Correlation between copy number variations of arm-level result and molecular subtypes

Overview

Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.

Summary

Testing the association between copy number variation 80 arm-level events and 12 molecular subtypes across 515 patients, 192 significant findings detected with P value < 0.05 and Q value < 0.25.

1p gain cnv correlated to 'CN_CNMF'.
1q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
2p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
2q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
3p gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
3q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
4p gain cnv correlated to 'CN_CNMF'.
5p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
5q gain cnv correlated to 'METHLYATION_CNMF'.
6p gain cnv correlated to 'METHLYATION_CNMF'.
7p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
7q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
8p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
8q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
9p gain cnv correlated to 'MRNASEQ_CNMF'.
10p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
10q gain cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
11p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
11q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
12p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
12q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
14q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
15q gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
17p gain cnv correlated to 'CN_CNMF'.
17q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
18p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
18q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
20p gain cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
20q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
21q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
1p loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
3p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
4p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
4q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
5q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
6q loss cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
8p loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
9p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
9q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
10p loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
10q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
11p loss cnv correlated to 'CN_CNMF'.
12p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
12q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
13q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
15q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
16p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
16q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
17p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
18p loss cnv correlated to 'CN_CNMF'.
18q loss cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
19p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
19q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
20p loss cnv correlated to 'CN_CNMF'.
21q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
22q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 192 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
12p gain	137 (27%)	378	0.22 (1.00)	0.0478 (1.00)	1e-05 (0.00946)	2e-05 (0.0169)	0.00802 (1.00)	0.357 (1.00)	1e-05 (0.00946)	1e-05 (0.00946)	1e-05 (0.00946)	1e-05 (0.00946)	0.371 (1.00)	2e-05 (0.0169)
12q gain	130 (25%)	385	0.22 (1.00)	0.137 (1.00)	1e-05 (0.00946)	1e-05 (0.00946)	0.0232 (1.00)	0.199 (1.00)	1e-05 (0.00946)	1e-05 (0.00946)	1e-05 (0.00946)	1e-05 (0.00946)	0.226 (1.00)	1e-05 (0.00946)
17q gain	191 (37%)	324	0.306 (1.00)	0.876 (1.00)	1e-05 (0.00946)	4e-05 (0.0326)	0.297 (1.00)	0.272 (1.00)	4e-05 (0.0326)	1e-05 (0.00946)	0.00012 (0.0935)	4e-05 (0.0326)	0.395 (1.00)	0.00029 (0.22)
20q gain	199 (39%)	316	0.00426 (1.00)	0.00892 (1.00)	1e-05 (0.00946)	1e-05 (0.00946)	0.109 (1.00)	0.249 (1.00)	2e-05 (0.0169)	1e-05 (0.00946)	2e-05 (0.0169)	0.00012 (0.0935)	0.161 (1.00)	1e-05 (0.00946)
4p loss	120 (23%)	395	0.184 (1.00)	0.382 (1.00)	3e-05 (0.0248)	1e-05 (0.00946)	0.523 (1.00)	0.693 (1.00)	0.0001 (0.0786)	2e-05 (0.0169)	2e-05 (0.0169)	1e-05 (0.00946)	0.191 (1.00)	0.0001 (0.0786)
4q loss	136 (26%)	379	0.00045 (0.335)	0.00678 (1.00)	1e-05 (0.00946)	1e-05 (0.00946)	0.273 (1.00)	0.337 (1.00)	1e-05 (0.00946)	1e-05 (0.00946)	1e-05 (0.00946)	1e-05 (0.00946)	0.0579 (1.00)	2e-05 (0.0169)
