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 82 arm-level events and 10 molecular subtypes across 90 patients, 244 significant findings detected with P value < 0.05 and Q value < 0.25.

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

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 82 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, 244 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
2q gain	13 (14%)	77	0.00322 (0.0264)	0.011 (0.0662)	0.828 (0.958)	0.00552 (0.0374)	0.00377 (0.0294)	0.00098 (0.01)	0.0389 (0.142)	0.0011 (0.0106)	0.0137 (0.0731)	9e-05 (0.00176)
20p gain	46 (51%)	44	2e-05 (0.000607)	0.00032 (0.0041)	0.0416 (0.147)	0.00852 (0.055)	0.00025 (0.00347)	7e-05 (0.00155)	0.00218 (0.019)	0.0886 (0.233)	0.00538 (0.0368)	0.00533 (0.0368)
14q gain	21 (23%)	69	0.00347 (0.0276)	0.0197 (0.0923)	0.141 (0.32)	0.427 (0.639)	0.00029 (0.00377)	0.00105 (0.0104)	0.00022 (0.00322)	0.00019 (0.00289)	2e-05 (0.000607)	2e-05 (0.000607)
20q gain	49 (54%)	41	3e-05 (0.00082)	0.00018 (0.00278)	0.0113 (0.0662)	0.0756 (0.218)	0.00015 (0.00251)	0.00027 (0.00363)	0.00355 (0.028)	0.273 (0.473)	0.0131 (0.0731)	0.0454 (0.158)
2p gain	13 (14%)	77	0.00273 (0.0233)	0.00702 (0.0461)	0.572 (0.766)	0.342 (0.555)	0.013 (0.0728)	0.00025 (0.00347)	0.0722 (0.21)	0.019 (0.0899)	0.0329 (0.13)	0.0113 (0.0662)
15q gain	11 (12%)	79	0.0141 (0.0739)	0.029 (0.121)	0.371 (0.588)	0.846 (0.97)	0.00971 (0.0608)	0.00495 (0.0353)	0.184 (0.376)	0.0007 (0.00765)	0.0165 (0.0821)	0.0429 (0.151)
17p loss	33 (37%)	57	0.00024 (0.00345)	0.00256 (0.0221)	0.456 (0.661)	0.195 (0.389)	0.004 (0.0301)	0.0152 (0.0767)	0.0875 (0.231)	0.00094 (0.00988)	0.0318 (0.127)	0.0005 (0.00612)
4q gain	35 (39%)	55	7e-05 (0.00155)	0.00445 (0.0323)	1 (1.00)	0.532 (0.721)	0.00012 (0.00209)	3e-05 (0.00082)	0.8 (0.939)	0.00028 (0.0037)	0.379 (0.597)	0.0248 (0.106)
5p gain	57 (63%)	33	4e-05 (0.00102)	0.00345 (0.0276)	0.0642 (0.195)	0.0343 (0.133)	0.00053 (0.0063)	1e-05 (0.000456)	0.135 (0.31)	0.226 (0.424)	0.00305 (0.0255)	0.159 (0.341)
5q gain	55 (61%)	35	1e-05 (0.000456)	0.00037 (0.00467)	0.19 (0.386)	0.0662 (0.197)	0.00018 (0.00278)	1e-05 (0.000456)	0.0382 (0.142)	0.0822 (0.221)	0.0101 (0.0631)	0.0904 (0.235)
7q gain	48 (53%)	42	0.00017 (0.00273)	0.00889 (0.0565)	0.0817 (0.22)	0.242 (0.442)	1e-05 (0.000456)	0.00012 (0.00209)	1 (1.00)	0.332 (0.541)	0.0149 (0.0764)	0.0218 (0.0984)
9p gain	21 (23%)	69	1e-05 (0.000456)	0.0116 (0.0667)	0.0483 (0.163)	0.121 (0.286)	0.017 (0.0831)	0.0137 (0.0731)	0.0788 (0.219)	0.436 (0.643)	0.028 (0.119)	0.144 (0.323)
9q gain	27 (30%)	63	2e-05 (0.000607)	0.00434 (0.0321)	0.0836 (0.223)	0.21 (0.405)	0.0355 (0.136)	0.00534 (0.0368)	0.019 (0.0899)	0.212 (0.405)	0.0146 (0.0753)	0.207 (0.404)
10p gain	25 (28%)	65	2e-05 (0.000607)	0.0895 (0.234)	0.0217 (0.0984)	0.0134 (0.0731)	1e-05 (0.000456)	0.00016 (0.00262)	0.0535 (0.176)	0.506 (0.702)	0.021 (0.0963)	0.548 (0.738)
10q gain	26 (29%)	64	1e-05 (0.000456)	0.288 (0.491)	0.0565 (0.18)	0.0145 (0.0753)	2e-05 (0.000607)	0.00042 (0.00522)	0.0311 (0.125)	0.343 (0.555)	0.0285 (0.119)	0.395 (0.613)
16p gain	50 (56%)	40	1e-05 (0.000456)	2e-05 (0.000607)	1 (1.00)	0.0637 (0.194)	5e-05 (0.00124)	1e-05 (0.000456)	0.114 (0.28)	0.0205 (0.0943)	0.0112 (0.0662)	0.0774 (0.219)
16q gain	47 (52%)	43	1e-05 (0.000456)	1e-05 (0.000456)	1 (1.00)	0.323 (0.53)	9e-05 (0.00176)	1e-05 (0.000456)	0.0552 (0.179)	0.0137 (0.0731)	0.00052 (0.00627)	0.0648 (0.195)
21q gain	31 (34%)	59	0.254 (0.452)	0.00424 (0.0316)	0.0782 (0.219)	0.231 (0.43)	0.033 (0.13)	0.00102 (0.0102)	0.0224 (0.0999)	0.02 (0.0929)	0.0188 (0.0899)	0.087 (0.23)
xp gain	43 (48%)	47	1e-05 (0.000456)	0.0297 (0.122)	0.431 (0.64)	0.0235 (0.102)	0.00288 (0.0243)	0.0155 (0.0773)	1 (1.00)	0.0613 (0.19)	0.313 (0.517)	0.00859 (0.055)
xq gain	41 (46%)	49	8e-05 (0.00164)	0.00514 (0.0363)	0.195 (0.389)	0.0329 (0.13)	0.00439 (0.0321)	0.024 (0.104)	0.883 (1.00)	0.103 (0.26)	0.347 (0.56)	0.0301 (0.122)
9p loss	20 (22%)	70	1e-05 (0.000456)	0.0119 (0.0679)	0.618 (0.805)	0.117 (0.282)	8e-05 (0.00164)	0.00097 (0.01)	0.0402 (0.144)	0.139 (0.318)	0.00308 (0.0255)	0.248 (0.448)
4p gain	38 (42%)	52	4e-05 (0.00102)	0.00728 (0.0474)	0.977 (1.00)	0.43 (0.64)	2e-05 (0.000607)	1e-05 (0.000456)	0.739 (0.89)	0.00153 (0.0138)	0.0585 (0.184)	0.128 (0.298)
7p gain	48 (53%)	42	0.0001 (0.00186)	0.046 (0.158)	0.0811 (0.22)	0.0928 (0.24)	8e-05 (0.00164)	0.00136 (0.0124)	1 (1.00)	0.548 (0.738)	0.0152 (0.0767)	0.0813 (0.22)
12p gain	64 (71%)	26	1e-05 (0.000456)	0.0133 (0.0731)	0.372 (0.588)	0.0672 (0.2)	0.00011 (0.002)	6e-05 (0.00141)	0.133 (0.307)	0.21 (0.405)	0.0409 (0.145)	0.117 (0.282)
12q gain	64 (71%)	26	1e-05 (0.000456)	0.0227 (0.101)	0.342 (0.555)	0.028 (0.119)	0.00058 (0.00661)	0.00013 (0.00222)	0.144 (0.323)	0.455 (0.66)	0.092 (0.239)	0.392 (0.612)
3q loss	19 (21%)	71	0.00107 (0.0104)	0.154 (0.335)	0.451 (0.657)	0.602 (0.793)	0.0137 (0.0731)	0.0293 (0.121)	0.0581 (0.184)	0.34 (0.553)	0.00673 (0.0445)	0.0385 (0.142)
8q loss	12 (13%)	78	0.0135 (0.0731)	0.128 (0.298)	0.407 (0.619)	0.0357 (0.136)	0.0246 (0.106)	0.128 (0.298)	0.0798 (0.22)	0.0352 (0.136)	0.0265 (0.113)	0.0744 (0.215)
17q loss	25 (28%)	65	0.0116 (0.0667)	0.0122 (0.0688)	0.583 (0.774)	0.515 (0.71)	0.0636 (0.194)	0.047 (0.16)	0.152 (0.332)	0.00895 (0.0565)	0.26 (0.458)	0.0454 (0.158)
xq loss	16 (18%)	74	0.0373 (0.14)	0.0173 (0.0838)	0.0166 (0.0822)	0.0595 (0.186)	0.0347 (0.134)	0.0361 (0.137)	0.355 (0.568)	0.15 (0.328)	0.277 (0.477)	0.231 (0.43)
19p gain	56 (62%)	34	3e-05 (0.00082)	0.184 (0.376)	0.108 (0.269)	0.0191 (0.0899)	0.00101 (0.0102)	0.00054 (0.00633)	0.429 (0.639)	0.467 (0.667)	0.0891 (0.233)	0.703 (0.862)
8p loss	16 (18%)	74	0.0394 (0.143)	0.063 (0.194)	0.0699 (0.204)	0.00058 (0.00661)	0.139 (0.318)	0.141 (0.32)	0.0658 (0.197)	0.023 (0.102)	0.055 (0.179)	0.0108 (0.0662)
6p gain	18 (20%)	72	0.048 (0.163)	0.504 (0.701)	0.689 (0.854)	0.872 (0.994)	0.0393 (0.143)	0.474 (0.671)	0.245 (0.446)	0.0553 (0.179)	0.0224 (0.0999)	0.162 (0.347)
19q gain	52 (58%)	38	1e-05 (0.000456)	0.251 (0.45)	0.664 (0.836)	0.0557 (0.179)	0.00027 (0.00363)	0.00115 (0.0108)	0.289 (0.491)	0.11 (0.272)	0.141 (0.32)	0.373 (0.588)
14q loss	18 (20%)	72	0.00077 (0.0082)	0.4 (0.613)	0.332 (0.541)	0.0527 (0.174)	0.0153 (0.0769)	0.0461 (0.158)	0.473 (0.671)	0.53 (0.721)	0.565 (0.758)	0.98 (1.00)
15q loss	21 (23%)	69	0.00074 (0.00798)	0.867 (0.99)	0.661 (0.834)	0.509 (0.704)	0.115 (0.28)	0.23 (0.43)	0.839 (0.967)	0.0404 (0.144)	0.732 (0.884)	0.0484 (0.163)
3q gain	16 (18%)	74	0.046 (0.158)	0.0114 (0.0662)	0.442 (0.647)	0.822 (0.958)	0.0766 (0.219)	0.795 (0.935)	0.627 (0.811)	0.246 (0.446)	0.149 (0.328)	0.352 (0.565)
