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 63 focal events and 10 molecular subtypes across 184 patients, 269 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p34.2 cnv correlated to 'RPPA_CHIERARCHICAL'.
amp_1q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_2q36.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3p12.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_3q26.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_4p16.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_6p21.31 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
amp_7q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_8p11.22 cnv correlated to 'CN_CNMF'.
amp_8p11.21 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_9p13.3 cnv correlated to 'CN_CNMF'.
amp_12p13.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_12p11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_12q15 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_15q26.1 cnv correlated to 'CN_CNMF'.
amp_17p11.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
amp_17q12 cnv correlated to 'CN_CNMF'.
amp_18q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19p13.2 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
amp_19q13.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_20p11.23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_xp22.11 cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_xq27.1 cnv correlated to 'CN_CNMF'.
del_1p36.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q14.3 cnv correlated to 'CN_CNMF'.
del_3p21.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_4p15.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q22.1 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q34.3 cnv correlated to 'CN_CNMF'.
del_5q14.2 cnv correlated to 'CN_CNMF'.
del_6p25.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6p22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_7q36.1 cnv correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.
del_8p23.2 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10p15.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q23.33 cnv correlated to 'CN_CNMF'.
del_11p15.4 cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.
del_12p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12q21.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12q24.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q14.2 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
del_14q11.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_15q15.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q23.1 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.
del_17p12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17q22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_18q21.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19q13.33 cnv correlated to 'CN_CNMF'.
del_21q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_22q13.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_22q13.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp21.1 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_xq11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 63 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 269 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
del 12p13 1	29 (16%)	155	3e-05 (0.00032)	0.00071 (0.00452)	0.00816 (0.0283)	0.05 (0.117)	0.0099 (0.0326)	0.00134 (0.00767)	0.00463 (0.0182)	6e-05 (0.000548)	0.0216 (0.0582)	0.00051 (0.00349)
del 12q21 33	44 (24%)	140	1e-05 (0.00014)	0.00137 (0.00778)	0.0127 (0.0389)	0.0206 (0.0567)	0.00726 (0.0258)	0.00179 (0.00917)	0.00585 (0.022)	0.00621 (0.023)	0.00339 (0.0146)	0.00141 (0.00793)
del 12q24 33	43 (23%)	141	2e-05 (0.000233)	0.00209 (0.0104)	0.0141 (0.0424)	0.0144 (0.0429)	0.00126 (0.00728)	0.00333 (0.0145)	0.00334 (0.0145)	0.00059 (0.00391)	0.00673 (0.0241)	0.00017 (0.00134)
del 6q25 3	91 (49%)	93	1e-05 (0.00014)	1e-05 (0.00014)	0.0125 (0.0385)	0.404 (0.509)	0.00056 (0.00375)	0.00476 (0.0185)	0.00465 (0.0182)	0.00016 (0.00128)	1e-05 (0.00014)	0.00015 (0.00126)
del xq11 2	23 (12%)	161	1e-05 (0.00014)	0.00271 (0.0124)	0.00163 (0.00863)	0.288 (0.396)	0.00894 (0.0301)	0.0206 (0.0567)	0.0043 (0.0174)	0.0234 (0.0618)	0.00447 (0.0178)	0.016 (0.0465)
amp 1q21 3	62 (34%)	122	0.00281 (0.0127)	1e-05 (0.00014)	0.0658 (0.141)	0.0767 (0.159)	0.00123 (0.00717)	0.011 (0.0345)	0.00147 (0.00812)	0.0157 (0.0459)	0.00038 (0.00272)	0.00258 (0.0121)
del 6p25 2	74 (40%)	110	1e-05 (0.00014)	2e-05 (0.000233)	0.00205 (0.0102)	0.18 (0.287)	0.0314 (0.0801)	0.0124 (0.0385)	0.0905 (0.177)	0.00045 (0.00319)	0.00143 (0.00797)	0.00016 (0.00128)
del 9p21 3	116 (63%)	68	1e-05 (0.00014)	1e-05 (0.00014)	0.151 (0.255)	0.568 (0.653)	1e-05 (0.00014)	0.0001 (0.000863)	1e-05 (0.00014)	1e-05 (0.00014)	1e-05 (0.00014)	1e-05 (0.00014)
del 12q12	25 (14%)	159	1e-05 (0.00014)	0.00018 (0.00137)	0.136 (0.235)	0.221 (0.328)	0.00405 (0.0167)	0.00098 (0.00588)	0.00237 (0.0113)	0.021 (0.0568)	0.00177 (0.00914)	0.00294 (0.0132)
del 17p12	89 (48%)	95	1e-05 (0.00014)	1e-05 (0.00014)	0.227 (0.334)	0.46 (0.561)	1e-05 (0.00014)	5e-05 (0.000485)	1e-05 (0.00014)	8e-05 (0.00072)	1e-05 (0.00014)	1e-05 (0.00014)
del 17q22	49 (27%)	135	1e-05 (0.00014)	0.00163 (0.00863)	0.00395 (0.0164)	0.0598 (0.132)	0.00999 (0.0326)	0.0136 (0.0411)	0.0086 (0.0291)	0.0258 (0.0669)	3e-05 (0.00032)	0.0537 (0.123)
del 18q21 2	126 (68%)	58	1e-05 (0.00014)	1e-05 (0.00014)	0.242 (0.351)	0.611 (0.686)	4e-05 (0.000406)	3e-05 (0.00032)	0.00018 (0.00137)	6e-05 (0.000548)	0.00998 (0.0326)	1e-05 (0.00014)
amp 18q11 2	56 (30%)	128	2e-05 (0.000233)	0.00016 (0.00128)	0.0745 (0.156)	0.103 (0.195)	0.0245 (0.0646)	0.0757 (0.158)	0.00268 (0.0124)	0.00064 (0.00416)	0.00378 (0.0158)	0.00022 (0.00163)
del 1p36 11	68 (37%)	116	1e-05 (0.00014)	1e-05 (0.00014)	0.0167 (0.048)	0.282 (0.39)	0.00215 (0.0106)	0.0179 (0.0505)	0.108 (0.2)	0.086 (0.171)	0.00827 (0.0283)	0.00558 (0.0214)
del 6p22 2	70 (38%)	114	1e-05 (0.00014)	9e-05 (0.000787)	0.0359 (0.0894)	0.561 (0.648)	0.0784 (0.161)	0.0221 (0.0589)	0.228 (0.335)	0.00098 (0.00588)	0.00262 (0.0122)	0.00014 (0.00119)
del 19p13 2	28 (15%)	156	3e-05 (0.00032)	3e-05 (0.00032)	0.569 (0.653)	0.083 (0.167)	0.00623 (0.023)	0.00359 (0.0154)	0.0533 (0.122)	0.00046 (0.00322)	1e-05 (0.00014)	0.00076 (0.00479)
del 22q13 31	60 (33%)	124	1e-05 (0.00014)	6e-05 (0.000548)	0.47 (0.57)	0.896 (0.926)	0.0133 (0.0402)	0.0798 (0.163)	0.0405 (0.1)	0.0168 (0.048)	9e-05 (0.000787)	0.00108 (0.00642)
amp 3q26 2	32 (17%)	152	6e-05 (0.000548)	2e-05 (0.000233)	0.211 (0.319)	0.0166 (0.048)	0.0409 (0.101)	0.0525 (0.121)	0.218 (0.326)	0.0176 (0.0499)	0.00674 (0.0241)	0.0869 (0.172)
amp 7q22 1	56 (30%)	128	1e-05 (0.00014)	0.0077 (0.0271)	0.0323 (0.0821)	0.683 (0.751)	0.143 (0.246)	0.313 (0.416)	0.0423 (0.104)	0.0393 (0.0976)	0.00587 (0.022)	0.0662 (0.141)
del 1p36 32	52 (28%)	132	4e-05 (0.000406)	1e-05 (0.00014)	0.0488 (0.115)	0.482 (0.576)	0.0102 (0.0331)	0.152 (0.256)	0.175 (0.281)	0.0644 (0.139)	0.015 (0.0443)	0.0176 (0.0499)
del 4p15 31	30 (16%)	154	0.011 (0.0345)	0.00053 (0.00359)	0.39 (0.496)	0.529 (0.622)	0.0357 (0.0892)	0.0265 (0.0684)	0.459 (0.561)	0.00973 (0.0323)	0.518 (0.611)	0.0105 (0.0338)
del 15q15 1	36 (20%)	148	1e-05 (0.00014)	0.0103 (0.0332)	0.268 (0.373)	0.437 (0.544)	0.0457 (0.11)	0.00328 (0.0145)	0.184 (0.291)	0.0335 (0.0845)	0.124 (0.22)	0.00571 (0.0218)
del 19p13 3	36 (20%)	148	2e-05 (0.000233)	2e-05 (0.000233)	0.782 (0.832)	0.251 (0.359)	0.0832 (0.167)	0.00175 (0.00911)	0.166 (0.274)	0.0086 (0.0291)	5e-05 (0.000485)	0.00411 (0.0168)
del 21q11 2	62 (34%)	122	1e-05 (0.00014)	0.0106 (0.0338)	0.343 (0.446)	0.21 (0.319)	0.00925 (0.0308)	0.0584 (0.13)	0.374 (0.479)	0.0218 (0.0582)	0.00033 (0.00242)	0.0187 (0.0523)
amp 2q36 2	26 (14%)	158	0.00016 (0.00128)	0.00095 (0.00581)	0.0565 (0.127)	0.314 (0.416)	0.0583 (0.13)	0.0207 (0.0567)	0.607 (0.683)	0.00376 (0.0158)	0.167 (0.275)	0.00301 (0.0134)
amp 12p11 21	43 (23%)	141	1e-05 (0.00014)	1e-05 (0.00014)	0.495 (0.59)	0.461 (0.561)	0.245 (0.354)	0.311 (0.416)	0.0194 (0.0538)	0.00759 (0.0269)	0.00378 (0.0158)	0.515 (0.609)
del 10p15 3	41 (22%)	143	0.00088 (0.00544)	0.233 (0.34)	0.897 (0.926)	0.677 (0.747)	0.028 (0.0718)	0.0129 (0.0396)	0.108 (0.2)	0.0249 (0.0653)	0.0572 (0.128)	0.0065 (0.0235)
amp 4p16 3	15 (8%)	169	0.0437 (0.106)	0.629 (0.7)	0.139 (0.24)	0.0705 (0.15)	0.0328 (0.0831)	0.019 (0.053)	0.13 (0.23)	0.0278 (0.0714)	0.644 (0.714)	0.138 (0.239)
amp 8q24 21	74 (40%)	110	1e-05 (0.00014)	1e-05 (0.00014)	0.104 (0.195)	0.144 (0.247)	0.132 (0.23)	0.0613 (0.134)	0.115 (0.209)	0.056 (0.127)	0.00272 (0.0124)	0.0065 (0.0235)
amp 20p11 23	38 (21%)	146	1e-05 (0.00014)	0.00155 (0.00849)	0.0778 (0.161)	0.118 (0.212)	0.725 (0.782)	0.392 (0.497)	0.388 (0.496)	0.0252 (0.066)	0.00087 (0.00543)	0.161 (0.266)
del 3p21 31	51 (28%)	133	2e-05 (0.000233)	0.00444 (0.0178)	0.241 (0.35)	0.542 (0.631)	0.208 (0.317)	0.788 (0.836)	0.0983 (0.189)	0.0446 (0.108)	0.0483 (0.114)	0.213 (0.319)
del 4q22 1	27 (15%)	157	0.13 (0.229)	0.0106 (0.0338)	0.337 (0.441)	0.145 (0.247)	0.00496 (0.0192)	0.0904 (0.177)	0.132 (0.23)	0.00159 (0.00863)	0.226 (0.334)	0.00574 (0.0218)
del 22q13 32	62 (34%)	122	1e-05 (0.00014)	0.00021 (0.00157)	0.861 (0.899)	0.941 (0.959)	0.152 (0.255)	0.179 (0.285)	0.155 (0.258)	0.286 (0.395)	0.00051 (0.00349)	0.0447 (0.108)
amp 12p13 33	39 (21%)	145	1e-05 (0.00014)	2e-05 (0.000233)	0.403 (0.509)	0.276 (0.383)	0.771 (0.823)	0.55 (0.638)	0.122 (0.219)	0.198 (0.304)	0.00067 (0.00431)	0.887 (0.919)
amp 12q15	29 (16%)	155	1e-05 (0.00014)	0.00163 (0.00863)	0.289 (0.396)	0.0744 (0.156)	0.805 (0.853)	0.327 (0.432)	0.0981 (0.189)	0.0761 (0.158)	0.0133 (0.0402)	0.404 (0.509)
amp 17p11 2	15 (8%)	169	0.00227 (0.011)	0.371 (0.475)	0.369 (0.474)	0.408 (0.512)	0.181 (0.287)	0.0495 (0.116)	0.047 (0.113)	0.112 (0.206)	0.886 (0.919)	0.311 (0.416)
amp xp22 11	11 (6%)	173	0.0146 (0.0435)	0.227 (0.334)	0.41 (0.513)	0.0502 (0.117)	0.108 (0.2)	0.076 (0.158)	0.0352 (0.0882)	0.0913 (0.178)	0.843 (0.887)	0.00817 (0.0283)
del 16q23 1	19 (10%)	165	0.0153 (0.0449)	0.528 (0.621)	0.19 (0.295)	0.00645 (0.0235)	0.56 (0.647)	0.0476 (0.113)	0.299 (0.404)	0.334 (0.439)	0.153 (0.256)	0.279 (0.386)
del xp21 1	29 (16%)	155	2e-05 (0.000233)	0.0951 (0.184)	0.0472 (0.113)	0.577 (0.658)	0.29 (0.397)	0.451 (0.556)	0.0564 (0.127)	0.779 (0.83)	0.0149 (0.044)	0.481 (0.576)
amp 3p12 2	12 (7%)	172	0.00826 (0.0283)	0.0122 (0.0382)	0.0835 (0.167)	0.767 (0.821)	1 (1.00)	0.92 (0.942)	0.834 (0.878)	1 (1.00)	1 (1.00)	0.717 (0.776)
amp 6p21 31	12 (7%)	172	0.00231 (0.0111)	0.185 (0.292)	0.681 (0.75)	0.685 (0.751)	0.297 (0.402)	0.853 (0.896)	0.479 (0.575)	0.716 (0.776)	0.00904 (0.0303)	0.145 (0.247)
amp 8p11 21	34 (18%)	150	0.00621 (0.023)	0.262 (0.37)	0.239 (0.348)	0.454 (0.559)	0.592 (0.671)	0.698 (0.762)	0.858 (0.898)	0.213 (0.319)	0.0209 (0.0568)	0.17 (0.277)
amp 19p13 2	18 (10%)	166	0.00169 (0.00887)	0.256 (0.363)	0.449 (0.556)	0.345 (0.447)	0.902 (0.93)	0.71 (0.774)	0.00457 (0.0181)	0.112 (0.206)	0.103 (0.195)	0.267 (0.373)
amp 19q13 2	47 (26%)	137	1e-05 (0.00014)	0.0255 (0.0664)	0.343 (0.446)	0.51 (0.604)	0.95 (0.966)	0.873 (0.908)	0.575 (0.658)	0.228 (0.335)	0.389 (0.496)	0.576 (0.658)
del 7q36 1	15 (8%)	169	0.00119 (0.00701)	0.169 (0.277)	0.154 (0.257)	0.0218 (0.0582)	0.211 (0.319)	0.601 (0.678)	0.905 (0.932)	0.338 (0.441)	0.0562 (0.127)	0.25 (0.357)
del 8p23 2	58 (32%)	126	0.00018 (0.00137)	0.0602 (0.132)	0.296 (0.402)	0.296 (0.402)	0.356 (0.46)	0.317 (0.419)	0.175 (0.281)	0.154 (0.257)	0.0209 (0.0568)	0.0663 (0.141)
del 11p15 4	29 (16%)	155	0.00063 (0.00413)	0.82 (0.865)	0.0019 (0.00965)	0.0832 (0.167)	0.929 (0.949)	0.785 (0.834)	0.464 (0.565)	0.552 (0.639)	0.17 (0.277)	1 (1.00)
del 13q14 2	20 (11%)	164	0.0031 (0.0138)	0.105 (0.196)	0.973 (0.986)	0.503 (0.598)	0.0622 (0.135)	0.263 (0.37)	0.122 (0.219)	0.0623 (0.135)	0.00196 (0.00988)	0.0903 (0.177)
del 14q11 2	20 (11%)	164	0.00371 (0.0158)	0.00825 (0.0283)	0.908 (0.933)	0.739 (0.795)	0.101 (0.192)	0.131 (0.23)	0.247 (0.355)	0.247 (0.355)	0.263 (0.37)	0.536 (0.627)
amp 1p34 2	13 (7%)	171	0.113 (0.206)	0.296 (0.402)	0.171 (0.278)	0.0435 (0.106)	0.862 (0.899)	0.264 (0.37)	0.929 (0.949)	0.917 (0.941)	0.475 (0.575)	0.424 (0.53)
amp 8p11 22	34 (18%)	150	0.0186 (0.0523)	0.479 (0.575)	0.124 (0.22)	0.333 (0.438)	1 (1.00)	0.698 (0.762)	0.81 (0.857)	0.686 (0.752)	0.05 (0.117)	0.506 (0.601)
amp 9p13 3	24 (13%)	160	0.00224 (0.0109)	0.714 (0.776)	0.948 (0.965)	0.313 (0.416)	0.146 (0.248)	0.39 (0.496)	0.62 (0.692)	0.0797 (0.163)	0.739 (0.795)	0.588 (0.67)
amp 15q26 1	22 (12%)	162	0.0108 (0.0341)	0.0555 (0.126)	0.333 (0.438)	0.667 (0.737)	0.212 (0.319)	0.111 (0.206)	0.451 (0.556)	0.537 (0.627)	0.363 (0.467)	0.3 (0.404)
amp 17q12	31 (17%)	153	5e-05 (0.000485)	0.114 (0.208)	0.959 (0.973)	0.986 (0.995)	0.131 (0.23)	0.213 (0.319)	0.0804 (0.163)	0.0589 (0.13)	0.253 (0.361)	0.127 (0.225)
amp xq27 1	21 (11%)	163	1e-05 (0.00014)	0.311 (0.416)	0.188 (0.293)	0.3 (0.404)	0.759 (0.814)	0.195 (0.301)	0.212 (0.319)	0.458 (0.561)	0.868 (0.904)	0.652 (0.722)
del 2q14 3	9 (5%)	175	4e-05 (0.000406)	0.118 (0.213)	0.338 (0.441)	0.197 (0.303)	1 (1.00)	0.476 (0.575)	0.485 (0.578)	0.72 (0.778)	0.0946 (0.183)	0.605 (0.682)
del 4q34 3	35 (19%)	149	0.00419 (0.017)	0.0614 (0.134)	0.105 (0.196)	0.0539 (0.123)	0.187 (0.293)	0.623 (0.694)	0.716 (0.776)	0.172 (0.279)	0.616 (0.69)	0.232 (0.339)
del 5q14 2	35 (19%)	149	1e-05 (0.00014)	0.0503 (0.117)	0.291 (0.397)	0.148 (0.251)	0.192 (0.298)	0.219 (0.327)	0.102 (0.194)	0.178 (0.285)	0.0797 (0.163)	0.0898 (0.177)
del 10q23 33	35 (19%)	149	0.00034 (0.00246)	0.405 (0.509)	0.568 (0.653)	0.312 (0.416)	0.451 (0.556)	0.177 (0.284)	0.758 (0.814)	0.537 (0.627)	0.631 (0.701)	0.0903 (0.177)
del 19q13 33	22 (12%)	162	0.0025 (0.0118)	0.151 (0.255)	0.589 (0.67)	0.531 (0.623)	0.194 (0.3)	0.227 (0.334)	0.186 (0.293)	0.0855 (0.171)	0.254 (0.361)	0.073 (0.154)
amp 1p12	27 (15%)	157	0.549 (0.638)	0.197 (0.303)	0.169 (0.277)	0.202 (0.309)	0.263 (0.37)	0.441 (0.548)	0.476 (0.575)	0.263 (0.37)	0.456 (0.56)	0.0986 (0.189)
del 9q22 33	47 (26%)	137	0.0658 (0.141)	0.25 (0.357)	0.479 (0.575)	0.174 (0.281)	0.135 (0.235)	0.429 (0.536)	0.0816 (0.165)	0.101 (0.192)	0.156 (0.258)	0.116 (0.209)
del 18p11 31	54 (29%)	130	0.35 (0.453)	0.601 (0.678)	0.266 (0.371)	0.185 (0.291)	0.614 (0.688)	0.975 (0.986)	0.188 (0.294)	0.855 (0.896)	0.59 (0.67)	0.112 (0.206)