5q loss	141 (27%)	374	0.064 (1.00)	0.035 (1.00)	1e-05 (0.00946)	1e-05 (0.00946)	0.0654 (1.00)	0.0544 (1.00)	2e-05 (0.0169)	0.0001 (0.0786)	1e-05 (0.00946)	1e-05 (0.00946)	0.467 (1.00)	2e-05 (0.0169)
22q loss	220 (43%)	295	0.126 (1.00)	0.168 (1.00)	1e-05 (0.00946)	1e-05 (0.00946)	0.89 (1.00)	0.62 (1.00)	1e-05 (0.00946)	1e-05 (0.00946)	7e-05 (0.0557)	3e-05 (0.0248)	0.112 (1.00)	0.00016 (0.123)
2p gain	155 (30%)	360	0.301 (1.00)	0.242 (1.00)	1e-05 (0.00946)	1e-05 (0.00946)	0.819 (1.00)	0.973 (1.00)	3e-05 (0.0248)	4e-05 (0.0326)	1e-05 (0.00946)	0.00049 (0.363)	0.0267 (1.00)	0.00016 (0.123)
7p gain	264 (51%)	251	0.853 (1.00)	0.538 (1.00)	1e-05 (0.00946)	0.0015 (1.00)	0.00077 (0.561)	0.00777 (1.00)	1e-05 (0.00946)	1e-05 (0.00946)	1e-05 (0.00946)	0.00035 (0.264)	0.00016 (0.123)	1e-05 (0.00946)
8q gain	246 (48%)	269	0.0236 (1.00)	0.0474 (1.00)	1e-05 (0.00946)	1e-05 (0.00946)	0.649 (1.00)	0.793 (1.00)	1e-05 (0.00946)	1e-05 (0.00946)	1e-05 (0.00946)	0.00362 (1.00)	0.0149 (1.00)	6e-05 (0.0481)
15q loss	242 (47%)	273	0.101 (1.00)	0.282 (1.00)	1e-05 (0.00946)	0.00013 (0.101)	0.0532 (1.00)	0.00547 (1.00)	1e-05 (0.00946)	1e-05 (0.00946)	3e-05 (0.0248)	0.00461 (1.00)	0.308 (1.00)	1e-05 (0.00946)
19p loss	244 (47%)	271	0.817 (1.00)	1 (1.00)	1e-05 (0.00946)	1e-05 (0.00946)	0.877 (1.00)	0.389 (1.00)	1e-05 (0.00946)	1e-05 (0.00946)	1e-05 (0.00946)	1e-05 (0.00946)	0.0312 (1.00)	0.00157 (1.00)
19q loss	159 (31%)	356	0.344 (1.00)	0.461 (1.00)	1e-05 (0.00946)	0.00012 (0.0935)	0.267 (1.00)	0.6 (1.00)	0.00015 (0.116)	5e-05 (0.0403)	5e-05 (0.0403)	2e-05 (0.0169)	0.284 (1.00)	0.00911 (1.00)
10p gain	112 (22%)	403	0.236 (1.00)	0.298 (1.00)	1e-05 (0.00946)	1e-05 (0.00946)	0.0314 (1.00)	0.169 (1.00)	5e-05 (0.0403)	1e-05 (0.00946)	0.00043 (0.321)	0.00018 (0.137)	0.306 (1.00)	0.00094 (0.683)
21q loss	165 (32%)	350	0.185 (1.00)	0.145 (1.00)	1e-05 (0.00946)	0.00048 (0.356)	0.0146 (1.00)	0.048 (1.00)	1e-05 (0.00946)	1e-05 (0.00946)	2e-05 (0.0169)	9e-05 (0.0709)	0.591 (1.00)	0.00044 (0.328)
3q gain	92 (18%)	423	0.0561 (1.00)	0.0708 (1.00)	5e-05 (0.0403)	0.00013 (0.101)	0.483 (1.00)	0.0994 (1.00)	1e-05 (0.00946)	1e-05 (0.00946)	0.0138 (1.00)	0.0328 (1.00)	0.143 (1.00)	0.00107 (0.766)
7q gain	217 (42%)	298	0.481 (1.00)	0.31 (1.00)	1e-05 (0.00946)	0.00975 (1.00)	0.0644 (1.00)	0.0538 (1.00)	1e-05 (0.00946)	1e-05 (0.00946)	0.00308 (1.00)	0.00125 (0.891)	0.149 (1.00)	2e-05 (0.0169)
11q gain	118 (23%)	397	0.0106 (1.00)	0.0172 (1.00)	1e-05 (0.00946)	0.0134 (1.00)	0.00854 (1.00)	0.773 (1.00)	0.00273 (1.00)	0.00032 (0.242)	0.00013 (0.101)	3e-05 (0.0248)	0.465 (1.00)	0.00311 (1.00)
14q gain	126 (24%)	389	0.804 (1.00)	0.846 (1.00)	1e-05 (0.00946)	0.00315 (1.00)	0.433 (1.00)	0.126 (1.00)	0.00016 (0.123)	5e-05 (0.0403)	7e-05 (0.0557)	0.00171 (1.00)	0.148 (1.00)	0.153 (1.00)
16q loss	140 (27%)	375	0.552 (1.00)	0.626 (1.00)	1e-05 (0.00946)	3e-05 (0.0248)	0.192 (1.00)	0.038 (1.00)	1e-05 (0.00946)	3e-05 (0.0248)	0.0104 (1.00)	0.00282 (1.00)	0.873 (1.00)	0.00069 (0.505)
18q loss	216 (42%)	299	0.517 (1.00)	0.425 (1.00)	1e-05 (0.00946)	0.23 (1.00)	0.00409 (1.00)	3e-05 (0.0248)	0.00011 (0.086)	0.00013 (0.101)	0.0427 (1.00)	0.635 (1.00)	0.594 (1.00)	0.167 (1.00)
5p gain	274 (53%)	241	0.798 (1.00)	0.361 (1.00)	1e-05 (0.00946)	0.0952 (1.00)	0.0509 (1.00)	0.00339 (1.00)	0.0414 (1.00)	1e-05 (0.00946)	0.0338 (1.00)	0.126 (1.00)	0.654 (1.00)	0.00016 (0.123)
18p gain	93 (18%)	422	0.877 (1.00)	0.637 (1.00)	4e-05 (0.0326)	1e-05 (0.00946)	0.183 (1.00)	0.894 (1.00)	0.0223 (1.00)	0.00327 (1.00)	0.0249 (1.00)	0.0178 (1.00)	0.15 (1.00)	0.00025 (0.189)
18q gain	71 (14%)	444	0.595 (1.00)	0.147 (1.00)	1e-05 (0.00946)	1e-05 (0.00946)	0.0714 (1.00)	0.234 (1.00)	2e-05 (0.0169)	0.0006 (0.442)	0.0127 (1.00)	0.00258 (1.00)	0.0439 (1.00)	0.0031 (1.00)
20p gain	173 (34%)	342	0.0701 (1.00)	0.139 (1.00)	0.00351 (1.00)	0.00012 (0.0935)	0.168 (1.00)	0.515 (1.00)	0.00037 (0.278)	1e-05 (0.00946)	6e-05 (0.0481)	0.00051 (0.376)	0.0632 (1.00)	0.00039 (0.292)
1p loss	82 (16%)	433	0.0811 (1.00)	0.126 (1.00)	1e-05 (0.00946)	0.00128 (0.911)	0.133 (1.00)	0.135 (1.00)	0.00015 (0.116)	1e-05 (0.00946)	0.226 (1.00)	0.0315 (1.00)	0.14 (1.00)	0.263 (1.00)
3p loss	213 (41%)	302	0.342 (1.00)	0.113 (1.00)	4e-05 (0.0326)	6e-05 (0.0481)	0.517 (1.00)	0.321 (1.00)	0.0406 (1.00)	1e-05 (0.00946)	0.0122 (1.00)	0.00985 (1.00)	0.256 (1.00)	0.018 (1.00)
8p loss	202 (39%)	313	0.131 (1.00)	0.0797 (1.00)	1e-05 (0.00946)	0.00989 (1.00)	0.266 (1.00)	0.00649 (1.00)	6e-05 (0.0481)	1e-05 (0.00946)	0.0056 (1.00)	0.0151 (1.00)	0.00763 (1.00)	0.00305 (1.00)