8p gain	32 (36%)	58	0.0033 (0.0268)	0.281 (0.484)	0.521 (0.713)	0.437 (0.643)	0.17 (0.36)	0.146 (0.326)	0.0775 (0.219)	0.172 (0.362)	0.0234 (0.102)	0.192 (0.387)
11q gain	6 (7%)	84	0.0301 (0.122)	0.259 (0.458)	0.2 (0.395)	0.483 (0.679)	0.0399 (0.143)	0.0787 (0.219)	0.457 (0.661)	0.369 (0.588)	0.204 (0.4)	0.0811 (0.22)
1q loss	21 (23%)	69	2e-05 (0.000607)	0.921 (1.00)	0.771 (0.916)	0.0109 (0.0662)	0.807 (0.944)	0.464 (0.666)	0.468 (0.667)	0.722 (0.877)	0.512 (0.707)	0.529 (0.721)
2p loss	16 (18%)	74	0.00205 (0.0181)	0.288 (0.491)	0.859 (0.982)	0.658 (0.833)	0.724 (0.877)	0.301 (0.504)	0.0358 (0.136)	0.639 (0.818)	0.25 (0.45)	0.518 (0.711)
2q loss	14 (16%)	76	0.00115 (0.0108)	0.145 (0.323)	0.77 (0.916)	0.885 (1.00)	0.19 (0.386)	0.0686 (0.202)	0.0337 (0.132)	0.648 (0.823)	0.12 (0.286)	0.578 (0.771)
4p loss	9 (10%)	81	0.0783 (0.219)	0.216 (0.411)	0.764 (0.913)	0.898 (1.00)	0.00397 (0.0301)	0.014 (0.0739)	0.373 (0.588)	0.705 (0.863)	0.057 (0.181)	0.452 (0.658)
11q loss	22 (24%)	68	0.00172 (0.0153)	0.0113 (0.0662)	0.758 (0.908)	0.395 (0.613)	0.195 (0.389)	0.149 (0.328)	0.174 (0.364)	0.766 (0.913)	0.256 (0.454)	0.577 (0.77)
12q loss	4 (4%)	86	0.407 (0.619)	0.0508 (0.17)	0.263 (0.459)	0.0828 (0.221)	0.408 (0.619)	0.0103 (0.0637)	0.148 (0.328)	0.241 (0.441)	0.151 (0.328)	0.0198 (0.0923)
19p loss	5 (6%)	85	0.149 (0.328)	0.416 (0.626)			0.108 (0.269)	0.0138 (0.0732)	0.395 (0.613)	0.716 (0.871)	0.255 (0.454)	0.0294 (0.121)
19q loss	4 (4%)	86	0.0445 (0.156)	0.587 (0.777)			0.773 (0.917)	0.117 (0.282)	0.395 (0.613)	0.207 (0.404)	0.254 (0.452)	0.0308 (0.124)
1q gain	8 (9%)	82	0.223 (0.42)	0.524 (0.717)	0.285 (0.488)	0.564 (0.758)	0.0479 (0.163)	0.0776 (0.219)	0.21 (0.405)	0.241 (0.441)	0.161 (0.346)	0.0932 (0.24)
6q gain	16 (18%)	74	6e-05 (0.00141)	0.915 (1.00)	0.66 (0.834)	0.688 (0.854)	0.148 (0.328)	0.293 (0.494)	0.177 (0.367)	0.196 (0.39)	0.236 (0.435)	0.489 (0.684)
8q gain	38 (42%)	52	0.00616 (0.0414)	0.323 (0.53)	0.429 (0.639)	0.468 (0.667)	0.32 (0.528)	0.231 (0.43)	0.421 (0.631)	0.263 (0.459)	0.213 (0.406)	0.174 (0.364)
13q gain	6 (7%)	84	0.894 (1.00)	0.323 (0.53)	0.699 (0.858)	0.724 (0.877)	0.0284 (0.119)	0.634 (0.815)	0.21 (0.405)	0.913 (1.00)	0.0557 (0.179)	0.646 (0.821)
17q gain	7 (8%)	83	0.00629 (0.0419)	0.438 (0.643)			0.684 (0.854)	0.145 (0.323)	0.292 (0.494)	0.793 (0.934)	0.608 (0.798)	0.669 (0.84)
1p loss	29 (32%)	61	0.00022 (0.00322)	0.184 (0.376)	0.904 (1.00)	0.131 (0.303)	0.407 (0.619)	0.0647 (0.195)	0.689 (0.854)	0.409 (0.619)	0.266 (0.463)	0.247 (0.446)
3p loss	19 (21%)	71	0.00521 (0.0365)	0.495 (0.691)	0.17 (0.361)	0.292 (0.494)	0.0809 (0.22)	0.135 (0.31)	0.226 (0.424)	0.391 (0.612)	0.116 (0.282)	0.122 (0.287)
4q loss	10 (11%)	80	0.0781 (0.219)	0.0794 (0.219)	0.455 (0.66)	0.619 (0.806)	0.0177 (0.0854)	0.0809 (0.22)	0.37 (0.588)	0.397 (0.613)	0.433 (0.642)	0.4 (0.613)
5p loss	7 (8%)	83	0.4 (0.613)	0.373 (0.588)	0.15 (0.328)	0.191 (0.386)	0.41 (0.619)	0.0218 (0.0984)	0.766 (0.913)	0.156 (0.336)	0.623 (0.81)	0.838 (0.967)
5q loss	5 (6%)	85	0.118 (0.282)	0.461 (0.664)			0.407 (0.619)	0.211 (0.405)	0.0334 (0.131)	0.0794 (0.219)	0.463 (0.665)	0.0942 (0.242)
6p loss	19 (21%)	71	0.00068 (0.00754)	0.81 (0.946)	0.613 (0.801)	0.235 (0.435)	0.612 (0.8)	0.694 (0.856)	0.734 (0.885)	0.1 (0.256)	0.47 (0.668)	0.261 (0.458)
6q loss	22 (24%)	68	0.0001 (0.00186)	0.636 (0.816)	0.749 (0.9)	0.274 (0.473)	0.592 (0.783)	0.691 (0.854)	0.595 (0.785)	0.176 (0.367)	0.389 (0.61)	0.19 (0.386)
7q loss	6 (7%)	84	0.0649 (0.195)	0.502 (0.699)	0.606 (0.796)	0.78 (0.924)	0.626 (0.811)	0.654 (0.829)	1 (1.00)	0.234 (0.435)	0.484 (0.679)	0.0386 (0.142)
9q loss	12 (13%)	78	0.038 (0.142)	0.0967 (0.248)	0.829 (0.958)	0.163 (0.349)	0.176 (0.367)	0.313 (0.517)	0.469 (0.667)	0.57 (0.764)	0.3 (0.503)	0.812 (0.947)
11p loss	23 (26%)	67	0.00125 (0.0116)	0.101 (0.258)	0.967 (1.00)	0.798 (0.937)	0.295 (0.496)	0.211 (0.405)	0.331 (0.541)	0.826 (0.958)	0.581 (0.772)	0.634 (0.815)
12p loss	5 (6%)	85	0.475 (0.671)	0.182 (0.373)	0.267 (0.463)	0.0823 (0.221)	0.626 (0.811)	0.0378 (0.142)	0.0516 (0.172)	0.516 (0.71)	0.348 (0.56)	0.0589 (0.184)
13q loss	39 (43%)	51	0.00127 (0.0117)	0.128 (0.298)	0.973 (1.00)	0.942 (1.00)	0.53 (0.721)	0.885 (1.00)	0.839 (0.967)	0.303 (0.507)	0.953 (1.00)	0.171 (0.361)
16p loss	4 (4%)	86	0.351 (0.564)	0.26 (0.458)	0.532 (0.721)	0.205 (0.402)	0.0397 (0.143)	0.0769 (0.219)	0.458 (0.662)	0.745 (0.896)	0.203 (0.4)	0.678 (0.848)
18p loss	37 (41%)	53	0.00387 (0.0299)	0.829 (0.958)	0.954 (1.00)	0.688 (0.854)	0.64 (0.818)	0.646 (0.821)	0.881 (1.00)	0.694 (0.856)	0.805 (0.943)	0.116 (0.282)
18q loss	35 (39%)	55	0.0039 (0.0299)	0.697 (0.857)	1 (1.00)	0.533 (0.721)	0.73 (0.883)	0.934 (1.00)	0.596 (0.786)	0.915 (1.00)	0.63 (0.813)	0.193 (0.388)
21q loss	15 (17%)	75	0.0169 (0.0829)	0.261 (0.458)	0.0629 (0.194)	0.052 (0.173)	0.246 (0.446)	0.253 (0.452)	0.238 (0.438)	0.507 (0.703)	0.476 (0.672)	0.932 (1.00)
22q loss	48 (53%)	42	0.00453 (0.0326)	0.246 (0.446)	0.975 (1.00)	0.482 (0.679)	0.679 (0.848)	0.282 (0.484)	0.716 (0.871)	0.826 (0.958)	0.786 (0.931)	0.461 (0.664)
xp loss	16 (18%)	74	0.00068 (0.00754)	0.104 (0.262)	0.165 (0.351)	0.062 (0.192)	0.0539 (0.177)	0.0679 (0.201)	0.695 (0.856)	0.104 (0.261)	0.294 (0.495)	0.307 (0.512)
1p gain	4 (4%)	86	0.156 (0.337)
3p gain	14 (16%)	76	0.0693 (0.203)	0.0587 (0.184)	0.215 (0.41)	0.884 (1.00)	0.384 (0.603)	0.364 (0.582)	0.4 (0.613)	0.109 (0.269)	0.313 (0.517)	0.273 (0.473)
11p gain	5 (6%)	85	0.118 (0.282)
17p gain	5 (6%)	85	0.114 (0.28)	0.439 (0.643)			0.686 (0.854)	0.144 (0.323)	0.289 (0.491)	0.793 (0.934)	0.61 (0.799)	0.671 (0.842)
18p gain	6 (7%)	84	0.755 (0.906)
18q gain	5 (6%)	85	0.397 (0.613)
22q gain	3 (3%)	87	0.22 (0.417)
7p loss	5 (6%)	85	0.102 (0.258)	0.788 (0.931)	0.405 (0.619)	0.205 (0.402)	0.909 (1.00)	0.891 (1.00)	0.541 (0.73)	0.413 (0.622)	0.258 (0.457)	0.104 (0.262)
10p loss	12 (13%)	78	0.437 (0.643)	0.888 (1.00)	1 (1.00)	0.0555 (0.179)	0.182 (0.373)	1 (1.00)	0.642 (0.818)	0.709 (0.866)	0.666 (0.837)	0.496 (0.692)
10q loss	10 (11%)	80	0.439 (0.643)	0.843 (0.968)	1 (1.00)	0.238 (0.438)	0.418 (0.628)	1 (1.00)	0.58 (0.772)	0.71 (0.866)	0.629 (0.813)	0.488 (0.684)
16q loss	5 (6%)	85	0.177 (0.367)	0.121 (0.286)	0.202 (0.399)	0.178 (0.367)	0.0681 (0.201)	0.0851 (0.226)	0.223 (0.42)	0.31 (0.516)	0.0736 (0.213)	0.841 (0.967)
20p loss	9 (10%)	81	0.106 (0.265)	0.22 (0.417)	0.52 (0.713)	0.856 (0.98)	0.193 (0.387)	0.126 (0.298)	0.128 (0.298)	0.446 (0.652)	0.116 (0.282)	0.641 (0.818)
20q loss	3 (3%)	87	0.171 (0.361)