'amp_1p34.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0435 (Fisher's exact test), Q value = 0.11

Table S1. Gene #1: 'amp_1p34.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	25	16	16	18
AMP PEAK 1(1P34.2) MUTATED	1	3	0	3	0
AMP PEAK 1(1P34.2) WILD-TYPE	46	22	16	13	18

Figure S1. Get High-res Image Gene #1: 'amp_1p34.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_1q21.3' versus 'CN_CNMF'

P value = 0.00281 (Fisher's exact test), Q value = 0.013

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 3(1Q21.3) MUTATED	18	35	9
AMP PEAK 3(1Q21.3) WILD-TYPE	67	40	15

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

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
AMP PEAK 3(1Q21.3) MUTATED	30	7	18	7
AMP PEAK 3(1Q21.3) WILD-TYPE	15	40	32	34

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

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 0.00123 (Fisher's exact test), Q value = 0.0072

Table S4. Gene #3: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	48	46
AMP PEAK 3(1Q21.3) MUTATED	36	17	6
AMP PEAK 3(1Q21.3) WILD-TYPE	47	31	40

Figure S4. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.034

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
AMP PEAK 3(1Q21.3) MUTATED	22	33	4
AMP PEAK 3(1Q21.3) WILD-TYPE	52	42	24

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

'amp_1q21.3' versus 'MIRSEQ_CNMF'

P value = 0.00147 (Fisher's exact test), Q value = 0.0081

Table S6. Gene #3: 'amp_1q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	40	35	33
AMP PEAK 3(1Q21.3) MUTATED	34	13	6	6
AMP PEAK 3(1Q21.3) WILD-TYPE	35	27	29	27

Figure S6. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0157 (Fisher's exact test), Q value = 0.046

Table S7. Gene #3: 'amp_1q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
AMP PEAK 3(1Q21.3) MUTATED	42	12	5
AMP PEAK 3(1Q21.3) WILD-TYPE	60	30	28

Figure S7. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0027

Table S8. Gene #3: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
AMP PEAK 3(1Q21.3) MUTATED	35	13	10
AMP PEAK 3(1Q21.3) WILD-TYPE	34	54	27

Figure S8. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00258 (Fisher's exact test), Q value = 0.012

Table S9. Gene #3: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
AMP PEAK 3(1Q21.3) MUTATED	33	20	5
AMP PEAK 3(1Q21.3) WILD-TYPE	53	27	35

Figure S9. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_2q36.2' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0013

Table S10. Gene #4: 'amp_2q36.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 4(2Q36.2) MUTATED	3	19	4
AMP PEAK 4(2Q36.2) WILD-TYPE	82	56	20

Figure S10. Get High-res Image Gene #4: 'amp_2q36.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2q36.2' versus 'METHLYATION_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.0058

Table S11. Gene #4: 'amp_2q36.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
AMP PEAK 4(2Q36.2) MUTATED	10	2	12	1
AMP PEAK 4(2Q36.2) WILD-TYPE	35	45	38	40

Figure S11. Get High-res Image Gene #4: 'amp_2q36.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_2q36.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0207 (Fisher's exact test), Q value = 0.057

Table S12. Gene #4: 'amp_2q36.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
AMP PEAK 4(2Q36.2) MUTATED	10	15	0
AMP PEAK 4(2Q36.2) WILD-TYPE	64	60	28

Figure S12. Get High-res Image Gene #4: 'amp_2q36.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_2q36.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00376 (Fisher's exact test), Q value = 0.016

Table S13. Gene #4: 'amp_2q36.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
AMP PEAK 4(2Q36.2) MUTATED	22	2	1
AMP PEAK 4(2Q36.2) WILD-TYPE	80	40	32

Figure S13. Get High-res Image Gene #4: 'amp_2q36.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_2q36.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00301 (Fisher's exact test), Q value = 0.013

Table S14. Gene #4: 'amp_2q36.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
AMP PEAK 4(2Q36.2) MUTATED	20	4	1
AMP PEAK 4(2Q36.2) WILD-TYPE	66	43	39

Figure S14. Get High-res Image Gene #4: 'amp_2q36.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3p12.2' versus 'CN_CNMF'