9q loss	248 (48%)	267	0.5 (1.00)	0.902 (1.00)	0.00011 (0.086)	0.00022 (0.167)	0.549 (1.00)	0.0866 (1.00)	0.135 (1.00)	0.00037 (0.278)	0.00237 (1.00)	2e-05 (0.0169)	0.174 (1.00)	0.00457 (1.00)
10p loss	110 (21%)	405	0.815 (1.00)	0.788 (1.00)	1e-05 (0.00946)	0.033 (1.00)	0.0624 (1.00)	0.0169 (1.00)	6e-05 (0.0481)	1e-05 (0.00946)	0.00314 (1.00)	0.277 (1.00)	0.0243 (1.00)	0.0324 (1.00)
13q loss	252 (49%)	263	0.106 (1.00)	0.625 (1.00)	1e-05 (0.00946)	0.054 (1.00)	0.00333 (1.00)	0.0163 (1.00)	1e-05 (0.00946)	1e-05 (0.00946)	0.00998 (1.00)	0.0225 (1.00)	0.234 (1.00)	0.00335 (1.00)
16p loss	111 (22%)	404	0.452 (1.00)	0.483 (1.00)	1e-05 (0.00946)	7e-05 (0.0557)	0.744 (1.00)	0.00301 (1.00)	8e-05 (0.0634)	0.00103 (0.742)	0.00358 (1.00)	0.00433 (1.00)	0.504 (1.00)	0.00225 (1.00)
2q gain	140 (27%)	375	0.126 (1.00)	0.289 (1.00)	1e-05 (0.00946)	2e-05 (0.0169)	0.915 (1.00)	0.707 (1.00)	0.0786 (1.00)	0.0145 (1.00)	0.0019 (1.00)	0.089 (1.00)	0.0153 (1.00)	0.00877 (1.00)
3p gain	41 (8%)	474			0.00186 (1.00)	0.0372 (1.00)	0.926 (1.00)	0.743 (1.00)	3e-05 (0.0248)	0.00015 (0.116)	0.111 (1.00)	0.117 (1.00)	0.557 (1.00)	0.0149 (1.00)
8p gain	126 (24%)	389	0.15 (1.00)	0.254 (1.00)	1e-05 (0.00946)	0.0952 (1.00)	0.59 (1.00)	0.253 (1.00)	0.00072 (0.526)	9e-05 (0.0709)	0.425 (1.00)	0.839 (1.00)	0.395 (1.00)	0.478 (1.00)
10q gain	78 (15%)	437			0.00229 (1.00)	2e-05 (0.0169)	0.36 (1.00)	0.195 (1.00)	0.00049 (0.363)	3e-05 (0.0248)	0.147 (1.00)	0.0415 (1.00)	0.984 (1.00)	0.064 (1.00)
11p gain	96 (19%)	419	0.0006 (0.442)	0.00098 (0.71)	2e-05 (0.0169)	0.327 (1.00)	0.00098 (0.71)	0.678 (1.00)	0.104 (1.00)	0.00045 (0.335)	0.00095 (0.69)	1e-05 (0.00946)	0.395 (1.00)	0.0279 (1.00)
15q gain	39 (8%)	476	0.193 (1.00)	0.147 (1.00)	0.798 (1.00)	0.137 (1.00)	0.272 (1.00)	0.349 (1.00)	1e-05 (0.00946)	1e-05 (0.00946)	0.737 (1.00)	0.661 (1.00)	0.145 (1.00)	0.902 (1.00)
6q loss	217 (42%)	298	0.247 (1.00)	0.542 (1.00)	0.00832 (1.00)	0.00011 (0.086)	0.2 (1.00)	0.235 (1.00)	0.131 (1.00)	0.00022 (0.167)	0.675 (1.00)	0.00136 (0.963)	0.744 (1.00)	0.173 (1.00)
10q loss	132 (26%)	383	0.816 (1.00)	0.789 (1.00)	4e-05 (0.0326)	0.0307 (1.00)	0.0295 (1.00)	0.0302 (1.00)	0.00136 (0.963)	1e-05 (0.00946)	0.00344 (1.00)	0.00613 (1.00)	0.0138 (1.00)	0.00119 (0.85)
12q loss	99 (19%)	416	0.555 (1.00)	0.425 (1.00)	4e-05 (0.0326)	0.0844 (1.00)	0.201 (1.00)	0.0822 (1.00)	0.00129 (0.917)	8e-05 (0.0634)	0.0956 (1.00)	0.227 (1.00)	0.906 (1.00)	0.213 (1.00)
17p loss	215 (42%)	300	0.551 (1.00)	0.362 (1.00)	1e-05 (0.00946)	0.0001 (0.0786)	0.0265 (1.00)	0.00902 (1.00)	0.00103 (0.742)	0.00132 (0.936)	0.297 (1.00)	0.128 (1.00)	0.77 (1.00)	0.0166 (1.00)
1p gain	141 (27%)	374	0.631 (1.00)	1 (1.00)	1e-05 (0.00946)	0.612 (1.00)	0.0133 (1.00)	0.0279 (1.00)	0.204 (1.00)	0.0484 (1.00)	0.0442 (1.00)	0.2 (1.00)	0.183 (1.00)	0.0968 (1.00)
1q gain	311 (60%)	204	0.121 (1.00)	1 (1.00)	0.0134 (1.00)	0.00805 (1.00)	0.00102 (0.735)	0.0067 (1.00)	0.128 (1.00)	0.00031 (0.234)	0.618 (1.00)	0.0594 (1.00)	0.0227 (1.00)	0.118 (1.00)
4p gain	83 (16%)	432	0.876 (1.00)	1 (1.00)	2e-05 (0.0169)	0.153 (1.00)	0.434 (1.00)	0.111 (1.00)	0.043 (1.00)	0.283 (1.00)	0.136 (1.00)	0.237 (1.00)	0.915 (1.00)	0.18 (1.00)
5q gain	129 (25%)	386	0.196 (1.00)	0.288 (1.00)	0.00954 (1.00)	8e-05 (0.0634)	0.372 (1.00)	0.313 (1.00)	0.00625 (1.00)	0.0267 (1.00)	0.158 (1.00)	0.00994 (1.00)	0.429 (1.00)	0.0721 (1.00)
6p gain	142 (28%)	373	0.353 (1.00)	0.0879 (1.00)	0.00034 (0.256)	1e-05 (0.00946)	0.031 (1.00)	0.856 (1.00)	0.0761 (1.00)	0.00895 (1.00)	0.0615 (1.00)	0.00732 (1.00)	0.642 (1.00)	0.00985 (1.00)
9p gain	45 (9%)	470			0.00129 (0.917)	0.137 (1.00)	0.939 (1.00)	0.277 (1.00)	0.00024 (0.182)	0.00473 (1.00)	0.15 (1.00)	0.639 (1.00)	0.0952 (1.00)	0.138 (1.00)
17p gain	85 (17%)	430	0.454 (1.00)	0.687 (1.00)	3e-05 (0.0248)	0.0618 (1.00)	0.96 (1.00)	0.691 (1.00)	0.0124 (1.00)	0.0384 (1.00)	0.0041 (1.00)	0.063 (1.00)	0.661 (1.00)	0.387 (1.00)
21q gain	97 (19%)	418	0.539 (1.00)	0.264 (1.00)	0.00515 (1.00)	0.673 (1.00)	0.431 (1.00)	0.0221 (1.00)	0.0298 (1.00)	7e-05 (0.0557)	0.682 (1.00)	0.743 (1.00)	0.456 (1.00)	0.406 (1.00)
9p loss	264 (51%)	251	0.0516 (1.00)	0.601 (1.00)	0.00049 (0.363)	0.0211 (1.00)	0.813 (1.00)	0.0567 (1.00)	0.00097 (0.703)	6e-05 (0.0481)	0.0172 (1.00)	0.00061 (0.448)	0.194 (1.00)	0.0684 (1.00)
11p loss	112 (22%)	403	0.0527 (1.00)	0.126 (1.00)	1e-05 (0.00946)	0.00815 (1.00)	0.707 (1.00)	0.755 (1.00)	0.00276 (1.00)	0.00705 (1.00)	0.0251 (1.00)	0.0418 (1.00)	0.202 (1.00)	0.0421 (1.00)
12p loss	113 (22%)	402	0.63 (1.00)	0.881 (1.00)	0.00101 (0.729)	0.244 (1.00)	0.0321 (1.00)	0.15 (1.00)	0.00608 (1.00)	0.0002 (0.152)	0.106 (1.00)	0.347 (1.00)	0.989 (1.00)	0.153 (1.00)
