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 79 arm-level events and 10 molecular subtypes across 369 patients, 184 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 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
2p gain cnv correlated to 'CN_CNMF'.
2q gain cnv correlated to 'CN_CNMF'.
5p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
6p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
6q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
7p gain cnv correlated to 'CN_CNMF'.
7q gain cnv correlated to 'CN_CNMF'.
8p gain cnv correlated to 'CN_CNMF'.
8q gain cnv correlated to 'MIRSEQ_MATURE_CNMF'.
10p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
10q gain cnv correlated to 'CN_CNMF'.
11q gain cnv correlated to 'CN_CNMF'.
13q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
14q gain cnv correlated to 'CN_CNMF'.
15q gain cnv correlated to 'CN_CNMF'.
18p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
20p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
xq gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
1p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
1q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
2p loss cnv correlated to 'CN_CNMF'.
2q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
3p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
3q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
4p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
4q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
5p loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
5q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
6p loss cnv correlated to 'CN_CNMF'.
6q loss cnv correlated to 'CN_CNMF'.
7p loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.
7q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
8p loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
9p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
9q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
10p loss cnv correlated to 'CN_CNMF'.
10q loss cnv correlated to 'CN_CNMF'.
11p loss cnv correlated to 'CN_CNMF'.
12p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
12q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
13q loss cnv correlated to 'CN_CNMF'.
14q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
15q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
16p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
16q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
17p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
17q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
18p loss cnv correlated to 'CN_CNMF'.
18q loss cnv correlated to 'CN_CNMF'.
19p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
19q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
20p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
21q loss cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
22q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
xq loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 79 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 184 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
5q loss	81 (22%)	288	1e-05 (0.0079)	1e-05 (0.0079)	0.62 (1.00)	0.977 (1.00)	1e-05 (0.0079)	3e-05 (0.0204)	2e-05 (0.0138)	1e-05 (0.0079)	2e-05 (0.0138)	1e-05 (0.0079)
16p loss	77 (21%)	292	1e-05 (0.0079)	0.00036 (0.22)	0.811 (1.00)	0.842 (1.00)	1e-05 (0.0079)	1e-05 (0.0079)	2e-05 (0.0138)	9e-05 (0.0591)	2e-05 (0.0138)	1e-05 (0.0079)
17p loss	131 (36%)	238	1e-05 (0.0079)	1e-05 (0.0079)	0.504 (1.00)	0.0286 (1.00)	1e-05 (0.0079)	1e-05 (0.0079)	0.00018 (0.115)	4e-05 (0.0268)	7e-05 (0.0463)	1e-05 (0.0079)
19p loss	93 (25%)	276	1e-05 (0.0079)	1e-05 (0.0079)	0.00397 (1.00)	0.0702 (1.00)	1e-05 (0.0079)	1e-05 (0.0079)	1e-05 (0.0079)	1e-05 (0.0079)	1e-05 (0.0079)	1e-05 (0.0079)
19q loss	72 (20%)	297	1e-05 (0.0079)	1e-05 (0.0079)	0.018 (1.00)	0.144 (1.00)	1e-05 (0.0079)	3e-05 (0.0204)	1e-05 (0.0079)	1e-05 (0.0079)	1e-05 (0.0079)	1e-05 (0.0079)
20q gain	231 (63%)	138	1e-05 (0.0079)	1e-05 (0.0079)	0.0525 (1.00)	0.227 (1.00)	1e-05 (0.0079)	1e-05 (0.0079)	0.00019 (0.12)	1e-05 (0.0079)	0.0147 (1.00)	1e-05 (0.0079)
9p loss	116 (31%)	253	1e-05 (0.0079)	1e-05 (0.0079)	0.00165 (0.912)	0.00028 (0.174)	1e-05 (0.0079)	0.00013 (0.0841)	0.00091 (0.536)	3e-05 (0.0204)	0.068 (1.00)	0.0001 (0.0654)
16q loss	86 (23%)	283	1e-05 (0.0079)	1e-05 (0.0079)	0.0468 (1.00)	0.0832 (1.00)	1e-05 (0.0079)	2e-05 (0.0138)	0.00028 (0.174)	0.00024 (0.15)	0.00445 (1.00)	3e-05 (0.0204)
6p gain	69 (19%)	300	1e-05 (0.0079)	1e-05 (0.0079)	0.0829 (1.00)	0.298 (1.00)	0.00024 (0.15)	0.00405 (1.00)	7e-05 (0.0463)	0.00054 (0.325)	0.00013 (0.0841)	1e-05 (0.0079)
12p loss	48 (13%)	321	1e-05 (0.0079)	1e-05 (0.0079)	0.264 (1.00)	0.0975 (1.00)	9e-05 (0.0591)	1e-05 (0.0079)	0.0618 (1.00)	1e-05 (0.0079)	0.0244 (1.00)	1e-05 (0.0079)
22q loss	116 (31%)	253	1e-05 (0.0079)	1e-05 (0.0079)	0.015 (1.00)	0.00714 (1.00)	0.00125 (0.715)	0.00432 (1.00)	4e-05 (0.0268)	1e-05 (0.0079)	0.0004 (0.243)	1e-05 (0.0079)
5p gain	84 (23%)	285	1e-05 (0.0079)	1e-05 (0.0079)	0.263 (1.00)	0.96 (1.00)	1e-05 (0.0079)	0.00469 (1.00)	0.00193 (1.00)	7e-05 (0.0463)	0.00156 (0.872)	1e-05 (0.0079)
6q gain	55 (15%)	314	1e-05 (0.0079)	1e-05 (0.0079)	0.119 (1.00)	0.247 (1.00)	0.00027 (0.168)	0.0081 (1.00)	0.00015 (0.0966)	0.0335 (1.00)	0.00011 (0.0717)	0.00099 (0.574)