P value = 0.00826 (Fisher's exact test), Q value = 0.028

Table S15. Gene #5: 'amp_3p12.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 5(3P12.2) MUTATED	2	5	5
AMP PEAK 5(3P12.2) WILD-TYPE	83	70	19

Figure S15. Get High-res Image Gene #5: 'amp_3p12.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3p12.2' versus 'METHLYATION_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.038

Table S16. Gene #5: 'amp_3p12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
AMP PEAK 5(3P12.2) MUTATED	7	1	4	0
AMP PEAK 5(3P12.2) WILD-TYPE	38	46	46	41

Figure S16. Get High-res Image Gene #5: 'amp_3p12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00055

Table S17. Gene #6: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 6(3Q26.2) MUTATED	4	18	10
AMP PEAK 6(3Q26.2) WILD-TYPE	81	57	14

Figure S17. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00023

Table S18. Gene #6: 'amp_3q26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
AMP PEAK 6(3Q26.2) MUTATED	12	1	17	2
AMP PEAK 6(3Q26.2) WILD-TYPE	33	46	33	39

Figure S18. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 0.048

Table S19. Gene #6: 'amp_3q26.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	25	16	16	18
AMP PEAK 6(3Q26.2) MUTATED	9	3	1	2	9
AMP PEAK 6(3Q26.2) WILD-TYPE	38	22	15	14	9

Figure S19. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_3q26.2' versus 'MRNASEQ_CNMF'

P value = 0.0409 (Fisher's exact test), Q value = 0.1

Table S20. Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	48	46
AMP PEAK 6(3Q26.2) MUTATED	21	6	4
AMP PEAK 6(3Q26.2) WILD-TYPE	62	42	42

Figure S20. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3q26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0176 (Fisher's exact test), Q value = 0.05

Table S21. Gene #6: 'amp_3q26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
AMP PEAK 6(3Q26.2) MUTATED	25	3	3
AMP PEAK 6(3Q26.2) WILD-TYPE	77	39	30

Figure S21. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00674 (Fisher's exact test), Q value = 0.024

Table S22. Gene #6: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
AMP PEAK 6(3Q26.2) MUTATED	19	5	6
AMP PEAK 6(3Q26.2) WILD-TYPE	50	62	31

Figure S22. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_4p16.3' versus 'CN_CNMF'

P value = 0.0437 (Fisher's exact test), Q value = 0.11

Table S23. Gene #7: 'amp_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 7(4P16.3) MUTATED	4	6	5
AMP PEAK 7(4P16.3) WILD-TYPE	81	69	19

Figure S23. Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4p16.3' versus 'MRNASEQ_CNMF'

P value = 0.0328 (Fisher's exact test), Q value = 0.083

Table S24. Gene #7: 'amp_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	48	46
AMP PEAK 7(4P16.3) MUTATED	6	1	8
AMP PEAK 7(4P16.3) WILD-TYPE	77	47	38

Figure S24. Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.019 (Fisher's exact test), Q value = 0.053

Table S25. Gene #7: 'amp_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
AMP PEAK 7(4P16.3) MUTATED	2	8	5
AMP PEAK 7(4P16.3) WILD-TYPE	72	67	23

Figure S25. Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0278 (Fisher's exact test), Q value = 0.071

Table S26. Gene #7: 'amp_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
AMP PEAK 7(4P16.3) MUTATED	10	0	5
AMP PEAK 7(4P16.3) WILD-TYPE	92	42	28

Figure S26. Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6p21.31' versus 'CN_CNMF'

P value = 0.00231 (Fisher's exact test), Q value = 0.011

Table S27. Gene #8: 'amp_6p21.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 8(6P21.31) MUTATED	1	6	5
AMP PEAK 8(6P21.31) WILD-TYPE	84	69	19

Figure S27. Get High-res Image Gene #8: 'amp_6p21.31' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p21.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00904 (Fisher's exact test), Q value = 0.03

Table S28. Gene #8: 'amp_6p21.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
AMP PEAK 8(6P21.31) MUTATED	7	0	4
AMP PEAK 8(6P21.31) WILD-TYPE	62	67	33

Figure S28. Get High-res Image Gene #8: 'amp_6p21.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S29. Gene #9: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 9(7Q22.1) MUTATED	12	28	16
AMP PEAK 9(7Q22.1) WILD-TYPE	73	47	8

Figure S29. Get High-res Image Gene #9: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q22.1' versus 'METHLYATION_CNMF'

P value = 0.0077 (Fisher's exact test), Q value = 0.027

Table S30. Gene #9: 'amp_7q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
AMP PEAK 9(7Q22.1) MUTATED	17	9	22	7
AMP PEAK 9(7Q22.1) WILD-TYPE	28	38	28	34

Figure S30. Get High-res Image Gene #9: 'amp_7q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q22.1' versus 'RPPA_CNMF'

P value = 0.0323 (Fisher's exact test), Q value = 0.082

Table S31. Gene #9: 'amp_7q22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	25	20	15	23
AMP PEAK 9(7Q22.1) MUTATED	14	8	1	2	9
AMP PEAK 9(7Q22.1) WILD-TYPE	25	17	19	13	14

Figure S31. Get High-res Image Gene #9: 'amp_7q22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_7q22.1' versus 'MIRSEQ_CNMF'

P value = 0.0423 (Fisher's exact test), Q value = 0.1

Table S32. Gene #9: 'amp_7q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	40	35	33
AMP PEAK 9(7Q22.1) MUTATED	29	8	7	9
AMP PEAK 9(7Q22.1) WILD-TYPE	40	32	28	24

Figure S32. Get High-res Image Gene #9: 'amp_7q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0393 (Fisher's exact test), Q value = 0.098

Table S33. Gene #9: 'amp_7q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
AMP PEAK 9(7Q22.1) MUTATED	38	7	8
AMP PEAK 9(7Q22.1) WILD-TYPE	64	35	25

Figure S33. Get High-res Image Gene #9: 'amp_7q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00587 (Fisher's exact test), Q value = 0.022

Table S34. Gene #9: 'amp_7q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
AMP PEAK 9(7Q22.1) MUTATED	27	11	14
AMP PEAK 9(7Q22.1) WILD-TYPE	42	56	23

Figure S34. Get High-res Image Gene #9: 'amp_7q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8p11.22' versus 'CN_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.052

Table S35. Gene #10: 'amp_8p11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 10(8P11.22) MUTATED	10	15	9
AMP PEAK 10(8P11.22) WILD-TYPE	75	60	15

Figure S35. Get High-res Image Gene #10: 'amp_8p11.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p11.21' versus 'CN_CNMF'

P value = 0.00621 (Fisher's exact test), Q value = 0.023

Table S36. Gene #11: 'amp_8p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 11(8P11.21) MUTATED	10	14	10
AMP PEAK 11(8P11.21) WILD-TYPE	75	61	14

Figure S36. Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0209 (Fisher's exact test), Q value = 0.057

Table S37. Gene #11: 'amp_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
AMP PEAK 11(8P11.21) MUTATED	14	6	11
AMP PEAK 11(8P11.21) WILD-TYPE	55	61	26

Figure S37. Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S38. Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 12(8Q24.21) MUTATED	14	41	19
AMP PEAK 12(8Q24.21) WILD-TYPE	71	34	5

Figure S38. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S39. Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
AMP PEAK 12(8Q24.21) MUTATED	26	11	29	7
AMP PEAK 12(8Q24.21) WILD-TYPE	19	36	21	34

Figure S39. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00272 (Fisher's exact test), Q value = 0.012

Table S40. Gene #12: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
AMP PEAK 12(8Q24.21) MUTATED	34	17	20
AMP PEAK 12(8Q24.21) WILD-TYPE	35	50	17

Figure S40. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0065 (Fisher's exact test), Q value = 0.024

Table S41. Gene #12: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
AMP PEAK 12(8Q24.21) MUTATED	41	22	8
AMP PEAK 12(8Q24.21) WILD-TYPE	45	25	32

Figure S41. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9p13.3' versus 'CN_CNMF'

P value = 0.00224 (Fisher's exact test), Q value = 0.011

Table S42. Gene #13: 'amp_9p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 13(9P13.3) MUTATED	5	11	8
AMP PEAK 13(9P13.3) WILD-TYPE	80	64	16

Figure S42. Get High-res Image Gene #13: 'amp_9p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S43. Gene #14: 'amp_12p13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 14(12P13.33) MUTATED	2	15	22
AMP PEAK 14(12P13.33) WILD-TYPE	83	60	2

Figure S43. Get High-res Image Gene #14: 'amp_12p13.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p13.33' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00023

Table S44. Gene #14: 'amp_12p13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
AMP PEAK 14(12P13.33) MUTATED	15	8	16	0
AMP PEAK 14(12P13.33) WILD-TYPE	30	39	34	41

Figure S44. Get High-res Image Gene #14: 'amp_12p13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12p13.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0043

Table S45. Gene #14: 'amp_12p13.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
AMP PEAK 14(12P13.33) MUTATED	19	5	13
AMP PEAK 14(12P13.33) WILD-TYPE	50	62	24

Figure S45. Get High-res Image Gene #14: 'amp_12p13.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_12p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S46. Gene #15: 'amp_12p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 15(12P11.21) MUTATED	2	21	20
AMP PEAK 15(12P11.21) WILD-TYPE	83	54	4

Figure S46. Get High-res Image Gene #15: 'amp_12p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S47. Gene #15: 'amp_12p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
AMP PEAK 15(12P11.21) MUTATED	20	7	15	1
AMP PEAK 15(12P11.21) WILD-TYPE	25	40	35	40

Figure S47. Get High-res Image Gene #15: 'amp_12p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12p11.21' versus 'MIRSEQ_CNMF'

P value = 0.0194 (Fisher's exact test), Q value = 0.054

Table S48. Gene #15: 'amp_12p11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	40	35	33
AMP PEAK 15(12P11.21) MUTATED	20	5	4	12
AMP PEAK 15(12P11.21) WILD-TYPE	49	35	31	21

Figure S48. Get High-res Image Gene #15: 'amp_12p11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_12p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00759 (Fisher's exact test), Q value = 0.027

Table S49. Gene #15: 'amp_12p11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
AMP PEAK 15(12P11.21) MUTATED	27	3	11
AMP PEAK 15(12P11.21) WILD-TYPE	75	39	22

Figure S49. Get High-res Image Gene #15: 'amp_12p11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_12p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00378 (Fisher's exact test), Q value = 0.016

Table S50. Gene #15: 'amp_12p11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
AMP PEAK 15(12P11.21) MUTATED	20	7	13
AMP PEAK 15(12P11.21) WILD-TYPE	49	60	24

Figure S50. Get High-res Image Gene #15: 'amp_12p11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_12q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S51. Gene #16: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 16(12Q15) MUTATED	2	10	17
AMP PEAK 16(12Q15) WILD-TYPE	83	65	7

Figure S51. Get High-res Image Gene #16: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 0.00163 (Fisher's exact test), Q value = 0.0086

Table S52. Gene #16: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
AMP PEAK 16(12Q15) MUTATED	10	7	12	0
AMP PEAK 16(12Q15) WILD-TYPE	35	40	38	41

Figure S52. Get High-res Image Gene #16: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12q15' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.04

Table S53. Gene #16: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
AMP PEAK 16(12Q15) MUTATED	11	5	11
AMP PEAK 16(12Q15) WILD-TYPE	58	62	26

Figure S53. Get High-res Image Gene #16: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_15q26.1' versus 'CN_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.034

Table S54. Gene #17: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 17(15Q26.1) MUTATED	4	13	5
AMP PEAK 17(15Q26.1) WILD-TYPE	81	62	19

Figure S54. Get High-res Image Gene #17: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17p11.2' versus 'CN_CNMF'

P value = 0.00227 (Fisher's exact test), Q value = 0.011

Table S55. Gene #18: 'amp_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 18(17P11.2) MUTATED	4	4	7
AMP PEAK 18(17P11.2) WILD-TYPE	81	71	17

Figure S55. Get High-res Image Gene #18: 'amp_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0495 (Fisher's exact test), Q value = 0.12

Table S56. Gene #18: 'amp_17p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
AMP PEAK 18(17P11.2) MUTATED	4	5	6
AMP PEAK 18(17P11.2) WILD-TYPE	70	70	22

Figure S56. Get High-res Image Gene #18: 'amp_17p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17p11.2' versus 'MIRSEQ_CNMF'

P value = 0.047 (Fisher's exact test), Q value = 0.11

Table S57. Gene #18: 'amp_17p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	40	35	33
AMP PEAK 18(17P11.2) MUTATED	4	3	1	7
AMP PEAK 18(17P11.2) WILD-TYPE	65	37	34	26

