41

Figure S182. Get High-res Image Gene #37: 'del_4q22.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q35.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S183. Gene #38: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 9(4Q35.1) MUTATED	43	94	35
DEL PEAK 9(4Q35.1) WILD-TYPE	66	30	102

Figure S183. Get High-res Image Gene #38: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q35.1' versus 'METHLYATION_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0013

Table S184. Gene #38: 'del_4q35.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
DEL PEAK 9(4Q35.1) MUTATED	31	70	71
DEL PEAK 9(4Q35.1) WILD-TYPE	57	97	44

Figure S184. Get High-res Image Gene #38: '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 = 9.5e-05

Table S185. Gene #38: 'del_4q35.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
DEL PEAK 9(4Q35.1) MUTATED	38	39	49	22	21
DEL PEAK 9(4Q35.1) WILD-TYPE	23	58	19	47	48

Figure S185. Get High-res Image Gene #38: 'del_4q35.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_4q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00067 (Fisher's exact test), Q value = 0.0026

Table S186. Gene #38: '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 S186. Get High-res Image Gene #38: 'del_4q35.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00595 (Fisher's exact test), Q value = 0.016

Table S187. Gene #38: '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 S187. Get High-res Image Gene #38: 'del_4q35.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0013

Table S188. Gene #38: 'del_4q35.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
DEL PEAK 9(4Q35.1) MUTATED	53	40	40	28
DEL PEAK 9(4Q35.1) WILD-TYPE	39	47	79	14

Figure S188. Get High-res Image Gene #38: 'del_4q35.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_4q35.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00453 (Fisher's exact test), Q value = 0.012

Table S189. Gene #38: 'del_4q35.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
DEL PEAK 9(4Q35.1) MUTATED	38	41	52	17	13
DEL PEAK 9(4Q35.1) WILD-TYPE	29	45	47	18	40

Figure S189. Get High-res Image Gene #38: 'del_4q35.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q27' versus 'CN_CNMF'

P value = 0.00878 (Fisher's exact test), Q value = 0.021

Table S190. Gene #39: 'del_6q27' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 10(6Q27) MUTATED	39	58	39
DEL PEAK 10(6Q27) WILD-TYPE	70	66	98

Figure S190. Get High-res Image Gene #39: 'del_6q27' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q27' versus 'METHLYATION_CNMF'

P value = 0.0272 (Fisher's exact test), Q value = 0.053

Table S191. Gene #39: 'del_6q27' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
DEL PEAK 10(6Q27) MUTATED	23	72	41
DEL PEAK 10(6Q27) WILD-TYPE	65	95	74

Figure S191. Get High-res Image Gene #39: 'del_6q27' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q27' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0397 (Fisher's exact test), Q value = 0.072

Table S192. Gene #39: '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 S192. Get High-res Image Gene #39: 'del_6q27' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S193. Gene #40: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 11(8P23.2) MUTATED	103	86	58
DEL PEAK 11(8P23.2) WILD-TYPE	6	38	79

Figure S193. Get High-res Image Gene #40: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 0.0443 (Fisher's exact test), Q value = 0.078

Table S194. Gene #40: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
DEL PEAK 11(8P23.2) MUTATED	49	118	80
DEL PEAK 11(8P23.2) WILD-TYPE	39	49	35

Figure S194. Get High-res Image Gene #40: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S195. Gene #41: 'del_8p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 12(8P12) MUTATED	100	86	56
DEL PEAK 12(8P12) WILD-TYPE	9	38	81

Figure S195. Get High-res Image Gene #41: 'del_8p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p12' versus 'METHLYATION_CNMF'

P value = 0.0239 (Fisher's exact test), Q value = 0.048

Table S196. Gene #41: 'del_8p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
DEL PEAK 12(8P12) MUTATED	48	110	84
DEL PEAK 12(8P12) WILD-TYPE	40	57	31

Figure S196. Get High-res Image Gene #41: 'del_8p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00022

Table S197. Gene #42: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 13(9P21.3) MUTATED	40	70	40
DEL PEAK 13(9P21.3) WILD-TYPE	69	54	97