13q gain	129 (35%)	240	1e-05 (0.0079)	0.00019 (0.12)	0.57 (1.00)	0.637 (1.00)	0.0223 (1.00)	6e-05 (0.04)	0.00954 (1.00)	0.00343 (1.00)	0.00018 (0.115)	7e-05 (0.0463)
4p loss	139 (38%)	230	1e-05 (0.0079)	2e-05 (0.0138)	0.28 (1.00)	0.102 (1.00)	0.00058 (0.348)	0.00021 (0.133)	0.00426 (1.00)	1e-05 (0.0079)	0.00161 (0.895)	1e-05 (0.0079)
15q loss	78 (21%)	291	1e-05 (0.0079)	0.00138 (0.781)	0.0103 (1.00)	0.648 (1.00)	0.00015 (0.0966)	0.00165 (0.912)	0.00394 (1.00)	0.00031 (0.192)	0.00031 (0.192)	0.00011 (0.0717)
18p gain	66 (18%)	303	1e-05 (0.0079)	1e-05 (0.0079)	0.0953 (1.00)	0.0455 (1.00)	0.0156 (1.00)	0.00272 (1.00)	0.00026 (0.162)	0.00023 (0.145)	0.00075 (0.445)	0.00077 (0.457)
20p gain	201 (54%)	168	1e-05 (0.0079)	0.00012 (0.0778)	0.0849 (1.00)	0.149 (1.00)	0.0007 (0.418)	1e-05 (0.0079)	0.00614 (1.00)	0.00054 (0.325)	0.0279 (1.00)	0.00011 (0.0717)
3q loss	47 (13%)	322	1e-05 (0.0079)	0.00244 (1.00)	0.208 (1.00)	0.272 (1.00)	0.0001 (0.0654)	2e-05 (0.0138)	0.00261 (1.00)	0.00195 (1.00)	0.00032 (0.197)	0.00176 (0.968)
4q loss	137 (37%)	232	1e-05 (0.0079)	3e-05 (0.0204)	0.0707 (1.00)	0.0222 (1.00)	0.00622 (1.00)	0.00107 (0.618)	0.00789 (1.00)	1e-05 (0.0079)	0.00314 (1.00)	1e-05 (0.0079)
17q loss	61 (17%)	308	1e-05 (0.0079)	1e-05 (0.0079)	0.398 (1.00)	0.00977 (1.00)	0.00105 (0.608)	0.00338 (1.00)	0.0424 (1.00)	0.00034 (0.208)	0.00531 (1.00)	2e-05 (0.0138)
1q gain	88 (24%)	281	1e-05 (0.0079)	0.00023 (0.145)	0.0398 (1.00)	0.177 (1.00)	5e-05 (0.0333)	0.00755 (1.00)	0.0147 (1.00)	0.00976 (1.00)	0.00085 (0.502)	0.0166 (1.00)
10p gain	85 (23%)	284	1e-05 (0.0079)	2e-05 (0.0138)	0.109 (1.00)	0.43 (1.00)	0.00164 (0.909)	0.148 (1.00)	0.199 (1.00)	0.00047 (0.284)	0.068 (1.00)	0.00028 (0.174)
21q gain	21 (6%)	348	3e-05 (0.0204)	0.00031 (0.192)	0.145 (1.00)	0.638 (1.00)	0.00977 (1.00)	0.0315 (1.00)	0.0196 (1.00)	0.00041 (0.249)	0.0195 (1.00)	0.00072 (0.429)
12q loss	38 (10%)	331	1e-05 (0.0079)	2e-05 (0.0138)	0.545 (1.00)	0.114 (1.00)	0.00338 (1.00)	0.00581 (1.00)	0.665 (1.00)	0.00492 (1.00)	0.178 (1.00)	0.00021 (0.133)
21q loss	143 (39%)	226	1e-05 (0.0079)	0.0232 (1.00)	0.101 (1.00)	0.297 (1.00)	0.0369 (1.00)	0.00167 (0.92)	0.00039 (0.238)	0.00526 (1.00)	0.00015 (0.0966)	0.00198 (1.00)
xq gain	44 (12%)	325	1e-05 (0.0079)	0.00017 (0.109)	0.748 (1.00)	0.507 (1.00)	0.0524 (1.00)	0.00042 (0.255)	0.0569 (1.00)	0.439 (1.00)	0.125 (1.00)	0.0469 (1.00)
1p loss	46 (12%)	323	1e-05 (0.0079)	0.00011 (0.0717)	0.0593 (1.00)	0.295 (1.00)	0.0363 (1.00)	0.0112 (1.00)	0.337 (1.00)	0.0243 (1.00)	0.129 (1.00)	0.00571 (1.00)
1q loss	21 (6%)	348	6e-05 (0.04)	0.00014 (0.0903)	0.0335 (1.00)	0.301 (1.00)	0.565 (1.00)	0.216 (1.00)	0.23 (1.00)	0.316 (1.00)	0.243 (1.00)	0.118 (1.00)
2q loss	24 (7%)	345	4e-05 (0.0268)	8e-05 (0.0526)	0.729 (1.00)	0.933 (1.00)	0.0113 (1.00)	0.412 (1.00)	0.123 (1.00)	0.0152 (1.00)	0.023 (1.00)	0.156 (1.00)
3p loss	74 (20%)	295	1e-05 (0.0079)	0.0174 (1.00)	0.36 (1.00)	0.199 (1.00)	0.00324 (1.00)	0.0003 (0.186)	0.00958 (1.00)	0.00503 (1.00)	0.0106 (1.00)	0.00533 (1.00)
5p loss	47 (13%)	322	1e-05 (0.0079)	0.00297 (1.00)	0.218 (1.00)	0.756 (1.00)	0.00452 (1.00)	0.0134 (1.00)	0.00474 (1.00)	0.00506 (1.00)	0.00092 (0.541)	0.00017 (0.109)
7q loss	26 (7%)	343	2e-05 (0.0138)	0.00265 (1.00)	0.653 (1.00)	0.374 (1.00)	0.0276 (1.00)	0.189 (1.00)	0.0462 (1.00)	0.066 (1.00)	0.00018 (0.115)	0.0438 (1.00)
8p loss	65 (18%)	304	1e-05 (0.0079)	0.0442 (1.00)	0.399 (1.00)	0.768 (1.00)	0.00862 (1.00)	0.00138 (0.781)	0.00512 (1.00)	0.00766 (1.00)	3e-05 (0.0204)	0.00095 (0.554)
9q loss	81 (22%)	288	1e-05 (0.0079)	0.00145 (0.813)	0.247 (1.00)	0.0165 (1.00)	0.00015 (0.0966)	0.0167 (1.00)	0.00148 (0.829)	0.00098 (0.569)	0.0058 (1.00)	0.00156 (0.872)
14q loss	88 (24%)	281	1e-05 (0.0079)	9e-05 (0.0591)	0.561 (1.00)	0.531 (1.00)	0.00111 (0.64)	0.00691 (1.00)	0.0365 (1.00)	0.00143 (0.804)	0.0134 (1.00)	0.00467 (1.00)
20p loss	19 (5%)	350	0.00033 (0.203)	0.00036 (0.22)	1 (1.00)	0.37 (1.00)	0.00044 (0.266)	0.0574 (1.00)	0.106 (1.00)	0.646 (1.00)	0.436 (1.00)	0.588 (1.00)
xq loss	43 (12%)	326	1e-05 (0.0079)	4e-05 (0.0268)	0.263 (1.00)	0.0696 (1.00)	0.0572 (1.00)	0.158 (1.00)	0.0458 (1.00)	0.795 (1.00)	0.0486 (1.00)	0.186 (1.00)
1p gain	44 (12%)	325	1e-05 (0.0079)	0.0522 (1.00)	0.00534 (1.00)	0.609 (1.00)	0.0174 (1.00)	0.402 (1.00)	0.0102 (1.00)	0.0853 (1.00)	0.00048 (0.289)	0.0472 (1.00)
2p gain	61 (17%)	308	1e-05 (0.0079)	0.00624 (1.00)	0.0216 (1.00)	0.118 (1.00)	0.143 (1.00)	0.0279 (1.00)	0.00096 (0.559)	0.0374 (1.00)	0.00273 (1.00)	0.00122 (0.699)
2q gain	52 (14%)	317	1e-05 (0.0079)	0.163 (1.00)	0.239 (1.00)	0.557 (1.00)	0.0448 (1.00)	0.0299 (1.00)	0.117 (1.00)	0.283 (1.00)	0.101 (1.00)	0.0584 (1.00)
7p gain	161 (44%)	208	1e-05 (0.0079)	0.00211 (1.00)	0.612 (1.00)	0.833 (1.00)	0.397 (1.00)	0.00079 (0.468)	0.0313 (1.00)	0.114 (1.00)	0.0154 (1.00)	0.00142 (0.799)
7q gain	139 (38%)	230	1e-05 (0.0079)	0.0384 (1.00)	0.842 (1.00)	0.608 (1.00)	0.508 (1.00)	0.00772 (1.00)	0.119 (1.00)	0.328 (1.00)	0.286 (1.00)	0.0459 (1.00)
8p gain	155 (42%)	214	2e-05 (0.0138)	0.0115 (1.00)	0.565 (1.00)	0.392 (1.00)	0.35 (1.00)	0.115 (1.00)	0.283 (1.00)	0.646 (1.00)	0.00808 (1.00)	0.21 (1.00)
8q gain	208 (56%)	161	0.00134 (0.76)	0.0166 (1.00)	0.788 (1.00)	0.299 (1.00)	0.0256 (1.00)	0.0199 (1.00)	0.00523 (1.00)	0.0275 (1.00)	0.00023 (0.145)	0.00341 (1.00)