Figure S57. Get High-res Image Gene #18: 'amp_17p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_17q12' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00048

Table S58. Gene #19: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 19(17Q12) MUTATED	4	20	7
AMP PEAK 19(17Q12) WILD-TYPE	81	55	17

Figure S58. Get High-res Image Gene #19: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18q11.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00023

Table S59. Gene #20: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 20(18Q11.2) MUTATED	10	36	10
AMP PEAK 20(18Q11.2) WILD-TYPE	75	39	14

Figure S59. Get High-res Image Gene #20: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0013

Table S60. Gene #20: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
AMP PEAK 20(18Q11.2) MUTATED	19	7	23	6
AMP PEAK 20(18Q11.2) WILD-TYPE	26	40	27	35

Figure S60. Get High-res Image Gene #20: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CNMF'

P value = 0.0245 (Fisher's exact test), Q value = 0.065

Table S61. Gene #20: 'amp_18q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	48	46
AMP PEAK 20(18Q11.2) MUTATED	33	13	8
AMP PEAK 20(18Q11.2) WILD-TYPE	50	35	38

Figure S61. Get High-res Image Gene #20: 'amp_18q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00268 (Fisher's exact test), Q value = 0.012

Table S62. Gene #20: 'amp_18q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	40	35	33
AMP PEAK 20(18Q11.2) MUTATED	32	10	5	7
AMP PEAK 20(18Q11.2) WILD-TYPE	37	30	30	26

Figure S62. Get High-res Image Gene #20: 'amp_18q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00064 (Fisher's exact test), Q value = 0.0042

Table S63. Gene #20: 'amp_18q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
AMP PEAK 20(18Q11.2) MUTATED	42	9	3
AMP PEAK 20(18Q11.2) WILD-TYPE	60	33	30

Figure S63. Get High-res Image Gene #20: 'amp_18q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00378 (Fisher's exact test), Q value = 0.016

Table S64. Gene #20: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
AMP PEAK 20(18Q11.2) MUTATED	31	13	9
AMP PEAK 20(18Q11.2) WILD-TYPE	38	54	28

Figure S64. Get High-res Image Gene #20: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.0016

Table S65. Gene #20: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
AMP PEAK 20(18Q11.2) MUTATED	36	14	3
AMP PEAK 20(18Q11.2) WILD-TYPE	50	33	37

Figure S65. Get High-res Image Gene #20: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

P value = 0.00169 (Fisher's exact test), Q value = 0.0089

Table S66. Gene #21: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 21(19P13.2) MUTATED	3	8	7
AMP PEAK 21(19P13.2) WILD-TYPE	82	67	17

Figure S66. Get High-res Image Gene #21: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19p13.2' versus 'MIRSEQ_CNMF'

P value = 0.00457 (Fisher's exact test), Q value = 0.018

Table S67. Gene #21: 'amp_19p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	40	35	33
AMP PEAK 21(19P13.2) MUTATED	11	1	0	6
AMP PEAK 21(19P13.2) WILD-TYPE	58	39	35	27

Figure S67. Get High-res Image Gene #21: 'amp_19p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_19q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S68. Gene #22: 'amp_19q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 22(19Q13.2) MUTATED	8	28	11
AMP PEAK 22(19Q13.2) WILD-TYPE	77	47	13

Figure S68. Get High-res Image Gene #22: 'amp_19q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q13.2' versus 'METHLYATION_CNMF'

P value = 0.0255 (Fisher's exact test), Q value = 0.066

Table S69. Gene #22: 'amp_19q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
AMP PEAK 22(19Q13.2) MUTATED	10	8	21	8
AMP PEAK 22(19Q13.2) WILD-TYPE	35	39	29	33

Figure S69. Get High-res Image Gene #22: 'amp_19q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S70. Gene #23: 'amp_20p11.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 23(20P11.23) MUTATED	7	15	16
AMP PEAK 23(20P11.23) WILD-TYPE	78	60	8

Figure S70. Get High-res Image Gene #23: 'amp_20p11.23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20p11.23' versus 'METHLYATION_CNMF'

P value = 0.00155 (Fisher's exact test), Q value = 0.0085

Table S71. Gene #23: 'amp_20p11.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
AMP PEAK 23(20P11.23) MUTATED	17	8	10	2
AMP PEAK 23(20P11.23) WILD-TYPE	28	39	40	39

Figure S71. Get High-res Image Gene #23: 'amp_20p11.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20p11.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0252 (Fisher's exact test), Q value = 0.066

Table S72. Gene #23: 'amp_20p11.23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
AMP PEAK 23(20P11.23) MUTATED	27	3	7
AMP PEAK 23(20P11.23) WILD-TYPE	75	39	26

Figure S72. Get High-res Image Gene #23: 'amp_20p11.23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20p11.23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0054

Table S73. Gene #23: 'amp_20p11.23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
AMP PEAK 23(20P11.23) MUTATED	18	5	13
AMP PEAK 23(20P11.23) WILD-TYPE	51	62	24

Figure S73. Get High-res Image Gene #23: 'amp_20p11.23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_xp22.11' versus 'CN_CNMF'

P value = 0.0146 (Fisher's exact test), Q value = 0.044

Table S74. Gene #24: 'amp_xp22.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 24(XP22.11) MUTATED	3	3	5
AMP PEAK 24(XP22.11) WILD-TYPE	82	72	19

Figure S74. Get High-res Image Gene #24: 'amp_xp22.11' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp22.11' versus 'MIRSEQ_CNMF'

P value = 0.0352 (Fisher's exact test), Q value = 0.088

Table S75. Gene #24: 'amp_xp22.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	40	35	33
AMP PEAK 24(XP22.11) MUTATED	3	1	1	6
AMP PEAK 24(XP22.11) WILD-TYPE	66	39	34	27

Figure S75. Get High-res Image Gene #24: 'amp_xp22.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_xp22.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00817 (Fisher's exact test), Q value = 0.028

Table S76. Gene #24: 'amp_xp22.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
AMP PEAK 24(XP22.11) MUTATED	4	0	6
AMP PEAK 24(XP22.11) WILD-TYPE	82	47	34

Figure S76. Get High-res Image Gene #24: 'amp_xp22.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xq27.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S77. Gene #25: 'amp_xq27.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 25(XQ27.1) MUTATED	2	9	10
AMP PEAK 25(XQ27.1) WILD-TYPE	83	66	14

Figure S77. Get High-res Image Gene #25: 'amp_xq27.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.32' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00041

Table S78. Gene #26: 'del_1p36.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 1(1P36.32) MUTATED	12	26	14
DEL PEAK 1(1P36.32) WILD-TYPE	73	49	10

Figure S78. Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S79. Gene #26: 'del_1p36.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
DEL PEAK 1(1P36.32) MUTATED	28	10	11	3
DEL PEAK 1(1P36.32) WILD-TYPE	17	37	39	38

Figure S79. Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.32' versus 'RPPA_CNMF'

P value = 0.0488 (Fisher's exact test), Q value = 0.12

Table S80. Gene #26: 'del_1p36.32' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	25	20	15	23
DEL PEAK 1(1P36.32) MUTATED	18	3	7	3	7
DEL PEAK 1(1P36.32) WILD-TYPE	21	22	13	12	16

Figure S80. Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_1p36.32' versus 'MRNASEQ_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.033

Table S81. Gene #26: 'del_1p36.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	48	46
DEL PEAK 1(1P36.32) MUTATED	28	15	5
DEL PEAK 1(1P36.32) WILD-TYPE	55	33	41

Figure S81. Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p36.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.015 (Fisher's exact test), Q value = 0.044

Table S82. Gene #26: 'del_1p36.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 1(1P36.32) MUTATED	22	10	14
DEL PEAK 1(1P36.32) WILD-TYPE	47	57	23

Figure S82. Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p36.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0176 (Fisher's exact test), Q value = 0.05

Table S83. Gene #26: 'del_1p36.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
DEL PEAK 1(1P36.32) MUTATED	28	14	4
DEL PEAK 1(1P36.32) WILD-TYPE	58	33	36

Figure S83. Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S84. Gene #27: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 2(1P36.11) MUTATED	16	36	16
DEL PEAK 2(1P36.11) WILD-TYPE	69	39	8

Figure S84. Get High-res Image Gene #27: '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 = 0.00014

Table S85. Gene #27: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
DEL PEAK 2(1P36.11) MUTATED	36	12	17	3
DEL PEAK 2(1P36.11) WILD-TYPE	9	35	33	38

Figure S85. Get High-res Image Gene #27: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.11' versus 'RPPA_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.048

Table S86. Gene #27: 'del_1p36.11' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	25	20	15	23
DEL PEAK 2(1P36.11) MUTATED	24	6	9	4	7
DEL PEAK 2(1P36.11) WILD-TYPE	15	19	11	11	16

Figure S86. Get High-res Image Gene #27: 'del_1p36.11' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 0.00215 (Fisher's exact test), Q value = 0.011

Table S87. Gene #27: 'del_1p36.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	48	46
DEL PEAK 2(1P36.11) MUTATED	36	21	7
DEL PEAK 2(1P36.11) WILD-TYPE	47	27	39

Figure S87. Get High-res Image Gene #27: 'del_1p36.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0179 (Fisher's exact test), Q value = 0.051

Table S88. Gene #27: 'del_1p36.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 2(1P36.11) MUTATED	27	33	4
DEL PEAK 2(1P36.11) WILD-TYPE	47	42	24

Figure S88. Get High-res Image Gene #27: 'del_1p36.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00827 (Fisher's exact test), Q value = 0.028

Table S89. Gene #27: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 2(1P36.11) MUTATED	29	15	18
DEL PEAK 2(1P36.11) WILD-TYPE	40	52	19

Figure S89. Get High-res Image Gene #27: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00558 (Fisher's exact test), Q value = 0.021

Table S90. Gene #27: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
DEL PEAK 2(1P36.11) MUTATED	36	20	6
DEL PEAK 2(1P36.11) WILD-TYPE	50	27	34

Figure S90. Get High-res Image Gene #27: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q14.3' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00041

Table S91. Gene #28: 'del_2q14.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 3(2Q14.3) MUTATED	0	3	6
DEL PEAK 3(2Q14.3) WILD-TYPE	85	72	18

Figure S91. Get High-res Image Gene #28: 'del_2q14.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p21.31' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00023

Table S92. Gene #29: 'del_3p21.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 4(3P21.31) MUTATED	11	26	14
DEL PEAK 4(3P21.31) WILD-TYPE	74	49	10

Figure S92. Get High-res Image Gene #29: 'del_3p21.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p21.31' versus 'METHLYATION_CNMF'

P value = 0.00444 (Fisher's exact test), Q value = 0.018

Table S93. Gene #29: 'del_3p21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
DEL PEAK 4(3P21.31) MUTATED	19	9	18	5
DEL PEAK 4(3P21.31) WILD-TYPE	26	38	32	36

Figure S93. Get High-res Image Gene #29: 'del_3p21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0446 (Fisher's exact test), Q value = 0.11

Table S94. Gene #29: 'del_3p21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 4(3P21.31) MUTATED	35	6	8
DEL PEAK 4(3P21.31) WILD-TYPE	67	36	25

Figure S94. Get High-res Image Gene #29: 'del_3p21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0483 (Fisher's exact test), Q value = 0.11

Table S95. Gene #29: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 4(3P21.31) MUTATED	25	12	11
DEL PEAK 4(3P21.31) WILD-TYPE	44	55	26

Figure S95. Get High-res Image Gene #29: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4p15.31' versus 'CN_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.034

Table S96. Gene #30: 'del_4p15.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 5(4P15.31) MUTATED	7	19	4
DEL PEAK 5(4P15.31) WILD-TYPE	78	56	20

Figure S96. Get High-res Image Gene #30: 'del_4p15.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_4p15.31' versus 'METHLYATION_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.0036

Table S97. Gene #30: 'del_4p15.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
DEL PEAK 5(4P15.31) MUTATED	14	1	11	4
DEL PEAK 5(4P15.31) WILD-TYPE	31	46	39	37

Figure S97. Get High-res Image Gene #30: 'del_4p15.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4p15.31' versus 'MRNASEQ_CNMF'

P value = 0.0357 (Fisher's exact test), Q value = 0.089

Table S98. Gene #30: 'del_4p15.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	48	46
DEL PEAK 5(4P15.31) MUTATED	20	4	5
DEL PEAK 5(4P15.31) WILD-TYPE	63	44	41

Figure S98. Get High-res Image Gene #30: 'del_4p15.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4p15.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0265 (Fisher's exact test), Q value = 0.068