Figure S197. Get High-res Image Gene #42: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 0.00787 (Fisher's exact test), Q value = 0.02

Table S198. Gene #42: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
DEL PEAK 13(9P21.3) MUTATED	29	61	60
DEL PEAK 13(9P21.3) WILD-TYPE	59	106	55

Figure S198. Get High-res Image Gene #42: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S199. Gene #42: 'del_9p21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
DEL PEAK 13(9P21.3) MUTATED	31	31	43	26	16
DEL PEAK 13(9P21.3) WILD-TYPE	30	66	25	43	53

Figure S199. Get High-res Image Gene #42: 'del_9p21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00199 (Fisher's exact test), Q value = 0.0064

Table S200. Gene #42: '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 13(9P21.3) MUTATED	28	20	38	46	15
DEL PEAK 13(9P21.3) WILD-TYPE	26	36	76	38	41

Figure S200. Get High-res Image Gene #42: 'del_9p21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00206 (Fisher's exact test), Q value = 0.0065

Table S201. Gene #42: '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 13(9P21.3) MUTATED	20	31	29	59	10
DEL PEAK 13(9P21.3) WILD-TYPE	24	64	27	63	38

Figure S201. Get High-res Image Gene #42: 'del_9p21.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.04

Table S202. Gene #42: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
DEL PEAK 13(9P21.3) MUTATED	42	36	39	25
DEL PEAK 13(9P21.3) WILD-TYPE	50	51	80	17

Figure S202. Get High-res Image Gene #42: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00773 (Fisher's exact test), Q value = 0.02

Table S203. Gene #42: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
DEL PEAK 13(9P21.3) MUTATED	37	29	47	15	14
DEL PEAK 13(9P21.3) WILD-TYPE	30	57	52	20	39

Figure S203. Get High-res Image Gene #42: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q31.3' versus 'CN_CNMF'

P value = 0.00199 (Fisher's exact test), Q value = 0.0064

Table S204. Gene #43: 'del_9q31.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 14(9Q31.3) MUTATED	29	55	35
DEL PEAK 14(9Q31.3) WILD-TYPE	80	69	102

Figure S204. Get High-res Image Gene #43: 'del_9q31.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q31.3' versus 'METHLYATION_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.031

Table S205. Gene #43: 'del_9q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
DEL PEAK 14(9Q31.3) MUTATED	22	48	49
DEL PEAK 14(9Q31.3) WILD-TYPE	66	119	66

Figure S205. Get High-res Image Gene #43: 'del_9q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9q31.3' versus 'MRNASEQ_CNMF'

P value = 0.00284 (Fisher's exact test), Q value = 0.0084

Table S206. Gene #43: 'del_9q31.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
DEL PEAK 14(9Q31.3) MUTATED	25	34	28	21	10
DEL PEAK 14(9Q31.3) WILD-TYPE	36	63	40	48	59

Figure S206. Get High-res Image Gene #43: '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 S207. Gene #43: '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 14(9Q31.3) MUTATED	21	16	38	37	6
DEL PEAK 14(9Q31.3) WILD-TYPE	33	40	76	47	50

Figure S207. Get High-res Image Gene #43: 'del_9q31.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_9q31.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00661 (Fisher's exact test), Q value = 0.018

Table S208. Gene #43: '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 14(9Q31.3) MUTATED	17	30	21	43	5
DEL PEAK 14(9Q31.3) WILD-TYPE	27	65	35	79	43

Figure S208. Get High-res Image Gene #43: 'del_9q31.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_9q31.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.001

Table S209. Gene #43: 'del_9q31.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
DEL PEAK 14(9Q31.3) MUTATED	28	26	36	16	5
DEL PEAK 14(9Q31.3) WILD-TYPE	39	60	63	19	48

Figure S209. Get High-res Image Gene #43: 'del_9q31.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 0.0306 (Fisher's exact test), Q value = 0.058