18p loss	181 (35%)	334	0.436 (1.00)	0.454 (1.00)	1e-05 (0.00946)	0.608 (1.00)	0.0229 (1.00)	0.021 (1.00)	0.0193 (1.00)	0.00234 (1.00)	0.0401 (1.00)	0.375 (1.00)	0.973 (1.00)	0.596 (1.00)
20p loss	117 (23%)	398	0.221 (1.00)	0.241 (1.00)	8e-05 (0.0634)	0.00039 (0.292)	0.00057 (0.42)	0.00263 (1.00)	0.00665 (1.00)	0.0011 (0.786)	0.951 (1.00)	0.959 (1.00)	0.252 (1.00)	0.0178 (1.00)
4q gain	47 (9%)	468	0.33 (1.00)	0.582 (1.00)	0.00142 (1.00)	0.84 (1.00)	0.68 (1.00)	0.163 (1.00)	0.00754 (1.00)	0.0035 (1.00)	0.071 (1.00)	0.274 (1.00)	0.506 (1.00)	0.198 (1.00)
6q gain	60 (12%)	455	1 (1.00)	1 (1.00)	0.0435 (1.00)	0.00335 (1.00)	0.431 (1.00)	0.846 (1.00)	0.163 (1.00)	0.0142 (1.00)	0.00922 (1.00)	0.00842 (1.00)	0.981 (1.00)	0.256 (1.00)
9q gain	34 (7%)	481			0.0306 (1.00)	0.452 (1.00)	0.773 (1.00)	0.705 (1.00)	0.0772 (1.00)	0.116 (1.00)	0.194 (1.00)	0.805 (1.00)	0.27 (1.00)	0.135 (1.00)
13q gain	43 (8%)	472	0.413 (1.00)	0.543 (1.00)	0.978 (1.00)	0.00691 (1.00)	0.0426 (1.00)	0.0341 (1.00)	0.0593 (1.00)	0.128 (1.00)	0.83 (1.00)	0.363 (1.00)	0.431 (1.00)	0.537 (1.00)
16p gain	136 (26%)	379	0.531 (1.00)	0.336 (1.00)	0.00924 (1.00)	0.0129 (1.00)	0.0863 (1.00)	0.0214 (1.00)	0.111 (1.00)	0.00484 (1.00)	0.00259 (1.00)	0.721 (1.00)	0.0265 (1.00)	0.101 (1.00)
16q gain	102 (20%)	413	0.439 (1.00)	0.154 (1.00)	0.00736 (1.00)	0.0829 (1.00)	0.0101 (1.00)	0.0268 (1.00)	0.45 (1.00)	0.0219 (1.00)	0.00147 (1.00)	0.11 (1.00)	0.16 (1.00)	0.13 (1.00)
19p gain	33 (6%)	482	0.192 (1.00)	0.0418 (1.00)	0.416 (1.00)	0.735 (1.00)	0.702 (1.00)	0.774 (1.00)	0.993 (1.00)	0.746 (1.00)	0.437 (1.00)	0.858 (1.00)	0.905 (1.00)	0.475 (1.00)
19q gain	76 (15%)	439	0.0497 (1.00)	0.04 (1.00)	0.00333 (1.00)	0.0168 (1.00)	0.872 (1.00)	0.927 (1.00)	0.216 (1.00)	0.0143 (1.00)	0.173 (1.00)	0.478 (1.00)	0.423 (1.00)	0.00228 (1.00)
22q gain	62 (12%)	453	0.11 (1.00)	0.119 (1.00)	0.00421 (1.00)	0.925 (1.00)	0.108 (1.00)	0.282 (1.00)	0.177 (1.00)	0.0964 (1.00)	0.449 (1.00)	0.564 (1.00)	0.278 (1.00)	0.538 (1.00)
xq gain	77 (15%)	438	0.658 (1.00)	0.247 (1.00)	0.00035 (0.264)	0.1 (1.00)	0.869 (1.00)	0.151 (1.00)	0.0516 (1.00)	0.0201 (1.00)	0.0448 (1.00)	0.158 (1.00)	0.268 (1.00)	0.0692 (1.00)
1q loss	27 (5%)	488			0.133 (1.00)	0.0194 (1.00)	0.106 (1.00)	0.026 (1.00)	0.0725 (1.00)	0.173 (1.00)	0.832 (1.00)	0.498 (1.00)	0.926 (1.00)	0.146 (1.00)
2p loss	23 (4%)	492	0.751 (1.00)	0.58 (1.00)	0.0645 (1.00)	0.173 (1.00)	0.549 (1.00)	0.989 (1.00)	0.974 (1.00)	0.909 (1.00)	0.0448 (1.00)	0.491 (1.00)	0.253 (1.00)	0.125 (1.00)
2q loss	24 (5%)	491			0.00066 (0.484)	0.0478 (1.00)	0.463 (1.00)	0.442 (1.00)	0.292 (1.00)	0.39 (1.00)	0.14 (1.00)	0.665 (1.00)	0.632 (1.00)	0.223 (1.00)
3q loss	146 (28%)	369	0.553 (1.00)	0.144 (1.00)	0.00705 (1.00)	0.0139 (1.00)	0.806 (1.00)	0.491 (1.00)	0.0741 (1.00)	0.00103 (0.742)	0.233 (1.00)	0.412 (1.00)	0.389 (1.00)	0.866 (1.00)
5p loss	44 (9%)	471	0.597 (1.00)	0.308 (1.00)	0.198 (1.00)	0.00922 (1.00)	0.0874 (1.00)	0.24 (1.00)	0.00706 (1.00)	0.00179 (1.00)	0.114 (1.00)	0.00178 (1.00)	0.624 (1.00)	0.00164 (1.00)
6p loss	105 (20%)	410	0.0129 (1.00)	0.00442 (1.00)	0.0163 (1.00)	0.219 (1.00)	0.522 (1.00)	0.264 (1.00)	0.154 (1.00)	0.254 (1.00)	0.336 (1.00)	0.0236 (1.00)	0.734 (1.00)	0.181 (1.00)
7p loss	35 (7%)	480	1 (1.00)	1 (1.00)	0.00212 (1.00)	0.0112 (1.00)	0.291 (1.00)	0.993 (1.00)	0.00534 (1.00)	0.00175 (1.00)	0.0906 (1.00)	0.141 (1.00)	0.065 (1.00)	0.0791 (1.00)
7q loss	42 (8%)	473	0.805 (1.00)	0.256 (1.00)	0.0586 (1.00)	0.0201 (1.00)	0.889 (1.00)	0.961 (1.00)	0.111 (1.00)	0.0375 (1.00)	0.388 (1.00)	0.143 (1.00)	0.728 (1.00)	0.825 (1.00)
8q loss	56 (11%)	459			0.031 (1.00)	0.664 (1.00)	0.492 (1.00)	0.249 (1.00)	0.23 (1.00)	0.0778 (1.00)	0.535 (1.00)	0.599 (1.00)	0.149 (1.00)	0.254 (1.00)
11q loss	90 (17%)	425	0.841 (1.00)	0.482 (1.00)	0.0007 (0.512)	0.0143 (1.00)	0.305 (1.00)	0.231 (1.00)	0.00104 (0.746)	0.00639 (1.00)	0.0423 (1.00)	0.0302 (1.00)	0.0364 (1.00)	0.213 (1.00)
14q loss	115 (22%)	400	0.929 (1.00)	0.411 (1.00)	0.0202 (1.00)	0.442 (1.00)	0.331 (1.00)	0.107 (1.00)	0.0308 (1.00)	0.00463 (1.00)	0.0238 (1.00)	0.17 (1.00)	0.191 (1.00)	0.0477 (1.00)
17q loss	58 (11%)	457	0.293 (1.00)	0.474 (1.00)	0.00086 (0.626)	0.0842 (1.00)	0.00885 (1.00)	0.0734 (1.00)	0.138 (1.00)	0.506 (1.00)	0.836 (1.00)	0.161 (1.00)	0.98 (1.00)	0.807 (1.00)
20q loss	69 (13%)	446	0.256 (1.00)	0.498 (1.00)	0.456 (1.00)	0.62 (1.00)	0.105 (1.00)	0.216 (1.00)	0.529 (1.00)	0.478 (1.00)	0.497 (1.00)	0.63 (1.00)	0.0928 (1.00)	0.897 (1.00)
xq loss	68 (13%)	447	0.172 (1.00)	0.254 (1.00)	0.00046 (0.342)	0.00477 (1.00)	0.399 (1.00)	0.813 (1.00)	0.324 (1.00)	0.58 (1.00)	0.209 (1.00)	0.13 (1.00)	0.84 (1.00)	0.455 (1.00)