Table S99. Gene #30: 'del_4p15.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 5(4P15.31) MUTATED	8	19	2
DEL PEAK 5(4P15.31) WILD-TYPE	66	56	26

Figure S99. Get High-res Image Gene #30: 'del_4p15.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4p15.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00973 (Fisher's exact test), Q value = 0.032

Table S100. Gene #30: 'del_4p15.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 5(4P15.31) MUTATED	24	2	3
DEL PEAK 5(4P15.31) WILD-TYPE	78	40	30

Figure S100. Get High-res Image Gene #30: 'del_4p15.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4p15.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.034

Table S101. Gene #30: 'del_4p15.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
DEL PEAK 5(4P15.31) MUTATED	21	5	2
DEL PEAK 5(4P15.31) WILD-TYPE	65	42	38

Figure S101. Get High-res Image Gene #30: 'del_4p15.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.034

Table S102. Gene #31: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
DEL PEAK 6(4Q22.1) MUTATED	11	1	8	7
DEL PEAK 6(4Q22.1) WILD-TYPE	34	46	42	34

Figure S102. Get High-res Image Gene #31: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00496 (Fisher's exact test), Q value = 0.019

Table S103. Gene #31: 'del_4q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	48	46
DEL PEAK 6(4Q22.1) MUTATED	15	1	10
DEL PEAK 6(4Q22.1) WILD-TYPE	68	47	36

Figure S103. Get High-res Image Gene #31: 'del_4q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00159 (Fisher's exact test), Q value = 0.0086

Table S104. Gene #31: 'del_4q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 6(4Q22.1) MUTATED	19	0	7
DEL PEAK 6(4Q22.1) WILD-TYPE	83	42	26

Figure S104. Get High-res Image Gene #31: 'del_4q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00574 (Fisher's exact test), Q value = 0.022

Table S105. Gene #31: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
DEL PEAK 6(4Q22.1) MUTATED	18	1	6
DEL PEAK 6(4Q22.1) WILD-TYPE	68	46	34

Figure S105. Get High-res Image Gene #31: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 0.00419 (Fisher's exact test), Q value = 0.017

Table S106. Gene #32: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 7(4Q34.3) MUTATED	9	23	3
DEL PEAK 7(4Q34.3) WILD-TYPE	76	52	21

Figure S106. Get High-res Image Gene #32: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S107. Gene #33: 'del_5q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 8(5Q14.2) MUTATED	4	24	7
DEL PEAK 8(5Q14.2) WILD-TYPE	81	51	17

Figure S107. Get High-res Image Gene #33: 'del_5q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S108. Gene #34: 'del_6p25.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 9(6P25.2) MUTATED	15	45	14
DEL PEAK 9(6P25.2) WILD-TYPE	70	30	10

Figure S108. Get High-res Image Gene #34: 'del_6p25.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00023

Table S109. Gene #34: 'del_6p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
DEL PEAK 9(6P25.2) MUTATED	26	9	29	9
DEL PEAK 9(6P25.2) WILD-TYPE	19	38	21	32

Figure S109. Get High-res Image Gene #34: 'del_6p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p25.2' versus 'RPPA_CNMF'

P value = 0.00205 (Fisher's exact test), Q value = 0.01

Table S110. Gene #34: 'del_6p25.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	25	20	15	23
DEL PEAK 9(6P25.2) MUTATED	26	5	8	4	8
DEL PEAK 9(6P25.2) WILD-TYPE	13	20	12	11	15

Figure S110. Get High-res Image Gene #34: 'del_6p25.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_6p25.2' versus 'MRNASEQ_CNMF'

P value = 0.0314 (Fisher's exact test), Q value = 0.08

Table S111. Gene #34: 'del_6p25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	48	46
DEL PEAK 9(6P25.2) MUTATED	39	20	11
DEL PEAK 9(6P25.2) WILD-TYPE	44	28	35

Figure S111. Get High-res Image Gene #34: 'del_6p25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6p25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0124 (Fisher's exact test), Q value = 0.038

Table S112. Gene #34: 'del_6p25.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 9(6P25.2) MUTATED	28	37	5
DEL PEAK 9(6P25.2) WILD-TYPE	46	38	23

Figure S112. Get High-res Image Gene #34: 'del_6p25.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6p25.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0032

Table S113. Gene #34: 'del_6p25.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 9(6P25.2) MUTATED	53	10	7
DEL PEAK 9(6P25.2) WILD-TYPE	49	32	26

Figure S113. Get High-res Image Gene #34: 'del_6p25.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6p25.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00143 (Fisher's exact test), Q value = 0.008

Table S114. Gene #34: 'del_6p25.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 9(6P25.2) MUTATED	36	16	18
DEL PEAK 9(6P25.2) WILD-TYPE	33	51	19

Figure S114. Get High-res Image Gene #34: 'del_6p25.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6p25.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.0013

Table S115. Gene #34: 'del_6p25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
DEL PEAK 9(6P25.2) MUTATED	46	18	6
DEL PEAK 9(6P25.2) WILD-TYPE	40	29	34

Figure S115. Get High-res Image Gene #34: 'del_6p25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S116. Gene #35: 'del_6p22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 10(6P22.2) MUTATED	16	41	13
DEL PEAK 10(6P22.2) WILD-TYPE	69	34	11

Figure S116. Get High-res Image Gene #35: 'del_6p22.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p22.2' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00079

Table S117. Gene #35: 'del_6p22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
DEL PEAK 10(6P22.2) MUTATED	24	9	27	9
DEL PEAK 10(6P22.2) WILD-TYPE	21	38	23	32

Figure S117. Get High-res Image Gene #35: 'del_6p22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p22.2' versus 'RPPA_CNMF'

P value = 0.0359 (Fisher's exact test), Q value = 0.089

Table S118. Gene #35: 'del_6p22.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	25	20	15	23
DEL PEAK 10(6P22.2) MUTATED	23	6	8	4	7
DEL PEAK 10(6P22.2) WILD-TYPE	16	19	12	11	16

Figure S118. Get High-res Image Gene #35: 'del_6p22.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_6p22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0221 (Fisher's exact test), Q value = 0.059

Table S119. Gene #35: 'del_6p22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 10(6P22.2) MUTATED	26	35	5
DEL PEAK 10(6P22.2) WILD-TYPE	48	40	23

Figure S119. Get High-res Image Gene #35: 'del_6p22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6p22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00098 (Fisher's exact test), Q value = 0.0059

Table S120. Gene #35: 'del_6p22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 10(6P22.2) MUTATED	50	9	7
DEL PEAK 10(6P22.2) WILD-TYPE	52	33	26

Figure S120. Get High-res Image Gene #35: 'del_6p22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6p22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00262 (Fisher's exact test), Q value = 0.012

Table S121. Gene #35: 'del_6p22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 10(6P22.2) MUTATED	33	15	18
DEL PEAK 10(6P22.2) WILD-TYPE	36	52	19

Figure S121. Get High-res Image Gene #35: 'del_6p22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6p22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.0012

Table S122. Gene #35: 'del_6p22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
DEL PEAK 10(6P22.2) MUTATED	45	15	6
DEL PEAK 10(6P22.2) WILD-TYPE	41	32	34

Figure S122. Get High-res Image Gene #35: 'del_6p22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q25.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S123. Gene #36: 'del_6q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 11(6Q25.3) MUTATED	21	54	16
DEL PEAK 11(6Q25.3) WILD-TYPE	64	21	8

Figure S123. Get High-res Image Gene #36: 'del_6q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q25.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S124. Gene #36: 'del_6q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
DEL PEAK 11(6Q25.3) MUTATED	29	12	36	13
DEL PEAK 11(6Q25.3) WILD-TYPE	16	35	14	28

Figure S124. Get High-res Image Gene #36: 'del_6q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q25.3' versus 'RPPA_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.039

Table S125. Gene #36: 'del_6q25.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	25	20	15	23
DEL PEAK 11(6Q25.3) MUTATED	27	8	11	4	13
DEL PEAK 11(6Q25.3) WILD-TYPE	12	17	9	11	10

Figure S125. Get High-res Image Gene #36: 'del_6q25.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_6q25.3' versus 'MRNASEQ_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0038

Table S126. Gene #36: 'del_6q25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	48	46
DEL PEAK 11(6Q25.3) MUTATED	52	21	13
DEL PEAK 11(6Q25.3) WILD-TYPE	31	27	33

Figure S126. Get High-res Image Gene #36: 'del_6q25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00476 (Fisher's exact test), Q value = 0.019

Table S127. Gene #36: 'del_6q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 11(6Q25.3) MUTATED	34	45	7
DEL PEAK 11(6Q25.3) WILD-TYPE	40	30	21

Figure S127. Get High-res Image Gene #36: 'del_6q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q25.3' versus 'MIRSEQ_CNMF'

P value = 0.00465 (Fisher's exact test), Q value = 0.018

Table S128. Gene #36: 'del_6q25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	40	35	33
DEL PEAK 11(6Q25.3) MUTATED	45	16	14	11
DEL PEAK 11(6Q25.3) WILD-TYPE	24	24	21	22

Figure S128. Get High-res Image Gene #36: 'del_6q25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6q25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.0013

Table S129. Gene #36: 'del_6q25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 11(6Q25.3) MUTATED	63	12	11
DEL PEAK 11(6Q25.3) WILD-TYPE	39	30	22

Figure S129. Get High-res Image Gene #36: 'del_6q25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q25.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S130. Gene #36: 'del_6q25.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 11(6Q25.3) MUTATED	47	17	21
DEL PEAK 11(6Q25.3) WILD-TYPE	22	50	16

Figure S130. Get High-res Image Gene #36: 'del_6q25.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6q25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.0013

Table S131. Gene #36: 'del_6q25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
DEL PEAK 11(6Q25.3) MUTATED	54	22	9
DEL PEAK 11(6Q25.3) WILD-TYPE	32	25	31

Figure S131. Get High-res Image Gene #36: 'del_6q25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q36.1' versus 'CN_CNMF'

P value = 0.00119 (Fisher's exact test), Q value = 0.007

Table S132. Gene #37: 'del_7q36.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 12(7Q36.1) MUTATED	1	10	4
DEL PEAK 12(7Q36.1) WILD-TYPE	84	65	20

Figure S132. Get High-res Image Gene #37: 'del_7q36.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q36.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 0.058

Table S133. Gene #37: 'del_7q36.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	25	16	16	18
DEL PEAK 12(7Q36.1) MUTATED	1	4	2	0	4
DEL PEAK 12(7Q36.1) WILD-TYPE	46	21	14	16	14

Figure S133. Get High-res Image Gene #37: 'del_7q36.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0014

Table S134. Gene #38: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 13(8P23.2) MUTATED	14	33	11
DEL PEAK 13(8P23.2) WILD-TYPE	71	42	13

Figure S134. Get High-res Image Gene #38: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0209 (Fisher's exact test), Q value = 0.057

Table S135. Gene #38: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 13(8P23.2) MUTATED	25	14	17
DEL PEAK 13(8P23.2) WILD-TYPE	44	53	20

Figure S135. Get High-res Image Gene #38: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S136. Gene #39: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 14(9P21.3) MUTATED	31	69	16
DEL PEAK 14(9P21.3) WILD-TYPE	54	6	8

Figure S136. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S137. Gene #39: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
DEL PEAK 14(9P21.3) MUTATED	38	15	45	17
DEL PEAK 14(9P21.3) WILD-TYPE	7	32	5	24

Figure S137. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S138. Gene #39: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	48	46
DEL PEAK 14(9P21.3) MUTATED	68	26	15
DEL PEAK 14(9P21.3) WILD-TYPE	15	22	31

Figure S138. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00086

Table S139. Gene #39: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 14(9P21.3) MUTATED	44	57	8
DEL PEAK 14(9P21.3) WILD-TYPE	30	18	20

Figure S139. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S140. Gene #39: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	40	35	33
DEL PEAK 14(9P21.3) MUTATED	60	20	18	11
DEL PEAK 14(9P21.3) WILD-TYPE	9	20	17	22

Figure S140. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S141. Gene #39: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 14(9P21.3) MUTATED	80	17	12
DEL PEAK 14(9P21.3) WILD-TYPE	22	25	21

Figure S141. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S142. Gene #39: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 14(9P21.3) MUTATED	60	26	22
DEL PEAK 14(9P21.3) WILD-TYPE	9	41	15

Figure S142. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S143. Gene #39: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
DEL PEAK 14(9P21.3) MUTATED	68	28	12
DEL PEAK 14(9P21.3) WILD-TYPE	18	19	28