Table S210. Gene #44: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 15(10Q23.31) MUTATED	19	40	38
DEL PEAK 15(10Q23.31) WILD-TYPE	90	84	99

Figure S210. Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 0.0139 (Fisher's exact test), Q value = 0.031

Table S211. Gene #44: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
DEL PEAK 15(10Q23.31) MUTATED	28	50	19
DEL PEAK 15(10Q23.31) WILD-TYPE	60	117	96

Figure S211. Get High-res Image Gene #44: '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 = 9.5e-05

Table S212. Gene #44: 'del_10q23.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
DEL PEAK 15(10Q23.31) MUTATED	35	34	5	15	5
DEL PEAK 15(10Q23.31) WILD-TYPE	26	63	63	54	64

Figure S212. Get High-res Image Gene #44: '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 = 9.5e-05

Table S213. Gene #44: '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 15(10Q23.31) MUTATED	27	9	41	11	6
DEL PEAK 15(10Q23.31) WILD-TYPE	27	47	73	73	50

Figure S213. Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 0.0312 (Fisher's exact test), Q value = 0.059

Table S214. Gene #44: 'del_10q23.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	127	49	124
DEL PEAK 15(10Q23.31) MUTATED	25	35	7	30
DEL PEAK 15(10Q23.31) WILD-TYPE	40	92	42	94

Figure S214. Get High-res Image Gene #44: '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 = 9.5e-05

Table S215. Gene #44: '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 15(10Q23.31) MUTATED	15	41	13	25	3
DEL PEAK 15(10Q23.31) WILD-TYPE	29	54	43	97	45

Figure S215. Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0481 (Fisher's exact test), Q value = 0.083

Table S216. Gene #44: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
DEL PEAK 15(10Q23.31) MUTATED	35	22	30	7
DEL PEAK 15(10Q23.31) WILD-TYPE	57	65	89	35

Figure S216. Get High-res Image Gene #44: '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 = 9.5e-05

Table S217. Gene #44: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
DEL PEAK 15(10Q23.31) MUTATED	21	39	19	13	2
DEL PEAK 15(10Q23.31) WILD-TYPE	46	47	80	22	51

Figure S217. Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q26.13' versus 'CN_CNMF'

P value = 0.00831 (Fisher's exact test), Q value = 0.021

Table S218. Gene #45: 'del_10q26.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 16(10Q26.13) MUTATED	19	41	45
DEL PEAK 16(10Q26.13) WILD-TYPE	90	83	92

Figure S218. Get High-res Image Gene #45: 'del_10q26.13' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q26.13' versus 'METHLYATION_CNMF'

P value = 0.048 (Fisher's exact test), Q value = 0.083

Table S219. Gene #45: 'del_10q26.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
DEL PEAK 16(10Q26.13) MUTATED	32	49	24
DEL PEAK 16(10Q26.13) WILD-TYPE	56	118	91

Figure S219. Get High-res Image Gene #45: '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 = 9.5e-05

Table S220. Gene #45: 'del_10q26.13' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
DEL PEAK 16(10Q26.13) MUTATED	34	37	9	17	5
DEL PEAK 16(10Q26.13) WILD-TYPE	27	60	59	52	64

Figure S220. Get High-res Image Gene #45: '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 = 9.5e-05

Table S221. Gene #45: '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 16(10Q26.13) MUTATED	30	11	41	14	6
DEL PEAK 16(10Q26.13) WILD-TYPE	24	45	73	70	50

Figure S221. Get High-res Image Gene #45: 'del_10q26.13' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S222. Gene #45: '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 16(10Q26.13) MUTATED	14	45	12	31	3
DEL PEAK 16(10Q26.13) WILD-TYPE	30	50	44	91	45

Figure S222. Get High-res Image Gene #45: '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 = 9.5e-05

Table S223. Gene #45: 'del_10q26.13' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
DEL PEAK 16(10Q26.13) MUTATED	22	41	24	13	2
DEL PEAK 16(10Q26.13) WILD-TYPE	45	45	75	22	51

Figure S223. Get High-res Image Gene #45: 'del_10q26.13' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q14.1' versus 'CN_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.026