'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
1P GAIN MUTATED	81	44	16
1P GAIN WILD-TYPE	110	185	79

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

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.23

Table S2. Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
1Q GAIN MUTATED	54	38	15	46	36	36	30	6	31
1Q GAIN WILD-TYPE	29	19	29	38	10	15	19	12	23

Figure S2. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S3. Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
2P GAIN MUTATED	76	38	41
2P GAIN WILD-TYPE	115	191	54

Figure S3. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S4. Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	125	108	116
2P GAIN MUTATED	10	58	32	27
2P GAIN WILD-TYPE	86	67	76	89

Figure S4. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S5. Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
2P GAIN MUTATED	40	18	26	49	16
2P GAIN WILD-TYPE	98	94	50	57	38

Figure S5. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.033

Table S6. Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
2P GAIN MUTATED	23	11	11	32	8	26	22	0	16
2P GAIN WILD-TYPE	60	46	33	52	38	25	27	18	38

Figure S6. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S7. Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
2P GAIN MUTATED	40	95	19
2P GAIN WILD-TYPE	149	133	74

Figure S7. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.12

Table S8. Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
2P GAIN MUTATED	16	92	19
2P GAIN WILD-TYPE	87	156	64

Figure S8. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S9. Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
2Q GAIN MUTATED	63	38	39
2Q GAIN WILD-TYPE	128	191	56

Figure S9. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S10. Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	125	108	116
2Q GAIN MUTATED	13	50	32	23
2Q GAIN WILD-TYPE	83	75	76	93

Figure S10. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S11. Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
3P GAIN MUTATED	20	0	3	12	5
3P GAIN WILD-TYPE	118	112	73	94	49

Figure S11. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.12

Table S12. Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
3P GAIN MUTATED	11	0	4	17	1	2	2	0	3
3P GAIN WILD-TYPE	72	57	40	67	45	49	47	18	51

Figure S12. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.04

Table S13. Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
3Q GAIN MUTATED	47	23	22
3Q GAIN WILD-TYPE	144	206	73

Figure S13. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.1

Table S14. Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	125	108	116
3Q GAIN MUTATED	4	31	23	22
3Q GAIN WILD-TYPE	92	94	85	94

Figure S14. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S15. Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
3Q GAIN MUTATED	35	2	16	23	10
3Q GAIN WILD-TYPE	103	110	60	83	44

Figure S15. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S16. Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
3Q GAIN MUTATED	17	2	10	35	2	6	8	2	4
3Q GAIN WILD-TYPE	66	55	34	49	44	45	41	16	50

Figure S16. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S17. Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
4P GAIN MUTATED	50	20	13
4P GAIN WILD-TYPE	141	209	82

Figure S17. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S18. Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
5P GAIN MUTATED	136	93	45
5P GAIN WILD-TYPE	55	136	50

Figure S18. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S19. Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
5P GAIN MUTATED	57	29	17	55	16	31	25	0	30
5P GAIN WILD-TYPE	26	28	27	29	30	20	24	18	24

Figure S19. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.12

Table S20. Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
5P GAIN MUTATED	37	149	49
5P GAIN WILD-TYPE	66	99	34

Figure S20. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.063

Table S21. Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	125	108	116
5Q GAIN MUTATED	43	27	21	23
5Q GAIN WILD-TYPE	53	98	87	93

Figure S21. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S22. Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	125	108	116
6P GAIN MUTATED	19	59	29	16
6P GAIN WILD-TYPE	77	66	79	100

Figure S22. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S23. Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
7P GAIN MUTATED	140	84	40
7P GAIN WILD-TYPE	51	145	55

Figure S23. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S24. Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
7P GAIN MUTATED	103	32	38	47	27
7P GAIN WILD-TYPE	35	80	38	59	27

Figure S24. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S25. Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
7P GAIN MUTATED	53	20	35	51	9	21	27	2	29
7P GAIN WILD-TYPE	30	37	9	33	37	30	22	16	25

Figure S25. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S26. Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
7P GAIN MUTATED	71	128	62
7P GAIN WILD-TYPE	118	100	31

Figure S26. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.12

Table S27. Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	198	91
7P GAIN MUTATED	61	102	63
7P GAIN WILD-TYPE	84	96	28

Figure S27. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S28. Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
7P GAIN MUTATED	29	147	50
7P GAIN WILD-TYPE	74	101	33

Figure S28. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S29. Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
7Q GAIN MUTATED	114	65	38
7Q GAIN WILD-TYPE	77	164	57

Figure S29. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S30. Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
7Q GAIN MUTATED	87	27	33	34	22
7Q GAIN WILD-TYPE	51	85	43	72	32

Figure S30. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S31. Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
7Q GAIN MUTATED	47	17	30	38	7	16	24	2	22
7Q GAIN WILD-TYPE	36	40	14	46	39	35	25	16	32

Figure S31. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S32. Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
7Q GAIN MUTATED	22	120	40
7Q GAIN WILD-TYPE	81	128	43

Figure S32. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S33. Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
8P GAIN MUTATED	38	39	49
8P GAIN WILD-TYPE	153	190	46

Figure S33. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.071

Table S34. Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
8P GAIN MUTATED	21	6	8	17	14	24	16	0	12
8P GAIN WILD-TYPE	62	51	36	67	32	27	33	18	42

Figure S34. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S35. Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
8Q GAIN MUTATED	98	68	80
8Q GAIN WILD-TYPE	93	161	15

Figure S35. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S36. Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	125	108	116
8Q GAIN MUTATED	31	82	56	47
8Q GAIN WILD-TYPE	65	43	52	69

Figure S36. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S37. Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
8Q GAIN MUTATED	69	33	32	73	21
8Q GAIN WILD-TYPE	69	79	44	33	33

Figure S37. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S38. Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
8Q GAIN MUTATED	35	17	28	43	19	40	25	0	21
8Q GAIN WILD-TYPE	48	40	16	41	27	11	24	18	33

Figure S38. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S39. Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
8Q GAIN MUTATED	63	131	50
8Q GAIN WILD-TYPE	126	97	43

Figure S39. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.048

Table S40. Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
8Q GAIN MUTATED	32	142	37
8Q GAIN WILD-TYPE	71	106	46

Figure S40. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.18

Table S41. Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
9P GAIN MUTATED	14	4	0	16	7
9P GAIN WILD-TYPE	124	108	76	90	47

Figure S41. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S42. Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
10P GAIN MUTATED	44	31	37
10P GAIN WILD-TYPE	147	198	58

Figure S42. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S43. Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	125	108	116
10P GAIN MUTATED	5	44	34	16
10P GAIN WILD-TYPE	91	81	74	100

Figure S43. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.04

Table S44. Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
10P GAIN MUTATED	28	10	21	37	9
10P GAIN WILD-TYPE	110	102	55	69	45

Figure S44. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S45. Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
10P GAIN MUTATED	13	3	10	16	13	22	17	0	11
10P GAIN WILD-TYPE	70	54	34	68	33	29	32	18	43

Figure S45. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.14

Table S46. Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
10P GAIN MUTATED	12	58	15	25
10P GAIN WILD-TYPE	59	140	126	75

Figure S46. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S47. Gene #20: '10q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	125	108	116
10Q GAIN MUTATED	4	33	23	10
10Q GAIN WILD-TYPE	92	92	85	106

Figure S47. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S48. Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
10Q GAIN MUTATED	10	2	7	7	13	16	13	0	7
10Q GAIN WILD-TYPE	73	55	37	77	33	35	36	18	47

Figure S48. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S49. Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
11P GAIN MUTATED	48	23	25
11P GAIN WILD-TYPE	143	206	70

Figure S49. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S50. Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
11P GAIN MUTATED	4	40	17	34
11P GAIN WILD-TYPE	67	158	124	66

Figure S50. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S51. Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
11Q GAIN MUTATED	68	25	25
11Q GAIN WILD-TYPE	123	204	70