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.0479 (Fisher's exact test), Q value = 0.16

Table S1. Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
1Q GAIN MUTATED	4	2	0	0
1Q GAIN WILD-TYPE	20	12	16	23

Figure S1. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 0.00273 (Fisher's exact test), Q value = 0.023

Table S2. Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
2P GAIN MUTATED	3	0	0	8	2	0	0
2P GAIN WILD-TYPE	16	18	13	10	9	6	5

Figure S2. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.00702 (Fisher's exact test), Q value = 0.046

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	16	14	8	17	9	12	2
2P GAIN MUTATED	6	1	2	0	0	0	0
2P GAIN WILD-TYPE	10	13	6	17	9	12	2

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

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.073

Table S4. Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
2P GAIN MUTATED	7	0	0	2
2P GAIN WILD-TYPE	17	14	16	21

Figure S4. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.0035

Table S5. Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
2P GAIN MUTATED	8	0	1	0
2P GAIN WILD-TYPE	15	23	6	24

Figure S5. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.019 (Fisher's exact test), Q value = 0.09

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	16	27	11	20	4
2P GAIN MUTATED	0	1	1	6	1
2P GAIN WILD-TYPE	16	26	10	14	3

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

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0329 (Fisher's exact test), Q value = 0.13

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	19	16	26
2P GAIN MUTATED	4	2	3	0
2P GAIN WILD-TYPE	12	17	13	26

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

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.066

Table S8. Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	6	24	11	14	11	11
2P GAIN MUTATED	0	1	1	6	1	0
2P GAIN WILD-TYPE	6	23	10	8	10	11

Figure S8. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 0.00322 (Fisher's exact test), Q value = 0.026

Table S9. Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
2Q GAIN MUTATED	3	0	0	8	2	0	0
2Q GAIN WILD-TYPE	16	18	13	10	9	6	5

Figure S9. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.066

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	16	14	8	17	9	12	2
2Q GAIN MUTATED	6	1	1	0	0	0	0
2Q GAIN WILD-TYPE	10	13	7	17	9	12	2

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

'2q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00552 (Fisher's exact test), Q value = 0.037

Table S11. Gene #4: '2q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	8	7	7	3	4	4	6	6
2Q GAIN MUTATED	1	1	1	3	0	0	0	0
2Q GAIN WILD-TYPE	7	6	6	0	4	4	6	6

Figure S11. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.00377 (Fisher's exact test), Q value = 0.029

Table S12. Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
2Q GAIN MUTATED	7	0	0	1
2Q GAIN WILD-TYPE	17	14	16	22

Figure S12. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00098 (Fisher's exact test), Q value = 0.01

Table S13. Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
2Q GAIN MUTATED	7	0	1	0
2Q GAIN WILD-TYPE	16	23	6	24

Figure S13. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CNMF'

P value = 0.0389 (Fisher's exact test), Q value = 0.14

Table S14. Gene #4: '2q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	24	25
2Q GAIN MUTATED	6	2	0
2Q GAIN WILD-TYPE	23	22	25

Figure S14. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0011 (Fisher's exact test), Q value = 0.011

Table S15. Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	16	27	11	20	4
2Q GAIN MUTATED	0	0	1	7	0
2Q GAIN WILD-TYPE	16	27	10	13	4

Figure S15. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.073

Table S16. Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	19	16	26
2Q GAIN MUTATED	4	1	3	0
2Q GAIN WILD-TYPE	12	18	13	26

Figure S16. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.0018

Table S17. Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	6	24	11	14	11	11
2Q GAIN MUTATED	0	0	1	7	0	0
2Q GAIN WILD-TYPE	6	24	10	7	11	11

Figure S17. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 0.046 (Fisher's exact test), Q value = 0.16

Table S18. Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
3Q GAIN MUTATED	3	1	5	3	0	3	1
3Q GAIN WILD-TYPE	16	17	8	15	11	3	4

Figure S18. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.066

Table S19. Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	16	14	8	17	9	12	2
3Q GAIN MUTATED	0	4	0	2	2	2	2
3Q GAIN WILD-TYPE	16	10	8	15	7	10	0

Figure S19. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.001

Table S20. Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
4P GAIN MUTATED	1	8	9	6	4	5	5
4P GAIN WILD-TYPE	18	10	4	12	7	1	0

Figure S20. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.00728 (Fisher's exact test), Q value = 0.047

Table S21. Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	16	14	8	17	9	12	2
4P GAIN MUTATED	2	3	3	12	6	5	1
4P GAIN WILD-TYPE	14	11	5	5	3	7	1

Figure S21. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00061

Table S22. Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
4P GAIN MUTATED	1	9	11	10
4P GAIN WILD-TYPE	23	5	5	13

Figure S22. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S23. Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
4P GAIN MUTATED	2	16	0	13
4P GAIN WILD-TYPE	21	7	7	11

Figure S23. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00153 (Fisher's exact test), Q value = 0.014

Table S24. Gene #7: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	16	27	11	20	4
4P GAIN MUTATED	11	10	6	2	3
4P GAIN WILD-TYPE	5	17	5	18	1

Figure S24. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.0016

Table S25. Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
4Q GAIN MUTATED	1	7	8	4	5	5	5
4Q GAIN WILD-TYPE	18	11	5	14	6	1	0