Table S224. Gene #46: 'del_11q14.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 17(11Q14.1) MUTATED	22	36	19
DEL PEAK 17(11Q14.1) WILD-TYPE	87	88	118

Figure S224. Get High-res Image Gene #46: 'del_11q14.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0016

Table S225. Gene #46: 'del_11q14.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
DEL PEAK 17(11Q14.1) MUTATED	33	12	16	10
DEL PEAK 17(11Q14.1) WILD-TYPE	59	75	103	32

Figure S225. Get High-res Image Gene #46: 'del_11q14.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_11q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0125 (Fisher's exact test), Q value = 0.028

Table S226. Gene #46: 'del_11q14.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
DEL PEAK 17(11Q14.1) MUTATED	23	21	15	6	6
DEL PEAK 17(11Q14.1) WILD-TYPE	44	65	84	29	47

Figure S226. Get High-res Image Gene #46: 'del_11q14.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q24.2' versus 'CN_CNMF'

P value = 0.00428 (Fisher's exact test), Q value = 0.012

Table S227. Gene #47: 'del_11q24.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 18(11Q24.2) MUTATED	24	45	26
DEL PEAK 18(11Q24.2) WILD-TYPE	85	79	111

Figure S227. Get High-res Image Gene #47: 'del_11q24.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q24.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.003

Table S228. Gene #47: 'del_11q24.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
DEL PEAK 18(11Q24.2) MUTATED	38	17	21	11
DEL PEAK 18(11Q24.2) WILD-TYPE	54	70	98	31

Figure S228. Get High-res Image Gene #47: 'del_11q24.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_11q24.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.0017

Table S229. Gene #47: 'del_11q24.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
DEL PEAK 18(11Q24.2) MUTATED	29	27	19	5	7
DEL PEAK 18(11Q24.2) WILD-TYPE	38	59	80	30	46

Figure S229. Get High-res Image Gene #47: 'del_11q24.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12p12.1' versus 'CN_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0019

Table S230. Gene #48: 'del_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 19(12P12.1) MUTATED	16	41	21
DEL PEAK 19(12P12.1) WILD-TYPE	93	83	116

Figure S230. Get High-res Image Gene #48: 'del_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p12.1' versus 'MRNASEQ_CNMF'

P value = 0.00211 (Fisher's exact test), Q value = 0.0066

Table S231. Gene #48: 'del_12p12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
DEL PEAK 19(12P12.1) MUTATED	24	24	10	10	10
DEL PEAK 19(12P12.1) WILD-TYPE	37	73	58	59	59

Figure S231. Get High-res Image Gene #48: 'del_12p12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_12p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0301 (Fisher's exact test), Q value = 0.058

Table S232. Gene #48: '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 19(12P12.1) MUTATED	14	27	8	21	6
DEL PEAK 19(12P12.1) WILD-TYPE	30	68	48	101	42

Figure S232. Get High-res Image Gene #48: 'del_12p12.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_12q24.33' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 6e-04

Table S233. Gene #49: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 20(12Q24.33) MUTATED	9	34	16
DEL PEAK 20(12Q24.33) WILD-TYPE	100	90	121

Figure S233. Get High-res Image Gene #49: '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 = 9.5e-05

Table S234. Gene #50: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 21(13Q14.2) MUTATED	35	92	52
DEL PEAK 21(13Q14.2) WILD-TYPE	74	32	85

Figure S234. Get High-res Image Gene #50: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0013

Table S235. Gene #50: 'del_13q14.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
DEL PEAK 21(13Q14.2) MUTATED	38	52	38	29	19
DEL PEAK 21(13Q14.2) WILD-TYPE	23	45	30	40	50

Figure S235. Get High-res Image Gene #50: '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 = 9.5e-05

Table S236. Gene #50: '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 21(13Q14.2) MUTATED	34	15	67	46	14
DEL PEAK 21(13Q14.2) WILD-TYPE	20	41	47	38	42