Figure S51. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.24

Table S52. Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
11Q GAIN MUTATED	22	15	11	27	1	18	9	1	9
11Q GAIN WILD-TYPE	61	42	33	57	45	33	40	17	45

Figure S52. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.1

Table S53. Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
11Q GAIN MUTATED	24	63	28
11Q GAIN WILD-TYPE	165	165	65

Figure S53. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S54. Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
11Q GAIN MUTATED	5	52	23	35
11Q GAIN WILD-TYPE	66	146	118	65

Figure S54. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S55. Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
12P GAIN MUTATED	56	37	44
12P GAIN WILD-TYPE	135	192	51

Figure S55. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S56. Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	125	108	116
12P GAIN MUTATED	10	52	28	30
12P GAIN WILD-TYPE	86	73	80	86

Figure S56. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S57. Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
12P GAIN MUTATED	41	5	30	42	12
12P GAIN WILD-TYPE	97	107	46	64	42

Figure S57. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S58. Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
12P GAIN MUTATED	17	5	16	26	3	27	24	2	10
12P GAIN WILD-TYPE	66	52	28	58	43	24	25	16	44

Figure S58. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S59. Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
12P GAIN MUTATED	29	82	24
12P GAIN WILD-TYPE	160	146	69

Figure S59. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S60. Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
12P GAIN MUTATED	10	58	20	47
12P GAIN WILD-TYPE	61	140	121	53

Figure S60. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S61. Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
12P GAIN MUTATED	10	89	18
12P GAIN WILD-TYPE	93	159	65

Figure S61. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S62. Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
12Q GAIN MUTATED	46	36	48
12Q GAIN WILD-TYPE	145	193	47

Figure S62. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S63. Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	125	108	116
12Q GAIN MUTATED	7	50	28	29
12Q GAIN WILD-TYPE	89	75	80	87

Figure S63. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S64. Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
12Q GAIN MUTATED	32	6	29	49	9
12Q GAIN WILD-TYPE	106	106	47	57	45

Figure S64. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S65. Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
12Q GAIN MUTATED	16	6	15	20	3	32	25	2	6
12Q GAIN WILD-TYPE	67	51	29	64	43	19	24	16	48

Figure S65. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S66. Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
12Q GAIN MUTATED	27	82	19
12Q GAIN WILD-TYPE	162	146	74

Figure S66. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S67. Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
12Q GAIN MUTATED	13	58	14	43
12Q GAIN WILD-TYPE	58	140	127	57

Figure S67. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S68. Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
12Q GAIN MUTATED	8	84	19
12Q GAIN WILD-TYPE	95	164	64

Figure S68. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S69. Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
14Q GAIN MUTATED	50	34	42
14Q GAIN WILD-TYPE	141	195	53

Figure S69. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.12

Table S70. Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
14Q GAIN MUTATED	37	19	9	42	11
14Q GAIN WILD-TYPE	101	93	67	64	43

Figure S70. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.04

Table S71. Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
14Q GAIN MUTATED	14	12	11	38	8	19	8	0	8
14Q GAIN WILD-TYPE	69	45	33	46	38	32	41	18	46

Figure S71. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.056

Table S72. Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
14Q GAIN MUTATED	27	62	34
14Q GAIN WILD-TYPE	162	166	59

Figure S72. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S73. Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
15Q GAIN MUTATED	3	5	19	6	2
15Q GAIN WILD-TYPE	135	107	57	100	52

Figure S73. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S74. Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
15Q GAIN MUTATED	2	1	0	3	3	4	15	3	4
15Q GAIN WILD-TYPE	81	56	44	81	43	47	34	15	50

Figure S74. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S75. Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
17P GAIN MUTATED	33	22	30
17P GAIN WILD-TYPE	158	207	65

Figure S75. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S76. Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
17Q GAIN MUTATED	99	47	45
17Q GAIN WILD-TYPE	92	182	50

Figure S76. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.033

Table S77. Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	125	108	116
17Q GAIN MUTATED	20	55	56	35
17Q GAIN WILD-TYPE	76	70	52	81

Figure S77. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.033

Table S78. Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
17Q GAIN MUTATED	72	28	20	44	18
17Q GAIN WILD-TYPE	66	84	56	62	36

Figure S78. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S79. Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
17Q GAIN MUTATED	40	19	21	41	5	26	14	0	16
17Q GAIN WILD-TYPE	43	38	23	43	41	25	35	18	38

Figure S79. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.093

Table S80. Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
17Q GAIN MUTATED	49	104	36
17Q GAIN WILD-TYPE	140	124	57

Figure S80. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.033

Table S81. Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
17Q GAIN MUTATED	19	87	34	49
17Q GAIN WILD-TYPE	52	111	107	51

Figure S81. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.22

Table S82. Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
17Q GAIN MUTATED	22	107	35
17Q GAIN WILD-TYPE	81	141	48

Figure S82. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.033

Table S83. Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
18P GAIN MUTATED	45	22	26
18P GAIN WILD-TYPE	146	207	69

Figure S83. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S84. Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	125	108	116
18P GAIN MUTATED	7	40	23	11
18P GAIN WILD-TYPE	89	85	85	105

Figure S84. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.19

Table S85. Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
18P GAIN MUTATED	6	57	16
18P GAIN WILD-TYPE	97	191	67

Figure S85. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S86. Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
18Q GAIN MUTATED	30	14	27
18Q GAIN WILD-TYPE	161	215	68

Figure S86. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S87. Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	125	108	116
18Q GAIN MUTATED	4	37	14	6
18Q GAIN WILD-TYPE	92	88	94	110

Figure S87. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S88. Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
18Q GAIN MUTATED	13	8	9	31	4
18Q GAIN WILD-TYPE	125	104	67	75	50

Figure S88. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.093

Table S89. Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	125	108	116
20P GAIN MUTATED	22	61	27	38
20P GAIN WILD-TYPE	74	64	81	78

Figure S89. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S90. Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
20P GAIN MUTATED	18	10	19	45	14	25	15	1	13
20P GAIN WILD-TYPE	65	47	25	39	32	26	34	17	41

Figure S90. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.048

Table S91. Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
20P GAIN MUTATED	41	90	40
20P GAIN WILD-TYPE	148	138	53

Figure S91. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S92. Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
20Q GAIN MUTATED	87	60	52
20Q GAIN WILD-TYPE	104	169	43

Figure S92. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S93. Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	125	108	116
20Q GAIN MUTATED	22	71	39	39
20Q GAIN WILD-TYPE	74	54	69	77

Figure S93. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S94. Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
20Q GAIN MUTATED	58	24	27	60	17
20Q GAIN WILD-TYPE	80	88	49	46	37

Figure S94. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S95. Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
20Q GAIN MUTATED	26	10	24	52	14	27	18	1	14
20Q GAIN WILD-TYPE	57	47	20	32	32	24	31	17	40

Figure S95. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S96. Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
20Q GAIN MUTATED	47	107	41
20Q GAIN WILD-TYPE	142	121	52

Figure S96. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.093

Table S97. Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
20Q GAIN MUTATED	16	85	42	52
20Q GAIN WILD-TYPE	55	113	99	48

Figure S97. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S98. Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
20Q GAIN MUTATED	19	121	31
20Q GAIN WILD-TYPE	84	127	52

Figure S98. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.056

Table S99. Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
21Q GAIN MUTATED	25	17	5	24	3	4	7	0	8
21Q GAIN WILD-TYPE	58	40	39	60	43	47	42	18	46