10q gain	59 (16%)	310	1e-05 (0.0079)	0.00648 (1.00)	0.129 (1.00)	0.743 (1.00)	0.0201 (1.00)	0.112 (1.00)	0.151 (1.00)	0.147 (1.00)	0.236 (1.00)	0.0401 (1.00)
11q gain	53 (14%)	316	1e-05 (0.0079)	0.00157 (0.874)	0.837 (1.00)	1 (1.00)	0.312 (1.00)	0.00622 (1.00)	0.00067 (0.401)	0.00093 (0.543)	0.00635 (1.00)	0.00125 (0.715)
14q gain	23 (6%)	346	0.00035 (0.214)	0.251 (1.00)	0.798 (1.00)	0.646 (1.00)	0.641 (1.00)	0.525 (1.00)	0.00893 (1.00)	0.637 (1.00)	0.0363 (1.00)	0.82 (1.00)
15q gain	31 (8%)	338	6e-05 (0.04)	0.00211 (1.00)	0.208 (1.00)	0.827 (1.00)	0.02 (1.00)	0.125 (1.00)	0.282 (1.00)	0.268 (1.00)	0.365 (1.00)	0.227 (1.00)
2p loss	20 (5%)	349	0.00017 (0.109)	0.00092 (0.541)	0.35 (1.00)	0.535 (1.00)	0.0155 (1.00)	0.491 (1.00)	0.126 (1.00)	0.164 (1.00)	0.0667 (1.00)	0.591 (1.00)
6p loss	43 (12%)	326	1e-05 (0.0079)	0.00313 (1.00)	0.15 (1.00)	0.913 (1.00)	0.0236 (1.00)	0.0123 (1.00)	0.109 (1.00)	0.00192 (1.00)	0.0651 (1.00)	0.00232 (1.00)
6q loss	56 (15%)	313	1e-05 (0.0079)	0.00191 (1.00)	0.765 (1.00)	0.681 (1.00)	0.0417 (1.00)	0.126 (1.00)	0.603 (1.00)	0.027 (1.00)	0.326 (1.00)	0.0717 (1.00)
7p loss	14 (4%)	355	0.00133 (0.755)	0.0074 (1.00)	0.443 (1.00)	0.403 (1.00)	0.00162 (0.899)	0.219 (1.00)	0.188 (1.00)	0.0177 (1.00)	0.0003 (0.186)	0.00244 (1.00)
10p loss	49 (13%)	320	3e-05 (0.0204)	0.0361 (1.00)	0.552 (1.00)	0.0893 (1.00)	0.015 (1.00)	0.0735 (1.00)	0.012 (1.00)	0.0116 (1.00)	0.0062 (1.00)	0.0145 (1.00)
10q loss	55 (15%)	314	1e-05 (0.0079)	0.0045 (1.00)	0.609 (1.00)	0.0318 (1.00)	0.00092 (0.541)	0.00256 (1.00)	0.00868 (1.00)	0.0191 (1.00)	0.0129 (1.00)	0.00112 (0.645)
11p loss	54 (15%)	315	2e-05 (0.0138)	0.0115 (1.00)	0.00911 (1.00)	0.136 (1.00)	0.0987 (1.00)	0.198 (1.00)	0.121 (1.00)	0.0192 (1.00)	0.132 (1.00)	0.00693 (1.00)
13q loss	31 (8%)	338	6e-05 (0.04)	0.694 (1.00)	0.686 (1.00)	0.304 (1.00)	0.28 (1.00)	0.601 (1.00)	0.728 (1.00)	0.911 (1.00)	0.335 (1.00)	0.603 (1.00)
18p loss	107 (29%)	262	1e-05 (0.0079)	0.631 (1.00)	0.505 (1.00)	0.62 (1.00)	0.394 (1.00)	0.258 (1.00)	0.187 (1.00)	0.422 (1.00)	0.363 (1.00)	0.207 (1.00)
18q loss	132 (36%)	237	1e-05 (0.0079)	0.0267 (1.00)	0.294 (1.00)	0.868 (1.00)	0.00708 (1.00)	0.0225 (1.00)	0.00514 (1.00)	0.00329 (1.00)	0.014 (1.00)	0.00129 (0.735)
3p gain	40 (11%)	329	0.00529 (1.00)	0.0118 (1.00)	0.791 (1.00)	0.0255 (1.00)	0.627 (1.00)	0.223 (1.00)	0.612 (1.00)	0.58 (1.00)	0.102 (1.00)	0.344 (1.00)
3q gain	69 (19%)	300	0.0134 (1.00)	0.317 (1.00)	0.874 (1.00)	0.149 (1.00)	0.168 (1.00)	0.0292 (1.00)	0.597 (1.00)	0.525 (1.00)	0.165 (1.00)	0.638 (1.00)
4p gain	13 (4%)	356	0.159 (1.00)	0.505 (1.00)	1 (1.00)	0.448 (1.00)	0.388 (1.00)	0.427 (1.00)	0.135 (1.00)	0.936 (1.00)	0.726 (1.00)	0.541 (1.00)
4q gain	9 (2%)	360	0.759 (1.00)	0.289 (1.00)	0.867 (1.00)	0.186 (1.00)	0.0916 (1.00)	0.539 (1.00)	0.486 (1.00)	0.455 (1.00)	0.27 (1.00)	0.26 (1.00)
5q gain	34 (9%)	335	0.00085 (0.502)	0.0952 (1.00)	0.658 (1.00)	0.106 (1.00)	0.105 (1.00)	0.35 (1.00)	0.69 (1.00)	0.474 (1.00)	0.495 (1.00)	0.471 (1.00)
9p gain	48 (13%)	321	0.097 (1.00)	1 (1.00)	0.568 (1.00)	0.924 (1.00)	0.373 (1.00)	0.582 (1.00)	0.243 (1.00)	0.827 (1.00)	0.0691 (1.00)	0.527 (1.00)
9q gain	61 (17%)	308	0.238 (1.00)	0.982 (1.00)	0.246 (1.00)	0.994 (1.00)	0.43 (1.00)	0.927 (1.00)	0.43 (1.00)	0.525 (1.00)	0.503 (1.00)	0.606 (1.00)
11p gain	45 (12%)	324	0.00121 (0.696)	0.0408 (1.00)	0.934 (1.00)	0.845 (1.00)	0.283 (1.00)	0.394 (1.00)	0.00585 (1.00)	0.00527 (1.00)	0.0179 (1.00)	0.0475 (1.00)
12p gain	77 (21%)	292	0.00289 (1.00)	0.242 (1.00)	0.238 (1.00)	0.337 (1.00)	0.168 (1.00)	0.102 (1.00)	0.00139 (0.784)	0.323 (1.00)	0.00702 (1.00)	0.115 (1.00)
12q gain	66 (18%)	303	0.0558 (1.00)	0.966 (1.00)	0.439 (1.00)	0.422 (1.00)	0.966 (1.00)	0.277 (1.00)	0.0964 (1.00)	0.544 (1.00)	0.273 (1.00)	0.43 (1.00)
16p gain	52 (14%)	317	0.00073 (0.434)	0.0096 (1.00)	0.393 (1.00)	0.113 (1.00)	0.0733 (1.00)	0.286 (1.00)	0.754 (1.00)	0.834 (1.00)	0.828 (1.00)	0.732 (1.00)
16q gain	42 (11%)	327	0.00671 (1.00)	0.202 (1.00)	0.673 (1.00)	0.262 (1.00)	0.188 (1.00)	0.624 (1.00)	0.57 (1.00)	0.93 (1.00)	0.32 (1.00)	0.854 (1.00)
17p gain	21 (6%)	348	0.0373 (1.00)	0.861 (1.00)	0.843 (1.00)	0.774 (1.00)	0.506 (1.00)	0.278 (1.00)	0.472 (1.00)	0.513 (1.00)	0.343 (1.00)	0.589 (1.00)
17q gain	46 (12%)	323	0.00092 (0.541)	0.212 (1.00)	0.941 (1.00)	0.902 (1.00)	0.531 (1.00)	0.201 (1.00)	0.289 (1.00)	0.662 (1.00)	0.221 (1.00)	0.462 (1.00)
18q gain	45 (12%)	324	0.00369 (1.00)	0.00621 (1.00)	0.597 (1.00)	0.237 (1.00)	0.371 (1.00)	0.033 (1.00)	0.0477 (1.00)	0.0596 (1.00)	0.131 (1.00)	0.0922 (1.00)
19p gain	46 (12%)	323	0.0195 (1.00)	0.929 (1.00)	0.657 (1.00)	0.0876 (1.00)	0.608 (1.00)	0.908 (1.00)	0.766 (1.00)	1 (1.00)	0.741 (1.00)	0.458 (1.00)
19q gain	61 (17%)	308	0.00131 (0.745)	0.361 (1.00)	0.297 (1.00)	0.0956 (1.00)	0.0186 (1.00)	0.345 (1.00)	0.184 (1.00)	0.0324 (1.00)	0.106 (1.00)	0.0677 (1.00)
22q gain	28 (8%)	341	0.00063 (0.377)	0.136 (1.00)	0.846 (1.00)	0.218 (1.00)	0.255 (1.00)	0.067 (1.00)	0.243 (1.00)	0.578 (1.00)	0.236 (1.00)	0.415 (1.00)
8q loss	20 (5%)	349	0.0198 (1.00)	0.423 (1.00)	0.942 (1.00)	0.24 (1.00)	0.7 (1.00)	0.959 (1.00)	0.367 (1.00)	0.631 (1.00)	0.408 (1.00)	0.753 (1.00)
11q loss	52 (14%)	317	0.00121 (0.696)	0.241 (1.00)	0.529 (1.00)	0.384 (1.00)	0.679 (1.00)	0.606 (1.00)	0.306 (1.00)	0.288 (1.00)	0.103 (1.00)	0.144 (1.00)