Figure S236. Get High-res Image Gene #50: 'del_13q14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 0.00271 (Fisher's exact test), Q value = 0.0081

Table S237. Gene #50: 'del_13q14.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	127	49	124
DEL PEAK 21(13Q14.2) MUTATED	41	49	19	68
DEL PEAK 21(13Q14.2) WILD-TYPE	24	78	30	56

Figure S237. Get High-res Image Gene #50: 'del_13q14.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00071 (Fisher's exact test), Q value = 0.0028

Table S238. Gene #50: '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 21(13Q14.2) MUTATED	28	53	26	59	11
DEL PEAK 21(13Q14.2) WILD-TYPE	16	42	30	63	37

Figure S238. Get High-res Image Gene #50: 'del_13q14.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00047

Table S239. Gene #50: 'del_13q14.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
DEL PEAK 21(13Q14.2) MUTATED	38	51	45	22	12
DEL PEAK 21(13Q14.2) WILD-TYPE	29	35	54	13	41

Figure S239. Get High-res Image Gene #50: '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 = 9.5e-05

Table S240. Gene #51: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 22(14Q23.3) MUTATED	21	78	32
DEL PEAK 22(14Q23.3) WILD-TYPE	88	46	105

Figure S240. Get High-res Image Gene #51: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q23.3' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00064

Table S241. Gene #51: 'del_14q23.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
DEL PEAK 22(14Q23.3) MUTATED	36	25	28	23	17
DEL PEAK 22(14Q23.3) WILD-TYPE	25	72	40	46	52

Figure S241. Get High-res Image Gene #51: 'del_14q23.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_14q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00027

Table S242. Gene #51: '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 22(14Q23.3) MUTATED	34	12	38	32	13
DEL PEAK 22(14Q23.3) WILD-TYPE	20	44	76	52	43

Figure S242. Get High-res Image Gene #51: 'del_14q23.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_14q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00665 (Fisher's exact test), Q value = 0.018

Table S243. Gene #51: 'del_14q23.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
DEL PEAK 22(14Q23.3) MUTATED	47	31	33	14
DEL PEAK 22(14Q23.3) WILD-TYPE	45	56	86	28

Figure S243. Get High-res Image Gene #51: '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 = 9.5e-05

Table S244. Gene #52: 'del_14q32.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 23(14Q32.33) MUTATED	20	77	35
DEL PEAK 23(14Q32.33) WILD-TYPE	89	47	102

Figure S244. Get High-res Image Gene #52: 'del_14q32.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.33' versus 'MRNASEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0012

Table S245. Gene #52: 'del_14q32.33' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
DEL PEAK 23(14Q32.33) MUTATED	35	25	28	25	17
DEL PEAK 23(14Q32.33) WILD-TYPE	26	72	40	44	52

Figure S245. Get High-res Image Gene #52: 'del_14q32.33' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_14q32.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00042

Table S246. Gene #52: '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 23(14Q32.33) MUTATED	33	12	36	35	14
DEL PEAK 23(14Q32.33) WILD-TYPE	21	44	78	49	42

Figure S246. Get High-res Image Gene #52: 'del_14q32.33' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.33' versus 'MIRSEQ_MATURE_CNMF'

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

Table S247. Gene #52: 'del_14q32.33' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
DEL PEAK 23(14Q32.33) MUTATED	43	35	31	16
DEL PEAK 23(14Q32.33) WILD-TYPE	49	52	88	26

Figure S247. Get High-res Image Gene #52: 'del_14q32.33' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_14q32.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0304 (Fisher's exact test), Q value = 0.058

Table S248. Gene #52: 'del_14q32.33' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
DEL PEAK 23(14Q32.33) MUTATED	31	25	39	17	13
DEL PEAK 23(14Q32.33) WILD-TYPE	36	61	60	18	40

Figure S248. Get High-res Image Gene #52: 'del_14q32.33' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q26.3' versus 'CN_CNMF'

P value = 0.0349 (Fisher's exact test), Q value = 0.065

Table S249. Gene #53: 'del_15q26.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 24(15Q26.3) MUTATED	17	36	26
DEL PEAK 24(15Q26.3) WILD-TYPE	92	88	111