Figure S25. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'METHLYATION_CNMF'

P value = 0.00445 (Fisher's exact test), Q value = 0.032

Table S26. Gene #8: '4q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	16	14	8	17	9	12	2
4Q GAIN MUTATED	2	3	3	12	6	4	0
4Q GAIN WILD-TYPE	14	11	5	5	3	8	2

Figure S26. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0021

Table S27. Gene #8: '4q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
4Q GAIN MUTATED	1	9	9	10
4Q GAIN WILD-TYPE	23	5	7	13

Figure S27. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00082

Table S28. Gene #8: '4q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
4Q GAIN MUTATED	2	15	0	12
4Q GAIN WILD-TYPE	21	8	7	12

Figure S28. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.0037

Table S29. Gene #8: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	16	27	11	20	4
4Q GAIN MUTATED	11	10	5	1	3
4Q GAIN WILD-TYPE	5	17	6	19	1

Figure S29. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0248 (Fisher's exact test), Q value = 0.11

Table S30. Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	6	24	11	14	11	11
4Q GAIN MUTATED	5	10	5	1	3	5
4Q GAIN WILD-TYPE	1	14	6	13	8	6

Figure S30. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.001

Table S31. Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
5P GAIN MUTATED	4	17	11	10	5	5	5
5P GAIN WILD-TYPE	15	1	2	8	6	1	0

Figure S31. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.00345 (Fisher's exact test), Q value = 0.028

Table S32. Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	16	14	8	17	9	12	2
5P GAIN MUTATED	5	8	3	13	8	11	2
5P GAIN WILD-TYPE	11	6	5	4	1	1	0

Figure S32. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0343 (Fisher's exact test), Q value = 0.13

Table S33. Gene #9: '5p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	8	7	7	3	4	4	6	6
5P GAIN MUTATED	4	5	6	1	4	4	5	1
5P GAIN WILD-TYPE	4	2	1	2	0	0	1	5

Figure S33. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.0063

Table S34. Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
5P GAIN MUTATED	7	11	13	18
5P GAIN WILD-TYPE	17	3	3	5

Figure S34. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S35. Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
5P GAIN MUTATED	6	18	3	22
5P GAIN WILD-TYPE	17	5	4	2

Figure S35. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00305 (Fisher's exact test), Q value = 0.026

Table S36. Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	19	16	26
5P GAIN MUTATED	5	10	14	20
5P GAIN WILD-TYPE	11	9	2	6

Figure S36. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S37. Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
5Q GAIN MUTATED	3	16	13	8	5	5	5
5Q GAIN WILD-TYPE	16	2	0	10	6	1	0

Figure S37. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0047

Table S38. Gene #10: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	16	14	8	17	9	12	2
5Q GAIN MUTATED	5	7	3	15	8	11	1
5Q GAIN WILD-TYPE	11	7	5	2	1	1	1

Figure S38. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0028

Table S39. Gene #10: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
5Q GAIN MUTATED	7	12	14	16
5Q GAIN WILD-TYPE	17	2	2	7

Figure S39. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S40. Gene #10: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
5Q GAIN MUTATED	5	20	3	21
5Q GAIN WILD-TYPE	18	3	4	3

Figure S40. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CNMF'

P value = 0.0382 (Fisher's exact test), Q value = 0.14

Table S41. Gene #10: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	24	25
5Q GAIN MUTATED	15	14	21
5Q GAIN WILD-TYPE	14	10	4

Figure S41. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.063

Table S42. Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	19	16	26
5Q GAIN MUTATED	5	11	13	20
5Q GAIN WILD-TYPE	11	8	3	6

Figure S42. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 0.048 (Fisher's exact test), Q value = 0.16

Table S43. Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
6P GAIN MUTATED	4	1	2	2	6	1	2
6P GAIN WILD-TYPE	15	17	11	16	5	5	3

Figure S43. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 0.0393 (Fisher's exact test), Q value = 0.14

Table S44. Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
6P GAIN MUTATED	6	0	6	3
6P GAIN WILD-TYPE	18	14	10	20

Figure S44. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0224 (Fisher's exact test), Q value = 0.1

Table S45. Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	19	16	26
6P GAIN MUTATED	4	1	7	3
6P GAIN WILD-TYPE	12	18	9	23

Figure S45. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0014

Table S46. Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
6Q GAIN MUTATED	5	1	0	0	7	1	2
6Q GAIN WILD-TYPE	14	17	13	18	4	5	3

Figure S46. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.0019

Table S47. Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
7P GAIN MUTATED	4	12	12	9	3	3	5
7P GAIN WILD-TYPE	15	6	1	9	8	3	0

Figure S47. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.046 (Fisher's exact test), Q value = 0.16

Table S48. Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	16	14	8	17	9	12	2
7P GAIN MUTATED	4	7	4	11	8	6	2
7P GAIN WILD-TYPE	12	7	4	6	1	6	0

Figure S48. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0016

Table S49. Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
7P GAIN MUTATED	6	13	12	11
7P GAIN WILD-TYPE	18	1	4	12

Figure S49. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00136 (Fisher's exact test), Q value = 0.012

Table S50. Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
7P GAIN MUTATED	7	19	2	14
7P GAIN WILD-TYPE	16	4	5	10

Figure S50. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.077

Table S51. Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	19	16	26
7P GAIN MUTATED	4	11	13	13
7P GAIN WILD-TYPE	12	8	3	13

Figure S51. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0027

Table S52. Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
7Q GAIN MUTATED	4	12	12	9	3	3	5
7Q GAIN WILD-TYPE	15	6	1	9	8	3	0

Figure S52. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.00889 (Fisher's exact test), Q value = 0.056

Table S53. Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	16	14	8	17	9	12	2
7Q GAIN MUTATED	3	7	4	12	8	6	2
7Q GAIN WILD-TYPE	13	7	4	5	1	6	0

Figure S53. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S54. Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
7Q GAIN MUTATED	5	14	12	11
7Q GAIN WILD-TYPE	19	0	4	12

Figure S54. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.0021

Table S55. Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
7Q GAIN MUTATED	6	20	2	14
7Q GAIN WILD-TYPE	17	3	5	10

Figure S55. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.076

Table S56. Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	19	16	26
7Q GAIN MUTATED	4	11	13	13
7Q GAIN WILD-TYPE	12	8	3	13

Figure S56. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 0.098

Table S57. Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	6	24	11	14	11	11
7Q GAIN MUTATED	4	16	9	3	5	4
7Q GAIN WILD-TYPE	2	8	2	11	6	7

Figure S57. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 0.0033 (Fisher's exact test), Q value = 0.027

Table S58. Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
8P GAIN MUTATED	1	12	6	6	3	3	1
8P GAIN WILD-TYPE	18	6	7	12	8	3	4

Figure S58. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0234 (Fisher's exact test), Q value = 0.1

Table S59. Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	19	16	26
8P GAIN MUTATED	5	2	8	13
8P GAIN WILD-TYPE	11	17	8	13

Figure S59. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 0.00616 (Fisher's exact test), Q value = 0.041

Table S60. Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
8Q GAIN MUTATED	2	12	8	9	3	3	1
8Q GAIN WILD-TYPE	17	6	5	9	8	3	4

Figure S60. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S61. Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
9P GAIN MUTATED	1	1	11	2	3	3	0
9P GAIN WILD-TYPE	18	17	2	16	8	3	5

Figure S61. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 0.067

Table S62. Gene #17: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	16	14	8	17	9	12	2
9P GAIN MUTATED	3	0	2	7	2	1	2
9P GAIN WILD-TYPE	13	14	6	10	7	11	0

Figure S62. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p gain' versus 'RPPA_CNMF'

P value = 0.0483 (Fisher's exact test), Q value = 0.16

Table S63. Gene #17: '9p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	10	11	10	14
9P GAIN MUTATED	1	4	0	6
9P GAIN WILD-TYPE	9	7	10	8

Figure S63. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 0.083

Table S64. Gene #17: '9p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
9P GAIN MUTATED	2	7	4	3
9P GAIN WILD-TYPE	22	7	12	20

Figure S64. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 0.073

Table S65. Gene #17: '9p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
9P GAIN MUTATED	4	10	0	2
9P GAIN WILD-TYPE	19	13	7	22

Figure S65. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.12

Table S66. Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	19	16	26
9P GAIN MUTATED	2	8	5	2
9P GAIN WILD-TYPE	14	11	11	24

Figure S66. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00061

Table S67. Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
9Q GAIN MUTATED	1	1	11	5	5	3	1
9Q GAIN WILD-TYPE	18	17	2	13	6	3	4

Figure S67. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'METHLYATION_CNMF'

P value = 0.00434 (Fisher's exact test), Q value = 0.032

Table S68. Gene #18: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	16	14	8	17	9	12	2
9Q GAIN MUTATED	6	0	2	8	2	1	2
9Q GAIN WILD-TYPE	10	14	6	9	7	11	0

Figure S68. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 0.0355 (Fisher's exact test), Q value = 0.14

Table S69. Gene #18: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
9Q GAIN MUTATED	5	8	4	3
9Q GAIN WILD-TYPE	19	6	12	20

Figure S69. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00534 (Fisher's exact test), Q value = 0.037

Table S70. Gene #18: '9q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
9Q GAIN MUTATED	7	11	0	2
9Q GAIN WILD-TYPE	16	12	7	22