Figure S143. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 0.00088 (Fisher's exact test), Q value = 0.0054

Table S144. Gene #41: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 16(10P15.3) MUTATED	10	20	11
DEL PEAK 16(10P15.3) WILD-TYPE	75	55	13

Figure S144. Get High-res Image Gene #41: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.072

Table S145. Gene #41: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	48	46
DEL PEAK 16(10P15.3) MUTATED	25	5	10
DEL PEAK 16(10P15.3) WILD-TYPE	58	43	36

Figure S145. Get High-res Image Gene #41: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0129 (Fisher's exact test), Q value = 0.04

Table S146. Gene #41: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 16(10P15.3) MUTATED	10	25	5
DEL PEAK 16(10P15.3) WILD-TYPE	64	50	23

Figure S146. Get High-res Image Gene #41: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0249 (Fisher's exact test), Q value = 0.065

Table S147. Gene #41: 'del_10p15.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 16(10P15.3) MUTATED	30	4	6
DEL PEAK 16(10P15.3) WILD-TYPE	72	38	27

Figure S147. Get High-res Image Gene #41: 'del_10p15.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0065 (Fisher's exact test), Q value = 0.024

Table S148. Gene #41: 'del_10p15.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
DEL PEAK 16(10P15.3) MUTATED	28	7	4
DEL PEAK 16(10P15.3) WILD-TYPE	58	40	36

Figure S148. Get High-res Image Gene #41: 'del_10p15.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.33' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0025

Table S149. Gene #42: 'del_10q23.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 17(10Q23.33) MUTATED	7	18	10
DEL PEAK 17(10Q23.33) WILD-TYPE	78	57	14

Figure S149. Get High-res Image Gene #42: 'del_10q23.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.4' versus 'CN_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.0041

Table S150. Gene #43: 'del_11p15.4' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 18(11P15.4) MUTATED	5	16	8
DEL PEAK 18(11P15.4) WILD-TYPE	80	59	16

Figure S150. Get High-res Image Gene #43: 'del_11p15.4' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.4' versus 'RPPA_CNMF'

P value = 0.0019 (Fisher's exact test), Q value = 0.0097

Table S151. Gene #43: 'del_11p15.4' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	25	20	15	23
DEL PEAK 18(11P15.4) MUTATED	10	1	0	1	8
DEL PEAK 18(11P15.4) WILD-TYPE	29	24	20	14	15

Figure S151. Get High-res Image Gene #43: 'del_11p15.4' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_12p13.1' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00032

Table S152. Gene #44: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 19(12P13.1) MUTATED	4	23	2
DEL PEAK 19(12P13.1) WILD-TYPE	81	52	22

Figure S152. Get High-res Image Gene #44: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0045

Table S153. Gene #44: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
DEL PEAK 19(12P13.1) MUTATED	9	1	15	4
DEL PEAK 19(12P13.1) WILD-TYPE	36	46	35	37

Figure S153. Get High-res Image Gene #44: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12p13.1' versus 'RPPA_CNMF'

P value = 0.00816 (Fisher's exact test), Q value = 0.028

Table S154. Gene #44: 'del_12p13.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	25	20	15	23
DEL PEAK 19(12P13.1) MUTATED	12	2	0	1	2
DEL PEAK 19(12P13.1) WILD-TYPE	27	23	20	14	21

Figure S154. Get High-res Image Gene #44: 'del_12p13.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_12p13.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.05 (Fisher's exact test), Q value = 0.12

Table S155. Gene #44: 'del_12p13.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	25	16	16	18
DEL PEAK 19(12P13.1) MUTATED	12	2	2	1	0
DEL PEAK 19(12P13.1) WILD-TYPE	35	23	14	15	18

Figure S155. Get High-res Image Gene #44: 'del_12p13.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_12p13.1' versus 'MRNASEQ_CNMF'

P value = 0.0099 (Fisher's exact test), Q value = 0.033

Table S156. Gene #44: 'del_12p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	48	46
DEL PEAK 19(12P13.1) MUTATED	20	4	3
DEL PEAK 19(12P13.1) WILD-TYPE	63	44	43

Figure S156. Get High-res Image Gene #44: 'del_12p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00134 (Fisher's exact test), Q value = 0.0077

Table S157. Gene #44: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 19(12P13.1) MUTATED	6	20	1
DEL PEAK 19(12P13.1) WILD-TYPE	68	55	27

Figure S157. Get High-res Image Gene #44: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_CNMF'

P value = 0.00463 (Fisher's exact test), Q value = 0.018

Table S158. Gene #44: 'del_12p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	40	35	33
DEL PEAK 19(12P13.1) MUTATED	19	2	4	2
DEL PEAK 19(12P13.1) WILD-TYPE	50	38	31	31

Figure S158. Get High-res Image Gene #44: 'del_12p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_12p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00055

Table S159. Gene #44: 'del_12p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 19(12P13.1) MUTATED	25	0	2
DEL PEAK 19(12P13.1) WILD-TYPE	77	42	31

Figure S159. Get High-res Image Gene #44: 'del_12p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0216 (Fisher's exact test), Q value = 0.058

Table S160. Gene #44: 'del_12p13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 19(12P13.1) MUTATED	17	6	3
DEL PEAK 19(12P13.1) WILD-TYPE	52	61	34

Figure S160. Get High-res Image Gene #44: 'del_12p13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_12p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.0035

Table S161. Gene #44: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
DEL PEAK 19(12P13.1) MUTATED	22	2	2
DEL PEAK 19(12P13.1) WILD-TYPE	64	45	38

Figure S161. Get High-res Image Gene #44: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S162. Gene #45: 'del_12q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 20(12Q12) MUTATED	1	23	1
DEL PEAK 20(12Q12) WILD-TYPE	84	52	23

Figure S162. Get High-res Image Gene #45: 'del_12q12' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q12' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0014

Table S163. Gene #45: 'del_12q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
DEL PEAK 20(12Q12) MUTATED	7	1	15	2
DEL PEAK 20(12Q12) WILD-TYPE	38	46	35	39

Figure S163. Get High-res Image Gene #45: 'del_12q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12q12' versus 'MRNASEQ_CNMF'

P value = 0.00405 (Fisher's exact test), Q value = 0.017

Table S164. Gene #45: 'del_12q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	48	46
DEL PEAK 20(12Q12) MUTATED	18	5	1
DEL PEAK 20(12Q12) WILD-TYPE	65	43	45

Figure S164. Get High-res Image Gene #45: 'del_12q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_12q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00098 (Fisher's exact test), Q value = 0.0059

Table S165. Gene #45: 'del_12q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 20(12Q12) MUTATED	6	18	0
DEL PEAK 20(12Q12) WILD-TYPE	68	57	28

Figure S165. Get High-res Image Gene #45: 'del_12q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12q12' versus 'MIRSEQ_CNMF'

P value = 0.00237 (Fisher's exact test), Q value = 0.011

Table S166. Gene #45: 'del_12q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	40	35	33
DEL PEAK 20(12Q12) MUTATED	18	3	2	1
DEL PEAK 20(12Q12) WILD-TYPE	51	37	33	32

Figure S166. Get High-res Image Gene #45: 'del_12q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_12q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.021 (Fisher's exact test), Q value = 0.057

Table S167. Gene #45: 'del_12q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 20(12Q12) MUTATED	20	3	1
DEL PEAK 20(12Q12) WILD-TYPE	82	39	32

Figure S167. Get High-res Image Gene #45: 'del_12q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_12q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00177 (Fisher's exact test), Q value = 0.0091

Table S168. Gene #45: 'del_12q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 20(12Q12) MUTATED	17	3	3
DEL PEAK 20(12Q12) WILD-TYPE	52	64	34

Figure S168. Get High-res Image Gene #45: 'del_12q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_12q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00294 (Fisher's exact test), Q value = 0.013

Table S169. Gene #45: 'del_12q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
DEL PEAK 20(12Q12) MUTATED	17	6	0
DEL PEAK 20(12Q12) WILD-TYPE	69	41	40

Figure S169. Get High-res Image Gene #45: 'del_12q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q21.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S170. Gene #46: 'del_12q21.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 21(12Q21.33) MUTATED	6	33	5
DEL PEAK 21(12Q21.33) WILD-TYPE	79	42	19

Figure S170. Get High-res Image Gene #46: 'del_12q21.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q21.33' versus 'METHLYATION_CNMF'

P value = 0.00137 (Fisher's exact test), Q value = 0.0078

Table S171. Gene #46: 'del_12q21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
DEL PEAK 21(12Q21.33) MUTATED	15	5	19	5
DEL PEAK 21(12Q21.33) WILD-TYPE	30	42	31	36

Figure S171. Get High-res Image Gene #46: 'del_12q21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12q21.33' versus 'RPPA_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.039

Table S172. Gene #46: 'del_12q21.33' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	25	20	15	23
DEL PEAK 21(12Q21.33) MUTATED	16	2	4	1	4
DEL PEAK 21(12Q21.33) WILD-TYPE	23	23	16	14	19

Figure S172. Get High-res Image Gene #46: 'del_12q21.33' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_12q21.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.0206 (Fisher's exact test), Q value = 0.057

Table S173. Gene #46: 'del_12q21.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	25	16	16	18
DEL PEAK 21(12Q21.33) MUTATED	15	2	2	1	7
DEL PEAK 21(12Q21.33) WILD-TYPE	32	23	14	15	11

Figure S173. Get High-res Image Gene #46: 'del_12q21.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_12q21.33' versus 'MRNASEQ_CNMF'

P value = 0.00726 (Fisher's exact test), Q value = 0.026

Table S174. Gene #46: 'del_12q21.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	48	46
DEL PEAK 21(12Q21.33) MUTATED	27	11	4
DEL PEAK 21(12Q21.33) WILD-TYPE	56	37	42

Figure S174. Get High-res Image Gene #46: 'del_12q21.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_12q21.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00179 (Fisher's exact test), Q value = 0.0092

Table S175. Gene #46: 'del_12q21.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 21(12Q21.33) MUTATED	15	26	1
DEL PEAK 21(12Q21.33) WILD-TYPE	59	49	27

Figure S175. Get High-res Image Gene #46: 'del_12q21.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12q21.33' versus 'MIRSEQ_CNMF'

P value = 0.00585 (Fisher's exact test), Q value = 0.022

Table S176. Gene #46: 'del_12q21.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	40	35	33
DEL PEAK 21(12Q21.33) MUTATED	26	8	4	4
DEL PEAK 21(12Q21.33) WILD-TYPE	43	32	31	29

Figure S176. Get High-res Image Gene #46: 'del_12q21.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_12q21.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00621 (Fisher's exact test), Q value = 0.023

Table S177. Gene #46: 'del_12q21.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 21(12Q21.33) MUTATED	33	6	3
DEL PEAK 21(12Q21.33) WILD-TYPE	69	36	30

Figure S177. Get High-res Image Gene #46: 'del_12q21.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_12q21.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00339 (Fisher's exact test), Q value = 0.015

Table S178. Gene #46: 'del_12q21.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 21(12Q21.33) MUTATED	25	8	8
DEL PEAK 21(12Q21.33) WILD-TYPE	44	59	29

Figure S178. Get High-res Image Gene #46: 'del_12q21.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_12q21.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00141 (Fisher's exact test), Q value = 0.0079

Table S179. Gene #46: 'del_12q21.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
DEL PEAK 21(12Q21.33) MUTATED	28	11	2
DEL PEAK 21(12Q21.33) WILD-TYPE	58	36	38

Figure S179. Get High-res Image Gene #46: 'del_12q21.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q24.33' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00023

Table S180. Gene #47: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 22(12Q24.33) MUTATED	7	30	6
DEL PEAK 22(12Q24.33) WILD-TYPE	78	45	18

Figure S180. Get High-res Image Gene #47: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q24.33' versus 'METHLYATION_CNMF'

P value = 0.00209 (Fisher's exact test), Q value = 0.01

Table S181. Gene #47: 'del_12q24.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
DEL PEAK 22(12Q24.33) MUTATED	14	5	19	5
DEL PEAK 22(12Q24.33) WILD-TYPE	31	42	31	36

Figure S181. Get High-res Image Gene #47: 'del_12q24.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12q24.33' versus 'RPPA_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.042

Table S182. Gene #47: 'del_12q24.33' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	25	20	15	23
DEL PEAK 22(12Q24.33) MUTATED	15	3	4	0	4
DEL PEAK 22(12Q24.33) WILD-TYPE	24	22	16	15	19

Figure S182. Get High-res Image Gene #47: 'del_12q24.33' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_12q24.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.043