Figure S249. Get High-res Image Gene #53: 'del_15q26.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q26.3' versus 'MRNASEQ_CNMF'

P value = 0.0045 (Fisher's exact test), Q value = 0.012

Table S250. Gene #53: 'del_15q26.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
DEL PEAK 24(15Q26.3) MUTATED	24	18	16	11	9
DEL PEAK 24(15Q26.3) WILD-TYPE	37	79	52	58	60

Figure S250. Get High-res Image Gene #53: 'del_15q26.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_15q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00839 (Fisher's exact test), Q value = 0.021

Table S251. Gene #53: '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 24(15Q26.3) MUTATED	21	6	22	19	10
DEL PEAK 24(15Q26.3) WILD-TYPE	33	50	92	65	46

Figure S251. Get High-res Image Gene #53: 'del_15q26.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_15q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00173 (Fisher's exact test), Q value = 0.0057

Table S252. Gene #53: 'del_15q26.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
DEL PEAK 24(15Q26.3) MUTATED	29	12	19	15
DEL PEAK 24(15Q26.3) WILD-TYPE	63	75	100	27

Figure S252. Get High-res Image Gene #53: '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 = 9.5e-05

Table S253. Gene #54: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 25(16Q23.1) MUTATED	45	78	39
DEL PEAK 25(16Q23.1) WILD-TYPE	64	46	98

Figure S253. Get High-res Image Gene #54: '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 = 9.5e-05

Table S254. Gene #54: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
DEL PEAK 25(16Q23.1) MUTATED	28	60	74
DEL PEAK 25(16Q23.1) WILD-TYPE	60	107	41

Figure S254. Get High-res Image Gene #54: '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 = 9.5e-05

Table S255. Gene #54: 'del_16q23.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
DEL PEAK 25(16Q23.1) MUTATED	32	42	58	18	10
DEL PEAK 25(16Q23.1) WILD-TYPE	29	55	10	51	59

Figure S255. Get High-res Image Gene #54: '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 = 9.5e-05

Table S256. Gene #54: '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 25(16Q23.1) MUTATED	25	18	52	57	8
DEL PEAK 25(16Q23.1) WILD-TYPE	29	38	62	27	48

Figure S256. Get High-res Image Gene #54: 'del_16q23.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S257. Gene #54: '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 25(16Q23.1) MUTATED	19	40	33	62	6
DEL PEAK 25(16Q23.1) WILD-TYPE	25	55	23	60	42

Figure S257. Get High-res Image Gene #54: 'del_16q23.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S258. Gene #54: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
DEL PEAK 25(16Q23.1) MUTATED	54	36	36	28
DEL PEAK 25(16Q23.1) WILD-TYPE	38	51	83	14

Figure S258. Get High-res Image Gene #54: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00027

Table S259. Gene #54: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
DEL PEAK 25(16Q23.1) MUTATED	42	37	50	15	10
DEL PEAK 25(16Q23.1) WILD-TYPE	25	49	49	20	43

Figure S259. Get High-res Image Gene #54: '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 = 9.5e-05

Table S260. Gene #55: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 26(17P13.1) MUTATED	46	105	75
DEL PEAK 26(17P13.1) WILD-TYPE	63	19	62

Figure S260. Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.1' versus 'METHLYATION_CNMF'

P value = 0.0214 (Fisher's exact test), Q value = 0.044

Table S261. Gene #55: 'del_17p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
DEL PEAK 26(17P13.1) MUTATED	48	115	63
DEL PEAK 26(17P13.1) WILD-TYPE	40	52	52

Figure S261. Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p13.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S262. Gene #55: 'del_17p13.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
DEL PEAK 26(17P13.1) MUTATED	49	69	36	34	33
DEL PEAK 26(17P13.1) WILD-TYPE	12	28	32	35	36

Figure S262. Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_17p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00056

Table S263. Gene #55: '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 26(17P13.1) MUTATED	40	28	85	42	26
DEL PEAK 26(17P13.1) WILD-TYPE	14	28	29	42	30