Figure S99. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S100. Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
1P LOSS MUTATED	17	31	34
1P LOSS WILD-TYPE	174	198	61

Figure S100. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.12

Table S101. Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
1P LOSS MUTATED	19	10	15	29	2
1P LOSS WILD-TYPE	119	102	61	77	52

Figure S101. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S102. Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
1P LOSS MUTATED	7	7	10	5	10	20	12	1	3
1P LOSS WILD-TYPE	76	50	34	79	36	31	37	17	51

Figure S102. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.033

Table S103. Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
3P LOSS MUTATED	89	71	53
3P LOSS WILD-TYPE	102	158	42

Figure S103. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.048

Table S104. Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	125	108	116
3P LOSS MUTATED	33	73	41	38
3P LOSS WILD-TYPE	63	52	67	78

Figure S104. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S105. Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
3P LOSS MUTATED	28	25	14	42	17	34	26	0	18
3P LOSS WILD-TYPE	55	32	30	42	29	17	23	18	36

Figure S105. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S106. Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
4P LOSS MUTATED	55	31	34
4P LOSS WILD-TYPE	136	198	61

Figure S106. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S107. Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	125	108	116
4P LOSS MUTATED	6	44	22	28
4P LOSS WILD-TYPE	90	81	86	88

Figure S107. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.079

Table S108. Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
4P LOSS MUTATED	30	12	22	40	11
4P LOSS WILD-TYPE	108	100	54	66	43

Figure S108. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S109. Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
4P LOSS MUTATED	16	9	7	35	2	20	14	2	10
4P LOSS WILD-TYPE	67	48	37	49	44	31	35	16	44

Figure S109. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S110. Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
4P LOSS MUTATED	22	75	22
4P LOSS WILD-TYPE	167	153	71

Figure S110. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S111. Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
4P LOSS MUTATED	6	54	22	37
4P LOSS WILD-TYPE	65	144	119	63

Figure S111. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.079

Table S112. Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
4P LOSS MUTATED	12	75	12
4P LOSS WILD-TYPE	91	173	71

Figure S112. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S113. Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
4Q LOSS MUTATED	61	35	40
4Q LOSS WILD-TYPE	130	194	55

Figure S113. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S114. Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	125	108	116
4Q LOSS MUTATED	6	56	20	32
4Q LOSS WILD-TYPE	90	69	88	84

Figure S114. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S115. Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
4Q LOSS MUTATED	33	12	25	49	11
4Q LOSS WILD-TYPE	105	100	51	57	43

Figure S115. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S116. Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
4Q LOSS MUTATED	17	6	6	38	5	28	19	1	10
4Q LOSS WILD-TYPE	66	51	38	46	41	23	30	17	44

Figure S116. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S117. Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
4Q LOSS MUTATED	25	85	25
4Q LOSS WILD-TYPE	164	143	68

Figure S117. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S118. Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
4Q LOSS MUTATED	8	61	20	46
4Q LOSS WILD-TYPE	63	137	121	54

Figure S118. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S119. Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
4Q LOSS MUTATED	13	84	16
4Q LOSS WILD-TYPE	90	164	67

Figure S119. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S120. Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
5Q LOSS MUTATED	68	34	39
5Q LOSS WILD-TYPE	123	195	56

Figure S120. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S121. Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	125	108	116
5Q LOSS MUTATED	9	50	34	26
5Q LOSS WILD-TYPE	87	75	74	90

Figure S121. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S122. Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
5Q LOSS MUTATED	44	12	22	44	9
5Q LOSS WILD-TYPE	94	100	54	62	45

Figure S122. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.079

Table S123. Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
5Q LOSS MUTATED	24	5	11	32	7	20	18	1	13
5Q LOSS WILD-TYPE	59	52	33	52	39	31	31	17	41

Figure S123. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S124. Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
5Q LOSS MUTATED	29	87	23
5Q LOSS WILD-TYPE	160	141	70

Figure S124. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S125. Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
5Q LOSS MUTATED	9	62	21	47
5Q LOSS WILD-TYPE	62	136	120	53

Figure S125. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S126. Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
5Q LOSS MUTATED	12	91	18
5Q LOSS WILD-TYPE	91	157	65

Figure S126. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.086

Table S127. Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	125	108	116
6Q LOSS MUTATED	47	56	57	29
6Q LOSS WILD-TYPE	49	69	51	87

Figure S127. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.17

Table S128. Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
6Q LOSS MUTATED	43	20	22	23	28	29	16	4	21
6Q LOSS WILD-TYPE	40	37	22	61	18	22	33	14	33

Figure S128. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S129. Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
8P LOSS MUTATED	114	58	30
8P LOSS WILD-TYPE	77	171	65

Figure S129. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.048

Table S130. Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
8P LOSS MUTATED	77	36	23	40	14
8P LOSS WILD-TYPE	61	76	53	66	40

Figure S130. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S131. Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
8P LOSS MUTATED	39	23	25	46	8	15	14	2	18
8P LOSS WILD-TYPE	44	34	19	38	38	36	35	16	36

Figure S131. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.048

Table S132. Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
9P LOSS MUTATED	36	30	18	51	19	24	41	8	23
9P LOSS WILD-TYPE	47	27	26	33	27	27	8	10	31

Figure S132. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.086

Table S133. Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
9Q LOSS MUTATED	108	87	53
9Q LOSS WILD-TYPE	83	142	42

Figure S133. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.17

Table S134. Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	125	108	116
9Q LOSS MUTATED	36	79	44	48
9Q LOSS WILD-TYPE	60	46	64	68

Figure S134. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S135. Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
9Q LOSS MUTATED	29	92	54	70
9Q LOSS WILD-TYPE	42	106	87	30

Figure S135. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S136. Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
10P LOSS MUTATED	67	29	14
10P LOSS WILD-TYPE	124	200	81

Figure S136. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.048

Table S137. Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
10P LOSS MUTATED	46	18	5	23	15
10P LOSS WILD-TYPE	92	94	71	83	39

Figure S137. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S138. Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
10P LOSS MUTATED	18	16	10	36	0	10	4	2	11
10P LOSS WILD-TYPE	65	41	34	48	46	41	45	16	43

Figure S138. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.033

Table S139. Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
10Q LOSS MUTATED	70	39	23
10Q LOSS WILD-TYPE	121	190	72

Figure S139. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S140. Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
10Q LOSS MUTATED	23	16	12	44	0	10	9	2	11
10Q LOSS WILD-TYPE	60	41	32	40	46	41	40	16	43

Figure S140. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S141. Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
11P LOSS MUTATED	55	28	29
11P LOSS WILD-TYPE	136	201	66

Figure S141. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.15

Table S142. Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
12P LOSS MUTATED	22	17	5	28	11	3	4	2	14
12P LOSS WILD-TYPE	61	40	39	56	35	48	45	16	40

Figure S142. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.033

Table S143. Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
12Q LOSS MUTATED	55	36	8
12Q LOSS WILD-TYPE	136	193	87

Figure S143. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.063

Table S144. Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
12Q LOSS MUTATED	23	12	4	24	10	1	3	2	14
12Q LOSS WILD-TYPE	60	45	40	60	36	50	46	16	40

Figure S144. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S145. Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
13Q LOSS MUTATED	125	66	61
13Q LOSS WILD-TYPE	66	163	34

Figure S145. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S146. Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
13Q LOSS MUTATED	86	40	24	66	23
13Q LOSS WILD-TYPE	52	72	52	40	31