Table S183. Gene #47: 'del_12q24.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	25	16	16	18
DEL PEAK 22(12Q24.33) MUTATED	14	3	2	0	7
DEL PEAK 22(12Q24.33) WILD-TYPE	33	22	14	16	11

Figure S183. Get High-res Image Gene #47: 'del_12q24.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_12q24.33' versus 'MRNASEQ_CNMF'

P value = 0.00126 (Fisher's exact test), Q value = 0.0073

Table S184. Gene #47: 'del_12q24.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	48	46
DEL PEAK 22(12Q24.33) MUTATED	28	10	3
DEL PEAK 22(12Q24.33) WILD-TYPE	55	38	43

Figure S184. Get High-res Image Gene #47: 'del_12q24.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_12q24.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00333 (Fisher's exact test), Q value = 0.015

Table S185. Gene #47: 'del_12q24.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 22(12Q24.33) MUTATED	15	25	1
DEL PEAK 22(12Q24.33) WILD-TYPE	59	50	27

Figure S185. Get High-res Image Gene #47: 'del_12q24.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12q24.33' versus 'MIRSEQ_CNMF'

P value = 0.00334 (Fisher's exact test), Q value = 0.015

Table S186. Gene #47: 'del_12q24.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	40	35	33
DEL PEAK 22(12Q24.33) MUTATED	26	7	5	3
DEL PEAK 22(12Q24.33) WILD-TYPE	43	33	30	30

Figure S186. Get High-res Image Gene #47: 'del_12q24.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_12q24.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00059 (Fisher's exact test), Q value = 0.0039

Table S187. Gene #47: 'del_12q24.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 22(12Q24.33) MUTATED	34	5	2
DEL PEAK 22(12Q24.33) WILD-TYPE	68	37	31

Figure S187. Get High-res Image Gene #47: 'del_12q24.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_12q24.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00673 (Fisher's exact test), Q value = 0.024

Table S188. Gene #47: 'del_12q24.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 22(12Q24.33) MUTATED	24	8	8
DEL PEAK 22(12Q24.33) WILD-TYPE	45	59	29

Figure S188. Get High-res Image Gene #47: 'del_12q24.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_12q24.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.0013

Table S189. Gene #47: 'del_12q24.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
DEL PEAK 22(12Q24.33) MUTATED	29	10	1
DEL PEAK 22(12Q24.33) WILD-TYPE	57	37	39

Figure S189. Get High-res Image Gene #47: 'del_12q24.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 0.0031 (Fisher's exact test), Q value = 0.014

Table S190. Gene #48: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 23(13Q14.2) MUTATED	3	11	6
DEL PEAK 23(13Q14.2) WILD-TYPE	82	64	18

Figure S190. Get High-res Image Gene #48: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00196 (Fisher's exact test), Q value = 0.0099

Table S191. Gene #48: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 23(13Q14.2) MUTATED	12	1	6
DEL PEAK 23(13Q14.2) WILD-TYPE	57	66	31

Figure S191. Get High-res Image Gene #48: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_14q11.2' versus 'CN_CNMF'

P value = 0.00371 (Fisher's exact test), Q value = 0.016

Table S192. Gene #49: 'del_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 24(14Q11.2) MUTATED	5	15	0
DEL PEAK 24(14Q11.2) WILD-TYPE	80	60	24

Figure S192. Get High-res Image Gene #49: 'del_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q11.2' versus 'METHLYATION_CNMF'

P value = 0.00825 (Fisher's exact test), Q value = 0.028

Table S193. Gene #49: 'del_14q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
DEL PEAK 24(14Q11.2) MUTATED	10	1	7	2
DEL PEAK 24(14Q11.2) WILD-TYPE	35	46	43	39

Figure S193. Get High-res Image Gene #49: 'del_14q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S194. Gene #50: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 25(15Q15.1) MUTATED	3	21	12
DEL PEAK 25(15Q15.1) WILD-TYPE	82	54	12

Figure S194. Get High-res Image Gene #50: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q15.1' versus 'METHLYATION_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.033

Table S195. Gene #50: 'del_15q15.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
DEL PEAK 25(15Q15.1) MUTATED	9	4	17	5
DEL PEAK 25(15Q15.1) WILD-TYPE	36	43	33	36

Figure S195. Get High-res Image Gene #50: 'del_15q15.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q15.1' versus 'MRNASEQ_CNMF'

P value = 0.0457 (Fisher's exact test), Q value = 0.11

Table S196. Gene #50: 'del_15q15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	48	46
DEL PEAK 25(15Q15.1) MUTATED	23	7	5
DEL PEAK 25(15Q15.1) WILD-TYPE	60	41	41

Figure S196. Get High-res Image Gene #50: 'del_15q15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00328 (Fisher's exact test), Q value = 0.014

Table S197. Gene #50: 'del_15q15.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 25(15Q15.1) MUTATED	11	23	1
DEL PEAK 25(15Q15.1) WILD-TYPE	63	52	27

Figure S197. Get High-res Image Gene #50: 'del_15q15.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0335 (Fisher's exact test), Q value = 0.085

Table S198. Gene #50: 'del_15q15.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 25(15Q15.1) MUTATED	27	5	3
DEL PEAK 25(15Q15.1) WILD-TYPE	75	37	30

Figure S198. Get High-res Image Gene #50: 'del_15q15.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00571 (Fisher's exact test), Q value = 0.022

Table S199. Gene #50: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
DEL PEAK 25(15Q15.1) MUTATED	24	7	2
DEL PEAK 25(15Q15.1) WILD-TYPE	62	40	38

Figure S199. Get High-res Image Gene #50: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.045

Table S200. Gene #51: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 26(16Q23.1) MUTATED	6	6	7
DEL PEAK 26(16Q23.1) WILD-TYPE	79	69	17

Figure S200. Get High-res Image Gene #51: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00645 (Fisher's exact test), Q value = 0.024

Table S201. Gene #51: 'del_16q23.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	25	16	16	18
DEL PEAK 26(16Q23.1) MUTATED	1	0	1	4	0
DEL PEAK 26(16Q23.1) WILD-TYPE	46	25	15	12	18

Figure S201. Get High-res Image Gene #51: 'del_16q23.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0476 (Fisher's exact test), Q value = 0.11

Table S202. Gene #51: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 26(16Q23.1) MUTATED	3	12	3
DEL PEAK 26(16Q23.1) WILD-TYPE	71	63	25

Figure S202. Get High-res Image Gene #51: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S203. Gene #52: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 27(17P12) MUTATED	12	66	11
DEL PEAK 27(17P12) WILD-TYPE	73	9	13

Figure S203. Get High-res Image Gene #52: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S204. Gene #52: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
DEL PEAK 27(17P12) MUTATED	29	8	40	12
DEL PEAK 27(17P12) WILD-TYPE	16	39	10	29

Figure S204. Get High-res Image Gene #52: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S205. Gene #52: 'del_17p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	48	46
DEL PEAK 27(17P12) MUTATED	54	24	8
DEL PEAK 27(17P12) WILD-TYPE	29	24	38

Figure S205. Get High-res Image Gene #52: 'del_17p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00048

Table S206. Gene #52: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 27(17P12) MUTATED	40	43	3
DEL PEAK 27(17P12) WILD-TYPE	34	32	25

Figure S206. Get High-res Image Gene #52: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S207. Gene #52: 'del_17p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	40	35	33
DEL PEAK 27(17P12) MUTATED	50	18	11	7
DEL PEAK 27(17P12) WILD-TYPE	19	22	24	26

Figure S207. Get High-res Image Gene #52: 'del_17p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00072

Table S208. Gene #52: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 27(17P12) MUTATED	63	16	7
DEL PEAK 27(17P12) WILD-TYPE	39	26	26

Figure S208. Get High-res Image Gene #52: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S209. Gene #52: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 27(17P12) MUTATED	50	17	18
DEL PEAK 27(17P12) WILD-TYPE	19	50	19

Figure S209. Get High-res Image Gene #52: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S210. Gene #52: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
DEL PEAK 27(17P12) MUTATED	54	24	7
DEL PEAK 27(17P12) WILD-TYPE	32	23	33

Figure S210. Get High-res Image Gene #52: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S211. Gene #53: 'del_17q22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 28(17Q22) MUTATED	4	40	5
DEL PEAK 28(17Q22) WILD-TYPE	81	35	19

Figure S211. Get High-res Image Gene #53: 'del_17q22' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q22' versus 'METHLYATION_CNMF'

P value = 0.00163 (Fisher's exact test), Q value = 0.0086

Table S212. Gene #53: 'del_17q22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
DEL PEAK 28(17Q22) MUTATED	17	6	20	6
DEL PEAK 28(17Q22) WILD-TYPE	28	41	30	35

Figure S212. Get High-res Image Gene #53: 'del_17q22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q22' versus 'RPPA_CNMF'

P value = 0.00395 (Fisher's exact test), Q value = 0.016

Table S213. Gene #53: 'del_17q22' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	25	20	15	23
DEL PEAK 28(17Q22) MUTATED	19	5	1	3	8
DEL PEAK 28(17Q22) WILD-TYPE	20	20	19	12	15

Figure S213. Get High-res Image Gene #53: 'del_17q22' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_17q22' versus 'MRNASEQ_CNMF'

P value = 0.00999 (Fisher's exact test), Q value = 0.033

Table S214. Gene #53: 'del_17q22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	48	46
DEL PEAK 28(17Q22) MUTATED	29	13	5
DEL PEAK 28(17Q22) WILD-TYPE	54	35	41

Figure S214. Get High-res Image Gene #53: 'del_17q22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17q22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.041

Table S215. Gene #53: 'del_17q22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 28(17Q22) MUTATED	19	26	2
DEL PEAK 28(17Q22) WILD-TYPE	55	49	26

Figure S215. Get High-res Image Gene #53: 'del_17q22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17q22' versus 'MIRSEQ_CNMF'

P value = 0.0086 (Fisher's exact test), Q value = 0.029

Table S216. Gene #53: 'del_17q22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	40	35	33
DEL PEAK 28(17Q22) MUTATED	28	8	7	4
DEL PEAK 28(17Q22) WILD-TYPE	41	32	28	29

Figure S216. Get High-res Image Gene #53: 'del_17q22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17q22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0258 (Fisher's exact test), Q value = 0.067

Table S217. Gene #53: 'del_17q22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 28(17Q22) MUTATED	35	7	5
DEL PEAK 28(17Q22) WILD-TYPE	67	35	28

Figure S217. Get High-res Image Gene #53: 'del_17q22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17q22' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00032

Table S218. Gene #53: 'del_17q22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 28(17Q22) MUTATED	31	7	8
DEL PEAK 28(17Q22) WILD-TYPE	38	60	29

Figure S218. Get High-res Image Gene #53: 'del_17q22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_18q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S219. Gene #55: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 30(18Q21.2) MUTATED	41	70	15
DEL PEAK 30(18Q21.2) WILD-TYPE	44	5	9

Figure S219. Get High-res Image Gene #55: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S220. Gene #55: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
DEL PEAK 30(18Q21.2) MUTATED	37	19	45	24
DEL PEAK 30(18Q21.2) WILD-TYPE	8	28	5	17

Figure S220. Get High-res Image Gene #55: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00041

Table S221. Gene #55: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	48	46
DEL PEAK 30(18Q21.2) MUTATED	67	34	19
DEL PEAK 30(18Q21.2) WILD-TYPE	16	14	27

Figure S221. Get High-res Image Gene #55: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00032

Table S222. Gene #55: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 30(18Q21.2) MUTATED	51	60	9
DEL PEAK 30(18Q21.2) WILD-TYPE	23	15	19

Figure S222. Get High-res Image Gene #55: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0014

Table S223. Gene #55: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	40	35	33
DEL PEAK 30(18Q21.2) MUTATED	59	26	19	16
DEL PEAK 30(18Q21.2) WILD-TYPE	10	14	16	17

Figure S223. Get High-res Image Gene #55: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00055

Table S224. Gene #55: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 30(18Q21.2) MUTATED	82	25	13
DEL PEAK 30(18Q21.2) WILD-TYPE	20	17	20

Figure S224. Get High-res Image Gene #55: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00998 (Fisher's exact test), Q value = 0.033

Table S225. Gene #55: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 30(18Q21.2) MUTATED	55	37	25
DEL PEAK 30(18Q21.2) WILD-TYPE	14	30	12

Figure S225. Get High-res Image Gene #55: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_18q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S226. Gene #55: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
DEL PEAK 30(18Q21.2) MUTATED	69	37	11
DEL PEAK 30(18Q21.2) WILD-TYPE	17	10	29