Figure S263. Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.1' versus 'MIRSEQ_CNMF'

P value = 0.00172 (Fisher's exact test), Q value = 0.0057

Table S264. Gene #55: 'del_17p13.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	127	49	124
DEL PEAK 26(17P13.1) MUTATED	53	76	27	68
DEL PEAK 26(17P13.1) WILD-TYPE	12	51	22	56

Figure S264. Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_17p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00031

Table S265. Gene #55: '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 26(17P13.1) MUTATED	38	67	30	66	23
DEL PEAK 26(17P13.1) WILD-TYPE	6	28	26	56	25

Figure S265. Get High-res Image Gene #55: '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 = 9.5e-05

Table S266. Gene #55: 'del_17p13.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
DEL PEAK 26(17P13.1) MUTATED	36	67	55	31	25
DEL PEAK 26(17P13.1) WILD-TYPE	31	19	44	4	28

Figure S266. Get High-res Image Gene #55: '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 = 9.5e-05

Table S267. Gene #56: 'del_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 27(17P11.2) MUTATED	40	90	65
DEL PEAK 27(17P11.2) WILD-TYPE	69	34	72

Figure S267. Get High-res Image Gene #56: 'del_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p11.2' versus 'MRNASEQ_CNMF'

P value = 0.00145 (Fisher's exact test), Q value = 0.005

Table S268. Gene #56: 'del_17p11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
DEL PEAK 27(17P11.2) MUTATED	44	57	32	31	28
DEL PEAK 27(17P11.2) WILD-TYPE	17	40	36	38	41

Figure S268. Get High-res Image Gene #56: 'del_17p11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_17p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00828 (Fisher's exact test), Q value = 0.021

Table S269. Gene #56: '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 27(17P11.2) MUTATED	37	27	68	37	23
DEL PEAK 27(17P11.2) WILD-TYPE	17	29	46	47	33

Figure S269. Get High-res Image Gene #56: 'del_17p11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_17p11.2' versus 'MIRSEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00056

Table S270. Gene #56: 'del_17p11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	127	49	124
DEL PEAK 27(17P11.2) MUTATED	51	61	22	59
DEL PEAK 27(17P11.2) WILD-TYPE	14	66	27	65

Figure S270. Get High-res Image Gene #56: 'del_17p11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_17p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.0013

Table S271. Gene #56: '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 27(17P11.2) MUTATED	36	54	25	56	22
DEL PEAK 27(17P11.2) WILD-TYPE	8	41	31	66	26

Figure S271. Get High-res Image Gene #56: 'del_17p11.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_17p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.0011

Table S272. Gene #56: 'del_17p11.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
DEL PEAK 27(17P11.2) MUTATED	32	54	47	29	22
DEL PEAK 27(17P11.2) WILD-TYPE	35	32	52	6	31

Figure S272. Get High-res Image Gene #56: 'del_17p11.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q21.2' versus 'CN_CNMF'

P value = 0.00138 (Fisher's exact test), Q value = 0.0049

Table S273. Gene #57: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 28(18Q21.2) MUTATED	21	46	27
DEL PEAK 28(18Q21.2) WILD-TYPE	88	78	110

Figure S273. Get High-res Image Gene #57: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0013

Table S274. Gene #57: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
DEL PEAK 28(18Q21.2) MUTATED	14	35	45
DEL PEAK 28(18Q21.2) WILD-TYPE	74	132	70

Figure S274. Get High-res Image Gene #57: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S275. Gene #57: '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 28(18Q21.2) MUTATED	9	5	28	39	13
DEL PEAK 28(18Q21.2) WILD-TYPE	45	51	86	45	43

Figure S275. Get High-res Image Gene #57: '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 = 9.5e-05

Table S276. Gene #58: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 29(19P13.3) MUTATED	18	51	18
DEL PEAK 29(19P13.3) WILD-TYPE	91	73	119

Figure S276. Get High-res Image Gene #58: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0013