Figure S70. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_CNMF'

P value = 0.019 (Fisher's exact test), Q value = 0.09

Table S71. Gene #18: '9q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	24	25
9Q GAIN MUTATED	9	10	2
9Q GAIN WILD-TYPE	20	14	23

Figure S71. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0146 (Fisher's exact test), Q value = 0.075

Table S72. Gene #18: '9q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	19	16	26
9Q GAIN MUTATED	4	9	6	2
9Q GAIN WILD-TYPE	12	10	10	24

Figure S72. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00061

Table S73. Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
10P GAIN MUTATED	3	0	9	10	1	1	1
10P GAIN WILD-TYPE	16	18	4	8	10	5	4

Figure S73. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'RPPA_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.098

Table S74. Gene #19: '10p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	10	11	10	14
10P GAIN MUTATED	3	3	0	8
10P GAIN WILD-TYPE	7	8	10	6

Figure S74. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'10p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.073

Table S75. Gene #19: '10p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	8	7	7	3	4	4	6	6
10P GAIN MUTATED	6	3	0	2	1	1	0	1
10P GAIN WILD-TYPE	2	4	7	1	3	3	6	5

Figure S75. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S76. Gene #19: '10p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
10P GAIN MUTATED	6	12	3	2
10P GAIN WILD-TYPE	18	2	13	21

Figure S76. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.0026

Table S77. Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
10P GAIN MUTATED	7	14	1	1
10P GAIN WILD-TYPE	16	9	6	23

Figure S77. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.021 (Fisher's exact test), Q value = 0.096

Table S78. Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	19	16	26
10P GAIN MUTATED	4	10	6	3
10P GAIN WILD-TYPE	12	9	10	23

Figure S78. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S79. Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
10Q GAIN MUTATED	2	0	8	12	2	1	1
10Q GAIN WILD-TYPE	17	18	5	6	9	5	4

Figure S79. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0145 (Fisher's exact test), Q value = 0.075

Table S80. Gene #20: '10q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	8	7	7	3	4	4	6	6
10Q GAIN MUTATED	6	2	0	2	1	1	0	1
10Q GAIN WILD-TYPE	2	5	7	1	3	3	6	5

Figure S80. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00061

Table S81. Gene #20: '10q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
10Q GAIN MUTATED	7	12	2	2
10Q GAIN WILD-TYPE	17	2	14	21

Figure S81. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.0052

Table S82. Gene #20: '10q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
10Q GAIN MUTATED	8	13	1	1
10Q GAIN WILD-TYPE	15	10	6	23

Figure S82. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_CNMF'

P value = 0.0311 (Fisher's exact test), Q value = 0.12

Table S83. Gene #20: '10q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	24	25
10Q GAIN MUTATED	9	11	3
10Q GAIN WILD-TYPE	20	13	22

Figure S83. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0285 (Fisher's exact test), Q value = 0.12

Table S84. Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	19	16	26
10Q GAIN MUTATED	5	10	5	3
10Q GAIN WILD-TYPE	11	9	11	23

Figure S84. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 0.0301 (Fisher's exact test), Q value = 0.12

Table S85. Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
11Q GAIN MUTATED	1	0	0	5	0	0	0
11Q GAIN WILD-TYPE	18	18	13	13	11	6	5

Figure S85. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 0.0399 (Fisher's exact test), Q value = 0.14

Table S86. Gene #22: '11q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
11Q GAIN MUTATED	4	0	0	0
11Q GAIN WILD-TYPE	20	14	16	23

Figure S86. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S87. Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
12P GAIN MUTATED	3	18	12	14	7	5	5
12P GAIN WILD-TYPE	16	0	1	4	4	1	0

Figure S87. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.073

Table S88. Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	16	14	8	17	9	12	2
12P GAIN MUTATED	8	8	4	14	8	12	1
12P GAIN WILD-TYPE	8	6	4	3	1	0	1

Figure S88. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.002

Table S89. Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
12P GAIN MUTATED	9	14	13	18
12P GAIN WILD-TYPE	15	0	3	5

Figure S89. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.0014

Table S90. Gene #23: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
12P GAIN MUTATED	10	20	2	22
12P GAIN WILD-TYPE	13	3	5	2

Figure S90. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0409 (Fisher's exact test), Q value = 0.15

Table S91. Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	19	16	26
12P GAIN MUTATED	8	11	14	21
12P GAIN WILD-TYPE	8	8	2	5

Figure S91. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S92. Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
12Q GAIN MUTATED	3	18	12	15	6	5	5
12Q GAIN WILD-TYPE	16	0	1	3	5	1	0

Figure S92. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.1

Table S93. Gene #24: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	16	14	8	17	9	12	2
12Q GAIN MUTATED	9	8	4	14	8	12	1
12Q GAIN WILD-TYPE	7	6	4	3	1	0	1

Figure S93. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.028 (Fisher's exact test), Q value = 0.12

Table S94. Gene #24: '12q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	8	7	7	3	4	4	6	6
12Q GAIN MUTATED	7	6	6	3	2	4	5	1
12Q GAIN WILD-TYPE	1	1	1	0	2	0	1	5

Figure S94. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.0066

Table S95. Gene #24: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
12Q GAIN MUTATED	10	14	13	18
12Q GAIN WILD-TYPE	14	0	3	5

Figure S95. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.0022

Table S96. Gene #24: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
12Q GAIN MUTATED	11	20	2	22
12Q GAIN WILD-TYPE	12	3	5	2

Figure S96. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 0.0284 (Fisher's exact test), Q value = 0.12

Table S97. Gene #25: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
13Q GAIN MUTATED	1	1	4	0
13Q GAIN WILD-TYPE	23	13	12	23

Figure S97. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 0.00347 (Fisher's exact test), Q value = 0.028

Table S98. Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
14Q GAIN MUTATED	1	2	8	4	4	0	2
14Q GAIN WILD-TYPE	18	16	5	14	7	6	3

Figure S98. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 0.0197 (Fisher's exact test), Q value = 0.092

Table S99. Gene #26: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	16	14	8	17	9	12	2
14Q GAIN MUTATED	3	0	3	8	2	1	1
14Q GAIN WILD-TYPE	13	14	5	9	7	11	1

Figure S99. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0038

Table S100. Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
14Q GAIN MUTATED	2	7	7	1
14Q GAIN WILD-TYPE	22	7	9	22

Figure S100. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00105 (Fisher's exact test), Q value = 0.01

Table S101. Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
14Q GAIN MUTATED	3	12	0	2
14Q GAIN WILD-TYPE	20	11	7	22

Figure S101. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0032

Table S102. Gene #26: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	24	25
14Q GAIN MUTATED	13	5	0
14Q GAIN WILD-TYPE	16	19	25

Figure S102. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.0029

Table S103. Gene #26: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	16	27	11	20	4
14Q GAIN MUTATED	7	0	3	5	3
14Q GAIN WILD-TYPE	9	27	8	15	1

Figure S103. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00061

Table S104. Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	19	16	26
14Q GAIN MUTATED	2	5	10	0
14Q GAIN WILD-TYPE	14	14	6	26

Figure S104. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00061

Table S105. Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	6	24	11	14	11	11
14Q GAIN MUTATED	4	0	6	3	4	0
14Q GAIN WILD-TYPE	2	24	5	11	7	11

Figure S105. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.074

Table S106. Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
15Q GAIN MUTATED	1	1	0	3	3	0	3
15Q GAIN WILD-TYPE	18	17	13	15	8	6	2

Figure S106. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

'15q gain' versus 'METHLYATION_CNMF'

P value = 0.029 (Fisher's exact test), Q value = 0.12

Table S107. Gene #27: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	16	14	8	17	9	12	2
15Q GAIN MUTATED	0	1	3	5	1	0	0
15Q GAIN WILD-TYPE	16	13	5	12	8	12	2

Figure S107. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 0.00971 (Fisher's exact test), Q value = 0.061

Table S108. Gene #27: '15q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
15Q GAIN MUTATED	0	3	5	2
15Q GAIN WILD-TYPE	24	11	11	21

Figure S108. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00495 (Fisher's exact test), Q value = 0.035

Table S109. Gene #27: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
15Q GAIN MUTATED	1	8	0	1
15Q GAIN WILD-TYPE	22	15	7	23

Figure S109. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.0077

Table S110. Gene #27: '15q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	16	27	11	20	4
15Q GAIN MUTATED	6	1	1	0	2
15Q GAIN WILD-TYPE	10	26	10	20	2

Figure S110. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.082

Table S111. Gene #27: '15q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	19	16	26
15Q GAIN MUTATED	0	3	5	1
15Q GAIN WILD-TYPE	16	16	11	25

Figure S111. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0429 (Fisher's exact test), Q value = 0.15

Table S112. Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	6	24	11	14	11	11
15Q GAIN MUTATED	1	1	4	0	2	1
15Q GAIN WILD-TYPE	5	23	7	14	9	10

Figure S112. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S113. Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
16P GAIN MUTATED	2	18	12	7	4	4	3
16P GAIN WILD-TYPE	17	0	1	11	7	2	2

Figure S113. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00061

Table S114. Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	16	14	8	17	9	12	2
16P GAIN MUTATED	2	5	5	13	5	12	1
16P GAIN WILD-TYPE	14	9	3	4	4	0	1