'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
1P GAIN MUTATED	4	6	11	2	21
1P GAIN WILD-TYPE	165	27	55	8	70

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

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
1Q GAIN MUTATED	12	12	18	6	40
1Q GAIN WILD-TYPE	157	21	48	4	51

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.14

Table S3. Gene #2: '1q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
1Q GAIN MUTATED	25	36	16
1Q GAIN WILD-TYPE	95	56	93

Figure S3. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.033

Table S4. Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
1Q GAIN MUTATED	11	7	8	9	30
1Q GAIN WILD-TYPE	54	55	38	28	32

Figure S4. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S5. Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
2P GAIN MUTATED	9	12	16	2	22
2P GAIN WILD-TYPE	160	21	50	8	69

Figure S5. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S6. Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
2Q GAIN MUTATED	9	12	14	1	16
2Q GAIN WILD-TYPE	160	21	52	9	75

Figure S6. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S7. Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
5P GAIN MUTATED	14	5	14	1	50
5P GAIN WILD-TYPE	155	28	52	9	41

Figure S7. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S8. Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
5P GAIN MUTATED	15	37	18
5P GAIN WILD-TYPE	105	55	91

Figure S8. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S9. Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
5P GAIN MUTATED	10	5	7	8	29
5P GAIN WILD-TYPE	55	57	39	29	33

Figure S9. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.046

Table S10. Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
5P GAIN MUTATED	34	10	40
5P GAIN WILD-TYPE	145	73	66

Figure S10. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S11. Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
5P GAIN MUTATED	31	4	35
5P GAIN WILD-TYPE	146	58	47