Figure S146. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S147. Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
13Q LOSS MUTATED	52	22	25	48	10	36	19	1	26
13Q LOSS WILD-TYPE	31	35	19	36	36	15	30	17	28

Figure S147. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S148. Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
15Q LOSS MUTATED	113	73	56
15Q LOSS WILD-TYPE	78	156	39

Figure S148. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.1

Table S149. Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	125	108	116
15Q LOSS MUTATED	27	65	63	53
15Q LOSS WILD-TYPE	69	60	45	63

Figure S149. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S150. Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
15Q LOSS MUTATED	92	37	13	61	26
15Q LOSS WILD-TYPE	46	75	63	45	28

Figure S150. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S151. Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
15Q LOSS MUTATED	48	23	31	49	7	34	9	0	28
15Q LOSS WILD-TYPE	35	34	13	35	39	17	40	18	26

Figure S151. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S152. Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
15Q LOSS MUTATED	63	122	55
15Q LOSS WILD-TYPE	126	106	38

Figure S152. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S153. Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
15Q LOSS MUTATED	27	133	46
15Q LOSS WILD-TYPE	76	115	37

Figure S153. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S154. Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
16P LOSS MUTATED	50	28	33
16P LOSS WILD-TYPE	141	201	62

Figure S154. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.056

Table S155. Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	125	108	116
16P LOSS MUTATED	7	36	35	20
16P LOSS WILD-TYPE	89	89	73	96

Figure S155. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.063

Table S156. Gene #68: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
16P LOSS MUTATED	42	10	14	35	8
16P LOSS WILD-TYPE	96	102	62	71	46

Figure S156. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S157. Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
16Q LOSS MUTATED	62	39	39
16Q LOSS WILD-TYPE	129	190	56

Figure S157. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S158. Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	125	108	116
16Q LOSS MUTATED	12	42	42	24
16Q LOSS WILD-TYPE	84	83	66	92

Figure S158. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S159. Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
16Q LOSS MUTATED	59	15	16	39	9
16Q LOSS WILD-TYPE	79	97	60	67	45

Figure S159. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S160. Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
16Q LOSS MUTATED	35	7	20	29	9	17	10	0	11
16Q LOSS WILD-TYPE	48	50	24	55	37	34	39	18	43

Figure S160. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S161. Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
17P LOSS MUTATED	117	58	40
17P LOSS WILD-TYPE	74	171	55

Figure S161. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.079

Table S162. Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	125	108	116
17P LOSS MUTATED	28	53	63	39
17P LOSS WILD-TYPE	68	72	45	77

Figure S162. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S163. Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
18P LOSS MUTATED	92	61	28
18P LOSS WILD-TYPE	99	168	67

Figure S163. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S164. Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
18Q LOSS MUTATED	116	74	26
18Q LOSS WILD-TYPE	75	155	69

Figure S164. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S165. Gene #73: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	40	33	45	31	32
18Q LOSS MUTATED	17	6	34	15	12
18Q LOSS WILD-TYPE	23	27	11	16	20

Figure S165. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.086

Table S166. Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
18Q LOSS MUTATED	80	39	33	32	20
18Q LOSS WILD-TYPE	58	73	43	74	34

Figure S166. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.1

Table S167. Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
18Q LOSS MUTATED	39	27	25	42	7	14	24	9	17
18Q LOSS WILD-TYPE	44	30	19	42	39	37	25	9	37

Figure S167. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S168. Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
19P LOSS MUTATED	109	72	63
19P LOSS WILD-TYPE	82	157	32

Figure S168. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S169. Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	125	108	116
19P LOSS MUTATED	31	87	46	43
19P LOSS WILD-TYPE	65	38	62	73

Figure S169. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S170. Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
19P LOSS MUTATED	63	39	42	73	17
19P LOSS WILD-TYPE	75	73	34	33	37

Figure S170. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S171. Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
19P LOSS MUTATED	29	17	21	50	31	35	33	4	14
19P LOSS WILD-TYPE	54	40	23	34	15	16	16	14	40

Figure S171. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S172. Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
19P LOSS MUTATED	65	135	39
19P LOSS WILD-TYPE	124	93	54

Figure S172. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S173. Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
19P LOSS MUTATED	31	97	43	68
19P LOSS WILD-TYPE	40	101	98	32

Figure S173. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S174. Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
19Q LOSS MUTATED	82	38	39
19Q LOSS WILD-TYPE	109	191	56

Figure S174. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.093

Table S175. Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	125	108	116
19Q LOSS MUTATED	17	54	37	26
19Q LOSS WILD-TYPE	79	71	71	90

Figure S175. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.12

Table S176. Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
19Q LOSS MUTATED	47	23	23	50	10
19Q LOSS WILD-TYPE	91	89	53	56	44

Figure S176. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.04

Table S177. Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
19Q LOSS MUTATED	20	13	17	34	17	23	21	0	8
19Q LOSS WILD-TYPE	63	44	27	50	29	28	28	18	46

Figure S177. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.04

Table S178. Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
19Q LOSS MUTATED	38	90	27
19Q LOSS WILD-TYPE	151	138	66

Figure S178. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S179. Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
19Q LOSS MUTATED	18	64	25	48
19Q LOSS WILD-TYPE	53	134	116	52

Figure S179. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.063

Table S180. Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
20P LOSS MUTATED	62	33	22
20P LOSS WILD-TYPE	129	196	73

Figure S180. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S181. Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
21Q LOSS MUTATED	52	59	54
21Q LOSS WILD-TYPE	139	170	41

Figure S181. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S182. Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
21Q LOSS MUTATED	40	14	30	58	11
21Q LOSS WILD-TYPE	98	98	46	48	43

Figure S182. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S183. Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
21Q LOSS MUTATED	14	8	17	31	11	32	24	4	12
21Q LOSS WILD-TYPE	69	49	27	53	35	19	25	14	42

Figure S183. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S184. Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
21Q LOSS MUTATED	39	96	27
21Q LOSS WILD-TYPE	150	132	66

Figure S184. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.071

Table S185. Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
21Q LOSS MUTATED	15	66	32	49
21Q LOSS WILD-TYPE	56	132	109	51

Figure S185. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S186. Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	191	229	95
22Q LOSS MUTATED	99	60	61
22Q LOSS WILD-TYPE	92	169	34

Figure S186. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S187. Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	96	125	108	116
22Q LOSS MUTATED	24	69	56	41
22Q LOSS WILD-TYPE	72	56	52	75

Figure S187. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S188. Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
22Q LOSS MUTATED	70	30	34	62	11
22Q LOSS WILD-TYPE	68	82	42	44	43

Figure S188. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S189. Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	83	57	44	84	46	51	49	18	54
22Q LOSS MUTATED	47	14	20	40	14	33	24	4	11
22Q LOSS WILD-TYPE	36	43	24	44	32	18	25	14	43

Figure S189. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.056

Table S190. Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	189	228	93
22Q LOSS MUTATED	58	119	39
22Q LOSS WILD-TYPE	131	109	54

Figure S190. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S191. Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	71	198	141	100
22Q LOSS MUTATED	21	100	41	54
22Q LOSS WILD-TYPE	50	98	100	46

Figure S191. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.12

Table S192. Gene #79: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	248	83
22Q LOSS MUTATED	28	128	31
22Q LOSS WILD-TYPE	75	120	52

Figure S192. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtypes file = LUAD-TP.transferedmergedcluster.txt
Number of patients = 515
Number of significantly arm-level cnvs = 80
Number of molecular subtypes = 12
Exclude genes that fewer than K tumors have mutations, 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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