Table S277. Gene #58: 'del_19p13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
DEL PEAK 29(19P13.3) MUTATED	29	18	15	12	12
DEL PEAK 29(19P13.3) WILD-TYPE	32	79	53	57	57

Figure S277. Get High-res Image Gene #58: 'del_19p13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00295 (Fisher's exact test), Q value = 0.0087

Table S278. Gene #58: '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 29(19P13.3) MUTATED	22	9	23	25	7
DEL PEAK 29(19P13.3) WILD-TYPE	32	47	91	59	49

Figure S278. Get High-res Image Gene #58: 'del_19p13.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.043

Table S279. Gene #58: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	92	87	119	42
DEL PEAK 29(19P13.3) MUTATED	32	19	20	12
DEL PEAK 29(19P13.3) WILD-TYPE	60	68	99	30

Figure S279. Get High-res Image Gene #58: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00251 (Fisher's exact test), Q value = 0.0076

Table S280. Gene #58: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	99	35	53
DEL PEAK 29(19P13.3) MUTATED	25	21	18	13	6
DEL PEAK 29(19P13.3) WILD-TYPE	42	65	81	22	47

Figure S280. Get High-res Image Gene #58: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20p12.1' versus 'CN_CNMF'

P value = 0.0437 (Fisher's exact test), Q value = 0.078

Table S281. Gene #59: 'del_20p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 30(20P12.1) MUTATED	12	4	13
DEL PEAK 30(20P12.1) WILD-TYPE	97	120	124

Figure S281. Get High-res Image Gene #59: 'del_20p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q12.1' versus 'CN_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 0.058

Table S282. Gene #60: 'del_22q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 31(22Q12.1) MUTATED	14	30	35
DEL PEAK 31(22Q12.1) WILD-TYPE	95	94	102

Figure S282. Get High-res Image Gene #60: 'del_22q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q12.1' versus 'MRNASEQ_CNMF'

P value = 0.00168 (Fisher's exact test), Q value = 0.0056

Table S283. Gene #60: 'del_22q12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
DEL PEAK 31(22Q12.1) MUTATED	25	21	9	14	10
DEL PEAK 31(22Q12.1) WILD-TYPE	36	76	59	55	59

Figure S283. Get High-res Image Gene #60: 'del_22q12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'CN_CNMF'

P value = 0.0049 (Fisher's exact test), Q value = 0.013

Table S284. Gene #61: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 32(22Q13.32) MUTATED	13	33	37
DEL PEAK 32(22Q13.32) WILD-TYPE	96	91	100

Figure S284. Get High-res Image Gene #61: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00031

Table S285. Gene #61: 'del_22q13.32' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	97	68	69	69
DEL PEAK 32(22Q13.32) MUTATED	27	27	7	12	10
DEL PEAK 32(22Q13.32) WILD-TYPE	34	70	61	57	59

Figure S285. Get High-res Image Gene #61: 'del_22q13.32' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.024

Table S286. Gene #61: '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 32(22Q13.32) MUTATED	16	6	36	16	9
DEL PEAK 32(22Q13.32) WILD-TYPE	38	50	78	68	47

Figure S286. Get High-res Image Gene #61: 'del_22q13.32' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_xq26.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S287. Gene #62: 'del_xq26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	109	124	137
DEL PEAK 33(XQ26.2) MUTATED	8	39	20
DEL PEAK 33(XQ26.2) WILD-TYPE	101	85	117

Figure S287. Get High-res Image Gene #62: 'del_xq26.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq26.2' versus 'METHLYATION_CNMF'

P value = 0.0469 (Fisher's exact test), Q value = 0.082

Table S288. Gene #62: 'del_xq26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	167	115
DEL PEAK 33(XQ26.2) MUTATED	9	31	27
DEL PEAK 33(XQ26.2) WILD-TYPE	79	136	88

Figure S288. Get High-res Image Gene #62: '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/19782292/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LIHC-TP/20139336/LIHC-TP.transferedmergedcluster.txt
Number of patients = 370
Number of significantly focal cnvs = 62
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.

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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