Figure S11. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S12. Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
6P GAIN MUTATED	6	7	14	2	40
6P GAIN WILD-TYPE	163	26	52	8	51

Figure S12. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S13. Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
6P GAIN MUTATED	14	35	7
6P GAIN WILD-TYPE	106	57	102

Figure S13. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.15

Table S14. Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
6P GAIN MUTATED	9	5	6	5	24
6P GAIN WILD-TYPE	56	57	40	32	38

Figure S14. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.046

Table S15. Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
6P GAIN MUTATED	19	8	41
6P GAIN WILD-TYPE	100	100	100

Figure S15. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.084

Table S16. Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
6P GAIN MUTATED	7	39	9
6P GAIN WILD-TYPE	70	105	91

Figure S16. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S17. Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
6P GAIN MUTATED	26	2	27
6P GAIN WILD-TYPE	151	60	55

Figure S17. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S18. Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
6Q GAIN MUTATED	5	5	10	2	33
6Q GAIN WILD-TYPE	164	28	56	8	58

Figure S18. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S19. Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
6Q GAIN MUTATED	13	27	5
6Q GAIN WILD-TYPE	107	65	104

Figure S19. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.17

Table S20. Gene #12: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
6Q GAIN MUTATED	5	4	5	5	21
6Q GAIN WILD-TYPE	60	58	41	32	41

Figure S20. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.097

Table S21. Gene #12: '6q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
6Q GAIN MUTATED	14	6	34
6Q GAIN WILD-TYPE	105	102	107

Figure S21. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.072

Table S22. Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
6Q GAIN MUTATED	4	33	7
6Q GAIN WILD-TYPE	73	111	93

Figure S22. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S23. Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
7P GAIN MUTATED	42	30	34	7	48
7P GAIN WILD-TYPE	127	3	32	3	43

Figure S23. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S24. Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
7Q GAIN MUTATED	41	28	27	6	37
7Q GAIN WILD-TYPE	128	5	39	4	54

Figure S24. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S25. Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
8P GAIN MUTATED	75	19	17	10	34
8P GAIN WILD-TYPE	94	14	49	0	57

Figure S25. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.14

Table S26. Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
8Q GAIN MUTATED	39	96	41
8Q GAIN WILD-TYPE	38	48	59

Figure S26. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S27. Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
10P GAIN MUTATED	10	8	33	0	34
10P GAIN WILD-TYPE	159	25	33	10	57

Figure S27. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S28. Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
10P GAIN MUTATED	20	37	16
10P GAIN WILD-TYPE	100	55	93

Figure S28. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.17

Table S29. Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
10P GAIN MUTATED	31	9	32
10P GAIN WILD-TYPE	146	53	50

Figure S29. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S30. Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
10Q GAIN MUTATED	8	3	29	0	19
10Q GAIN WILD-TYPE	161	30	37	10	72

Figure S30. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S31. Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
11Q GAIN MUTATED	8	5	16	2	22
11Q GAIN WILD-TYPE	161	28	50	8	69

Figure S31. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S32. Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
13Q GAIN MUTATED	34	26	16	4	49
13Q GAIN WILD-TYPE	135	7	50	6	42

Figure S32. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.12

Table S33. Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
13Q GAIN MUTATED	34	48	29
13Q GAIN WILD-TYPE	86	44	80

Figure S33. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.04

Table S34. Gene #25: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
13Q GAIN MUTATED	3	5	16	16	24	19	6
13Q GAIN WILD-TYPE	35	16	33	46	17	21	15

Figure S34. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.11

Table S35. Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
13Q GAIN MUTATED	18	67	25
13Q GAIN WILD-TYPE	59	77	75

Figure S35. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.046

Table S36. Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
13Q GAIN MUTATED	51	15	44
13Q GAIN WILD-TYPE	126	47	38

Figure S36. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.21

Table S37. Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
14Q GAIN MUTATED	4	5	1	1	12
14Q GAIN WILD-TYPE	165	28	65	9	79

Figure S37. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'15q gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.04

Table S38. Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
15Q GAIN MUTATED	4	2	14	0	11
15Q GAIN WILD-TYPE	165	31	52	10	80

Figure S38. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S39. Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
18P GAIN MUTATED	12	4	17	2	31
18P GAIN WILD-TYPE	157	29	49	8	60

Figure S39. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S40. Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
18P GAIN MUTATED	12	34	12
18P GAIN WILD-TYPE	108	58	97

Figure S40. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.16

Table S41. Gene #32: '18p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
18P GAIN MUTATED	15	11	40
18P GAIN WILD-TYPE	104	97	101

Figure S41. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.14

Table S42. Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
18P GAIN MUTATED	24	9	33
18P GAIN WILD-TYPE	155	74	73

Figure S42. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S43. Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
20P GAIN MUTATED	55	27	47	7	65
20P GAIN WILD-TYPE	114	6	19	3	26

Figure S43. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.078

Table S44. Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
20P GAIN MUTATED	56	67	51
20P GAIN WILD-TYPE	64	25	58

Figure S44. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S45. Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
20P GAIN MUTATED	16	19	17	28	28	32	2
20P GAIN WILD-TYPE	22	2	32	34	13	8	19

Figure S45. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.072

Table S46. Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
20P GAIN MUTATED	87	26	60
20P GAIN WILD-TYPE	90	36	22

Figure S46. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S47. Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
20Q GAIN MUTATED	63	30	53	8	77
20Q GAIN WILD-TYPE	106	3	13	2	14

Figure S47. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S48. Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
20Q GAIN MUTATED	61	81	61
20Q GAIN WILD-TYPE	59	11	48

Figure S48. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S49. Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
20Q GAIN MUTATED	30	31	27	24	56
20Q GAIN WILD-TYPE	35	31	19	13	6

Figure S49. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S50. Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
20Q GAIN MUTATED	22	19	19	38	31	37	2
20Q GAIN WILD-TYPE	16	2	30	24	10	3	19

Figure S50. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.12

Table S51. Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
20Q GAIN MUTATED	66	57	107
20Q GAIN WILD-TYPE	53	51	34

Figure S51. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S52. Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
20Q GAIN MUTATED	97	42	91
20Q GAIN WILD-TYPE	82	41	15

Figure S52. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S53. Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
20Q GAIN MUTATED	100	28	74
20Q GAIN WILD-TYPE	77	34	8

Figure S53. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S54. Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
21Q GAIN MUTATED	1	1	5	0	14
21Q GAIN WILD-TYPE	168	32	61	10	77

Figure S54. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.19

Table S55. Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
21Q GAIN MUTATED	4	14	2
21Q GAIN WILD-TYPE	116	78	107

Figure S55. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.25

Table S56. Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
21Q GAIN MUTATED	8	0	13
21Q GAIN WILD-TYPE	171	83	93

Figure S56. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S57. Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
XQ GAIN MUTATED	7	11	5	3	18
XQ GAIN WILD-TYPE	162	22	61	7	73