Figure S114. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0012

Table S115. Gene #28: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
16P GAIN MUTATED	4	11	12	16
16P GAIN WILD-TYPE	20	3	4	7

Figure S115. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S116. Gene #28: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
16P GAIN MUTATED	4	20	1	18
16P GAIN WILD-TYPE	19	3	6	6

Figure S116. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0205 (Fisher's exact test), Q value = 0.094

Table S117. Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	16	27	11	20	4
16P GAIN MUTATED	12	17	6	5	3
16P GAIN WILD-TYPE	4	10	5	15	1

Figure S117. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.066

Table S118. Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	19	16	26
16P GAIN MUTATED	3	11	10	18
16P GAIN WILD-TYPE	13	8	6	8

Figure S118. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S119. Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
16Q GAIN MUTATED	2	18	11	6	4	4	2
16Q GAIN WILD-TYPE	17	0	2	12	7	2	3

Figure S119. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S120. Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	16	14	8	17	9	12	2
16Q GAIN MUTATED	2	5	5	13	4	12	1
16Q GAIN WILD-TYPE	14	9	3	4	5	0	1

Figure S120. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.0018

Table S121. Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
16Q GAIN MUTATED	4	10	12	16
16Q GAIN WILD-TYPE	20	4	4	7

Figure S121. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S122. Gene #29: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
16Q GAIN MUTATED	4	19	1	18
16Q GAIN WILD-TYPE	19	4	6	6

Figure S122. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 0.073

Table S123. Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	16	27	11	20	4
16Q GAIN MUTATED	13	16	6	5	2
16Q GAIN WILD-TYPE	3	11	5	15	2

Figure S123. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0063

Table S124. Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	19	16	26
16Q GAIN MUTATED	2	9	12	18
16Q GAIN WILD-TYPE	14	10	4	8

Figure S124. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 0.00629 (Fisher's exact test), Q value = 0.042

Table S125. Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
17Q GAIN MUTATED	1	0	0	3	0	3	0
17Q GAIN WILD-TYPE	18	18	13	15	11	3	5

Figure S125. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00082

Table S126. Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
19P GAIN MUTATED	4	8	13	14	7	5	5
19P GAIN WILD-TYPE	15	10	0	4	4	1	0

Figure S126. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0191 (Fisher's exact test), Q value = 0.09

Table S127. Gene #34: '19p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	8	7	7	3	4	4	6	6
19P GAIN MUTATED	8	7	4	2	1	3	4	2
19P GAIN WILD-TYPE	0	0	3	1	3	1	2	4

Figure S127. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.00101 (Fisher's exact test), Q value = 0.01

Table S128. Gene #34: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
19P GAIN MUTATED	11	14	12	11
19P GAIN WILD-TYPE	13	0	4	12

Figure S128. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.0063

Table S129. Gene #34: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
19P GAIN MUTATED	14	21	1	12
19P GAIN WILD-TYPE	9	2	6	12

Figure S129. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S130. Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
19Q GAIN MUTATED	2	8	12	14	7	4	5
19Q GAIN WILD-TYPE	17	10	1	4	4	2	0

Figure S130. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0036

Table S131. Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
19Q GAIN MUTATED	10	14	11	9
19Q GAIN WILD-TYPE	14	0	5	14

Figure S131. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00115 (Fisher's exact test), Q value = 0.011

Table S132. Gene #35: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
19Q GAIN MUTATED	12	20	1	11
19Q GAIN WILD-TYPE	11	3	6	13

Figure S132. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00061

Table S133. Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
20P GAIN MUTATED	2	16	8	8	3	5	4
20P GAIN WILD-TYPE	17	2	5	10	8	1	1

Figure S133. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0041

Table S134. Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	16	14	8	17	9	12	2
20P GAIN MUTATED	4	7	1	10	5	12	1
20P GAIN WILD-TYPE	12	7	7	7	4	0	1

Figure S134. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CNMF'

P value = 0.0416 (Fisher's exact test), Q value = 0.15

Table S135. Gene #36: '20p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	10	11	10	14
20P GAIN MUTATED	6	2	8	7
20P GAIN WILD-TYPE	4	9	2	7

Figure S135. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'20p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00852 (Fisher's exact test), Q value = 0.055

Table S136. Gene #36: '20p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	8	7	7	3	4	4	6	6
20P GAIN MUTATED	5	2	6	1	1	4	4	0
20P GAIN WILD-TYPE	3	5	1	2	3	0	2	6

Figure S136. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0035

Table S137. Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
20P GAIN MUTATED	4	9	8	18
20P GAIN WILD-TYPE	20	5	8	5

Figure S137. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.0016

Table S138. Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
20P GAIN MUTATED	6	12	1	20
20P GAIN WILD-TYPE	17	11	6	4

Figure S138. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 0.00218 (Fisher's exact test), Q value = 0.019

Table S139. Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	24	25
20P GAIN MUTATED	10	10	20
20P GAIN WILD-TYPE	19	14	5

Figure S139. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00538 (Fisher's exact test), Q value = 0.037

Table S140. Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	19	16	26
20P GAIN MUTATED	4	9	6	20
20P GAIN WILD-TYPE	12	10	10	6

Figure S140. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00533 (Fisher's exact test), Q value = 0.037

Table S141. Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	6	24	11	14	11	11
20P GAIN MUTATED	2	18	5	4	2	8
20P GAIN WILD-TYPE	4	6	6	10	9	3

Figure S141. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00082

Table S142. Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
20Q GAIN MUTATED	3	16	9	9	3	5	4
20Q GAIN WILD-TYPE	16	2	4	9	8	1	1

Figure S142. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0028

Table S143. Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	16	14	8	17	9	12	2
20Q GAIN MUTATED	4	8	1	12	5	12	1
20Q GAIN WILD-TYPE	12	6	7	5	4	0	1

Figure S143. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.066

Table S144. Gene #37: '20q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	10	11	10	14
20Q GAIN MUTATED	8	2	8	7
20Q GAIN WILD-TYPE	2	9	2	7

Figure S144. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0025

Table S145. Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
20Q GAIN MUTATED	5	11	8	18
20Q GAIN WILD-TYPE	19	3	8	5

Figure S145. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.0036

Table S146. Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
20Q GAIN MUTATED	6	14	2	20
20Q GAIN WILD-TYPE	17	9	5	4

Figure S146. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 0.00355 (Fisher's exact test), Q value = 0.028

Table S147. Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	24	25
20Q GAIN MUTATED	10	13	20
20Q GAIN WILD-TYPE	19	11	5

Figure S147. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.073

Table S148. Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	19	16	26
20Q GAIN MUTATED	5	11	6	20
20Q GAIN WILD-TYPE	11	8	10	6

Figure S148. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0454 (Fisher's exact test), Q value = 0.16

Table S149. Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	6	24	11	14	11	11
20Q GAIN MUTATED	3	18	5	4	4	8
20Q GAIN WILD-TYPE	3	6	6	10	7	3

Figure S149. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.00424 (Fisher's exact test), Q value = 0.032

Table S150. Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	16	14	8	17	9	12	2
21Q GAIN MUTATED	7	2	2	12	2	1	0
21Q GAIN WILD-TYPE	9	12	6	5	7	11	2

Figure S150. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 0.033 (Fisher's exact test), Q value = 0.13

Table S151. Gene #38: '21q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
21Q GAIN MUTATED	7	9	6	4
21Q GAIN WILD-TYPE	17	5	10	19

Figure S151. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00102 (Fisher's exact test), Q value = 0.01

Table S152. Gene #38: '21q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
21Q GAIN MUTATED	7	15	1	3
21Q GAIN WILD-TYPE	16	8	6	21

Figure S152. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 0.0224 (Fisher's exact test), Q value = 0.1

Table S153. Gene #38: '21q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	24	25
21Q GAIN MUTATED	15	7	4
21Q GAIN WILD-TYPE	14	17	21

Figure S153. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.02 (Fisher's exact test), Q value = 0.093

Table S154. Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	16	27	11	20	4
21Q GAIN MUTATED	10	4	4	6	2
21Q GAIN WILD-TYPE	6	23	7	14	2

Figure S154. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.09

Table S155. Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	19	16	26
21Q GAIN MUTATED	5	6	10	4
21Q GAIN WILD-TYPE	11	13	6	22

Figure S155. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S156. Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
XP GAIN MUTATED	3	17	9	6	3	1	4
XP GAIN WILD-TYPE	16	1	4	12	8	5	1

Figure S156. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.12

Table S157. Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	16	14	8	17	9	12	2
XP GAIN MUTATED	5	5	2	9	6	10	2
XP GAIN WILD-TYPE	11	9	6	8	3	2	0

Figure S157. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0235 (Fisher's exact test), Q value = 0.1

Table S158. Gene #40: 'xp gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	8	7	7	3	4	4	6	6
XP GAIN MUTATED	6	5	5	0	3	3	4	0
XP GAIN WILD-TYPE	2	2	2	3	1	1	2	6

Figure S158. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 0.00288 (Fisher's exact test), Q value = 0.024

Table S159. Gene #40: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
XP GAIN MUTATED	5	11	10	12
XP GAIN WILD-TYPE	19	3	6	11

Figure S159. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0155 (Fisher's exact test), Q value = 0.077

Table S160. Gene #40: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
XP GAIN MUTATED	6	14	2	16
XP GAIN WILD-TYPE	17	9	5	8

Figure S160. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00859 (Fisher's exact test), Q value = 0.055