Figure S226. Get High-res Image Gene #55: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00023

Table S227. Gene #56: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 31(19P13.3) MUTATED	4	25	7
DEL PEAK 31(19P13.3) WILD-TYPE	81	50	17

Figure S227. Get High-res Image Gene #56: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00023

Table S228. Gene #56: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
DEL PEAK 31(19P13.3) MUTATED	11	1	19	5
DEL PEAK 31(19P13.3) WILD-TYPE	34	46	31	36

Figure S228. Get High-res Image Gene #56: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00175 (Fisher's exact test), Q value = 0.0091

Table S229. Gene #56: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 31(19P13.3) MUTATED	11	24	1
DEL PEAK 31(19P13.3) WILD-TYPE	63	51	27

Figure S229. Get High-res Image Gene #56: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0086 (Fisher's exact test), Q value = 0.029

Table S230. Gene #56: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 31(19P13.3) MUTATED	29	4	3
DEL PEAK 31(19P13.3) WILD-TYPE	73	38	30

Figure S230. Get High-res Image Gene #56: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00048

Table S231. Gene #56: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 31(19P13.3) MUTATED	25	4	6
DEL PEAK 31(19P13.3) WILD-TYPE	44	63	31

Figure S231. Get High-res Image Gene #56: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00411 (Fisher's exact test), Q value = 0.017

Table S232. Gene #56: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
DEL PEAK 31(19P13.3) MUTATED	25	8	2
DEL PEAK 31(19P13.3) WILD-TYPE	61	39	38

Figure S232. Get High-res Image Gene #56: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.2' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00032

Table S233. Gene #57: 'del_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 32(19P13.2) MUTATED	2	19	7
DEL PEAK 32(19P13.2) WILD-TYPE	83	56	17

Figure S233. Get High-res Image Gene #57: 'del_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.2' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00032

Table S234. Gene #57: 'del_19p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
DEL PEAK 32(19P13.2) MUTATED	8	1	17	2
DEL PEAK 32(19P13.2) WILD-TYPE	37	46	33	39

Figure S234. Get High-res Image Gene #57: 'del_19p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.2' versus 'MRNASEQ_CNMF'

P value = 0.00623 (Fisher's exact test), Q value = 0.023

Table S235. Gene #57: 'del_19p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	48	46
DEL PEAK 32(19P13.2) MUTATED	20	5	2
DEL PEAK 32(19P13.2) WILD-TYPE	63	43	44

Figure S235. Get High-res Image Gene #57: 'del_19p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00359 (Fisher's exact test), Q value = 0.015

Table S236. Gene #57: 'del_19p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 32(19P13.2) MUTATED	9	18	0
DEL PEAK 32(19P13.2) WILD-TYPE	65	57	28

Figure S236. Get High-res Image Gene #57: 'del_19p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.0032

Table S237. Gene #57: 'del_19p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 32(19P13.2) MUTATED	24	3	0
DEL PEAK 32(19P13.2) WILD-TYPE	78	39	33

Figure S237. Get High-res Image Gene #57: 'del_19p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S238. Gene #57: 'del_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 32(19P13.2) MUTATED	21	1	4
DEL PEAK 32(19P13.2) WILD-TYPE	48	66	33

Figure S238. Get High-res Image Gene #57: 'del_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00076 (Fisher's exact test), Q value = 0.0048

Table S239. Gene #57: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
DEL PEAK 32(19P13.2) MUTATED	20	6	0
DEL PEAK 32(19P13.2) WILD-TYPE	66	41	40

Figure S239. Get High-res Image Gene #57: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.33' versus 'CN_CNMF'

P value = 0.0025 (Fisher's exact test), Q value = 0.012

Table S240. Gene #58: 'del_19q13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 33(19Q13.33) MUTATED	3	14	5
DEL PEAK 33(19Q13.33) WILD-TYPE	82	61	19

Figure S240. Get High-res Image Gene #58: 'del_19q13.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S241. Gene #59: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 34(21Q11.2) MUTATED	12	40	10
DEL PEAK 34(21Q11.2) WILD-TYPE	73	35	14

Figure S241. Get High-res Image Gene #59: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.034

Table S242. Gene #59: 'del_21q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
DEL PEAK 34(21Q11.2) MUTATED	18	10	24	9
DEL PEAK 34(21Q11.2) WILD-TYPE	27	37	26	32

Figure S242. Get High-res Image Gene #59: 'del_21q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00925 (Fisher's exact test), Q value = 0.031

Table S243. Gene #59: 'del_21q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	48	46
DEL PEAK 34(21Q11.2) MUTATED	33	18	7
DEL PEAK 34(21Q11.2) WILD-TYPE	50	30	39

Figure S243. Get High-res Image Gene #59: 'del_21q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_21q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 0.058

Table S244. Gene #59: 'del_21q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 34(21Q11.2) MUTATED	41	12	5
DEL PEAK 34(21Q11.2) WILD-TYPE	61	30	28

Figure S244. Get High-res Image Gene #59: 'del_21q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0024

Table S245. Gene #59: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 34(21Q11.2) MUTATED	33	11	12
DEL PEAK 34(21Q11.2) WILD-TYPE	36	56	25

Figure S245. Get High-res Image Gene #59: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_21q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0187 (Fisher's exact test), Q value = 0.052

Table S246. Gene #59: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
DEL PEAK 34(21Q11.2) MUTATED	31	19	6
DEL PEAK 34(21Q11.2) WILD-TYPE	55	28	34

Figure S246. Get High-res Image Gene #59: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S247. Gene #60: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 35(22Q13.31) MUTATED	8	40	12
DEL PEAK 35(22Q13.31) WILD-TYPE	77	35	12

Figure S247. Get High-res Image Gene #60: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.31' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00055

Table S248. Gene #60: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
DEL PEAK 35(22Q13.31) MUTATED	20	8	26	6
DEL PEAK 35(22Q13.31) WILD-TYPE	25	39	24	35

Figure S248. Get High-res Image Gene #60: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.31' versus 'MRNASEQ_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.04

Table S249. Gene #60: 'del_22q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	48	46
DEL PEAK 35(22Q13.31) MUTATED	32	18	7
DEL PEAK 35(22Q13.31) WILD-TYPE	51	30	39

Figure S249. Get High-res Image Gene #60: 'del_22q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.31' versus 'MIRSEQ_CNMF'

P value = 0.0405 (Fisher's exact test), Q value = 0.1

Table S250. Gene #60: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	40	35	33
DEL PEAK 35(22Q13.31) MUTATED	30	13	8	6
DEL PEAK 35(22Q13.31) WILD-TYPE	39	27	27	27

Figure S250. Get High-res Image Gene #60: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.048

Table S251. Gene #60: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 35(22Q13.31) MUTATED	41	11	5
DEL PEAK 35(22Q13.31) WILD-TYPE	61	31	28

Figure S251. Get High-res Image Gene #60: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00079

Table S252. Gene #60: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 35(22Q13.31) MUTATED	29	9	18
DEL PEAK 35(22Q13.31) WILD-TYPE	40	58	19

Figure S252. Get High-res Image Gene #60: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00108 (Fisher's exact test), Q value = 0.0064

Table S253. Gene #60: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
DEL PEAK 35(22Q13.31) MUTATED	35	17	4
DEL PEAK 35(22Q13.31) WILD-TYPE	51	30	36

Figure S253. Get High-res Image Gene #60: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S254. Gene #61: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 36(22Q13.32) MUTATED	9	40	13
DEL PEAK 36(22Q13.32) WILD-TYPE	76	35	11

Figure S254. Get High-res Image Gene #61: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.32' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0016

Table S255. Gene #61: 'del_22q13.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
DEL PEAK 36(22Q13.32) MUTATED	21	10	25	6
DEL PEAK 36(22Q13.32) WILD-TYPE	24	37	25	35

Figure S255. Get High-res Image Gene #61: 'del_22q13.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0035

Table S256. Gene #61: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 36(22Q13.32) MUTATED	29	11	18
DEL PEAK 36(22Q13.32) WILD-TYPE	40	56	19

Figure S256. Get High-res Image Gene #61: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0447 (Fisher's exact test), Q value = 0.11

Table S257. Gene #61: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
DEL PEAK 36(22Q13.32) MUTATED	33	18	7
DEL PEAK 36(22Q13.32) WILD-TYPE	53	29	33

Figure S257. Get High-res Image Gene #61: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp21.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00023

Table S258. Gene #62: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 37(XP21.1) MUTATED	3	18	8
DEL PEAK 37(XP21.1) WILD-TYPE	82	57	16

Figure S258. Get High-res Image Gene #62: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp21.1' versus 'RPPA_CNMF'

P value = 0.0472 (Fisher's exact test), Q value = 0.11

Table S259. Gene #62: 'del_xp21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	25	20	15	23
DEL PEAK 37(XP21.1) MUTATED	8	0	1	2	5
DEL PEAK 37(XP21.1) WILD-TYPE	31	25	19	13	18

Figure S259. Get High-res Image Gene #62: 'del_xp21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_xp21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.044

Table S260. Gene #62: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 37(XP21.1) MUTATED	15	4	8
DEL PEAK 37(XP21.1) WILD-TYPE	54	63	29

Figure S260. Get High-res Image Gene #62: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xq11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S261. Gene #63: 'del_xq11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 38(XQ11.2) MUTATED	0	16	7
DEL PEAK 38(XQ11.2) WILD-TYPE	85	59	17

Figure S261. Get High-res Image Gene #63: 'del_xq11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq11.2' versus 'METHLYATION_CNMF'

P value = 0.00271 (Fisher's exact test), Q value = 0.012

Table S262. Gene #63: 'del_xq11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	47	50	41
DEL PEAK 38(XQ11.2) MUTATED	8	4	11	0
DEL PEAK 38(XQ11.2) WILD-TYPE	37	43	39	41

Figure S262. Get High-res Image Gene #63: 'del_xq11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq11.2' versus 'RPPA_CNMF'

P value = 0.00163 (Fisher's exact test), Q value = 0.0086

Table S263. Gene #63: 'del_xq11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	25	20	15	23
DEL PEAK 38(XQ11.2) MUTATED	10	0	0	0	3
DEL PEAK 38(XQ11.2) WILD-TYPE	29	25	20	15	20

Figure S263. Get High-res Image Gene #63: 'del_xq11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_xq11.2' versus 'MRNASEQ_CNMF'

P value = 0.00894 (Fisher's exact test), Q value = 0.03

Table S264. Gene #63: 'del_xq11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	48	46
DEL PEAK 38(XQ11.2) MUTATED	16	4	1
DEL PEAK 38(XQ11.2) WILD-TYPE	67	44	45

Figure S264. Get High-res Image Gene #63: 'del_xq11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xq11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0206 (Fisher's exact test), Q value = 0.057

Table S265. Gene #63: 'del_xq11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 38(XQ11.2) MUTATED	5	15	1
DEL PEAK 38(XQ11.2) WILD-TYPE	69	60	27

Figure S265. Get High-res Image Gene #63: 'del_xq11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xq11.2' versus 'MIRSEQ_CNMF'

P value = 0.0043 (Fisher's exact test), Q value = 0.017

Table S266. Gene #63: 'del_xq11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	40	35	33
DEL PEAK 38(XQ11.2) MUTATED	16	2	2	1
DEL PEAK 38(XQ11.2) WILD-TYPE	53	38	33	32

Figure S266. Get High-res Image Gene #63: 'del_xq11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xq11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0234 (Fisher's exact test), Q value = 0.062

Table S267. Gene #63: 'del_xq11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 38(XQ11.2) MUTATED	18	2	1
DEL PEAK 38(XQ11.2) WILD-TYPE	84	40	32

Figure S267. Get High-res Image Gene #63: 'del_xq11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xq11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00447 (Fisher's exact test), Q value = 0.018

Table S268. Gene #63: 'del_xq11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 38(XQ11.2) MUTATED	14	2	4
DEL PEAK 38(XQ11.2) WILD-TYPE	55	65	33

Figure S268. Get High-res Image Gene #63: 'del_xq11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xq11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.016 (Fisher's exact test), Q value = 0.046

Table S269. Gene #63: 'del_xq11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
DEL PEAK 38(XQ11.2) MUTATED	16	3	1
DEL PEAK 38(XQ11.2) WILD-TYPE	70	44	39

Figure S269. Get High-res Image Gene #63: 'del_xq11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

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/PAAD-TP/19783030/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PAAD-TP/20139891/PAAD-TP.transferedmergedcluster.txt
Number of patients = 184
Number of significantly focal cnvs = 63
Number of molecular subtypes = 10
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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