Figure S57. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.11

Table S58. Gene #40: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
XQ GAIN MUTATED	13	21	4
XQ GAIN WILD-TYPE	107	71	105

Figure S58. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S59. Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
1P LOSS MUTATED	2	4	15	1	24
1P LOSS WILD-TYPE	167	29	51	9	67

Figure S59. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.072

Table S60. Gene #41: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
1P LOSS MUTATED	11	24	6
1P LOSS WILD-TYPE	109	68	103

Figure S60. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.04

Table S61. Gene #42: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
1Q LOSS MUTATED	1	0	8	1	11
1Q LOSS WILD-TYPE	168	33	58	9	80

Figure S61. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.09

Table S62. Gene #42: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
1Q LOSS MUTATED	5	14	1
1Q LOSS WILD-TYPE	115	78	108

Figure S62. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.11

Table S63. Gene #43: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
2P LOSS MUTATED	1	1	6	0	12
2P LOSS WILD-TYPE	168	32	60	10	79

Figure S63. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.027

Table S64. Gene #44: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
2Q LOSS MUTATED	1	2	6	0	15
2Q LOSS WILD-TYPE	168	31	60	10	76

Figure S64. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.053

Table S65. Gene #44: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
2Q LOSS MUTATED	4	15	2
2Q LOSS WILD-TYPE	116	77	107

Figure S65. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S66. Gene #45: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
3P LOSS MUTATED	10	14	19	1	30
3P LOSS WILD-TYPE	159	19	47	9	61

Figure S66. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.19

Table S67. Gene #45: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
3P LOSS MUTATED	5	2	4	9	13	15	0
3P LOSS WILD-TYPE	33	19	45	53	28	25	21

Figure S67. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S68. Gene #46: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
3Q LOSS MUTATED	4	9	9	1	24
3Q LOSS WILD-TYPE	165	24	57	9	67

Figure S68. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.065

Table S69. Gene #46: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
3Q LOSS MUTATED	2	3	2	6	17
3Q LOSS WILD-TYPE	63	59	44	31	45

Figure S69. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S70. Gene #46: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
3Q LOSS MUTATED	3	0	1	3	10	13	0
3Q LOSS WILD-TYPE	35	21	48	59	31	27	21

Figure S70. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.2

Table S71. Gene #46: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
3Q LOSS MUTATED	3	31	9
3Q LOSS WILD-TYPE	74	113	91

Figure S71. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S72. Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
4P LOSS MUTATED	22	15	44	3	55
4P LOSS WILD-TYPE	147	18	22	7	36

Figure S72. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S73. Gene #47: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
4P LOSS MUTATED	32	53	35
4P LOSS WILD-TYPE	88	39	74

Figure S73. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.13

Table S74. Gene #47: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
4P LOSS MUTATED	11	2	18	17	18	25	3
4P LOSS WILD-TYPE	27	19	31	45	23	15	18

Figure S74. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S75. Gene #47: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
4P LOSS MUTATED	51	26	62
4P LOSS WILD-TYPE	128	57	44

Figure S75. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S76. Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
4P LOSS MUTATED	52	18	51
4P LOSS WILD-TYPE	125	44	31

Figure S76. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S77. Gene #48: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
4Q LOSS MUTATED	21	14	46	3	53
4Q LOSS WILD-TYPE	148	19	20	7	38

Figure S77. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S78. Gene #48: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
4Q LOSS MUTATED	34	55	32
4Q LOSS WILD-TYPE	86	37	77

Figure S78. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S79. Gene #48: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
4Q LOSS MUTATED	51	25	61
4Q LOSS WILD-TYPE	128	58	45

Figure S79. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S80. Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
4Q LOSS MUTATED	54	18	50
4Q LOSS WILD-TYPE	123	44	32

Figure S80. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S81. Gene #49: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
5P LOSS MUTATED	4	8	14	4	17
5P LOSS WILD-TYPE	165	25	52	6	74

Figure S81. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.11

Table S82. Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
5P LOSS MUTATED	19	2	22
5P LOSS WILD-TYPE	158	60	60

Figure S82. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S83. Gene #50: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
5Q LOSS MUTATED	6	11	19	5	40
5Q LOSS WILD-TYPE	163	22	47	5	51

Figure S83. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S84. Gene #50: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
5Q LOSS MUTATED	19	42	13
5Q LOSS WILD-TYPE	101	50	96

Figure S84. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S85. Gene #50: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
5Q LOSS MUTATED	11	3	5	7	28
5Q LOSS WILD-TYPE	54	59	41	30	34

Figure S85. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S86. Gene #50: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
5Q LOSS MUTATED	6	3	2	13	8	20	2
5Q LOSS WILD-TYPE	32	18	47	49	33	20	19

Figure S86. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S87. Gene #50: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
5Q LOSS MUTATED	20	12	49
5Q LOSS WILD-TYPE	99	96	92

Figure S87. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S88. Gene #50: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
5Q LOSS MUTATED	28	9	44
5Q LOSS WILD-TYPE	151	74	62

Figure S88. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S89. Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
5Q LOSS MUTATED	12	51	12
5Q LOSS WILD-TYPE	65	93	88

Figure S89. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S90. Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
5Q LOSS MUTATED	27	4	44
5Q LOSS WILD-TYPE	150	58	38

Figure S90. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S91. Gene #51: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
6P LOSS MUTATED	4	4	19	0	16
6P LOSS WILD-TYPE	165	29	47	10	75

Figure S91. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S92. Gene #52: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
6Q LOSS MUTATED	8	5	24	0	19
6Q LOSS WILD-TYPE	161	28	42	10	72

Figure S92. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'7p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.19

Table S93. Gene #53: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
7P LOSS MUTATED	0	11	0
7P LOSS WILD-TYPE	77	133	100

Figure S93. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S94. Gene #54: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
7Q LOSS MUTATED	1	1	9	1	14
7Q LOSS WILD-TYPE	168	32	57	9	77

Figure S94. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

'7q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.11

Table S95. Gene #54: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
7Q LOSS MUTATED	1	20	2
7Q LOSS WILD-TYPE	76	124	98

Figure S95. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S96. Gene #55: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
8P LOSS MUTATED	9	6	24	0	26
8P LOSS WILD-TYPE	160	27	42	10	65

Figure S96. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S97. Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
8P LOSS MUTATED	10	41	7
8P LOSS WILD-TYPE	67	103	93

Figure S97. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S98. Gene #57: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
9P LOSS MUTATED	12	13	48	4	39
9P LOSS WILD-TYPE	157	20	18	6	52

Figure S98. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S99. Gene #57: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
9P LOSS MUTATED	26	50	28
9P LOSS WILD-TYPE	94	42	81

Figure S99. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.17

Table S100. Gene #57: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
9P LOSS MUTATED	6	36	7	32
9P LOSS WILD-TYPE	28	47	48	59