Table S161. Gene #40: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	6	24	11	14	11	11
XP GAIN MUTATED	5	16	7	2	4	4
XP GAIN WILD-TYPE	1	8	4	12	7	7

Figure S161. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0016

Table S162. Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
XQ GAIN MUTATED	4	16	8	5	3	1	4
XQ GAIN WILD-TYPE	15	2	5	13	8	5	1

Figure S162. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 0.00514 (Fisher's exact test), Q value = 0.036

Table S163. Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	16	14	8	17	9	12	2
XQ GAIN MUTATED	4	5	1	9	6	10	2
XQ GAIN WILD-TYPE	12	9	7	8	3	2	0

Figure S163. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0329 (Fisher's exact test), Q value = 0.13

Table S164. Gene #41: 'xq gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	8	7	7	3	4	4	6	6
XQ GAIN MUTATED	6	4	5	0	3	3	4	0
XQ GAIN WILD-TYPE	2	3	2	3	1	1	2	6

Figure S164. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.00439 (Fisher's exact test), Q value = 0.032

Table S165. Gene #41: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
XQ GAIN MUTATED	5	11	9	12
XQ GAIN WILD-TYPE	19	3	7	11

Figure S165. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.024 (Fisher's exact test), Q value = 0.1

Table S166. Gene #41: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
XQ GAIN MUTATED	6	13	2	16
XQ GAIN WILD-TYPE	17	10	5	8

Figure S166. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0301 (Fisher's exact test), Q value = 0.12

Table S167. Gene #41: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	6	24	11	14	11	11
XQ GAIN MUTATED	4	16	6	2	4	4
XQ GAIN WILD-TYPE	2	8	5	12	7	7

Figure S167. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0032

Table S168. Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
1P LOSS MUTATED	4	1	3	12	3	5	1
1P LOSS WILD-TYPE	15	17	10	6	8	1	4

Figure S168. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00061

Table S169. Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
1Q LOSS MUTATED	0	1	2	11	2	4	1
1Q LOSS WILD-TYPE	19	17	11	7	9	2	4

Figure S169. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.066

Table S170. Gene #43: '1q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	8	7	7	3	4	4	6	6
1Q LOSS MUTATED	0	0	0	2	1	0	2	3
1Q LOSS WILD-TYPE	8	7	7	1	3	4	4	3

Figure S170. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 0.00205 (Fisher's exact test), Q value = 0.018

Table S171. Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
2P LOSS MUTATED	1	0	3	4	4	4	0
2P LOSS WILD-TYPE	18	18	10	14	7	2	5

Figure S171. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 0.0358 (Fisher's exact test), Q value = 0.14

Table S172. Gene #44: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	24	25
2P LOSS MUTATED	6	1	8
2P LOSS WILD-TYPE	23	23	17

Figure S172. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 0.00115 (Fisher's exact test), Q value = 0.011

Table S173. Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
2Q LOSS MUTATED	1	0	3	2	4	4	0
2Q LOSS WILD-TYPE	18	18	10	16	7	2	5

Figure S173. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.0337 (Fisher's exact test), Q value = 0.13

Table S174. Gene #45: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	24	25
2Q LOSS MUTATED	4	1	8
2Q LOSS WILD-TYPE	25	23	17

Figure S174. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 0.00521 (Fisher's exact test), Q value = 0.037

Table S175. Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
3P LOSS MUTATED	2	1	2	6	7	0	1
3P LOSS WILD-TYPE	17	17	11	12	4	6	4

Figure S175. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'CN_CNMF'

P value = 0.00107 (Fisher's exact test), Q value = 0.01

Table S176. Gene #47: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
3Q LOSS MUTATED	4	0	1	6	7	0	1
3Q LOSS WILD-TYPE	15	18	12	12	4	6	4

Figure S176. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.073

Table S177. Gene #47: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
3Q LOSS MUTATED	7	0	7	3
3Q LOSS WILD-TYPE	17	14	9	20

Figure S177. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0293 (Fisher's exact test), Q value = 0.12

Table S178. Gene #47: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
3Q LOSS MUTATED	8	7	1	1
3Q LOSS WILD-TYPE	15	16	6	23

Figure S178. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00673 (Fisher's exact test), Q value = 0.045

Table S179. Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	19	16	26
3Q LOSS MUTATED	5	3	7	1
3Q LOSS WILD-TYPE	11	16	9	25

Figure S179. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0385 (Fisher's exact test), Q value = 0.14

Table S180. Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	6	24	11	14	11	11
3Q LOSS MUTATED	0	3	5	6	1	1
3Q LOSS WILD-TYPE	6	21	6	8	10	10

Figure S180. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.00397 (Fisher's exact test), Q value = 0.03

Table S181. Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
4P LOSS MUTATED	7	0	0	1
4P LOSS WILD-TYPE	17	14	16	22

Figure S181. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 0.074

Table S182. Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
4P LOSS MUTATED	6	0	1	1
4P LOSS WILD-TYPE	17	23	6	23

Figure S182. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.085

Table S183. Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
4Q LOSS MUTATED	7	0	1	1
4Q LOSS WILD-TYPE	17	14	15	22

Figure S183. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 0.098

Table S184. Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
5P LOSS MUTATED	5	1	0	0
5P LOSS WILD-TYPE	18	22	7	24

Figure S184. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 0.0334 (Fisher's exact test), Q value = 0.13

Table S185. Gene #51: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	24	25
5Q LOSS MUTATED	4	0	0
5Q LOSS WILD-TYPE	25	24	25

Figure S185. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6p loss' versus 'CN_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.0075

Table S186. Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
6P LOSS MUTATED	4	0	3	8	0	4	0
6P LOSS WILD-TYPE	15	18	10	10	11	2	5

Figure S186. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.0019

Table S187. Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
6Q LOSS MUTATED	4	0	4	10	0	4	0
6Q LOSS WILD-TYPE	15	18	9	8	11	2	5

Figure S187. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'7q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0386 (Fisher's exact test), Q value = 0.14

Table S188. Gene #55: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	6	24	11	14	11	11
7Q LOSS MUTATED	0	0	0	3	0	2
7Q LOSS WILD-TYPE	6	24	11	11	11	9

Figure S188. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 0.0394 (Fisher's exact test), Q value = 0.14

Table S189. Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
8P LOSS MUTATED	4	0	3	4	5	0	0
8P LOSS WILD-TYPE	15	18	10	14	6	6	5

Figure S189. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.0066

Table S190. Gene #56: '8p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	8	7	7	3	4	4	6	6
8P LOSS MUTATED	1	1	0	2	0	0	0	5
8P LOSS WILD-TYPE	7	6	7	1	4	4	6	1

Figure S190. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.023 (Fisher's exact test), Q value = 0.1

Table S191. Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	16	27	11	20	4
8P LOSS MUTATED	2	2	1	5	3
8P LOSS WILD-TYPE	14	25	10	15	1

Figure S191. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0108 (Fisher's exact test), Q value = 0.066

Table S192. Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	6	24	11	14	11	11
8P LOSS MUTATED	0	1	4	4	4	0
8P LOSS WILD-TYPE	6	23	7	10	7	11

Figure S192. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.073

Table S193. Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
8Q LOSS MUTATED	1	0	3	3	5	0	0
8Q LOSS WILD-TYPE	18	18	10	15	6	6	5

Figure S193. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0357 (Fisher's exact test), Q value = 0.14

Table S194. Gene #57: '8q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	8	7	7	3	4	4	6	6
8Q LOSS MUTATED	1	1	0	2	0	0	0	3
8Q LOSS WILD-TYPE	7	6	7	1	4	4	6	3

Figure S194. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 0.11

Table S195. Gene #57: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
8Q LOSS MUTATED	3	2	5	0
8Q LOSS WILD-TYPE	21	12	11	23

Figure S195. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0352 (Fisher's exact test), Q value = 0.14

Table S196. Gene #57: '8q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	16	27	11	20	4
8Q LOSS MUTATED	1	1	1	5	2
8Q LOSS WILD-TYPE	15	26	10	15	2

Figure S196. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0265 (Fisher's exact test), Q value = 0.11

Table S197. Gene #57: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	19	16	26
8Q LOSS MUTATED	2	4	4	0
8Q LOSS WILD-TYPE	14	15	12	26

Figure S197. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S198. Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
9P LOSS MUTATED	8	0	0	10	1	0	1
9P LOSS WILD-TYPE	11	18	13	8	10	6	4

Figure S198. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.068

Table S199. Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	16	14	8	17	9	12	2
9P LOSS MUTATED	7	5	4	3	0	0	0
9P LOSS WILD-TYPE	9	9	4	14	9	12	2

Figure S199. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0016

Table S200. Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
9P LOSS MUTATED	14	1	3	1
9P LOSS WILD-TYPE	10	13	13	22

Figure S200. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00097 (Fisher's exact test), Q value = 0.01

Table S201. Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
9P LOSS MUTATED	12	4	2	1
9P LOSS WILD-TYPE	11	19	5	23

Figure S201. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 0.0402 (Fisher's exact test), Q value = 0.14

Table S202. Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	24	25
9P LOSS MUTATED	8	9	2
9P LOSS WILD-TYPE	21	15	23

Figure S202. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00308 (Fisher's exact test), Q value = 0.026

Table S203. Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	19	16	26
9P LOSS MUTATED	9	5	1	3
9P LOSS WILD-TYPE	7	14	15	23