Figure S100. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S101. Gene #57: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
9P LOSS MUTATED	6	13	19	9	35
9P LOSS WILD-TYPE	59	49	27	28	27

Figure S101. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.084

Table S102. Gene #57: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
9P LOSS MUTATED	13	1	10	23	13	21	1
9P LOSS WILD-TYPE	25	20	39	39	28	19	20

Figure S102. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S103. Gene #57: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
9P LOSS MUTATED	40	23	52
9P LOSS WILD-TYPE	139	60	54

Figure S103. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.065

Table S104. Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
9P LOSS MUTATED	46	15	43
9P LOSS WILD-TYPE	131	47	39

Figure S104. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S105. Gene #58: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
9Q LOSS MUTATED	11	10	30	3	27
9Q LOSS WILD-TYPE	158	23	36	7	64

Figure S105. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.097

Table S106. Gene #58: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
9Q LOSS MUTATED	6	10	13	4	25
9Q LOSS WILD-TYPE	59	52	33	33	37

Figure S106. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S107. Gene #59: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
10P LOSS MUTATED	7	7	10	1	24
10P LOSS WILD-TYPE	162	26	56	9	67

Figure S107. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S108. Gene #60: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
10Q LOSS MUTATED	6	10	8	2	29
10Q LOSS WILD-TYPE	163	23	58	8	62

Figure S108. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S109. Gene #61: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
11P LOSS MUTATED	9	4	15	0	26
11P LOSS WILD-TYPE	160	29	51	10	65

Figure S109. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S110. Gene #63: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
12P LOSS MUTATED	1	2	11	1	33
12P LOSS WILD-TYPE	168	31	55	9	58

Figure S110. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S111. Gene #63: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
12P LOSS MUTATED	3	29	6
12P LOSS WILD-TYPE	117	63	103

Figure S111. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.059

Table S112. Gene #63: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
12P LOSS MUTATED	3	4	6	3	20
12P LOSS WILD-TYPE	62	58	40	34	42

Figure S112. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S113. Gene #63: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
12P LOSS MUTATED	2	0	3	10	4	17	0
12P LOSS WILD-TYPE	36	21	46	52	37	23	21

Figure S113. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S114. Gene #63: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
12P LOSS MUTATED	13	6	29
12P LOSS WILD-TYPE	166	77	77

Figure S114. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S115. Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
12P LOSS MUTATED	10	3	25
12P LOSS WILD-TYPE	167	59	57

Figure S115. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S116. Gene #64: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
12Q LOSS MUTATED	0	2	10	1	25
12Q LOSS WILD-TYPE	169	31	56	9	66

Figure S116. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S117. Gene #64: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
12Q LOSS MUTATED	4	22	5
12Q LOSS WILD-TYPE	116	70	104

Figure S117. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.13

Table S118. Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
12Q LOSS MUTATED	10	3	18
12Q LOSS WILD-TYPE	167	59	64

Figure S118. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.04

Table S119. Gene #65: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
13Q LOSS MUTATED	7	0	16	1	7
13Q LOSS WILD-TYPE	162	33	50	9	84

Figure S119. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S120. Gene #66: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
14Q LOSS MUTATED	17	7	30	2	32
14Q LOSS WILD-TYPE	152	26	36	8	59

Figure S120. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.059

Table S121. Gene #66: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
14Q LOSS MUTATED	20	38	19
14Q LOSS WILD-TYPE	100	54	90

Figure S121. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S122. Gene #67: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
15Q LOSS MUTATED	10	12	21	3	32
15Q LOSS WILD-TYPE	159	21	45	7	59

Figure S122. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.097

Table S123. Gene #67: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
15Q LOSS MUTATED	8	4	9	4	23
15Q LOSS WILD-TYPE	57	58	37	33	39

Figure S123. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.19

Table S124. Gene #67: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
15Q LOSS MUTATED	33	9	36
15Q LOSS WILD-TYPE	146	74	70

Figure S124. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.19

Table S125. Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
15Q LOSS MUTATED	11	47	13
15Q LOSS WILD-TYPE	66	97	87

Figure S125. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.072

Table S126. Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
15Q LOSS MUTATED	35	5	31
15Q LOSS WILD-TYPE	142	57	51

Figure S126. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S127. Gene #68: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
16P LOSS MUTATED	8	3	24	0	42
16P LOSS WILD-TYPE	161	30	42	10	49

Figure S127. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.22

Table S128. Gene #68: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
16P LOSS MUTATED	18	33	16
16P LOSS WILD-TYPE	102	59	93

Figure S128. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S129. Gene #68: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
16P LOSS MUTATED	7	5	5	4	31
16P LOSS WILD-TYPE	58	57	41	33	31

Figure S129. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S130. Gene #68: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
16P LOSS MUTATED	7	0	4	9	8	21	3
16P LOSS WILD-TYPE	31	21	45	53	33	19	18

Figure S130. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S131. Gene #68: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
16P LOSS MUTATED	13	16	48
16P LOSS WILD-TYPE	106	92	93

Figure S131. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.059

Table S132. Gene #68: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
16P LOSS MUTATED	27	12	38
16P LOSS WILD-TYPE	152	71	68

Figure S132. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S133. Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
16P LOSS MUTATED	6	48	14
16P LOSS WILD-TYPE	71	96	86

Figure S133. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S134. Gene #68: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
16P LOSS MUTATED	29	6	33
16P LOSS WILD-TYPE	148	56	49

Figure S134. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S135. Gene #69: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
16Q LOSS MUTATED	12	3	24	2	45
16Q LOSS WILD-TYPE	157	30	42	8	46

Figure S135. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S136. Gene #69: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
16Q LOSS MUTATED	14	38	22
16Q LOSS WILD-TYPE	106	54	87

Figure S136. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S137. Gene #69: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
16Q LOSS MUTATED	6	10	10	5	32
16Q LOSS WILD-TYPE	59	52	36	32	30

Figure S137. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S138. Gene #69: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
16Q LOSS MUTATED	8	0	8	14	8	23	2
16Q LOSS WILD-TYPE	30	21	41	48	33	17	19

Figure S138. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.17

Table S139. Gene #69: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
16Q LOSS MUTATED	17	20	49
16Q LOSS WILD-TYPE	102	88	92

Figure S139. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.15

Table S140. Gene #69: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
16Q LOSS MUTATED	30	16	40
16Q LOSS WILD-TYPE	149	67	66

Figure S140. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S141. Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
16Q LOSS MUTATED	31	9	35
16Q LOSS WILD-TYPE	146	53	47

Figure S141. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S142. Gene #70: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
17P LOSS MUTATED	12	21	37	3	58
17P LOSS WILD-TYPE	157	12	29	7	33

Figure S142. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S143. Gene #70: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
17P LOSS MUTATED	34	60	21
17P LOSS WILD-TYPE	86	32	88

Figure S143. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S144. Gene #70: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
17P LOSS MUTATED	14	10	18	12	37
17P LOSS WILD-TYPE	51	52	28	25	25

Figure S144. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S145. Gene #70: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
17P LOSS MUTATED	14	2	7	22	17	27	2
17P LOSS WILD-TYPE	24	19	42	40	24	13	19

Figure S145. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.11

Table S146. Gene #70: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
17P LOSS MUTATED	40	24	66
17P LOSS WILD-TYPE	79	84	75

Figure S146. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.027

Table S147. Gene #70: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
17P LOSS MUTATED	57	18	55
17P LOSS WILD-TYPE	122	65	51

Figure S147. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.046

Table S148. Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
17P LOSS MUTATED	22	71	22
17P LOSS WILD-TYPE	55	73	78

Figure S148. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S149. Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
17P LOSS MUTATED	56	10	49
17P LOSS WILD-TYPE	121	52	33

Figure S149. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S150. Gene #71: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
17Q LOSS MUTATED	5	7	17	2	30
17Q LOSS WILD-TYPE	164	26	49	8	61

Figure S150. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S151. Gene #71: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
17Q LOSS MUTATED	13	29	8
17Q LOSS WILD-TYPE	107	63	101

Figure S151. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.21

Table S152. Gene #71: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
17Q LOSS MUTATED	24	6	30
17Q LOSS WILD-TYPE	155	77	76

Figure S152. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S153. Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
17Q LOSS MUTATED	19	4	27
17Q LOSS WILD-TYPE	158	58	55

Figure S153. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S154. Gene #72: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
18P LOSS MUTATED	27	15	30	2	33
18P LOSS WILD-TYPE	142	18	36	8	58

Figure S154. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S155. Gene #73: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
18Q LOSS MUTATED	29	16	36	2	49
18Q LOSS WILD-TYPE	140	17	30	8	42

Figure S155. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S156. Gene #74: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
19P LOSS MUTATED	3	9	23	4	54
19P LOSS WILD-TYPE	166	24	43	6	37

Figure S156. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S157. Gene #74: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
19P LOSS MUTATED	19	51	12
19P LOSS WILD-TYPE	101	41	97

Figure S157. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S158. Gene #74: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
19P LOSS MUTATED	8	3	8	4	34
19P LOSS WILD-TYPE	57	59	38	33	28

Figure S158. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S159. Gene #74: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
19P LOSS MUTATED	5	2	3	14	10	23	0
19P LOSS WILD-TYPE	33	19	46	48	31	17	21

Figure S159. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S160. Gene #74: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
19P LOSS MUTATED	21	12	59
19P LOSS WILD-TYPE	98	96	82

Figure S160. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S161. Gene #74: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
19P LOSS MUTATED	29	8	55
19P LOSS WILD-TYPE	150	75	51

Figure S161. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S162. Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
19P LOSS MUTATED	12	58	11
19P LOSS WILD-TYPE	65	86	89

Figure S162. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S163. Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
19P LOSS MUTATED	32	5	44
19P LOSS WILD-TYPE	145	57	38

Figure S163. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S164. Gene #75: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
19Q LOSS MUTATED	2	7	17	4	42
19Q LOSS WILD-TYPE	167	26	49	6	49

Figure S164. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S165. Gene #75: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
19Q LOSS MUTATED	15	39	8
19Q LOSS WILD-TYPE	105	53	101

Figure S165. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S166. Gene #75: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
19Q LOSS MUTATED	5	2	8	5	25
19Q LOSS WILD-TYPE	60	60	38	32	37

Figure S166. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S167. Gene #75: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
19Q LOSS MUTATED	3	1	2	13	9	17	0
19Q LOSS WILD-TYPE	35	20	47	49	32	23	21

Figure S167. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S168. Gene #75: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
19Q LOSS MUTATED	17	8	47
19Q LOSS WILD-TYPE	102	100	94

Figure S168. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S169. Gene #75: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
19Q LOSS MUTATED	23	7	42
19Q LOSS WILD-TYPE	156	76	64

Figure S169. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S170. Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
19Q LOSS MUTATED	12	45	6
19Q LOSS WILD-TYPE	65	99	94

Figure S170. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S171. Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
19Q LOSS MUTATED	25	4	34
19Q LOSS WILD-TYPE	152	58	48

Figure S171. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.2

Table S172. Gene #76: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
20P LOSS MUTATED	1	1	8	0	9
20P LOSS WILD-TYPE	168	32	58	10	82

Figure S172. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.22

Table S173. Gene #76: '20p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
20P LOSS MUTATED	1	12	4
20P LOSS WILD-TYPE	119	80	105

Figure S173. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S174. Gene #77: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
21Q LOSS MUTATED	28	16	44	7	48
21Q LOSS WILD-TYPE	141	17	22	3	43

Figure S174. Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.24

Table S175. Gene #77: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
21Q LOSS MUTATED	37	33	73
21Q LOSS WILD-TYPE	82	75	68

Figure S175. Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.097

Table S176. Gene #77: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
21Q LOSS MUTATED	21	75	30
21Q LOSS WILD-TYPE	56	69	70

Figure S176. Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S177. Gene #78: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
22Q LOSS MUTATED	13	10	38	5	50
22Q LOSS WILD-TYPE	156	23	28	5	41

Figure S177. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S178. Gene #78: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
22Q LOSS MUTATED	30	49	24
22Q LOSS WILD-TYPE	90	43	85

Figure S178. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.027

Table S179. Gene #78: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	108	141
22Q LOSS MUTATED	23	27	65
22Q LOSS WILD-TYPE	96	81	76

Figure S179. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S180. Gene #78: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	83	106
22Q LOSS MUTATED	40	19	56
22Q LOSS WILD-TYPE	139	64	50

Figure S180. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.24

Table S181. Gene #78: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	144	100
22Q LOSS MUTATED	15	62	25
22Q LOSS WILD-TYPE	62	82	75

Figure S181. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S182. Gene #78: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	62	82
22Q LOSS MUTATED	45	11	46
22Q LOSS WILD-TYPE	132	51	36

Figure S182. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S183. Gene #79: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	33	66	10	91
XQ LOSS MUTATED	4	5	17	1	16
XQ LOSS WILD-TYPE	165	28	49	9	75

Figure S183. Get High-res Image Gene #79: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.027

Table S184. Gene #79: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	92	109
XQ LOSS MUTATED	15	18	2
XQ LOSS WILD-TYPE	105	74	107

Figure S184. Get High-res Image Gene #79: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtypes file = STAD-TP.transferedmergedcluster.txt
Number of patients = 369
Number of significantly arm-level cnvs = 79
Number of molecular subtypes = 10
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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