Figure S203. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 0.038 (Fisher's exact test), Q value = 0.14

Table S204. Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
9Q LOSS MUTATED	5	0	0	5	1	0	1
9Q LOSS WILD-TYPE	14	18	13	13	10	6	4

Figure S204. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 0.00125 (Fisher's exact test), Q value = 0.012

Table S205. Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
11P LOSS MUTATED	2	1	3	5	6	5	1
11P LOSS WILD-TYPE	17	17	10	13	5	1	4

Figure S205. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 0.00172 (Fisher's exact test), Q value = 0.015

Table S206. Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
11Q LOSS MUTATED	3	1	3	3	6	5	1
11Q LOSS WILD-TYPE	16	17	10	15	5	1	4

Figure S206. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.066

Table S207. Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	16	14	8	17	9	12	2
11Q LOSS MUTATED	1	2	4	9	3	1	0
11Q LOSS WILD-TYPE	15	12	4	8	6	11	2

Figure S207. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0378 (Fisher's exact test), Q value = 0.14

Table S208. Gene #64: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
12P LOSS MUTATED	2	1	2	0
12P LOSS WILD-TYPE	21	22	5	24

Figure S208. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.064

Table S209. Gene #65: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
12Q LOSS MUTATED	2	0	2	0
12Q LOSS WILD-TYPE	21	23	5	24

Figure S209. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0198 (Fisher's exact test), Q value = 0.092

Table S210. Gene #65: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	6	24	11	14	11	11
12Q LOSS MUTATED	0	0	1	0	3	0
12Q LOSS WILD-TYPE	6	24	10	14	8	11

Figure S210. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 0.00127 (Fisher's exact test), Q value = 0.012

Table S211. Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
13Q LOSS MUTATED	6	2	5	10	9	5	2
13Q LOSS WILD-TYPE	13	16	8	8	2	1	3

Figure S211. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.0082

Table S212. Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
14Q LOSS MUTATED	4	1	0	6	2	5	0
14Q LOSS WILD-TYPE	15	17	13	12	9	1	5

Figure S212. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.077

Table S213. Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
14Q LOSS MUTATED	7	0	1	8
14Q LOSS WILD-TYPE	17	14	15	15

Figure S213. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0461 (Fisher's exact test), Q value = 0.16

Table S214. Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
14Q LOSS MUTATED	5	1	3	7
14Q LOSS WILD-TYPE	18	22	4	17

Figure S214. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.008

Table S215. Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
15Q LOSS MUTATED	2	1	2	8	3	5	0
15Q LOSS WILD-TYPE	17	17	11	10	8	1	5

Figure S215. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0404 (Fisher's exact test), Q value = 0.14

Table S216. Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	16	27	11	20	4
15Q LOSS MUTATED	0	7	2	8	1
15Q LOSS WILD-TYPE	16	20	9	12	3

Figure S216. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0484 (Fisher's exact test), Q value = 0.16

Table S217. Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	6	24	11	14	11	11
15Q LOSS MUTATED	0	5	0	7	3	3
15Q LOSS WILD-TYPE	6	19	11	7	8	8

Figure S217. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 0.0397 (Fisher's exact test), Q value = 0.14

Table S218. Gene #69: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
16P LOSS MUTATED	4	0	0	0
16P LOSS WILD-TYPE	20	14	16	23

Figure S218. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0035

Table S219. Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
17P LOSS MUTATED	5	1	4	11	9	1	2
17P LOSS WILD-TYPE	14	17	9	7	2	5	3

Figure S219. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00256 (Fisher's exact test), Q value = 0.022

Table S220. Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	16	14	8	17	9	12	2
17P LOSS MUTATED	10	5	3	10	0	1	0
17P LOSS WILD-TYPE	6	9	5	7	9	11	2

Figure S220. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.004 (Fisher's exact test), Q value = 0.03

Table S221. Gene #71: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
17P LOSS MUTATED	15	4	7	3
17P LOSS WILD-TYPE	9	10	9	20

Figure S221. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0152 (Fisher's exact test), Q value = 0.077

Table S222. Gene #71: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
17P LOSS MUTATED	12	11	3	3
17P LOSS WILD-TYPE	11	12	4	21

Figure S222. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00094 (Fisher's exact test), Q value = 0.0099

Table S223. Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	16	27	11	20	4
17P LOSS MUTATED	5	8	0	14	2
17P LOSS WILD-TYPE	11	19	11	6	2

Figure S223. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0318 (Fisher's exact test), Q value = 0.13

Table S224. Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	19	16	26
17P LOSS MUTATED	8	10	6	4
17P LOSS WILD-TYPE	8	9	10	22

Figure S224. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.0061

Table S225. Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	6	24	11	14	11	11
17P LOSS MUTATED	1	6	3	12	5	1
17P LOSS WILD-TYPE	5	18	8	2	6	10

Figure S225. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 0.067

Table S226. Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
17Q LOSS MUTATED	4	1	4	7	7	0	2
17Q LOSS WILD-TYPE	15	17	9	11	4	6	3

Figure S226. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.069

Table S227. Gene #72: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	16	14	8	17	9	12	2
17Q LOSS MUTATED	6	4	4	10	0	1	0
17Q LOSS WILD-TYPE	10	10	4	7	9	11	2

Figure S227. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.047 (Fisher's exact test), Q value = 0.16

Table S228. Gene #72: '17q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
17Q LOSS MUTATED	9	11	2	3
17Q LOSS WILD-TYPE	14	12	5	21

Figure S228. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00895 (Fisher's exact test), Q value = 0.056

Table S229. Gene #72: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	16	27	11	20	4
17Q LOSS MUTATED	6	6	0	11	2
17Q LOSS WILD-TYPE	10	21	11	9	2

Figure S229. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0454 (Fisher's exact test), Q value = 0.16

Table S230. Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	6	24	11	14	11	11
17Q LOSS MUTATED	1	5	4	9	4	1
17Q LOSS WILD-TYPE	5	19	7	5	7	10

Figure S230. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.00387 (Fisher's exact test), Q value = 0.03

Table S231. Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
18P LOSS MUTATED	7	2	6	9	6	6	1
18P LOSS WILD-TYPE	12	16	7	9	5	0	4

Figure S231. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 0.0039 (Fisher's exact test), Q value = 0.03

Table S232. Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
18Q LOSS MUTATED	6	2	6	9	5	6	1
18Q LOSS WILD-TYPE	13	16	7	9	6	0	4

Figure S232. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0138 (Fisher's exact test), Q value = 0.073

Table S233. Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
19P LOSS MUTATED	1	0	2	0
19P LOSS WILD-TYPE	22	23	5	24

Figure S233. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0294 (Fisher's exact test), Q value = 0.12

Table S234. Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	6	24	11	14	11	11
19P LOSS MUTATED	1	0	0	0	2	0
19P LOSS WILD-TYPE	5	24	11	14	9	11

Figure S234. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 0.0445 (Fisher's exact test), Q value = 0.16

Table S235. Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
19Q LOSS MUTATED	4	0	0	0	0	0	0
19Q LOSS WILD-TYPE	15	18	13	18	11	6	5

Figure S235. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0308 (Fisher's exact test), Q value = 0.12

Table S236. Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	6	24	11	14	11	11
19Q LOSS MUTATED	1	0	0	0	2	0
19Q LOSS WILD-TYPE	5	24	11	14	9	11

Figure S236. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.083

Table S237. Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
21Q LOSS MUTATED	4	1	0	4	2	4	0
21Q LOSS WILD-TYPE	15	17	13	14	9	2	5

Figure S237. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 0.00453 (Fisher's exact test), Q value = 0.033

Table S238. Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
22Q LOSS MUTATED	10	4	5	13	8	6	2
22Q LOSS WILD-TYPE	9	14	8	5	3	0	3

Figure S238. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'CN_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.0075

Table S239. Gene #81: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
XP LOSS MUTATED	8	0	0	2	5	1	0
XP LOSS WILD-TYPE	11	18	13	16	6	5	5

Figure S239. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 0.0373 (Fisher's exact test), Q value = 0.14

Table S240. Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	19	18	13	18	11	6	5
XQ LOSS MUTATED	7	1	0	3	4	1	0
XQ LOSS WILD-TYPE	12	17	13	15	7	5	5

Figure S240. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 0.084

Table S241. Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	16	14	8	17	9	12	2
XQ LOSS MUTATED	4	1	5	2	1	0	0
XQ LOSS WILD-TYPE	12	13	3	15	8	12	2

Figure S241. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.082

Table S242. Gene #82: 'xq loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	10	11	10	14
XQ LOSS MUTATED	0	5	0	2
XQ LOSS WILD-TYPE	10	6	10	12

Figure S242. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 0.0347 (Fisher's exact test), Q value = 0.13

Table S243. Gene #82: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	14	16	23
XQ LOSS MUTATED	8	0	3	2
XQ LOSS WILD-TYPE	16	14	13	21

Figure S243. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0361 (Fisher's exact test), Q value = 0.14

Table S244. Gene #82: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
XQ LOSS MUTATED	8	3	1	1
XQ LOSS WILD-TYPE	15	20	6	23

Figure S244. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = broad_values_by_arm.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ACC-TP/22522856/transformed.cor.cli.txt
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/ACC-TP/22541000/ACC-TP.transferedmergedcluster.txt
Number of patients = 90
Number of significantly arm-level cnvs = 82
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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